Merged with trunk and removed unnecessary files

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/witness@934 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: d0ec52d222d22c102e9fe57590882cd0024c82d5
author: skachano <skachano@636b058d-ea47-450e-bf9e-a15bfbe3eedb> 2015-12-07 14:45:43 +0000
committer: skachano <skachano@636b058d-ea47-450e-bf9e-a15bfbe3eedb> 2015-12-07 14:45:43 +0000
commit: c4078affdbf6fac7150c10ade96fcb72270ac013 (patch)
tree: 1ad197bb90078a56036a49c6ee3766a032f85e63
parent: f70e386fc98f1dbd8287d1cb7cc715710a8f751b (diff)
parent: 061e43a2a48525bc5a69482a1ea80f20ff505e55 (diff)
165 files changed, 10570 insertions, 18212 deletions
diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
new file mode 100644
index 00000000..19d10535
--- /dev/null
+++ b/CMakeGUDHIVersion.txt
@@ -0,0 +1,6 @@
+set (GUDHI_MAJOR_VERSION 1)
+set (GUDHI_MINOR_VERSION 2)
+set (GUDHI_PATCH_VERSION 0)
+set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
+
+message(STATUS "GUDHI version : ${GUDHI_VERSION}")
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 57cb14d4..609b5eb7 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,6 +1,10 @@
 cmake_minimum_required(VERSION 2.6)
 project(GUDHIdev)
 
+include(CMakeGUDHIVersion.txt)
+# Generate GUDHI official version file
+configure_file(GUDHIVersion.cmake.in "${PROJECT_BINARY_DIR}/GUDHIVersion.cmake" @ONLY)
+
 find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework chrono timer program_options thread REQUIRED)
 
 set(CMAKE_PREFIX_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/")
@@ -23,7 +27,6 @@ set(Boost_USE_STATIC_LIBS        ON)
 set(Boost_USE_MULTITHREADED      ON)
 set(Boost_USE_STATIC_RUNTIME    OFF)
 
-find_package(Boost)
 #find_package(GMP)
 #if(GMP_FOUND)
 	#find_package(GMPXX)
@@ -67,9 +70,9 @@ else()
   LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})                      
 
   message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS})
+  message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS})
 
   include_directories(src/common/include/)
-  include_directories(src/Alpha_shapes/include/)
   include_directories(src/Bottleneck/include/)
   include_directories(src/Contraction/include/)
   include_directories(src/Hasse_complex/include/)
@@ -85,17 +88,21 @@ else()
   add_subdirectory(src/Skeleton_blocker/test) 
   add_subdirectory(src/Skeleton_blocker/example) 
   add_subdirectory(src/Contraction/example)
-  add_subdirectory(src/Hasse_complex/example)
+  # add_subdirectory(src/Hasse_complex/example)
   add_subdirectory(src/Witness_complex/test)
   add_subdirectory(src/Witness_complex/example)
-  add_subdirectory(src/Alpha_shapes/example)
-  add_subdirectory(src/Alpha_shapes/test)
+  # add_subdirectory(src/Alpha_shapes/example)
+  # add_subdirectory(src/Alpha_shapes/test)
   add_subdirectory(src/Bottleneck/example)
   add_subdirectory(src/Bottleneck/test)
 
   # data points generator
   add_subdirectory(data/points/generator)
 
+  # Please let GudhUI in last compilation position as QT is known to modify CMAKE_CXX_FLAGS
+  # GudhUI
+  add_subdirectory(src/GudhUI)
+
 endif()  
 
 
diff --git a/GUDHIVersion.cmake.in b/GUDHIVersion.cmake.in
new file mode 100644
index 00000000..2f433c1c
--- /dev/null
+++ b/GUDHIVersion.cmake.in
@@ -0,0 +1 @@
+@GUDHI_VERSION@
diff --git a/Version.txt b/Version.txt
deleted file mode 100644
index 9084fa2f..00000000
--- a/Version.txt
+++ /dev/null
@@ -1 +0,0 @@
-1.1.0
diff --git a/biblio/how_to_cite_gudhi.bib b/biblio/how_to_cite_gudhi.bib
new file mode 100644
index 00000000..851dd5d9
--- /dev/null
+++ b/biblio/how_to_cite_gudhi.bib
@@ -0,0 +1,44 @@
+@book{gudhi:urm
+, title        = "{GUDHI} User and Reference Manual"
+, author      = "{The GUDHI Project}"
+, publisher     = "{GUDHI Editorial Board}"
+, year         = 2015
+, url =    "http://gudhi.gforge.inria.fr/doc/latest/"
+}
+
+@incollection{gudhi:FilteredComplexes
+, author =  "Cl\'ement Maria"
+, title =   "Filtered Complexes"
+, publisher =  "{GUDHI Editorial Board}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "http://gudhi.gforge.inria.fr/doc/latest/group__simplex__tree.html"
+, year =        2015
+}
+
+@incollection{gudhi:PersistentCohomology
+, author =  "Cl\'ement Maria"
+, title =   "Persistent Cohomology"
+, publisher =  "{GUDHI Editorial Board}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "http://gudhi.gforge.inria.fr/doc/latest/group__persistent__cohomology.html"
+, year =        2015
+}
+
+@incollection{gudhi:Contraction
+, author =  "David Salinas"
+, title =   "Contraction"
+, publisher =  "{GUDHI Editorial Board}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "http://gudhi.gforge.inria.fr/doc/latest/group__contr.html"
+, year =        2015
+}
+
+@incollection{gudhi:Skeleton-Blocker
+, author =  "David Salinas"
+, title =   "Skeleton-Blocker"
+, publisher =  "{GUDHI Editorial Board}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "http://gudhi.gforge.inria.fr/doc/latest/group__skbl.html"
+, year =        2015
+}
+
diff --git a/data/points/generator/CMakeLists.txt b/data/points/generator/CMakeLists.txt
index 0f2674c4..26b44446 100644
--- a/data/points/generator/CMakeLists.txt
+++ b/data/points/generator/CMakeLists.txt
@@ -4,7 +4,22 @@ project(GUDHIPointsGenerator)
 if(CGAL_FOUND)
   if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
     message(STATUS "CGAL version: ${CGAL_VERSION}.")
+
     include( ${CGAL_USE_FILE} )
+    # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten.
+    # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
+    # A workaround is to add "-std=c++11" again.
+    # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html 
+    # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
+    # but it implies to use cmake version 3.1 at least.
+    if(NOT MSVC)
+      include(CheckCXXCompilerFlag)
+      CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11)
+      if(COMPILER_SUPPORTS_CXX11)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+      endif()
+    endif()
+    # - End of workaround
 
     find_package(Eigen3 3.1.0)
     if (EIGEN3_FOUND)
@@ -21,6 +36,6 @@ if(CGAL_FOUND)
       add_test(hypergenerator_in_cube_50000_2 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator in cube inCube.off 50000 3)
       endif()
   else()
-    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
+    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile hypergenerator. Version 4.6.0 is required.")
   endif ()
 endif()
diff --git a/data/points/generator/hypergenerator.cpp b/data/points/generator/hypergenerator.cpp
index f4ea6b07..60890b44 100644
--- a/data/points/generator/hypergenerator.cpp
+++ b/data/points/generator/hypergenerator.cpp
@@ -35,8 +35,9 @@ typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > K;
 typedef K::Point_d Point;
 
 void usage(char * const progName) {
-  std::cerr << "Usage: " << progName << " in|on sphere|cube off_file_name points_number[integer > 0] dimension[integer > 1] radius[double > 0.0 | default = 1.0]" << std::endl;
-  exit(-1); // ----- >>
+  std::cerr << "Usage: " << progName << " in|on sphere|cube off_file_name points_number[integer > 0] " <<
+      "dimension[integer > 1] radius[double > 0.0 | default = 1.0]" << std::endl;
+  exit(-1);
 }
 
 int main(int argc, char **argv) {
@@ -86,8 +87,13 @@ int main(int argc, char **argv) {
   }
 
   std::ofstream diagram_out(argv[3]);
-  diagram_out << "OFF" << std::endl;
-  diagram_out << points_number << " 0 0" << std::endl;
+  if (dimension == 3) {
+    diagram_out << "OFF" << std::endl;
+    diagram_out << points_number << " 0 0" << std::endl;
+  } else {
+    diagram_out << "nOFF" << std::endl;
+    diagram_out << dimension << " " << points_number << " 0 0" << std::endl;
+  }
 
   if (diagram_out.is_open()) {
     // Instanciate a random point generator
@@ -114,7 +120,7 @@ int main(int argc, char **argv) {
 
     for (auto thePoint : points) {
       int i = 0;
-      for (;i < dimension - 1; i++) {
+      for (; i < dimension - 1; i++) {
         diagram_out << thePoint[i] << " ";
       }
       diagram_out << thePoint[i] << std::endl;  // last point + Carriage Return
diff --git a/scripts/generate_version.sh b/scripts/generate_version.sh
index 4d28cf53..323396dc 100755
--- a/scripts/generate_version.sh
+++ b/scripts/generate_version.sh
@@ -2,19 +2,22 @@
 #usage bash generate_version.sh : dont generate if svn st non empty
 #usage bash generate_version.sh -f : generate even if svn is empty
 #usage bash generate_version.sh -f DIR : generate even if svn is empty and save library in dir
+#
+# 23/06/2015 - Remove source, add biblio, and doc
+# 06/10/2015 - Replace static Version.txt with generated GUDHIVersion.cmake file
 # VERSION CHECK
 ROOT_DIR=..
-VERSION_FILE="$ROOT_DIR/Version.txt"
+VERSION_FILE="$ROOT_DIR/GUDHIVersion.cmake"
 
 if [ ! -f $VERSION_FILE ]; then
-    echo "File not found! : $VERSION_FILE"
+    echo "File not found! : $VERSION_FILE - Please launch cmake first to generate file"
     exit 1
 fi
 
 # SVN STATUS CHECK OR IF FORCED BY USER
 if [ "$1" != "-f" ]
 then
-  SVN_STATUS=`svn status $ROOT_DIR`
+  SVN_STATUS=`svn status $ROOT_DIR | grep -v $VERSION_FILE`
   echo $SVN_STATUS
 fi
 
@@ -42,22 +45,29 @@ mkdir "$VERSION_DIR"
 
 # TOP LEVEL FILE COPY
 cp $VERSION_FILE $VERSION_DIR
+cp $ROOT_DIR/CMakeGUDHIVersion.txt $VERSION_DIR
 cp $ROOT_DIR/README $VERSION_DIR
 cp $ROOT_DIR/Conventions.txt $VERSION_DIR
 cp $ROOT_DIR/COPYING $VERSION_DIR
 cp -R $ROOT_DIR/data $VERSION_DIR
 cp $ROOT_DIR/src/CMakeLists.txt $VERSION_DIR
 cp $ROOT_DIR/src/Doxyfile $VERSION_DIR
+cp -R $ROOT_DIR/biblio $VERSION_DIR
+cp $ROOT_DIR/src/GUDHIConfigVersion.cmake.in $VERSION_DIR
+cp $ROOT_DIR/src/GUDHIConfig.cmake.in $VERSION_DIR
+cp $ROOT_DIR/GUDHIVersion.cmake.in $VERSION_DIR
 
 # PACKAGE LEVEL COPY
 PACKAGE_INC_DIR="/include"
-PACKAGE_SRC_DIR="/source"
+#PACKAGE_SRC_DIR="/source"
 PACKAGE_EX_DIR="/example"
+PACKAGE_CONCEPT_DIR="/concept"
+PACKAGE_DOC_DIR="/doc"
 for package in `ls $ROOT_DIR/src/`
 do
-  echo $package
-  if [ -d "$ROOT_DIR/src/$package" ]
+  if [ -d "$ROOT_DIR/src/$package" ] && [ $package != "Bottleneck" ]
   then
+    echo $package
     if [ "$package" == "cmake" ]
     then
       # SPECIFIC FOR CMAKE MODULES
@@ -77,20 +87,21 @@ do
         fi
         cp -R $ROOT_DIR/src/$package$PACKAGE_INC_DIR/* $VERSION_DIR$PACKAGE_INC_DIR/
       fi
-      if [ -d "$ROOT_DIR/src/$package$PACKAGE_SRC_DIR" ]
-      then
-        if [ ! -d "$VERSION_DIR$PACKAGE_SRC_DIR" ]
-        then
-          # MUST CREATE DIRECTORY ON FIRST LOOP
-          mkdir $VERSION_DIR$PACKAGE_INC_DIR
-        fi
-        cp -R $ROOT_DIR/src/$package$PACKAGE_SRC_DIR/* $VERSION_DIR$PACKAGE_SRC_DIR/
-      fi
       if [ -d "$ROOT_DIR/src/$package$PACKAGE_EX_DIR" ]
       then
         mkdir -p $VERSION_DIR$PACKAGE_EX_DIR/$package
         cp -R $ROOT_DIR/src/$package$PACKAGE_EX_DIR/* $VERSION_DIR$PACKAGE_EX_DIR/$package
       fi
+      if [ -d "$ROOT_DIR/src/$package$PACKAGE_CONCEPT_DIR" ]
+      then
+        mkdir -p $VERSION_DIR$PACKAGE_CONCEPT_DIR/$package
+        cp -R $ROOT_DIR/src/$package$PACKAGE_CONCEPT_DIR/* $VERSION_DIR$PACKAGE_CONCEPT_DIR/$package
+      fi
+      if [ -d "$ROOT_DIR/src/$package$PACKAGE_DOC_DIR" ]
+      then
+        mkdir -p $VERSION_DIR$PACKAGE_DOC_DIR/$package
+        cp -R $ROOT_DIR/src/$package$PACKAGE_DOC_DIR/* $VERSION_DIR$PACKAGE_DOC_DIR/$package
+      fi
     fi
   fi
 done
diff --git a/src/Alpha_shapes/example/CMakeLists.txt b/src/Alpha_shapes/example/CMakeLists.txt
deleted file mode 100644
index 753238a5..00000000
--- a/src/Alpha_shapes/example/CMakeLists.txt
+++ /dev/null
@@ -1,32 +0,0 @@
-cmake_minimum_required(VERSION 2.6)
-project(GUDHIAlphaShapesExample)
-
-# need CGAL 4.6
-# cmake -DCGAL_DIR=~/workspace/CGAL-4.6-beta1 ../../..
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    message(STATUS "CGAL version: ${CGAL_VERSION}.")
-
-    include( ${CGAL_USE_FILE} )
- 
-    find_package(Eigen3 3.1.0)
-    if (EIGEN3_FOUND)
-      message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
-      include( ${EIGEN3_USE_FILE} )
-      include_directories (BEFORE "../../include")
-
-      add_executable ( dtoffrw Delaunay_triangulation_off_rw.cpp )
-      target_link_libraries(dtoffrw  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-      add_test(dtoffrw_tore3D ${CMAKE_CURRENT_BINARY_DIR}/dtoffrw ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 3)
-
-      # uncomment to display debug traces
-      # add_definitions(-DDEBUG_TRACES)
-      add_executable ( stfromdt Simplex_tree_from_delaunay_triangulation.cpp )
-      target_link_libraries(stfromdt  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-    else()
-      message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")
-    endif()
-  else()
-    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
-  endif ()
-endif()
diff --git a/src/Alpha_shapes/example/Delaunay_triangulation_off_rw.cpp b/src/Alpha_shapes/example/Delaunay_triangulation_off_rw.cpp
deleted file mode 100644
index 03f6440d..00000000
--- a/src/Alpha_shapes/example/Delaunay_triangulation_off_rw.cpp
+++ /dev/null
@@ -1,105 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Vincent Rouvreau
- *
- *    Copyright (C) 2014  INRIA Saclay (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-// to construct a Delaunay_triangulation from a OFF file
-#include "gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h"
-
-#include <CGAL/Delaunay_triangulation.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/point_generators_d.h>
-#include <CGAL/algorithm.h>
-#include <CGAL/assertions.h>
-
-#include <iostream>
-#include <iterator>
-#include <vector>
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string>
-
-// Use dynamic_dimension_tag for the user to be able to set dimension
-typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > K;
-typedef CGAL::Delaunay_triangulation<K> T;
-// The triangulation uses the default instanciation of the 
-// TriangulationDataStructure template parameter
-
-void usage(char * const progName) {
-  std::cerr << "Usage: " << progName << " filename.off dimension" << std::endl;
-  exit(-1); // ----- >>
-}
-
-int main(int argc, char **argv) {
-  if (argc != 3) {
-    std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl;
-    usage(argv[0]);
-  }
-
-  int dimension = 0;
-  int returnedScanValue = sscanf(argv[2], "%d", &dimension);
-  if ((returnedScanValue == EOF) || (dimension <= 0)) {
-    std::cerr << "Error: " << argv[2] << " is not correct" << std::endl;
-    usage(argv[0]);
-  }
-
-  T dt(dimension);
-  std::string offFileName(argv[1]);
-  Gudhi::alphashapes::Delaunay_triangulation_off_reader<T> off_reader(offFileName, dt, true, true);
-  if (!off_reader.is_valid()) {
-    std::cerr << "Unable to read file " << offFileName << std::endl;
-    exit(-1); // ----- >>
-  }
-
-  std::cout << "number of vertices=" << dt.number_of_vertices() << std::endl;
-  std::cout << "number of full cells=" << dt.number_of_full_cells() << std::endl;
-  std::cout << "number of finite full cells=" << dt.number_of_finite_full_cells() << std::endl;
-
-  // Points list
-  /*for (T::Vertex_iterator vit = dt.vertices_begin(); vit != dt.vertices_end(); ++vit) {
-        for (auto Coord = vit->point().cartesian_begin(); Coord != vit->point().cartesian_end(); ++Coord) {
-          std::cout << *Coord << " ";
-        }
-        std::cout << std::endl;
-  }
-  std::cout << std::endl;*/
- 
-  int i = 0, j = 0;
-  typedef T::Full_cell_iterator Full_cell_iterator;
-  typedef T::Facet Facet;
-
-  for (Full_cell_iterator cit = dt.full_cells_begin(); cit != dt.full_cells_end(); ++cit) {
-    if (!dt.is_infinite(cit)) {
-      j++;
-      continue;
-    }
-    Facet fct(cit, cit->index(dt.infinite_vertex()));
-    i++;
-  }
-  std::cout << "There are " << i << " facets on the convex hull." << std::endl;
-  std::cout << "There are " << j << " facets not on the convex hull." << std::endl;
-
-
-  std::string offOutputFile("out.off");
-  Gudhi::alphashapes::Delaunay_triangulation_off_writer<T> off_writer(offOutputFile, dt);
-
-  return 0;
-}
-\ No newline at end of file
diff --git a/src/Alpha_shapes/example/Simplex_tree_from_delaunay_triangulation.cpp b/src/Alpha_shapes/example/Simplex_tree_from_delaunay_triangulation.cpp
deleted file mode 100644
index 3a17b519..00000000
--- a/src/Alpha_shapes/example/Simplex_tree_from_delaunay_triangulation.cpp
+++ /dev/null
@@ -1,103 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Vincent Rouvreau
- *
- *    Copyright (C) 2014  INRIA Saclay (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-// to construct a Delaunay_triangulation from a OFF file
-#include "gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h"
-#include "gudhi/Alpha_shapes.h"
-
-// to construct a simplex_tree from Delaunay_triangulation
-#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Simplex_tree.h"
-
-#include <CGAL/Delaunay_triangulation.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/point_generators_d.h>
-#include <CGAL/algorithm.h>
-#include <CGAL/assertions.h>
-
-#include <iostream>
-#include <iterator>
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string>
-
-// Use dynamic_dimension_tag for the user to be able to set dimension
-typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > K;
-typedef CGAL::Delaunay_triangulation<K> T;
-// The triangulation uses the default instanciation of the 
-// TriangulationDataStructure template parameter
-
-void usage(char * const progName) {
-  std::cerr << "Usage: " << progName << " filename.off dimension" << std::endl;
-  exit(-1); // ----- >>
-}
-
-int main(int argc, char **argv) {
-  if (argc != 3) {
-    std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl;
-    usage(argv[0]);
-  }
-
-  int dimension = 0;
-  int returnedScanValue = sscanf(argv[2], "%d", &dimension);
-  if ((returnedScanValue == EOF) || (dimension <= 0)) {
-    std::cerr << "Error: " << argv[2] << " is not correct" << std::endl;
-    usage(argv[0]);
-  }
-
-  // ----------------------------------------------------------------------------
-  //
-  // Init of an alpha-shape from a Delaunay triangulation
-  //
-  // ----------------------------------------------------------------------------
-  T dt(dimension);
-  std::string off_file_name(argv[1]);
-
-  Gudhi::alphashapes::Delaunay_triangulation_off_reader<T> off_reader(off_file_name, dt, false, false);
-  if (!off_reader.is_valid()) {
-    std::cerr << "Unable to read file " << off_file_name << std::endl;
-    exit(-1); // ----- >>
-  }
-
-  std::cout << "number of vertices=" << dt.number_of_vertices() << std::endl;
-  std::cout << "number of full cells=" << dt.number_of_full_cells() << std::endl;
-  std::cout << "number of finite full cells=" << dt.number_of_finite_full_cells() << std::endl;
-
-  Gudhi::alphashapes::Alpha_shapes alpha_shapes_from_dt(dt);
-  //std::cout << alpha_shapes_from_dt << std::endl;
-
-  // ----------------------------------------------------------------------------
-  //
-  // Init of an alpha-shape from a OFF file
-  //
-  // ----------------------------------------------------------------------------
-  Gudhi::alphashapes::Alpha_shapes alpha_shapes_from_file(off_file_name, dimension);
-  //std::cout << alpha_shapes_from_file << std::endl;
-  
-  std::cout << "alpha_shapes_from_file.dimension()=" << alpha_shapes_from_file.dimension() << std::endl;
-  std::cout << "alpha_shapes_from_file.filtration()=" << alpha_shapes_from_file.filtration() << std::endl;
-  std::cout << "alpha_shapes_from_file.num_simplices()=" << alpha_shapes_from_file.num_simplices() << std::endl;
-  std::cout << "alpha_shapes_from_file.num_vertices()=" << alpha_shapes_from_file.num_vertices() << std::endl;
-
-  return 0;
-}
-\ No newline at end of file
diff --git a/src/Alpha_shapes/include/gudhi/Alpha_shapes.h b/src/Alpha_shapes/include/gudhi/Alpha_shapes.h
deleted file mode 100644
index b8efdb4d..00000000
--- a/src/Alpha_shapes/include/gudhi/Alpha_shapes.h
+++ /dev/null
@@ -1,200 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Vincent Rouvreau
- *
- *    Copyright (C) 2015  INRIA Saclay (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#ifndef SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_H_
-#define SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_H_
-
-// to construct a Delaunay_triangulation from a OFF file
-#include <gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h>
-
-// to construct a simplex_tree from Delaunay_triangulation
-#include <gudhi/graph_simplicial_complex.h>
-#include <gudhi/Simplex_tree.h>
-
-#include <stdio.h>
-#include <stdlib.h>
-
-#include <CGAL/Delaunay_triangulation.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/algorithm.h>
-#include <CGAL/assertions.h>
-
-#include <iostream>
-#include <iterator>
-#include <vector>
-#include <string>
-
-namespace Gudhi {
-
-namespace alphashapes {
-
-/** \defgroup alpha_shapes Alpha shapes in dimension N
- *
- <DT>Implementations:</DT>
- Alpha shapes in dimension N are a subset of Delaunay Triangulation in dimension N.
-
-
- * \author    Vincent Rouvreau
- * \version   1.0
- * \date      2015
- * \copyright GNU General Public License v3.
- * @{
- */
-
-/**
- * \brief Alpha shapes data structure.
- *
- * \details Every simplex \f$[v_0, \cdots ,v_d]\f$ admits a canonical orientation
- * induced by the order relation on vertices \f$ v_0 < \cdots < v_d \f$.
- *
- * Details may be found in \cite boissonnatmariasimplextreealgorithmica.
- *
- * \implements FilteredComplex
- *
- */
-class Alpha_shapes {
- private:
-  // From Simplex_tree
-  /** \brief Type required to insert into a simplex_tree (with or without subfaces).*/
-  typedef std::vector<Vertex_handle> typeVectorVertex;
-
-  // From CGAL
-  /** \brief Kernel for the Delaunay_triangulation.
-   * Dimension can be set dynamically.
-   */
-  typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel;
-  /** \brief Delaunay_triangulation type required to create an alpha-shape.
-   */
-  typedef CGAL::Delaunay_triangulation<Kernel> Delaunay_triangulation;
-
- private:
-  /** \brief Upper bound on the simplex tree of the simplicial complex.*/
-  Gudhi::Simplex_tree<> _st;
-
- public:
-
-  Alpha_shapes(std::string off_file_name, int dimension) {
-    Delaunay_triangulation dt(dimension);
-    Gudhi::alphashapes::Delaunay_triangulation_off_reader<Delaunay_triangulation>
-        off_reader(off_file_name, dt, true, true);
-    if (!off_reader.is_valid()) {
-      std::cerr << "Unable to read file " << off_file_name << std::endl;
-      exit(-1); // ----- >>
-    }
-#ifdef DEBUG_TRACES
-    std::cout << "number of vertices=" << dt.number_of_vertices() << std::endl;
-    std::cout << "number of full cells=" << dt.number_of_full_cells() << std::endl;
-    std::cout << "number of finite full cells=" << dt.number_of_finite_full_cells() << std::endl;
-#endif  // DEBUG_TRACES
-    init<Delaunay_triangulation>(dt);
-  }
-
-  template<typename T>
-  Alpha_shapes(T triangulation) {
-    init<T>(triangulation);
-  }
-
-  ~Alpha_shapes() { }
-
- private:
-
-  template<typename T>
-  void init(T triangulation) {
-    _st.set_dimension(triangulation.maximal_dimension());
-    _st.set_filtration(0.0);
-    // triangulation points list
-    for (auto vit = triangulation.finite_vertices_begin();
-         vit != triangulation.finite_vertices_end(); ++vit) {
-      typeVectorVertex vertexVector;
-      Vertex_handle vertexHdl = std::distance(triangulation.finite_vertices_begin(), vit);
-      vertexVector.push_back(vertexHdl);
-
-      // Insert each point in the simplex tree
-      _st.insert_simplex(vertexVector, 0.0);
-
-#ifdef DEBUG_TRACES
-      std::cout << "P" << vertexHdl << ":";
-      for (auto Coord = vit->point().cartesian_begin(); Coord != vit->point().cartesian_end(); ++Coord) {
-        std::cout << *Coord << " ";
-      }
-      std::cout << std::endl;
-#endif  // DEBUG_TRACES
-    }
-    // triangulation finite full cells list
-    for (auto cit = triangulation.finite_full_cells_begin();
-         cit != triangulation.finite_full_cells_end(); ++cit) {
-      typeVectorVertex vertexVector;
-      for (auto vit = cit->vertices_begin(); vit != cit->vertices_end(); ++vit) {
-        // Vertex handle is distance - 1
-        Vertex_handle vertexHdl = std::distance(triangulation.vertices_begin(), *vit) - 1;
-        vertexVector.push_back(vertexHdl);
-      }
-      // Insert each point in the simplex tree
-      _st.insert_simplex_and_subfaces(vertexVector, 0.0);
-
-#ifdef DEBUG_TRACES
-      std::cout << "C" << std::distance(triangulation.finite_full_cells_begin(), cit) << ":";
-      for (auto value : vertexVector) {
-        std::cout << value << ' ';
-      }
-      std::cout << std::endl;
-#endif  // DEBUG_TRACES
-    }
-  }
-
- public:
-
-  /** \brief Returns the number of vertices in the complex. */
-  size_t num_vertices() {
-    return _st.num_vertices();
-  }
-
-  /** \brief Returns the number of simplices in the complex.
-   *
-   * Does not count the empty simplex. */
-  const unsigned int& num_simplices() const {
-    return _st.num_simplices();
-  }
-
-  /** \brief Returns an upper bound on the dimension of the simplicial complex. */
-  int dimension() {
-    return _st.dimension();
-  }
-
-  /** \brief Returns an upper bound of the filtration values of the simplices. */
-  Filtration_value filtration() {
-    return _st.filtration();
-  }
-
-  friend std::ostream& operator<<(std::ostream& os, const Alpha_shapes& alpha_shape) {
-    // TODO: Program terminated with signal SIGABRT, Aborted - Maybe because of copy constructor
-    Gudhi::Simplex_tree<> st = alpha_shape._st;
-    os << st << std::endl;
-    return os;
-  }
-};
-
-} // namespace alphashapes
-
-} // namespace Gudhi
-
-#endif  // SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_H_
diff --git a/src/Alpha_shapes/include/gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h b/src/Alpha_shapes/include/gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h
deleted file mode 100644
index 693b393e..00000000
--- a/src/Alpha_shapes/include/gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h
+++ /dev/null
@@ -1,213 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Vincent Rouvreau
- *
- *    Copyright (C) 2015  INRIA Saclay (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-#ifndef SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_DELAUNAY_TRIANGULATION_OFF_IO_H_
-#define SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_DELAUNAY_TRIANGULATION_OFF_IO_H_
-
-#include <string>
-#include <vector>
-#include <fstream>
-
-#include "gudhi/Off_reader.h"
-
-namespace Gudhi {
-
-namespace alphashapes {
-
-/**
- *@brief Off reader visitor with flag that can be passed to Off_reader to read a Delaunay_triangulation_complex.
- */
-template<typename Complex>
-class Delaunay_triangulation_off_flag_visitor_reader {
-  Complex& complex_;
-  typedef typename Complex::Point Point;
-
-  const bool load_only_points_;
-
- public:
-  explicit Delaunay_triangulation_off_flag_visitor_reader(Complex& complex, bool load_only_points = false) :
-      complex_(complex),
-      load_only_points_(load_only_points) { }
-
-  void init(int dim, int num_vertices, int num_faces, int num_edges) {
-#ifdef DEBUG_TRACES
-    std::cout << "init" << std::endl;
-#endif  // DEBUG_TRACES
-  }
-
-  void point(const std::vector<double>& point) {
-#ifdef DEBUG_TRACES
-    std::cout << "p ";
-    for (auto coordinate: point) {
-      std::cout << coordinate << " | ";
-    }
-    std::cout << std::endl;
-#endif  // DEBUG_TRACES
-    complex_.insert(Point(point.size(), point.begin(), point.end()));
-  }
-
-  void maximal_face(const std::vector<int>& face) {
-    // For alpha shapes, only points are read
-  }
-
-  void done() {
-#ifdef DEBUG_TRACES
-    std::cout << "done" << std::endl;
-#endif  // DEBUG_TRACES
-  }
-};
-
-/**
- *@brief Off reader visitor that can be passed to Off_reader to read a Delaunay_triangulation_complex.
- */
-template<typename Complex>
-class Delaunay_triangulation_off_visitor_reader {
-  Complex& complex_;
-  // typedef typename Complex::Vertex_handle Vertex_handle;
-  // typedef typename Complex::Simplex_handle Simplex_handle;
-  typedef typename Complex::Point Point;
-
-  const bool load_only_points_;
-  std::vector<Point> points_;
-  // std::vector<Simplex_handle> maximal_faces_;
-
- public:
-  explicit Delaunay_triangulation_off_visitor_reader(Complex& complex, bool load_only_points = false) :
-      complex_(complex),
-      load_only_points_(load_only_points) { }
-
-  void init(int dim, int num_vertices, int num_faces, int num_edges) {
-#ifdef DEBUG_TRACES
-    std::cout << "init - " << num_vertices << std::endl;
-#endif  // DEBUG_TRACES
-    // maximal_faces_.reserve(num_faces);
-    points_.reserve(num_vertices);
-  }
-
-  void point(const std::vector<double>& point) {
-#ifdef DEBUG_TRACES
-    std::cout << "p ";
-    for (auto coordinate: point) {
-      std::cout << coordinate << " | ";
-    }
-    std::cout << std::endl;
-#endif  // DEBUG_TRACES
-    points_.emplace_back(Point(point.size(), point.begin(), point.end()));
-  }
-
-  void maximal_face(const std::vector<int>& face) {
-    // For alpha shapes, only points are read
-  }
-
-  void done() {
-    complex_.insert(points_.begin(), points_.end());
-#ifdef DEBUG_TRACES
-    std::cout << "done" << std::endl;
-#endif  // DEBUG_TRACES
-  }
-};
-
-/**
- *@brief Class that allows to load a Delaunay_triangulation_complex from an off file.
- */
-template<typename Complex>
-class Delaunay_triangulation_off_reader {
- public:
-  /**
-   * name_file : file to read
-   * read_complex : complex that will receive the file content
-   * read_only_points : specify true if only the points must be read
-   */
-  Delaunay_triangulation_off_reader(const std::string & name_file, Complex& read_complex, bool read_only_points = false,
-                                    bool is_flag = false) : valid_(false) {
-    std::ifstream stream(name_file);
-    if (stream.is_open()) {
-      if (is_flag) {
-        // For alpha shapes, only points are read
-        Delaunay_triangulation_off_flag_visitor_reader<Complex> off_visitor(read_complex, true);
-        Off_reader off_reader(stream);
-        valid_ = off_reader.read(off_visitor);
-      } else {
-        // For alpha shapes, only points are read
-        Delaunay_triangulation_off_visitor_reader<Complex> off_visitor(read_complex, true);
-        Off_reader off_reader(stream);
-        valid_ = off_reader.read(off_visitor);
-      }
-    }
-  }
-
-  /**
-   * return true if reading did not meet problems.
-   */
-  bool is_valid() const {
-    return valid_;
-  }
-
- private:
-  bool valid_;
-};
-
-template<typename Complex>
-class Delaunay_triangulation_off_writer {
- public:
-  /**
-   * name_file : file where the off will be written
-   * save_complex : complex that be outputted in the file
-   * for now only save triangles.
-   */
-  Delaunay_triangulation_off_writer(const std::string & name_file, const Complex& save_complex) {
-    std::ofstream stream(name_file);
-    if (stream.is_open()) {
-      // OFF header
-      stream << "OFF" << std::endl;
-      // no endl on next line - don't know why...
-      stream << save_complex.number_of_vertices() << " " << save_complex.number_of_finite_full_cells() << " 0";
-
-      // Points list
-      for (auto vit = save_complex.vertices_begin(); vit != save_complex.vertices_end(); ++vit) {
-        for (auto Coord = vit->point().cartesian_begin(); Coord != vit->point().cartesian_end(); ++Coord) {
-          stream << *Coord << " ";
-        }
-        stream << std::endl;
-      }
-
-      // Finite cells list
-      for (auto cit = save_complex.finite_full_cells_begin(); cit != save_complex.finite_full_cells_end(); ++cit) {
-        stream << std::distance(cit->vertices_begin(), cit->vertices_end()) << " ";  // Dimension
-        for (auto vit = cit->vertices_begin(); vit != cit->vertices_end(); ++vit) {
-          auto vertexHdl = *vit;
-          // auto vertexHdl = std::distance(save_complex.vertices_begin(), *vit) - 1;
-          // stream << std::distance(save_complex.vertices_begin(), *(vit)) - 1 << " ";
-        }
-        stream << std::endl;
-      }
-      stream.close();
-    } else {
-      std::cerr << "could not open file " << name_file << std::endl;
-    }
-  }
-};
-
-}  // namespace alphashapes
-
-}  // namespace Gudhi
-
-#endif  // SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_DELAUNAY_TRIANGULATION_OFF_IO_H_
diff --git a/src/Alpha_shapes/test/Alpha_shapes_unit_test.cpp b/src/Alpha_shapes/test/Alpha_shapes_unit_test.cpp
deleted file mode 100644
index b4c32321..00000000
--- a/src/Alpha_shapes/test/Alpha_shapes_unit_test.cpp
+++ /dev/null
@@ -1,126 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Vincent Rouvreau
- *
- *    Copyright (C) 2015  INRIA Saclay (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#define BOOST_TEST_MODULE alpha_shapes test
-#include <boost/test/included/unit_test.hpp>
-#include <boost/system/error_code.hpp>
-#include <boost/chrono/thread_clock.hpp>
-// to construct a Delaunay_triangulation from a OFF file
-#include "gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h"
-#include "gudhi/Alpha_shapes.h"
-
-// to construct a simplex_tree from Delaunay_triangulation
-#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Simplex_tree.h"
-
-#include <CGAL/Delaunay_triangulation.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/point_generators_d.h>
-#include <CGAL/algorithm.h>
-#include <CGAL/assertions.h>
-
-#include <iostream>
-#include <iterator>
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string>
-
-// Use dynamic_dimension_tag for the user to be able to set dimension
-typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > K;
-typedef CGAL::Delaunay_triangulation<K> T;
-// The triangulation uses the default instanciation of the 
-// TriangulationDataStructure template parameter
-
-BOOST_AUTO_TEST_CASE( OFF_file ) {
-  // ----------------------------------------------------------------------------
-  //
-  // Init of an alpha-shape from a OFF file
-  //
-  // ----------------------------------------------------------------------------
-  std::string off_file_name("S4_100.off");
-  std::cout << "========== OFF FILE NAME = " << off_file_name << " ==========" << std::endl;
-  
-  Gudhi::alphashapes::Alpha_shapes alpha_shapes_from_file(off_file_name, 4);
-
-  const int DIMENSION = 4;
-  std::cout << "alpha_shapes_from_file.dimension()=" << alpha_shapes_from_file.dimension() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_file.dimension() == DIMENSION);
-  
-  const double FILTRATION = 0.0;
-  std::cout << "alpha_shapes_from_file.filtration()=" << alpha_shapes_from_file.filtration() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_file.filtration() == FILTRATION);
-  
-  const int NUMBER_OF_VERTICES = 100;
-  std::cout << "alpha_shapes_from_file.num_vertices()=" << alpha_shapes_from_file.num_vertices() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_file.num_vertices() == NUMBER_OF_VERTICES);
-  
-  const int NUMBER_OF_SIMPLICES = 6779;
-  std::cout << "alpha_shapes_from_file.num_simplices()=" << alpha_shapes_from_file.num_simplices() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
-
-}
-
-BOOST_AUTO_TEST_CASE( Delaunay_triangulation ) {
-  // ----------------------------------------------------------------------------
-  //
-  // Init of an alpha-shape from a Delauny triangulation
-  //
-  // ----------------------------------------------------------------------------
-  T dt(8);
-  std::string off_file_name("S8_10.off");
-  std::cout << "========== OFF FILE NAME = " << off_file_name << " ==========" << std::endl;
-  
-  Gudhi::alphashapes::Delaunay_triangulation_off_reader<T> off_reader(off_file_name, dt, true, true);
-  std::cout << "off_reader.is_valid()=" << off_reader.is_valid() << std::endl;
-  BOOST_CHECK(off_reader.is_valid());
-
-  const int NUMBER_OF_VERTICES = 10;
-  std::cout << "dt.number_of_vertices()=" << dt.number_of_vertices() << std::endl;
-  BOOST_CHECK(dt.number_of_vertices() == NUMBER_OF_VERTICES);
-  
-  const int NUMBER_OF_FULL_CELLS = 30;
-  std::cout << "dt.number_of_full_cells()=" << dt.number_of_full_cells() << std::endl;
-  BOOST_CHECK(dt.number_of_full_cells() == NUMBER_OF_FULL_CELLS);
-  
-  const int NUMBER_OF_FINITE_FULL_CELLS = 6;
-  std::cout << "dt.number_of_finite_full_cells()=" << dt.number_of_finite_full_cells() << std::endl;
-  BOOST_CHECK(dt.number_of_finite_full_cells() == NUMBER_OF_FINITE_FULL_CELLS);
-
-  Gudhi::alphashapes::Alpha_shapes alpha_shapes_from_dt(dt);
-
-  const int DIMENSION = 8;
-  std::cout << "alpha_shapes_from_dt.dimension()=" << alpha_shapes_from_dt.dimension() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_dt.dimension() == DIMENSION);
-  
-  const double FILTRATION = 0.0;
-  std::cout << "alpha_shapes_from_dt.filtration()=" << alpha_shapes_from_dt.filtration() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_dt.filtration() == FILTRATION);
-  
-  std::cout << "alpha_shapes_from_dt.num_vertices()=" << alpha_shapes_from_dt.num_vertices() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_dt.num_vertices() == NUMBER_OF_VERTICES);
-  
-  const int NUMBER_OF_SIMPLICES = 997;
-  std::cout << "alpha_shapes_from_dt.num_simplices()=" << alpha_shapes_from_dt.num_simplices() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_dt.num_simplices() == NUMBER_OF_SIMPLICES);
-}
-
diff --git a/src/Alpha_shapes/test/CMakeLists.txt b/src/Alpha_shapes/test/CMakeLists.txt
deleted file mode 100644
index e0d33827..00000000
--- a/src/Alpha_shapes/test/CMakeLists.txt
+++ /dev/null
@@ -1,48 +0,0 @@
-cmake_minimum_required(VERSION 2.6)
-project(GUDHIAlphaShapesUT)
-
-# need CGAL 4.6
-# cmake -DCGAL_DIR=~/workspace/CGAL-4.6-beta1 ../../..
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    message(STATUS "CGAL version: ${CGAL_VERSION}.")
-
-    include( ${CGAL_USE_FILE} )
- 
-    find_package(Eigen3 3.1.0)
-    if (EIGEN3_FOUND)
-      message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
-      include( ${EIGEN3_USE_FILE} )
-      include_directories (BEFORE "../../include")
-
-      if (GCOVR_PATH)
-        # for gcovr to make coverage reports - Corbera Jenkins plugin
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-        set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")
-        set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage")
-      endif()
-      if (GPROF_PATH)
-        # for gprof to make coverage reports - Jenkins
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-        set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg")
-        set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg")
-      endif()
-
-      # uncomment to display debug traces
-      # add_definitions(-DDEBUG_TRACES)
-      add_executable ( AlphaShapesUT Alpha_shapes_unit_test.cpp )
-      target_link_libraries(AlphaShapesUT  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
-      add_test(NAME AlphaShapesUT 
-        COMMAND ${CMAKE_CURRENT_BINARY_DIR}/AlphaShapesUT
-        # XML format for Jenkins xUnit plugin 
-        --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/AlphaShapesUT.xml --log_level=test_suite --report_level=no)
-
-
-    else()
-      message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")
-    endif()
-  else()
-    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
-  endif ()
-endif()
-
diff --git a/src/Alpha_shapes/test/README b/src/Alpha_shapes/test/README
deleted file mode 100644
index cddd46ca..00000000
--- a/src/Alpha_shapes/test/README
+++ /dev/null
@@ -1,14 +0,0 @@
-To compile:
-***********
-
-cd /path-to-gudhi/
-cmake .
-cd /path-to-test/
-make
-
-To launch with details:
-***********************
-
-./AlphaShapesUT --report_level=detailed --log_level=all 
-
-   ==> echo $? returns 0 in case of success (non-zero otherwise)
diff --git a/src/Alpha_shapes/test/S4_100.off b/src/Alpha_shapes/test/S4_100.off
deleted file mode 100644
index 0a5dc58c..00000000
--- a/src/Alpha_shapes/test/S4_100.off
+++ /dev/null
@@ -1,102 +0,0 @@
-OFF
-100 0 0
-0.562921 -0.735261 -0.256472 0.277007
--0.803733 -0.0527915 -0.315125 0.501918
--0.24946 -0.354982 -0.410773 -0.801887
-0.916381 -0.0512295 0.371049 0.141223
-0.182222 0.940836 -0.171362 -0.228599
--0.787145 -0.129213 0.568102 -0.202402
-0.0187866 -0.22093 -0.832882 -0.507095
--0.4702 -0.533814 0.353776 0.607286
--0.159798 -0.504771 0.263586 0.806346
-0.295546 0.162541 0.452931 0.825279
-0.242043 -0.107437 -0.913612 -0.308521
-0.875759 -0.113035 -0.469189 -0.0114505
-0.547877 -0.762247 -0.256972 -0.229729
--0.172302 0.521057 0.412013 -0.727363
--0.724729 -0.0574074 -0.0290602 0.686023
-0.700434 -0.102636 0.687285 0.162779
--0.681386 0.0946893 0.610047 0.393178
--0.847553 -0.357132 0.383743 0.0827718
-0.72297 -0.161631 -0.608517 0.284424
-0.757394 0.141549 0.196065 -0.606528
-0.78094 0.00901997 0.434536 0.448586
-0.14166 -0.619339 0.614589 -0.467582
-0.473105 -0.537832 -0.0103746 0.697711
--0.208004 0.536218 0.818027 0.00605288
-0.743694 -0.628926 0.188072 0.126488
--0.462228 -0.278147 0.35514 -0.76345
--0.17361 0.249211 0.758567 -0.57648
-0.416958 -0.254924 -0.576373 -0.654946
--0.590751 -0.286089 -0.424896 0.623402
--0.639538 -0.739693 -0.203745 0.0482932
-0.0731787 0.132121 0.864022 0.480266
--0.149644 -0.164724 -0.249746 -0.94239
--0.348592 0.0120379 -0.928656 -0.126239
-0.395328 -0.54513 0.149976 -0.723917
--0.974164 0.14707 0.157191 0.068302
--0.166425 0.119943 -0.627304 -0.751269
-0.031947 -0.358518 -0.708301 -0.607251
-0.93781 -0.155368 -0.30951 0.0240237
-0.276094 -0.753155 -0.597088 -0.00387459
--0.642876 -0.200551 -0.263517 -0.690687
-0.178711 0.604987 -0.262989 0.729993
--0.520347 0.497922 -0.676144 0.155374
--0.703999 0.500219 -0.484381 0.139789
--0.131013 0.835735 0.506779 0.166004
--0.536116 -0.566557 0.229226 0.582279
--0.334105 0.158252 0.926091 0.0754059
--0.0362677 0.296076 0.897108 0.325915
--0.57486 0.798575 0.15324 -0.0912754
-0.498602 0.0186805 0.72824 0.469801
--0.960329 0.0473356 0.261005 -0.0860505
-0.899134 -0.381392 -0.214508 0.00921711
-0.570576 0.567224 0.393019 -0.445237
--0.761763 -0.614589 -0.0546476 -0.197513
-0.188584 0.289531 0.174031 0.922129
--0.458506 -0.583876 0.639297 -0.2004
-0.785343 -0.21571 0.0794082 -0.574804
-0.0819036 0.65961 -0.247426 0.704973
-0.573125 0.49706 0.373026 0.534145
--0.513286 -0.626226 0.208535 -0.548536
-0.460558 0.468686 0.507832 -0.55707
-0.716158 -0.488201 0.388209 -0.313164
-0.881074 0.152441 0.380128 -0.236589
-0.885793 0.0386389 0.161009 -0.433537
--0.365162 0.298384 0.292846 0.831784
-0.364934 0.632269 -0.197205 -0.654346
--0.31469 -0.429991 0.665304 -0.522923
--0.734198 0.462914 -0.135691 -0.477756
--0.422885 0.674444 -0.364143 -0.483419
-0.829218 -0.154622 -0.381147 0.378439
-0.887881 0.310479 -0.109528 0.321363
--0.354398 -0.693974 0.456019 -0.429941
--0.492045 -0.160008 0.044387 0.854587
-0.0595532 0.158421 0.412577 -0.895062
--0.211441 0.491794 -0.153521 0.83058
--0.33558 -0.504711 0.353831 -0.71236
--0.735211 -0.197714 0.525626 0.379593
-0.465818 -0.424245 0.769469 -0.104627
--0.641071 -0.286339 -0.704442 -0.103923
--0.00446569 0.0249849 -0.194417 -0.980591
--0.610081 -0.252448 0.176698 -0.729966
--0.0859217 -0.154471 0.715027 0.676382
-0.091315 0.0723382 -0.855023 -0.505337
-0.165362 0.200983 -0.428242 -0.865373
--0.587465 0.303019 -0.152442 0.734729
-0.454946 -0.319828 0.437063 -0.706902
--0.384368 0.277509 0.879225 -0.0470385
-0.523335 -0.330233 -0.208592 0.757335
-0.895086 0.0448492 0.268089 -0.353466
--0.0272491 -0.567336 -0.72254 -0.39411
--0.0745014 -0.121818 -0.882466 0.448179
-0.382304 -0.240135 0.851109 -0.267941
--0.418057 -0.852847 -0.3128 0.00606452
--0.554046 0.304237 0.272381 -0.725453
-0.155115 -0.0894732 -0.245017 -0.952838
-0.114459 -0.130722 0.953669 0.245614
-0.0913002 -0.462466 0.244433 0.847374
--0.198849 0.0785111 0.131441 -0.967997
--0.303154 -0.686484 0.639333 0.167604
-0.521455 0.256835 -0.0584503 -0.811606
--0.109787 0.870544 0.161523 0.451676
diff --git a/src/Alpha_shapes/test/S8_10.off b/src/Alpha_shapes/test/S8_10.off
deleted file mode 100644
index 1d67e10f..00000000
--- a/src/Alpha_shapes/test/S8_10.off
+++ /dev/null
@@ -1,12 +0,0 @@
-OFF
-10 0 0
-0.440036 -0.574754 -0.200485 0.216537 -0.501251 -0.0329236 -0.196529 0.313023
--0.129367 -0.184089 -0.213021 -0.415848 0.783529 -0.0438025 0.317256 0.120749
-0.132429 0.683748 -0.124536 -0.166133 -0.540695 -0.0887576 0.390234 -0.139031
-0.0137399 -0.161581 -0.609142 -0.370872 -0.320669 -0.364053 0.24127 0.41416
--0.115313 -0.36425 0.190208 0.581871 0.204605 0.112527 0.313562 0.571337
-0.168272 -0.0746917 -0.635156 -0.214488 0.629498 -0.0812499 -0.337255 -0.00823068
-0.369896 -0.514626 -0.173493 -0.1551 -0.127105 0.384377 0.303936 -0.536566
--0.49013 -0.0388242 -0.0196532 0.463953 0.515962 -0.0756047 0.506276 0.119908
--0.434258 0.060347 0.388793 0.250579 -0.653127 -0.275207 0.295714 0.0637842
-0.596172 -0.133284 -0.501793 0.234541 0.428452 0.0800735 0.110912 -0.343109
diff --git a/src/Bottleneck/test/bottleneck_unit_test.cpp b/src/Bottleneck/test/bottleneck_unit_test.cpp
index 068b8690..c60f5d8a 100644
--- a/src/Bottleneck/test/bottleneck_unit_test.cpp
+++ b/src/Bottleneck/test/bottleneck_unit_test.cpp
@@ -1,6 +1,6 @@
-#define BOOST_TEST_MODULE bottleneck test
-
-#include <boost/test/included/unit_test.hpp>
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "bottleneck"
+#include <boost/test/unit_test.hpp>
 
 #include "gudhi/Graph_matching.h"
 #include <iostream>
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 70fc9a45..864ee040 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,11 +1,14 @@
 cmake_minimum_required(VERSION 2.6)
 project(GUDHI)
 
+include("CMakeGUDHIVersion.txt")
+
+enable_testing()
+
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules/")
 
 find_package(Boost REQUIRED COMPONENTS system filesystem program_options chrono timer REQUIRED)
 
-
 if (NOT CMAKE_BUILD_TYPE)
  set(CMAKE_BUILD_TYPE "Release")
 endif()
@@ -19,7 +22,6 @@ set(Boost_USE_STATIC_LIBS        ON)
 set(Boost_USE_MULTITHREADED      ON)
 set(Boost_USE_STATIC_RUNTIME    OFF)
 
-find_package(Boost)
 find_package(GMP)
 if(GMP_FOUND)
   find_package(GMPXX)
@@ -36,22 +38,53 @@ else()
   add_definitions(-DBOOST_ALL_NO_LIB)
 
   INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
-  LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})                      
-  include_directories(include/)
-	
+  LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
+
+  #---------------------------------------------------------------------------------------
+  # Gudhi compilation part
+  include_directories(include)
+
   add_subdirectory(example/Simplex_tree)                   
   add_subdirectory(example/Persistent_cohomology)                   
   add_subdirectory(example/Skeleton_blocker)                   
   add_subdirectory(example/Contraction)                   
   add_subdirectory(example/Hasse_complex)
   add_subdirectort(example/Witness_complex)
-  add_subdirectory(example/Alpha_shapes)
+  # add_subdirectory(example/Alpha_shapes)
   add_subdirectory(example/Bottleneck)
 
+  # data points generator
+  add_subdirectory(data/points/generator)
+
+  # Please let GudhUI in last compilation position as QT is known to modify CMAKE_CXX_FLAGS
   # GudhUI
   add_subdirectory(GudhUI)
+  #---------------------------------------------------------------------------------------
 
-  # data points generator
-  add_subdirectory(data/points/generator)
+  #---------------------------------------------------------------------------------------
+  # GUDHIConfig.cmake
+  # Export the package for use from the build-tree
+  # (this registers the build-tree with a global CMake-registry)
+  export(PACKAGE GUDHI)
+
+  # Create the GUDHIConfig.cmake and GUDHIConfigVersion files
+  set(CONF_INCLUDE_DIRS "${PROJECT_SOURCE_DIR}/include")
+  configure_file(GUDHIConfig.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfig.cmake" @ONLY)
+  configure_file(GUDHIConfigVersion.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfigVersion.cmake" @ONLY)
+
+  #---------------------------------------------------------------------------------------
+
+  #---------------------------------------------------------------------------------------
+  # Gudhi installation part
+
+  # Install the GUDHIConfig.cmake and GUDHIConfigVersion.cmake
+  install(FILES
+    "${PROJECT_BINARY_DIR}/GUDHIConfig.cmake"
+    "${PROJECT_BINARY_DIR}/GUDHIConfigVersion.cmake"
+    DESTINATION share/gudhi)
+
+  # install the include file on "make install"
+  install(DIRECTORY include/gudhi DESTINATION include)
+  #---------------------------------------------------------------------------------------
 
 endif()  
diff --git a/src/Contraction/example/Garland_heckbert.cpp b/src/Contraction/example/Garland_heckbert.cpp
index a41f65aa..b545a066 100644
--- a/src/Contraction/example/Garland_heckbert.cpp
+++ b/src/Contraction/example/Garland_heckbert.cpp
@@ -1,7 +1,4 @@
-/*
- * Garland_heckbert.h
- *  Created on: Feb 10, 2015
- * This file is part of the Gudhi Library. The Gudhi library 
+/* This file is part of the Gudhi Library. The Gudhi library 
  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
  *    library for computational topology.
  *
@@ -28,12 +25,13 @@
 #ifndef GARLAND_HECKBERT_H_
 #define GARLAND_HECKBERT_H_
 
+#include <gudhi/Point.h>
+#include <gudhi/Edge_contraction.h>
+#include <gudhi/Skeleton_blocker.h>
+#include <gudhi/Off_reader.h>
+
 #include <boost/timer/timer.hpp>
 #include <iostream>
-#include "gudhi/Point.h"
-#include "gudhi/Edge_contraction.h"
-#include "gudhi/Skeleton_blocker.h"
-#include "gudhi/Off_reader.h"
 
 #include "Garland_heckbert/Error_quadric.h"
 
@@ -51,7 +49,6 @@ struct Geometry_trait {
  */
 struct Garland_heckbert_traits : public Skeleton_blocker_simple_geometric_traits<Geometry_trait> {
  public:
-
   struct Garland_heckbert_vertex : public Simple_geometric_vertex {
     Error_quadric<Geometry_trait::Point> quadric;
   };
@@ -68,6 +65,7 @@ typedef Skeleton_blocker_contractor<Complex> Complex_contractor;
  */
 class GH_placement : public Gudhi::contraction::Placement_policy<EdgeProfile> {
   Complex& complex_;
+
  public:
   typedef Gudhi::contraction::Placement_policy<EdgeProfile>::Placement_type Placement_type;
 
@@ -91,8 +89,8 @@ class GH_placement : public Gudhi::contraction::Placement_policy<EdgeProfile> {
  */
 class GH_cost : public Gudhi::contraction::Cost_policy<EdgeProfile> {
   Complex& complex_;
- public:
 
+ public:
   typedef Gudhi::contraction::Cost_policy<EdgeProfile>::Cost_type Cost_type;
 
   GH_cost(Complex& complex) : complex_(complex) { }
@@ -115,13 +113,13 @@ class GH_cost : public Gudhi::contraction::Cost_policy<EdgeProfile> {
  */
 class GH_visitor : public Gudhi::contraction::Contraction_visitor<EdgeProfile> {
   Complex& complex_;
- public:
 
+ public:
   GH_visitor(Complex& complex) : complex_(complex) { }
 
-  //Compute quadrics for every vertex v
-  //The quadric of v consists in the sum of quadric
-  //of every triangles passing through v weighted by its area
+  // Compute quadrics for every vertex v
+  // The quadric of v consists in the sum of quadric
+  // of every triangles passing through v weighted by its area
 
   void on_started(Complex & complex) override {
     for (auto v : complex.vertex_range()) {
@@ -147,11 +145,13 @@ class GH_visitor : public Gudhi::contraction::Contraction_visitor<EdgeProfile> {
 
 int main(int argc, char *argv[]) {
   if (argc != 4) {
-    std::cerr << "Usage " << argv[0] << " input.off output.off N to load the file input.off, contract N edges and save the result to output.off.\n";
+    std::cerr << "Usage " << argv[0] <<
+        " input.off output.off N to load the file input.off, contract N edges and save the result to output.off.\n";
     return EXIT_FAILURE;
   }
 
   Complex complex;
+  typedef Complex::Vertex_handle Vertex_handle;
 
   // load the points
   Skeleton_blocker_off_reader<Complex> off_reader(argv[1], complex);
@@ -160,8 +160,12 @@ int main(int argc, char *argv[]) {
     return EXIT_FAILURE;
   }
 
-  std::cout << "Load complex with " << complex.num_vertices() << " vertices" << std::endl;
+  if (!complex.empty() && !(complex.point(Vertex_handle(0)).dimension() == 3)) {
+    std::cerr << "Only points of dimension 3 are supported." << std::endl;
+    return EXIT_FAILURE;
+  }
 
+  std::cout << "Load complex with " << complex.num_vertices() << " vertices" << std::endl;
 
   int num_contractions = atoi(argv[3]);
 
@@ -172,23 +176,24 @@ int main(int argc, char *argv[]) {
                                 new GH_cost(complex),
                                 new GH_placement(complex),
                                 contraction::make_link_valid_contraction<EdgeProfile>(),
-                                new GH_visitor(complex)
-                                );
+                                new GH_visitor(complex));
 
   std::cout << "Contract " << num_contractions << " edges" << std::endl;
   contractor.contract_edges(num_contractions);
 
   std::cout << "Final complex has " <<
       complex.num_vertices() << " vertices, " <<
-      complex.num_edges() << " edges and" <<
+      complex.num_edges() << " edges and " <<
       complex.num_triangles() << " triangles." << std::endl;
 
-  //write simplified complex
+  // write simplified complex
   Skeleton_blocker_off_writer<Complex> off_writer(argv[2], complex);
 
   return EXIT_SUCCESS;
 }
 
+#endif  // GARLAND_HECKBERT_H_
+
+
 
 
-#endif /* GARLAND_HECKBERT_H_ */
diff --git a/src/Contraction/example/Garland_heckbert/Error_quadric.h b/src/Contraction/example/Garland_heckbert/Error_quadric.h
index 725a3a56..a033aa00 100644
--- a/src/Contraction/example/Garland_heckbert/Error_quadric.h
+++ b/src/Contraction/example/Garland_heckbert/Error_quadric.h
@@ -1,164 +1,182 @@
-/*
- * Error_quadric.h
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
  *
- *  Created on: 24 janv. 2014
- *      Author: dsalinas
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-M�diterran�e (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
  */
 
 #ifndef ERROR_QUADRIC_H_
 #define ERROR_QUADRIC_H_
 
-#include <vector>
-#include <utility>
 #include <boost/optional/optional.hpp>
 
+#include <vector>
+#include <utility>
 
-template <typename Point> class Error_quadric{
-private :
-	double coeff[10];
-
-public :
-	Error_quadric(){
-		clear();
-	}
-
-	/**
-	 * Quadric corresponding to the L2 distance to the plane.
-	 *
-	 * According to the notation of Garland Heckbert, they
-	 * denote a quadric symetric matrix as :
-	 * Q = [ q11 q12 q13 q14]
-	 *     [ q12 q22 q23 q24]
-	 *     [ q13 q23 q33 q34]
-	 *     [ q14 q24 q34 q44]
-	 *
-	 * which is represented by a vector with 10 elts that
-	 * are denoted ci for clarity with :
-	 * Q = [ c0  c1  c2  c3 ]
-	 *     [ c1  c4  c5  c6 ]
-	 *     [ c2  c5  c7  c8 ]
-	 *     [ c3  c6  c8  c9 ]
-	 *
-	 * The constructor return the quadrics that represents
-	 * the squared distance to the plane defined by triangle p0,p1,p2
-	 * times the area of triangle p0,p1,p2.
-	 */
-	Error_quadric(const Point & p0,const Point & p1,const Point & p2){
-
-		Point normal(unit_normal(p0,p1,p2));
-		double a=normal[0];
-		double b=normal[1];
-		double c=normal[2];
-		double d= -a*p0[0]-b*p0[1]-c*p0[2];
-		coeff[0] = a*a ;
-		coeff[1] = a*b ;
-		coeff[2] = a*c ;
-		coeff[3] = a*d ;
-		coeff[4] = b*b ;
-		coeff[5] = b*c ;
-		coeff[6] = b*d ;
-		coeff[7] = c*c ;
-		coeff[8] = c*d ;
-		coeff[9] = d*d ;
-
-		double area_p0p1p2 = std::sqrt(squared_area(p0,p1,p2));
-		for(auto& x : coeff)
-			x*= area_p0p1p2;
-	}
-
-
-	inline double squared_area(const Point& p0,const Point& p1,const Point& p2) {
-		//if (x1,x2,x3) = p1-p0 and (y1,y2,y3) = p2-p0
-		//then the squared area is = (u^2+v^2+w^2)/4
-		//with:		u = x2 * y3 - x3 * y2;
-		//		    v = x3 * y1 - x1 * y3;
-		//	     	w = x1 * y2 - x2 * y1;
-		Point p0p1(p1-p0);
-		Point p0p2(p2-p0);
-		double A = p0p1[1] * p0p2[2] - p0p1[2] * p0p2[1];
-		double B = p0p1[2] * p0p2[0] - p0p1[0] * p0p2[2];
-		double C = p0p1[0] * p0p2[1] - p0p1[1] * p0p2[0];
-		return 1./4. * (A*A+B*B+C*C);
-	}
-
-
-	void clear(){
-		for(auto& x:coeff)
-			x=0;
-	}
-
-	Error_quadric& operator+=(const Error_quadric& other){
-		if(this!=&other)
-			for(int i = 0 ; i < 10; ++i)
-				coeff[i] += other.coeff[i];
-		return *this;
-	}
-
-	/**
-	 * @return The quadric quost defined by the scalar product v^T Q v where Q is the quadratic form of Garland/Heckbert
-	 */
-	inline double cost(const Point& point) const{
-		double cost =
-				coeff[0]*point.x()*point.x()+coeff[4]*point.y()*point.y()+coeff[7]*point.z()*point.z()
-				+2*(coeff[1]*point.x()*point.y()+coeff[5]*point.y()*point.z()+coeff[2]*point.z()*point.x())
-				+2*(coeff[3]*point.x()+coeff[6]*point.y()+coeff[8]*point.z())
-				+coeff[9];
-		if(cost<0) return 0;
-		else {
-			return cost;
-		}
-	}
-
-	inline double grad_determinant() const{
-		return
-				coeff[0] * coeff[4] * coeff[7]
-				                            -  coeff[0] * coeff[5] * coeff[5]
-				                                                           -  coeff[1] * coeff[1] * coeff[7]
-				                                                                                          +2*coeff[1] * coeff[5] * coeff[2]
-				                                                                                                                         -  coeff[4] * coeff[2] * coeff[2];
-	}
-
-	/**
-	 * Return the point such that it minimizes the gradient of the quadric.
-	 * Det must be passed with the determinant value of the gradient (should be non zero).
-	 */
-	inline Point solve_linear_gradient(double det = grad_determinant()) const{
-		return Point({
-				(-coeff[1]*coeff[5]*coeff[8]+coeff[1]*coeff[7]*coeff[6]+coeff[2]*coeff[8]*coeff[4]-coeff[2]*coeff[5]*coeff[6]-coeff[3]*coeff[4]*coeff[7]+coeff[3]*coeff[5]*coeff[5])/ det,
-				(coeff[0]*coeff[5]*coeff[8]-coeff[0]*coeff[7]*coeff[6]-coeff[5]*coeff[2]*coeff[3]-coeff[1]*coeff[2]*coeff[8]+coeff[6]*coeff[2]*coeff[2]+coeff[1]*coeff[3]*coeff[7])/det,
-				(-coeff[8]*coeff[0]*coeff[4]+coeff[8]*coeff[1]*coeff[1]+coeff[2]*coeff[3]*coeff[4]+coeff[5]*coeff[0]*coeff[6]-coeff[5]*coeff[1]*coeff[3]-coeff[1]*coeff[2]*coeff[6])/det
-		});
-	}
-
-
-	/**
-	 * returns the point that minimizes the quadric.
-	 * It inverses the quadric if its determinant is higher that a given threshold .
-	 * If the determinant is lower than this value the returned value is uninitialized.
-	 */
-	boost::optional<Point> min_cost(double scale=1) const{
-		//		const double min_determinant = 1e-4 * scale*scale;
-		const double min_determinant = 1e-5;
-		boost::optional<Point> pt_res;
-		double det = grad_determinant();
-		if (std::abs(det)>min_determinant)
-			pt_res = solve_linear_gradient(det);
-		return pt_res;
-	}
-
-	friend std::ostream& operator<< (std::ostream& stream, const Error_quadric& quadric) {
-		stream << "\n[ "<<quadric.coeff[0]<<","<<quadric.coeff[1]<<","<<quadric.coeff[2]<<","<<quadric.coeff[3]<<";\n";
-		stream <<    " "<<quadric.coeff[1]<<","<<quadric.coeff[4]<<","<<quadric.coeff[5]<<","<<quadric.coeff[6]<<";\n";
-		stream <<    " "<<quadric.coeff[2]<<","<<quadric.coeff[5]<<","<<quadric.coeff[7]<<","<<quadric.coeff[8]<<";\n";
-		stream <<    " "<<quadric.coeff[3]<<","<<quadric.coeff[6]<<","<<quadric.coeff[8]<<","<<quadric.coeff[9]<<"]";
-		return stream;
-	}
-
-
+template <typename Point> class Error_quadric {
+ private:
+  double coeff[10];
+
+ public:
+  Error_quadric() {
+    clear();
+  }
+
+  /**
+   * Quadric corresponding to the L2 distance to the plane.
+   *
+   * According to the notation of Garland Heckbert, they
+   * denote a quadric symetric matrix as :
+   * Q = [ q11 q12 q13 q14]
+   *     [ q12 q22 q23 q24]
+   *     [ q13 q23 q33 q34]
+   *     [ q14 q24 q34 q44]
+   *
+   * which is represented by a vector with 10 elts that
+   * are denoted ci for clarity with :
+   * Q = [ c0  c1  c2  c3 ]
+   *     [ c1  c4  c5  c6 ]
+   *     [ c2  c5  c7  c8 ]
+   *     [ c3  c6  c8  c9 ]
+   *
+   * The constructor return the quadrics that represents
+   * the squared distance to the plane defined by triangle p0,p1,p2
+   * times the area of triangle p0,p1,p2.
+   */
+  Error_quadric(const Point & p0, const Point & p1, const Point & p2) {
+    Point normal(unit_normal(p0, p1, p2));
+    double a = normal[0];
+    double b = normal[1];
+    double c = normal[2];
+    double d = -a * p0[0] - b * p0[1] - c * p0[2];
+    coeff[0] = a*a;
+    coeff[1] = a*b;
+    coeff[2] = a*c;
+    coeff[3] = a*d;
+    coeff[4] = b*b;
+    coeff[5] = b*c;
+    coeff[6] = b*d;
+    coeff[7] = c*c;
+    coeff[8] = c*d;
+    coeff[9] = d*d;
+
+    double area_p0p1p2 = std::sqrt(squared_area(p0, p1, p2));
+    for (auto& x : coeff)
+      x *= area_p0p1p2;
+  }
+
+  inline double squared_area(const Point& p0, const Point& p1, const Point& p2) {
+    // if (x1,x2,x3) = p1-p0 and (y1,y2,y3) = p2-p0
+    // then the squared area is = (u^2+v^2+w^2)/4
+    // with: u = x2 * y3 - x3 * y2;
+    //       v = x3 * y1 - x1 * y3;
+    //       w = x1 * y2 - x2 * y1;
+    Point p0p1(p1 - p0);
+    Point p0p2(p2 - p0);
+    double A = p0p1[1] * p0p2[2] - p0p1[2] * p0p2[1];
+    double B = p0p1[2] * p0p2[0] - p0p1[0] * p0p2[2];
+    double C = p0p1[0] * p0p2[1] - p0p1[1] * p0p2[0];
+    return 1. / 4. * (A * A + B * B + C * C);
+  }
+
+  void clear() {
+    for (auto& x : coeff)
+      x = 0;
+  }
+
+  Error_quadric& operator+=(const Error_quadric& other) {
+    if (this != &other) {
+      for (int i = 0; i < 10; ++i)
+        coeff[i] += other.coeff[i];
+    }
+    return *this;
+  }
+
+  /**
+   * @return The quadric quost defined by the scalar product v^T Q v where Q is the quadratic form of Garland/Heckbert
+   */
+  inline double cost(const Point& point) const {
+    double cost =
+        coeff[0] * point.x() * point.x() + coeff[4] * point.y() * point.y() + coeff[7] * point.z() * point.z()
+        + 2 * (coeff[1] * point.x() * point.y() + coeff[5] * point.y() * point.z() + coeff[2] * point.z() * point.x())
+        + 2 * (coeff[3] * point.x() + coeff[6] * point.y() + coeff[8] * point.z())
+        + coeff[9];
+    if (cost < 0) {
+      return 0;
+    } else {
+      return cost;
+    }
+  }
+
+  inline double grad_determinant() const {
+    return
+    coeff[0] * coeff[4] * coeff[7]
+        - coeff[0] * coeff[5] * coeff[5]
+        - coeff[1] * coeff[1] * coeff[7]
+        + 2 * coeff[1] * coeff[5] * coeff[2]
+        - coeff[4] * coeff[2] * coeff[2];
+  }
+
+  /**
+   * Return the point such that it minimizes the gradient of the quadric.
+   * Det must be passed with the determinant value of the gradient (should be non zero).
+   */
+  inline Point solve_linear_gradient(double det) const {
+    return Point({
+                 (-coeff[1] * coeff[5] * coeff[8] + coeff[1] * coeff[7] * coeff[6] + coeff[2] * coeff[8] * coeff[4] -
+                     coeff[2] * coeff[5] * coeff[6] - coeff[3] * coeff[4] * coeff[7] + coeff[3] * coeff[5] * coeff[5])
+                     / det,
+                 (coeff[0] * coeff[5] * coeff[8] - coeff[0] * coeff[7] * coeff[6] - coeff[5] * coeff[2] * coeff[3] -
+                     coeff[1] * coeff[2] * coeff[8] + coeff[6] * coeff[2] * coeff[2] + coeff[1] * coeff[3] * coeff[7])
+                     / det,
+                 (-coeff[8] * coeff[0] * coeff[4] + coeff[8] * coeff[1] * coeff[1] + coeff[2] * coeff[3] * coeff[4] +
+                     coeff[5] * coeff[0] * coeff[6] - coeff[5] * coeff[1] * coeff[3] - coeff[1] * coeff[2] * coeff[6])
+                     / det
+    });
+  }
+
+  /**
+   * returns the point that minimizes the quadric.
+   * It inverses the quadric if its determinant is higher that a given threshold .
+   * If the determinant is lower than this value the returned value is uninitialized.
+   */
+  boost::optional<Point> min_cost(double scale = 1) const {
+    // const double min_determinant = 1e-4 * scale*scale;
+    const double min_determinant = 1e-5;
+    boost::optional<Point> pt_res;
+    double det = grad_determinant();
+    if (std::abs(det) > min_determinant)
+      pt_res = solve_linear_gradient(det);
+    return pt_res;
+  }
+
+  friend std::ostream& operator<<(std::ostream& stream, const Error_quadric& quadric) {
+    stream << "\n[ " << quadric.coeff[0] << "," << quadric.coeff[1] << "," << quadric.coeff[2] << "," <<
+        quadric.coeff[3] << ";\n";
+    stream << " " << quadric.coeff[1] << "," << quadric.coeff[4] << "," << quadric.coeff[5] << "," <<
+        quadric.coeff[6] << ";\n";
+    stream << " " << quadric.coeff[2] << "," << quadric.coeff[5] << "," << quadric.coeff[7] << "," <<
+        quadric.coeff[8] << ";\n";
+    stream << " " << quadric.coeff[3] << "," << quadric.coeff[6] << "," << quadric.coeff[8] << "," <<
+        quadric.coeff[9] << "]";
+    return stream;
+  }
 };
 
-
-
-
-#endif /* ERROR_QUADRIC_H_ */
-
+#endif  // ERROR_QUADRIC_H_
diff --git a/src/Contraction/example/Rips_contraction.cpp b/src/Contraction/example/Rips_contraction.cpp
index bd0a8b8c..f80cc2dc 100644
--- a/src/Contraction/example/Rips_contraction.cpp
+++ b/src/Contraction/example/Rips_contraction.cpp
@@ -19,24 +19,23 @@
  *    You should have received a copy of the GNU General Public License
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
+#include <gudhi/Edge_contraction.h>
+#include <gudhi/Skeleton_blocker.h>
+#include <gudhi/Off_reader.h>
+#include <gudhi/Point.h>
+
 #include <boost/timer/timer.hpp>
 #include <iostream>
-#include "gudhi/Edge_contraction.h"
-#include "gudhi/Skeleton_blocker.h"
-#include "gudhi/Off_reader.h"
-#include "gudhi/Point.h"
 
 using namespace std;
 using namespace Gudhi;
 using namespace skbl;
 using namespace contraction;
 
-
-struct Geometry_trait{
-	typedef Point_d Point;
+struct Geometry_trait {
+  typedef Point_d Point;
 };
 
-
 typedef Geometry_trait::Point Point;
 typedef Skeleton_blocker_simple_geometric_traits<Geometry_trait> Complex_geometric_traits;
 typedef Skeleton_blocker_geometric_complex< Complex_geometric_traits > Complex;
@@ -44,62 +43,62 @@ typedef Edge_profile<Complex> Profile;
 typedef Skeleton_blocker_contractor<Complex> Complex_contractor;
 
 template<typename ComplexType>
-void build_rips(ComplexType& complex, double offset){
-	if (offset<=0) return;
-	auto vertices = complex.vertex_range();
-	for (auto p = vertices.begin(); p != vertices.end(); ++p)
-		for (auto q = p; ++q != vertices.end(); /**/){
-			if ( squared_dist(complex.point(*p), complex.point(*q)) < 4 * offset * offset)
-				complex.add_edge(*p,*q);
-		}
+void build_rips(ComplexType& complex, double offset) {
+  if (offset <= 0) return;
+  auto vertices = complex.vertex_range();
+  for (auto p = vertices.begin(); p != vertices.end(); ++p)
+    for (auto q = p; ++q != vertices.end(); /**/) {
+      if (squared_dist(complex.point(*p), complex.point(*q)) < 4 * offset * offset)
+        complex.add_edge_without_blockers(*p, *q);
+    }
 }
 
-int main (int argc, char *argv[])
-{
-	if (argc!=3){
-		std::cerr << "Usage "<<argv[0]<<" ../../../data/meshes/SO3_10000.off 0.3 to load the file ../../data/SO3_10000.off and contract the Rips complex built with paremeter 0.3.\n";
-		return -1;
-	}
+int main(int argc, char *argv[]) {
+  if (argc != 3) {
+    std::cerr << "Usage " << argv[0] << " ../../../data/meshes/SO3_10000.off 0.3 to load the file " <<
+        "../../data/SO3_10000.off and contract the Rips complex built with paremeter 0.3.\n";
+    return -1;
+  }
 
-	Complex complex;
+  Complex complex;
 
-	// load only the points
-	Skeleton_blocker_off_reader<Complex> off_reader(argv[1],complex,true);
-	if(!off_reader.is_valid()){
-		std::cerr << "Unable to read file:"<<argv[1]<<std::endl;
-		return EXIT_FAILURE;
-	}
+  // load only the points
+  Skeleton_blocker_off_reader<Complex> off_reader(argv[1], complex, true);
+  if (!off_reader.is_valid()) {
+    std::cerr << "Unable to read file:" << argv[1] << std::endl;
+    return EXIT_FAILURE;
+  }
 
-	std::cout << "Build the Rips complex with "<<complex.num_vertices()<<" vertices"<<std::endl;
+  std::cout << "Build the Rips complex with " << complex.num_vertices() << " vertices" << std::endl;
 
-	build_rips(complex,atof(argv[2]));
+  build_rips(complex, atof(argv[2]));
 
-	boost::timer::auto_cpu_timer t;
+  boost::timer::auto_cpu_timer t;
 
-	std::cout << "Initial complex has "<<
-			complex.num_vertices()<<" vertices and "<<
-			complex.num_edges()<<" edges"<<std::endl;
+  std::cout << "Initial complex has " <<
+      complex.num_vertices() << " vertices and " <<
+      complex.num_edges() << " edges" << std::endl;
 
-	Complex_contractor contractor(complex,
-			new Edge_length_cost<Profile>,
-			contraction::make_first_vertex_placement<Profile>(),
-			contraction::make_link_valid_contraction<Profile>(),
-			contraction::make_remove_popable_blockers_visitor<Profile>());
-	contractor.contract_edges();
+  Complex_contractor contractor(complex,
+                                new Edge_length_cost<Profile>,
+                                contraction::make_first_vertex_placement<Profile>(),
+                                contraction::make_link_valid_contraction<Profile>(),
+                                contraction::make_remove_popable_blockers_visitor<Profile>());
+  contractor.contract_edges();
 
-	std::cout << "Counting final number of simplices \n";
-	unsigned num_simplices = std::distance(complex.simplex_range().begin(),complex.simplex_range().end());
+  std::cout << "Counting final number of simplices \n";
+  unsigned num_simplices = std::distance(complex.complex_simplex_range().begin(), complex.complex_simplex_range().end());
 
-	std::cout << "Final complex has "<<
-			complex.num_vertices()<<" vertices, "<<
-			complex.num_edges()<<" edges, "<<
-			complex.num_blockers()<<" blockers and "<<
-			num_simplices<<" simplices"<<std::endl;
+  std::cout << "Final complex has " <<
+      complex.num_vertices() << " vertices, " <<
+      complex.num_edges() << " edges, " <<
+      complex.num_blockers() << " blockers and " <<
+      num_simplices << " simplices" << std::endl;
 
 
-	std::cout << "Time to simplify and enumerate simplices:\n";
+  std::cout << "Time to simplify and enumerate simplices:\n";
 
-	return EXIT_SUCCESS;
+  return EXIT_SUCCESS;
 }
 
 
diff --git a/src/Contraction/include/gudhi/Contraction/CGAL_queue/Modifiable_priority_queue.h b/src/Contraction/include/gudhi/Contraction/CGAL_queue/Modifiable_priority_queue.h
index 10b89e13..5a55c513 100644
--- a/src/Contraction/include/gudhi/Contraction/CGAL_queue/Modifiable_priority_queue.h
+++ b/src/Contraction/include/gudhi/Contraction/CGAL_queue/Modifiable_priority_queue.h
@@ -16,76 +16,86 @@
 //
 // Author(s)     : Fernando Cacciola <fernando.cacciola@geometryfactory.com>
 //
-#ifndef CGAL_MODIFIABLE_PRIORITY_QUEUE_H
-#define CGAL_MODIFIABLE_PRIORITY_QUEUE_H
+#ifndef CONTRACTION_CGAL_QUEUE_MODIFIABLE_PRIORITY_QUEUE_H_
+#define CONTRACTION_CGAL_QUEUE_MODIFIABLE_PRIORITY_QUEUE_H_
 
 #define CGAL_SURFACE_MESH_SIMPLIFICATION_USE_RELAXED_HEAP
 
-#include <climits> // Neeeded by the following Boost header for CHAR_BIT.
 #include <boost/optional.hpp>
 #include <boost/pending/relaxed_heap.hpp>
 
-namespace CGAL {
+#include <climits>  // Neeeded by the following Boost header for CHAR_BIT.
+#include <functional>  // for less
 
-template <class IndexedType_ 
-         ,class Compare_ = std::less<IndexedType_>
-         ,class ID_      = boost::identity_property_map
-         >
-class Modifiable_priority_queue
-{
-public:
+namespace CGAL {
 
+template <class IndexedType_, class Compare_ = std::less<IndexedType_>, class ID_ = boost::identity_property_map>
+class Modifiable_priority_queue {
+ public:
   typedef Modifiable_priority_queue Self;
-  
-  typedef IndexedType_ IndexedType ;
-  typedef Compare_     Compare;
-  typedef ID_          ID ;
-  
-  typedef boost::relaxed_heap<IndexedType,Compare,ID> Heap;
+
+  typedef IndexedType_ IndexedType;
+  typedef Compare_ Compare;
+  typedef ID_ ID;
+
+  typedef boost::relaxed_heap<IndexedType, Compare, ID> Heap;
   typedef typename Heap::value_type value_type;
-  typedef typename Heap::size_type  size_type;
-  
-  typedef bool handle ;
-  
-public:
-
-  Modifiable_priority_queue( size_type largest_ID, Compare const& c, ID const& id ) : mHeap(largest_ID,c,id) {}
-  
-  handle push ( value_type const& v ) { mHeap.push(v) ; return handle(true) ; }
-  
-  handle update ( value_type const& v, handle h ) { mHeap.update(v); return h ; }
-  
-  handle erase ( value_type const& v, handle  ) { mHeap.remove(v); return null_handle() ; }
-
-  value_type top() const { return mHeap.top() ; }
-  
-  void pop() { mHeap.pop(); }
-  
-  bool empty() const { return mHeap.empty() ; }
-
-  bool contains ( value_type const& v ) { return mHeap.contains(v) ; }
-
-  boost::optional<value_type> extract_top()
-  {
-    boost::optional<value_type> r ;
-    if ( !empty() )
-    {
+  typedef typename Heap::size_type size_type;
+
+  typedef bool handle;
+
+ public:
+  Modifiable_priority_queue(size_type largest_ID, Compare const& c, ID const& id) : mHeap(largest_ID, c, id) { }
+
+  handle push(value_type const& v) {
+    mHeap.push(v);
+    return handle(true);
+  }
+
+  handle update(value_type const& v, handle h) {
+    mHeap.update(v);
+    return h;
+  }
+
+  handle erase(value_type const& v, handle) {
+    mHeap.remove(v);
+    return null_handle();
+  }
+
+  value_type top() const {
+    return mHeap.top();
+  }
+
+  void pop() {
+    mHeap.pop();
+  }
+
+  bool empty() const {
+    return mHeap.empty();
+  }
+
+  bool contains(value_type const& v) {
+    return mHeap.contains(v);
+  }
+
+  boost::optional<value_type> extract_top() {
+    boost::optional<value_type> r;
+    if (!empty()) {
       value_type v = top();
       pop();
-      r = boost::optional<value_type>(v) ;
-    }  
-    return r ;
+      r = boost::optional<value_type>(v);
+    }
+    return r;
+  }
+
+  static handle null_handle() {
+    return handle(false);
   }
-  
-  static handle null_handle() { return handle(false); }
-  
-private:
 
-  Heap mHeap ;  
-    
-} ;
+ private:
+  Heap mHeap;
+};
 
-} //namespace CGAL
+}  // namespace CGAL
 
-#endif
- 
+#endif  // CONTRACTION_CGAL_QUEUE_MODIFIABLE_PRIORITY_QUEUE_H_
diff --git a/src/Contraction/include/gudhi/Contraction/Edge_profile.h b/src/Contraction/include/gudhi/Contraction/Edge_profile.h
index f90bd71a..e4910b27 100644
--- a/src/Contraction/include/gudhi/Contraction/Edge_profile.h
+++ b/src/Contraction/include/gudhi/Contraction/Edge_profile.h
@@ -1,130 +1,130 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-
-#ifndef GUDHI_EDGE_PROFILE_H_
-#define GUDHI_EDGE_PROFILE_H_
-//#include "combinatorics/Skeleton_blocker/Simplex.h"
-
-
-namespace Gudhi{
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef CONTRACTION_EDGE_PROFILE_H_
+#define CONTRACTION_EDGE_PROFILE_H_
+
+#include <ostream>
+
+namespace Gudhi {
 
 namespace contraction {
-template<typename GeometricSimplifiableComplex> class Edge_profile{
 
-public:
-	typedef GeometricSimplifiableComplex Complex;
-	typedef typename Complex::GT GT;
+template<typename GeometricSimplifiableComplex> class Edge_profile {
+ public:
+  typedef GeometricSimplifiableComplex Complex;
+  typedef typename Complex::GT GT;
 
-	typedef typename GeometricSimplifiableComplex::Vertex_handle Vertex_handle;
-	typedef typename GeometricSimplifiableComplex::Root_vertex_handle Root_vertex_handle;
+  typedef typename GeometricSimplifiableComplex::Vertex_handle Vertex_handle;
+  typedef typename GeometricSimplifiableComplex::Root_vertex_handle Root_vertex_handle;
 
 
-	typedef typename GeometricSimplifiableComplex::Edge_handle Edge_handle;
-	typedef typename GeometricSimplifiableComplex::Graph_vertex Graph_vertex;
-	typedef typename GeometricSimplifiableComplex::Graph_edge Graph_edge;
-	typedef typename GeometricSimplifiableComplex::Point Point;
+  typedef typename GeometricSimplifiableComplex::Edge_handle Edge_handle;
+  typedef typename GeometricSimplifiableComplex::Graph_vertex Graph_vertex;
+  typedef typename GeometricSimplifiableComplex::Graph_edge Graph_edge;
+  typedef typename GeometricSimplifiableComplex::Point Point;
 
+  Edge_profile(GeometricSimplifiableComplex& complex, Edge_handle edge) : complex_(complex), edge_handle_(edge),
+      v0_(complex_.first_vertex(edge_handle_)), v1_(complex_.second_vertex(edge_handle_)) {
+    assert(complex_.get_address(complex_[edge_handle_].first()));
+    assert(complex_.get_address(complex_[edge_handle_].second()));
+    assert(complex_.contains_edge(v0_handle(), v1_handle()));
+    assert(v0_handle() != v1_handle());
+  }
 
+  virtual ~Edge_profile() { }
 
+  GeometricSimplifiableComplex& complex() const {
+    return complex_;
+  }
 
-	Edge_profile( GeometricSimplifiableComplex& complex,Edge_handle edge):complex_(complex),edge_handle_(edge),
-			v0_(complex_.first_vertex(edge_handle_)),v1_(complex_.second_vertex(edge_handle_))
-{
-		assert(complex_.get_address(complex_[edge_handle_].first()));
-		assert(complex_.get_address(complex_[edge_handle_].second()));
-		assert(complex_.contains_edge(v0_handle(),v1_handle()));
-		assert(v0_handle() != v1_handle());
-}
+  Edge_handle edge_handle() const {
+    return edge_handle_;
+  }
 
-	virtual ~Edge_profile(){	}
+  Graph_edge& edge() const {
+    return complex_[edge_handle_];
+  }
 
+  Graph_vertex& v0() const {
+    return complex_[v0_handle()];
+  }
 
-	GeometricSimplifiableComplex& complex() const {
-		return complex_;
-	}
+  Graph_vertex& v1() const {
+    return complex_[v1_handle()];
+  }
 
-	Edge_handle edge_handle() const{
-		return edge_handle_;
-	}
+  Vertex_handle v0_handle() const {
+    return v0_;
+    // Root_vertex_handle root = complex_[edge_handle_].first();
+    // assert(complex_.get_address(root));
+    // return *complex_.get_address(root);
+  }
 
-	Graph_edge& edge() const{
-		return complex_[edge_handle_];
-	}
+  Vertex_handle v1_handle() const {
+    return v1_;
+    // Root_vertex_handle root = complex_[edge_handle_].second();
+    // assert(complex_.get_address(root));
+    // return *complex_.get_address(root);
+  }
 
+  const Point& p0() const {
+    return complex_.point(v0_handle());
+  }
 
-	Graph_vertex& v0() const{return complex_[v0_handle()];}
-	Graph_vertex& v1() const{return complex_[v1_handle()];}
+  const Point& p1() const {
+    return complex_.point(v1_handle());
+  }
 
+  friend std::ostream& operator<<(std::ostream& o, const Edge_profile& v) {
+    return o << "v0:" << v.v0_handle() << " v1:" << v.v1_handle();
+  }
 
-	Vertex_handle v0_handle() const{
-		return v0_;
-//		Root_vertex_handle root = complex_[edge_handle_].first();
-//		assert(complex_.get_address(root));
-//		return *complex_.get_address(root);
-	}
+ private:
+  GeometricSimplifiableComplex& complex_;
 
-	Vertex_handle v1_handle() const{
-		return v1_;
-//		Root_vertex_handle root = complex_[edge_handle_].second();
-//		assert(complex_.get_address(root));
-//		return *complex_.get_address(root);
-	}
+  Edge_handle edge_handle_;
 
-	const Point& p0() const {return complex_.point(v0_handle());}
+  Vertex_handle v0_;
 
-	const Point& p1() const {return complex_.point(v1_handle());}
-
-	friend std::ostream& operator << (std::ostream& o, const Edge_profile & v){
-		o << "v0:"<<v.v0_handle() << " v1:"<<v.v1_handle();
-		return o;
-	}
-private:
-
-	GeometricSimplifiableComplex& complex_;
-
-	Edge_handle edge_handle_;
-
-	Vertex_handle v0_;
+  Vertex_handle v1_;
+};
 
-	Vertex_handle v1_;
+template<typename EdgeProfile> class Edge_profile_factory {
+ public:
+  typedef typename EdgeProfile::Edge_handle Edge_handle_;
+  typedef typename EdgeProfile::Complex Complex_;
 
-};
+  virtual EdgeProfile make_profile(
+                                   Complex_& complex,
+                                   Edge_handle_ edge) const {
+    return EdgeProfile(complex, edge);
+  }
 
-template<typename EdgeProfile> class Edge_profile_factory{
-public:
-	typedef typename EdgeProfile::Edge_handle Edge_handle_;
-	typedef typename EdgeProfile::Complex Complex_;
-	virtual EdgeProfile make_profile(
-			Complex_& complex,
-			Edge_handle_ edge) const{
-		return EdgeProfile(complex,edge);
-	}
-
-	virtual ~Edge_profile_factory(){};
+  virtual ~Edge_profile_factory() { }
 };
 
-
 }  // namespace contraction
 
-}  // namespace GUDHI
+}  // namespace Gudhi
 
-#endif /* GUDHI_EDGE_PROFILE_H_ */
+#endif  // CONTRACTION_EDGE_PROFILE_H_
diff --git a/src/Contraction/include/gudhi/Contraction/policies/Contraction_visitor.h b/src/Contraction/include/gudhi/Contraction/policies/Contraction_visitor.h
index b8b1e87a..7ee05aad 100644
--- a/src/Contraction/include/gudhi/Contraction/policies/Contraction_visitor.h
+++ b/src/Contraction/include/gudhi/Contraction/policies/Contraction_visitor.h
@@ -1,32 +1,32 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-
-#ifndef GUDHI_CONTRACTION_VISITOR_H_
-#define GUDHI_CONTRACTION_VISITOR_H_
-
-#include "gudhi/Contraction/Edge_profile.h"
-#include "boost/optional.hpp"
-
-namespace Gudhi{
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef CONTRACTION_POLICIES_CONTRACTION_VISITOR_H_
+#define CONTRACTION_POLICIES_CONTRACTION_VISITOR_H_
+
+#include <gudhi/Contraction/Edge_profile.h>
+#include <boost/optional.hpp>
+
+namespace Gudhi {
 
 namespace contraction {
 
@@ -36,66 +36,56 @@ namespace contraction {
  *@ingroup contr
  */
 template <typename EdgeProfile>
-class Contraction_visitor {//: public Dummy_complex_visitor<typename EdgeProfile::Vertex_handle>  {
-public:
-	//typedef typename ComplexType::GeometryTrait GT;
-	typedef EdgeProfile Profile;
-	typedef double FT;
-	typedef typename Profile::Complex Complex;
-	typedef Complex ComplexType;
-	typedef typename ComplexType::Point Point;
-
-
-	virtual ~Contraction_visitor(){};
-
-	/**
-	 * @brief Called before the edge contraction process starts.
-	 */
-	virtual void on_started (ComplexType & complex){}
-
-	/**
-	 * @brief Called when the algorithm stops.
-	 */
-	virtual void on_stop_condition_reached (){}
-
-
-	/**
-	 * @brief Called during the collecting phase (when a cost is assigned to the edges), for each edge collected.
-	 */
-	virtual void on_collected (const Profile &profile, boost::optional< FT > cost){}
-
-	/**
-	 * @brief Called during the processing phase (when edges are contracted), for each edge that is selected.
-	 */
-	virtual void on_selected (const Profile &profile, boost::optional< FT > cost, int initial_count, int current_count){}
-
-
-	/**
-	 * @brief Called when an edge is about to be contracted and replaced by a vertex whose position is *placement.
-	 */
-	virtual void on_contracting(const Profile &profile, boost::optional< Point > placement){
-	}
-
-
-
-	/**
-	 * @brief Called when after an edge has been contracted onto a new point placement.
-	 * A possibility would to remove popable blockers at this point for instance.
-	 */
-	virtual void on_contracted(const Profile  &profile, boost::optional< Point > placement){
-
-	}
-
-
-	/**
-	 * @brief Called for each selected edge which cannot be contracted because the ValidContractionPredicate is false
-	 */
-	virtual void on_non_valid(const Profile  &profile){}
-
+class Contraction_visitor {  // : public Dummy_complex_visitor<typename EdgeProfile::Vertex_handle>  {
+ public:
+  // typedef typename ComplexType::GeometryTrait GT;
+  typedef EdgeProfile Profile;
+  typedef double FT;
+  typedef typename Profile::Complex Complex;
+  typedef Complex ComplexType;
+  typedef typename ComplexType::Point Point;
+
+  virtual ~Contraction_visitor() { }
+
+  /**
+   * @brief Called before the edge contraction process starts.
+   */
+  virtual void on_started(ComplexType & complex) { }
+
+  /**
+   * @brief Called when the algorithm stops.
+   */
+  virtual void on_stop_condition_reached() { }
+
+  /**
+   * @brief Called during the collecting phase (when a cost is assigned to the edges), for each edge collected.
+   */
+  virtual void on_collected(const Profile &profile, boost::optional< FT > cost) { }
+
+  /**
+   * @brief Called during the processing phase (when edges are contracted), for each edge that is selected.
+   */
+  virtual void on_selected(const Profile &profile, boost::optional< FT > cost, int initial_count, int current_count) { }
+
+  /**
+   * @brief Called when an edge is about to be contracted and replaced by a vertex whose position is *placement.
+   */
+  virtual void on_contracting(const Profile &profile, boost::optional< Point > placement) { }
+
+  /**
+   * @brief Called when after an edge has been contracted onto a new point placement.
+   * A possibility would to remove popable blockers at this point for instance.
+   */
+  virtual void on_contracted(const Profile &profile, boost::optional< Point > placement) { }
+
+  /**
+   * @brief Called for each selected edge which cannot be contracted because the ValidContractionPredicate is false
+   */
+  virtual void on_non_valid(const Profile &profile) { }
 };
 
 }  // namespace contraction
 
-}  // namespace GUDHI
+}  // namespace Gudhi
 
-#endif /* GUDHI_CONTRACTION_VISITOR_H_ */
+#endif  // CONTRACTION_POLICIES_CONTRACTION_VISITOR_H_
diff --git a/src/Contraction/include/gudhi/Contraction/policies/Cost_policy.h b/src/Contraction/include/gudhi/Contraction/policies/Cost_policy.h
index 3cb18c86..f4d343ec 100644
--- a/src/Contraction/include/gudhi/Contraction/policies/Cost_policy.h
+++ b/src/Contraction/include/gudhi/Contraction/policies/Cost_policy.h
@@ -1,51 +1,53 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-
-#ifndef GUDHI_COST_POLICY_H_
-#define GUDHI_COST_POLICY_H_
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef CONTRACTION_POLICIES_COST_POLICY_H_
+#define CONTRACTION_POLICIES_COST_POLICY_H_
 
 #include <boost/optional.hpp>
 
-namespace Gudhi{
+namespace Gudhi {
 
 namespace contraction {
 
 /**
-*@brief Policy to specify the cost of contracting an edge.
+ *@brief Policy to specify the cost of contracting an edge.
  *@ingroup contr
-*/ 
-template< typename EdgeProfile> class Cost_policy{
-public:
-	typedef typename EdgeProfile::Point Point;
-	typedef typename EdgeProfile::Graph_vertex Graph_vertex;
+ */
+template< typename EdgeProfile>
+class Cost_policy {
+ public:
+  typedef typename EdgeProfile::Point Point;
+  typedef typename EdgeProfile::Graph_vertex Graph_vertex;
 
-	typedef boost::optional<double> Cost_type;
+  typedef boost::optional<double> Cost_type;
 
-	virtual Cost_type operator()(const EdgeProfile& profile, const boost::optional<Point>& placement) const =0;
-	virtual ~Cost_policy(){
-	};
+  virtual Cost_type operator()(const EdgeProfile& profile, const boost::optional<Point>& placement) const = 0;
+
+  virtual ~Cost_policy() { }
 };
 
 }  // namespace contraction
 
-}  // namespace GUDHI
-#endif /* GUDHI_COST_POLICY_H_ */
+}  // namespace Gudhi
+
+#endif  // CONTRACTION_POLICIES_COST_POLICY_H_
diff --git a/src/Contraction/include/gudhi/Contraction/policies/Dummy_valid_contraction.h b/src/Contraction/include/gudhi/Contraction/policies/Dummy_valid_contraction.h
index de473944..5d329496 100644
--- a/src/Contraction/include/gudhi/Contraction/policies/Dummy_valid_contraction.h
+++ b/src/Contraction/include/gudhi/Contraction/policies/Dummy_valid_contraction.h
@@ -1,51 +1,49 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-
-#ifndef GUDHI_DUMMY_VALID_CONTRACTION_H_
-#define GUDHI_DUMMY_VALID_CONTRACTION_H_
-
-#include "Valid_contraction_policy.h"
-
-namespace Gudhi{
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef CONTRACTION_POLICIES_DUMMY_VALID_CONTRACTION_H_
+#define CONTRACTION_POLICIES_DUMMY_VALID_CONTRACTION_H_
+
+#include <gudhi/Contraction/policies/Valid_contraction_policy.h>
+
+namespace Gudhi {
 
 namespace contraction {
 
-
-
-  /**
-  *@brief Policy that accept all edge contraction.
-  */
-template< typename EdgeProfile> class Dummy_valid_contraction : public Valid_contraction_policy<EdgeProfile>{
-public:
-	typedef typename EdgeProfile::Point Point;
-	bool operator()(const EdgeProfile& profile,const boost::optional<Point>& placement){
-		return true;
-	}
+/**
+ *@brief Policy that accept all edge contraction.
+ */
+template< typename EdgeProfile>
+class Dummy_valid_contraction : public Valid_contraction_policy<EdgeProfile> {
+ public:
+  typedef typename EdgeProfile::Point Point;
+
+  bool operator()(const EdgeProfile& profile, const boost::optional<Point>& placement) {
+    return true;
+  }
 };
 
 }  // namespace contraction
 
-}  // namespace GUDHI
-
-
+}  // namespace Gudhi
 
-#endif /* GUDHI_DUMMY_VALID_CONTRACTION_H_ */
+#endif  // CONTRACTION_POLICIES_DUMMY_VALID_CONTRACTION_H_
diff --git a/src/Contraction/include/gudhi/Contraction/policies/Edge_length_cost.h b/src/Contraction/include/gudhi/Contraction/policies/Edge_length_cost.h
index b22ada0d..dac2d448 100644
--- a/src/Contraction/include/gudhi/Contraction/policies/Edge_length_cost.h
+++ b/src/Contraction/include/gudhi/Contraction/policies/Edge_length_cost.h
@@ -1,56 +1,56 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-
-#ifndef GUDHI_EDGE_LENGTH_COST_H_
-#define GUDHI_EDGE_LENGTH_COST_H_
-
-#include "Cost_policy.h"
-
-namespace Gudhi{
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
 
-namespace contraction {
+#ifndef CONTRACTION_POLICIES_EDGE_LENGTH_COST_H_
+#define CONTRACTION_POLICIES_EDGE_LENGTH_COST_H_
+
+#include <gudhi/Contraction/policies/Cost_policy.h>
 
+namespace Gudhi {
+
+namespace contraction {
 
 /**
  * @brief return a cost corresponding to the squared length of the edge
  */
-template< typename EdgeProfile> class Edge_length_cost : public Cost_policy<EdgeProfile>{
-public:
-	typedef typename Cost_policy<EdgeProfile>::Cost_type Cost_type;
-	typedef typename EdgeProfile::Point Point;
-	Cost_type operator()(const EdgeProfile& profile, const boost::optional<Point>& placement) const override{
-		double res = 0;
-		auto p0_coord = profile.p0().begin();
-		auto p1_coord = profile.p1().begin();
-		for(; p0_coord != profile.p0().end(); p0_coord++, p1_coord++){
-			res += (*p0_coord - *p1_coord) * (*p0_coord - *p1_coord);
-		}
-		return res;
-	}
-
+template< typename EdgeProfile>
+class Edge_length_cost : public Cost_policy<EdgeProfile> {
+ public:
+  typedef typename Cost_policy<EdgeProfile>::Cost_type Cost_type;
+  typedef typename EdgeProfile::Point Point;
+
+  Cost_type operator()(const EdgeProfile& profile, const boost::optional<Point>& placement) const override {
+    double res = 0;
+    auto p0_coord = profile.p0().begin();
+    auto p1_coord = profile.p1().begin();
+    for (; p0_coord != profile.p0().end(); p0_coord++, p1_coord++) {
+      res += (*p0_coord - *p1_coord) * (*p0_coord - *p1_coord);
+    }
+    return res;
+  }
 };
 
 }  // namespace contraction
 
-}  // namespace GUDHI
+}  // namespace Gudhi
 
-#endif /* GUDHI_EDGE_LENGTH_COST_H_ */
+#endif  // CONTRACTION_POLICIES_EDGE_LENGTH_COST_H_
diff --git a/src/Contraction/include/gudhi/Contraction/policies/First_vertex_placement.h b/src/Contraction/include/gudhi/Contraction/policies/First_vertex_placement.h
index 93abac35..1f68db0d 100644
--- a/src/Contraction/include/gudhi/Contraction/policies/First_vertex_placement.h
+++ b/src/Contraction/include/gudhi/Contraction/policies/First_vertex_placement.h
@@ -1,53 +1,52 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-
-#ifndef GUDHI_FIRST_VERTEX_PLACEMENT_H_
-#define GUDHI_FIRST_VERTEX_PLACEMENT_H_
-
-#include "Placement_policy.h"
-
-namespace Gudhi{
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
 
-namespace contraction {
+#ifndef CONTRACTION_POLICIES_FIRST_VERTEX_PLACEMENT_H_
+#define CONTRACTION_POLICIES_FIRST_VERTEX_PLACEMENT_H_
+
+#include <gudhi/Contraction/policies/Placement_policy.h>
+
+namespace Gudhi {
 
+namespace contraction {
 
 /**
  * @brief Places the contracted point onto the first point of the edge
  */
-template< typename EdgeProfile> class First_vertex_placement : public Placement_policy<EdgeProfile>{
-
-public:
-	typedef typename EdgeProfile::Point Point;
-	typedef typename EdgeProfile::Edge_handle Edge_handle;
+template< typename EdgeProfile>
+class First_vertex_placement : public Placement_policy<EdgeProfile> {
+ public:
+  typedef typename EdgeProfile::Point Point;
+  typedef typename EdgeProfile::Edge_handle Edge_handle;
 
-	typedef typename Placement_policy<EdgeProfile>::Placement_type Placement_type;
+  typedef typename Placement_policy<EdgeProfile>::Placement_type Placement_type;
 
-	Placement_type operator()(const EdgeProfile& profile) const override{
-		return Placement_type(profile.p0());
-	}
+  Placement_type operator()(const EdgeProfile& profile) const override {
+    return Placement_type(profile.p0());
+  }
 };
-}  // namespace contraction
 
-}  // namespace GUDHI
+}  // namespace contraction
 
+}  // namespace Gudhi
 
-#endif /* GUDHI_FIRST_VERTEX_PLACEMENT_H_ */
+#endif  // CONTRACTION_POLICIES_FIRST_VERTEX_PLACEMENT_H_
diff --git a/src/Contraction/include/gudhi/Contraction/policies/Link_condition_valid_contraction.h b/src/Contraction/include/gudhi/Contraction/policies/Link_condition_valid_contraction.h
index c901e629..919df243 100644
--- a/src/Contraction/include/gudhi/Contraction/policies/Link_condition_valid_contraction.h
+++ b/src/Contraction/include/gudhi/Contraction/policies/Link_condition_valid_contraction.h
@@ -1,54 +1,56 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-
-#ifndef GUDHI_LINK_CONDITION_VALID_CONTRACTION_H_
-#define GUDHI_LINK_CONDITION_VALID_CONTRACTION_H_
-
-#include "gudhi/Utils.h"
-#include "Valid_contraction_policy.h"
-
-
-namespace Gudhi{
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef CONTRACTION_POLICIES_LINK_CONDITION_VALID_CONTRACTION_H_
+#define CONTRACTION_POLICIES_LINK_CONDITION_VALID_CONTRACTION_H_
+
+#include <gudhi/Utils.h>
+#include <gudhi/Contraction/policies/Valid_contraction_policy.h>
+
+
+namespace Gudhi {
 
 namespace contraction {
 
-
-  /**
-  *@brief Policy that only accept edges verifying the link condition (and therefore whose contraction preserving homotopy type). 
-  *@ingroup contr
-  */
-template< typename EdgeProfile> class Link_condition_valid_contraction : public Valid_contraction_policy<EdgeProfile>{
-public:
-	typedef typename EdgeProfile::Edge_handle Edge_handle;
-	typedef typename EdgeProfile::Point Point;
-	//typedef typename EdgeProfile::Edge_handle Edge_handle;
-	bool operator()(const EdgeProfile& profile,const boost::optional<Point>& placement) const override{
-		Edge_handle edge(profile.edge_handle());
-		DBGMSG("Link_condition_valid_contraction:",profile.complex().link_condition(edge));
-		return profile.complex().link_condition(edge);
-	}
+/**
+ *@brief Policy that only accept edges verifying the link condition (and therefore whose contraction preserving homotopy type). 
+ *@ingroup contr
+ */
+template< typename EdgeProfile>
+class Link_condition_valid_contraction : public Valid_contraction_policy<EdgeProfile> {
+ public:
+  typedef typename EdgeProfile::Edge_handle Edge_handle;
+  typedef typename EdgeProfile::Point Point;
+  // typedef typename EdgeProfile::Edge_handle Edge_handle;
+
+  bool operator()(const EdgeProfile& profile, const boost::optional<Point>& placement) const override {
+    Edge_handle edge(profile.edge_handle());
+    DBGMSG("Link_condition_valid_contraction:", profile.complex().link_condition(edge));
+    return profile.complex().link_condition(edge);
+  }
 };
+
 }  // namespace contraction
 
-}  // namespace GUDHI
+}  // namespace Gudhi
 
-#endif /* GUDHI_LINK_CONDITION_VALID_CONTRACTION_H_ */
+#endif  // CONTRACTION_POLICIES_LINK_CONDITION_VALID_CONTRACTION_H_
diff --git a/src/Contraction/include/gudhi/Contraction/policies/Middle_placement.h b/src/Contraction/include/gudhi/Contraction/policies/Middle_placement.h
index 30f0a570..4b59f1b5 100644
--- a/src/Contraction/include/gudhi/Contraction/policies/Middle_placement.h
+++ b/src/Contraction/include/gudhi/Contraction/policies/Middle_placement.h
@@ -1,52 +1,51 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-
-#ifndef GUDHI_MIDDLE_PLACEMENT_H_
-#define GUDHI_MIDDLE_PLACEMENT_H_
-
-#include "Placement_policy.h"
-
-
-namespace Gudhi{
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef CONTRACTION_POLICIES_MIDDLE_PLACEMENT_H_
+#define CONTRACTION_POLICIES_MIDDLE_PLACEMENT_H_
+
+#include <gudhi/Contraction/policies/Placement_policy.h>
+
+namespace Gudhi {
 
 namespace contraction {
 
+template< typename EdgeProfile>
+class Middle_placement : public Placement_policy<EdgeProfile> {
+ public:
+  typedef typename EdgeProfile::Point Point;
+  typedef typename EdgeProfile::Edge_handle Edge_handle;
+  typedef typename EdgeProfile::Graph_vertex Graph_vertex;
 
-  
-template< typename EdgeProfile> class Middle_placement : public Placement_policy<EdgeProfile>{
+  typedef typename Placement_policy<EdgeProfile>::Placement_type Placement_type;
 
-public:
-	typedef typename EdgeProfile::Point Point;
-	typedef typename EdgeProfile::Edge_handle Edge_handle;
-	typedef typename EdgeProfile::Graph_vertex Graph_vertex;
-
-	typedef typename Placement_policy<EdgeProfile>::Placement_type Placement_type;
-
-	Placement_type operator()(const EdgeProfile& profile) const override{
-		//todo compute the middle
-		return Placement_type(profile.p0());
-	}
+  Placement_type operator()(const EdgeProfile& profile) const override {
+    // todo compute the middle
+    return Placement_type(profile.p0());
+  }
 };
+
 }  // namespace contraction
-}  // namespace GUDHI
 
-#endif /* GUDHI_MIDDLE_PLACEMENT_H_ */
+}  // namespace Gudhi
+
+#endif  // CONTRACTION_POLICIES_MIDDLE_PLACEMENT_H_
diff --git a/src/Contraction/include/gudhi/Contraction/policies/Placement_policy.h b/src/Contraction/include/gudhi/Contraction/policies/Placement_policy.h
index 3a804cf0..34ffa49f 100644
--- a/src/Contraction/include/gudhi/Contraction/policies/Placement_policy.h
+++ b/src/Contraction/include/gudhi/Contraction/policies/Placement_policy.h
@@ -1,49 +1,51 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-
-#ifndef GUDHI_PLACEMENT_POLICY_H_
-#define GUDHI_PLACEMENT_POLICY_H_
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef CONTRACTION_POLICIES_PLACEMENT_POLICY_H_
+#define CONTRACTION_POLICIES_PLACEMENT_POLICY_H_
 
 #include <boost/optional.hpp>
 
 namespace Gudhi {
+
 namespace contraction {
 
+/**
+ *@brief Policy to specify where the merged point had to be placed after an edge contraction. 
+ *@ingroup contr
+ */
+template< typename EdgeProfile>
+class Placement_policy {
+ public:
+  typedef typename EdgeProfile::Point Point;
+  typedef boost::optional<Point> Placement_type;
 
-  /**
-  *@brief Policy to specify where the merged point had to be placed after an edge contraction. 
-  *@ingroup contr
-  */
-template< typename EdgeProfile> class Placement_policy{
-public:
-	typedef typename EdgeProfile::Point Point;
-	typedef boost::optional<Point> Placement_type;
+  virtual Placement_type operator()(const EdgeProfile& profile) const = 0;
 
-	virtual Placement_type operator()(const EdgeProfile& profile) const=0;
-	virtual ~Placement_policy(){};
+  virtual ~Placement_policy() { }
 };
 
-
 }  // namespace contraction
-}  // namespace GUDHI
 
-#endif /* GUDHI_PLACEMENT_POLICY_H_ */
+}  // namespace Gudhi
+
+#endif  // CONTRACTION_POLICIES_PLACEMENT_POLICY_H_
diff --git a/src/Contraction/include/gudhi/Contraction/policies/Valid_contraction_policy.h b/src/Contraction/include/gudhi/Contraction/policies/Valid_contraction_policy.h
index bee2ecd7..78d61173 100644
--- a/src/Contraction/include/gudhi/Contraction/policies/Valid_contraction_policy.h
+++ b/src/Contraction/include/gudhi/Contraction/policies/Valid_contraction_policy.h
@@ -1,47 +1,51 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-
-#ifndef GUDHI_VALID_CONTRACTION_POLICY_H_
-#define GUDHI_VALID_CONTRACTION_POLICY_H_
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef CONTRACTION_POLICIES_VALID_CONTRACTION_POLICY_H_
+#define CONTRACTION_POLICIES_VALID_CONTRACTION_POLICY_H_
 
 namespace Gudhi {
+
 namespace contraction {
 
-  /**
-  *@brief Policy to specify if an edge contraction is valid or not. 
-  *@ingroup contr
-  */
-template< typename EdgeProfile> class Valid_contraction_policy{
-public:
-	typedef typename EdgeProfile::Point Point;
-	typedef typename EdgeProfile::Edge_handle Edge_handle;
-	typedef typename EdgeProfile::Graph_vertex Graph_vertex;
-
-	virtual bool operator()(const EdgeProfile& profile,const boost::optional<Point>& placement) const =0;
-	virtual ~Valid_contraction_policy(){};
+/**
+ *@brief Policy to specify if an edge contraction is valid or not. 
+ *@ingroup contr
+ */
+template< typename EdgeProfile>
+class Valid_contraction_policy {
+ public:
+  typedef typename EdgeProfile::Point Point;
+  typedef typename EdgeProfile::Edge_handle Edge_handle;
+  typedef typename EdgeProfile::Graph_vertex Graph_vertex;
+
+  virtual bool operator()(const EdgeProfile& profile, const boost::optional<Point>& placement) const = 0;
+
+  virtual ~Valid_contraction_policy() { }
 };
 
 }  // namespace contraction
-}  // namespace GUDHI
+
+}  // namespace Gudhi
 
 
-#endif /* GUDHI_VALID_CONTRACTION_POLICY_H_ */
+#endif  // CONTRACTION_POLICIES_VALID_CONTRACTION_POLICY_H_
diff --git a/src/Contraction/include/gudhi/Edge_contraction.h b/src/Contraction/include/gudhi/Edge_contraction.h
index 2c254710..ee3e3de1 100644
--- a/src/Contraction/include/gudhi/Edge_contraction.h
+++ b/src/Contraction/include/gudhi/Edge_contraction.h
@@ -20,24 +20,24 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef GUDHI_EDGE_CONTRACTION_H_
-#define GUDHI_EDGE_CONTRACTION_H_
+#ifndef EDGE_CONTRACTION_H_
+#define EDGE_CONTRACTION_H_
 
 
-#include "gudhi/Skeleton_blocker_contractor.h"
-#include "gudhi/Contraction/policies/Edge_length_cost.h"
-#include "gudhi/Contraction/policies/First_vertex_placement.h"
-#include "gudhi/Contraction/policies/Valid_contraction_policy.h"
-#include "gudhi/Contraction/policies/Dummy_valid_contraction.h"
-#include "gudhi/Contraction/policies/Link_condition_valid_contraction.h"
-#include "gudhi/Utils.h"
+#include <gudhi/Skeleton_blocker_contractor.h>
+#include <gudhi/Contraction/policies/Edge_length_cost.h>
+#include <gudhi/Contraction/policies/First_vertex_placement.h>
+#include <gudhi/Contraction/policies/Valid_contraction_policy.h>
+#include <gudhi/Contraction/policies/Dummy_valid_contraction.h>
+#include <gudhi/Contraction/policies/Link_condition_valid_contraction.h>
+#include <gudhi/Utils.h>
 
+namespace Gudhi {
 
-namespace Gudhi{
-namespace contraction{
+namespace contraction {
 
 
-/** \defgroup contr Contraction
+/** \defgroup contr Edge contraction
 
 \author David Salinas
 
@@ -120,9 +120,9 @@ while ensuring its homotopy type is preserved during the contraction (edge are c
   \code{.cpp}
 #include <boost/timer/timer.hpp>
 #include <iostream>
-#include "gudhi/Edge_contraction.h"
-#include "gudhi/Skeleton_blocker.h"
-#include "gudhi/Off_reader.h"
+#include <gudhi/Edge_contraction.h>
+#include <gudhi/Skeleton_blocker.h>
+#include <gudhi/Off_reader.h>
 
 
 using namespace std;
@@ -158,7 +158,7 @@ void build_rips(ComplexType& complex, double offset){
 	for (auto p = vertices.begin(); p != vertices.end(); ++p)
 		for (auto q = p; ++q != vertices.end(); )
 			if (eucl_distance(complex.point(*p), complex.point(*q)) < 2 * offset)
-				complex.add_edge(*p,*q);
+				complex.add_edge_without_blockers(*p,*q);
 }
 
 int main (int argc, char *argv[])
@@ -194,7 +194,7 @@ int main (int argc, char *argv[])
 	contractor.contract_edges();
 
 	std::cout << "Counting final number of simplices \n";
-	unsigned num_simplices = std::distance(complex.simplex_range().begin(),complex.simplex_range().end());
+	unsigned num_simplices = std::distance(complex.star_simplex_range().begin(),complex.star_simplex_range().end());
 
 	std::cout << "Final complex has "<<
 			complex.num_vertices()<<" vertices, "<<
@@ -226,11 +226,11 @@ Time to simplify and enumerate simplices:
 
 
 \copyright GNU General Public License v3.                         
-\verbatim  Contact: David Salinas,     david.salinas@inria.fr \endverbatim
+\verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
 */
-/** @} */  // end defgroup 
+/** @} */  // end defgroup
+}  // namespace contraction
 
-}
-}
+}  // namespace Gudhi
 
-#endif /* GUDHI_EDGE_CONTRACTION_H_ */
+#endif  // EDGE_CONTRACTION_H_
diff --git a/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h b/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h
index dcc05c22..d6350a2c 100644
--- a/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h
+++ b/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h
@@ -20,80 +20,69 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef GUDHI_SKELETON_BLOCKER_CONTRACTOR_H_
-#define GUDHI_SKELETON_BLOCKER_CONTRACTOR_H_
-
-#include <memory>
-#include <cassert>
+#ifndef SKELETON_BLOCKER_CONTRACTOR_H_
+#define SKELETON_BLOCKER_CONTRACTOR_H_
 
 // todo remove the queue to be independent from cgald
-#include "gudhi/Contraction/CGAL_queue/Modifiable_priority_queue.h"
-
-
-#include <list>
-#include <boost/scoped_array.hpp>
-#include <boost/scoped_ptr.hpp>
-
+#include <gudhi/Contraction/CGAL_queue/Modifiable_priority_queue.h>
 
-#include "gudhi/Contraction/Edge_profile.h"
-#include "gudhi/Contraction/policies/Cost_policy.h"
-#include "gudhi/Contraction/policies/Edge_length_cost.h"
-#include "gudhi/Contraction/policies/Placement_policy.h"
-#include "gudhi/Contraction/policies/First_vertex_placement.h"
+#include <gudhi/Contraction/Edge_profile.h>
+#include <gudhi/Contraction/policies/Cost_policy.h>
+#include <gudhi/Contraction/policies/Edge_length_cost.h>
+#include <gudhi/Contraction/policies/Placement_policy.h>
+#include <gudhi/Contraction/policies/First_vertex_placement.h>
+#include <gudhi/Contraction/policies/Valid_contraction_policy.h>
+#include <gudhi/Contraction/policies/Dummy_valid_contraction.h>  // xxx remove
+#include <gudhi/Contraction/policies/Link_condition_valid_contraction.h>  // xxx remove
+#include <gudhi/Contraction/policies/Contraction_visitor.h>
 
-#include "gudhi/Contraction/policies/Valid_contraction_policy.h"
-#include "gudhi/Contraction/policies/Dummy_valid_contraction.h" //xxx remove
-#include "gudhi/Contraction/policies/Link_condition_valid_contraction.h" //xxx remove
+#include <gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h>
+#include <gudhi/Utils.h>
 
-#include "gudhi/Contraction/policies/Contraction_visitor.h"
 
-#include "gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h"
+#include <boost/scoped_array.hpp>
+#include <boost/scoped_ptr.hpp>
 
-#include "gudhi/Utils.h"
+#include <memory>
+#include <cassert>
+#include <list>
+#include <utility>  // for pair
+#include <vector>
 
-namespace Gudhi{
+namespace Gudhi {
 
 namespace contraction {
 
-
-
-
 template <class Profile>
-Placement_policy<Profile>* make_first_vertex_placement(){
-	return new First_vertex_placement<Profile>();
+Placement_policy<Profile>* make_first_vertex_placement() {
+  return new First_vertex_placement<Profile>();
 }
 
 template <class Profile>
-Valid_contraction_policy<Profile>* make_link_valid_contraction(){
-	return new Link_condition_valid_contraction<Profile>();
+Valid_contraction_policy<Profile>* make_link_valid_contraction() {
+  return new Link_condition_valid_contraction<Profile>();
 }
 
-
 /**
-*@brief Visitor to remove popable blockers after an edge contraction.
-*/
+ *@brief Visitor to remove popable blockers after an edge contraction.
+ */
 template <class Profile>
-class Contraction_visitor_remove_popable : public Contraction_visitor<Profile>{
-public:
-	typedef typename Profile::Point Point;
-	typedef typename Profile::Complex Complex;
-	typedef typename Complex::Vertex_handle Vertex_handle;
-
-	void on_contracted(const Profile  &profile, boost::optional< Point > placement) override{
-		profile.complex().remove_all_popable_blockers(profile.v0_handle());
-	}
+class Contraction_visitor_remove_popable : public Contraction_visitor<Profile> {
+ public:
+  typedef typename Profile::Point Point;
+  typedef typename Profile::Complex Complex;
+  typedef typename Complex::Vertex_handle Vertex_handle;
+
+  void on_contracted(const Profile &profile, boost::optional< Point > placement) override {
+    profile.complex().remove_all_popable_blockers(profile.v0_handle());
+  }
 };
 
 template <class Profile>
-Contraction_visitor<Profile>* make_remove_popable_blockers_visitor(){
-	return new Contraction_visitor_remove_popable<Profile>();
+Contraction_visitor<Profile>* make_remove_popable_blockers_visitor() {
+  return new Contraction_visitor_remove_popable<Profile>();
 }
 
-
-
-
-
-
 /**
  *@class Skeleton_blocker_contractor
  *@brief Class that allows to contract iteratively edges of a simplicial complex.
@@ -110,519 +99,484 @@ Contraction_visitor<Profile>* make_remove_popable_blockers_visitor(){
  *  a topological condition (link condition) or a geometrical condition (normals messed up).
  *
  */
-template<
-class GeometricSimplifiableComplex,
-class EdgeProfile = Edge_profile<GeometricSimplifiableComplex>
->
-class Skeleton_blocker_contractor : private skbl::Dummy_complex_visitor<typename GeometricSimplifiableComplex::Vertex_handle>{
-
-	GeometricSimplifiableComplex& complex_;
-
-public:
-	typedef typename GeometricSimplifiableComplex::Graph_vertex Graph_vertex;
-	typedef typename GeometricSimplifiableComplex::Vertex_handle Vertex_handle;
-	typedef typename GeometricSimplifiableComplex::Simplex_handle Simplex_handle;
-	typedef typename GeometricSimplifiableComplex::Simplex_handle_iterator Simplex_handle_iterator;
-
-
+template<class GeometricSimplifiableComplex, class EdgeProfile = Edge_profile<GeometricSimplifiableComplex>>
+class Skeleton_blocker_contractor : private skbl::Dummy_complex_visitor<
+typename GeometricSimplifiableComplex::Vertex_handle> {
+  GeometricSimplifiableComplex& complex_;
 
-	typedef typename GeometricSimplifiableComplex::Root_vertex_handle Root_vertex_handle;
+ public:
+  typedef typename GeometricSimplifiableComplex::Graph_vertex Graph_vertex;
+  typedef typename GeometricSimplifiableComplex::Vertex_handle Vertex_handle;
+  typedef typename GeometricSimplifiableComplex::Simplex Simplex;
+  typedef typename GeometricSimplifiableComplex::Root_vertex_handle Root_vertex_handle;
+  typedef typename GeometricSimplifiableComplex::Graph_edge Graph_edge;
+  typedef typename GeometricSimplifiableComplex::Edge_handle Edge_handle;
+  typedef typename GeometricSimplifiableComplex::Point Point;
 
-	typedef typename GeometricSimplifiableComplex::Graph_edge Graph_edge;
-	typedef typename GeometricSimplifiableComplex::Edge_handle Edge_handle;
-	typedef typename GeometricSimplifiableComplex::Point Point;
+  typedef EdgeProfile Profile;
 
-	typedef EdgeProfile  Profile;
 
+  typedef Cost_policy<Profile> Cost_policy_;
+  typedef Placement_policy<Profile> Placement_policy_;
+  typedef Valid_contraction_policy<Profile> Valid_contraction_policy_;
+  typedef Contraction_visitor<EdgeProfile> Contraction_visitor_;
+  typedef Edge_profile_factory<EdgeProfile> Edge_profile_factory_;
 
-	typedef Cost_policy<Profile> Cost_policy_;
-	typedef Placement_policy<Profile> Placement_policy_;
-	typedef Valid_contraction_policy<Profile> Valid_contraction_policy_;
-	typedef Contraction_visitor<EdgeProfile> Contraction_visitor_;
-	typedef Edge_profile_factory<EdgeProfile> Edge_profile_factory_;
 
 
+  typedef boost::optional<double> Cost_type;
+  typedef boost::optional<Point> Placement_type;
 
-	typedef boost::optional<double> Cost_type;
-	typedef boost::optional<Point> Placement_type ;
+  typedef size_t size_type;
 
-	typedef size_t size_type;
+  typedef Skeleton_blocker_contractor Self;
 
-	typedef Skeleton_blocker_contractor Self ;
+ private:
+  struct Compare_id {
+    Compare_id() : algorithm_(0) { }
 
+    Compare_id(Self const* aAlgorithm) : algorithm_(aAlgorithm) { }
 
+    bool operator()(Edge_handle a, Edge_handle b) const {
+      return algorithm_->get_undirected_edge_id(a) < algorithm_->get_undirected_edge_id(b);
+    }
 
-private:
+    Self const* algorithm_;
+  };
 
-	struct Compare_id
-	{
-		Compare_id() : algorithm_(0) {}
+  struct Compare_cost {
+    Compare_cost() : algorithm_(0) { }
 
-		Compare_id( Self const* aAlgorithm ) : algorithm_(aAlgorithm) {}
+    Compare_cost(Self const* aAlgorithm) : algorithm_(aAlgorithm) { }
 
-		bool operator() ( Edge_handle a, Edge_handle b ) const
-		{
-			return algorithm_->get_undirected_edge_id(a) < algorithm_->get_undirected_edge_id(b);
-		}
+    bool operator()(Edge_handle a, Edge_handle b) const {
+      // NOTE: A cost is an optional<> value.
+      // Absent optionals are ordered first; that is, "none < T" and "T > none" for any defined T != none.
+      // In consequence, edges with undefined costs will be promoted to the top of the priority queue and popped out
+      // first.
+      return algorithm_->get_data(a).cost() < algorithm_->get_data(b).cost();
+    }
 
-		Self const* algorithm_ ;
-	} ;
+    Self const* algorithm_;
+  };
 
-	struct Compare_cost
-	{
-		Compare_cost() : algorithm_(0) {
-		}
+  struct Undirected_edge_id : boost::put_get_helper<size_type, Undirected_edge_id> {
+    typedef boost::readable_property_map_tag category;
+    typedef size_type value_type;
+    typedef size_type reference;
+    typedef Edge_handle key_type;
 
-		Compare_cost( Self const* aAlgorithm ) : algorithm_(aAlgorithm) {
-		}
+    Undirected_edge_id() : algorithm_(0) { }
 
-		bool operator() ( Edge_handle a, Edge_handle b ) const
-		{
-			// NOTE: A cost is an optional<> value.
-			// Absent optionals are ordered first; that is, "none < T" and "T > none" for any defined T != none.
-			// In consequence, edges with undefined costs will be promoted to the top of the priority queue and poped out first.
-			return algorithm_->get_data(a).cost() < algorithm_->get_data(b).cost();
-		}
+    Undirected_edge_id(Self const* aAlgorithm) : algorithm_(aAlgorithm) { }
 
-		Self const* algorithm_ ;
+    size_type operator[](Edge_handle e) const {
+      return algorithm_->get_undirected_edge_id(e);
+    }
 
-	} ;
+    Self const* algorithm_;
+  };
+
+  typedef CGAL::Modifiable_priority_queue<Edge_handle, Compare_cost, Undirected_edge_id> PQ;
+  typedef typename PQ::handle pq_handle;
+
+
+  // An Edge_data is associated with EVERY edge in the complex (collapsible or not).
+  // It relates the edge with the PQ-handle needed to update the priority queue
+  // It also relates the edge with a policy-based cache
 
-	struct Undirected_edge_id : boost::put_get_helper<size_type, Undirected_edge_id>
-	{
-		typedef boost::readable_property_map_tag category;
-		typedef size_type                        value_type;
-		typedef size_type                        reference;
-		typedef Edge_handle                  key_type;
+  class Edge_data {
+   public:
+    Edge_data() : PQHandle_(), cost_() { }
 
-		Undirected_edge_id() : algorithm_(0) {}
+    Cost_type const& cost() const {
+      return cost_;
+    }
+
+    Cost_type & cost() {
+      return cost_;
+    }
+
+    pq_handle PQ_handle() const {
+      return PQHandle_;
+    }
+
+    bool is_in_PQ() const {
+      return PQHandle_ != PQ::null_handle();
+    }
+
+    void set_PQ_handle(pq_handle h) {
+      PQHandle_ = h;
+    }
 
-		Undirected_edge_id( Self const* aAlgorithm ) : algorithm_(aAlgorithm) {}
-
-		size_type operator[] ( Edge_handle e ) const { return algorithm_->get_undirected_edge_id(e); }
-
-		Self const* algorithm_ ;
-	} ;
-
-	typedef CGAL::Modifiable_priority_queue<Edge_handle,Compare_cost,Undirected_edge_id> PQ ;
-	typedef typename PQ::handle pq_handle ;
-
-
-	// An Edge_data is associated with EVERY edge in the complex (collapsible or not).
-	// It relates the edge with the PQ-handle needed to update the priority queue
-	// It also relates the edge with a policy-based cache
-	class Edge_data
-	{
-	public :
-
-		Edge_data() : PQHandle_(),cost_() {}
-
-		Cost_type const& cost() const { return cost_ ; }
-		Cost_type      & cost()       { return cost_ ; }
-
-		pq_handle PQ_handle() const { return PQHandle_ ;}
-
-		bool is_in_PQ() const { return PQHandle_ != PQ::null_handle() ; }
-
-		void set_PQ_handle( pq_handle h ) { PQHandle_ = h ; }
-
-		void reset_PQ_handle() { PQHandle_ = PQ::null_handle() ; }
-
-	private:
-		pq_handle PQHandle_ ;
-		Cost_type cost_ ;
-
-	} ;
-	typedef Edge_data* Edge_data_ptr ;
-	typedef boost::scoped_array<Edge_data> Edge_data_array ;
-
-
-	int get_undirected_edge_id ( Edge_handle edge ) const {
-		return complex_[edge].index() ;
-	}
-
-
-	const Edge_data& get_data ( Edge_handle edge ) const
-	{
-		return edge_data_array_[get_undirected_edge_id(edge)];
-	}
-
-
-	Edge_data& get_data ( Edge_handle edge )
-	{
-		return edge_data_array_[get_undirected_edge_id(edge)];
-	}
-
-	Cost_type get_cost(const Profile & profile) const{
-		return (*cost_policy_)(profile,get_placement(profile));
-	}
-
-	Profile create_profile(Edge_handle edge) const{
-		if(edge_profile_factory_)
-			return edge_profile_factory_->make_profile(complex_,edge);
-		else
-			return Profile(complex_,edge);
-	}
-
-
-	void insert_in_PQ( Edge_handle edge, Edge_data& data )
-	{
-		data.set_PQ_handle(heap_PQ_->push(edge));
-		++current_num_edges_heap_;
-	}
-
-	void update_in_PQ( Edge_handle edge, Edge_data& data )
-	{
-		data.set_PQ_handle(heap_PQ_->update(edge,data.PQ_handle())) ;
-	}
-
-	void remove_from_PQ( Edge_handle edge, Edge_data& data )
-	{
-		data.set_PQ_handle(heap_PQ_->erase(edge,data.PQ_handle()));
-		--current_num_edges_heap_;
-	}
-
-	boost::optional<Edge_handle> pop_from_PQ()	{
-		boost::optional<Edge_handle> edge = heap_PQ_->extract_top();
-		if ( edge )
-			get_data(*edge).reset_PQ_handle();
-		return edge ;
-	}
-
-
-
-private:
-
-	/**
-	 * @brief Collect edges.
-	 *
-	 * Iterates over all edges of the simplicial complex and
-	 * 1) inserts them in the priority queue sorted according to the Cost policy.
-	 * 2) set the id() field of each edge
-	 */
-	void collect_edges(){
-		//
-		// Loop over all the edges in the complex in the heap
-		//
-		size_type size = complex_.num_edges();
-		DBG("Collecting edges ...");
-		DBGMSG("num edges :",size);
-
-		edge_data_array_.reset( new Edge_data[size] ) ;
-
-		heap_PQ_.reset( new PQ (size, Compare_cost(this), Undirected_edge_id(this) ) ) ;
-
-		std::size_t id = 0 ;
-
-		//xxx do a parralel for
-		for(auto edge : complex_.edge_range()){
-			complex_[edge].index() = id++;
-			Profile const& profile = create_profile(edge);
-			Edge_data& data = get_data(edge);
-			data.cost() = get_cost(profile) ;
-			++initial_num_edges_heap_;
-			insert_in_PQ(edge,data);
-			if(contraction_visitor_) contraction_visitor_->on_collected(profile,data.cost());
-		}
-
-		DBG("Edges collected.");
-
-	}
-
-	bool should_stop(double lCost,const Profile &profile) const{
-		return false;
-	}
-
-	boost::optional<Point> get_placement(const Profile& profile) const{
-		return (*placement_policy_)(profile);
-	}
-
-	bool is_contraction_valid( Profile const& profile, Placement_type placement ) const{
-		if(!valid_contraction_policy_) return true;
-		return (*valid_contraction_policy_)(profile,placement);
-	}
-
-
-public:
-	/**
-	 * \brief Contract edges.
-	 *
-	 * While the heap is not empty, it extracts the edge with the minimum
-	 * cost in the heap then try to contract it.
-	 * It stops when the Stop policy says so or when the number of contractions
-	 * given by 'num_max_contractions' is reached (if this number is positive).
-	 */
-	void contract_edges(int num_max_contractions=-1){
-
-		DBG("\n\nContract edges");
-		int num_contraction = 0 ;
-
-		bool unspecified_num_contractions = (num_max_contractions == -1);
-		//
-		// Pops and processes each edge from the PQ
-		//
-		boost::optional<Edge_handle> edge ;
-		while ( (edge = pop_from_PQ())&& ((num_contraction<num_max_contractions)||(unspecified_num_contractions)))
-		{
-			Profile const& profile = create_profile(*edge);
-			Cost_type cost(get_data(*edge).cost());
-			if(contraction_visitor_) contraction_visitor_->on_selected(profile,cost,0,0);
-
-			DBGMSG("\n\n---- Pop edge - num vertices :",complex_.num_vertices());
-
-			if (cost){
-				DBGMSG("sqrt(cost):",std::sqrt(*cost));
-				if (should_stop(*cost,profile) )
-				{
-					if(contraction_visitor_) contraction_visitor_->on_stop_condition_reached();
-					DBG("should_stop");
-					break ;
-				}
-				Placement_type placement = get_placement(profile);
-				if ( is_contraction_valid(profile,placement) && placement )
-				{
-					DBG("contraction_valid");
-					contract_edge(profile,placement);
-					++ num_contraction;
-				}
-				else
-				{
-					DBG("contraction not valid");
-					if(contraction_visitor_) contraction_visitor_->on_non_valid(profile);
-				}
-			}
-			else
-				DBG("uncomputable cost");
-		}
-		if(contraction_visitor_) contraction_visitor_->on_stop_condition_reached();		
-	}
-
-
-	bool is_in_heap(Edge_handle edge) const{
-		if(heap_PQ_->empty()) return false;
-		else{
-			return edge_data_array_[get_undirected_edge_id(edge)].is_in_PQ();
-		}
-	}
-
-	bool is_heap_empty() const{
-		return heap_PQ_->empty();
-	}
-
-
-	/**
-	 * @brief Returns an Edge_handle and a Placement_type. This pair consists in
-	 * the edge with the lowest cost in the heap together with its placement.
-	 * The returned value is initialized iff the heap is non-empty.
-	 */
-	boost::optional<std::pair<Edge_handle,Placement_type > > top_edge(){
-		boost::optional<std::pair<Edge_handle,Placement_type > > res;
-
-		if(!heap_PQ_->empty()) {
-			auto edge = heap_PQ_->top();
-			Profile const& profile = create_profile(edge);
-			Placement_type placement = get_placement(profile);
-			res = make_pair(edge,placement);
-			DBGMSG("top edge:",complex_[edge]);
-
-		}
-		return res;
-	}
-
-
-	/**
-	 * @brief Constructor with default policies.
-	 *
-	 * @details The default cost, placement, valid and visitor policies
-	 * are respectively : the edge length, the first point, the link condition
-	 */
-	Skeleton_blocker_contractor(GeometricSimplifiableComplex& complex)
-	:complex_(complex),
-	 cost_policy_(new Edge_length_cost<Profile>),
-	 placement_policy_(new First_vertex_placement<Profile>),
-	 valid_contraction_policy_(new Link_condition_valid_contraction<Profile>),
-	 contraction_visitor_(new Contraction_visitor_()),
-	 edge_profile_factory_(0),
-	 initial_num_edges_heap_(0),
-	 current_num_edges_heap_(0)
-	{
-		complex_.set_visitor(this);
-		if(contraction_visitor_) contraction_visitor_->on_started(complex);
-		collect_edges();
-	}
-
-	/**
-	 * @brief Constructor with customed policies.
-	 * @remark Policies destruction is handle by the class with smart pointers.
-	 */
-	Skeleton_blocker_contractor(GeometricSimplifiableComplex& complex,
-			Cost_policy_ *cost_policy,
-			Placement_policy_ * placement_policy = new First_vertex_placement<Profile>,
-			Valid_contraction_policy_ * valid_contraction_policy = new Link_condition_valid_contraction<Profile>,
-			Contraction_visitor_* contraction_visitor = new Contraction_visitor_(),
-			Edge_profile_factory_* edge_profile_factory = NULL
-	):
-		complex_(complex),
-		cost_policy_(cost_policy),
-		placement_policy_(placement_policy),
-		valid_contraction_policy_(valid_contraction_policy),
-		contraction_visitor_(contraction_visitor),
-		edge_profile_factory_(edge_profile_factory),
-		initial_num_edges_heap_(0),
-		current_num_edges_heap_(0)
-	{
-		complex_.set_visitor(this);
-		if(contraction_visitor) contraction_visitor->on_started(complex);
-		collect_edges();
-	}
-
-
-	~Skeleton_blocker_contractor(){
-		complex_.set_visitor(0);
-	}
-
-private:
-
-
-	void contract_edge(const Profile& profile, Placement_type placement ) {
-		if(contraction_visitor_) contraction_visitor_->on_contracting(profile,placement);
-
-		assert(complex_.contains_vertex(profile.v0_handle()));
-		assert(complex_.contains_vertex(profile.v1_handle()));
-		assert(placement);
-
-		profile.complex().point(profile.v0_handle()) = *placement;
-
-		// remark : this is not necessary since v1 will be deactivated
-		//	profile.complex().point(profile.v1_handle()) = *placement;
-
-		complex_.contract_edge(profile.v0_handle(),profile.v1_handle());
-
-		assert(complex_.contains_vertex(profile.v0_handle()));
-		assert(!complex_.contains_vertex(profile.v1_handle()));
-
-		update_changed_edges();
-
-		// the visitor could do something as complex_.remove_popable_blockers();
-		if(contraction_visitor_) contraction_visitor_->on_contracted(profile,placement);
-	}
-
-private:
-
-	// every time the visitor's method on_changed_edge is called, it adds an
-	// edge to changed_edges_
-	std::vector< Edge_handle > changed_edges_;
-
-	/**
-	 * @brief we update the cost and the position in the heap of an edge that has
-	 * been changed
-	 */
-	inline void on_changed_edge(Vertex_handle a,Vertex_handle b) override{
-		boost::optional<Edge_handle> ab(complex_[std::make_pair(a,b)]);
-		assert(ab);
-		changed_edges_.push_back(*ab);
-	}
-
-	void update_changed_edges(){
-		//xxx do a parralel for
-
-		DBG("update edges");
-
-		//		sequential loop
-		for(auto ab : changed_edges_){
-			//1-get the Edge_handle corresponding to ab
-			//2-change the data in mEdgeArray[ab.id()]
-			//3-update the heap
-			Edge_data& data = get_data(ab);
-			Profile const& profile = create_profile(ab);
-			data.cost() = get_cost(profile) ;
-			if ( data.is_in_PQ()){
-				update_in_PQ(ab,data);
-			}
-			else{
-				insert_in_PQ(ab,data);
-			}
-		}
-		changed_edges_.clear();
-	}
-
-
-private:
-	void on_remove_edge(Vertex_handle a,Vertex_handle b) override{
-
-		boost::optional<Edge_handle> ab((complex_[std::make_pair(a,b)]));
-		assert(ab);
-		Edge_data& lData = get_data(*ab) ;
-		if ( lData.is_in_PQ() )
-		{
-			remove_from_PQ(*ab,lData) ;
-		}
-	}
-private:
-	/**
-	 * @brief Called when the edge 'ax' has been added while the edge 'bx'
-	 * is still there but will be removed on next instruction.
-	 * We assign the index of 'bx' to the edge index of 'ax'
-	 */
-	void on_swaped_edge(Vertex_handle a,Vertex_handle b,Vertex_handle x) override{
-		boost::optional<Edge_handle> ax(complex_[std::make_pair(a,x)]);
-		boost::optional<Edge_handle> bx(complex_[std::make_pair(b,x)]);
-		assert(ax&& bx);
-		complex_[*ax].index() =complex_[*bx].index();
-	}
-private:
-	/**
-	 * @brief Called when a blocker is removed.
-	 * All the edges that passes through the blocker may be edge-contractible
-	 * again and are thus reinserted in the heap.
-	 */
-	void on_delete_blocker(const Simplex_handle * blocker) override{
-		// we go for all pairs xy that belongs to the blocker
-		// note that such pairs xy are necessarily edges of the complex
-		// by definition of a blocker
-
-		// todo uniqument utile pour la link condition
-		// laisser � l'utilisateur? booleen update_heap_on_removed_blocker?
-		Simplex_handle blocker_copy(*blocker);
-		for (auto x = blocker_copy.begin(); x!= blocker_copy.end(); ++x){
-			for(auto y=x ; ++y != blocker_copy.end(); ){
-				auto edge_descr(complex_[std::make_pair(*x,*y)]);
-				assert(edge_descr);
-				Edge_data& data = get_data(*edge_descr);
-				Profile const& profile = create_profile(*edge_descr);
-				data.cost() = get_cost(profile) ;
-
-				// If the edge is already in the heap
-				// its priority has not changed.
-				// If the edge is not present, we reinsert it
-				// remark : we could also reinsert the edge
-				// only if it is valid
-				if ( !data.is_in_PQ() ){
-					insert_in_PQ(*edge_descr,data);
-				}
-			}
-		}
-	}
-
-
-private:
-	std::shared_ptr<Cost_policy_> cost_policy_;
-	std::shared_ptr<Placement_policy_> placement_policy_;
-	std::shared_ptr<Valid_contraction_policy_> valid_contraction_policy_;
-	std::shared_ptr<Contraction_visitor_> contraction_visitor_;
-
-	//in case the user wants to do something special when the edge profile
-	//are created (for instance add some info)
-	std::shared_ptr<Edge_profile_factory_> edge_profile_factory_;
-	Edge_data_array edge_data_array_ ;
-
-	boost::scoped_ptr<PQ> heap_PQ_ ;
-	int initial_num_edges_heap_;
-	int current_num_edges_heap_;
+    void reset_PQ_handle() {
+      PQHandle_ = PQ::null_handle();
+    }
 
+   private:
+    pq_handle PQHandle_;
+    Cost_type cost_;
+  };
+  typedef Edge_data* Edge_data_ptr;
+  typedef boost::scoped_array<Edge_data> Edge_data_array;
+
+  int get_undirected_edge_id(Edge_handle edge) const {
+    return complex_[edge].index();
+  }
+
+  const Edge_data& get_data(Edge_handle edge) const {
+    return edge_data_array_[get_undirected_edge_id(edge)];
+  }
+
+  Edge_data& get_data(Edge_handle edge) {
+    return edge_data_array_[get_undirected_edge_id(edge)];
+  }
+
+  Cost_type get_cost(const Profile & profile) const {
+    return (*cost_policy_)(profile, get_placement(profile));
+  }
+
+  Profile create_profile(Edge_handle edge) const {
+    if (edge_profile_factory_)
+      return edge_profile_factory_->make_profile(complex_, edge);
+    else
+      return Profile(complex_, edge);
+  }
+
+  void insert_in_PQ(Edge_handle edge, Edge_data& data) {
+    data.set_PQ_handle(heap_PQ_->push(edge));
+    ++current_num_edges_heap_;
+  }
+
+  void update_in_PQ(Edge_handle edge, Edge_data& data) {
+    data.set_PQ_handle(heap_PQ_->update(edge, data.PQ_handle()));
+  }
+
+  void remove_from_PQ(Edge_handle edge, Edge_data& data) {
+    data.set_PQ_handle(heap_PQ_->erase(edge, data.PQ_handle()));
+    --current_num_edges_heap_;
+  }
+
+  boost::optional<Edge_handle> pop_from_PQ() {
+    boost::optional<Edge_handle> edge = heap_PQ_->extract_top();
+    if (edge)
+      get_data(*edge).reset_PQ_handle();
+    return edge;
+  }
+
+ private:
+  /**
+   * @brief Collect edges.
+   *
+   * Iterates over all edges of the simplicial complex and
+   * 1) inserts them in the priority queue sorted according to the Cost policy.
+   * 2) set the id() field of each edge
+   */
+  void collect_edges() {
+    //
+    // Loop over all the edges in the complex in the heap
+    //
+    size_type size = complex_.num_edges();
+    DBG("Collecting edges ...");
+    DBGMSG("num edges :", size);
+
+    edge_data_array_.reset(new Edge_data[size]);
+
+    heap_PQ_.reset(new PQ(size, Compare_cost(this), Undirected_edge_id(this)));
+
+    std::size_t id = 0;
+
+    // xxx do a parralel for
+    for (auto edge : complex_.edge_range()) {
+      complex_[edge].index() = id++;
+      Profile const& profile = create_profile(edge);
+      Edge_data& data = get_data(edge);
+      data.cost() = get_cost(profile);
+      ++initial_num_edges_heap_;
+      insert_in_PQ(edge, data);
+      if (contraction_visitor_) contraction_visitor_->on_collected(profile, data.cost());
+    }
+
+    DBG("Edges collected.");
+  }
+
+  bool should_stop(double lCost, const Profile &profile) const {
+    return false;
+  }
+
+  boost::optional<Point> get_placement(const Profile& profile) const {
+    return (*placement_policy_)(profile);
+  }
+
+  bool is_contraction_valid(Profile const& profile, Placement_type placement) const {
+    if (!valid_contraction_policy_) return true;
+    return (*valid_contraction_policy_)(profile, placement);
+  }
+
+
+ public:
+  /**
+   * \brief Contract edges.
+   *
+   * While the heap is not empty, it extracts the edge with the minimum
+   * cost in the heap then try to contract it.
+   * It stops when the Stop policy says so or when the number of contractions
+   * given by 'num_max_contractions' is reached (if this number is positive).
+   */
+  void contract_edges(int num_max_contractions = -1) {
+    DBG("\n\nContract edges");
+    int num_contraction = 0;
+
+    bool unspecified_num_contractions = (num_max_contractions == -1);
+    //
+    // Pops and processes each edge from the PQ
+    //
+    boost::optional<Edge_handle> edge;
+    while ((edge = pop_from_PQ()) && ((num_contraction < num_max_contractions) || (unspecified_num_contractions))) {
+      Profile const& profile = create_profile(*edge);
+      Cost_type cost(get_data(*edge).cost());
+      if (contraction_visitor_) contraction_visitor_->on_selected(profile, cost, 0, 0);
+
+      DBGMSG("\n\n---- Pop edge - num vertices :", complex_.num_vertices());
+
+      if (cost) {
+        DBGMSG("sqrt(cost):", std::sqrt(*cost));
+        if (should_stop(*cost, profile)) {
+          if (contraction_visitor_) contraction_visitor_->on_stop_condition_reached();
+          DBG("should_stop");
+          break;
+        }
+        Placement_type placement = get_placement(profile);
+        if (is_contraction_valid(profile, placement) && placement) {
+          DBG("contraction_valid");
+          contract_edge(profile, placement);
+          ++num_contraction;
+        } else {
+          DBG("contraction not valid");
+          if (contraction_visitor_) contraction_visitor_->on_non_valid(profile);
+        }
+      } else {
+        DBG("uncomputable cost");
+      }
+    }
+    if (contraction_visitor_) contraction_visitor_->on_stop_condition_reached();
+  }
+
+  bool is_in_heap(Edge_handle edge) const {
+    if (heap_PQ_->empty()) {
+      return false;
+    } else {
+      return edge_data_array_[get_undirected_edge_id(edge)].is_in_PQ();
+    }
+  }
+
+  bool is_heap_empty() const {
+    return heap_PQ_->empty();
+  }
+
+  /**
+   * @brief Returns an Edge_handle and a Placement_type. This pair consists in
+   * the edge with the lowest cost in the heap together with its placement.
+   * The returned value is initialized iff the heap is non-empty.
+   */
+  boost::optional<std::pair<Edge_handle, Placement_type > > top_edge() {
+    boost::optional<std::pair<Edge_handle, Placement_type > > res;
+
+    if (!heap_PQ_->empty()) {
+      auto edge = heap_PQ_->top();
+      Profile const& profile = create_profile(edge);
+      Placement_type placement = get_placement(profile);
+      res = std::make_pair(edge, placement);
+      DBGMSG("top edge:", complex_[edge]);
+    }
+    return res;
+  }
+
+  /**
+   * @brief Constructor with default policies.
+   *
+   * @details The default cost, placement, valid and visitor policies
+   * are respectively : the edge length, the first point, the link condition
+   */
+  Skeleton_blocker_contractor(GeometricSimplifiableComplex& complex)
+      : complex_(complex),
+      cost_policy_(new Edge_length_cost<Profile>),
+      placement_policy_(new First_vertex_placement<Profile>),
+      valid_contraction_policy_(new Link_condition_valid_contraction<Profile>),
+      contraction_visitor_(new Contraction_visitor_()),
+      edge_profile_factory_(0),
+      initial_num_edges_heap_(0),
+      current_num_edges_heap_(0) {
+    complex_.set_visitor(this);
+    if (contraction_visitor_) contraction_visitor_->on_started(complex);
+    collect_edges();
+  }
+
+  /**
+   * @brief Constructor with customed policies.
+   * @remark Policies destruction is handle by the class with smart pointers.
+   */
+  Skeleton_blocker_contractor(GeometricSimplifiableComplex& complex,
+                              Cost_policy_ *cost_policy,
+                              Placement_policy_ * placement_policy = new First_vertex_placement<Profile>,
+                              Valid_contraction_policy_ * valid_contraction_policy =
+                              new Link_condition_valid_contraction<Profile>,
+                              Contraction_visitor_* contraction_visitor = new Contraction_visitor_(),
+                              Edge_profile_factory_* edge_profile_factory = NULL) :
+      complex_(complex),
+      cost_policy_(cost_policy),
+      placement_policy_(placement_policy),
+      valid_contraction_policy_(valid_contraction_policy),
+      contraction_visitor_(contraction_visitor),
+      edge_profile_factory_(edge_profile_factory),
+      initial_num_edges_heap_(0),
+      current_num_edges_heap_(0) {
+    complex_.set_visitor(this);
+    if (contraction_visitor) contraction_visitor->on_started(complex);
+    collect_edges();
+  }
+
+  ~Skeleton_blocker_contractor() {
+    complex_.set_visitor(0);
+  }
+
+ private:
+  void contract_edge(const Profile& profile, Placement_type placement) {
+    if (contraction_visitor_) contraction_visitor_->on_contracting(profile, placement);
+
+    assert(complex_.contains_vertex(profile.v0_handle()));
+    assert(complex_.contains_vertex(profile.v1_handle()));
+    assert(placement);
+
+    profile.complex().point(profile.v0_handle()) = *placement;
+
+    // remark : this is not necessary since v1 will be deactivated
+    // profile.complex().point(profile.v1_handle()) = *placement;
+
+    complex_.contract_edge(profile.v0_handle(), profile.v1_handle());
+
+    assert(complex_.contains_vertex(profile.v0_handle()));
+    assert(!complex_.contains_vertex(profile.v1_handle()));
+
+    update_changed_edges();
+
+    // the visitor could do something as complex_.remove_popable_blockers();
+    if (contraction_visitor_) contraction_visitor_->on_contracted(profile, placement);
+  }
+
+ private:
+  // every time the visitor's method on_changed_edge is called, it adds an
+  // edge to changed_edges_
+  std::vector< Edge_handle > changed_edges_;
+
+  /**
+   * @brief we update the cost and the position in the heap of an edge that has
+   * been changed
+   */
+  inline void on_changed_edge(Vertex_handle a, Vertex_handle b) override {
+    boost::optional<Edge_handle> ab(complex_[std::make_pair(a, b)]);
+    assert(ab);
+    changed_edges_.push_back(*ab);
+  }
+
+  void update_changed_edges() {
+    // xxx do a parralel for
+    DBG("update edges");
+
+    // sequential loop
+    for (auto ab : changed_edges_) {
+      // 1-get the Edge_handle corresponding to ab
+      // 2-change the data in mEdgeArray[ab.id()]
+      // 3-update the heap
+      Edge_data& data = get_data(ab);
+      Profile const& profile = create_profile(ab);
+      data.cost() = get_cost(profile);
+      if (data.is_in_PQ()) {
+        update_in_PQ(ab, data);
+      } else {
+        insert_in_PQ(ab, data);
+      }
+    }
+    changed_edges_.clear();
+  }
+
+
+ private:
+  void on_remove_edge(Vertex_handle a, Vertex_handle b) override {
+    boost::optional<Edge_handle> ab((complex_[std::make_pair(a, b)]));
+    assert(ab);
+    Edge_data& lData = get_data(*ab);
+    if (lData.is_in_PQ()) {
+      remove_from_PQ(*ab, lData);
+    }
+  }
+
+ private:
+  /**
+   * @brief Called when the edge 'ax' has been added while the edge 'bx'
+   * is still there but will be removed on next instruction.
+   * We assign the index of 'bx' to the edge index of 'ax'
+   */
+  void on_swaped_edge(Vertex_handle a, Vertex_handle b, Vertex_handle x) override {
+    boost::optional<Edge_handle> ax(complex_[std::make_pair(a, x)]);
+    boost::optional<Edge_handle> bx(complex_[std::make_pair(b, x)]);
+    assert(ax && bx);
+    complex_[*ax].index() = complex_[*bx].index();
+  }
+
+ private:
+  /**
+   * @brief Called when a blocker is removed.
+   * All the edges that passes through the blocker may be edge-contractible
+   * again and are thus reinserted in the heap.
+   */
+  void on_delete_blocker(const Simplex * blocker) override {
+    // we go for all pairs xy that belongs to the blocker
+    // note that such pairs xy are necessarily edges of the complex
+    // by definition of a blocker
+
+    // todo uniqument utile pour la link condition
+    // laisser a l'utilisateur ? booleen update_heap_on_removed_blocker?
+    Simplex blocker_copy(*blocker);
+    for (auto x = blocker_copy.begin(); x != blocker_copy.end(); ++x) {
+      for (auto y = x; ++y != blocker_copy.end();) {
+        auto edge_descr(complex_[std::make_pair(*x, *y)]);
+        assert(edge_descr);
+        Edge_data& data = get_data(*edge_descr);
+        Profile const& profile = create_profile(*edge_descr);
+        data.cost() = get_cost(profile);
+
+        // If the edge is already in the heap
+        // its priority has not changed.
+        // If the edge is not present, we reinsert it
+        // remark : we could also reinsert the edge
+        // only if it is valid
+        if (!data.is_in_PQ()) {
+          insert_in_PQ(*edge_descr, data);
+        }
+      }
+    }
+  }
+
+
+ private:
+  std::shared_ptr<Cost_policy_> cost_policy_;
+  std::shared_ptr<Placement_policy_> placement_policy_;
+  std::shared_ptr<Valid_contraction_policy_> valid_contraction_policy_;
+  std::shared_ptr<Contraction_visitor_> contraction_visitor_;
+
+  // in case the user wants to do something special when the edge profile
+  // are created (for instance add some info)
+  std::shared_ptr<Edge_profile_factory_> edge_profile_factory_;
+  Edge_data_array edge_data_array_;
+
+  boost::scoped_ptr<PQ> heap_PQ_;
+  int initial_num_edges_heap_;
+  int current_num_edges_heap_;
 };
 
 }  // namespace contraction
-} // namespace GUDHI
 
-#endif /* GUDHI_SKELETON_BLOCKER_CONTRACTOR_H_ */
+}  // namespace Gudhi
+
+#endif  // SKELETON_BLOCKER_CONTRACTOR_H_
diff --git a/src/Doxyfile b/src/Doxyfile
index 62412627..faa0d3fe 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile
@@ -38,7 +38,7 @@ PROJECT_NAME           = "Gudhi"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = "1.1.0"
+PROJECT_NUMBER         = "1.2.0"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -672,7 +672,8 @@ LAYOUT_FILE            =
 # search path. Do not use file names with spaces, bibtex cannot handle them. See
 # also \cite for info how to create references.
 
-CITE_BIB_FILES         = ../biblio/bibliography.bib
+CITE_BIB_FILES         = biblio/bibliography.bib \
+                        biblio/how_to_cite_gudhi.bib
 
 #---------------------------------------------------------------------------
 # Configuration options related to warning and progress messages
@@ -811,7 +812,7 @@ EXCLUDE_SYMBOLS        =
 # that contain example code fragments that are included (see the \include
 # command).
 
-EXAMPLE_PATH           =
+EXAMPLE_PATH           = biblio/
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
@@ -831,9 +832,9 @@ EXAMPLE_RECURSIVE      = NO
 # that contain images that are to be included in the documentation (see the
 # \image command).
 
-IMAGE_PATH             = Skeleton_blocker/doc/ \
-	common/doc/ \
-	Contraction/doc/
+IMAGE_PATH             = doc/Skeleton_blocker/ \
+	doc/common/ \
+	doc/Contraction/
 
 
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
@@ -1338,7 +1339,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-DISABLE_INDEX          = NO
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information. If the tag
@@ -1355,7 +1356,7 @@ DISABLE_INDEX          = NO
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-GENERATE_TREEVIEW      = NO
+GENERATE_TREEVIEW      = YES
 
 # The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
 # doxygen will group on one line in the generated HTML documentation.
diff --git a/src/GUDHIConfig.cmake.in b/src/GUDHIConfig.cmake.in
new file mode 100644
index 00000000..02b540dc
--- /dev/null
+++ b/src/GUDHIConfig.cmake.in
@@ -0,0 +1,7 @@
+# - Config file for the GUDHI package
+# It defines the following variables
+#  GUDHI_INCLUDE_DIRS - include directories for GUDHI
+
+# Compute paths
+set(GUDHI_INCLUDE_DIRS "@CONF_INCLUDE_DIRS@")
+
diff --git a/src/GUDHIConfigVersion.cmake.in b/src/GUDHIConfigVersion.cmake.in
new file mode 100644
index 00000000..6d443ef6
--- /dev/null
+++ b/src/GUDHIConfigVersion.cmake.in
@@ -0,0 +1,11 @@
+set(PACKAGE_VERSION "@GUDHI_VERSION@")
+
+# Check whether the requested PACKAGE_FIND_VERSION is compatible
+if("${PACKAGE_VERSION}" VERSION_LESS "${PACKAGE_FIND_VERSION}")
+  set(PACKAGE_VERSION_COMPATIBLE FALSE)
+else()
+  set(PACKAGE_VERSION_COMPATIBLE TRUE)
+  if ("${PACKAGE_VERSION}" VERSION_EQUAL "${PACKAGE_FIND_VERSION}")
+    set(PACKAGE_VERSION_EXACT TRUE)
+  endif()
+endif()
diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt
index ddbae969..71f4fd1a 100644
--- a/src/GudhUI/CMakeLists.txt
+++ b/src/GudhUI/CMakeLists.txt
@@ -5,9 +5,6 @@ find_package(CGAL  COMPONENTS Qt4)
 find_package(Qt4)
 find_package(QGLViewer)
 find_package(OpenGL)
-message("CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS}")
-message("CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG}")
-message("CMAKE_CXX_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE}")
 
 if ( CGAL_FOUND AND QT4_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND )
   set( QT_USE_QTXML    TRUE )
@@ -21,7 +18,23 @@ if ( CGAL_FOUND AND QT4_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND )
   LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
   
   include(${QT_USE_FILE})
+
   include(${CGAL_USE_FILE})
+  # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten.
+  # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
+  # A workaround is to add "-std=c++11" again.
+  # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html 
+  # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
+  # but it implies to use cmake version 3.1 at least.
+  if(NOT MSVC)
+    include(CheckCXXCompilerFlag)
+    CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11)
+    if(COMPILER_SUPPORTS_CXX11)
+      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+    endif()
+  endif()
+  # - End of workaround
+
   include_directories (${QGLVIEWER_INCLUDE_DIR})
   include_directories(.)	
  
@@ -66,5 +79,5 @@ if ( CGAL_FOUND AND QT4_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND )
   target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} )	
 
 else()
-  message(STATUS "NOTICE: This demo requires CGAL, the QGLViewer, OpenGL and Qt4, and will not be compiled.")
+  message(STATUS "NOTICE: GudhUI requires CGAL, the QGLViewer, OpenGL and Qt4, and will not be compiled.")
 endif()
diff --git a/src/GudhUI/gui/MainWindow.cpp b/src/GudhUI/gui/MainWindow.cpp
index e41b15ba..779ccd33 100644
--- a/src/GudhUI/gui/MainWindow.cpp
+++ b/src/GudhUI/gui/MainWindow.cpp
@@ -1,3 +1,25 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
 #include "MainWindow.h"
 
 #include <QWidget>
@@ -6,292 +28,271 @@
 
 #include <fenv.h>
 
-
 #include "gui/Menu_k_nearest_neighbors.h"
 #include "gui/Menu_uniform_neighbors.h"
 #include "gui/Menu_edge_contraction.h"
 #include "gui/Menu_persistence.h"
 
+MainWindow::MainWindow(QWidget* parent) :
+    menu_k_nearest_neighbors_(new Menu_k_nearest_neighbors(this)),
+    menu_uniform_neighbors_(new Menu_uniform_neighbors(this)),
+    menu_edge_contraction_(new Menu_edge_contraction(this, model_)),
+    menu_persistence_(new Menu_persistence(this)) {
+  // #ifndef NDEBUG // catch nan
+  // feenableexcept(FE_DIVBYZERO | FE_INVALID | FE_OVERFLOW);
+  // #endif
 
-MainWindow::MainWindow(QWidget* parent):
-menu_k_nearest_neighbors_(new Menu_k_nearest_neighbors(this)),
-menu_uniform_neighbors_(new Menu_uniform_neighbors(this)),
-menu_edge_contraction_(new Menu_edge_contraction(this,model_)),
-menu_persistence_(new Menu_persistence(this))
-{
-//#ifndef NDEBUG // catch nan
-//feenableexcept(FE_DIVBYZERO | FE_INVALID | FE_OVERFLOW);
-//#endif
+  setupUi(this);
 
-	setupUi(this);
+  viewer_instructor_ = new Viewer_instructor(
+                                             this,
+                                             this->viewer,
+                                             model_.complex_);
 
-	viewer_instructor_ = new Viewer_instructor(
-			this,
-			this->viewer,
-			model_.complex_
-	);
+  connectActions();
 
-	connectActions();
-
-	update_view();
+  update_view();
 }
 
-void 
-MainWindow::closeEvent(QCloseEvent *event){
-	exit(0);
+void
+MainWindow::closeEvent(QCloseEvent *event) {
+  exit(0);
 }
 
-
-void 
-MainWindow::connectActions(){
-	QObject::connect(this->actionLoad_complex, SIGNAL(triggered()), this,
-			SLOT(off_file_open()));
-	QObject::connect(this->actionLoad_points, SIGNAL(triggered()), this,
-			SLOT(off_points_open()));
-	QObject::connect(this->actionSave_complex, SIGNAL(triggered()), this,
-			SLOT(off_file_save()));
-	QObject::connect(this->actionSave_points, SIGNAL(triggered()), this,
-			SLOT(off_points_save()));
-
-	QObject::connect(this->actionShow_graph_stats, SIGNAL(triggered()), this,
-			SLOT(show_graph_stats()));
-	QObject::connect(this->actionShow_complex_stats, SIGNAL(triggered()), this,
-			SLOT(show_complex_stats()));
-	QObject::connect(this->actionShow_complex_dimension, SIGNAL(triggered()), this,
-			SLOT(show_complex_dimension()));
-
-	QObject::connect(this->actionUniform_proximity_graph, SIGNAL(triggered()), this,
-			SLOT(build_rips_menu()));
-	QObject::connect(this->actionK_nearest_neighbors_graph, SIGNAL(triggered()), this,
-			SLOT(build_k_nearest_neighbors_menu()));
-
-
-	QObject::connect(this->actionContract_edges, SIGNAL(triggered()), this,
-			SLOT(contract_edge_menu()));
-
-	QObject::connect(this->actionCollapse_vertices, SIGNAL(triggered()), this,
-			SLOT(collapse_vertices()));
-
-	QObject::connect(this->actionCollapse_edges, SIGNAL(triggered()), this,
-			SLOT(collapse_edges()));
-
-	QObject::connect(this->actionNoise, SIGNAL(triggered()), this,
-				SLOT(uniform_noise()));
-	QObject::connect(this->actionLloyd, SIGNAL(triggered()), this,
-				SLOT(lloyd()));
-
-
-	//view
-	QObject::connect(this->actionPoints, SIGNAL(triggered()), this->viewer_instructor_,
-				SLOT(change_draw_vertices()));
-	QObject::connect(this->actionEdges, SIGNAL(triggered()), this->viewer_instructor_,
-					SLOT(change_draw_edges()));
-	QObject::connect(this->actionTriangles, SIGNAL(triggered()), this->viewer_instructor_,
-					SLOT(change_draw_triangles()));
-
-	//topology
-	QObject::connect(this->actionShow_homology_group, SIGNAL(triggered()), this,
-			SLOT(show_homology_group()));
-	QObject::connect(this->actionEuler_characteristic, SIGNAL(triggered()), this,
-				SLOT(show_euler_characteristic()));
-	QObject::connect(this->actionPersistence, SIGNAL(triggered()), this,
-				SLOT(persistence_menu()));
-	QObject::connect(this->actionEstimate_topological_changes, SIGNAL(triggered()), this,
-				SLOT(critical_points_menu()));
-	QObject::connect(this->actionIs_manifold, SIGNAL(triggered()), this,
-				SLOT(is_manifold_menu()));
-
-
-	QObject::connect(this, SIGNAL(sceneChanged()), this->viewer_instructor_,
-			SLOT(sceneChanged()));
-
+void
+MainWindow::connectActions() {
+  QObject::connect(this->actionLoad_complex, SIGNAL(triggered()), this,
+                   SLOT(off_file_open()));
+  QObject::connect(this->actionLoad_points, SIGNAL(triggered()), this,
+                   SLOT(off_points_open()));
+  QObject::connect(this->actionSave_complex, SIGNAL(triggered()), this,
+                   SLOT(off_file_save()));
+  QObject::connect(this->actionSave_points, SIGNAL(triggered()), this,
+                   SLOT(off_points_save()));
+
+  QObject::connect(this->actionShow_graph_stats, SIGNAL(triggered()), this,
+                   SLOT(show_graph_stats()));
+  QObject::connect(this->actionShow_complex_stats, SIGNAL(triggered()), this,
+                   SLOT(show_complex_stats()));
+  QObject::connect(this->actionShow_complex_dimension, SIGNAL(triggered()), this,
+                   SLOT(show_complex_dimension()));
+
+  QObject::connect(this->actionUniform_proximity_graph, SIGNAL(triggered()), this,
+                   SLOT(build_rips_menu()));
+  QObject::connect(this->actionK_nearest_neighbors_graph, SIGNAL(triggered()), this,
+                   SLOT(build_k_nearest_neighbors_menu()));
+
+
+  QObject::connect(this->actionContract_edges, SIGNAL(triggered()), this,
+                   SLOT(contract_edge_menu()));
+
+  QObject::connect(this->actionCollapse_vertices, SIGNAL(triggered()), this,
+                   SLOT(collapse_vertices()));
+
+  QObject::connect(this->actionCollapse_edges, SIGNAL(triggered()), this,
+                   SLOT(collapse_edges()));
+
+  QObject::connect(this->actionNoise, SIGNAL(triggered()), this,
+                   SLOT(uniform_noise()));
+  QObject::connect(this->actionLloyd, SIGNAL(triggered()), this,
+                   SLOT(lloyd()));
+
+
+  // view
+  QObject::connect(this->actionPoints, SIGNAL(triggered()), this->viewer_instructor_,
+                   SLOT(change_draw_vertices()));
+  QObject::connect(this->actionEdges, SIGNAL(triggered()), this->viewer_instructor_,
+                   SLOT(change_draw_edges()));
+  QObject::connect(this->actionTriangles, SIGNAL(triggered()), this->viewer_instructor_,
+                   SLOT(change_draw_triangles()));
+
+  // topology
+  QObject::connect(this->actionShow_homology_group, SIGNAL(triggered()), this,
+                   SLOT(show_homology_group()));
+  QObject::connect(this->actionEuler_characteristic, SIGNAL(triggered()), this,
+                   SLOT(show_euler_characteristic()));
+  QObject::connect(this->actionPersistence, SIGNAL(triggered()), this,
+                   SLOT(persistence_menu()));
+  QObject::connect(this->actionEstimate_topological_changes, SIGNAL(triggered()), this,
+                   SLOT(critical_points_menu()));
+  QObject::connect(this->actionIs_manifold, SIGNAL(triggered()), this,
+                   SLOT(is_manifold_menu()));
+
+
+  QObject::connect(this, SIGNAL(sceneChanged()), this->viewer_instructor_,
+                   SLOT(sceneChanged()));
 }
 
 void
-MainWindow::init_view() const{
-	viewer_instructor_->initialize_bounding_box();
-	viewer_instructor_->show_entire_scene();
-	update_view();
+MainWindow::init_view() const {
+  viewer_instructor_->initialize_bounding_box();
+  viewer_instructor_->show_entire_scene();
+  update_view();
 }
 
-
 void
-MainWindow::update_view() const{
-	emit (sceneChanged());
+MainWindow::update_view() const {
+  emit(sceneChanged());
 }
 
-
-
 /**
  * open a file chooser to choose an off to load
  */
-void 
-MainWindow::off_file_open(){
-	QString fileName = QFileDialog::getOpenFileName(this, tr("Open off File"),
-			"~/", tr("off files (*.off)"));
-	if (!fileName.isEmpty()){
-		model_.off_file_open(fileName.toStdString());
-		init_view();
-	}
+void
+MainWindow::off_file_open() {
+  QString fileName = QFileDialog::getOpenFileName(this, tr("Open off File"),
+                                                  "~/", tr("off files (*.off)"));
+  if (!fileName.isEmpty()) {
+    model_.off_file_open(fileName.toStdString());
+    init_view();
+  }
 }
 
 void
-MainWindow::off_points_open(){
-	QString fileName = QFileDialog::getOpenFileName(this, tr("Open points in a off file"),
-			"~/", tr("off files (*.off)"));
-	if (!fileName.isEmpty()){
-		model_.off_points_open(fileName.toStdString());
-		init_view();
-	}
+MainWindow::off_points_open() {
+  QString fileName = QFileDialog::getOpenFileName(this, tr("Open points in a off file"),
+                                                  "~/", tr("off files (*.off)"));
+  if (!fileName.isEmpty()) {
+    model_.off_points_open(fileName.toStdString());
+    init_view();
+  }
 }
 
-
 /**
  * open a file chooser to choose an off to save
  */
-void 
-MainWindow::off_file_save(){
-	QString fileName = QFileDialog::getOpenFileName(this, tr("Save to off File"),
-			"~/", tr("off files (*.off)"));
-	if (!fileName.isEmpty())
-	{
-		model_.off_file_save(fileName.toStdString());
-	}
+void
+MainWindow::off_file_save() {
+  QString fileName = QFileDialog::getOpenFileName(this, tr("Save to off File"),
+                                                  "~/", tr("off files (*.off)"));
+  if (!fileName.isEmpty()) {
+    model_.off_file_save(fileName.toStdString());
+  }
 }
 
 /**
  * open a file chooser to choose an off to save
  */
 void
-MainWindow::off_points_save(){
-	QString fileName = QFileDialog::getOpenFileName(this, tr("Save to off File"),
-			"~/", tr("off files (*.off)"));
-	if (!fileName.isEmpty())
-	{
-		model_.off_points_save(fileName.toStdString());
-	}
+MainWindow::off_points_save() {
+  QString fileName = QFileDialog::getOpenFileName(this, tr("Save to off File"),
+                                                  "~/", tr("off files (*.off)"));
+  if (!fileName.isEmpty()) {
+    model_.off_points_save(fileName.toStdString());
+  }
 }
 
-
 void
-MainWindow::show_graph_stats(){
-	model_.show_graph_stats();
+MainWindow::show_graph_stats() {
+  model_.show_graph_stats();
 }
 
 void
-MainWindow::show_complex_stats(){
-	model_.show_complex_stats();
+MainWindow::show_complex_stats() {
+  model_.show_complex_stats();
 }
 
-void 
-MainWindow::show_complex_dimension(){
-	model_.show_complex_dimension();
+void
+MainWindow::show_complex_dimension() {
+  model_.show_complex_dimension();
 }
 
-
 void
-MainWindow::build_rips_menu(){
-	menu_uniform_neighbors_->show();
+MainWindow::build_rips_menu() {
+  menu_uniform_neighbors_->show();
 }
 
 void
-MainWindow::build_rips(double alpha){
-	model_.build_rips(alpha);
-	update_view();
+MainWindow::build_rips(double alpha) {
+  model_.build_rips(alpha);
+  update_view();
 }
 
 void
-MainWindow::build_k_nearest_neighbors_menu(){
-	menu_k_nearest_neighbors_->show();
+MainWindow::build_k_nearest_neighbors_menu() {
+  menu_k_nearest_neighbors_->show();
 }
 
 void
-MainWindow::build_k_nearest_neighbors(unsigned k){
-	model_.build_k_nearest_neighbors(k);
-	update_view();
+MainWindow::build_k_nearest_neighbors(unsigned k) {
+  model_.build_k_nearest_neighbors(k);
+  update_view();
 }
 
 void
-MainWindow::contract_edge_menu(){
-	menu_edge_contraction_->show();
+MainWindow::contract_edge_menu() {
+  menu_edge_contraction_->show();
 }
 
 void
-MainWindow::contract_edges(unsigned num_collapses){
-	std::cerr <<"Collapse "<<num_collapses<< " vertices\n";
-	model_.contract_edges(num_collapses);
-	update_view();
+MainWindow::contract_edges(unsigned num_collapses) {
+  std::cerr << "Collapse " << num_collapses << " vertices\n";
+  model_.contract_edges(num_collapses);
+  update_view();
 }
 
-
 void
-MainWindow::collapse_edges(){
-	model_.collapse_edges(model_.num_edges());
-	update_view();
+MainWindow::collapse_edges() {
+  model_.collapse_edges(model_.num_edges());
+  update_view();
 }
 
-
-
 void
-MainWindow::collapse_vertices(){
-	std::cerr <<"Collapse vertices edges\n";
-	model_.collapse_vertices(0);
-	update_view();
+MainWindow::collapse_vertices() {
+  std::cerr << "Collapse vertices edges\n";
+  model_.collapse_vertices(0);
+  update_view();
 }
 
-
 void
-MainWindow::uniform_noise(){
-	bool ok;
-	double amplitude = QInputDialog::getDouble(this, tr("Uniform noise"),
-			tr("Amplitude:"), 0, 0, 10000, 3, &ok);
-	srand(time(NULL));
-	if (ok)
-		model_.uniform_noise(amplitude);
+MainWindow::uniform_noise() {
+  bool ok;
+  double amplitude = QInputDialog::getDouble(this, tr("Uniform noise"),
+                                             tr("Amplitude:"), 0, 0, 10000, 3, &ok);
+  srand(time(NULL));
+  if (ok)
+    model_.uniform_noise(amplitude);
 }
 
-
 void
-MainWindow::lloyd(){
-	//todo 1 ask lloyd parameters
-	model_.lloyd(0,0);
-	update_view();
+MainWindow::lloyd() {
+  // todo 1 ask lloyd parameters
+  model_.lloyd(0, 0);
+  update_view();
 }
 
 void
-MainWindow::show_homology_group(){
-	model_.show_homology_group();
+MainWindow::show_homology_group() {
+  model_.show_homology_group();
 }
 
 void
-MainWindow::show_euler_characteristic(){
-	model_.show_euler_characteristic();
+MainWindow::show_euler_characteristic() {
+  model_.show_euler_characteristic();
 }
 
-
-
 void
-MainWindow::persistence_menu(){
-	menu_persistence_->show();
+MainWindow::persistence_menu() {
+  menu_persistence_->show();
 }
 
 void
-MainWindow::compute_persistence(int p,double threshold,int max_dim,double min_pers){
-	model_.show_persistence(p,threshold,max_dim,min_pers);
+MainWindow::compute_persistence(int p, double threshold, int max_dim, double min_pers) {
+  model_.show_persistence(p, threshold, max_dim, min_pers);
 }
 
 void
-MainWindow::critical_points_menu(){
-	bool ok;
-	double max_length = QInputDialog::getDouble(this, tr("Maximal edge length for the Rips"),
-			tr("Maximal edge length:"), 0, 0, 10000, 3, &ok);
-	if (ok)
-		model_.show_critical_points(max_length);
+MainWindow::critical_points_menu() {
+  bool ok;
+  double max_length = QInputDialog::getDouble(this, tr("Maximal edge length for the Rips"),
+                                              tr("Maximal edge length:"), 0, 0, 10000, 3, &ok);
+  if (ok)
+    model_.show_critical_points(max_length);
 }
 
 void
-MainWindow::is_manifold_menu(){
-	model_.show_is_manifold();
+MainWindow::is_manifold_menu() {
+  model_.show_is_manifold();
 }
 
 
diff --git a/src/GudhUI/gui/MainWindow.h b/src/GudhUI/gui/MainWindow.h
index 587f1c6f..c8c3fcf6 100644
--- a/src/GudhUI/gui/MainWindow.h
+++ b/src/GudhUI/gui/MainWindow.h
@@ -1,6 +1,30 @@
-#ifndef MAIN_WINDOW_H
-#define MAIN_WINDOW_H
-
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef GUI_MAINWINDOW_H_
+#define GUI_MAINWINDOW_H_
+
+// Workaround for moc-qt4 not parsing boost headers
+#include <CGAL/config.h>
 
 #include <QMainWindow>
 #include "ui_main_window.h"
@@ -13,86 +37,82 @@ class Menu_uniform_neighbors;
 class Menu_edge_contraction;
 class Menu_persistence;
 
-class MainWindow : public QMainWindow,public Ui::MainWindow{
-	Q_OBJECT
-
-private:
-	Model model_;
-	Viewer_instructor* viewer_instructor_;
-	Menu_k_nearest_neighbors* menu_k_nearest_neighbors_;
-	Menu_uniform_neighbors* menu_uniform_neighbors_;
-	Menu_edge_contraction* menu_edge_contraction_;
-	Menu_persistence* menu_persistence_;
-
-public:
-	MainWindow(QWidget* parent = 0);
-	void connectActions();
-
-	/**
-	 * compute the bounding box and calls update view
-	 */
-	void init_view() const;
-	void update_view() const;
+class MainWindow : public QMainWindow, public Ui::MainWindow {
+  Q_OBJECT
 
+ private:
+  Model model_;
+  Viewer_instructor* viewer_instructor_;
+  Menu_k_nearest_neighbors* menu_k_nearest_neighbors_;
+  Menu_uniform_neighbors* menu_uniform_neighbors_;
+  Menu_edge_contraction* menu_edge_contraction_;
+  Menu_persistence* menu_persistence_;
 
-protected:
-	void closeEvent(QCloseEvent *event);
-	void keyPressEvent(QKeyEvent *event){}
+ public:
+  MainWindow(QWidget* parent = 0);
+  void connectActions();
 
-public:
+  /**
+   * compute the bounding box and calls update view
+   */
+  void init_view() const;
+  void update_view() const;
 
-	public slots:
 
+ protected:
+  void closeEvent(QCloseEvent *event);
 
-	/**
-	 * open a file chooser to choose an off to load
-	 */
-	void off_file_open();
+  void keyPressEvent(QKeyEvent *event) { }
 
-	void off_points_open();
+ public:
+ public slots:
+  /**
+   * open a file chooser to choose an off to load
+   */
+  void off_file_open();
 
-	/**
-	 * open a file chooser to choose an off to save
-	 */
-	void off_file_save();
-	void off_points_save();
+  void off_points_open();
 
-	void show_graph_stats();
-	void show_complex_stats();
-	void show_complex_dimension();
+  /**
+   * open a file chooser to choose an off to save
+   */
+  void off_file_save();
+  void off_points_save();
 
+  void show_graph_stats();
+  void show_complex_stats();
+  void show_complex_dimension();
 
-	void build_rips_menu();
-	void build_rips(double alpha);
-	void build_k_nearest_neighbors_menu();
-	void build_k_nearest_neighbors(unsigned k);
 
+  void build_rips_menu();
+  void build_rips(double alpha);
+  void build_k_nearest_neighbors_menu();
+  void build_k_nearest_neighbors(unsigned k);
 
-	void contract_edge_menu();
-	void contract_edges(unsigned num_collapses);
 
+  void contract_edge_menu();
+  void contract_edges(unsigned num_collapses);
 
-	void collapse_vertices();
-	void collapse_edges();
 
+  void collapse_vertices();
+  void collapse_edges();
 
-	void uniform_noise();
-	void lloyd();
 
-	void show_homology_group();
-	void show_euler_characteristic();
-	void persistence_menu();
-	void compute_persistence(int p,double threshold,int max_dim,double min_pers);
-	void critical_points_menu();
-	void is_manifold_menu();
+  void uniform_noise();
+  void lloyd();
 
+  void show_homology_group();
+  void show_euler_characteristic();
+  void persistence_menu();
+  void compute_persistence(int p, double threshold, int max_dim, double min_pers);
+  void critical_points_menu();
+  void is_manifold_menu();
 
-public:
-	signals:
-	void sceneChanged() const;
-	
 
+ public:
+ signals:
+  void sceneChanged() const;
 };
 
 
-#endif
+#endif  // GUI_MAINWINDOW_H_
diff --git a/src/GudhUI/gui/Menu_edge_contraction.cpp b/src/GudhUI/gui/Menu_edge_contraction.cpp
index dd2621be..a679b0bf 100644
--- a/src/GudhUI/gui/Menu_edge_contraction.cpp
+++ b/src/GudhUI/gui/Menu_edge_contraction.cpp
@@ -1,91 +1,97 @@
-/*
- * Menu_edge_contraction.cpp
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
  *
- *  Created on: Sep 11, 2014
- *      Author: dsalinas
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef MENU_EDGE_CONTRACTION_CPP_
-#define MENU_EDGE_CONTRACTION_CPP_
-
+#ifndef GUI_MENU_EDGE_CONTRACTION_CPP_
+#define GUI_MENU_EDGE_CONTRACTION_CPP_
 
 #include "Menu_edge_contraction.h"
 
-Menu_edge_contraction::Menu_edge_contraction(MainWindow* parent,const Model& model):
-parent_(parent),model_(model)
-{
-	setupUi(this);
-	connectActions(parent_);
+Menu_edge_contraction::Menu_edge_contraction(MainWindow* parent, const Model& model) :
+    parent_(parent), model_(model) {
+  setupUi(this);
+  connectActions(parent_);
 }
 
-void Menu_edge_contraction::connectActions(MainWindow* parent)
-{
-	QObject::connect(
-			this->horizontalSlider,
-			SIGNAL(valueChanged(int)),
-			this,
-			SLOT(slider_value_changed(int))
-	);
+void Menu_edge_contraction::connectActions(MainWindow* parent) {
+  QObject::connect(
+                   this->horizontalSlider,
+                   SIGNAL(valueChanged(int)),
+                   this,
+                   SLOT(slider_value_changed(int)));
 
 
-	QObject::connect(this, SIGNAL(contract_edges(unsigned)), parent, SLOT(contract_edges(unsigned)));
-
-	QObject::connect(this->pushButton_collapse, SIGNAL(clicked()), this, SLOT(send_contract_edges()));
+  QObject::connect(this, SIGNAL(contract_edges(unsigned)), parent, SLOT(contract_edges(unsigned)));
 
+  QObject::connect(this->pushButton_collapse, SIGNAL(clicked()), this, SLOT(send_contract_edges()));
 }
 
-void Menu_edge_contraction::slider_value_changed(int new_slider_value){
-	int num_collapses =
-			(horizontalSlider->value()==1)? 1 : horizontalSlider->value() * model_.num_vertices() / 100 ;
-	this->txt_nb_vertices->setNum((int)model_.num_vertices());
-	this->txt_nb_collapses->setNum(num_collapses);
-	this->spinBox_nb_remaining_vertices->setValue(model_.num_vertices()-num_collapses);
+void Menu_edge_contraction::slider_value_changed(int new_slider_value) {
+  int num_collapses =
+      (horizontalSlider->value() == 1) ? 1 : horizontalSlider->value() * model_.num_vertices() / 100;
+  this->txt_nb_vertices->setNum(static_cast<int>(model_.num_vertices()));
+  this->txt_nb_collapses->setNum(num_collapses);
+  this->spinBox_nb_remaining_vertices->setValue(model_.num_vertices() - num_collapses);
 }
 
-
 void
-Menu_edge_contraction::update_slider_value(){
-	int num_vertices = model_.num_vertices();
-	int num_collapses = (horizontalSlider->value()==1)? 1 : horizontalSlider->value() * num_vertices / 100 ;
-	int horizontal_slider_position = num_vertices>0?  num_collapses/(double)num_vertices * 100 : 1  ;
-	horizontalSlider->setValue(horizontal_slider_position);
+Menu_edge_contraction::update_slider_value() {
+  int num_vertices = model_.num_vertices();
+  int num_collapses = (horizontalSlider->value() == 1) ? 1 : horizontalSlider->value() * num_vertices / 100;
+  int horizontal_slider_position = num_vertices > 0 ? num_collapses / static_cast<double>(num_vertices * 100) : 1;
+  horizontalSlider->setValue(horizontal_slider_position);
 }
 
-
 void
-Menu_edge_contraction::update_gui_numbers(){
-	update_slider_value();
-	bool ok;
-	int num_collapses = this->txt_nb_collapses->text().toInt(&ok,10);
-	if(!ok) return;
-	this->txt_nb_vertices->setNum((int)model_.num_vertices());
-	this->txt_nb_collapses->setNum(num_collapses);
-	this->spinBox_nb_remaining_vertices->setValue(model_.num_vertices()-num_collapses);
+Menu_edge_contraction::update_gui_numbers() {
+  update_slider_value();
+  bool ok;
+  int num_collapses = this->txt_nb_collapses->text().toInt(&ok, 10);
+  if (!ok) return;
+  this->txt_nb_vertices->setNum(static_cast<int>(model_.num_vertices()));
+  this->txt_nb_collapses->setNum(num_collapses);
+  this->spinBox_nb_remaining_vertices->setValue(model_.num_vertices() - num_collapses);
 }
 
 void
-Menu_edge_contraction::update_gui_numbers(int new_value){
-	update_gui_numbers();
+Menu_edge_contraction::update_gui_numbers(int new_value) {
+  update_gui_numbers();
 }
 
-
 void
-Menu_edge_contraction::send_contract_edges(){
-	emit(contract_edges(num_collapses()));
-	update_gui_numbers();
+Menu_edge_contraction::send_contract_edges() {
+  emit(contract_edges(num_collapses()));
+  update_gui_numbers();
 }
 
 unsigned
-Menu_edge_contraction::num_vertices(){
-	return model_.num_vertices();
+Menu_edge_contraction::num_vertices() {
+  return model_.num_vertices();
 }
 
 unsigned
-Menu_edge_contraction::num_collapses(){
-	return (horizontalSlider->value()==1)? 1 : horizontalSlider->value() * num_vertices() / 100 ;
+Menu_edge_contraction::num_collapses() {
+  return (horizontalSlider->value() == 1) ? 1 : horizontalSlider->value() * num_vertices() / 100;
 }
 
-
 #include "Menu_edge_contraction.moc"
 
-#endif /* MENU_EDGE_CONTRACTION_CPP_ */
+#endif  // GUI_MENU_EDGE_CONTRACTION_CPP_
diff --git a/src/GudhUI/gui/Menu_edge_contraction.h b/src/GudhUI/gui/Menu_edge_contraction.h
index e497a90f..08f0bf67 100644
--- a/src/GudhUI/gui/Menu_edge_contraction.h
+++ b/src/GudhUI/gui/Menu_edge_contraction.h
@@ -1,52 +1,63 @@
-/*
- * Menu_edge_contraction.h
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
  *
- *  Created on: Sep 11, 2014
- *      Author: dsalinas
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef MENU_EDGE_CONTRACTION_H_
-#define MENU_EDGE_CONTRACTION_H_
+#ifndef GUI_MENU_EDGE_CONTRACTION_H_
+#define GUI_MENU_EDGE_CONTRACTION_H_
 
+// Workaround for moc-qt4 not parsing boost headers
+#include <CGAL/config.h>
 
 #include "gui/MainWindow.h"
 #include "gui/ui_MenuEdgeContraction.h"
 
 #include "model/Model.h"
 
+class Menu_edge_contraction : public QDialog, public Ui::MenuEdgeContraction {
+  Q_OBJECT
 
-class Menu_edge_contraction : public QDialog,public Ui::MenuEdgeContraction{
-	Q_OBJECT
-private:
-	MainWindow* parent_;
-	const Model& model_;
-
+ private:
+  MainWindow* parent_;
+  const Model& model_;
 
-	void update_slider_value();
-public:
+  void update_slider_value();
 
-	Menu_edge_contraction(MainWindow* parent,const Model& model);
+ public:
+  Menu_edge_contraction(MainWindow* parent, const Model& model);
 
-	void connectActions(MainWindow* parent);
+  void connectActions(MainWindow* parent);
 
+ private:
+  unsigned num_vertices();
+  unsigned num_collapses();
 
-private:
-	unsigned num_vertices();
-	unsigned num_collapses();
+ public slots:
+  void slider_value_changed(int new_slider_value);
+  void update_gui_numbers();
+  void update_gui_numbers(int gui_numbers);
 
-	public slots:
-
-	void slider_value_changed(int new_slider_value);
-	void update_gui_numbers();
-	void update_gui_numbers(int);
-
-	void send_contract_edges();
-	signals:
-
-	void contract_edges(unsigned num_collapses);
+  void send_contract_edges();
 
+ signals:
+  void contract_edges(unsigned num_collapses);
 };
 
-
-
-#endif /* MENU_EDGE_CONTRACTION_H_ */
+#endif  // GUI_MENU_EDGE_CONTRACTION_H_
diff --git a/src/GudhUI/gui/Menu_k_nearest_neighbors.cpp b/src/GudhUI/gui/Menu_k_nearest_neighbors.cpp
index 21c67b2a..e24865f2 100644
--- a/src/GudhUI/gui/Menu_k_nearest_neighbors.cpp
+++ b/src/GudhUI/gui/Menu_k_nearest_neighbors.cpp
@@ -1,55 +1,59 @@
-/*
- * Menu_k_nearest_neighbors.cpp
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
  *
- *  Created on: Sep 11, 2014
- *      Author: dsalinas
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-
 #include "Menu_k_nearest_neighbors.h"
 
-Menu_k_nearest_neighbors::Menu_k_nearest_neighbors(QMainWindow* parent_):
-parent(parent_)
-{
-	setupUi(this);
-	connectActions(parent_);
+Menu_k_nearest_neighbors::Menu_k_nearest_neighbors(QMainWindow* parent_)
+    : parent(parent_) {
+  setupUi(this);
+  connectActions(parent_);
 }
 
-void Menu_k_nearest_neighbors::connectActions(QMainWindow* parent){
-
-	QObject::connect(
-			this->pushButtonCompute,
-			SIGNAL(clicked()),
-			this,
-			SLOT(send_compute_k_nearest_neighbors())
-	);
-	QObject::connect(
-			this->spinBoxK,
-			SIGNAL(valueChanged(int)),
-			this,
-			SLOT(update_k(int))
-	);
-	QObject::connect(
-			this,
-			SIGNAL(compute_k_nearest_neighbors(unsigned)),
-			parent,
-			SLOT(build_k_nearest_neighbors(unsigned))
-	);
-
+void Menu_k_nearest_neighbors::connectActions(QMainWindow* parent) {
+  QObject::connect(this->pushButtonCompute,
+                   SIGNAL(clicked()),
+                   this,
+                   SLOT(send_compute_k_nearest_neighbors()));
+  QObject::connect(this->spinBoxK,
+                   SIGNAL(valueChanged(int)),
+                   this,
+                   SLOT(update_k(int)));
+  QObject::connect(this,
+                   SIGNAL(compute_k_nearest_neighbors(unsigned)),
+                   parent,
+                   SLOT(build_k_nearest_neighbors(unsigned)));
 }
 
-void Menu_k_nearest_neighbors::send_compute_k_nearest_neighbors(){
-	emit(compute_k_nearest_neighbors((unsigned)spinBoxK->value()));
+void Menu_k_nearest_neighbors::send_compute_k_nearest_neighbors() {
+  emit(compute_k_nearest_neighbors((unsigned) spinBoxK->value()));
 }
 
-void Menu_k_nearest_neighbors::accept(){
-	send_compute_k_nearest_neighbors();
+void Menu_k_nearest_neighbors::accept() {
+  send_compute_k_nearest_neighbors();
 }
 
-void Menu_k_nearest_neighbors::update_k(int new_k_value){
-	if(checkBoxAutoUpdate->isChecked())
-		emit(compute_k_nearest_neighbors((unsigned)spinBoxK->value()));
+void Menu_k_nearest_neighbors::update_k(int new_k_value) {
+  if (checkBoxAutoUpdate->isChecked())
+    emit(compute_k_nearest_neighbors((unsigned) spinBoxK->value()));
 }
 
-
 #include "Menu_k_nearest_neighbors.moc"
diff --git a/src/GudhUI/gui/Menu_k_nearest_neighbors.h b/src/GudhUI/gui/Menu_k_nearest_neighbors.h
index d72b0074..8088b768 100644
--- a/src/GudhUI/gui/Menu_k_nearest_neighbors.h
+++ b/src/GudhUI/gui/Menu_k_nearest_neighbors.h
@@ -1,39 +1,51 @@
-/*
- * Menu_k_nearest_neighbors.h
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
  *
- *  Created on: Sep 11, 2014
- *      Author: dsalinas
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef MENU_K_NEAREST_NEIGHBORS_H_
-#define MENU_K_NEAREST_NEIGHBORS_H_
+#ifndef GUI_MENU_K_NEAREST_NEIGHBORS_H_
+#define GUI_MENU_K_NEAREST_NEIGHBORS_H_
 
 #include <QMainWindow>
 #include "gui/ui_KNearestNeighborsMenu.h"
 
 class QWidget;
 
+class Menu_k_nearest_neighbors : public QDialog, public Ui::KNearestNeighborsMenu {
+  Q_OBJECT
 
-class Menu_k_nearest_neighbors : public QDialog,public Ui::KNearestNeighborsMenu{
-	Q_OBJECT
-private:
-	QMainWindow* parent;
+ private:
+  QMainWindow* parent;
 
-public:
+ public:
+  Menu_k_nearest_neighbors(QMainWindow* parent_);
 
-	Menu_k_nearest_neighbors(QMainWindow* parent_);
+  void connectActions(QMainWindow* parent);
 
-	void connectActions(QMainWindow* parent);
-
-	public slots:
-	void send_compute_k_nearest_neighbors();
-	void update_k(int);
-	void accept();
-
-	signals:
-	void compute_k_nearest_neighbors(unsigned k);
+ public slots:
+  void send_compute_k_nearest_neighbors();
+  void update_k(int k);
+  void accept();
 
+ signals:
+  void compute_k_nearest_neighbors(unsigned k);
 };
 
-
-#endif /* MENU_K_NEAREST_NEIGHBORS_H_ */
+#endif  // GUI_MENU_K_NEAREST_NEIGHBORS_H_
diff --git a/src/GudhUI/gui/Menu_persistence.cpp b/src/GudhUI/gui/Menu_persistence.cpp
index fae3a0e6..016c076b 100644
--- a/src/GudhUI/gui/Menu_persistence.cpp
+++ b/src/GudhUI/gui/Menu_persistence.cpp
@@ -1,13 +1,10 @@
-/*
- * Menu_persistence.cpp
- *  Created on: Jan 27, 2015
- * This file is part of the Gudhi Library. The Gudhi library 
+/* This file is part of the Gudhi Library. The Gudhi library 
  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
  *    library for computational topology.
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-M�diterran�e (France)
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
@@ -27,34 +24,30 @@
 
 #include "Menu_persistence.h"
 
-Menu_persistence::Menu_persistence(QMainWindow* parent_):parent(parent_)
-{
-	setupUi(this);
-	connectActions(parent_);
+Menu_persistence::Menu_persistence(QMainWindow* parent_) : parent(parent_) {
+  setupUi(this);
+  connectActions(parent_);
 }
 
-void Menu_persistence::connectActions(QMainWindow* parent){
-	QObject::connect(
-			this,
-			SIGNAL(compute_persistence(int,double,int,double)),
-			parent,
-			SLOT(compute_persistence(int,double,int,double))
-	);
+void Menu_persistence::connectActions(QMainWindow* parent) {
+  QObject::connect(this,
+                   SIGNAL(compute_persistence(int, double, int, double)),
+                   parent,
+                   SLOT(compute_persistence(int, double, int, double)));
 }
 
-void Menu_persistence::send_compute_persistence(){
-	emit(compute_persistence(p_spinBox->value(),threshold_doubleSpinBox->value(),
-			maxdimension_spinBox->value(),minpersistence_doubleSpinBox->value()));
+void Menu_persistence::send_compute_persistence() {
+  emit(compute_persistence(p_spinBox->value(), threshold_doubleSpinBox->value(),
+                           maxdimension_spinBox->value(), minpersistence_doubleSpinBox->value()));
 }
 
-void Menu_persistence::accept(){
-	send_compute_persistence();
+void Menu_persistence::accept() {
+  send_compute_persistence();
 }
 
-//void Menu_persistence::compute_persistence(int p_fied,double threshold,int dim_max,double min_persistence){
-////	if(checkBoxAutoUpdate->isChecked())
-////		emit(compute_k_nearest_neighbors((unsigned)spinBoxK->value()));
-//}
-
+// void Menu_persistence::compute_persistence(int p_fied,double threshold,int dim_max,double min_persistence) {
+//  if(checkBoxAutoUpdate->isChecked())
+//    emit(compute_k_nearest_neighbors((unsigned)spinBoxK->value()));
+// }
 
 #include "Menu_persistence.moc"
diff --git a/src/GudhUI/gui/Menu_persistence.h b/src/GudhUI/gui/Menu_persistence.h
index 67b64afa..8c4df158 100644
--- a/src/GudhUI/gui/Menu_persistence.h
+++ b/src/GudhUI/gui/Menu_persistence.h
@@ -1,13 +1,10 @@
-/*
- * Menu_persistence.h
- *  Created on: Jan 27, 2015
- * This file is part of the Gudhi Library. The Gudhi library 
+/* This file is part of the Gudhi Library. The Gudhi library 
  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
  *    library for computational topology.
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-M�diterran�e (France)
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
@@ -24,36 +21,31 @@
  * 
  */
 
-
-#ifndef MENU_PERSISTENCE_H_
-#define MENU_PERSISTENCE_H_
-
+#ifndef GUI_MENU_PERSISTENCE_H_
+#define GUI_MENU_PERSISTENCE_H_
 
 #include <QMainWindow>
 #include "gui/ui_PersistenceMenu.h"
 
 class QWidget;
 
+class Menu_persistence : public QDialog, public Ui::PersistenceMenu {
+  Q_OBJECT
 
-class Menu_persistence : public QDialog,public Ui::PersistenceMenu{
-	Q_OBJECT
-private:
-	QMainWindow* parent;
-
-public:
+ private:
+  QMainWindow* parent;
 
-	Menu_persistence(QMainWindow* parent_);
+ public:
+  Menu_persistence(QMainWindow* parent_);
 
-	void connectActions(QMainWindow* parent);
+  void connectActions(QMainWindow* parent);
 
-	public slots:
-	void send_compute_persistence();
-	void accept();
-	signals:
-	void compute_persistence(int p_fied,double threshold,int dim_max,double min_persistence);
+ public slots:
+  void send_compute_persistence();
+  void accept();
 
+ signals:
+  void compute_persistence(int p_fied, double threshold, int dim_max, double min_persistence);
 };
 
-
-
-#endif /* MENU_PERSISTENCE_H_ */
+#endif  // GUI_MENU_PERSISTENCE_H_
diff --git a/src/GudhUI/gui/Menu_uniform_neighbors.cpp b/src/GudhUI/gui/Menu_uniform_neighbors.cpp
index 86e2593e..20e4f98f 100644
--- a/src/GudhUI/gui/Menu_uniform_neighbors.cpp
+++ b/src/GudhUI/gui/Menu_uniform_neighbors.cpp
@@ -1,59 +1,60 @@
-/*
- * Menu_uniform_neighbors.cpp
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
  *
- *  Created on: Sep 11, 2014
- *      Author: dsalinas
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
  */
 
-
-
-
-
 #include "Menu_uniform_neighbors.h"
 
-Menu_uniform_neighbors::Menu_uniform_neighbors(QMainWindow* parent_):
-parent(parent_)
-{
-	setupUi(this);
-	connectActions(parent_);
+Menu_uniform_neighbors::Menu_uniform_neighbors(QMainWindow* parent_) :
+    parent(parent_) {
+  setupUi(this);
+  connectActions(parent_);
 }
 
-void Menu_uniform_neighbors::connectActions(QMainWindow* parent){
-
-	QObject::connect(
-			this->pushButtonCompute,
-			SIGNAL(clicked()),
-			this,
-			SLOT(send_compute_uniform_neighbors())
-	);
-	QObject::connect(
-			this->doubleSpinBoxAlpha,
-			SIGNAL(valueChanged(double)),
-			this,
-			SLOT(update_alpha(double))
-	);
-	QObject::connect(
-			this,
-			SIGNAL(compute_uniform_neighbors(double)),
-			parent,
-			SLOT(build_rips(double))
-	);
-
+void Menu_uniform_neighbors::connectActions(QMainWindow* parent) {
+  QObject::connect(this->pushButtonCompute,
+                   SIGNAL(clicked()),
+                   this,
+                   SLOT(send_compute_uniform_neighbors()));
+  QObject::connect(this->doubleSpinBoxAlpha,
+                   SIGNAL(valueChanged(double)),
+                   this,
+                   SLOT(update_alpha(double)));
+  QObject::connect(this,
+                   SIGNAL(compute_uniform_neighbors(double)),
+                   parent,
+                   SLOT(build_rips(double)));
 }
 
-void Menu_uniform_neighbors::send_compute_uniform_neighbors(){
-	emit(compute_uniform_neighbors(doubleSpinBoxAlpha->value()));
+void Menu_uniform_neighbors::send_compute_uniform_neighbors() {
+  emit(compute_uniform_neighbors(doubleSpinBoxAlpha->value()));
 }
 
-void Menu_uniform_neighbors::accept(){
-	send_compute_uniform_neighbors();
+void Menu_uniform_neighbors::accept() {
+  send_compute_uniform_neighbors();
 }
 
-void Menu_uniform_neighbors::update_alpha(double alpha){
-	if(checkBoxAutoUpdate->isChecked())
-		emit(compute_uniform_neighbors(doubleSpinBoxAlpha->value()));
+void Menu_uniform_neighbors::update_alpha(double alpha) {
+  if (checkBoxAutoUpdate->isChecked())
+    emit(compute_uniform_neighbors(doubleSpinBoxAlpha->value()));
 }
 
-
-
 #include "Menu_uniform_neighbors.moc"
diff --git a/src/GudhUI/gui/Menu_uniform_neighbors.h b/src/GudhUI/gui/Menu_uniform_neighbors.h
index cb90cc88..0b6f65fe 100644
--- a/src/GudhUI/gui/Menu_uniform_neighbors.h
+++ b/src/GudhUI/gui/Menu_uniform_neighbors.h
@@ -1,36 +1,51 @@
-/*
- * Menu_uniform_neighbors.h
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
  *
- *  Created on: Sep 11, 2014
- *      Author: dsalinas
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
  */
 
-#ifndef MENU_UNIFORM_NEIGHBORS_H_
-#define MENU_UNIFORM_NEIGHBORS_H_
+#ifndef GUI_MENU_UNIFORM_NEIGHBORS_H_
+#define GUI_MENU_UNIFORM_NEIGHBORS_H_
 
 #include <QMainWindow>
 #include "gui/ui_UniformNeighborsMenu.h"
 
-class Menu_uniform_neighbors : public QDialog,public Ui::UniformMenu {
-	Q_OBJECT
-private:
-	QMainWindow* parent;
-
-public:
+class Menu_uniform_neighbors : public QDialog, public Ui::UniformMenu {
+  Q_OBJECT
 
-	Menu_uniform_neighbors(QMainWindow* parent_);
+ private:
+  QMainWindow* parent;
 
-	void connectActions(QMainWindow* parent);
+ public:
+  Menu_uniform_neighbors(QMainWindow* parent_);
 
-	public slots:
-	void send_compute_uniform_neighbors();
-	void update_alpha(double);
-	void accept();
+  void connectActions(QMainWindow* parent);
 
-	signals:
-	void compute_uniform_neighbors(double alpha);
+ public slots:
+  void send_compute_uniform_neighbors();
+  void update_alpha(double alpha);
+  void accept();
 
+ signals:
+  void compute_uniform_neighbors(double alpha);
 };
 
 
-#endif /* MENU_UNIFORM_NEIGHBORS_H_ */
+#endif  // GUI_MENU_UNIFORM_NEIGHBORS_H_
diff --git a/src/GudhUI/gui/Viewer.cpp b/src/GudhUI/gui/Viewer.cpp
deleted file mode 100644
index e69de29b..00000000
--- a/src/GudhUI/gui/Viewer.cpp
+++ /dev/null
diff --git a/src/GudhUI/gui/Viewer_instructor.cpp b/src/GudhUI/gui/Viewer_instructor.cpp
deleted file mode 100644
index e69de29b..00000000
--- a/src/GudhUI/gui/Viewer_instructor.cpp
+++ /dev/null
diff --git a/src/GudhUI/gui/gudhui.cpp b/src/GudhUI/gui/gudhui.cpp
index 8d90270f..377cd2f2 100644
--- a/src/GudhUI/gui/gudhui.cpp
+++ b/src/GudhUI/gui/gudhui.cpp
@@ -1,15 +1,36 @@
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
 #include "MainWindow.h"
 #include <QApplication>
 #include <CGAL/Qt/resources.h>
 
+int main(int argc, char** argv) {
+  QApplication application(argc, argv);
+  application.setOrganizationDomain("inria.fr");
+  application.setOrganizationName("INRIA");
+  application.setApplicationName("GudhUI");
 
-int main(int argc, char** argv)
-{
- QApplication application(argc,argv);
- application.setOrganizationDomain("inria.fr");
- application.setOrganizationName("INRIA");
- application.setApplicationName("GudhUI");
-  
   MainWindow mw;
   application.setQuitOnLastWindowClosed(false);
   mw.show();
diff --git a/src/GudhUI/model/Complex_typedefs.h b/src/GudhUI/model/Complex_typedefs.h
index b6404d62..c310d4a6 100644
--- a/src/GudhUI/model/Complex_typedefs.h
+++ b/src/GudhUI/model/Complex_typedefs.h
@@ -1,39 +1,49 @@
-/*
- * Complex_typedefs.h
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
  *
- *  Created on: Aug 26, 2014
- *      Author: dsalinas
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
  */
 
-#ifndef COMPLEX_TYPEDEFS_H_
-#define COMPLEX_TYPEDEFS_H_
-
+#ifndef MODEL_COMPLEX_TYPEDEFS_H_
+#define MODEL_COMPLEX_TYPEDEFS_H_
 
-
-#include "gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h"
-#include "gudhi/Skeleton_blocker_geometric_complex.h"
+#include <gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h>
+#include <gudhi/Skeleton_blocker_geometric_complex.h>
 
 #include <CGAL/Kernel_d/Point_d.h>
-
 #include <CGAL/Cartesian.h>
 #include <CGAL/Cartesian_d.h>
 
-
 struct Geometry_trait : public CGAL::Cartesian_d<double> {
-	typedef CGAL::Cartesian<double>::Point_3 Point_3;
-	typedef CGAL::Cartesian<double>::Vector_3 Vector_3;
-	typedef CGAL::Point_d<Cartesian_d<double>> Point;
-	typedef CGAL::Vector_d<Cartesian_d<double>> Vector;
+  typedef CGAL::Cartesian<double>::Point_3 Point_3;
+  typedef CGAL::Cartesian<double>::Vector_3 Vector_3;
+  typedef CGAL::Point_d<Cartesian_d<double>> Point;
+  typedef CGAL::Vector_d<Cartesian_d<double>> Vector;
 };
 
 typedef Geometry_trait::Point Point;
 
-
 using namespace Gudhi;
 using namespace Gudhi::skbl;
 
 typedef Skeleton_blocker_simple_geometric_traits<Geometry_trait> Complex_geometric_traits;
 typedef Skeleton_blocker_geometric_complex< Complex_geometric_traits > Complex;
 
-
-#endif /* COMPLEX_TYPEDEFS_H_ */
+#endif  // MODEL_COMPLEX_TYPEDEFS_H_
diff --git a/src/GudhUI/model/Model.h b/src/GudhUI/model/Model.h
index 17a7d278..07a67a0c 100644
--- a/src/GudhUI/model/Model.h
+++ b/src/GudhUI/model/Model.h
@@ -1,16 +1,41 @@
-/*
- * Model.h
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
  *
- *  Created on: Aug 25, 2014
- *      Author: david
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
  */
 
-#ifndef MODEL_H_
-#define MODEL_H_
+#ifndef MODEL_MODEL_H_
+#define MODEL_MODEL_H_
+
+#include <gudhi/Clock.h>
+#include <gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h>
+#include <gudhi/Skeleton_blocker_geometric_complex.h>
+#include <gudhi/Off_reader.h>
+
+#include <CGAL/Euclidean_distance.h>
 
 #include <fstream>
 #include <limits>
-#include "gudhi/Clock.h"
+#include <string>
+#include <vector>
+
 #include "utils/UI_utils.h"
 #include "utils/Lloyd_builder.h"
 #include "utils/Rips_builder.h"
@@ -22,328 +47,309 @@
 #include "utils/Critical_points.h"
 #include "utils/Is_manifold.h"
 
-#include "gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h"
-#include "gudhi/Skeleton_blocker_geometric_complex.h"
-
-#include "gudhi/Off_reader.h"
-
 #include "Complex_typedefs.h"
 
-
-#include <CGAL/Euclidean_distance.h>
-
-
 template<typename Complex>
-class CGAL_geometric_flag_complex_wrapper{
-	Complex& complex_;
-	typedef typename Complex::Vertex_handle Vertex_handle;
-	typedef typename Complex::Point Point;
-
-	const bool load_only_points_;
-
-public:
-	CGAL_geometric_flag_complex_wrapper(Complex& complex,bool load_only_points = false):
-		complex_(complex),
-		load_only_points_(load_only_points){
-	}
-
-	void init(int dim,int num_vertices,int num_max_faces,int num_edges) const{
-	}
-
-	void point(const std::vector<double>& coords){
-		Point p(coords.size(),coords.begin(),coords.end());
-		complex_.add_vertex(p);
-	}
-
-	void maximal_face(std::vector<int> vertices){
-		if (!load_only_points_){
-			std::cout<<"size:"<<vertices.size()<<std::endl;
-			for (int i = 0; i<vertices.size() ; ++i)
-				for (int j = i+1; j<vertices.size() ; ++j)
-					complex_.add_edge(Vertex_handle(vertices[i]),Vertex_handle(vertices[j]));
-		}
-	}
-	void done() const{}
+class CGAL_geometric_flag_complex_wrapper {
+  Complex& complex_;
+  typedef typename Complex::Vertex_handle Vertex_handle;
+  typedef typename Complex::Point Point;
+
+  const bool load_only_points_;
+
+ public:
+  CGAL_geometric_flag_complex_wrapper(Complex& complex, bool load_only_points = false) :
+      complex_(complex),
+      load_only_points_(load_only_points) { }
+
+  void init(int dim, int num_vertices, int num_max_faces, int num_edges) const { }
+
+  void point(const std::vector<double>& coords) {
+    Point p(coords.size(), coords.begin(), coords.end());
+    complex_.add_vertex(p);
+  }
+
+  void maximal_face(std::vector<int> vertices) {
+    if (!load_only_points_) {
+      std::cout << "size:" << vertices.size() << std::endl;
+      for (int i = 0; i < vertices.size(); ++i)
+        for (int j = i + 1; j < vertices.size(); ++j)
+          complex_.add_edge(Vertex_handle(vertices[i]), Vertex_handle(vertices[j]));
+    }
+  }
+
+  void done() const { }
 };
 
-
-class Model{
-
-public:
-	Complex complex_;
-	typedef Complex::Vertex_handle Vertex_handle;
-
-	Model():complex_(){
-	}
-
-public:
-	void off_file_open(const std::string& name_file){
-		UIDBGMSG("load off file",name_file);
-		complex_.clear();
-		CGAL_geometric_flag_complex_wrapper<Complex> read_wraper(complex_,false);
-		Gudhi::read_off(name_file,read_wraper);
-	}
-
-	void off_points_open(const std::string& name_file){
-		UIDBGMSG("load off points",name_file);
-		complex_.clear();
-		CGAL_geometric_flag_complex_wrapper<Complex> read_wraper(complex_,true);
-		Gudhi::read_off(name_file,read_wraper);
-	}
-
-	void off_file_save(const std::string& name_file){
-		UIDBG("save off file");
-		UIDBG("save off off_points_save");
-		std::ofstream file(name_file);
-		if(file.is_open()){
-			file<<"OFF\n";
-			file<<complex_.num_vertices()<<" "<<complex_.num_edges()<<" 0\n";
-			for(auto v : complex_.vertex_range()){
-				const auto& pt(complex_.point(v));
-				for(auto it = pt.cartesian_begin();it!=pt.cartesian_end();++it)
-					file<<*it<<" ";
-				file<<std::endl;
-			}
-			for(auto e : complex_.edge_range())
-				file<<"2 "<<complex_.first_vertex(e)<<" "<<complex_.second_vertex(e)<<"\n";
-			file.close();
-		}
-		else std::cerr << "Could not open file "<<name_file<<std::endl;
-
-	}
-
-	void off_points_save(const std::string& name_file){
-		UIDBG("save off off_points_save");
-		std::ofstream file(name_file);
-		if(file.is_open()){
-			file<<"OFF\n";
-			file<<complex_.num_vertices()<<" 0 0\n";
-			for(auto v : complex_.vertex_range()){
-				const auto& pt(complex_.point(v));
-				for(auto it = pt.cartesian_begin();it!=pt.cartesian_end();++it)
-					file<<*it<<" ";
-				file<<std::endl;
-			}
-			file.close();
-		}
-		else std::cerr << "Could not open file "<<name_file<<std::endl;
-
-	}
-
-	// point sets operations
-	void uniform_noise(double amplitude){
-		UIDBG("unif noise");
-		for (auto v : complex_.vertex_range())
-			complex_.point(v) = add_uniform_noise(complex_.point(v),amplitude);
-	}
-
-private:
-	Point add_uniform_noise(const Point& point,double amplitude){
-		std::vector<double> new_point(point.dimension());
-		for(int i  = 0 ; i < point.dimension();++i){
-			new_point[i] = point[i] + (rand() % 2 - .5) * amplitude;
-		}
-		return Point(point.dimension(), new_point.begin(),new_point.end());
-	}
-
-public:
-
-	void lloyd(int num_iterations,int num_closest_neighbors){
-		UIDBG("lloyd");
-		Lloyd_builder<Complex> lloyd_builder(complex_,1);
-	}
-
-	double squared_eucl_distance(const Point& p1,const Point& p2) const{
-		return Geometry_trait::Squared_distance_d()(p1,p2);
-	}
-
-	// complex operations from points
-	void build_rips(double alpha){
-		UIDBG("build_rips");
-		Rips_builder<Complex> rips_builder(complex_,alpha);
-	}
-
-	void build_k_nearest_neighbors(unsigned k){
-		UIDBG("build_k_nearest");
-		complex_.keep_only_vertices();
-		K_nearest_builder<Complex> k_nearest_builder(complex_,k);
-	}
-
-	void build_delaunay(){
-		UIDBG("build_delaunay");
-		complex_.keep_only_vertices();
-	}
-
-
-
-	void contract_edges(unsigned num_contractions){
-		Clock c;
-		Edge_contractor<Complex> contractor(complex_,num_contractions);
-		std::cout<<"Time to simplify: "<<c.num_seconds()<<"s"<<std::endl;
-	}
-
-
-	void collapse_vertices(unsigned num_collapses){
-
-		auto old_num_vertices = complex_.num_vertices();
-		Vertex_collapsor<Complex> collapsor(complex_,complex_.num_vertices());
-		UIDBGMSG("num vertices collapsed:",old_num_vertices - complex_.num_vertices());
-	}
-
-	void collapse_edges(unsigned num_collapses){
-		Edge_collapsor<Complex> collapsor(complex_,num_collapses);
-	}
-
-
-	void show_graph_stats(){
-		std::cout << "++++++ Graph stats +++++++"<< std::endl;
-		std::cout << "Num vertices : " << complex_.num_vertices()<<std::endl;
-		std::cout << "Num edges : " << complex_.num_edges()<<std::endl;
-		std::cout << "Num connected components : " << complex_.num_connected_components()<<std::endl;
-		std::cout << "Min/avg/max degree : " << min_degree()<<"/"<<avg_degree()<<"/"<<max_degree()<<std::endl;
-		std::cout << "Num connected components : " << complex_.num_connected_components()<<std::endl;
-		std::cout << "Num connected components : " << complex_.num_connected_components()<<std::endl;
-		std::cout << "+++++++++++++++++++++++++"<< std::endl;
-	}
-
-private:
-	int min_degree() const{
-		int res = (std::numeric_limits<int>::max)();
-		for(auto v : complex_.vertex_range())
-			res= (std::min)(res,complex_.degree(v));
-		return res;
-	}
-
-	int max_degree() const{
-		int res = 0;
-		for(auto v : complex_.vertex_range())
-			res= (std::max)(res,complex_.degree(v));
-		return res;
-	}
-
-	int avg_degree() const{
-		int res = 0;
-		for(auto v : complex_.vertex_range())
-			res+= complex_.degree(v);
-		return res / complex_.num_vertices();
-	}
-
-public:
-
-
-
-	void show_complex_stats(){
-		std::cout << "++++++ Mesh stats +++++++"<< std::endl;
-		std::cout << "Num vertices : " << complex_.num_vertices()<<std::endl;
-		std::cout << "Num edges : " << complex_.num_edges()<<std::endl;
-		std::cout << "Num connected components : " << complex_.num_connected_components()<<std::endl;
-		std::cout << "+++++++++++++++++++++++++"<< std::endl;
-
-	}
-
-	void show_complex_dimension(){
-		unsigned num_simplices = 0;
-		int euler = 0;
-		int dimension = 0;
-		Clock clock;
-		for(const auto &s : complex_.simplex_range()){
-			num_simplices++;
-			dimension = (std::max)(s.dimension(),dimension);
-			if(s.dimension()%2==0)
-				euler+=1;
-			else
-				euler-=1;
-		}
-		clock.end();
-		std::cout << "++++++ Mesh dimension +++++++"<< std::endl;
-		std::cout << "Dimension : " << dimension<<std::endl;
-		std::cout << "Euler characteristic : " << euler<<std::endl;
-		std::cout << "Num simplices : " << num_simplices <<std::endl;
-		std::cout << "Total time: " << clock <<std::endl;
-		std::cout << "Time per simplex: " << clock.num_seconds()/num_simplices <<" s"<<std::endl;
-		std::cout << "+++++++++++++++++++++++++"<< std::endl;
-	}
-
-
-	void show_homology_group(){
+class Model {
+ public:
+  Complex complex_;
+  typedef Complex::Vertex_handle Vertex_handle;
+
+  Model() : complex_() { }
+
+ public:
+  void off_file_open(const std::string& name_file) {
+    UIDBGMSG("load off file", name_file);
+    complex_.clear();
+    CGAL_geometric_flag_complex_wrapper<Complex> read_wraper(complex_, false);
+    Gudhi::read_off(name_file, read_wraper);
+  }
+
+  void off_points_open(const std::string& name_file) {
+    UIDBGMSG("load off points", name_file);
+    complex_.clear();
+    CGAL_geometric_flag_complex_wrapper<Complex> read_wraper(complex_, true);
+    Gudhi::read_off(name_file, read_wraper);
+  }
+
+  void off_file_save(const std::string& name_file) {
+    UIDBG("save off file");
+    UIDBG("save off off_points_save");
+    std::ofstream file(name_file);
+    if (file.is_open()) {
+      file << "OFF\n";
+      file << complex_.num_vertices() << " " << complex_.num_edges() << " 0\n";
+      for (auto v : complex_.vertex_range()) {
+        const auto& pt(complex_.point(v));
+        for (auto it = pt.cartesian_begin(); it != pt.cartesian_end(); ++it)
+          file << *it << " ";
+        file << std::endl;
+      }
+      for (auto e : complex_.edge_range())
+        file << "2 " << complex_.first_vertex(e) << " " << complex_.second_vertex(e) << "\n";
+      file.close();
+    } else {
+      std::cerr << "Could not open file " << name_file << std::endl;
+    }
+  }
+
+  void off_points_save(const std::string& name_file) {
+    UIDBG("save off off_points_save");
+    std::ofstream file(name_file);
+    if (file.is_open()) {
+      file << "OFF\n";
+      file << complex_.num_vertices() << " 0 0\n";
+      for (auto v : complex_.vertex_range()) {
+        const auto& pt(complex_.point(v));
+        for (auto it = pt.cartesian_begin(); it != pt.cartesian_end(); ++it)
+          file << *it << " ";
+        file << std::endl;
+      }
+      file.close();
+    } else {
+      std::cerr << "Could not open file " << name_file << std::endl;
+    }
+  }
+
+  // point sets operations
+  void uniform_noise(double amplitude) {
+    UIDBG("unif noise");
+    for (auto v : complex_.vertex_range())
+      complex_.point(v) = add_uniform_noise(complex_.point(v), amplitude);
+  }
+
+ private:
+  Point add_uniform_noise(const Point& point, double amplitude) {
+    std::vector<double> new_point(point.dimension());
+    for (int i = 0; i < point.dimension(); ++i) {
+      new_point[i] = point[i] + (rand() % 2 - .5) * amplitude;
+    }
+    return Point(point.dimension(), new_point.begin(), new_point.end());
+  }
+
+ public:
+  void lloyd(int num_iterations, int num_closest_neighbors) {
+    UIDBG("lloyd");
+    Lloyd_builder<Complex> lloyd_builder(complex_, 1);
+  }
+
+  double squared_eucl_distance(const Point& p1, const Point& p2) const {
+    return Geometry_trait::Squared_distance_d()(p1, p2);
+  }
+
+  // complex operations from points
+
+  void build_rips(double alpha) {
+    UIDBG("build_rips");
+    Rips_builder<Complex> rips_builder(complex_, alpha);
+  }
+
+  void build_k_nearest_neighbors(unsigned k) {
+    UIDBG("build_k_nearest");
+    complex_.keep_only_vertices();
+    K_nearest_builder<Complex> k_nearest_builder(complex_, k);
+  }
+
+  void build_delaunay() {
+    UIDBG("build_delaunay");
+    complex_.keep_only_vertices();
+  }
+
+  void contract_edges(unsigned num_contractions) {
+    Clock c;
+    Edge_contractor<Complex> contractor(complex_, num_contractions);
+    std::cout << "Time to simplify: " << c.num_seconds() << "s" << std::endl;
+  }
+
+  void collapse_vertices(unsigned num_collapses) {
+    auto old_num_vertices = complex_.num_vertices();
+    Vertex_collapsor<Complex> collapsor(complex_, complex_.num_vertices());
+    UIDBGMSG("num vertices collapsed:", old_num_vertices - complex_.num_vertices());
+  }
+
+  void collapse_edges(unsigned num_collapses) {
+    Edge_collapsor<Complex> collapsor(complex_, num_collapses);
+  }
+
+  void show_graph_stats() {
+    std::cout << "++++++ Graph stats +++++++" << std::endl;
+    std::cout << "Num vertices : " << complex_.num_vertices() << std::endl;
+    std::cout << "Num edges : " << complex_.num_edges() << std::endl;
+    std::cout << "Num connected components : " << complex_.num_connected_components() << std::endl;
+    std::cout << "Min/avg/max degree : " << min_degree() << "/" << avg_degree() << "/" << max_degree() << std::endl;
+    std::cout << "Num connected components : " << complex_.num_connected_components() << std::endl;
+    std::cout << "Num connected components : " << complex_.num_connected_components() << std::endl;
+    std::cout << "+++++++++++++++++++++++++" << std::endl;
+  }
+
+ private:
+  int min_degree() const {
+    int res = (std::numeric_limits<int>::max)();
+    for (auto v : complex_.vertex_range())
+      res = (std::min)(res, complex_.degree(v));
+    return res;
+  }
+
+  int max_degree() const {
+    int res = 0;
+    for (auto v : complex_.vertex_range())
+      res = (std::max)(res, complex_.degree(v));
+    return res;
+  }
+
+  int avg_degree() const {
+    int res = 0;
+    for (auto v : complex_.vertex_range())
+      res += complex_.degree(v);
+    return res / complex_.num_vertices();
+  }
+
+ public:
+  void show_complex_stats() {
+    std::cout << "++++++ Mesh stats +++++++" << std::endl;
+    std::cout << "Num vertices : " << complex_.num_vertices() << std::endl;
+    std::cout << "Num edges : " << complex_.num_edges() << std::endl;
+    std::cout << "Num connected components : " << complex_.num_connected_components() << std::endl;
+    std::cout << "+++++++++++++++++++++++++" << std::endl;
+  }
+
+  void show_complex_dimension() {
+    unsigned num_simplices = 0;
+    int euler = 0;
+    int dimension = 0;
+    Clock clock;
+    for (const auto &s : complex_.complex_simplex_range()) {
+      num_simplices++;
+      dimension = (std::max)(s.dimension(), dimension);
+      if (s.dimension() % 2 == 0)
+        euler += 1;
+      else
+        euler -= 1;
+    }
+    clock.end();
+    std::cout << "++++++ Mesh dimension +++++++" << std::endl;
+    std::cout << "Dimension : " << dimension << std::endl;
+    std::cout << "Euler characteristic : " << euler << std::endl;
+    std::cout << "Num simplices : " << num_simplices << std::endl;
+    std::cout << "Total time: " << clock << std::endl;
+    std::cout << "Time per simplex: " << clock.num_seconds() / num_simplices << " s" << std::endl;
+    std::cout << "+++++++++++++++++++++++++" << std::endl;
+  }
+
+  void show_homology_group() {
 #ifdef _WIN32
-		std::cout << "Works only on linux x64 for the moment\n";
+    std::cout << "Works only on linux x64 for the moment\n";
 #else
-		Clock clock;
-		run_chomp();
-		clock.end();
+    Clock clock;
+    run_chomp();
+    clock.end();
 #endif
-	}
-
-	void show_euler_characteristic(){
-		unsigned num_simplices = 0;
-		int euler = 0;
-		int dimension = 0;
-		for(const auto &s : complex_.simplex_range()){
-			num_simplices++;
-			dimension = (std::max)(s.dimension(),dimension);
-			if(s.dimension()%2==0)
-				euler+=1;
-			else
-				euler-=1;
-		}
-		std::cout << "Saw "<<num_simplices<<" simplices with maximum dimension " << dimension<<std::endl;
-		std::cout << "The euler characteristic is : " << euler<<std::endl;
-	}
-
-	void show_persistence(	int p,double threshold,int max_dim,double min_pers){
-		Persistence_compute<Complex> persistence(complex_,std::cout,Persistence_params(p,threshold,max_dim,min_pers));
-	}
-
-	void show_critical_points(double max_distance){
-		Critical_points<Complex> critical_points(complex_,std::cout,max_distance);
-	}
-
-	void show_is_manifold(){
-		unsigned dim;
-		bool is_manifold;
-		Is_manifold<Complex> test_manifold(complex_,dim,is_manifold);
-
-		if(is_manifold) std::cout << "The complex is a "<<dim<<"-manifold\n";
-		else
-			if(dim<4) std::cout << "The complex has dimension greater than "<<dim<<" and is not a manifold\n";
-			else std::cout << "The complex has dimension>=4 and may or may not be a manifold\n";
-	}
-
-
-private:
-	void run_chomp(){
-		save_complex_in_file_for_chomp();
-		std::cout << "Call CHOMP library\n";
-		int returnValue = system("utils/homsimpl chomp.sim");
-		std::cout << "CHOMP returns" << returnValue << std::endl;
-	}
-
-	void save_complex_in_file_for_chomp(){
-		std::ofstream file;
-		file.open("chomp.sim");
-		for(const auto &s : complex_.simplex_range()){
-			bool first = true;
-			file<<"(";
-			for(auto x : s){
-				if(first) first = false;
-				else file<<",";
-				file << x;
-			}
-			file<<")\n";
-		}
-	}
-public:
-
-
-	unsigned num_vertices() const{
-		return  complex_.num_vertices();
-	}
-
-	unsigned num_edges() const{
-		return  complex_.num_edges();
-	}
-
+  }
+
+  void show_euler_characteristic() {
+    unsigned num_simplices = 0;
+    int euler = 0;
+    int dimension = 0;
+    for (const auto &s : complex_.complex_simplex_range()) {
+      num_simplices++;
+      dimension = (std::max)(s.dimension(), dimension);
+      if (s.dimension() % 2 == 0)
+        euler += 1;
+      else
+        euler -= 1;
+    }
+    std::cout << "Saw " << num_simplices << " simplices with maximum dimension " << dimension << std::endl;
+    std::cout << "The euler characteristic is : " << euler << std::endl;
+  }
+
+  void show_persistence(int p, double threshold, int max_dim, double min_pers) {
+    Persistence_compute<Complex> persistence(complex_, std::cout, Persistence_params(p, threshold, max_dim, min_pers));
+  }
+
+  void show_critical_points(double max_distance) {
+    Critical_points<Complex> critical_points(complex_, std::cout, max_distance);
+  }
+
+  void show_is_manifold() {
+    unsigned dim;
+    bool is_manifold;
+    Is_manifold<Complex> test_manifold(complex_, dim, is_manifold);
+
+    if (is_manifold) {
+      std::cout << "The complex is a " << dim << "-manifold\n";
+    } else {
+      if (dim < 4) {
+        std::cout << "The complex has dimension greater than " << dim << " and is not a manifold\n";
+      } else {
+        std::cout << "The complex has dimension>=4 and may or may not be a manifold\n";
+      }
+    }
+  }
+
+ private:
+  void run_chomp() {
+    save_complex_in_file_for_chomp();
+    std::cout << "Call CHOMP library\n";
+    int returnValue = system("utils/homsimpl chomp.sim");
+    std::cout << "CHOMP returns" << returnValue << std::endl;
+  }
+
+  void save_complex_in_file_for_chomp() {
+    std::ofstream file;
+    file.open("chomp.sim");
+    for (const auto &s : complex_.complex_simplex_range()) {
+      bool first = true;
+      file << "(";
+      for (auto x : s) {
+        if (first)
+          first = false;
+        else
+          file << ",";
+        file << x;
+      }
+      file << ")\n";
+    }
+  }
+
+ public:
+  unsigned num_vertices() const {
+    return complex_.num_vertices();
+  }
+
+  unsigned num_edges() const {
+    return complex_.num_edges();
+  }
 };
 
-#endif /* MODEL_H_ */
+#endif  // MODEL_MODEL_H_
diff --git a/src/GudhUI/utils/Critical_points.h b/src/GudhUI/utils/Critical_points.h
index 92392d4a..3021a5fe 100644
--- a/src/GudhUI/utils/Critical_points.h
+++ b/src/GudhUI/utils/Critical_points.h
@@ -1,13 +1,10 @@
-/*
- * Critical_points.h
- *  Created on: Jan 27, 2015
- * This file is part of the Gudhi Library. The Gudhi library 
+/* This file is part of the Gudhi Library. The Gudhi library 
  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
  *    library for computational topology.
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-M�diterran�e (France)
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
@@ -24,11 +21,13 @@
  * 
  */
 
-
-#ifndef CRITICAL_POINTS_H_
-#define CRITICAL_POINTS_H_
+#ifndef UTILS_CRITICAL_POINTS_H_
+#define UTILS_CRITICAL_POINTS_H_
 
 #include <deque>
+#include <utility>  // for pair<>
+#include <algorithm>  // for sort
+
 #include "utils/Edge_contractor.h"
 
 /**
@@ -37,101 +36,97 @@
  *
  * todo do a sparsification with some parameter eps while growing
  */
-template<typename SkBlComplex> class Critical_points{
-private:
-	SkBlComplex filled_complex_;
-	const SkBlComplex& input_complex_;
-	double max_length_;
-	std::ostream& stream_;
-public:
-	typedef typename SkBlComplex::Vertex_handle Vertex_handle;
-	typedef typename SkBlComplex::Edge_handle Edge_handle;
-	typedef typename std::pair<Vertex_handle,Vertex_handle> Edge;
-
-	/**
-	 * @brief check all pair of points with length smaller than max_length
-	 */
-	Critical_points(const SkBlComplex& input_complex,std::ostream& stream,double max_length):
-		input_complex_(input_complex),max_length_(max_length),stream_(stream)
-	{
-
-		std::deque<Edge> edges;
-		auto vertices = input_complex.vertex_range();
-		for(auto p = vertices.begin(); p!= vertices.end(); ++p){
-			filled_complex_.add_vertex(input_complex.point(*p));
-			for (auto q = p; ++q != vertices.end(); /**/)
-				if (squared_eucl_distance(input_complex.point(*p),input_complex.point(*q)) < max_length_*max_length_)
-					edges.emplace_back(*p,*q);
-		}
-
-		std::sort(edges.begin(),edges.end(),
-				[&](Edge e1,Edge e2){
-			return squared_edge_length(e1) < squared_edge_length(e2);
-		});
-
-		anti_collapse_edges(edges);
-
-	}
-
-private:
-	double squared_eucl_distance(const Point& p1,const Point& p2) const{
-		return Geometry_trait::Squared_distance_d()(p1,p2);
-	}
-
-
-	void anti_collapse_edges(const std::deque<Edge>& edges){
-		unsigned pos = 0;
-		for(Edge e : edges){
-			std::cout<<"edge "<<pos++<<"/"<<edges.size()<<"\n";
-			auto eh = filled_complex_.add_edge(e.first,e.second);
-			int is_contractible(is_link_reducible(eh));
-
-			switch (is_contractible) {
-				case 0:
-					stream_<<"alpha="<<std::sqrt(squared_edge_length(e))<< " topological change"<<std::endl;
-					break;
-				case 2:
-					stream_<<"alpha="<<std::sqrt(squared_edge_length(e))<< " maybe a topological change"<<std::endl;
-					break;
-				default:
-					break;
-			}
-		}
-
-	}
-
-
-	//0 -> not
-	//1 -> yes
-	//2 -> maybe
-	int is_link_reducible(Edge_handle e){
-		auto link = filled_complex_.link(e);
-
-		if(link.empty()) return 0;
-
-		Edge_contractor<Complex> contractor(link,link.num_vertices()-1);
-
-		if(link.num_connected_components()>1) return 0; //one than more CC -> not contractible
-
-		if (link.num_vertices()==1) return 1; //reduced to one point -> contractible
-		else return 2; //we dont know
-	}
-
-
-	double squared_edge_length(Edge_handle e) const{
-		return squared_eucl_distance(input_complex_.point(input_complex_.first_vertex(e)),input_complex_.point(input_complex_.second_vertex(e)));
-	}
-
-	double squared_edge_length(Edge e) const{
-		return squared_eucl_distance(input_complex_.point(e.first),input_complex_.point(e.second));
-	}
-
-
-
+template<typename SkBlComplex> class Critical_points {
+ private:
+  SkBlComplex filled_complex_;
+  const SkBlComplex& input_complex_;
+  double max_length_;
+  std::ostream& stream_;
+
+ public:
+  typedef typename SkBlComplex::Vertex_handle Vertex_handle;
+  typedef typename SkBlComplex::Edge_handle Edge_handle;
+  typedef typename std::pair<Vertex_handle, Vertex_handle> Edge;
+
+  /**
+   * @brief check all pair of points with length smaller than max_length
+   */
+  Critical_points(const SkBlComplex& input_complex, std::ostream& stream, double max_length) :
+      input_complex_(input_complex), max_length_(max_length), stream_(stream) {
+    std::deque<Edge> edges;
+    auto vertices = input_complex.vertex_range();
+    for (auto p = vertices.begin(); p != vertices.end(); ++p) {
+      filled_complex_.add_vertex(input_complex.point(*p));
+      for (auto q = p; ++q != vertices.end(); /**/)
+        if (squared_eucl_distance(input_complex.point(*p), input_complex.point(*q)) < max_length_ * max_length_)
+          edges.emplace_back(*p, *q);
+    }
+
+    std::sort(edges.begin(), edges.end(),
+              [&](Edge e1, Edge e2) {
+                return squared_edge_length(e1) < squared_edge_length(e2);
+              });
+
+    anti_collapse_edges(edges);
+  }
+
+ private:
+  double squared_eucl_distance(const Point& p1, const Point& p2) const {
+    return Geometry_trait::Squared_distance_d()(p1, p2);
+  }
+
+  void anti_collapse_edges(const std::deque<Edge>& edges) {
+    unsigned pos = 0;
+    for (Edge e : edges) {
+      std::cout << "edge " << pos++ << "/" << edges.size() << "\n";
+      auto eh = filled_complex_.add_edge(e.first, e.second);
+      int is_contractible(is_link_reducible(eh));
+
+      switch (is_contractible) {
+        case 0:
+          stream_ << "alpha=" << std::sqrt(squared_edge_length(e)) << " topological change" << std::endl;
+          break;
+        case 2:
+          stream_ << "alpha=" << std::sqrt(squared_edge_length(e)) << " maybe a topological change" << std::endl;
+          break;
+        default:
+          break;
+      }
+    }
+  }
+
+  // 0 -> not
+  // 1 -> yes
+  // 2 -> maybe
+
+  int is_link_reducible(Edge_handle e) {
+    auto link = filled_complex_.link(e);
+
+    if (link.empty())
+      return 0;
+
+    Edge_contractor<Complex> contractor(link, link.num_vertices() - 1);
+
+    if (link.num_connected_components() > 1)
+      // one than more CC -> not contractible
+      return 0;
+
+    if (link.num_vertices() == 1)
+      // reduced to one point -> contractible
+      return 1;
+    else
+      // we dont know
+      return 2;
+  }
+
+  double squared_edge_length(Edge_handle e) const {
+    return squared_eucl_distance(input_complex_.point(input_complex_.first_vertex(e)),
+                                 input_complex_.point(input_complex_.second_vertex(e)));
+  }
+
+  double squared_edge_length(Edge e) const {
+    return squared_eucl_distance(input_complex_.point(e.first), input_complex_.point(e.second));
+  }
 };
 
-
-
-
-
-#endif /* CRITICAL_POINTS_H_ */
+#endif  // UTILS_CRITICAL_POINTS_H_
diff --git a/src/GudhUI/utils/Edge_collapsor.h b/src/GudhUI/utils/Edge_collapsor.h
index 4dcd18ac..151e9b01 100644
--- a/src/GudhUI/utils/Edge_collapsor.h
+++ b/src/GudhUI/utils/Edge_collapsor.h
@@ -1,12 +1,28 @@
-/*
- * Collapsor.h
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
  *
- *  Created on: Sep 25, 2014
- *      Author: dsalinas
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
  */
 
-#ifndef COLLAPSOR_H_
-#define COLLAPSOR_H_
+#ifndef UTILS_EDGE_COLLAPSOR_H_
+#define UTILS_EDGE_COLLAPSOR_H_
 
 #include <list>
 #include "utils/Edge_contractor.h"
@@ -15,71 +31,67 @@
 /**
  * Iteratively puts every vertex at the center of its neighbors
  */
-template<typename SkBlComplex> class Edge_collapsor{
-private:
-	SkBlComplex& complex_;
-	unsigned num_collapses_;
-public:
-	typedef typename SkBlComplex::Vertex_handle Vertex_handle;
-	typedef typename SkBlComplex::Edge_handle Edge_handle;
-
-	/**
-	 * @brief Collapse num_collapses edges. If num_collapses<0 then it collapses all possible edges.
-	 * Largest edges are collapsed first.
-	 *
-	 */
-	Edge_collapsor(SkBlComplex& complex,unsigned num_collapses):
-		complex_(complex),num_collapses_(num_collapses)
-	{
-		std::list<Edge_handle> edges;
-		edges.insert(edges.begin(),complex_.edge_range().begin(),complex_.edge_range().end());
-
-		edges.sort(
-				[&](Edge_handle e1,Edge_handle e2){
-			return squared_edge_length(e1) < squared_edge_length(e2);
-		});
-
-		collapse_edges(edges);
-
-	}
-
-private:
-
-	void collapse_edges(std::list<Edge_handle>& edges){
-		while(!edges.empty() && num_collapses_--){
-			Edge_handle current_edge = edges.front();
-			edges.pop_front();
-			if(is_link_reducible(current_edge))
-				complex_.remove_edge(current_edge);
-		}
-
-	}
-
-	bool is_link_reducible(Edge_handle e){
-		auto link = complex_.link(e);
-
-		if(link.empty()) return false;
-
-		if(link.is_cone()) return true;
-
-		if(link.num_connected_components()>1) return false;
-
-		Edge_contractor<SkBlComplex> contractor(link,link.num_vertices()-1);
-
-		return (link.num_vertices()==1);
-	}
-
-
-	double squared_edge_length(Edge_handle e) const{
-		return squared_eucl_distance(complex_.point(complex_.first_vertex(e)),complex_.point(complex_.second_vertex(e)));
-	}
-
-	double squared_eucl_distance(const Point& p1,const Point& p2) const{
-		return Geometry_trait::Squared_distance_d()(p1,p2);
-	}
-
+template<typename SkBlComplex> class Edge_collapsor {
+ private:
+  SkBlComplex& complex_;
+  unsigned num_collapses_;
+
+ public:
+  typedef typename SkBlComplex::Vertex_handle Vertex_handle;
+  typedef typename SkBlComplex::Edge_handle Edge_handle;
+
+  /**
+   * @brief Collapse num_collapses edges. If num_collapses<0 then it collapses all possible edges.
+   * Largest edges are collapsed first.
+   *
+   */
+  Edge_collapsor(SkBlComplex& complex, unsigned num_collapses) :
+      complex_(complex), num_collapses_(num_collapses) {
+    std::list<Edge_handle> edges;
+    edges.insert(edges.begin(), complex_.edge_range().begin(), complex_.edge_range().end());
+
+    edges.sort(
+               [&](Edge_handle e1, Edge_handle e2) {
+                 return squared_edge_length(e1) < squared_edge_length(e2);
+               });
+
+    collapse_edges(edges);
+  }
+
+ private:
+  void collapse_edges(std::list<Edge_handle>& edges) {
+    while (!edges.empty() && num_collapses_--) {
+      Edge_handle current_edge = edges.front();
+      edges.pop_front();
+      if (is_link_reducible(current_edge))
+        complex_.remove_edge(current_edge);
+    }
+  }
+
+  bool is_link_reducible(Edge_handle e) {
+    auto link = complex_.link(e);
+
+    if (link.empty())
+      return false;
+
+    if (link.is_cone())
+      return true;
+
+    if (link.num_connected_components() > 1)
+      return false;
+
+    Edge_contractor<SkBlComplex> contractor(link, link.num_vertices() - 1);
+
+    return (link.num_vertices() == 1);
+  }
+
+  double squared_edge_length(Edge_handle e) const {
+    return squared_eucl_distance(complex_.point(complex_.first_vertex(e)), complex_.point(complex_.second_vertex(e)));
+  }
+
+  double squared_eucl_distance(const Point& p1, const Point& p2) const {
+    return Geometry_trait::Squared_distance_d()(p1, p2);
+  }
 };
 
-
-
-#endif /* COLLAPSOR_H_ */
+#endif  // UTILS_EDGE_COLLAPSOR_H_
diff --git a/src/GudhUI/utils/Edge_contractor.h b/src/GudhUI/utils/Edge_contractor.h
index d0a1f866..45079a40 100644
--- a/src/GudhUI/utils/Edge_contractor.h
+++ b/src/GudhUI/utils/Edge_contractor.h
@@ -1,85 +1,97 @@
-/*
- * Contractor.h
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
  *
- *  Created on: Sep 25, 2014
- *      Author: dsalinas
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
  */
 
-#ifndef EDGE_CONTRACTOR_H_
-#define EDGE_CONTRACTOR_H_
+#ifndef UTILS_EDGE_CONTRACTOR_H_
+#define UTILS_EDGE_CONTRACTOR_H_
 
 
-#include "gudhi/Skeleton_blocker_contractor.h"
-
-#include "gudhi/Contraction/Edge_profile.h"
-#include "gudhi/Contraction/policies/Cost_policy.h"
+#include <gudhi/Skeleton_blocker_contractor.h>
+#include <gudhi/Contraction/Edge_profile.h>
+#include <gudhi/Contraction/policies/Cost_policy.h>
 
+#include <vector>
 
 /**
  * Iteratively puts every vertex at the center of its neighbors
  */
-template<typename SkBlComplex> class Edge_contractor{
-private:
-	SkBlComplex& complex_;
-	unsigned num_contractions_;
-
-	/**
-	 * @brief return a cost corresponding to the squared length of the edge
-	 */
-	template< typename EdgeProfile> class Length_cost : public contraction::Cost_policy<EdgeProfile>{
-	public:
-		typedef typename contraction::Cost_policy<EdgeProfile>::Cost_type Cost_type;
-		typedef typename EdgeProfile::Point Point;
-		Cost_type operator()(const EdgeProfile& profile, const boost::optional<Point>& placement) const override{
-			Cost_type res;
-			if(!placement) return res;
-			return Geometry_trait::Squared_distance_d()(profile.p0(),profile.p1()); //not working??
-		}
-	};
-
-
-	/**
-	* @brief return a cost corresponding to the squared length of the edge
-	*/
-	template< typename EdgeProfile> class Middle_placement : public contraction::Placement_policy<EdgeProfile>{
-	public:
-		typedef typename contraction::Placement_policy<EdgeProfile>::Placement_type Placement_type;
-		typedef typename EdgeProfile::Point Point;
-		Placement_type operator()(const EdgeProfile& profile) const override{
-			std::vector<double> mid_coords(profile.p0().dimension(),0);
-			for (size_t i = 0; i < profile.p0().dimension(); ++i){
-				mid_coords[i] = (profile.p0()[i] + profile.p1()[i]) / 2.;
-			}
-			return Point(profile.p0().dimension(),mid_coords.begin(), mid_coords.end());			
-		}
-	};
-
-	public:
-	typedef typename SkBlComplex::Vertex_handle Vertex_handle;
-	typedef typename SkBlComplex::Edge_handle Edge_handle;
-
-	/**
-	 * @brief Modify complex to be the expansion of the k-nearest neighbor
-	 * symetric graph.
-	 */
-	Edge_contractor(SkBlComplex& complex,unsigned num_contractions):
-		complex_(complex),num_contractions_(num_contractions)
-	{
-		typedef typename contraction::Edge_profile<Complex> Profile;
-		num_contractions = (std::min)((int)num_contractions,(int)(complex_.num_vertices()-1));
-		contraction::Skeleton_blocker_contractor<Complex> contractor(
-				complex_,
-				new Length_cost<contraction::Edge_profile<Complex>>(),
-				new Middle_placement<contraction::Edge_profile<Complex>>(),
-				contraction::make_link_valid_contraction<Profile>(),
-				contraction::make_remove_popable_blockers_visitor<Profile>()
-		);
-		contractor.contract_edges(num_contractions);
-	}
-
-
+template<typename SkBlComplex> class Edge_contractor {
+ private:
+  SkBlComplex& complex_;
+  unsigned num_contractions_;
+
+  /**
+   * @brief return a cost corresponding to the squared length of the edge
+   */
+  template< typename EdgeProfile> class Length_cost : public contraction::Cost_policy<EdgeProfile> {
+   public:
+    typedef typename contraction::Cost_policy<EdgeProfile>::Cost_type Cost_type;
+    typedef typename EdgeProfile::Point Point;
+
+    Cost_type operator()(const EdgeProfile& profile, const boost::optional<Point>& placement) const override {
+      Cost_type res;
+      if (!placement)
+        return res;
+      return Geometry_trait::Squared_distance_d()(profile.p0(), profile.p1());  // not working??
+    }
+  };
+
+  /**
+   * @brief return a cost corresponding to the squared length of the edge
+   */
+  template< typename EdgeProfile> class Middle_placement : public contraction::Placement_policy<EdgeProfile> {
+   public:
+    typedef typename contraction::Placement_policy<EdgeProfile>::Placement_type Placement_type;
+    typedef typename EdgeProfile::Point Point;
+
+    Placement_type operator()(const EdgeProfile& profile) const override {
+      std::vector<double> mid_coords(profile.p0().dimension(), 0);
+      for (size_t i = 0; i < profile.p0().dimension(); ++i) {
+        mid_coords[i] = (profile.p0()[i] + profile.p1()[i]) / 2.;
+      }
+      return Point(profile.p0().dimension(), mid_coords.begin(), mid_coords.end());
+    }
+  };
+
+ public:
+  typedef typename SkBlComplex::Vertex_handle Vertex_handle;
+  typedef typename SkBlComplex::Edge_handle Edge_handle;
+
+  /**
+   * @brief Modify complex to be the expansion of the k-nearest neighbor
+   * symetric graph.
+   */
+  Edge_contractor(SkBlComplex& complex, unsigned num_contractions) :
+      complex_(complex), num_contractions_(num_contractions) {
+    typedef typename contraction::Edge_profile<Complex> Profile;
+    num_contractions = (std::min)(static_cast<int>(num_contractions), static_cast<int>(complex_.num_vertices() - 1));
+    typedef typename contraction::Skeleton_blocker_contractor<Complex> Contractor;
+    Contractor contractor(complex_,
+                          new Length_cost<contraction::Edge_profile < Complex >> (),
+                          new Middle_placement<contraction::Edge_profile < Complex >> (),
+                          contraction::make_link_valid_contraction<Profile>(),
+                          contraction::make_remove_popable_blockers_visitor<Profile>());
+    contractor.contract_edges(num_contractions);
+  }
 };
 
-
-
-#endif /* EDGE_CONTRACTOR_H_ */
+#endif  // UTILS_EDGE_CONTRACTOR_H_
diff --git a/src/GudhUI/utils/Furthest_point_epsilon_net.h b/src/GudhUI/utils/Furthest_point_epsilon_net.h
index 590b65c4..f2a216f6 100644
--- a/src/GudhUI/utils/Furthest_point_epsilon_net.h
+++ b/src/GudhUI/utils/Furthest_point_epsilon_net.h
@@ -1,134 +1,132 @@
-/*
- * Furthest_point_epsilon_net.h
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
  *
- *  Created on: Sep 26, 2014
- *      Author: dsalinas
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
  */
 
-#ifndef FURTHEST_POINT_EPSILON_NET_H_
-#define FURTHEST_POINT_EPSILON_NET_H_
+#ifndef UTILS_FURTHEST_POINT_EPSILON_NET_H_
+#define UTILS_FURTHEST_POINT_EPSILON_NET_H_
 
-#include "utils/UI_utils.h"
 #include <vector>
+#include <algorithm>  // for sort
+
+#include "utils/UI_utils.h"
 
 /**
  * Computes an epsilon net with furthest point strategy.
  */
-template<typename SkBlComplex> class Furthest_point_epsilon_net{
-private:
-	SkBlComplex& complex_;
-	typedef typename SkBlComplex::Vertex_handle Vertex_handle;
-	typedef typename SkBlComplex::Edge_handle Edge_handle;
-
-	/**
-	 * Let V be the set of vertices.
-	 * Initially v0 is one arbitrarly vertex and the set V0 is {v0}.
-	 * Then Vk is computed as follows.
-	 * First we compute the vertex pk that is the furthest from Vk
-	 * then Vk = Vk \cup pk.
-	 * The radius of pk is its distance to Vk and its meeting vertex
-	 * is the vertex of Vk for which this distance is achieved.
-	 */
-	struct Net_filtration_vertex{
-		Vertex_handle vertex_handle;
-		Vertex_handle meeting_vertex;
-		double radius;
-
-
-		Net_filtration_vertex(
-				Vertex_handle vertex_handle_,
-				Vertex_handle meeting_vertex_,
-				double radius_):
-					vertex_handle(vertex_handle_),meeting_vertex(meeting_vertex_),radius(radius_)
-		{}
-
-		bool operator<(const Net_filtration_vertex& other ) const{
-			return radius < other.radius;
-		}
-
-	};
-
-public:
-
-
-	std::vector<Net_filtration_vertex> net_filtration_;
-
-	/**
-	 * @brief Modify complex to be the expansion of the k-nearest neighbor
-	 * symetric graph.
-	 */
-	Furthest_point_epsilon_net(SkBlComplex& complex):
-		complex_(complex)
-	{
-		if(!complex.empty()){
-			init_filtration();
-			for(int k = 2; k < net_filtration_.size(); ++k){
-				update_radius_value(k);
-			}
-		}
-	}
-
-	//xxx does not work if complex not full
-	double radius(Vertex_handle v){
-		return net_filtration_[v.vertex].radius;
-	}
-
-
-
-
-private:
-
-	void init_filtration(){
-		Vertex_handle v0 = *(complex_.vertex_range().begin());
-		net_filtration_.reserve(complex_.num_vertices());
-		for(auto v : complex_.vertex_range()){
-			if(v != v0)
-				net_filtration_.push_back(
-						Net_filtration_vertex(v,
-								Vertex_handle(-1),
-								squared_eucl_distance(v,v0))
-				);
-		}
-		net_filtration_.push_back(Net_filtration_vertex(v0,Vertex_handle(-1),1e10));
-		auto n = net_filtration_.size();
-		sort_filtration(n-1);
-	}
-
-	void update_radius_value(int k){
-		int n = net_filtration_.size();
-		int index_to_update = n-k;
-		for(int i = 0; i< index_to_update; ++i){
-			net_filtration_[i].radius = (std::min)(net_filtration_[i].radius ,
-					squared_eucl_distance(
-							net_filtration_[i].vertex_handle,
-							net_filtration_[index_to_update].vertex_handle
-					)
-			);
-		}
-		sort_filtration(n-k);
-	}
-
-	/**
-	 * sort all i first elements.
-	 */
-	void sort_filtration(int i){
-		std::sort(net_filtration_.begin(),net_filtration_.begin()+ i);
-	}
-
-	double squared_eucl_distance(Vertex_handle v1,Vertex_handle v2) const{
-		return std::sqrt(Geometry_trait::Squared_distance_d()(
-				complex_.point(v1),complex_.point(v2))
-		);
-	}
-
-	void print_filtration() const{
-		for(auto v : net_filtration_){
-			std::cerr <<"v="<<v.vertex_handle<<"-> d="<<v.radius<<std::endl;
-		}
-	}
-
+template<typename SkBlComplex> class Furthest_point_epsilon_net {
+ private:
+  SkBlComplex& complex_;
+  typedef typename SkBlComplex::Vertex_handle Vertex_handle;
+  typedef typename SkBlComplex::Edge_handle Edge_handle;
+
+  /**
+   * Let V be the set of vertices.
+   * Initially v0 is one arbitrarly vertex and the set V0 is {v0}.
+   * Then Vk is computed as follows.
+   * First we compute the vertex pk that is the furthest from Vk
+   * then Vk = Vk \cup pk.
+   * The radius of pk is its distance to Vk and its meeting vertex
+   * is the vertex of Vk for which this distance is achieved.
+   */
+  struct Net_filtration_vertex {
+    Vertex_handle vertex_handle;
+    Vertex_handle meeting_vertex;
+    double radius;
+
+    Net_filtration_vertex(Vertex_handle vertex_handle_,
+                          Vertex_handle meeting_vertex_,
+                          double radius_) :
+        vertex_handle(vertex_handle_), meeting_vertex(meeting_vertex_), radius(radius_) { }
+
+    bool operator<(const Net_filtration_vertex& other) const {
+      return radius < other.radius;
+    }
+  };
+
+ public:
+  std::vector<Net_filtration_vertex> net_filtration_;
+
+  /**
+   * @brief Modify complex to be the expansion of the k-nearest neighbor
+   * symetric graph.
+   */
+  Furthest_point_epsilon_net(SkBlComplex& complex) :
+      complex_(complex) {
+    if (!complex.empty()) {
+      init_filtration();
+      for (int k = 2; k < net_filtration_.size(); ++k) {
+        update_radius_value(k);
+      }
+    }
+  }
+
+  // xxx does not work if complex not full
+
+  double radius(Vertex_handle v) {
+    return net_filtration_[v.vertex].radius;
+  }
+
+ private:
+  void init_filtration() {
+    Vertex_handle v0 = *(complex_.vertex_range().begin());
+    net_filtration_.reserve(complex_.num_vertices());
+    for (auto v : complex_.vertex_range()) {
+      if (v != v0)
+        net_filtration_.push_back(Net_filtration_vertex(v,
+                                                        Vertex_handle(-1),
+                                                        squared_eucl_distance(v, v0)));
+    }
+    net_filtration_.push_back(Net_filtration_vertex(v0, Vertex_handle(-1), 1e10));
+    auto n = net_filtration_.size();
+    sort_filtration(n - 1);
+  }
+
+  void update_radius_value(int k) {
+    int n = net_filtration_.size();
+    int index_to_update = n - k;
+    for (int i = 0; i < index_to_update; ++i) {
+      net_filtration_[i].radius = (std::min)(net_filtration_[i].radius,
+                                             squared_eucl_distance(net_filtration_[i].vertex_handle,
+                                                                   net_filtration_[index_to_update].vertex_handle));
+    }
+    sort_filtration(n - k);
+  }
+
+  /**
+   * sort all i first elements.
+   */
+  void sort_filtration(int i) {
+    std::sort(net_filtration_.begin(), net_filtration_.begin() + i);
+  }
+
+  double squared_eucl_distance(Vertex_handle v1, Vertex_handle v2) const {
+    return std::sqrt(Geometry_trait::Squared_distance_d()(complex_.point(v1), complex_.point(v2)));
+  }
+
+  void print_filtration() const {
+    for (auto v : net_filtration_) {
+      std::cerr << "v=" << v.vertex_handle << "-> d=" << v.radius << std::endl;
+    }
+  }
 };
 
-
-
-#endif /* FURTHEST_POINT_EPSILON_NET_H_ */
+#endif  // UTILS_FURTHEST_POINT_EPSILON_NET_H_
diff --git a/src/GudhUI/utils/Is_manifold.h b/src/GudhUI/utils/Is_manifold.h
index e708a6a4..0640ea47 100644
--- a/src/GudhUI/utils/Is_manifold.h
+++ b/src/GudhUI/utils/Is_manifold.h
@@ -7,7 +7,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-M�diterran�e (France)
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
@@ -25,11 +25,10 @@
  */
 
 
-#ifndef IS_MANIFOLD_H_
-#define IS_MANIFOLD_H_
+#ifndef UTILS_IS_MANIFOLD_H_
+#define UTILS_IS_MANIFOLD_H_
 
 #include "utils/UI_utils.h"
-
 #include "utils/Edge_contractor.h"
 
 /**
@@ -38,67 +37,67 @@
  *
  * todo do a sparsification with some parameter eps while growing
  */
-template<typename SkBlComplex> class Is_manifold{
-private:
-	const SkBlComplex& input_complex_;
-	typedef typename SkBlComplex::Vertex_handle Vertex_handle;
+template<typename SkBlComplex> class Is_manifold {
+ private:
+  const SkBlComplex& input_complex_;
+  typedef typename SkBlComplex::Vertex_handle Vertex_handle;
 
+ public:
+  /*
+   * return dim the maximum dimension around one simplex and res which is true if the complex is a manifold.
+   * If the complex has dimension <= 3 then if res is false, the complex is not a manifold.
+   * For d-manifold with d>=4, res may be false while the complex is a manifold.
+   */
+  Is_manifold(const SkBlComplex& input_complex, unsigned& dim, bool & res) : input_complex_(input_complex) {
+    res = true;
+    dim = -1;
+    if (!input_complex_.empty()) {
+      for (auto v : input_complex_.vertex_range()) {
+        dim = local_dimension(v);
+        break;
+      }
+      // check that the link of every vertex is a dim-1 sphere
+      for (auto v : input_complex_.vertex_range()) {
+        if (!is_k_sphere(v, dim - 1)) {
+          res = false;
+          break;
+        }
+      }
+    }
+  }
 
-public:
-	/*
-	 * return dim the maximum dimension around one simplex and res which is true if the complex is a manifold.
-	 * If the complex has dimension <= 3 then if res is false, the complex is not a manifold.
-	 * For d-manifold with d>=4, res may be false while the complex is a manifold.
-	 */
-	Is_manifold(const SkBlComplex& input_complex,unsigned& dim,bool & res):input_complex_(input_complex){
-		res = true;
-		dim = -1;
-		if(!input_complex_.empty()){
-			for(auto v : input_complex_.vertex_range()){
-				dim = local_dimension(v);
-				break;
-			}
-			//check that the link of every vertex is a dim-1 sphere
-			for(auto v : input_complex_.vertex_range()){
-				if(!is_k_sphere(v,dim-1)) {
-					res = false;
-					break;
-				}
-			}
-		}
-	}
+ private:
+  unsigned local_dimension(Vertex_handle v) {
+    unsigned dim = 0;
+    for (const auto& s : input_complex_.star_simplex_range(v))
+      dim = (std::max)(dim, (unsigned) s.dimension());
+    return dim;
+  }
 
-private:
-	unsigned local_dimension(Vertex_handle v){
-		unsigned dim = 0;
-		for(const auto& s: input_complex_.simplex_range(v))
-			dim = (std::max)(dim,(unsigned)s.dimension());
-		return dim;
-	}
+  bool is_k_sphere(Vertex_handle v, int k) {
+    auto link = input_complex_.link(v);
+    Edge_contractor<Complex> contractor(link, link.num_vertices() - 1);
+    return (is_sphere_simplex(link) == k);
+  }
 
-	bool is_k_sphere(Vertex_handle v,int k){
-		auto link = input_complex_.link(v);
-		Edge_contractor<Complex> contractor(link,link.num_vertices()-1);
-		return (is_sphere_simplex(link)==k);
-	}
+  // A minimal sphere is a complex that contains vertices v1...vn and all faces
+  // made upon this set except the face {v1,...,vn}
+  // return -2 if not a minimal sphere
+  // and d otherwise if complex is a d minimal sphere
 
-	// A minimal sphere is a complex that contains vertices v1...vn and all faces
-	// made upon this set except the face {v1,...,vn}
-	// return -2 if not a minimal sphere
-	// and d otherwise if complex is a d minimal sphere
-	template<typename SubComplex>
-	int is_sphere_simplex(const SubComplex& complex){
-		if(complex.empty()) return -1;
-		if(complex.num_blockers()!=1) return -2;
+  template<typename SubComplex>
+  int is_sphere_simplex(const SubComplex& complex) {
+    if (complex.empty()) return -1;
+    if (complex.num_blockers() != 1) return -2;
 
-		//necessary and sufficient condition : there exists a unique blocker that passes through all vertices
-		auto first_blocker = *(complex.const_blocker_range().begin());
+    // necessary and sufficient condition : there exists a unique blocker that passes through all vertices
+    auto first_blocker = *(complex.const_blocker_range().begin());
 
-		if (first_blocker->dimension()+1 != complex.num_vertices())
-			return -2;
-		else
-			return (first_blocker->dimension()-1);
-	}
+    if (first_blocker->dimension() + 1 != complex.num_vertices())
+      return -2;
+    else
+      return (first_blocker->dimension() - 1);
+  }
 };
 
-#endif /* IS_MANIFOLD_H_ */
+#endif  // UTILS_IS_MANIFOLD_H_
diff --git a/src/GudhUI/utils/K_nearest_builder.h b/src/GudhUI/utils/K_nearest_builder.h
index b65a79e0..cab24b7c 100644
--- a/src/GudhUI/utils/K_nearest_builder.h
+++ b/src/GudhUI/utils/K_nearest_builder.h
@@ -1,81 +1,92 @@
-/*
- * K_nearest_builder.h
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
  *
- *  Created on: Sep 10, 2014
- *      Author: dsalinas
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
  */
 
-#ifndef K_NEAREST_BUILDER_H_
-#define K_NEAREST_BUILDER_H_
+#ifndef UTILS_K_NEAREST_BUILDER_H_
+#define UTILS_K_NEAREST_BUILDER_H_
 
-#include <unordered_map>
-#include <boost/iterator/iterator_facade.hpp>
 #include <CGAL/Euclidean_distance.h>
 #include <CGAL/Orthogonal_k_neighbor_search.h>
 #include <CGAL/Search_traits_d.h>
 #include <CGAL/Search_traits_adapter.h>
-#include <CGAL/property_map.h>
+#include <CGAL/property_map.h>
+#include <boost/iterator/iterator_facade.hpp>
 #include <boost/iterator/zip_iterator.hpp>
 
+#include <unordered_map>
+#include <tuple>
+#include <list>
+
 #include "utils/UI_utils.h"
 #include "model/Complex_typedefs.h"
 
-
-
-template<typename SkBlComplex> class K_nearest_builder{
-private:
-
-	typedef Geometry_trait Kernel;
-	typedef Point Point_d;
-	typedef boost::tuple<Point_d, unsigned> Point_d_with_id;
-	typedef CGAL::Search_traits_d<Kernel> Traits_base;
-	typedef CGAL::Search_traits_adapter<Point_d_with_id, CGAL::Nth_of_tuple_property_map<0, Point_d_with_id>, Traits_base> Traits;
-	typedef CGAL::Orthogonal_k_neighbor_search<Traits> Neighbor_search;
-	typedef Neighbor_search::Tree Tree;
-	typedef Neighbor_search::Distance Distance;
-
-	SkBlComplex& complex_;
-public:
-
-	/**
-	 * @brief Modify complex to be the expansion of the k-nearest neighbor
-	 * symetric graph.
-	 */
-	K_nearest_builder(SkBlComplex& complex,unsigned k):complex_(complex){
-		complex.keep_only_vertices();
-		compute_edges(k);
-	}
-
-private:
-
-
-
-	double squared_eucl_distance(const Point& p1,const Point& p2) const{
-		return Geometry_trait::Squared_distance_d()(p1,p2);
-	}
-
-	void compute_edges(unsigned k){
-
-		std::list<Point_d_with_id> points_with_id;
-		for(auto v: complex_.vertex_range()){
-			Point_d_with_id point_v(complex_.point(v),v.vertex);
-			points_with_id.push_back(point_v);
-		}
-
-		Tree tree(points_with_id.begin(),points_with_id.end());
-
-		typedef typename SkBlComplex::Vertex_handle Vertex_handle;
-		for (auto p : complex_.vertex_range()){
-			Neighbor_search search(tree, complex_.point(p),k+1);
-			for(auto it = ++search.begin(); it != search.end(); ++it){
-				Vertex_handle q(boost::get<1>(it->first));
-				if (p != q && complex_.contains_vertex(p) && complex_.contains_vertex(q))
-					complex_.add_edge(p,q);
-			}
-		}
-	}
-
-
+template<typename SkBlComplex> class K_nearest_builder {
+ private:
+  typedef Geometry_trait Kernel;
+  typedef Point Point_d;
+  typedef boost::tuple<Point_d, unsigned> Point_d_with_id;
+  typedef CGAL::Search_traits_d<Kernel> Traits_base;
+  typedef CGAL::Search_traits_adapter<Point_d_with_id, CGAL::Nth_of_tuple_property_map<0, Point_d_with_id>,
+      Traits_base> Traits;
+  typedef CGAL::Orthogonal_k_neighbor_search<Traits> Neighbor_search;
+  typedef Neighbor_search::Tree Tree;
+  typedef Neighbor_search::Distance Distance;
+
+  SkBlComplex& complex_;
+
+ public:
+  /**
+   * @brief Modify complex to be the expansion of the k-nearest neighbor
+   * symetric graph.
+   */
+  K_nearest_builder(SkBlComplex& complex, unsigned k) : complex_(complex) {
+    complex.keep_only_vertices();
+    compute_edges(k);
+  }
+
+ private:
+  double squared_eucl_distance(const Point& p1, const Point& p2) const {
+    return Geometry_trait::Squared_distance_d()(p1, p2);
+  }
+
+  void compute_edges(unsigned k) {
+    std::list<Point_d_with_id> points_with_id;
+    for (auto v : complex_.vertex_range()) {
+      Point_d_with_id point_v(complex_.point(v), v.vertex);
+      points_with_id.push_back(point_v);
+    }
+
+    Tree tree(points_with_id.begin(), points_with_id.end());
+
+    typedef typename SkBlComplex::Vertex_handle Vertex_handle;
+    for (auto p : complex_.vertex_range()) {
+      Neighbor_search search(tree, complex_.point(p), k + 1);
+      for (auto it = ++search.begin(); it != search.end(); ++it) {
+        Vertex_handle q(boost::get<1>(it->first));
+        if (p != q && complex_.contains_vertex(p) && complex_.contains_vertex(q))
+          complex_.add_edge(p, q);
+      }
+    }
+  }
 };
 
-#endif /* K_NEAREST_BUILDER_H_ */
+#endif  // UTILS_K_NEAREST_BUILDER_H_
diff --git a/src/GudhUI/utils/Lloyd_builder.h b/src/GudhUI/utils/Lloyd_builder.h
index db2a7973..18ec9fac 100644
--- a/src/GudhUI/utils/Lloyd_builder.h
+++ b/src/GudhUI/utils/Lloyd_builder.h
@@ -1,78 +1,91 @@
-/*
- * Lloyd.h
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
  *
- *  Created on: Sep 25, 2014
- *      Author: dsalinas
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
  */
 
-#ifndef LLOYD_H_
-#define LLOYD_H_
-
+#ifndef UTILS_LLOYD_BUILDER_H_
+#define UTILS_LLOYD_BUILDER_H_
 
 #include <vector>
+#include <list>
 
 /**
  * Iteratively puts every vertex at the center of its neighbors
  */
-template<typename SkBlComplex> class Lloyd_builder{
-private:
-	SkBlComplex& complex_;
-	int dim;
-public:
-	typedef typename SkBlComplex::Vertex_handle Vertex_handle;
-	/**
-	 * @brief Modify complex to be the expansion of the k-nearest neighbor
-	 * symetric graph.
-	 */
-	Lloyd_builder(SkBlComplex& complex,unsigned num_iterations):complex_(complex),dim(-1){
-		if(!complex_.empty()){
-			dim = get_dimension();
-			while(num_iterations--){
-				std::list<Point> new_points;
-				for(auto v : complex.vertex_range())
-					new_points.push_back(barycenter_neighbors(v));
-
-				auto new_points_it = new_points.begin();
-				for(auto v : complex.vertex_range())
-					complex_.point(v) = *(new_points_it++);
-			}
-		}
-	}
+template<typename SkBlComplex> class Lloyd_builder {
+ private:
+  SkBlComplex& complex_;
+  int dim;
 
-private:
+ public:
+  typedef typename SkBlComplex::Vertex_handle Vertex_handle;
 
-	int get_dimension(){
-		assert(!complex_.empty());
-		for(auto v : complex_.vertex_range())
-			return complex_.point(v).dimension();
-		return -1;
-	}
+  /**
+   * @brief Modify complex to be the expansion of the k-nearest neighbor
+   * symetric graph.
+   */
+  Lloyd_builder(SkBlComplex& complex, unsigned num_iterations) : complex_(complex), dim(-1) {
+    if (!complex_.empty()) {
+      dim = get_dimension();
+      while (num_iterations--) {
+        std::list<Point> new_points;
+        for (auto v : complex.vertex_range())
+          new_points.push_back(barycenter_neighbors(v));
 
-	Point barycenter_neighbors(Vertex_handle v) const{
-		if(complex_.degree(v)==0)
-			return complex_.point(v);
+        auto new_points_it = new_points.begin();
+        for (auto v : complex.vertex_range())
+          complex_.point(v) = *(new_points_it++);
+      }
+    }
+  }
 
-		std::vector<double> res(dim,0);
-		unsigned num_points = 0;
-		for(auto nv : complex_.vertex_range(v)){
-			++num_points;
-			const Point& point = complex_.point(nv);
-			assert(point.dimension() == dim);
-			for(int i = 0; i < point.dimension() ; ++i)
-				res[i] += point[i];
-		}
-		for(auto& x : res)
-			x/= num_points;
-		return Point(dim,res.begin(),res.end());
-	}
+ private:
+  int get_dimension() {
+    assert(!complex_.empty());
+    for (auto v : complex_.vertex_range())
+      return complex_.point(v).dimension();
+    return -1;
+  }
 
+  Point barycenter_neighbors(Vertex_handle v) const {
+    if (complex_.degree(v) == 0)
+      return complex_.point(v);
 
+    std::vector<double> res(dim, 0);
+    unsigned num_points = 0;
+    for (auto nv : complex_.vertex_range(v)) {
+      ++num_points;
+      const Point& point = complex_.point(nv);
+      assert(point.dimension() == dim);
+      for (int i = 0; i < point.dimension(); ++i)
+        res[i] += point[i];
+    }
+    for (auto& x : res)
+      x /= num_points;
+    return Point(dim, res.begin(), res.end());
+  }
 
-	double squared_eucl_distance(const Point& p1,const Point& p2) const{
-		return Geometry_trait::Squared_distance_d()(p1,p2);
-	}
-
+  double squared_eucl_distance(const Point& p1, const Point& p2) const {
+    return Geometry_trait::Squared_distance_d()(p1, p2);
+  }
 };
 
-
-#endif /* LLOYD_H_ */
+#endif  // UTILS_LLOYD_BUILDER_H_
diff --git a/src/GudhUI/utils/MClock.h b/src/GudhUI/utils/MClock.h
index b5c7d191..e8d8918a 100644
--- a/src/GudhUI/utils/MClock.h
+++ b/src/GudhUI/utils/MClock.h
@@ -1,57 +1,70 @@
-/*
- * Clock.h
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
  *
- *  Created on: Jun 17, 2014
- *      Author: dsalinas
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
  */
 
-#ifndef CLOCK_H_
-#define CLOCK_H_
+#ifndef UTILS_MCLOCK_H_
+#define UTILS_MCLOCK_H_
 
 #include <sys/time.h>
 
+class MClock {
+ public:
+  MClock() {
+    end_called = false;
+    begin();
+  }
 
-class MClock{
-
-public:
-	MClock(){
-		end_called = false;
-		begin();
-	}
-
-	void begin() const{
-		end_called = false;
-		gettimeofday(&startTime, NULL);
-	}
-
-	void end() const{
-		end_called = true;
-		gettimeofday(&endTime, NULL);
-	}
-
-	friend std::ostream& operator<< (std::ostream& stream,const MClock& clock){
-		//		if(!clock.end_called) clock.end();
-		if(!clock.end_called) stream << "end not called";
-		else{
-			long totalTime =  (clock.endTime.tv_sec - clock.startTime.tv_sec) * 1000000L;
-			totalTime += (clock.endTime.tv_usec - clock.startTime.tv_usec);
-			stream << clock.num_seconds() <<"s";
-		}
-		return stream;
-
-	}
-
-	double num_seconds() const{
-		if(!end_called) end();
-		long totalTime =  (endTime.tv_sec - startTime.tv_sec) * 1000000L;
-		totalTime += (endTime.tv_usec - startTime.tv_usec);
-		return (totalTime / 1000L)/(double) 1000;
-	}
-
-private:
-	mutable struct timeval startTime, endTime;
-	mutable bool end_called;
-};
+  void begin() const {
+    end_called = false;
+    gettimeofday(&startTime, NULL);
+  }
 
+  void end() const {
+    end_called = true;
+    gettimeofday(&endTime, NULL);
+  }
+
+  friend std::ostream& operator<<(std::ostream& stream, const MClock& clock) {
+    // if(!clock.end_called) clock.end();
+    if (!clock.end_called) {
+      stream << "end not called";
+    } else {
+      long totalTime = (clock.endTime.tv_sec - clock.startTime.tv_sec) * 1000000L;
+      totalTime += (clock.endTime.tv_usec - clock.startTime.tv_usec);
+      stream << clock.num_seconds() << "s";
+    }
+    return stream;
+  }
+
+  double num_seconds() const {
+    if (!end_called) end();
+    long totalTime = (endTime.tv_sec - startTime.tv_sec) * 1000000L;
+    totalTime += (endTime.tv_usec - startTime.tv_usec);
+    return (totalTime / 1000L) / static_cast<double>(1000);
+  }
+
+ private:
+  mutable struct timeval startTime, endTime;
+  mutable bool end_called;
+};
 
-#endif /* CLOCK_H_ */
+#endif  // UTILS_MCLOCK_H_
diff --git a/src/GudhUI/utils/Persistence_compute.h b/src/GudhUI/utils/Persistence_compute.h
index 50d340b8..0b9961d3 100644
--- a/src/GudhUI/utils/Persistence_compute.h
+++ b/src/GudhUI/utils/Persistence_compute.h
@@ -1,13 +1,10 @@
-/*
- * Persistence_compute.h
- *  Created on: Jan 26, 2015
- * This file is part of the Gudhi Library. The Gudhi library 
+/* This file is part of the Gudhi Library. The Gudhi library 
  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
  *    library for computational topology.
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-M�diterran�e (France)
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
@@ -25,83 +22,76 @@
  */
 
 
-#ifndef PERSISTENCE_COMPUTE_H_
-#define PERSISTENCE_COMPUTE_H_
+#ifndef UTILS_PERSISTENCE_COMPUTE_H_
+#define UTILS_PERSISTENCE_COMPUTE_H_
 
+#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/distance_functions.h>
+#include <gudhi/Persistent_cohomology.h>
 
-#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Simplex_tree.h"
-#include "gudhi/distance_functions.h"
-#include "gudhi/Persistent_cohomology.h"
+#include <vector>
 
+struct Persistence_params {
+  int p;
+  double threshold;
+  int max_dim;
+  double min_pers;
 
-struct Persistence_params{
-	int p;
-	double threshold;
-	int max_dim;
-	double min_pers;
-
-	Persistence_params(int p_,double th_,int max_dim_=10,double min_pers_=0)
-	:p(p_),threshold(th_),max_dim(max_dim_),min_pers(min_pers_){}
+  Persistence_params(int p_, double th_, int max_dim_ = 10, double min_pers_ = 0)
+      : p(p_), threshold(th_), max_dim(max_dim_), min_pers(min_pers_) { }
 };
 
-
 /**
  * Show persistence into output stream
  */
-template<typename SkBlComplex> class Persistence_compute{
-private:
-	SkBlComplex& complex_;
-	std::ostream& stream_;
-public:
-	typedef typename SkBlComplex::Vertex_handle Vertex_handle;
-	typedef typename SkBlComplex::Edge_handle Edge_handle;
-
-	/**
-	 * @brief Compute persistence
-	 * parameters :
-	 * unsigned dim_max
-	 * double threshold
-	 * int p for coefficient Z_p
-	 */
-	Persistence_compute(SkBlComplex& complex,std::ostream& stream,const Persistence_params& params):
-//
-//			double threshold = 0.5,unsigned dim_max = 8):
-		complex_(complex),stream_(stream){
-
-		//for now everything is copied, todo boost adapt iterators to points of SkBlComplex instead of copying to an intial vector
-		typedef std::vector<double> Point_t;
-		std::vector< Point_t > points;
-		points.reserve(complex.num_vertices());
-		for(auto v :  complex.vertex_range()){
-			const auto & pt = complex.point(v);
-			Point_t pt_to_add(pt.cartesian_begin(),pt.cartesian_end());
-			points.emplace_back(std::move(pt_to_add));
-		}
-
-
-		Graph_t prox_graph = compute_proximity_graph( points, params.threshold, euclidean_distance<Point_t> );
-		Gudhi::Simplex_tree<> st;
-		st.insert_graph(prox_graph);
-		st.expansion( params.max_dim );
-
-		Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::Simplex_tree<>,Gudhi::persistent_cohomology::Field_Zp > pcoh (st);
-		pcoh.init_coefficients( params.p ); //initilizes the coefficient field for homology
-		pcoh.compute_persistent_cohomology( params.min_pers ); //put params.min_pers
-		stream_<<"persistence: \n";
-		stream_<<"p dimension birth death: \n";
-
-		pcoh.output_diagram(stream_);
-	}
-
-private:
-
-
+template<typename SkBlComplex> class Persistence_compute {
+ private:
+  SkBlComplex& complex_;
+  std::ostream& stream_;
+
+ public:
+  typedef typename SkBlComplex::Vertex_handle Vertex_handle;
+  typedef typename SkBlComplex::Edge_handle Edge_handle;
+
+  /**
+   * @brief Compute persistence
+   * parameters :
+   * unsigned dim_max
+   * double threshold
+   * int p for coefficient Z_p
+   */
+  Persistence_compute(SkBlComplex& complex, std::ostream& stream, const Persistence_params& params) :
+      // double threshold = 0.5,unsigned dim_max = 8):
+      complex_(complex), stream_(stream) {
+    // for now everything is copied, todo boost adapt iterators to points of SkBlComplex instead of copying to an
+    // initial vector
+    typedef std::vector<double> Point_t;
+    std::vector< Point_t > points;
+    points.reserve(complex.num_vertices());
+    for (auto v : complex.vertex_range()) {
+      const auto & pt = complex.point(v);
+      Point_t pt_to_add(pt.cartesian_begin(), pt.cartesian_end());
+      points.emplace_back(std::move(pt_to_add));
+    }
+
+
+    Graph_t prox_graph = compute_proximity_graph(points, params.threshold, euclidean_distance<Point_t>);
+    Gudhi::Simplex_tree<> st;
+    st.insert_graph(prox_graph);
+    st.expansion(params.max_dim);
+
+    Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::Simplex_tree<>,
+        Gudhi::persistent_cohomology::Field_Zp > pcoh(st);
+    // initializes the coefficient field for homology
+    pcoh.init_coefficients(params.p);
+    // put params.min_pers
+    pcoh.compute_persistent_cohomology(params.min_pers);
+    stream_ << "persistence: \n";
+    stream_ << "p dimension birth death: \n";
+
+    pcoh.output_diagram(stream_);
+  }
 };
 
-
-
-
-
-
-#endif /* PERSISTENCE_COMPUTE_H_ */
+#endif  // UTILS_PERSISTENCE_COMPUTE_H_
diff --git a/src/GudhUI/utils/Rips_builder.h b/src/GudhUI/utils/Rips_builder.h
index 9484f9ab..b22f4db6 100644
--- a/src/GudhUI/utils/Rips_builder.h
+++ b/src/GudhUI/utils/Rips_builder.h
@@ -1,56 +1,69 @@
-/*
- * Rips_builder.h
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
  *
- *  Created on: Sep 10, 2014
- *      Author: dsalinas
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
  */
 
-#ifndef RIPS_BUILDER_H_
-#define RIPS_BUILDER_H_
+#ifndef UTILS_RIPS_BUILDER_H_
+#define UTILS_RIPS_BUILDER_H_
 
 #include <boost/iterator/iterator_facade.hpp>
 
-#include "utils/UI_utils.h"
-#include "model/Complex_typedefs.h"
 #include <CGAL/Euclidean_distance.h>
-
 #include <CGAL/Orthogonal_k_neighbor_search.h>
 #include <CGAL/Search_traits_d.h>
 
-template<typename SkBlComplex> class Rips_builder{
-private:
-	SkBlComplex& complex_;
-public:
-
-	/**
-	 * @brief Modify complex to be the Rips complex
-	 * of its points with offset alpha.
-	 */
-	Rips_builder(SkBlComplex& complex,double alpha):complex_(complex){
-		complex.keep_only_vertices();
-		if (alpha<=0) return;
-		compute_edges(alpha);
-	}
-
-private:
-
-
-	double squared_eucl_distance(const Point& p1,const Point& p2) const{
-		return Geometry_trait::Squared_distance_d()(p1,p2);
-	}
-
-	void compute_edges(double alpha){
-		auto vertices = complex_.vertex_range();
-		for(auto p = vertices.begin(); p!= vertices.end(); ++p){
-			std::cout << *p << " "; std::cout.flush();
-			for (auto q = p; ++q != vertices.end(); /**/)
-				if (squared_eucl_distance(complex_.point(*p),complex_.point(*q)) < 4*alpha*alpha)
-					complex_.add_edge(*p,*q);
-		}
-		std::cout << std::endl;
-	}
+#include "utils/UI_utils.h"
+#include "model/Complex_typedefs.h"
 
-};
+template<typename SkBlComplex> class Rips_builder {
+ private:
+  SkBlComplex& complex_;
 
+ public:
+  /**
+   * @brief Modify complex to be the Rips complex
+   * of its points with offset alpha.
+   */
+  Rips_builder(SkBlComplex& complex, double alpha) : complex_(complex) {
+    complex.keep_only_vertices();
+    if (alpha <= 0) return;
+    compute_edges(alpha);
+  }
+
+ private:
+  double squared_eucl_distance(const Point& p1, const Point& p2) const {
+    return Geometry_trait::Squared_distance_d()(p1, p2);
+  }
+
+  void compute_edges(double alpha) {
+    auto vertices = complex_.vertex_range();
+    for (auto p = vertices.begin(); p != vertices.end(); ++p) {
+      std::cout << *p << " ";
+      std::cout.flush();
+      for (auto q = p; ++q != vertices.end(); /**/)
+        if (squared_eucl_distance(complex_.point(*p), complex_.point(*q)) < 4 * alpha * alpha)
+          complex_.add_edge(*p, *q);
+    }
+    std::cout << std::endl;
+  }
+};
 
-#endif /* RIPS_BUILDER_H_ */
+#endif  // UTILS_RIPS_BUILDER_H_
diff --git a/src/GudhUI/utils/UI_utils.h b/src/GudhUI/utils/UI_utils.h
index a7c0689f..9cc209d3 100644
--- a/src/GudhUI/utils/UI_utils.h
+++ b/src/GudhUI/utils/UI_utils.h
@@ -1,33 +1,45 @@
-/*
- * UI_utils.h
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
  *
- *  Created on: Aug 25, 2014
- *      Author: david
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
  */
 
-#ifndef UI_UTILS_H_
-#define UI_UTILS_H_
-
-#define PRINT(a) std::cerr << #a << ": " << (a) << " (DISP)"<<std::endl
+#ifndef UTILS_UI_UTILS_H_
+#define UTILS_UI_UTILS_H_
 
 #define UIDBG_VERBOSE
 
-
 #ifdef UIDBG_VERBOSE
-#define UIDBG(a) std::cerr << "UIDBG: " << (a)<<std::endl
-#define UIDBGMSG(a,b) std::cerr << "UIDBG: " << a<<b<<std::endl
-#define UIDBGVALUE(a) std::cerr << "UIDBG: " <<  #a << ": " << a<<std::endl
-#define UIDBGCONT(a) std::cerr << "UIDBG: container "<< #a<<" -> "; for(auto x:a) std::cerr<< x << ","; std::cerr<<std::endl
+#define UIDBG(a) std::cerr << "UIDBG: " << (a) << std::endl
+#define UIDBGMSG(a, b) std::cerr << "UIDBG: " << a << b << std::endl
+#define UIDBGVALUE(a) std::cerr << "UIDBG: " <<  #a << ": " << a << std::endl
+#define UIDBGCONT(a) std::cerr << "UIDBG: container " << #a << " -> "; for (auto x : a) std::cerr << x << ","; std::cerr << std::endl }
 #else
-//#define DBG(a) a
-//#define DBGMSG(a,b) b
-//#define DBGVALUE(a) a
-//#define DBGCONT(a) a
+// #define DBG(a) a
+// #define DBGMSG(a, b) b
+// #define DBGVALUE(a) a
+// #define DBGCONT(a) a
 #define UIDBG(a)
-#define UIDBGMSG(a,b)
+#define UIDBGMSG(a, b)
 #define UIDBGVALUE(a)
 #define UIDBGCONT(a)
 #endif
 
-
-#endif /* UI_UTILS_H_ */
+#endif  // UTILS_UI_UTILS_H_
diff --git a/src/GudhUI/utils/Vertex_collapsor.h b/src/GudhUI/utils/Vertex_collapsor.h
index d4911a35..2b36cb3a 100644
--- a/src/GudhUI/utils/Vertex_collapsor.h
+++ b/src/GudhUI/utils/Vertex_collapsor.h
@@ -1,76 +1,88 @@
-/*
- * Vertex_collapsor.h
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
  *
- *  Created on: Sep 25, 2014
- *      Author: dsalinas
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
  */
 
-#ifndef VERTEX_COLLAPSOR_H_
-#define VERTEX_COLLAPSOR_H_
+#ifndef UTILS_VERTEX_COLLAPSOR_H_
+#define UTILS_VERTEX_COLLAPSOR_H_
+
+#include <list>
 
 #include "utils/Edge_contractor.h"
 #include "utils/Furthest_point_epsilon_net.h"
 #include "utils/UI_utils.h"
+
 /**
  * Iteratively puts every vertex at the center of its neighbors
  */
-template<typename SkBlComplex> class Vertex_collapsor{
-private:
-	SkBlComplex& complex_;
-	size_t num_collapses_;
-public:
-	typedef typename SkBlComplex::Vertex_handle Vertex_handle;
-	typedef typename SkBlComplex::Edge_handle Edge_handle;
-
-	/**
-	 * @brief Modify complex to be the expansion of the k-nearest neighbor
-	 * symetric graph.
-	 */
-	Vertex_collapsor(SkBlComplex& complex, size_t num_collapses) :
-		complex_(complex),num_collapses_(num_collapses)
-	{
-//		std::list<Vertex_handle> vertices;
-//		vertices.insert(vertices.begin(),complex_.vertex_range().begin(),complex_.vertex_range().end());
-//		UIDBG("Collapse vertices");
-//		collapse_vertices(vertices);
-
-		std::list<Vertex_handle> vertices;
-
-		UIDBG("Compute eps net");
-		Furthest_point_epsilon_net<Complex> eps_net(complex_);
-
-		for(auto vh : eps_net.net_filtration_)
-			vertices.push_back(vh.vertex_handle);
-
-		UIDBG("Collapse vertices");
-		collapse_vertices(vertices);
-
-
-
-	}
-
-private:
-
-
-	void collapse_vertices(std::list<Vertex_handle>& vertices){
-		while(!vertices.empty() && num_collapses_--){
-			Vertex_handle current_vertex = vertices.front();
-			vertices.pop_front();
-			if(is_link_reducible(current_vertex))
-				complex_.remove_vertex(current_vertex);
-		}
-	}
-
-	bool is_link_reducible(Vertex_handle v){
-		auto link = complex_.link(v);
-		if(link.empty()) return false;
-		if(link.is_cone()) return true;
-		if(link.num_connected_components()>1) return false;
-		Edge_contractor<Complex> contractor(link,link.num_vertices()-1);
-		return (link.num_vertices()==1);
-	}
-
+template<typename SkBlComplex> class Vertex_collapsor {
+ private:
+  SkBlComplex& complex_;
+  size_t num_collapses_;
+
+ public:
+  typedef typename SkBlComplex::Vertex_handle Vertex_handle;
+  typedef typename SkBlComplex::Edge_handle Edge_handle;
+
+  /**
+   * @brief Modify complex to be the expansion of the k-nearest neighbor
+   * symetric graph.
+   */
+  Vertex_collapsor(SkBlComplex& complex, size_t num_collapses) :
+      complex_(complex), num_collapses_(num_collapses) {
+    // std::list<Vertex_handle> vertices;
+    // vertices.insert(vertices.begin(),complex_.vertex_range().begin(),complex_.vertex_range().end());
+    // UIDBG("Collapse vertices");
+    // collapse_vertices(vertices);
+
+    std::list<Vertex_handle> vertices;
+
+    UIDBG("Compute eps net");
+    Furthest_point_epsilon_net<Complex> eps_net(complex_);
+
+    for (auto vh : eps_net.net_filtration_)
+      vertices.push_back(vh.vertex_handle);
+
+    UIDBG("Collapse vertices");
+    collapse_vertices(vertices);
+  }
+
+ private:
+  void collapse_vertices(std::list<Vertex_handle>& vertices) {
+    while (!vertices.empty() && num_collapses_--) {
+      Vertex_handle current_vertex = vertices.front();
+      vertices.pop_front();
+      if (is_link_reducible(current_vertex))
+        complex_.remove_vertex(current_vertex);
+    }
+  }
+
+  bool is_link_reducible(Vertex_handle v) {
+    auto link = complex_.link(v);
+    if (link.empty()) return false;
+    if (link.is_cone()) return true;
+    if (link.num_connected_components() > 1) return false;
+    Edge_contractor<Complex> contractor(link, link.num_vertices() - 1);
+    return (link.num_vertices() == 1);
+  }
 };
 
-
-#endif /* VERTEX_COLLAPSOR_H_ */
+#endif  // UTILS_VERTEX_COLLAPSOR_H_
diff --git a/src/GudhUI/view/Color.h b/src/GudhUI/view/Color.h
index a63456cb..ba0592e1 100644
--- a/src/GudhUI/view/Color.h
+++ b/src/GudhUI/view/Color.h
@@ -1,21 +1,35 @@
-/*
- * Color.h
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
  *
- *  Created on: Aug 26, 2014
- *      Author: dsalinas
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
  */
 
-#ifndef COLOR_H_
-#define COLOR_H_
-
+#ifndef VIEW_COLOR_H_
+#define VIEW_COLOR_H_
 
+struct Color {
+  double r;
+  double g;
+  double b;
 
-struct Color{
-	double r;
-	double g;
-	double b;
-	Color(double r_,double g_,double b_):r(r_),g(g_),b(b_){}
+  Color(double r_, double g_, double b_) : r(r_), g(g_), b(b_) { }
 };
 
-
-#endif /* COLOR_H_ */
+#endif  // VIEW_COLOR_H_
diff --git a/src/GudhUI/view/FirstCoordProjector.h b/src/GudhUI/view/FirstCoordProjector.h
index 2659eef1..529d2d42 100644
--- a/src/GudhUI/view/FirstCoordProjector.h
+++ b/src/GudhUI/view/FirstCoordProjector.h
@@ -1,24 +1,40 @@
-/*
- * FirstCoordProjector.h
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
  *
- *  Created on: Aug 27, 2014
- *      Author: dsalinas
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
  */
 
-#ifndef FIRSTCOORDPROJECTOR_H_
-#define FIRSTCOORDPROJECTOR_H_
+#ifndef VIEW_FIRSTCOORDPROJECTOR_H_
+#define VIEW_FIRSTCOORDPROJECTOR_H_
 
 #include "utils/UI_utils.h"
 #include "Projector3D.h"
 
-class FirstCoordProjector3D : public Projector3D{
-	typedef Projector3D::Point Point;
-	typedef Projector3D::Point_3 Point_3;
+class FirstCoordProjector3D : public Projector3D {
+  typedef Projector3D::Point Point;
+  typedef Projector3D::Point_3 Point_3;
 
-	Point_3 operator()(const Point& p) const{
-		assert(p.dimension()>=3);
-		return Point_3(p.x(),p.y(),p.z());
-	}
+  Point_3 operator()(const Point& p) const {
+    assert(p.dimension() >= 3);
+    return Point_3(p.x(), p.y(), p.z());
+  }
 };
 
-#endif /* FIRSTCOORDPROJECTOR_H_ */
+#endif  // VIEW_FIRSTCOORDPROJECTOR_H_
diff --git a/src/GudhUI/view/Projector3D.h b/src/GudhUI/view/Projector3D.h
index 503b35c5..2a756541 100644
--- a/src/GudhUI/view/Projector3D.h
+++ b/src/GudhUI/view/Projector3D.h
@@ -1,28 +1,39 @@
-/*
- * Projector.h
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
  *
- *  Created on: Aug 27, 2014
- *      Author: dsalinas
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
  */
 
-#ifndef PROJECTOR3D_H_
-#define PROJECTOR3D_H_
+#ifndef VIEW_PROJECTOR3D_H_
+#define VIEW_PROJECTOR3D_H_
 
 #include "model/Complex_typedefs.h"
 
+class Projector3D {
+ public:
+  typedef Geometry_trait::Point Point;
+  typedef Geometry_trait::Point_3 Point_3;
 
-class Projector3D{
-public:
-	typedef Geometry_trait::Point Point;
-	typedef Geometry_trait::Point_3 Point_3;
-
-	virtual Point_3 operator()(const Point&) const  = 0;
-
-	virtual ~Projector3D(){
-	}
+  virtual Point_3 operator()(const Point&) const = 0;
 
+  virtual ~Projector3D() { }
 };
 
-
-
-#endif /* PROJECTOR3D_H_ */
+#endif  // VIEW_PROJECTOR3D_H_
diff --git a/src/GudhUI/view/View_parameter.h b/src/GudhUI/view/View_parameter.h
index 39c5d7dd..9805abc2 100644
--- a/src/GudhUI/view/View_parameter.h
+++ b/src/GudhUI/view/View_parameter.h
@@ -1,13 +1,28 @@
-/*
- * View_parameter.h
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
  *
- *  Created on: Mar 10, 2014 
- *      Author: David Salinas
- *  Copyright 2013 INRIA. All rights reserved
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
  */
 
-#ifndef VIEW_PARAMETER_H_
-#define VIEW_PARAMETER_H_
+#ifndef VIEW_VIEW_PARAMETER_H_
+#define VIEW_VIEW_PARAMETER_H_
 
 #include <iostream>
 
@@ -15,123 +30,122 @@
  * Different parameters for the view such as the camera angle,
  * the light, options for vertices/edges/triangles.
  */
-class View_parameter{
-public:
-	bool light;
-	bool relative_light;
-
-	double size_vertices;
-	double size_edges;
-	double light_edges; // in 0-1
-	double light_triangles;// in 0-1
-
-	/**
-	 * light angle
-	 */
-	double theta;
-	double phi;
-
-	enum VERTEX_MODE{ V_NONE,V_SIMPLE,V_COUNT};
-	enum EDGE_MODE{ E_NONE,E_SIMPLE,E_COUNT};
-	enum TRIANGLE_MODE{ T_NONE,T_SIMPLE,T_COUNT};
-
-
-
-
-	VERTEX_MODE vertex_mode;
-	EDGE_MODE edge_mode;
-	TRIANGLE_MODE triangle_mode;
-
-	void change_vertex_mode(){
-		int current_value = vertex_mode;
-		vertex_mode = static_cast<VERTEX_MODE>(++current_value % V_COUNT);
-		std::cout<<"Vertex mode : ";
-		switch (vertex_mode) {
-		case V_NONE:
-			std::cout<<"empty\n";
-			break;
-		case V_SIMPLE:
-			std::cout<<"simple\n";
-			break;
-		default:
-			break;
-		}
-	}
-
-	void change_vertex_mode(int new_mode){
-		vertex_mode = static_cast<VERTEX_MODE>(new_mode % V_COUNT);
-	}
-
-	void change_edge_mode(){
-		int current_value = edge_mode;
-		edge_mode = static_cast<EDGE_MODE>(++current_value % E_COUNT);
-	}
-
-	void change_edge_mode(int new_mode){
-		edge_mode = static_cast<EDGE_MODE>(new_mode % E_COUNT);
-	}
-
-
-	void change_triangle_mode(){
-		int current_value = triangle_mode;
-		triangle_mode = static_cast<TRIANGLE_MODE>(++current_value % T_COUNT);
-	}
-
-
-
-
-
-	View_parameter(){
-		light = true;
-		relative_light = true;
-		vertex_mode = V_SIMPLE;
-		edge_mode = E_SIMPLE;
-		triangle_mode = T_NONE;
-
-		size_vertices = 3;
-		size_edges = 2;
-
-		light_edges = 0.3;
-		light_triangles = 0.85;
-		theta = 0;
-		phi = 0;
-	}
-
-	friend std::ostream& operator<<(std::ostream& stream, const View_parameter& param){
-		stream << param.light<< " ";
-		stream << param.relative_light<< " ";
-		stream << param.vertex_mode<< " ";
-		stream << param.edge_mode<< " ";
-		stream << param.triangle_mode<< " ";
-		stream << param.size_vertices<< " ";
-		stream << param.size_edges<< " ";
-		stream << param.light_edges<< " ";
-		stream << param.light_triangles<< " ";
-		stream << param.theta<< " ";
-		stream << param.phi<< " ";
-		return stream;
-	}
-
-	friend std::istream& operator>>(std::istream& stream, View_parameter& param){
-		stream >> param.light;
-		stream >> param.relative_light;
-		int a;
-		stream>>a;
-		param.vertex_mode = static_cast<VERTEX_MODE>(a % V_COUNT);
-		stream>>a;
-		param.edge_mode = static_cast<EDGE_MODE>(a % E_COUNT);
-		stream>>a;
-		param.triangle_mode = static_cast<TRIANGLE_MODE>(a % T_COUNT);
-		stream>>a;
-		stream >> param.size_vertices;
-		stream >> param.size_edges;
-		stream >> param.light_edges;
-		stream >> param.light_triangles;
-		stream >> param.theta;
-		stream >> param.phi;
-		return stream;
-	}
-
+class View_parameter {
+ public:
+  bool light;
+  bool relative_light;
+
+  double size_vertices;
+  double size_edges;
+  double light_edges;  // in 0-1
+  double light_triangles;  // in 0-1
+
+  /**
+   * light angle
+   */
+  double theta;
+  double phi;
+
+  enum VERTEX_MODE {
+    V_NONE, V_SIMPLE, V_COUNT
+  };
+
+  enum EDGE_MODE {
+    E_NONE, E_SIMPLE, E_COUNT
+  };
+
+  enum TRIANGLE_MODE {
+    T_NONE, T_SIMPLE, T_COUNT
+  };
+
+  VERTEX_MODE vertex_mode;
+  EDGE_MODE edge_mode;
+  TRIANGLE_MODE triangle_mode;
+
+  void change_vertex_mode() {
+    int current_value = vertex_mode;
+    vertex_mode = static_cast<VERTEX_MODE> (++current_value % V_COUNT);
+    std::cout << "Vertex mode : ";
+    switch (vertex_mode) {
+      case V_NONE:
+        std::cout << "empty\n";
+        break;
+      case V_SIMPLE:
+        std::cout << "simple\n";
+        break;
+      default:
+        break;
+    }
+  }
+
+  void change_vertex_mode(int new_mode) {
+    vertex_mode = static_cast<VERTEX_MODE> (new_mode % V_COUNT);
+  }
+
+  void change_edge_mode() {
+    int current_value = edge_mode;
+    edge_mode = static_cast<EDGE_MODE> (++current_value % E_COUNT);
+  }
+
+  void change_edge_mode(int new_mode) {
+    edge_mode = static_cast<EDGE_MODE> (new_mode % E_COUNT);
+  }
+
+  void change_triangle_mode() {
+    int current_value = triangle_mode;
+    triangle_mode = static_cast<TRIANGLE_MODE> (++current_value % T_COUNT);
+  }
+
+  View_parameter() {
+    light = true;
+    relative_light = true;
+    vertex_mode = V_SIMPLE;
+    edge_mode = E_SIMPLE;
+    triangle_mode = T_NONE;
+
+    size_vertices = 3;
+    size_edges = 2;
+
+    light_edges = 0.3;
+    light_triangles = 0.85;
+    theta = 0;
+    phi = 0;
+  }
+
+  friend std::ostream& operator<<(std::ostream& stream, const View_parameter& param) {
+    stream << param.light << " ";
+    stream << param.relative_light << " ";
+    stream << param.vertex_mode << " ";
+    stream << param.edge_mode << " ";
+    stream << param.triangle_mode << " ";
+    stream << param.size_vertices << " ";
+    stream << param.size_edges << " ";
+    stream << param.light_edges << " ";
+    stream << param.light_triangles << " ";
+    stream << param.theta << " ";
+    stream << param.phi << " ";
+    return stream;
+  }
+
+  friend std::istream& operator>>(std::istream& stream, View_parameter& param) {
+    stream >> param.light;
+    stream >> param.relative_light;
+    int a;
+    stream >> a;
+    param.vertex_mode = static_cast<VERTEX_MODE> (a % V_COUNT);
+    stream >> a;
+    param.edge_mode = static_cast<EDGE_MODE> (a % E_COUNT);
+    stream >> a;
+    param.triangle_mode = static_cast<TRIANGLE_MODE> (a % T_COUNT);
+    stream >> a;
+    stream >> param.size_vertices;
+    stream >> param.size_edges;
+    stream >> param.light_edges;
+    stream >> param.light_triangles;
+    stream >> param.theta;
+    stream >> param.phi;
+    return stream;
+  }
 };
 
-#endif /* VIEW_PARAMETER_H_ */
+#endif  // VIEW_VIEW_PARAMETER_H_
diff --git a/src/GudhUI/view/Viewer.cpp b/src/GudhUI/view/Viewer.cpp
index d8a35faf..c6c2b345 100644
--- a/src/GudhUI/view/Viewer.cpp
+++ b/src/GudhUI/view/Viewer.cpp
@@ -1,197 +1,186 @@
-/*
- * Viewer.cpp
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
  *
- *  Created on: Aug 26, 2014
- *      Author: dsalinas
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
  */
 
 #include "Viewer.h"
 #include "utils/UI_utils.h"
 
-Viewer::Viewer(QWidget* parent): QGLViewer(QGLFormat(QGL::SampleBuffers),parent),instructor(0),theta(0),phi(0){
-}
+Viewer::Viewer(QWidget* parent) : QGLViewer(QGLFormat(QGL::SampleBuffers), parent), instructor(0), theta(0), phi(0) { }
 
-void
-Viewer::set_instructor(Viewer_instructor* instructor_){
-	instructor = instructor_;
+void Viewer::set_instructor(Viewer_instructor* instructor_) {
+  instructor = instructor_;
 }
 
-void
-Viewer::show_entire_scene(){
-	this->showEntireScene();
+void Viewer::show_entire_scene() {
+  this->showEntireScene();
 }
 
-void
-Viewer::draw(){
-	instructor->give_instructions();
+void Viewer::draw() {
+  instructor->give_instructions();
 }
 
-
-void
-Viewer::set_bounding_box(const Point_3 & lower_left,const Point_3 & upper_right){
-	this->camera()->setSceneBoundingBox(
-			qglviewer::Vec(lower_left[0], lower_left[1], lower_left[2]),
-			qglviewer::Vec(upper_right[0], upper_right[1], upper_right[2])
-	);
+void Viewer::set_bounding_box(const Point_3 & lower_left, const Point_3 & upper_right) {
+  this->camera()->setSceneBoundingBox(qglviewer::Vec(lower_left[0], lower_left[1], lower_left[2]),
+                                      qglviewer::Vec(upper_right[0], upper_right[1], upper_right[2]));
 }
 
-void
-Viewer::update_GL(){
-	this->updateGL();
-
+void Viewer::update_GL() {
+  this->updateGL();
 }
 
-void
-Viewer::init_scene(){
-	this->setBackgroundColor(Qt::white);
-	::glEnable(GL_LINE_SMOOTH);
-	init_light();
+void Viewer::init_scene() {
+  this->setBackgroundColor(Qt::white);
+  ::glEnable(GL_LINE_SMOOTH);
+  init_light();
 }
 
-void
-Viewer::init_light(){
-	::glLightModeli(GL_LIGHT_MODEL_TWO_SIDE, GL_TRUE);
+void Viewer::init_light() {
+  ::glLightModeli(GL_LIGHT_MODEL_TWO_SIDE, GL_TRUE);
 }
 
-void
-Viewer::set_light(){
-	if(theta>=0 && phi >=0){
-		const GLfloat pos[4] = {(float)(sin(phi)*cos(theta)),(float)(sin(phi)*sin(theta)),(float)(cos(phi)),0.};
-		glLightfv(GL_LIGHT0, GL_POSITION, pos);
-	}
+void Viewer::set_light() {
+  if (theta >= 0 && phi >= 0) {
+    const GLfloat pos[4] = {static_cast<float> (sin(phi) * cos(theta)),
+                            static_cast<float> (sin(phi) * sin(theta)),
+                            static_cast<float> (cos(phi)), 0.};
+    glLightfv(GL_LIGHT0, GL_POSITION, pos);
+  }
 }
 
-void
-Viewer::set_light_direction(double theta_,double phi_){
-	theta = theta_;
-	phi = phi_;
+void Viewer::set_light_direction(double theta_, double phi_) {
+  theta = theta_;
+  phi = phi_;
 }
 
 /**
  * set the light in the direction of the observer
  */
-void
-Viewer::set_light_direction(){
-	theta = -1;
-	phi = -1;
+void Viewer::set_light_direction() {
+  theta = -1;
+  phi = -1;
 }
 
+void Viewer::postSelection(const QPoint& point) {
+  bool found;
 
-void
-Viewer::postSelection(const QPoint& point){
-	bool found;
+  auto vec = this->camera()->pointUnderPixel(point, found);
 
-	auto vec = this->camera()->pointUnderPixel(point,found);
-
-	if(found){
-		Point_3 position(vec[0],vec[1],vec[2]);
-		emit(click(position));
-	}
+  if (found) {
+    Point_3 position(vec[0], vec[1], vec[2]);
+    emit(click(position));
+  }
 }
 
 ////////////////////////
 // draw
 ////////////////////////
-void
-Viewer::set_size_point(double size_points){
-	::glPointSize(size_points);
-}
-
-void
-Viewer::draw_point(const Point_3& p,const Color& color,double size_points){
-	::glColor3f(color.r,color.g,color.b);
-	::glDisable(GL_LIGHTING);
-	::glEnable(GL_POINT_SMOOTH);
-	::glPointSize(size_points);
-	::glBegin(GL_POINTS);
-	::glVertex3d(p.x(), p.y(), p.z());
-	::glEnd();
-	::glDisable(GL_POINT_SMOOTH);
-}
-
-void
-Viewer::begin_draw_points(double size,bool light){
-	light?glEnable(GL_LIGHTING):glDisable(GL_LIGHTING);
-	::glEnable(GL_POINT_SMOOTH);
-	::glPointSize(size);
-	::glBegin(GL_POINTS);
-}
-
-void
-Viewer::set_color(const Color& color){
-	::glColor3f(color.r,color.g,color.b);
-}
-
-void
-Viewer::draw_points(const Point_3 & point){
-	::glVertex3d(point.x(),point.y(),point.z());
-}
-
-void
-Viewer::end_draw_points(){
-	::glEnd();
-	::glDisable(GL_POINT_SMOOTH);
-}
-
-void
-Viewer::draw_edge(const Point_3 &a,const Point_3 &b,const Color& color,double size){
-	::glColor3f(color.r,color.g,color.b);
-	::glPointSize(3.0);
-	::glLineWidth(size);
-	::glBegin(GL_LINES);
-	::glVertex3f(a.x(),a.y(),a.z());
-	::glVertex3f(b.x(),b.y(),b.z());
-	::glEnd();
-}
-
-void
-Viewer::begin_draw_edges(double size,bool light){
-	::glLineWidth(size);
-	::glPolygonMode(GL_FRONT_AND_BACK,GL_LINE);
-	::glEnable(GL_POLYGON_OFFSET_LINE);
-	::glPolygonOffset(3.0f,-3.0f);
-	light?glEnable(GL_LIGHTING):glDisable(GL_LIGHTING);
-	::glBegin(GL_LINES);
-}
-
-void
-Viewer::draw_edges(const Point_3 &a,const Point_3 &b){
-	::glVertex3f(a.x(),a.y(),a.z());
-	::glVertex3f(b.x(),b.y(),b.z());
-}
-
-void
-Viewer::end_draw_edges(){
-	::glEnd();
-}
-
-void
-Viewer::begin_draw_triangles(double size,bool light,bool transparent){
-	if(transparent){
-		::glEnable (GL_BLEND);
-		::glBlendFunc (GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);
-	}
-	::glPolygonMode(GL_FRONT_AND_BACK,GL_FILL);
-	::glEnable(GL_POLYGON_OFFSET_FILL);
-	::glPolygonOffset(3.0f,-3.0f);
-	light?glEnable(GL_LIGHTING):glDisable(GL_LIGHTING);
-	::glBegin(GL_TRIANGLES);
-}
-
-void
-Viewer::draw_triangles(const Point_3& p1,const Point_3& p2,const Point_3& p3){
-	if(!CGAL::collinear(p1,p2,p3)){
-		auto triangle_normal = CGAL::unit_normal(p1,p2,p3);
-		::glNormal3d(triangle_normal.x(),triangle_normal.y(),triangle_normal.z());
-		::glVertex3d(p1.x(),p1.y(),p1.z());
-		::glVertex3d(p2.x(),p2.y(),p2.z());
-		::glVertex3d(p3.x(),p3.y(),p3.z());
-	}
-}
-
-void
-Viewer::end_draw_triangles(){
-	::glEnd();
+
+void Viewer::set_size_point(double size_points) {
+  ::glPointSize(size_points);
+}
+
+void Viewer::draw_point(const Point_3& p, const Color& color, double size_points) {
+  ::glColor3f(color.r, color.g, color.b);
+  ::glDisable(GL_LIGHTING);
+  ::glEnable(GL_POINT_SMOOTH);
+  ::glPointSize(size_points);
+  ::glBegin(GL_POINTS);
+  ::glVertex3d(p.x(), p.y(), p.z());
+  ::glEnd();
+  ::glDisable(GL_POINT_SMOOTH);
+}
+
+void Viewer::begin_draw_points(double size, bool light) {
+  light ? glEnable(GL_LIGHTING) : glDisable(GL_LIGHTING);
+  ::glEnable(GL_POINT_SMOOTH);
+  ::glPointSize(size);
+  ::glBegin(GL_POINTS);
+}
+
+void Viewer::set_color(const Color& color) {
+  ::glColor3f(color.r, color.g, color.b);
+}
+
+void Viewer::draw_points(const Point_3 & point) {
+  ::glVertex3d(point.x(), point.y(), point.z());
+}
+
+void Viewer::end_draw_points() {
+  ::glEnd();
+  ::glDisable(GL_POINT_SMOOTH);
+}
+
+void Viewer::draw_edge(const Point_3 &a, const Point_3 &b, const Color& color, double size) {
+  ::glColor3f(color.r, color.g, color.b);
+  ::glPointSize(3.0);
+  ::glLineWidth(size);
+  ::glBegin(GL_LINES);
+  ::glVertex3f(a.x(), a.y(), a.z());
+  ::glVertex3f(b.x(), b.y(), b.z());
+  ::glEnd();
+}
+
+void Viewer::begin_draw_edges(double size, bool light) {
+  ::glLineWidth(size);
+  ::glPolygonMode(GL_FRONT_AND_BACK, GL_LINE);
+  ::glEnable(GL_POLYGON_OFFSET_LINE);
+  ::glPolygonOffset(3.0f, -3.0f);
+  light ? glEnable(GL_LIGHTING) : glDisable(GL_LIGHTING);
+  ::glBegin(GL_LINES);
+}
+
+void Viewer::draw_edges(const Point_3 &a, const Point_3 &b) {
+  ::glVertex3f(a.x(), a.y(), a.z());
+  ::glVertex3f(b.x(), b.y(), b.z());
+}
+
+void Viewer::end_draw_edges() {
+  ::glEnd();
+}
+
+void Viewer::begin_draw_triangles(double size, bool light, bool transparent) {
+  if (transparent) {
+    ::glEnable(GL_BLEND);
+    ::glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);
+  }
+  ::glPolygonMode(GL_FRONT_AND_BACK, GL_FILL);
+  ::glEnable(GL_POLYGON_OFFSET_FILL);
+  ::glPolygonOffset(3.0f, -3.0f);
+  light ? glEnable(GL_LIGHTING) : glDisable(GL_LIGHTING);
+  ::glBegin(GL_TRIANGLES);
+}
+
+void Viewer::draw_triangles(const Point_3& p1, const Point_3& p2, const Point_3& p3) {
+  if (!CGAL::collinear(p1, p2, p3)) {
+    auto triangle_normal = CGAL::unit_normal(p1, p2, p3);
+    ::glNormal3d(triangle_normal.x(), triangle_normal.y(), triangle_normal.z());
+    ::glVertex3d(p1.x(), p1.y(), p1.z());
+    ::glVertex3d(p2.x(), p2.y(), p2.z());
+    ::glVertex3d(p3.x(), p3.y(), p3.z());
+  }
+}
+
+void Viewer::end_draw_triangles() {
+  ::glEnd();
 }
 
 #include "Viewer.moc"
diff --git a/src/GudhUI/view/Viewer.h b/src/GudhUI/view/Viewer.h
index 5639aa56..276ccd3c 100644
--- a/src/GudhUI/view/Viewer.h
+++ b/src/GudhUI/view/Viewer.h
@@ -1,7 +1,36 @@
-#ifndef VIEWER_H
-#define VIEWER_H
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+#ifndef VIEW_VIEWER_H_
+#define VIEW_VIEWER_H_
+
+// Workaround for moc-qt4 not parsing boost headers
+#include <CGAL/config.h>
 
 #include <QGLViewer/qglviewer.h>
+
+#include <vector>
+
 #include "View_parameter.h"
 #include "model/Complex_typedefs.h"
 #include "Color.h"
@@ -10,87 +39,82 @@
 class Viewer_instructor;
 
 class Viewer : public QGLViewer {
-	Q_OBJECT
-
-	Viewer_instructor * instructor;
-
-	/**
-	 * light angles
-	 */
-	double theta,phi;
-	typedef Complex::GT Gudhi_kernel;
-	typedef Gudhi_kernel::Point_3 Point_3;
-public:
-	Viewer(QWidget* parent);
+  Q_OBJECT
 
-	void set_instructor(Viewer_instructor* instructor_);
+  Viewer_instructor * instructor;
 
-	void show_entire_scene();
+  /**
+   * light angles
+   */
+  double theta, phi;
+  typedef Complex::GT Gudhi_kernel;
+  typedef Gudhi_kernel::Point_3 Point_3;
 
-	void draw();
+ public:
+  Viewer(QWidget* parent);
 
+  void set_instructor(Viewer_instructor* instructor_);
 
-	void set_bounding_box(const Point_3 & lower_left,const Point_3 & upper_right);
+  void show_entire_scene();
 
-	void update_GL();
+  void draw();
 
-	void init_scene();
+  void set_bounding_box(const Point_3 & lower_left, const Point_3 & upper_right);
 
-	void init_light();
+  void update_GL();
 
-	void set_light();
+  void init_scene();
 
-	void set_light_direction(double theta,double phi);
+  void init_light();
 
-	/**
-	 * set the light in the direction of the observer
-	 */
-	void set_light_direction();
+  void set_light();
 
+  void set_light_direction(double theta, double phi);
 
-protected:
-	virtual void postSelection(const QPoint& point);
+  /**
+   * set the light in the direction of the observer
+   */
+  void set_light_direction();
 
+ protected:
+  virtual void postSelection(const QPoint& point);
 
-public:
+ public:
+  ////////////////////////
+  // draw
+  ////////////////////////
+  void set_size_point(double size_points);
 
-	////////////////////////
-	// draw
-	////////////////////////
-	void set_size_point(double size_points);
+  void set_color(const Color& color);
 
-	void set_color(const Color& color);
+  void draw_point(const Point_3& p, const Color& color, double size_points);
 
-	void draw_point(const Point_3& p,const Color& color,double size_points);
+  void begin_draw_points(double size, bool light = false);
 
-	void begin_draw_points(double size,bool light=false);
+  void draw_points(const Point_3 & point);
 
-	void draw_points(const Point_3 & point);
+  void end_draw_points();
 
-	void end_draw_points();
+  void draw_edge(const Point_3 &a, const Point_3 &b, const Color& color, double size);
 
-	void draw_edge(const Point_3 &a,const Point_3 &b,const Color& color,double size);
+  void begin_draw_edges(double size, bool light = false);
 
-	void begin_draw_edges(double size,bool light=false);
+  void draw_edges(const Point_3 &a, const Point_3 &b);
 
-	void draw_edges(const Point_3 &a,const Point_3 &b);
+  void end_draw_edges();
 
-	void end_draw_edges();
+  void begin_draw_triangles(double size, bool light, bool transparent = false);
 
-	void begin_draw_triangles(double size,bool light,bool transparent = false);
+  void draw_triangles(const Point_3& p1, const Point_3& p2, const Point_3& p3);
 
-	void draw_triangles(const Point_3& p1,const Point_3& p2,const Point_3& p3);
+  // todo remove
+  void draw_triangles(const std::vector<Point_3*>& points);
 
-	//todo remove
-	void draw_triangles(const  std::vector<Point_3*>& points);
+  void end_draw_triangles();
 
-	void end_draw_triangles();
 
-
-	signals:
-	void click(const Point_3& position);
+ signals:
+  void click(const Point_3& position);
 };
 
-
-
-#endif
+#endif  // VIEW_VIEWER_H_
diff --git a/src/GudhUI/view/Viewer_instructor.cpp b/src/GudhUI/view/Viewer_instructor.cpp
index 3cb8f152..1ddd4d8b 100644
--- a/src/GudhUI/view/Viewer_instructor.cpp
+++ b/src/GudhUI/view/Viewer_instructor.cpp
@@ -1,206 +1,192 @@
-/*
- * Viewer_instructor.cpp
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
  *
- *  Created on: Aug 26, 2014
- *      Author: dsalinas
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
  */
 
 #include <utility>
+
 #include "Viewer_instructor.h"
 #include "utils/UI_utils.h"
 #include "FirstCoordProjector.h"
 
-
 Viewer_instructor::Viewer_instructor(QWidget* parent,
-		Viewer* viewer,
-		const Complex& mesh
-):viewer_(viewer),mesh_(mesh),projector_(new FirstCoordProjector3D()){
-	viewer_->set_instructor(this);
+                                     Viewer* viewer,
+                                     const Complex& mesh
+                                     )
+    : viewer_(viewer), mesh_(mesh), projector_(new FirstCoordProjector3D()) {
+  viewer_->set_instructor(this);
+}
+
+void Viewer_instructor::initialize_bounding_box() {
+  auto pair_bounding_box = compute_bounding_box_corners();
+  viewer_->set_bounding_box(proj(pair_bounding_box.first), proj(pair_bounding_box.second));
+  viewer_->init_scene();
 }
 
+std::pair<Complex::Point, Complex::Point> Viewer_instructor::compute_bounding_box_corners() {
+  if (mesh_.empty()) {
+    return std::make_pair(Point(-1, -1, -1, 1), Point(1, 1, 1, 1));
+  } else {
+    double x_min = 1e10;
+    double y_min = 1e10;
+    double z_min = 1e10;
+    double x_max = -1e10;
+    double y_max = -1e10;
+    double z_max = -1e10;
+    for (auto vi : mesh_.vertex_range()) {
+      auto pt = proj(mesh_.point(vi));
+      x_min = (std::min)(x_min, pt.x());
+      y_min = (std::min)(y_min, pt.y());
+      z_min = (std::min)(z_min, pt.z());
 
-void
-Viewer_instructor::initialize_bounding_box(){
-	auto pair_bounding_box = compute_bounding_box_corners();
-	viewer_->set_bounding_box(proj(pair_bounding_box.first),proj(pair_bounding_box.second));
-	viewer_->init_scene();
-}
-
-std::pair<Complex::Point,Complex::Point>
-Viewer_instructor::compute_bounding_box_corners(){
-	if(mesh_.empty()){
-		return std::make_pair(Point(-1,-1,-1,1),Point(1,1,1,1));
-	}
-	else{
-		double x_min = 1e10;
-		double y_min = 1e10;
-		double z_min = 1e10;
-		double x_max = -1e10;
-		double y_max = -1e10;
-		double z_max = -1e10;
-		for( auto vi : mesh_.vertex_range())
-		{
-			auto pt = proj(mesh_.point(vi));
-			x_min = (std::min)(x_min,pt.x());
-			y_min = (std::min)(y_min,pt.y());
-			z_min = (std::min)(z_min,pt.z());
-
-			x_max = (std::max)(x_max,pt.x());
-			y_max = (std::max)(y_max,pt.y());
-			z_max = (std::max)(z_max,pt.z());
-
-		}
-		return std::make_pair(
-				Point(x_min,y_min,z_min,1.),
-				Point(x_max,y_max,z_max,1.)
-		);
-	}
+      x_max = (std::max)(x_max, pt.x());
+      y_max = (std::max)(y_max, pt.y());
+      z_max = (std::max)(z_max, pt.z());
+    }
+    return std::make_pair(Point(x_min, y_min, z_min, 1.),
+                          Point(x_max, y_max, z_max, 1.));
+  }
 }
 
-void
-Viewer_instructor::show_entire_scene(){
-	viewer_->show_entire_scene();
+void Viewer_instructor::show_entire_scene() {
+  viewer_->show_entire_scene();
 }
 
-const qglviewer::Camera*
-Viewer_instructor::camera() const{
-	return viewer_->camera();
+const qglviewer::Camera* Viewer_instructor::camera() const {
+  return viewer_->camera();
 }
 
 int
-Viewer_instructor::width() const{
-	return viewer_->width();
+Viewer_instructor::width() const {
+  return viewer_->width();
 }
+
 int
-Viewer_instructor::height() const{
-	return viewer_->height();
+Viewer_instructor::height() const {
+  return viewer_->height();
 }
 
 /**
  * to change display parameters
  */
-View_parameter&
-Viewer_instructor::view_params(){
-	return view_params_;
+View_parameter& Viewer_instructor::view_params() {
+  return view_params_;
 }
 
-
 void
-Viewer_instructor::give_instructions(){
-	if(view_params_.relative_light)
-		viewer_->set_light_direction();
-	else
-		viewer_->set_light_direction(view_params_.theta,view_params_.phi);
-	viewer_->set_light();
-
-	if (view_params_.edge_mode) draw_edges();
-	if (view_params_.triangle_mode)	draw_triangles();
-	if (view_params_.vertex_mode) draw_points();
+Viewer_instructor::give_instructions() {
+  if (view_params_.relative_light)
+    viewer_->set_light_direction();
+  else
+    viewer_->set_light_direction(view_params_.theta, view_params_.phi);
+  viewer_->set_light();
 
+  if (view_params_.edge_mode) draw_edges();
+  if (view_params_.triangle_mode) draw_triangles();
+  if (view_params_.vertex_mode) draw_points();
 }
 
-void
-Viewer_instructor::draw_edges(){
-	viewer_->begin_draw_edges(view_params_.size_edges,false);
+void Viewer_instructor::draw_edges() {
+  viewer_->begin_draw_edges(view_params_.size_edges, false);
 
-	for(auto edge : mesh_.edge_range()){
-		set_color_edge(edge);
-		const Point& a = mesh_.point(mesh_.first_vertex(edge));
-		const Point& b = mesh_.point(mesh_.second_vertex(edge)) ;
-		viewer_->draw_edges(proj(a),proj(b));
-	}
+  for (auto edge : mesh_.edge_range()) {
+    set_color_edge(edge);
+    const Point& a = mesh_.point(mesh_.first_vertex(edge));
+    const Point& b = mesh_.point(mesh_.second_vertex(edge));
+    viewer_->draw_edges(proj(a), proj(b));
+  }
 
-	viewer_->end_draw_edges();
+  viewer_->end_draw_edges();
 }
 
-void
-Viewer_instructor::draw_triangles(){
-	const double size_triangles = 1.0;
-	viewer_->begin_draw_triangles(size_triangles,view_params_.light);
-
-	for(const auto& fit : mesh_.triangle_range()) {
-		set_color_triangle(fit);
-		if(view_params_.triangle_mode){
-			auto fit_it  = fit.begin();
-			const Point& p1 = mesh_.point(*fit_it);
-			const Point& p2 = mesh_.point(*(++fit_it));
-			const Point& p3 = mesh_.point(*(++fit_it));
-			viewer_->draw_triangles(proj(p1),proj(p2),proj(p3));
-		}
-	}
-	viewer_->end_draw_triangles();
-}
+void Viewer_instructor::draw_triangles() {
+  const double size_triangles = 1.0;
+  viewer_->begin_draw_triangles(size_triangles, view_params_.light);
 
-void
-Viewer_instructor::draw_points(){
-	viewer_->begin_draw_points(	view_params_.size_vertices);
-	for( auto vi : mesh_.vertex_range())
-	{
-		viewer_->set_size_point(view_params_.size_vertices);
-		set_color_vertex(vi);
-		viewer_->draw_points(proj(mesh_.point(vi)));
-	}
-	viewer_->end_draw_points();
+  for (const auto& fit : mesh_.triangle_range()) {
+    set_color_triangle(fit);
+    if (view_params_.triangle_mode) {
+      auto fit_it = fit.begin();
+      const Point& p1 = mesh_.point(*fit_it);
+      const Point& p2 = mesh_.point(*(++fit_it));
+      const Point& p3 = mesh_.point(*(++fit_it));
+      viewer_->draw_triangles(proj(p1), proj(p2), proj(p3));
+    }
+  }
+  viewer_->end_draw_triangles();
 }
 
-
-void
-Viewer_instructor::draw_edge(const Point&,const Point&){
-
+void Viewer_instructor::draw_points() {
+  viewer_->begin_draw_points(view_params_.size_vertices);
+  for (auto vi : mesh_.vertex_range()) {
+    viewer_->set_size_point(view_params_.size_vertices);
+    set_color_vertex(vi);
+    viewer_->draw_points(proj(mesh_.point(vi)));
+  }
+  viewer_->end_draw_points();
 }
 
-void
-Viewer_instructor::draw_point(const Point&){
-
-}
+void Viewer_instructor::draw_edge(const Point&, const Point&) { }
 
+void Viewer_instructor::draw_point(const Point&) { }
 
 /**
  * set the right color of vertex/edge/triangle considering the view_params choice
  */
-void
-Viewer_instructor::set_color_vertex(Vertex_handle vh){
-	viewer_->set_color(Color(view_params_.light_edges,view_params_.light_edges,view_params_.light_edges));
+void Viewer_instructor::set_color_vertex(Vertex_handle vh) {
+  viewer_->set_color(Color(view_params_.light_edges, view_params_.light_edges, view_params_.light_edges));
 }
 
-void
-Viewer_instructor::set_color_edge(Edge_handle eh)	{
-	viewer_->set_color(Color(view_params_.light_edges,view_params_.light_edges,view_params_.light_edges));
+void Viewer_instructor::set_color_edge(Edge_handle eh) {
+  viewer_->set_color(Color(view_params_.light_edges, view_params_.light_edges, view_params_.light_edges));
 }
 
-void
-Viewer_instructor::set_color_triangle(const Simplex_handle& triangle){
-	viewer_->set_color(Color(view_params_.light_triangles,view_params_.light_triangles,view_params_.light_triangles));
+void Viewer_instructor::set_color_triangle(const Simplex& triangle) {
+  viewer_->set_color(Color(view_params_.light_triangles, view_params_.light_triangles, view_params_.light_triangles));
 }
 
-
 Viewer_instructor::Point_3
-Viewer_instructor::proj(const Point& p) const{
-	return (*projector_)(p);
+Viewer_instructor::proj(const Point& p) const {
+  return (*projector_)(p);
 }
 
-
-void
-Viewer_instructor::sceneChanged(){
-	UIDBG("sceneChanged");
-	viewer_->update_GL();
+void Viewer_instructor::sceneChanged() {
+  UIDBG("sceneChanged");
+  viewer_->update_GL();
 }
 
-void
-Viewer_instructor::change_draw_vertices(){
-	view_params_.change_vertex_mode();
+void Viewer_instructor::change_draw_vertices() {
+  view_params_.change_vertex_mode();
 }
-void
-Viewer_instructor::change_draw_edges(){
-	view_params_.change_edge_mode();
+
+void Viewer_instructor::change_draw_edges() {
+  view_params_.change_edge_mode();
 }
-void
-Viewer_instructor::change_draw_triangles(){
-	view_params_.change_triangle_mode();
+
+void Viewer_instructor::change_draw_triangles() {
+  view_params_.change_triangle_mode();
 }
-void
-Viewer_instructor::change_light(){
-	view_params_.light =! view_params_.light ;
+
+void Viewer_instructor::change_light() {
+  view_params_.light = !view_params_.light;
 }
 
 #include "Viewer_instructor.moc"
diff --git a/src/GudhUI/view/Viewer_instructor.h b/src/GudhUI/view/Viewer_instructor.h
index 9a2a236b..82c8e346 100644
--- a/src/GudhUI/view/Viewer_instructor.h
+++ b/src/GudhUI/view/Viewer_instructor.h
@@ -1,15 +1,40 @@
-#ifndef VIEWER_INSTRUCTOR_H
-#define VIEWER_INSTRUCTOR_H
+/* This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+#ifndef VIEW_VIEWER_INSTRUCTOR_H_
+#define VIEW_VIEWER_INSTRUCTOR_H_
 
 // todo do a viewer instructor that have directely a pointer to a QGLviewer and buffer ot not triangles
 
-
-#include <memory>
+// Workaround for moc-qt4 not parsing boost headers
+#include <CGAL/config.h>
 
 #include <QFileDialog>
 #include <QKeyEvent>
 #include <QGLViewer/camera.h>
 
+#include <memory>
+#include <utility>  // for pair<>
 
 #include "model/Complex_typedefs.h"
 
@@ -20,89 +45,73 @@
 class Viewer;
 class Viewer_parameter;
 
-class Viewer_instructor : public QWidget{
-	Q_OBJECT
-
-	typedef Geometry_trait::Point_3 Point_3;
-	typedef Complex::Point Point;
-	typedef Complex::Vertex_handle Vertex_handle;
-	typedef Complex::Edge_handle Edge_handle;
-	typedef Complex::Simplex_handle Simplex_handle;
-
-
-	Viewer* viewer_;
-	View_parameter view_params_;
-	const Complex& mesh_;
-	std::unique_ptr<Projector3D> projector_;
-
-
-public:
-
-	Viewer_instructor(QWidget* parent,
-			Viewer* viewer,
-			const Complex& mesh
-	);
-
-
-	void initialize_bounding_box();
-
-	std::pair<Point,Point> compute_bounding_box_corners();
-
-	void show_entire_scene();
-
-	const qglviewer::Camera* camera() const;
-
-	int width() const;
-	int height() const;
-
-	/**
-	 * to change display parameters
-	 */
-	View_parameter& view_params();
+class Viewer_instructor : public QWidget {
+  Q_OBJECT
 
+  typedef Geometry_trait::Point_3 Point_3;
+  typedef Complex::Point Point;
+  typedef Complex::Vertex_handle Vertex_handle;
+  typedef Complex::Edge_handle Edge_handle;
+  typedef Complex::Simplex Simplex;
 
-public:
+  Viewer* viewer_;
+  View_parameter view_params_;
+  const Complex& mesh_;
+  std::unique_ptr<Projector3D> projector_;
 
-	/**
-	 * gives instructions to the viewer
-	 */
-	void give_instructions();
+ public:
+  Viewer_instructor(QWidget* parent, Viewer* viewer, const Complex& mesh);
 
-	void draw_edges();
-	void draw_triangles();
-	void draw_points();
+  void initialize_bounding_box();
 
+  std::pair<Point, Point> compute_bounding_box_corners();
 
-	void draw_edge(const Point&,const Point&);
+  void show_entire_scene();
 
-	void draw_point(const Point&);
+  const qglviewer::Camera* camera() const;
 
+  int width() const;
+  int height() const;
 
-	/**
-	 * set the right color of vertex/edge/triangle considering the view_params choice
-	 */
-	void set_color_vertex(Vertex_handle vh);
-	void set_color_edge(Edge_handle eh);
+  /**
+   * to change display parameters
+   */
+  View_parameter& view_params();
 
-	void set_color_triangle(const Simplex_handle& triangle);
+ public:
+  /**
+   * gives instructions to the viewer
+   */
+  void give_instructions();
 
-private:
-	/**
-	 * Projection to 3D needed for the viewer.
-	 */
-	Point_3 proj(const Point& p) const;
+  void draw_edges();
+  void draw_triangles();
+  void draw_points();
 
-	public slots :
+  void draw_edge(const Point&, const Point&);
 
-	void sceneChanged();
+  void draw_point(const Point&);
 
-	void change_draw_vertices();
-	void change_draw_edges();
-	void change_draw_triangles();
-	void change_light();
+  /**
+   * set the right color of vertex/edge/triangle considering the view_params choice
+   */
+  void set_color_vertex(Vertex_handle vh);
+  void set_color_edge(Edge_handle eh);
 
+  void set_color_triangle(const Simplex& triangle);
 
+ private:
+  /**
+   * Projection to 3D needed for the viewer.
+   */
+  Point_3 proj(const Point& p) const;
 
+ public slots:
+  void sceneChanged();
+  void change_draw_vertices();
+  void change_draw_edges();
+  void change_draw_triangles();
+  void change_light();
 };
 
-#endif //VIEWER_INSTRUCTOR_H
+#endif  // VIEW_VIEWER_INSTRUCTOR_H_
diff --git a/src/Hasse_complex/example/CMakeLists.txt b/src/Hasse_complex/example/CMakeLists.txt
deleted file mode 100644
index 564df49d..00000000
--- a/src/Hasse_complex/example/CMakeLists.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-cmake_minimum_required(VERSION 2.6)
-project(GUDHIHasseComplexExample)
-
-add_executable ( hasse_complex_from_simplex_tree hasse_complex_from_simplex_tree.cpp )
-add_test(hasse_complex_from_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/hasse_complex_from_simplex_tree)
diff --git a/src/Hasse_complex/example/hasse_complex_from_simplex_tree.cpp b/src/Hasse_complex/example/hasse_complex_from_simplex_tree.cpp
deleted file mode 100644
index 1de43ab7..00000000
--- a/src/Hasse_complex/example/hasse_complex_from_simplex_tree.cpp
+++ /dev/null
@@ -1,124 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Vincent Rouvreau
- *
- *    Copyright (C) 2014  INRIA Saclay (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <iostream>
-#include <ctime>
-#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Simplex_tree.h"
-
-using namespace Gudhi;
-
-typedef std::vector< Vertex_handle > typeVectorVertex;
-typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
-typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
-typedef Simplex_tree<> typeST;
-
-int main(int argc, char * const argv[]) {
-  // TEST OF INSERTION
-  std::cout << "********************************************************************" << std::endl;
-  std::cout << "TEST OF INSERTION" << std::endl;
-  typeST st;
-
-  // ++ FIRST
-  std::cout << "   - INSERT (2,1,0)" << std::endl;
-  typeVectorVertex SimplexVector1;
-  SimplexVector1.push_back(2);
-  SimplexVector1.push_back(1);
-  SimplexVector1.push_back(0);
-  st.insert_simplex_and_subfaces(SimplexVector1, 0.3);
-
-  // ++ SECOND
-  std::cout << "   - INSERT 3" << std::endl;
-  typeVectorVertex SimplexVector2;
-  SimplexVector2.push_back(3);
-  st.insert_simplex_and_subfaces(SimplexVector2, 0.1);
-
-  // ++ THIRD
-  std::cout << "   - INSERT (0,3)" << std::endl;
-  typeVectorVertex SimplexVector3;
-  SimplexVector3.push_back(3);
-  SimplexVector3.push_back(0);
-  st.insert_simplex_and_subfaces(SimplexVector3, 0.2);
-
-  // ++ FOURTH
-  std::cout << "   - INSERT (1,0) (already inserted)" << std::endl;
-  typeVectorVertex SimplexVector4;
-  SimplexVector4.push_back(1);
-  SimplexVector4.push_back(0);
-  st.insert_simplex_and_subfaces(SimplexVector4, 0.2);
-
-  // ++ FIFTH
-  std::cout << "   - INSERT (3,4,5)" << std::endl;
-  typeVectorVertex SimplexVector5;
-  SimplexVector5.push_back(3);
-  SimplexVector5.push_back(4);
-  SimplexVector5.push_back(5);
-  st.insert_simplex_and_subfaces(SimplexVector5, 0.3);
-
-  // ++ SIXTH
-  std::cout << "   - INSERT (0,1,6,7)" << std::endl;
-  typeVectorVertex SimplexVector6;
-  SimplexVector6.push_back(0);
-  SimplexVector6.push_back(1);
-  SimplexVector6.push_back(6);
-  SimplexVector6.push_back(7);
-  st.insert_simplex_and_subfaces(SimplexVector6, 0.4);
-
-  /* Inserted simplex:         */
-  /*    1   6                  */
-  /*    o---o                  */
-  /*   /X\7/      4            */
-  /*  o---o---o---o            */
-  /*  2   0   3\X/             */
-  /*            o              */
-  /*            5              */
-
-  /* In other words:          */
-  /*   A facet [2,1,0]        */
-  /*   An edge [0,3]          */
-  /*   A facet [3,4,5]        */
-  /*   A cell  [0,1,6,7]      */
-  /*   A cell  [4,5,8,9]      */
-  /*   A facet [9,10,11]      */
-  /*   An edge [11,6]         */
-  /*   An edge [10,12,2]      */
-
-  // ++ GENERAL VARIABLE SET
-  st.set_filtration(0.4); // Max filtration value
-  st.set_dimension(3); // Max dimension = 3 -> (0,1,6,7)
-
-  std::cout << "The complex contains " << st.num_simplices() << " simplices - " << st.num_vertices() << " vertices " << std::endl;
-  std::cout << "   - dimension " << st.dimension() << "   - filtration " << st.filtration() << std::endl;
-  std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
-  std::cout << "**************************************************************" << std::endl;
-
-  for( auto f_simplex : st.filtration_simplex_range() )
-  {
-    std::cout << "   " << "[" << st.filtration(f_simplex) << "] ";
-    for( auto vertex : st.simplex_vertex_range(f_simplex) )
-    {
-      std::cout << (int)vertex;
-    }
-  }
-
-  return 0;
-}
diff --git a/src/Hasse_complex/include/gudhi/Hasse_complex.h b/src/Hasse_complex/include/gudhi/Hasse_complex.h
index 427d9916..67079687 100644
--- a/src/Hasse_complex/include/gudhi/Hasse_complex.h
+++ b/src/Hasse_complex/include/gudhi/Hasse_complex.h
@@ -1,208 +1,234 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       Clément Maria
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-
-#ifndef GUDHI_HASSE_DIAGRAM_H
-#define GUDHI_HASSE_DIAGRAM_H
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       Clément Maria
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef HASSE_COMPLEX_H_
+#define HASSE_COMPLEX_H_
 
-#include <algorithm>
 #include <boost/iterator/counting_iterator.hpp>
 
-namespace Gudhi{
+#include <algorithm>
+#include <utility>  // for pair
+#include <vector>
+
+namespace Gudhi {
 
 template < class HasseCpx >
-struct Hasse_simplex 
-{
-//Complex_ds must verify that cpx->key(sh) is the order of sh in the filtration
+struct Hasse_simplex {
+  // Complex_ds must verify that cpx->key(sh) is the order of sh in the filtration
+
   template< class Complex_ds >
-  Hasse_simplex ( Complex_ds &                        cpx
-                , typename Complex_ds::Simplex_handle sh )
-  : key_(cpx.key(sh))
-  , filtration_(cpx.filtration(sh))
-  , boundary_()
-  {
-    boundary_.reserve(cpx.dimension(sh)+1);
-    for( auto b_sh : cpx.boundary_simplex_range(sh) )
-    { boundary_.push_back( cpx.key(b_sh) ); }
-  }
-
-  Hasse_simplex ( typename HasseCpx::Simplex_key key
+  Hasse_simplex(Complex_ds & cpx
+                , typename Complex_ds::Simplex_handle sh)
+      : key_(cpx.key(sh))
+      , filtration_(cpx.filtration(sh))
+      , boundary_() {
+    boundary_.reserve(cpx.dimension(sh) + 1);
+    for (auto b_sh : cpx.boundary_simplex_range(sh)) {
+      boundary_.push_back(cpx.key(b_sh));
+    }
+  }
+
+  Hasse_simplex(typename HasseCpx::Simplex_key key
                 , typename HasseCpx::Filtration_value fil
                 , std::vector<typename HasseCpx::Simplex_handle> boundary)
-  : key_(key)
-  , filtration_(fil)
-  , boundary_(boundary) {}
+      : key_(key)
+      , filtration_(fil)
+      , boundary_(boundary) { }
 
-  typename HasseCpx::Simplex_key                 key_;
-  typename HasseCpx::Filtration_value            filtration_;
+  typename HasseCpx::Simplex_key key_;
+  typename HasseCpx::Filtration_value filtration_;
   std::vector<typename HasseCpx::Simplex_handle> boundary_;
 };
 
-
-
-/** \brief Data structure representing a Hasse diagram, i.e. 
-  * a complex where all codimension 1 incidence 
-  * relations are explicitly encoded.
-  *
-  * \implements FilteredComplex
-  * \ingroup simplex_tree
-  */
-template < typename FiltrationValue     = double
-         , typename SimplexKey          = int   
-         , typename VertexHandle        = int 
-         >
-class Hasse_complex 
-{
-public:
-
-  typedef Hasse_simplex<Hasse_complex>         Hasse_simp;
-  typedef FiltrationValue                      Filtration_value;
-  typedef SimplexKey                           Simplex_key;
-  typedef int                                  Simplex_handle; //index in vector complex_
-
-  typedef boost::counting_iterator< Simplex_handle >          Filtration_simplex_iterator;
-  typedef boost::iterator_range<Filtration_simplex_iterator>  Filtration_simplex_range;  
-
-  typedef typename std::vector< Simplex_handle >::iterator    Boundary_simplex_iterator;
-  typedef boost::iterator_range<Boundary_simplex_iterator>    Boundary_simplex_range;  
-
-  typedef typename std::vector< Simplex_handle >::iterator    Skeleton_simplex_iterator;
-  typedef boost::iterator_range< Skeleton_simplex_iterator >  Skeleton_simplex_range;
-
-
-/*  only dimension 0 skeleton_simplex_range(...) */
-  Skeleton_simplex_range skeleton_simplex_range( int dim = 0 ) {
-    if(dim != 0) { std::cerr << "Dimension must be 0 \n"; }
-    return Skeleton_simplex_range(vertices_.begin(),vertices_.end());
+/** \private 
+ * \brief Data structure representing a Hasse diagram, i.e. 
+ * a complex where all codimension 1 incidence 
+ * relations are explicitly encoded.
+ *
+ * \implements FilteredComplex
+ * \ingroup simplex_tree
+ */
+template < typename FiltrationValue = double
+, typename SimplexKey = int
+, typename VertexHandle = int
+>
+class Hasse_complex {
+ public:
+  typedef Hasse_simplex<Hasse_complex> Hasse_simp;
+  typedef FiltrationValue Filtration_value;
+  typedef SimplexKey Simplex_key;
+  typedef int Simplex_handle;  // index in vector complex_
+
+  typedef boost::counting_iterator< Simplex_handle > Filtration_simplex_iterator;
+  typedef boost::iterator_range<Filtration_simplex_iterator> Filtration_simplex_range;
+
+  typedef typename std::vector< Simplex_handle >::iterator Boundary_simplex_iterator;
+  typedef boost::iterator_range<Boundary_simplex_iterator> Boundary_simplex_range;
+
+  typedef typename std::vector< Simplex_handle >::iterator Skeleton_simplex_iterator;
+  typedef boost::iterator_range< Skeleton_simplex_iterator > Skeleton_simplex_range;
+
+  /*  only dimension 0 skeleton_simplex_range(...) */
+  Skeleton_simplex_range skeleton_simplex_range(int dim = 0) {
+    if (dim != 0) {
+      std::cerr << "Dimension must be 0 \n";
+    }
+    return Skeleton_simplex_range(vertices_.begin(), vertices_.end());
   }
 
   template < class Complex_ds >
   Hasse_complex(Complex_ds & cpx)
-  : complex_()
-  , vertices_()
-  , threshold_(cpx.filtration())
-  , num_vertices_()
-  , dim_max_(cpx.dimension())
-  {
+      : complex_()
+      , vertices_()
+      , threshold_(cpx.filtration())
+      , num_vertices_()
+      , dim_max_(cpx.dimension()) {
     complex_.reserve(cpx.num_simplices());
     int idx = 0;
-    for(auto cpx_sh : cpx.filtration_simplex_range())
-    { 
-      complex_.push_back(Hasse_simp(cpx,cpx_sh)); 
-      if(dimension(idx) == 0) { vertices_.push_back(idx); } 
-      ++idx; 
+    for (auto cpx_sh : cpx.filtration_simplex_range()) {
+      complex_.push_back(Hasse_simp(cpx, cpx_sh));
+      if (dimension(idx) == 0) {
+        vertices_.push_back(idx);
+      }
+      ++idx;
     }
   }
 
   Hasse_complex()
-  : complex_()
-  , vertices_()
-  , threshold_(0)
-  , num_vertices_(0)
-  , dim_max_(-1) {}
-
-  size_t num_simplices() { return complex_.size(); }
+      : complex_()
+      , vertices_()
+      , threshold_(0)
+      , num_vertices_(0)
+      , dim_max_(-1) { }
+
+  size_t num_simplices() {
+    return complex_.size();
+  }
 
-  Filtration_simplex_range filtration_simplex_range() 
-  { return Filtration_simplex_range( Filtration_simplex_iterator(0)
-                                   , Filtration_simplex_iterator(complex_.size()) ); }
+  Filtration_simplex_range filtration_simplex_range() {
+    return Filtration_simplex_range(Filtration_simplex_iterator(0)
+                                    , Filtration_simplex_iterator(complex_.size()));
+  }
 
-  Simplex_key key( Simplex_handle sh ) { return complex_[sh].key_; }
+  Simplex_key key(Simplex_handle sh) {
+    return complex_[sh].key_;
+  }
 
-  Simplex_key null_key() { return -1; }
+  Simplex_key null_key() {
+    return -1;
+  }
 
-  Simplex_handle simplex( Simplex_key key ) 
-  {
-    if(key == null_key()) return null_simplex();
+  Simplex_handle simplex(Simplex_key key) {
+    if (key == null_key()) return null_simplex();
     return key;
   }
 
-  Simplex_handle null_simplex() { return -1; }
+  Simplex_handle null_simplex() {
+    return -1;
+  }
 
-  Filtration_value filtration( Simplex_handle sh ) {
-    if( sh == null_simplex() ) { return filtration(); }
+  Filtration_value filtration(Simplex_handle sh) {
+    if (sh == null_simplex()) {
+      return filtration();
+    }
     return complex_[sh].filtration_;
   }
 
-  Filtration_value filtration() { return threshold_; }
+  Filtration_value filtration() {
+    return threshold_;
+  }
+
+  int dimension(Simplex_handle sh) {
+    if (complex_[sh].boundary_.empty()) return 0;
+    return complex_[sh].boundary_.size() - 1;
+  }
 
-  int dimension ( Simplex_handle sh ) { 
-    if(complex_[sh].boundary_.empty()) return 0;
-    return complex_[sh].boundary_.size()-1; 
+  int dimension() {
+    return dim_max_;
   }
-  int dimension () { return dim_max_; }
 
-  std::pair<Simplex_handle,Simplex_handle> endpoints( Simplex_handle sh ) 
-  { return std::pair<Simplex_handle,Simplex_handle>( complex_[sh].boundary_[0]
-                                                   , complex_[sh].boundary_[1] ) ;}
+  std::pair<Simplex_handle, Simplex_handle> endpoints(Simplex_handle sh) {
+    return std::pair<Simplex_handle, Simplex_handle>(complex_[sh].boundary_[0]
+                                                     , complex_[sh].boundary_[1]);
+  }
 
-  void assign_key( Simplex_handle sh, Simplex_key key) { complex_[sh].key_ = key; }
+  void assign_key(Simplex_handle sh, Simplex_key key) {
+    complex_[sh].key_ = key;
+  }
 
-  Boundary_simplex_range boundary_simplex_range ( Simplex_handle sh ) 
-  { return Boundary_simplex_range( complex_[sh].boundary_.begin()
-                                 , complex_[sh].boundary_.end() ); }
+  Boundary_simplex_range boundary_simplex_range(Simplex_handle sh) {
+    return Boundary_simplex_range(complex_[sh].boundary_.begin()
+                                  , complex_[sh].boundary_.end());
+  }
 
-  void display_simplex(Simplex_handle sh)
-  {
+  void display_simplex(Simplex_handle sh) {
     std::cout << dimension(sh) << "  ";
-    for(auto sh_b : boundary_simplex_range(sh)) std::cout << sh_b << " ";
+    for (auto sh_b : boundary_simplex_range(sh)) std::cout << sh_b << " ";
     std::cout << "  " << filtration(sh) << "         key=" << key(sh);
   }
 
-  void initialize_filtration()
-  {
+  void initialize_filtration() {
     Simplex_key key = 0;
-    for(auto & h_simp : complex_) { h_simp.key_ = key; ++key; }
+    for (auto & h_simp : complex_) {
+      h_simp.key_ = key;
+      ++key;
+    }
   }
 
-  std::vector< Hasse_simp >   complex_;
+  std::vector< Hasse_simp > complex_;
   std::vector<Simplex_handle> vertices_;
-  Filtration_value            threshold_;
-  size_t                      num_vertices_;
-  int                         dim_max_;
+  Filtration_value threshold_;
+  size_t num_vertices_;
+  int dim_max_;
 };
 
 template< typename T1, typename T2, typename T3 >
-std::istream& operator>> ( std::istream                & is 
-                         , Hasse_complex< T1, T2, T3 > & hcpx )
-{
+std::istream& operator>>(std::istream & is
+                         , Hasse_complex< T1, T2, T3 > & hcpx) {
   assert(hcpx.num_simplices() == 0);
 
   size_t num_simp;
   is >> num_simp;
-  hcpx.complex_.reserve(num_simp); 
-
-  std::vector< typename Hasse_complex<T1,T2,T3>::Simplex_key >  boundary;
-  typename Hasse_complex<T1,T2,T3>::Filtration_value            fil;
-  typename Hasse_complex<T1,T2,T3>::Filtration_value            max_fil = 0 ;
-  int                                                           max_dim = -1;
-  int                                                           key     = 0 ;
-  while(read_hasse_simplex( is, boundary, fil )) //read all simplices in the file as a list of vertices
-  {
-    //insert every simplex in the simplex tree
-    hcpx.complex_.push_back( Hasse_simplex< Hasse_complex<T1,T2,T3> >(key,fil,boundary));
-
-    if(max_dim < hcpx.dimension(key)) { max_dim = hcpx.dimension(key); }
-    if(hcpx.dimension(key) == 0)      { hcpx.vertices_.push_back(key); }
-    if(max_fil < fil)                 { max_fil = fil;                 }
+  hcpx.complex_.reserve(num_simp);
+
+  std::vector< typename Hasse_complex<T1, T2, T3>::Simplex_key > boundary;
+  typename Hasse_complex<T1, T2, T3>::Filtration_value fil;
+  typename Hasse_complex<T1, T2, T3>::Filtration_value max_fil = 0;
+  int max_dim = -1;
+  int key = 0;
+  // read all simplices in the file as a list of vertices
+  while (read_hasse_simplex(is, boundary, fil)) {
+    // insert every simplex in the simplex tree
+    hcpx.complex_.push_back(Hasse_simplex< Hasse_complex<T1, T2, T3> >(key, fil, boundary));
+
+    if (max_dim < hcpx.dimension(key)) {
+      max_dim = hcpx.dimension(key);
+    }
+    if (hcpx.dimension(key) == 0) {
+      hcpx.vertices_.push_back(key);
+    }
+    if (max_fil < fil) {
+      max_fil = fil;
+    }
 
     ++key;
     boundary.clear();
@@ -214,6 +240,6 @@ std::istream& operator>> ( std::istream                & is
   return is;
 }
 
-}  // namespace GUDHI
+}  // namespace Gudhi
 
-#endif // GUDHI_HASSE_DIAGRAM_H
+#endif  // HASSE_COMPLEX_H_
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index 9487cce6..50d10025 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -2,39 +2,47 @@ cmake_minimum_required(VERSION 2.6)
 project(GUDHIExPersCohom)
 
 # problem with Visual Studio link on Boost program_options
-if (NOT MSVC)
-   add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp)
-   target_link_libraries(persistence_from_simple_simplex_tree ${Boost_SYSTEM_LIBRARY})
+add_definitions( -DBOOST_ALL_NO_LIB )
+add_definitions( -DBOOST_ALL_DYN_LINK )
 
-   add_executable(rips_persistence rips_persistence.cpp)
-   target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
-   
-   add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 3 -m 100)
-   
-   add_executable(persistence_from_file persistence_from_file.cpp)
-   target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
-   add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 2 -m 0)
-   add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100)
-   
-   if(GMPXX_FOUND AND GMP_FOUND)
-      message("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
-      message("GMP_LIBRARIES = ${GMP_LIBRARIES}")
-   
-      add_executable(rips_multifield_persistence rips_multifield_persistence.cpp )
-      target_link_libraries(rips_multifield_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
-      add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 71 -m 100)
+add_executable(plain_homology plain_homology.cpp)
+target_link_libraries(plain_homology ${Boost_SYSTEM_LIBRARY})
+add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology)
+
+add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp)
+target_link_libraries(persistence_from_simple_simplex_tree ${Boost_SYSTEM_LIBRARY})
+add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0)
+
+add_executable(rips_persistence rips_persistence.cpp)
+target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
    
-      add_executable ( performance_rips_persistence performance_rips_persistence.cpp )
-      target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 3 -m 100)
    
-      if(CGAL_FOUND)
-         # uncomment to display debug traces
-         # add_definitions(-DDEBUG_TRACES)
-         add_executable(alpha_shapes_persistence alpha_shapes_persistence.cpp)
-         target_link_libraries(alpha_shapes_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY})
-         add_test(alpha_shapes_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5)
-         #add_test(alpha_shapes_persistence_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100)
-      endif()
+add_executable(persistence_from_file persistence_from_file.cpp)
+target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 2 -m 0)
+add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100)
    
+if(GMPXX_FOUND AND GMP_FOUND)
+   message("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
+   message("GMP_LIBRARIES = ${GMP_LIBRARIES}")
+
+   add_executable(rips_multifield_persistence rips_multifield_persistence.cpp )
+   target_link_libraries(rips_multifield_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+   add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 71 -m 100)
+
+   add_executable ( performance_rips_persistence performance_rips_persistence.cpp )
+   target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+
+   if(CGAL_FOUND)
+     if (CMAKE_BUILD_TYPE MATCHES Debug)
+       # For programs to be more verbose
+       add_definitions(-DDEBUG_TRACES)
+     endif()
+     add_executable(alpha_shapes_persistence alpha_shapes_persistence.cpp)
+     target_link_libraries(alpha_shapes_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY})
+     add_test(alpha_shapes_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5)
+     #add_test(alpha_shapes_persistence_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100)
    endif()
+   
 endif()
diff --git a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp b/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp
index 3a50c84c..6d5eebcf 100644
--- a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp
@@ -1,24 +1,29 @@
- /*    This file is part of the Gudhi Library. The Gudhi library
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++
-  *    library for computational topology.
-  *
-  *    Author(s):       Vincent Rouvreau
-  *
-  *    Copyright (C) 2014  INRIA Saclay (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2014  INRIA Saclay (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <boost/variant.hpp>
 
 #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
 #include <CGAL/Delaunay_triangulation_3.h>
@@ -27,36 +32,37 @@
 
 #include <fstream>
 #include <cmath>
-
-#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Simplex_tree.h"
-#include "gudhi/Persistent_cohomology.h"
-#include <boost/variant.hpp>
+#include <string>
+#include <tuple>
+#include <map>
+#include <utility>
+#include <list>
+#include <vector>
 
 using namespace Gudhi;
 using namespace Gudhi::persistent_cohomology;
 
 // Alpha_shape_3 templates type definitions
 typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel;
-typedef CGAL::Alpha_shape_vertex_base_3<Kernel>             Vb;
-typedef CGAL::Alpha_shape_cell_base_3<Kernel>               Fb;
-typedef CGAL::Triangulation_data_structure_3<Vb,Fb>         Tds;
-typedef CGAL::Delaunay_triangulation_3<Kernel,Tds>          Triangulation_3;
-typedef CGAL::Alpha_shape_3<Triangulation_3>                Alpha_shape_3;
+typedef CGAL::Alpha_shape_vertex_base_3<Kernel> Vb;
+typedef CGAL::Alpha_shape_cell_base_3<Kernel> Fb;
+typedef CGAL::Triangulation_data_structure_3<Vb, Fb> Tds;
+typedef CGAL::Delaunay_triangulation_3<Kernel, Tds> Triangulation_3;
+typedef CGAL::Alpha_shape_3<Triangulation_3> Alpha_shape_3;
 
 // From file type definition
-typedef Kernel::Point_3                                     Point_3;
+typedef Kernel::Point_3 Point_3;
 
 // filtration with alpha values needed type definition
 typedef Alpha_shape_3::FT Alpha_value_type;
-typedef CGAL::Object      Object;
+typedef CGAL::Object Object;
 typedef CGAL::Dispatch_output_iterator<
-  CGAL::cpp11::tuple<Object, Alpha_value_type>,
-  CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >, std::back_insert_iterator< std::vector<Alpha_value_type> >
-                     > > Dispatch;
-typedef Alpha_shape_3::Cell_handle   Cell_handle;
-typedef Alpha_shape_3::Facet         Facet;
-typedef Alpha_shape_3::Edge          Edge_3;
+CGAL::cpp11::tuple<Object, Alpha_value_type>,
+CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >,
+    std::back_insert_iterator< std::vector<Alpha_value_type> > > > Dispatch;
+typedef Alpha_shape_3::Cell_handle Cell_handle;
+typedef Alpha_shape_3::Facet Facet;
+typedef Alpha_shape_3::Edge Edge_3;
 typedef std::list<Alpha_shape_3::Vertex_handle> Vertex_list;
 
 // gudhi type definition
@@ -65,70 +71,60 @@ typedef std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex > Alpha_shape
 typedef std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex> Alpha_shape_simplex_tree_pair;
 typedef std::vector< Simplex_tree_vertex > Simplex_tree_vector_vertex;
 
-//#define DEBUG_TRACES
-
-Vertex_list from (const Cell_handle& ch)
-{
+Vertex_list from(const Cell_handle& ch) {
   Vertex_list the_list;
-  for (auto i = 0; i < 4; i++)
-  {
+  for (auto i = 0; i < 4; i++) {
 #ifdef DEBUG_TRACES
     std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl;
-#endif // DEBUG_TRACES
+#endif  // DEBUG_TRACES
     the_list.push_back(ch->vertex(i));
   }
   return the_list;
 }
-Vertex_list from (const Facet& fct)
-{
+
+Vertex_list from(const Facet& fct) {
   Vertex_list the_list;
-  for (auto i = 0; i < 4; i++)
-  {
-    if (fct.second != i)
-    {
+  for (auto i = 0; i < 4; i++) {
+    if (fct.second != i) {
 #ifdef DEBUG_TRACES
       std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl;
-#endif // DEBUG_TRACES
+#endif  // DEBUG_TRACES
       the_list.push_back(fct.first->vertex(i));
     }
   }
   return the_list;
 }
-Vertex_list from (const Edge_3& edg)
-{
+
+Vertex_list from(const Edge_3& edg) {
   Vertex_list the_list;
-  for (auto i = 0; i < 4; i++)
-  {
-    if ((edg.second == i) ||(edg.third == i))
-    {
+  for (auto i = 0; i < 4; i++) {
+    if ((edg.second == i) || (edg.third == i)) {
 #ifdef DEBUG_TRACES
       std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl;
-#endif // DEBUG_TRACES
+#endif  // DEBUG_TRACES
       the_list.push_back(edg.first->vertex(i));
     }
   }
   return the_list;
 }
-Vertex_list from (const Alpha_shape_3::Vertex_handle& vh)
-{
+
+Vertex_list from(const Alpha_shape_3::Vertex_handle& vh) {
   Vertex_list the_list;
 #ifdef DEBUG_TRACES
   std::cout << "from vertex=" << vh->point() << std::endl;
-#endif // DEBUG_TRACES
+#endif  // DEBUG_TRACES
   the_list.push_back(vh);
   return the_list;
 }
 
-void usage(char * const progName)
-{
-  std::cerr << "Usage: " << progName << " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
-  exit(-1); // ----- >>
+void usage(char * const progName) {
+  std::cerr << "Usage: " << progName <<
+      " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
+  exit(-1);
 }
 
-int main (int argc, char * const argv[])
-{
-
-  int coeff_field_characteristic=0;
+int main(int argc, char * const argv[]) {
+  int coeff_field_characteristic = 0;
   int returnedScanValue = sscanf(argv[2], "%d", &coeff_field_characteristic);
   if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) {
     std::cerr << "Error: " << argv[2] << " is not correct\n";
@@ -149,102 +145,96 @@ int main (int argc, char * const argv[])
   }
 
   // Read points from file
-  std::string filegraph   = argv[1];
+  std::string filegraph = argv[1];
   std::list<Point_3> lp;
   std::ifstream is(filegraph.c_str());
   int n;
   is >> n;
 #ifdef DEBUG_TRACES
   std::cout << "Reading " << n << " points " << std::endl;
-#endif // DEBUG_TRACES
+#endif  // DEBUG_TRACES
   Point_3 p;
-  for( ; n>0 ; n--)    {
+  for (; n > 0; n--) {
     is >> p;
     lp.push_back(p);
   }
 
   // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode.
-  Alpha_shape_3 as(lp.begin(),lp.end(),0,Alpha_shape_3::GENERAL);
+  Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL);
 #ifdef DEBUG_TRACES
   std::cout << "Alpha shape computed in GENERAL mode" << std::endl;
-#endif // DEBUG_TRACES
+#endif  // DEBUG_TRACES
 
   // filtration with alpha values from alpha shape
   std::vector<Object> the_objects;
   std::vector<Alpha_value_type> the_alpha_values;
 
-  Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>( std::back_inserter(the_objects), std::back_inserter(the_alpha_values));
+  Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>(std::back_inserter(the_objects),
+                                                                  std::back_inserter(the_alpha_values));
 
   as.filtration_with_alpha_values(disp);
 #ifdef DEBUG_TRACES
   std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl;
-#endif // DEBUG_TRACES
+#endif  // DEBUG_TRACES
 
   Alpha_shape_3::size_type count_vertices = 0;
-  Alpha_shape_3::size_type count_edges    = 0;
-  Alpha_shape_3::size_type count_facets   = 0;
-  Alpha_shape_3::size_type count_cells    = 0;
+  Alpha_shape_3::size_type count_edges = 0;
+  Alpha_shape_3::size_type count_facets = 0;
+  Alpha_shape_3::size_type count_cells = 0;
 
   // Loop on objects vector
   Vertex_list vertex_list;
   Simplex_tree<> simplex_tree;
   Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
   std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
-  int dim_max=0;
-  Filtration_value filtration_max=0.0;
-  for(auto object_iterator: the_objects)
-  {
+  int dim_max = 0;
+  Filtration_value filtration_max = 0.0;
+  for (auto object_iterator : the_objects) {
     // Retrieve Alpha shape vertex list from object
-    if (const Cell_handle* cell = CGAL::object_cast<Cell_handle>(&object_iterator))
-    {
+    if (const Cell_handle * cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
       vertex_list = from(*cell);
       count_cells++;
       if (dim_max < 3) {
-        dim_max=3; // Cell is of dim 3
+        // Cell is of dim 3
+        dim_max = 3;
       }
-    }
-    else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator))
-    {
+    } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) {
       vertex_list = from(*facet);
       count_facets++;
       if (dim_max < 2) {
-        dim_max=2; // Facet is of dim 2
+        // Facet is of dim 2
+        dim_max = 2;
       }
-    }
-    else if (const Edge_3* edge = CGAL::object_cast<Edge_3>(&object_iterator))
-    {
+    } else if (const Edge_3 * edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
       vertex_list = from(*edge);
       count_edges++;
       if (dim_max < 1) {
-        dim_max=1; // Edge_3 is of dim 1
+        // Edge_3 is of dim 1
+        dim_max = 1;
       }
-    }
-    else if (const Alpha_shape_3::Vertex_handle* vertex = CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator))
-    {
+    } else if (const Alpha_shape_3::Vertex_handle * vertex =
+               CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator)) {
       count_vertices++;
       vertex_list = from(*vertex);
     }
     // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
     Simplex_tree_vector_vertex the_simplex_tree;
-    for (auto the_alpha_shape_vertex:vertex_list)
-    {
+    for (auto the_alpha_shape_vertex : vertex_list) {
       Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
-      if (the_map_iterator == map_cgal_simplex_tree.end())
-      {
+      if (the_map_iterator == map_cgal_simplex_tree.end()) {
         // alpha shape not found
         Simplex_tree_vertex vertex = map_cgal_simplex_tree.size();
 #ifdef DEBUG_TRACES
         std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
-#endif // DEBUG_TRACES
+#endif  // DEBUG_TRACES
         the_simplex_tree.push_back(vertex);
-        map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex,vertex));
-      } else
-      {
+        map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex));
+      } else {
         // alpha shape found
         Simplex_tree_vertex vertex = the_map_iterator->second;
 #ifdef DEBUG_TRACES
         std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
-#endif // DEBUG_TRACES
+#endif  // DEBUG_TRACES
         the_simplex_tree.push_back(vertex);
       }
     }
@@ -252,7 +242,7 @@ int main (int argc, char * const argv[])
     Filtration_value filtr = std::sqrt(*the_alpha_value_iterator);
 #ifdef DEBUG_TRACES
     std::cout << "filtration = " << filtr << std::endl;
-#endif // DEBUG_TRACES
+#endif  // DEBUG_TRACES
     if (filtr > filtration_max) {
       filtration_max = filtr;
     }
@@ -263,14 +253,13 @@ int main (int argc, char * const argv[])
       std::cout << "This shall not happen" << std::endl;
   }
   simplex_tree.set_filtration(filtration_max);
-  simplex_tree.set_num_simplices(count_vertices + count_edges + count_facets + count_cells);
   simplex_tree.set_dimension(dim_max);
 
 #ifdef DEBUG_TRACES
   std::cout << "vertices \t\t" << count_vertices << std::endl;
-  std::cout << "edges \t\t"    << count_edges << std::endl;
-  std::cout << "facets \t\t"   << count_facets << std::endl;
-  std::cout << "cells \t\t"    << count_cells << std::endl;
+  std::cout << "edges \t\t" << count_edges << std::endl;
+  std::cout << "facets \t\t" << count_facets << std::endl;
+  std::cout << "cells \t\t" << count_cells << std::endl;
 
 
   std::cout << "Information of the Simplex Tree: " << std::endl;
@@ -278,23 +267,25 @@ int main (int argc, char * const argv[])
   std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
   std::cout << "  Dimension = " << simplex_tree.dimension() << " ";
   std::cout << "  filtration = " << simplex_tree.filtration() << std::endl << std::endl;
-#endif // DEBUG_TRACES
+#endif  // DEBUG_TRACES
 
 #ifdef DEBUG_TRACES
   std::cout << "Iterator on vertices: " << std::endl;
-  for( auto vertex : simplex_tree.complex_vertex_range() )
-  { std::cout << vertex << " "; }
-#endif // DEBUG_TRACES
+  for (auto vertex : simplex_tree.complex_vertex_range()) {
+    std::cout << vertex << " ";
+  }
+#endif  // DEBUG_TRACES
 
   // Sort the simplices in the order of the filtration
   simplex_tree.initialize_filtration();
 
   std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
   // Compute the persistence diagram of the complex
-  Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh( simplex_tree );
-  pcoh.init_coefficients( coeff_field_characteristic ); //initializes the coefficient field for homology
+  Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(simplex_tree);
+  // initializes the coefficient field for homology
+  pcoh.init_coefficients(coeff_field_characteristic);
 
-  pcoh.compute_persistent_cohomology( min_persistence );
+  pcoh.compute_persistent_cohomology(min_persistence);
 
   pcoh.output_diagram();
 
diff --git a/src/Persistent_cohomology/example/performance_rips_persistence.cpp b/src/Persistent_cohomology/example/performance_rips_persistence.cpp
index 077c2b07..fc48d6b1 100644
--- a/src/Persistent_cohomology/example/performance_rips_persistence.cpp
+++ b/src/Persistent_cohomology/example/performance_rips_persistence.cpp
@@ -1,49 +1,51 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       Clément Maria
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-
-#include "gudhi/reader_utils.h"
-#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/distance_functions.h"
-#include "gudhi/Simplex_tree.h"
-#include "gudhi/Persistent_cohomology.h"
-#include "gudhi/Persistent_cohomology/Multi_field.h"
-#include "gudhi/Hasse_complex.h"
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       Clément Maria
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <gudhi/reader_utils.h>
+#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/distance_functions.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Persistent_cohomology/Multi_field.h>
+#include <gudhi/Hasse_complex.h>
 
 #include <chrono>
+#include <string>
+#include <vector>
 
 using namespace Gudhi;
 using namespace Gudhi::persistent_cohomology;
 
 /* Compute the persistent homology of the complex cpx with coefficients in Z/pZ. */
 template< typename FilteredComplex>
-void timing_persistence( FilteredComplex & cpx
-                       , int               p );
+void timing_persistence(FilteredComplex & cpx
+                        , int p);
 
 /* Compute multi-field persistent homology of the complex cpx with coefficients in
  * Z/rZ for all prime number r in [p;q].*/
 template< typename FilteredComplex>
-void timing_persistence( FilteredComplex & cpx
-                       , int               p 
-                       , int               q );
+void timing_persistence(FilteredComplex & cpx
+                        , int p
+                        , int q);
 
 /* Timings for the computation of persistent homology with different 
  * representations of a Rips complex and different coefficient fields. The 
@@ -59,111 +61,154 @@ void timing_persistence( FilteredComplex & cpx
  * We present also timings for the computation of multi-field persistent 
  * homology in all fields Z/rZ for r prime between 2 and 1223.
  */
-int main (int argc, char * argv[]) 
-{
+int main(int argc, char * argv[]) {
   std::chrono::time_point<std::chrono::system_clock> start, end;
-  int enlapsed_sec;
+  int elapsed_sec;
+  {
 
-  std::string      filepoints      = "../examples/Kl.txt";
-  Filtration_value threshold       = 0.3;
-  int              dim_max         = 3;
-  int              p               = 2;
-  int              q               = 1223;
+  std::string filepoints = "../../../data/points/Kl.txt";
+  Filtration_value threshold = 0.27;
+  int dim_max = 3;
+  int p = 2;
+  int q = 1223;
 
-// Extract the points from the file filepoints
+  // Extract the points from the file filepoints
   typedef std::vector<double> Point_t;
   std::vector< Point_t > points;
-  read_points( filepoints, points );
+  read_points(filepoints, points);
 
-// Compute the proximity graph of the points
+  // Compute the proximity graph of the points
   start = std::chrono::system_clock::now();
-  Graph_t prox_graph = compute_proximity_graph( points, threshold
-                                              , euclidean_distance<Point_t> );
+  Graph_t prox_graph = compute_proximity_graph(points, threshold
+                                               , euclidean_distance<Point_t>);
   end = std::chrono::system_clock::now();
-  enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count();
-  std::cout << "Compute Rips graph in " << enlapsed_sec << " sec.\n";
+  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+  std::cout << "Compute Rips graph in " << elapsed_sec << " ms.\n";
 
-// Construct the Rips complex in a Simplex Tree
-  Simplex_tree<> st;        
+  // Construct the Rips complex in a Simplex Tree
+  Simplex_tree<> st;
   start = std::chrono::system_clock::now();
 
-  st.insert_graph(prox_graph); // insert the proximity graph in the simplex tree
-  st.expansion( dim_max ); // expand the graph until dimension dim_max
+  // insert the proximity graph in the simplex tree
+  st.insert_graph(prox_graph);
+  // expand the graph until dimension dim_max
+  st.expansion(dim_max);
 
   end = std::chrono::system_clock::now();
-  enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count();
-  std::cout << "Compute Rips complex in " << enlapsed_sec << " sec.\n";
+  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+  std::cout << "Compute Rips complex in " << elapsed_sec << " ms.\n";
   std::cout << "  - dimension           = " << st.dimension() << std::endl;
   std::cout << "  - number of simplices = " << st.num_simplices() << std::endl;
 
-// Sort the simplices in the order of the filtration
+  // Sort the simplices in the order of the filtration
   start = std::chrono::system_clock::now();
   st.initialize_filtration();
   end = std::chrono::system_clock::now();
-  enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count();
-  std::cout << "Order the simplices of the filtration in " << enlapsed_sec << " sec.\n";
+  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+  std::cout << "Order the simplices of the filtration in " << elapsed_sec << " ms.\n";
+
+  // Copy the keys inside the simplices
+  start = std::chrono::system_clock::now();
+  {
+    int count = 0;
+    for (auto sh : st.filtration_simplex_range())
+      st.assign_key(sh, count++);
+  }
+  end = std::chrono::system_clock::now();
+  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+  std::cout << "Copied the keys inside the simplices in " << elapsed_sec << " ms.\n";
 
-// Convert the simplex tree into a hasse diagram
+  // Convert the simplex tree into a hasse diagram
   start = std::chrono::system_clock::now();
   Hasse_complex<> hcpx(st);
   end = std::chrono::system_clock::now();
-  enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count();
-  std::cout << "Convert the simplex tree into a Hasse diagram in " << enlapsed_sec << " sec.\n";
+  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+  std::cout << "Convert the simplex tree into a Hasse diagram in " << elapsed_sec << " ms.\n";
 
 
   std::cout << "Timings when using a simplex tree: \n";
-  timing_persistence(st,p);
-  timing_persistence(st,q);
-  timing_persistence(st,p,q);
+  timing_persistence(st, p);
+  timing_persistence(st, q);
+  timing_persistence(st, p, q);
 
   std::cout << "Timings when using a Hasse complex: \n";
-  timing_persistence(hcpx,p);
-  timing_persistence(hcpx,q);
-  timing_persistence(hcpx,p,q);
+  timing_persistence(hcpx, p);
+  timing_persistence(hcpx, q);
+  timing_persistence(hcpx, p, q);
 
+  start = std::chrono::system_clock::now();
+  }
+  end = std::chrono::system_clock::now();
+  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+  std::cout << "Running the complex destructors in " << elapsed_sec << " ms.\n";
   return 0;
 }
 
-
 template< typename FilteredComplex>
 void
-timing_persistence( FilteredComplex & cpx
-                  , int               p )
-{
+timing_persistence(FilteredComplex & cpx
+                   , int p) {
   std::chrono::time_point<std::chrono::system_clock> start, end;
-  int enlapsed_sec;
+  int elapsed_sec;
+  {
+  start = std::chrono::system_clock::now();
+  Persistent_cohomology< FilteredComplex, Field_Zp > pcoh(cpx);
+  end = std::chrono::system_clock::now();
+  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+  std::cout << "  Initialize pcoh in " << elapsed_sec << " ms.\n";
+  // initializes the coefficient field for homology
+  start = std::chrono::system_clock::now();
+  pcoh.init_coefficients(p);
+  end = std::chrono::system_clock::now();
+  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+  std::cout << "  Initialize the coefficient field in " << elapsed_sec << " ms.\n";
 
-  Persistent_cohomology< FilteredComplex, Field_Zp > pcoh (cpx);
-  pcoh.init_coefficients( p ); //initilizes the coefficient field for homology
-  
   start = std::chrono::system_clock::now();
- 
-  pcoh.compute_persistent_cohomology( INFINITY );
- 
+
+  pcoh.compute_persistent_cohomology(INFINITY);
+
+  end = std::chrono::system_clock::now();
+  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+  std::cout << "  Compute persistent homology in Z/" << p << "Z in " << elapsed_sec << " ms.\n";
+  start = std::chrono::system_clock::now();
+  }
   end = std::chrono::system_clock::now();
-  enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count();
-  std::cout << "  Compute persistent homology in Z/"<<p<<"Z in " << enlapsed_sec << " sec.\n";
+  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+  std::cout << "  Run the persistence destructors in " << elapsed_sec << " ms.\n";
 }
 
 template< typename FilteredComplex>
 void
-timing_persistence( FilteredComplex & cpx
-                  , int               p 
-                  , int               q )
-{
+timing_persistence(FilteredComplex & cpx
+                   , int p
+                   , int q) {
   std::chrono::time_point<std::chrono::system_clock> start, end;
-  int enlapsed_sec;
-
-  Persistent_cohomology< FilteredComplex, Multi_field > pcoh (cpx);
-  pcoh.init_coefficients( p, q ); //initilizes the coefficient field for homology
+  int elapsed_sec;
+  {
+  start = std::chrono::system_clock::now();
+  Persistent_cohomology< FilteredComplex, Multi_field > pcoh(cpx);
+  end = std::chrono::system_clock::now();
+  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+  std::cout << "  Initialize pcoh in " << elapsed_sec << " ms.\n";
+  // initializes the coefficient field for homology
+  start = std::chrono::system_clock::now();
+  pcoh.init_coefficients(p, q);
+  end = std::chrono::system_clock::now();
+  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+  std::cout << "  Initialize the coefficient field in " << elapsed_sec << " ms.\n";
   // compute persistent homology, disgarding persistent features of life shorter than min_persistence
 
   start = std::chrono::system_clock::now();
 
-  pcoh.compute_persistent_cohomology( INFINITY );
+  pcoh.compute_persistent_cohomology(INFINITY);
 
   end = std::chrono::system_clock::now();
-  enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count();
+  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
   std::cout << "  Compute multi-field persistent homology in all coefficient fields Z/pZ "
-            << "with p in ["<<p<<";"<<q<<"] in " << enlapsed_sec << " sec.\n";
+      << "with p in [" << p << ";" << q << "] in " << elapsed_sec << " ms.\n";
+  start = std::chrono::system_clock::now();
+  }
+  end = std::chrono::system_clock::now();
+  elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+  std::cout << "  Run the persistence destructors in " << elapsed_sec << " ms.\n";
 }
diff --git a/src/Persistent_cohomology/example/persistence_from_file.cpp b/src/Persistent_cohomology/example/persistence_from_file.cpp
index e886aea7..8eb8d0f3 100644
--- a/src/Persistent_cohomology/example/persistence_from_file.cpp
+++ b/src/Persistent_cohomology/example/persistence_from_file.cpp
@@ -1,141 +1,144 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       Vincent Rouvreau
-  *
-  *    Copyright (C) 2014  INRIA Saclay (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-
-#include "gudhi/reader_utils.h"
-#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/distance_functions.h"
-#include "gudhi/Simplex_tree.h"
-#include "gudhi/Persistent_cohomology.h"
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2014  INRIA Saclay (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <gudhi/reader_utils.h>
+#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/distance_functions.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
 
 #include <boost/program_options.hpp>
 
+#include <string>
+
 using namespace Gudhi;
 using namespace Gudhi::persistent_cohomology;
 
-typedef int        Vertex_handle;
-typedef double     Filtration_value;
-
-void program_options( int argc, char *   argv[] 
-                    , std::string      & simplex_tree_file
-                    , std::string      & output_file
-                    , int              & p
-                    , Filtration_value & min_persistence );
-
-int main (int argc, char * argv[]) 
-{
-	std::string      simplex_tree_file;
-	std::string      output_file  ;
-	int              p         ;
-	Filtration_value min_persistence;
-
-	program_options(argc,argv,simplex_tree_file,output_file,p,min_persistence);
-
-	std::cout << "Simplex_tree from file=" << simplex_tree_file.c_str() << " - output_file=" << output_file.c_str() << std::endl;
-	std::cout << "     - p=" << p << " - min_persistence=" << min_persistence << std::endl;
-
-	// Construct the Rips complex in a Simplex Tree
-	Simplex_tree<> simplex_tree;
-
-	std::ifstream simplex_tree_stream(simplex_tree_file);
-	simplex_tree_stream >> simplex_tree;
-
-	std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices" << std::endl;
-	std::cout << "   - dimension " << simplex_tree.dimension() << "   - filtration " << simplex_tree.filtration() << std::endl;
-
-	/*
-	std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
-	for( auto f_simplex : simplex_tree.filtration_simplex_range() )
-	{ std::cout << "   " << "[" << simplex_tree.filtration(f_simplex) << "] ";
-	for( auto vertex : simplex_tree.simplex_vertex_range(f_simplex) )
-	{ std::cout << vertex << " "; }
-	std::cout << std::endl;
-	}*/
-
-	// Sort the simplices in the order of the filtration
-	simplex_tree.initialize_filtration();
-
-	// Compute the persistence diagram of the complex
-	Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh( simplex_tree );
-	pcoh.init_coefficients( p ); //initilizes the coefficient field for homology
-
-	pcoh.compute_persistent_cohomology( min_persistence );
-
-	// Output the diagram in output_file
-	if(output_file.empty()) {  pcoh.output_diagram(); }
-	else {
-		std::ofstream out(output_file);
-		pcoh.output_diagram(out);
-		out.close(); }
+typedef int Vertex_handle;
+typedef double Filtration_value;
+
+void program_options(int argc, char * argv[]
+                     , std::string & simplex_tree_file
+                     , std::string & output_file
+                     , int & p
+                     , Filtration_value & min_persistence);
+
+int main(int argc, char * argv[]) {
+  std::string simplex_tree_file;
+  std::string output_file;
+  int p;
+  Filtration_value min_persistence;
+
+  program_options(argc, argv, simplex_tree_file, output_file, p, min_persistence);
+
+  std::cout << "Simplex_tree from file=" << simplex_tree_file.c_str() << " - output_file=" << output_file.c_str()
+      << std::endl;
+  std::cout << "     - p=" << p << " - min_persistence=" << min_persistence << std::endl;
+
+  // Construct the Rips complex in a Simplex Tree
+  Simplex_tree<> simplex_tree;
+
+  std::ifstream simplex_tree_stream(simplex_tree_file);
+  simplex_tree_stream >> simplex_tree;
+
+  std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices" << std::endl;
+  std::cout << "   - dimension " << simplex_tree.dimension() << "   - filtration " << simplex_tree.filtration()
+      << std::endl;
+
+  /*
+  std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
+  for( auto f_simplex : simplex_tree.filtration_simplex_range() )
+  { std::cout << "   " << "[" << simplex_tree.filtration(f_simplex) << "] ";
+  for( auto vertex : simplex_tree.simplex_vertex_range(f_simplex) )
+  { std::cout << vertex << " "; }
+  std::cout << std::endl;
+  }*/
+
+  // Sort the simplices in the order of the filtration
+  simplex_tree.initialize_filtration();
+
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(simplex_tree);
+  // initializes the coefficient field for homology
+  pcoh.init_coefficients(p);
+
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  // Output the diagram in output_file
+  if (output_file.empty()) {
+    pcoh.output_diagram();
+  } else {
+    std::ofstream out(output_file);
+    pcoh.output_diagram(out);
+    out.close();
+  }
 
-	return 0;
+  return 0;
 }
 
-
-
-void program_options( int argc, char *   argv[] 
-                    , std::string      & simplex_tree_file
-                    , std::string      & output_file
-                    , int              & p
-                    , Filtration_value & min_persistence )
-{
+void program_options(int argc, char * argv[]
+                     , std::string & simplex_tree_file
+                     , std::string & output_file
+                     , int & p
+                     , Filtration_value & min_persistence) {
   namespace po = boost::program_options;
-  po::options_description     hidden("Hidden options");
+  po::options_description hidden("Hidden options");
   hidden.add_options()
-        ("input-file",  po::value<std::string>(&simplex_tree_file),
-          "Name of file containing a simplex set. Format is one simplex per line (cf. reader_utils.h - read_simplex):   Dim1 X11 X12 ... X1d Fil1  ");
-    
+      ("input-file", po::value<std::string>(&simplex_tree_file),
+       "Name of file containing a simplex set. Format is one simplex per line (cf. reader_utils.h - read_simplex): Dim1 X11 X12 ... X1d Fil1  ");
+
   po::options_description visible("Allowed options", 100);
   visible.add_options()
-        ("help,h",          "produce help message")
-        ("output-file,o", po::value<std::string>(&output_file)->default_value(std::string()),
-                   "Name of file in which the persistence diagram is written. Default print in std::cout")
-        ("field-charac,p", po::value<int>(&p)->default_value(11),                  
-                  "Characteristic p of the coefficient field Z/pZ for computing homology.")
-        ("min-persistence,m", po::value<Filtration_value>(&min_persistence), 
-                  "Minimal lifetime of homology feature to be recorded. Default is 0");
+      ("help,h", "produce help message")
+      ("output-file,o", po::value<std::string>(&output_file)->default_value(std::string()),
+       "Name of file in which the persistence diagram is written. Default print in std::cout")
+      ("field-charac,p", po::value<int>(&p)->default_value(11),
+       "Characteristic p of the coefficient field Z/pZ for computing homology.")
+      ("min-persistence,m", po::value<Filtration_value>(&min_persistence),
+       "Minimal lifetime of homology feature to be recorded. Default is 0");
 
   po::positional_options_description pos;
   pos.add("input-file", 1);
-  
-  po::options_description all; all.add(visible).add(hidden);
+
+  po::options_description all;
+  all.add(visible).add(hidden);
 
   po::variables_map vm;
   po::store(po::command_line_parser(argc, argv).
-                options(all).positional(pos).run(), vm);
+            options(all).positional(pos).run(), vm);
   po::notify(vm);
 
-  if (vm.count("help") || !vm.count("input-file"))
-  { 
-      std::cout << std::endl;
-      std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
-      std::cout << "of a Rips complex defined on a set of input points.\n \n";
-      std::cout << "The output diagram contains one bar per line, written with the convention: \n";
-      std::cout << "   p   dim b d \n";
-      std::cout << "where dim is the dimension of the homological feature,\n";
-      std::cout << "b and d are respectively the birth and death of the feature and \n";
-      std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
-
-      std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
-      std::cout << visible << std::endl; 
-      std::abort();
+  if (vm.count("help") || !vm.count("input-file")) {
+    std::cout << std::endl;
+    std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
+    std::cout << "of a Rips complex defined on a set of input points.\n \n";
+    std::cout << "The output diagram contains one bar per line, written with the convention: \n";
+    std::cout << "   p   dim b d \n";
+    std::cout << "where dim is the dimension of the homological feature,\n";
+    std::cout << "b and d are respectively the birth and death of the feature and \n";
+    std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
+
+    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+    std::cout << visible << std::endl;
+    std::abort();
   }
 }
diff --git a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
index ba82e4e6..ba772f04 100644
--- a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
+++ b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
@@ -20,11 +20,14 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
+#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+
 #include <iostream>
 #include <ctime>
-#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Simplex_tree.h"
-#include "gudhi/Persistent_cohomology.h"
+#include <utility>
+#include <vector>
 
 using namespace Gudhi;
 using namespace Gudhi::persistent_cohomology;
@@ -34,15 +37,19 @@ typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
 typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
 typedef Simplex_tree<> typeST;
 
-void usage(char * const progName)
-{
+void usage(char * const progName) {
   std::cerr << "Usage: " << progName << " coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
-  exit(-1); // ----- >>
+  exit(-1);
 }
 
-int main (int argc, char * const argv[])
-{
-  int coeff_field_characteristic=0;
+int main(int argc, char * const argv[]) {
+  // program args management
+  if (argc != 3) {
+    std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
+    usage(argv[0]);
+  }
+
+  int coeff_field_characteristic = 0;
   int returnedScanValue = sscanf(argv[1], "%d", &coeff_field_characteristic);
   if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) {
     std::cerr << "Error: " << argv[1] << " is not correct\n";
@@ -56,101 +63,65 @@ int main (int argc, char * const argv[])
     usage(argv[0]);
   }
 
-  // program args management
-  if (argc != 3) {
-    std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
-    usage(argv[0]);
-  }
-
   // TEST OF INSERTION
   std::cout << "********************************************************************" << std::endl;
   std::cout << "TEST OF INSERTION" << std::endl;
   typeST st;
 
   // ++ FIRST
-  std::cout << "   - INSERT (2,1,0)" << std::endl;
-  typeVectorVertex SimplexVector1;
-  SimplexVector1.push_back(2);
-  SimplexVector1.push_back(1);
-  SimplexVector1.push_back(0);
-  st.insert_simplex_and_subfaces ( SimplexVector1, 0.3);
+  std::cout << "   - INSERT (0,1,2)" << std::endl;
+  typeVectorVertex SimplexVector = {0, 1, 2};
+  st.insert_simplex_and_subfaces(SimplexVector, 0.3);
 
   // ++ SECOND
   std::cout << "   - INSERT 3" << std::endl;
-  typeVectorVertex SimplexVector2;
-  SimplexVector2.push_back(3);
-  st.insert_simplex_and_subfaces ( SimplexVector2, 0.1);
+  SimplexVector = {3};
+  st.insert_simplex_and_subfaces(SimplexVector, 0.1);
 
   // ++ THIRD
   std::cout << "   - INSERT (0,3)" << std::endl;
-  typeVectorVertex SimplexVector3;
-  SimplexVector3.push_back(3);
-  SimplexVector3.push_back(0);
-  st.insert_simplex_and_subfaces ( SimplexVector3, 0.2);
+  SimplexVector = {0, 3};
+  st.insert_simplex_and_subfaces(SimplexVector, 0.2);
 
   // ++ FOURTH
-  std::cout << "   - INSERT (1,0) (already inserted)" << std::endl;
-  typeVectorVertex SimplexVector4;
-  SimplexVector4.push_back(1);
-  SimplexVector4.push_back(0);
-  st.insert_simplex_and_subfaces ( SimplexVector4, 0.2);
+  std::cout << "   - INSERT (0,1) (already inserted)" << std::endl;
+  SimplexVector = {0, 1};
+  st.insert_simplex_and_subfaces(SimplexVector, 0.2);
 
   // ++ FIFTH
   std::cout << "   - INSERT (3,4,5)" << std::endl;
-  typeVectorVertex SimplexVector5;
-  SimplexVector5.push_back(3);
-  SimplexVector5.push_back(4);
-  SimplexVector5.push_back(5);
-  st.insert_simplex_and_subfaces ( SimplexVector5, 0.3);
+  SimplexVector = {3, 4, 5};
+  st.insert_simplex_and_subfaces(SimplexVector, 0.3);
 
   // ++ SIXTH
   std::cout << "   - INSERT (0,1,6,7)" << std::endl;
-  typeVectorVertex SimplexVector6;
-  SimplexVector6.push_back(0);
-  SimplexVector6.push_back(1);
-  SimplexVector6.push_back(6);
-  SimplexVector6.push_back(7);
-  st.insert_simplex_and_subfaces ( SimplexVector6, 0.4);
+  SimplexVector = {0, 1, 6, 7};
+  st.insert_simplex_and_subfaces(SimplexVector, 0.4);
 
   // ++ SEVENTH
   std::cout << "   - INSERT (4,5,8,9)" << std::endl;
-  typeVectorVertex SimplexVector7;
-  SimplexVector7.push_back(4);
-  SimplexVector7.push_back(5);
-  SimplexVector7.push_back(8);
-  SimplexVector7.push_back(9);
-  st.insert_simplex_and_subfaces ( SimplexVector7, 0.4);
+  SimplexVector = {4, 5, 8, 9};
+  st.insert_simplex_and_subfaces(SimplexVector, 0.4);
 
   // ++ EIGHTH
   std::cout << "   - INSERT (9,10,11)" << std::endl;
-  typeVectorVertex SimplexVector8;
-  SimplexVector8.push_back(9);
-  SimplexVector8.push_back(10);
-  SimplexVector8.push_back(11);
-  st.insert_simplex_and_subfaces ( SimplexVector8, 0.3);
-  
+  SimplexVector = {9, 10, 11};
+  st.insert_simplex_and_subfaces(SimplexVector, 0.3);
+
   // ++ NINETH
   std::cout << "   - INSERT (2,10,12)" << std::endl;
-  typeVectorVertex SimplexVector9;
-  SimplexVector9.push_back(2);
-  SimplexVector9.push_back(10);
-  SimplexVector9.push_back(12);
-  st.insert_simplex_and_subfaces ( SimplexVector9, 0.3);
-  
+  SimplexVector = {2, 10, 12};
+  st.insert_simplex_and_subfaces(SimplexVector, 0.3);
+
   // ++ TENTH
   std::cout << "   - INSERT (11,6)" << std::endl;
-  typeVectorVertex SimplexVector10;
-  SimplexVector10.push_back(11);
-  SimplexVector10.push_back(6);
-  st.insert_simplex_and_subfaces ( SimplexVector10, 0.2);
+  SimplexVector = {6, 11};
+  st.insert_simplex_and_subfaces(SimplexVector, 0.2);
 
   // ++ ELEVENTH
   std::cout << "   - INSERT (13,14,15)" << std::endl;
-  typeVectorVertex SimplexVector11;
-  SimplexVector11.push_back(13);
-  SimplexVector11.push_back(14);
-  SimplexVector11.push_back(15);
-  st.insert_simplex_and_subfaces ( SimplexVector11, 0.25);
+  SimplexVector = {13, 14, 15};
+  st.insert_simplex_and_subfaces(SimplexVector, 0.25);
 
   /* Inserted simplex:         */
   /*    1   6                  */
@@ -175,33 +146,31 @@ int main (int argc, char * const argv[])
   st.set_dimension(2);
   st.set_filtration(0.4);
 
-  std::cout << "The complex contains " << st.num_simplices() << " simplices - " << st.num_vertices() << " vertices " << std::endl;
+  std::cout << "The complex contains " << st.num_simplices() << " simplices - " << st.num_vertices() << " vertices "
+      << std::endl;
   std::cout << "   - dimension " << st.dimension() << "   - filtration " << st.filtration() << std::endl;
-  std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
+  std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:"
+      << std::endl;
   std::cout << "**************************************************************" << std::endl;
   std::cout << "strict graph G { " << std::endl;
 
-  for( auto f_simplex : st.filtration_simplex_range() )
-  {
+  for (auto f_simplex : st.filtration_simplex_range()) {
     std::cout << "   " << "[" << st.filtration(f_simplex) << "] ";
-    for( auto vertex : st.simplex_vertex_range(f_simplex) )
-    {
-      std::cout << (int)vertex << " -- ";
+    for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+      std::cout << static_cast<int>(vertex) << " -- ";
     }
     std::cout << ";" << std::endl;
   }
 
   std::cout << "}" << std::endl;
-  //std::cout << "**************************************************************" << std::endl;
-  //st.print_hasse(std::cout);
   std::cout << "**************************************************************" << std::endl;
 
-
   // Compute the persistence diagram of the complex
   persistent_cohomology::Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(st);
-  pcoh.init_coefficients( coeff_field_characteristic ); //initiliazes the coefficient field for homology
+  // initializes the coefficient field for homology
+  pcoh.init_coefficients(coeff_field_characteristic);
 
-  pcoh.compute_persistent_cohomology( min_persistence );
+  pcoh.compute_persistent_cohomology(min_persistence);
 
   // Output the diagram in filediag
   pcoh.output_diagram();
diff --git a/src/Persistent_cohomology/example/plain_homology.cpp b/src/Persistent_cohomology/example/plain_homology.cpp
new file mode 100644
index 00000000..0a692717
--- /dev/null
+++ b/src/Persistent_cohomology/example/plain_homology.cpp
@@ -0,0 +1,84 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Marc Glisse
+ *
+ *    Copyright (C) 2015  INRIA Saclay - Ile-de-France (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+
+#include <iostream>
+
+using namespace Gudhi;
+
+/* We could perfectly well use the default Simplex_tree<> (which uses
+ * Simplex_tree_options_full_featured), the following simply demonstrates
+ * how to save on storage by not storing a filtration value.  */
+
+struct MyOptions : Simplex_tree_options_full_featured {
+  // Implicitly use 0 as filtration value for all simplices
+  static const bool store_filtration = false;
+  // The persistence algorithm needs this
+  static const bool store_key = true;
+  // I have few vertices
+  typedef short Vertex_handle;
+};
+typedef Simplex_tree<MyOptions> ST;
+
+int main() {
+  ST st;
+
+  /* Complex to build. */
+  /*    1   3          */
+  /*    o---o          */
+  /*   /X\ /           */
+  /*  o---o   o        */
+  /*  2   0   4        */
+
+  const short triangle012[] = {0, 1, 2};
+  const short edge03[] = {0, 3};
+  const short edge13[] = {1, 3};
+  const short vertex4[] = {4};
+  st.insert_simplex_and_subfaces(triangle012);
+  st.insert_simplex_and_subfaces(edge03);
+  st.insert_simplex(edge13);
+  st.insert_simplex(vertex4);
+  // FIXME: Remove this line
+  st.set_dimension(2);
+
+  // Sort the simplices in the order of the filtration
+  st.initialize_filtration();
+
+  // Class for homology computation
+  persistent_cohomology::Persistent_cohomology<ST, persistent_cohomology::Field_Zp> pcoh(st);
+
+  // Initialize the coefficient field Z/2Z for homology
+  pcoh.init_coefficients(2);
+
+  // Compute the persistence diagram of the complex
+  pcoh.compute_persistent_cohomology();
+
+  // Print the result. The format is, on each line: 2 dim 0 inf
+  // where 2 represents the field, dim the dimension of the feature.
+  // 2  0 0 inf 
+  // 2  0 0 inf 
+  // 2  1 0 inf 
+  // means that in Z/2Z-homology, the Betti numbers are b0=2 and b1=1.
+  pcoh.output_diagram();
+}
diff --git a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
index 297a8f98..5277bf7a 100644
--- a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
@@ -1,153 +1,157 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       Clément Maria
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-
-#include "gudhi/reader_utils.h"
-#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/distance_functions.h"
-#include "gudhi/Simplex_tree.h"
-#include "gudhi/Persistent_cohomology.h"
-#include "gudhi/Persistent_cohomology/Multi_field.h"
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       Clément Maria
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <gudhi/reader_utils.h>
+#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/distance_functions.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Persistent_cohomology/Multi_field.h>
 
 #include <boost/program_options.hpp>
 
+#include <string>
+#include <vector>
+
 using namespace Gudhi;
 using namespace Gudhi::persistent_cohomology;
 
-typedef int    Vertex_handle;
+typedef int Vertex_handle;
 typedef double Filtration_value;
 
-void program_options( int argc, char *   argv[] 
-                    , std::string      & filepoints
-                    , std::string      & filediag
-                    , Filtration_value & threshold
-                    , int              & dim_max
-                    , int              & min_p
-                    , int              & max_p
-                    , Filtration_value & min_persistence );
-
-int main (int argc, char * argv[]) 
-{
-  std::string      filepoints;
-  std::string      filediag;
+void program_options(int argc, char * argv[]
+                     , std::string & filepoints
+                     , std::string & filediag
+                     , Filtration_value & threshold
+                     , int & dim_max
+                     , int & min_p
+                     , int & max_p
+                     , Filtration_value & min_persistence);
+
+int main(int argc, char * argv[]) {
+  std::string filepoints;
+  std::string filediag;
   Filtration_value threshold;
-  int              dim_max;
-  int              min_p;
-  int              max_p;
+  int dim_max;
+  int min_p;
+  int max_p;
   Filtration_value min_persistence;
 
-  program_options(argc,argv,filepoints,filediag,threshold,dim_max,min_p,max_p,min_persistence);
+  program_options(argc, argv, filepoints, filediag, threshold, dim_max, min_p, max_p, min_persistence);
 
-// Extract the points from the file filepoints
+  // Extract the points from the file filepoints
   typedef std::vector<double> Point_t;
   std::vector< Point_t > points;
-  read_points( filepoints, points );
+  read_points(filepoints, points);
 
-// Compute the proximity graph of the points
-  Graph_t prox_graph = compute_proximity_graph( points, threshold
-                                              , euclidean_distance<Point_t> );
+  // Compute the proximity graph of the points
+  Graph_t prox_graph = compute_proximity_graph(points, threshold
+                                               , euclidean_distance<Point_t>);
 
-// Construct the Rips complex in a Simplex Tree
-  Simplex_tree<> st;        
-  st.insert_graph(prox_graph); // insert the proximity graph in the simplex tree
-  st.expansion( dim_max ); // expand the graph until dimension dim_max
+  // Construct the Rips complex in a Simplex Tree
+  Simplex_tree<> st;
+  // insert the proximity graph in the simplex tree
+  st.insert_graph(prox_graph);
+  // expand the graph until dimension dim_max
+  st.expansion(dim_max);
 
-// Sort the simplices in the order of the filtration
+  // Sort the simplices in the order of the filtration
   st.initialize_filtration();
 
-// Compute the persistence diagram of the complex
-  Persistent_cohomology< Simplex_tree<>, Multi_field > pcoh( st );
-  pcoh.init_coefficients( min_p, max_p ); //initilizes the coefficient field for homology
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology< Simplex_tree<>, Multi_field > pcoh(st);
+  // initializes the coefficient field for homology
+  pcoh.init_coefficients(min_p, max_p);
   // compute persistent homology, disgarding persistent features of life shorter than min_persistence
-  pcoh.compute_persistent_cohomology( min_persistence );
-
-// Output the diagram in filediag
-  if(filediag.empty()) {  pcoh.output_diagram(); }
-  else {
-   std::ofstream out(filediag);
-   pcoh.output_diagram(out);
-   out.close(); }
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  // Output the diagram in filediag
+  if (filediag.empty()) {
+    pcoh.output_diagram();
+  } else {
+    std::ofstream out(filediag);
+    pcoh.output_diagram(out);
+    out.close();
+  }
 
   return 0;
 }
 
-
-
-void program_options( int argc, char *   argv[] 
-                    , std::string      & filepoints
-                    , std::string      & filediag
-                    , Filtration_value & threshold
-                    , int              & dim_max
-                    , int              & min_p
-                    , int              & max_p
-                    , Filtration_value & min_persistence )
-{
+void program_options(int argc, char * argv[]
+                     , std::string & filepoints
+                     , std::string & filediag
+                     , Filtration_value & threshold
+                     , int & dim_max
+                     , int & min_p
+                     , int & max_p
+                     , Filtration_value & min_persistence) {
   namespace po = boost::program_options;
-  po::options_description     hidden("Hidden options");
+  po::options_description hidden("Hidden options");
   hidden.add_options()
-        ("input-file",  po::value<std::string>(&filepoints), 
-          "Name of file containing a point set. Format is one point per line:   X1 ... Xd \n");
-    
+      ("input-file", po::value<std::string>(&filepoints),
+       "Name of file containing a point set. Format is one point per line:   X1 ... Xd \n");
+
   po::options_description visible("Allowed options");
   visible.add_options()
-        ("help,h",          "produce help message")
-        ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()), 
-                   "Name of file in which the persistence diagram is written. Default print in std::cout")
-        ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0), 
-                   "Maximal length of an edge for the Rips complex construction.")
-        ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),        
-                  "Maximal dimension of the Rips complex we want to compute.")
-        ("min-field-charac,p", po::value<int>(&min_p)->default_value(2),                  
-                  "Minimal characteristic p of the coefficient field Z/pZ.")
-        ("max-field-charac,q", po::value<int>(&max_p)->default_value(1223),                  
-                  "Minimial characteristic q of the coefficient field Z/pZ.")
-        ("min-persistence,m", po::value<Filtration_value>(&min_persistence), 
-                  "Minimal lifetime of homology feature to be recorded. Default is 0");
+      ("help,h", "produce help message")
+      ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
+       "Name of file in which the persistence diagram is written. Default print in std::cout")
+      ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0),
+       "Maximal length of an edge for the Rips complex construction.")
+      ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
+       "Maximal dimension of the Rips complex we want to compute.")
+      ("min-field-charac,p", po::value<int>(&min_p)->default_value(2),
+       "Minimal characteristic p of the coefficient field Z/pZ.")
+      ("max-field-charac,q", po::value<int>(&max_p)->default_value(1223),
+       "Minimial characteristic q of the coefficient field Z/pZ.")
+      ("min-persistence,m", po::value<Filtration_value>(&min_persistence),
+       "Minimal lifetime of homology feature to be recorded. Default is 0");
 
   po::positional_options_description pos;
   pos.add("input-file", 1);
-  
-  po::options_description all; all.add(visible).add(hidden);
+
+  po::options_description all;
+  all.add(visible).add(hidden);
 
   po::variables_map vm;
   po::store(po::command_line_parser(argc, argv).
-                options(all).positional(pos).run(), vm);
+            options(all).positional(pos).run(), vm);
   po::notify(vm);
 
-  if (vm.count("help") || !vm.count("input-file"))
-  { 
-      std::cout << std::endl;
-      std::cout << "Compute the persistent homology with various coefficient fields \n";
-      std::cout << "of a Rips complex defined on a set of input points. The coefficient \n";
-      std::cout << "fields are all the Z/rZ for a prime number r contained in the \n";
-      std::cout << "specified range [p,q]\n \n";
-      std::cout << "The output diagram contains one bar per line, written with the convention: \n";
-      std::cout << "   p1*...*pr   dim b d \n";
-      std::cout << "where dim is the dimension of the homological feature,\n";
-      std::cout << "b and d are respectively the birth and death of the feature and \n";
-      std::cout << "p1*...*pr is the product of prime numbers pi such that the homology \n";
-      std::cout << "feature exists in homology with Z/piZ coefficients."<< std::endl << std::endl;
-
-      std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
-      std::cout << visible << std::endl; 
-      std::abort();
+  if (vm.count("help") || !vm.count("input-file")) {
+    std::cout << std::endl;
+    std::cout << "Compute the persistent homology with various coefficient fields \n";
+    std::cout << "of a Rips complex defined on a set of input points. The coefficient \n";
+    std::cout << "fields are all the Z/rZ for a prime number r contained in the \n";
+    std::cout << "specified range [p,q]\n \n";
+    std::cout << "The output diagram contains one bar per line, written with the convention: \n";
+    std::cout << "   p1*...*pr   dim b d \n";
+    std::cout << "where dim is the dimension of the homological feature,\n";
+    std::cout << "b and d are respectively the birth and death of the feature and \n";
+    std::cout << "p1*...*pr is the product of prime numbers pi such that the homology \n";
+    std::cout << "feature exists in homology with Z/piZ coefficients." << std::endl << std::endl;
+
+    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+    std::cout << visible << std::endl;
+    std::abort();
   }
 }
diff --git a/src/Persistent_cohomology/example/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp
index 4253def9..9b1ef42f 100644
--- a/src/Persistent_cohomology/example/rips_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence.cpp
@@ -1,147 +1,151 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       Clément Maria
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-
-#include "gudhi/reader_utils.h"
-#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/distance_functions.h"
-#include "gudhi/Simplex_tree.h"
-#include "gudhi/Persistent_cohomology.h"
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       Clément Maria
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <gudhi/reader_utils.h>
+#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/distance_functions.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
 
 #include <boost/program_options.hpp>
 
+#include <string>
+#include <vector>
+
 using namespace Gudhi;
 using namespace Gudhi::persistent_cohomology;
 
-typedef int        Vertex_handle;
-typedef double     Filtration_value;
-
-void program_options( int argc, char *   argv[] 
-                    , std::string      & filepoints
-                    , std::string      & filediag
-                    , Filtration_value & threshold
-                    , int              & dim_max
-                    , int              & p
-                    , Filtration_value & min_persistence );
-
-int main (int argc, char * argv[]) 
-{
-  std::string      filepoints;
-  std::string      filediag  ;
-  Filtration_value threshold ;
-  int              dim_max   ;
-  int              p         ;
+typedef int Vertex_handle;
+typedef double Filtration_value;
+
+void program_options(int argc, char * argv[]
+                     , std::string & filepoints
+                     , std::string & filediag
+                     , Filtration_value & threshold
+                     , int & dim_max
+                     , int & p
+                     , Filtration_value & min_persistence);
+
+int main(int argc, char * argv[]) {
+  std::string filepoints;
+  std::string filediag;
+  Filtration_value threshold;
+  int dim_max;
+  int p;
   Filtration_value min_persistence;
 
-  program_options(argc,argv,filepoints,filediag,threshold,dim_max,p,min_persistence);
+  program_options(argc, argv, filepoints, filediag, threshold, dim_max, p, min_persistence);
 
-// Extract the points from the file filepoints
+  // Extract the points from the file filepoints
   typedef std::vector<double> Point_t;
   std::vector< Point_t > points;
-  read_points( filepoints, points );
+  read_points(filepoints, points);
 
-// Compute the proximity graph of the points
-  Graph_t prox_graph = compute_proximity_graph( points, threshold
-                                              , euclidean_distance<Point_t> );
+  // Compute the proximity graph of the points
+  Graph_t prox_graph = compute_proximity_graph(points, threshold
+                                               , euclidean_distance<Point_t>);
 
-// Construct the Rips complex in a Simplex Tree
-  Simplex_tree<> st;        
-  st.insert_graph(prox_graph); // insert the proximity graph in the simplex tree
-  st.expansion( dim_max ); // expand the graph until dimension dim_max
+  // Construct the Rips complex in a Simplex Tree
+  Simplex_tree<> st;
+  // insert the proximity graph in the simplex tree
+  st.insert_graph(prox_graph);
+  // expand the graph until dimension dim_max
+  st.expansion(dim_max);
 
   std::cout << "The complex contains " << st.num_simplices() << " simplices \n";
   std::cout << "   and has dimension " << st.dimension() << " \n";
 
-// Sort the simplices in the order of the filtration
+  // Sort the simplices in the order of the filtration
   st.initialize_filtration();
 
-// Compute the persistence diagram of the complex
+  // Compute the persistence diagram of the complex
   persistent_cohomology::Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(st);
-  pcoh.init_coefficients( p ); //initilizes the coefficient field for homology
-  
-  pcoh.compute_persistent_cohomology( min_persistence );
-
-// Output the diagram in filediag
-  if(filediag.empty()) {  pcoh.output_diagram(); }
-  else {
-   std::ofstream out(filediag);
-   pcoh.output_diagram(out);
-   out.close(); }
+  // initializes the coefficient field for homology
+  pcoh.init_coefficients(p);
+
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  // Output the diagram in filediag
+  if (filediag.empty()) {
+    pcoh.output_diagram();
+  } else {
+    std::ofstream out(filediag);
+    pcoh.output_diagram(out);
+    out.close();
+  }
 
   return 0;
 }
 
-
-
-void program_options( int argc, char *   argv[] 
-                    , std::string      & filepoints
-                    , std::string      & filediag
-                    , Filtration_value & threshold
-                    , int              & dim_max
-                    , int              & p
-                    , Filtration_value & min_persistence )
-{
+void program_options(int argc, char * argv[]
+                     , std::string & filepoints
+                     , std::string & filediag
+                     , Filtration_value & threshold
+                     , int & dim_max
+                     , int & p
+                     , Filtration_value & min_persistence) {
   namespace po = boost::program_options;
-  po::options_description     hidden("Hidden options");
+  po::options_description hidden("Hidden options");
   hidden.add_options()
-        ("input-file",  po::value<std::string>(&filepoints), 
-          "Name of file containing a point set. Format is one point per line:   X1 ... Xd ");
-    
+      ("input-file", po::value<std::string>(&filepoints),
+       "Name of file containing a point set. Format is one point per line:   X1 ... Xd ");
+
   po::options_description visible("Allowed options", 100);
   visible.add_options()
-        ("help,h",          "produce help message")
-        ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()), 
-                   "Name of file in which the persistence diagram is written. Default print in std::cout")
-        ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0), 
-                   "Maximal length of an edge for the Rips complex construction.")
-        ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),        
-                  "Maximal dimension of the Rips complex we want to compute.")
-        ("field-charac,p", po::value<int>(&p)->default_value(11),                  
-                  "Characteristic p of the coefficient field Z/pZ for computing homology.")
-        ("min-persistence,m", po::value<Filtration_value>(&min_persistence), 
-                  "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals");
+      ("help,h", "produce help message")
+      ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
+       "Name of file in which the persistence diagram is written. Default print in std::cout")
+      ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0),
+       "Maximal length of an edge for the Rips complex construction.")
+      ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
+       "Maximal dimension of the Rips complex we want to compute.")
+      ("field-charac,p", po::value<int>(&p)->default_value(11),
+       "Characteristic p of the coefficient field Z/pZ for computing homology.")
+      ("min-persistence,m", po::value<Filtration_value>(&min_persistence),
+       "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals");
 
   po::positional_options_description pos;
   pos.add("input-file", 1);
-  
-  po::options_description all; all.add(visible).add(hidden);
+
+  po::options_description all;
+  all.add(visible).add(hidden);
 
   po::variables_map vm;
   po::store(po::command_line_parser(argc, argv).
-                options(all).positional(pos).run(), vm);
+            options(all).positional(pos).run(), vm);
   po::notify(vm);
 
-  if (vm.count("help") || !vm.count("input-file"))
-  { 
-      std::cout << std::endl;
-      std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
-      std::cout << "of a Rips complex defined on a set of input points.\n \n";
-      std::cout << "The output diagram contains one bar per line, written with the convention: \n";
-      std::cout << "   p   dim b d \n";
-      std::cout << "where dim is the dimension of the homological feature,\n";
-      std::cout << "b and d are respectively the birth and death of the feature and \n";
-      std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
-
-      std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
-      std::cout << visible << std::endl; 
-      std::abort();
+  if (vm.count("help") || !vm.count("input-file")) {
+    std::cout << std::endl;
+    std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
+    std::cout << "of a Rips complex defined on a set of input points.\n \n";
+    std::cout << "The output diagram contains one bar per line, written with the convention: \n";
+    std::cout << "   p   dim b d \n";
+    std::cout << "where dim is the dimension of the homological feature,\n";
+    std::cout << "b and d are respectively the birth and death of the feature and \n";
+    std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
+
+    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+    std::cout << visible << std::endl;
+    std::abort();
   }
 }
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index b0d68f09..2a405830 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -20,23 +20,28 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_H_
-#define SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_H_
+#ifndef PERSISTENT_COHOMOLOGY_H_
+#define PERSISTENT_COHOMOLOGY_H_
 
 #include <gudhi/Persistent_cohomology/Persistent_cohomology_column.h>
 #include <gudhi/Persistent_cohomology/Field_Zp.h>
+#include <gudhi/Simple_object_pool.h>
 
 #include <boost/tuple/tuple.hpp>
 #include <boost/intrusive/set.hpp>
 #include <boost/pending/disjoint_sets.hpp>
 #include <boost/intrusive/list.hpp>
-#include <boost/pool/object_pool.hpp>
 
 #include <map>
 #include <utility>
 #include <list>
 #include <vector>
 #include <set>
+#include <fstream>  // std::ofstream
+#include <limits>  // for numeric_limits<>
+#include <tuple>
+#include <algorithm>
+#include <string>
 
 namespace Gudhi {
 
@@ -229,9 +234,10 @@ class Persistent_cohomology {
       : cpx_(&cpx),
         dim_max_(cpx.dimension()),                       // upper bound on the dimension of the simplices
         coeff_field_(),                                  // initialize the field coefficient structure.
-        ds_rank_(cpx_->num_simplices()),                 // union-find
-        ds_parent_(cpx_->num_simplices()),               // union-find
-        ds_repr_(cpx_->num_simplices(), NULL),           // union-find -> annotation vectors
+        num_simplices_(cpx_->num_simplices()),           // num_simplices save to avoid to call thrice the function
+        ds_rank_(num_simplices_),                        // union-find
+        ds_parent_(num_simplices_),                      // union-find
+        ds_repr_(num_simplices_, NULL),                  // union-find -> annotation vectors
         dsets_(&ds_rank_[0], &ds_parent_[0]),            // union-find
         cam_(),                                          // collection of annotation vectors
         zero_cocycles_(),                                // union-find -> Simplex_key of creator for 0-homology
@@ -241,7 +247,7 @@ class Persistent_cohomology {
         column_pool_(),  // memory pools for the CAM
         cell_pool_() {
     Simplex_key idx_fil = 0;
-    for (auto & sh : cpx_->filtration_simplex_range()) {
+    for (auto sh : cpx_->filtration_simplex_range()) {
       cpx_->assign_key(sh, idx_fil);
       ++idx_fil;
       dsets_.make_set(cpx_->key(sh));
@@ -264,13 +270,10 @@ class Persistent_cohomology {
   }
 
   ~Persistent_cohomology() {
-// Clean the remaining columns in the matrix.
-    for (auto & cam_ref : cam_) {
-      cam_ref.col_.clear();
-    }
-// Clean the transversal lists
+    // Clean the transversal lists
     for (auto & transverse_ref : transverse_idx_) {
-      transverse_ref.second.row_->clear();
+      // Destruct all the cells
+      transverse_ref.second.row_->clear_and_dispose([&](Cell*p){p->~Cell();});
       delete transverse_ref.second.row_;
     }
   }
@@ -335,18 +338,18 @@ class Persistent_cohomology {
 
       if (ds_parent_[key] == key  // root of its tree
       && zero_cocycles_.find(key) == zero_cocycles_.end()) {
-        persistent_pairs_.push_back(
-            Persistent_interval(cpx_->simplex(key), cpx_->null_simplex(), coeff_field_.characteristic()));
+        persistent_pairs_.emplace_back(
+            cpx_->simplex(key), cpx_->null_simplex(), coeff_field_.characteristic());
       }
     }
     for (auto zero_idx : zero_cocycles_) {
-      persistent_pairs_.push_back(
-          Persistent_interval(cpx_->simplex(zero_idx.second), cpx_->null_simplex(), coeff_field_.characteristic()));
+      persistent_pairs_.emplace_back(
+          cpx_->simplex(zero_idx.second), cpx_->null_simplex(), coeff_field_.characteristic());
     }
 // Compute infinite interval of dimension > 0
     for (auto cocycle : transverse_idx_) {
-      persistent_pairs_.push_back(
-          Persistent_interval(cpx_->simplex(cocycle.first), cpx_->null_simplex(), cocycle.second.characteristics_));
+      persistent_pairs_.emplace_back(
+          cpx_->simplex(cocycle.first), cpx_->null_simplex(), cocycle.second.characteristics_);
     }
   }
 
@@ -386,8 +389,8 @@ class Persistent_cohomology {
       if (cpx_->filtration(cpx_->simplex(idx_coc_u))
           < cpx_->filtration(cpx_->simplex(idx_coc_v))) {  // Kill cocycle [idx_coc_v], which is younger.
         if (interval_length_policy(cpx_->simplex(idx_coc_v), sigma)) {
-          persistent_pairs_.push_back(
-              Persistent_interval(cpx_->simplex(idx_coc_v), sigma, coeff_field_.characteristic()));
+          persistent_pairs_.emplace_back(
+              cpx_->simplex(idx_coc_v), sigma, coeff_field_.characteristic());
         }
         // Maintain the index of the 0-cocycle alive.
         if (kv != idx_coc_v) {
@@ -401,8 +404,8 @@ class Persistent_cohomology {
         }
       } else {  // Kill cocycle [idx_coc_u], which is younger.
         if (interval_length_policy(cpx_->simplex(idx_coc_u), sigma)) {
-          persistent_pairs_.push_back(
-              Persistent_interval(cpx_->simplex(idx_coc_u), sigma, coeff_field_.characteristic()));
+          persistent_pairs_.emplace_back(
+              cpx_->simplex(idx_coc_u), sigma, coeff_field_.characteristic());
         }
         // Maintain the index of the 0-cocycle alive.
         if (ku != idx_coc_u) {
@@ -428,9 +431,12 @@ class Persistent_cohomology {
       std::map<Simplex_key, Arith_element> & map_a_ds, Simplex_handle sigma,
       int dim_sigma) {
     // traverses the boundary of sigma, keeps track of the annotation vectors,
-    // with multiplicity, in a map.
-    std::map<Column *, int> annotations_in_boundary;
-    std::pair<typename std::map<Column *, int>::iterator, bool> result_insert_bound;
+    // with multiplicity. We used to sum the coefficients directly in
+    // annotations_in_boundary by using a map, we now do it later.
+    typedef std::pair<Column *, int> annotation_t;
+    // Danger: not thread-safe!
+    static std::vector<annotation_t> annotations_in_boundary;
+    annotations_in_boundary.clear();
     int sign = 1 - 2 * (dim_sigma % 2);  // \in {-1,1} provides the sign in the
                                          // alternate sum in the boundary.
     Simplex_key key;
@@ -442,22 +448,29 @@ class Persistent_cohomology {
         // Find its annotation vector
         curr_col = ds_repr_[dsets_.find_set(key)];
         if (curr_col != NULL) {  // and insert it in annotations_in_boundary with multyiplicative factor "sign".
-          result_insert_bound = annotations_in_boundary.insert(std::pair<Column *, int>(curr_col, sign));
-          if (!(result_insert_bound.second)) {
-            result_insert_bound.first->second += sign;
-          }
+	  annotations_in_boundary.emplace_back(curr_col, sign);
         }
       }
       sign = -sign;
     }
+    // Place identical annotations consecutively so we can easily sum their multiplicities.
+    std::sort(annotations_in_boundary.begin(), annotations_in_boundary.end(),
+	[](annotation_t const& a, annotation_t const& b) { return a.first < b.first; });
+
     // Sum the annotations with multiplicity, using a map<key,coeff>
     // to represent a sparse vector.
     std::pair<typename std::map<Simplex_key, Arith_element>::iterator, bool> result_insert_a_ds;
 
-    for (auto ann_ref : annotations_in_boundary) {
-      if (ann_ref.second != coeff_field_.additive_identity()) {  // For all columns in the boundary,
-        for (auto cell_ref : ann_ref.first->col_) {  // insert every cell in map_a_ds with multiplicity
-          Arith_element w_y = coeff_field_.times(cell_ref.coefficient_, ann_ref.second);  // coefficient * multiplicity
+    for (auto ann_it = annotations_in_boundary.begin(); ann_it != annotations_in_boundary.end(); /**/) {
+      Column* col = ann_it->first;
+      int mult = ann_it->second;
+      while (++ann_it != annotations_in_boundary.end() && ann_it->first == col) {
+	mult += ann_it->second;
+      }
+      // The following test is just a heuristic, it is not required, and it is fine that is misses p == 0.
+      if (mult != coeff_field_.additive_identity()) {  // For all columns in the boundary,
+        for (auto cell_ref : col->col_) {  // insert every cell in map_a_ds with multiplicity
+          Arith_element w_y = coeff_field_.times(cell_ref.coefficient_, mult);  // coefficient * multiplicity
 
           if (w_y != coeff_field_.additive_identity()) {  // if != 0
             result_insert_a_ds = map_a_ds.insert(std::pair<Simplex_key, Arith_element>(cell_ref.key_, w_y));
@@ -525,8 +538,8 @@ class Persistent_cohomology {
                       Arith_element charac) {
     Simplex_key key = cpx_->key(sigma);
     // Create a column containing only one cell,
-    Column * new_col = column_pool_.construct(Column(key));
-    Cell * new_cell = cell_pool_.construct(Cell(key, x, new_col));
+    Column * new_col = column_pool_.construct(key);
+    Cell * new_cell = cell_pool_.construct(key, x, new_col);
     new_col->col_.push_back(*new_cell);
     // and insert it in the matrix, in constant time thanks to the hint cam_.end().
     // Indeed *new_col has the biggest lexicographic value because key is the
@@ -552,9 +565,9 @@ class Persistent_cohomology {
                        Arith_element charac) {
     // Create a finite persistent interval for which the interval exists
     if (interval_length_policy(cpx_->simplex(death_key), sigma)) {
-      persistent_pairs_.push_back(Persistent_interval(cpx_->simplex(death_key)  // creator
-          , sigma                                                               // destructor
-          , charac));                                                           // fields
+      persistent_pairs_.emplace_back(cpx_->simplex(death_key)  // creator
+          , sigma                                              // destructor
+          , charac);                                           // fields
     }
 
     auto death_key_row = transverse_idx_.find(death_key);  // Find the beginning of the row.
@@ -570,9 +583,8 @@ class Persistent_cohomology {
         Column * curr_col = row_cell_it->self_col_;
         ++row_cell_it;
         // Disconnect the column from the rows in the CAM.
-        for (auto col_cell_it = curr_col->col_.begin();
-            col_cell_it != curr_col->col_.end(); ++col_cell_it) {
-          col_cell_it->base_hook_cam_h::unlink();
+        for (auto& col_cell : curr_col->col_) {
+          col_cell.base_hook_cam_h::unlink();
         }
 
         // Remove the column from the CAM before modifying its value
@@ -587,9 +599,9 @@ class Persistent_cohomology {
           // Find whether the column obtained is already in the CAM
           result_insert_cam = cam_.insert(*curr_col);
           if (result_insert_cam.second) {  // If it was not in the CAM before: insertion has succeeded
-            for (auto col_cell_it = curr_col->col_.begin(); col_cell_it != curr_col->col_.end(); ++col_cell_it) {
+            for (auto& col_cell : curr_col->col_) {
               // re-establish the row links
-              transverse_idx_[col_cell_it->key_].row_->push_front(*col_cell_it);
+              transverse_idx_[col_cell.key_].row_->push_front(col_cell);
             }
           } else {  // There is already an identical column in the CAM:
             // merge two disjoint sets.
@@ -599,6 +611,8 @@ class Persistent_cohomology {
             Simplex_key key_tmp = dsets_.find_set(curr_col->class_key_);
             ds_repr_[key_tmp] = &(*(result_insert_cam.first));
             result_insert_cam.first->class_key_ = key_tmp;
+            // intrusive containers don't own their elements, we have to release them manually
+            curr_col->col_.clear_and_dispose([&](Cell*p){cell_pool_.destroy(p);});
             column_pool_.destroy(curr_col);  // delete curr_col;
           }
         }
@@ -694,7 +708,7 @@ class Persistent_cohomology {
   void output_diagram(std::ostream& ostream = std::cout) {
 
     cmp_intervals_by_length cmp(cpx_);
-    persistent_pairs_.sort(cmp);
+    std::sort(std::begin(persistent_pairs_), std::end(persistent_pairs_), cmp);
     bool has_infinity = std::numeric_limits<Filtration_value>::has_infinity;
     for (auto pair : persistent_pairs_) {
       // Special case on windows, inf is "1.#INF" (cf. unitary tests and R package TDA)
@@ -709,13 +723,11 @@ class Persistent_cohomology {
     }
   }
 
-  void write_output_diagram(std::string diagram_name)
-  {
-    std::ofstream           diagram_out(diagram_name.c_str());
-    cmp_intervals_by_length cmp( cpx_ );
-    persistent_pairs_.sort( cmp );
-    for(auto pair : persistent_pairs_)
-    {
+  void write_output_diagram(std::string diagram_name) {
+    std::ofstream diagram_out(diagram_name.c_str());
+    cmp_intervals_by_length cmp(cpx_);
+    std::sort(std::begin(persistent_pairs_), std::end(persistent_pairs_), cmp);
+    for (auto pair : persistent_pairs_) {
     diagram_out << cpx_->dimension(get<0>(pair)) << " "
           << cpx_->filtration(get<0>(pair)) << " "
           << cpx_->filtration(get<1>(pair)) << std::endl;
@@ -742,6 +754,7 @@ class Persistent_cohomology {
   Complex_ds * cpx_;
   int dim_max_;
   CoefficientField coeff_field_;
+  size_t num_simplices_;
 
   /*  Disjoint sets data structure to link the model of FilteredComplex
    * with the compressed annotation matrix.
@@ -760,11 +773,11 @@ class Persistent_cohomology {
   /*  Key -> row. */
   std::map<Simplex_key, cocycle> transverse_idx_;
   /* Persistent intervals. */
-  std::list<Persistent_interval> persistent_pairs_;
+  std::vector<Persistent_interval> persistent_pairs_;
   length_interval interval_length_policy;
 
-  boost::object_pool<Column> column_pool_;
-  boost::object_pool<Cell> cell_pool_;
+  Simple_object_pool<Column> column_pool_;
+  Simple_object_pool<Cell> cell_pool_;
 };
 
 /** @} */  // end defgroup persistent_cohomology
@@ -773,4 +786,4 @@ class Persistent_cohomology {
 
 }  // namespace Gudhi
 
-#endif  // SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_H_
+#endif  // PERSISTENT_COHOMOLOGY_H_
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h
index 2a4c8692..6db16e69 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_FIELD_ZP_H_
-#define SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_FIELD_ZP_H_
+#ifndef PERSISTENT_COHOMOLOGY_FIELD_ZP_H_
+#define PERSISTENT_COHOMOLOGY_FIELD_ZP_H_
 
 #include <utility>
 #include <vector>
@@ -41,9 +41,7 @@ class Field_Zp {
 
   Field_Zp()
       : Prime(0),
-        inverse_(),
-        mult_id_all(1),
-        add_id_all(0) {
+        inverse_() {
   }
 
   void init(int charac) {
@@ -81,14 +79,14 @@ class Field_Zp {
   }
 
   /** \brief Returns the additive idendity \f$0_{\Bbbk}\f$ of the field.*/
-  const Element& additive_identity() const {
-    return add_id_all;
+  Element additive_identity() const {
+    return 0;
   }
   /** \brief Returns the multiplicative identity \f$1_{\Bbbk}\f$ of the field.*/
-  const Element& multiplicative_identity(Element = 0) const {
-    return mult_id_all;
+  Element multiplicative_identity(Element = 0) const {
+    return 1;
   }
-  /** Returns the inverse in the field. Modifies P.*/
+  /** Returns the inverse in the field. Modifies P. ??? */
   std::pair<Element, Element> inverse(Element x, Element P) {
     return std::pair<Element, Element>(inverse_[x], P);
   }  // <------ return the product of field characteristic for which x is invertible
@@ -101,7 +99,7 @@ class Field_Zp {
   }
 
   /** \brief Returns the characteristic \f$p\f$ of the field.*/
-  const int& characteristic() const {
+  int characteristic() const {
     return Prime;
   }
 
@@ -109,12 +107,10 @@ class Field_Zp {
   int Prime;
   /** Property map Element -> Element, which associate to an element its inverse in the field.*/
   std::vector<Element> inverse_;
-  const Element mult_id_all;
-  const Element add_id_all;
 };
 
 }  // namespace persistent_cohomology
 
 }  // namespace Gudhi
 
-#endif  // SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_FIELD_ZP_H_
+#endif  // PERSISTENT_COHOMOLOGY_FIELD_ZP_H_
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h
index c6fd5282..38bc08d1 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_MULTI_FIELD_H_
-#define SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_MULTI_FIELD_H_
+#ifndef PERSISTENT_COHOMOLOGY_MULTI_FIELD_H_
+#define PERSISTENT_COHOMOLOGY_MULTI_FIELD_H_
 
 #include <gmpxx.h>
 
@@ -81,8 +81,7 @@ class Multi_field {
     // set m to primorial(bound_prime)
     prod_characteristics_ = 1;
     for (auto p : primes_) {
-      mpz_mul_ui(prod_characteristics_.get_mpz_t(),
-                 prod_characteristics_.get_mpz_t(), p);
+      prod_characteristics_ *= p;
     }
 
     // Uvect_
@@ -142,7 +141,7 @@ class Multi_field {
     return prod_characteristics_;
   }
 
-  /** Returns the inverse in the field. Modifies P.*/
+  /** Returns the inverse in the field. Modifies P. ??? */
   std::pair<Element, Element> inverse(Element x, Element QS) {
     Element QR;
     mpz_gcd(QR.get_mpz_t(), x.get_mpz_t(), QS.get_mpz_t());  // QR <- gcd(x,QS)
@@ -153,12 +152,12 @@ class Multi_field {
     mpz_invert(inv_qt.get_mpz_t(), x.get_mpz_t(), QT.get_mpz_t());
 
     assert(prod_characteristics_ > 0);  // division by zero + non negative values
-    return std::pair<Element, Element>(
-        (inv_qt * multiplicative_identity(QT)) % prod_characteristics_, QT);
+    return { (inv_qt * multiplicative_identity(QT)) % prod_characteristics_, QT };
   }
   /** Returns -x * y.*/
   Element times_minus(const Element& x, const Element& y) {
     assert(prod_characteristics_ > 0);  // division by zero + non negative values
+    /* This assumes that (x*y)%pc cannot be zero, but Field_Zp has specific code for the 0 case ??? */
     return prod_characteristics_ - ((x * y) % prod_characteristics_);
   }
 
@@ -183,4 +182,4 @@ class Multi_field {
 
 }  // namespace Gudhi
 
-#endif  // SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_MULTI_FIELD_H_
+#endif  // PERSISTENT_COHOMOLOGY_MULTI_FIELD_H_
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h
index fcec819a..612658e6 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h
@@ -20,14 +20,14 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_
-#define SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_
+#ifndef PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_
+#define PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_
 
-#include <list>
+#include <boost/tuple/tuple.hpp>
+#include <boost/intrusive/set.hpp>
+#include <boost/intrusive/list.hpp>
 
-#include "boost/tuple/tuple.hpp"
-#include "boost/intrusive/set.hpp"
-#include "boost/intrusive/list.hpp"
+#include <list>
 
 namespace Gudhi {
 
@@ -80,40 +80,33 @@ class Persistent_cohomology_cell : public base_hook_cam_h,
  * The non-zero coefficients of the column are stored in a
  * boost::intrusive::list. Contains a hook to be stored in a
  * boost::intrusive::set.
+ *
+ * Movable but not Copyable.
  */
 template<typename SimplexKey, typename ArithmeticElement>
 class Persistent_cohomology_column : public boost::intrusive::set_base_hook<
     boost::intrusive::link_mode<boost::intrusive::normal_link> > {
- private:
   template<class T1, class T2> friend class Persistent_cohomology;
 
+ public:
   typedef Persistent_cohomology_cell<SimplexKey, ArithmeticElement> Cell;
   typedef boost::intrusive::list<Cell,
       boost::intrusive::constant_time_size<false>,
       boost::intrusive::base_hook<base_hook_cam_v> > Col_type;
 
   /** \brief Creates an empty column.*/
-  explicit Persistent_cohomology_column(SimplexKey key) {
-    class_key_ = key;
-    col_ = Col_type();
-  }
- public:
-  /** Copy constructor.*/
-  Persistent_cohomology_column(Persistent_cohomology_column const &other)
+  explicit Persistent_cohomology_column(SimplexKey key)
       : col_(),
-        class_key_(other.class_key_) {
-    if (!other.col_.empty())
-      std::cerr << "Copying a non-empty column.\n";
-  }
+        class_key_(key) {}
 
   /** \brief Returns true iff the column is null.*/
-  bool is_null() {
+  bool is_null() const {
     return col_.empty();
   }
   /** \brief Returns the key of the representative simplex of
    * the set of simplices having this column as annotation vector
    * in the compressed annotation matrix.*/
-  SimplexKey class_key() {
+  SimplexKey class_key() const {
     return class_key_;
   }
 
@@ -145,4 +138,4 @@ class Persistent_cohomology_column : public boost::intrusive::set_base_hook<
 
 }  // namespace Gudhi
 
-#endif  // SRC_PERSISTENT_COHOMOLOGY_INCLUDE_GUDHI_PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_
+#endif  // PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_
diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
index 55bc7066..194b3e74 100644
--- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
+++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
@@ -1,15 +1,14 @@
-#define BOOST_TEST_MODULE persistent_cohomology test
-#include <boost/test/included/unit_test.hpp>
-#include <boost/system/error_code.hpp>
-#include <boost/chrono/thread_clock.hpp>
 #include <iostream>
 #include <string>
-
+#include <algorithm>
 #include <utility> // std::pair, std::make_pair
-
 #include <cmath> // float comparison
 #include <limits>
 
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "persistent_cohomology"
+#include <boost/test/unit_test.hpp>
+
 #include "gudhi/graph_simplicial_complex.h"
 #include "gudhi/reader_utils.h"
 #include "gudhi/Simplex_tree.h"
diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp
index 18a4725e..703682e1 100644
--- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp
+++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp
@@ -1,15 +1,14 @@
-#define BOOST_TEST_MODULE persistent_cohomology_multi_field test
-#include <boost/test/included/unit_test.hpp>
-#include <boost/system/error_code.hpp>
-#include <boost/chrono/thread_clock.hpp>
 #include <iostream>
 #include <string>
-
+#include <algorithm>
 #include <utility> // std::pair, std::make_pair
-
 #include <cmath> // float comparison
 #include <limits>
 
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "persistent_cohomology_multi_field"
+#include <boost/test/unit_test.hpp>
+
 #include "gudhi/graph_simplicial_complex.h"
 #include "gudhi/reader_utils.h"
 #include "gudhi/Simplex_tree.h"
diff --git a/src/Simplex_tree/concept/IndexingTag.h b/src/Simplex_tree/concept/IndexingTag.h
index d690da11..1dcdd756 100644
--- a/src/Simplex_tree/concept/IndexingTag.h
+++ b/src/Simplex_tree/concept/IndexingTag.h
@@ -25,6 +25,6 @@
   * continuous maps to a cell complex, and compute its persistent
   * homology.
   *
-  * Must be linear_indexing_tag. 
+  * Must be `Gudhi::linear_indexing_tag`. 
   */
 struct IndexingTag {};
diff --git a/src/Simplex_tree/concept/SimplexKey.h b/src/Simplex_tree/concept/SimplexKey.h
index ce5b2382..7fdbdd84 100644
--- a/src/Simplex_tree/concept/SimplexKey.h
+++ b/src/Simplex_tree/concept/SimplexKey.h
@@ -22,7 +22,7 @@
 
  /** \brief Key type used as simplex identifier.
   *
-  * Must be <CODE>int</CODE>
+  * Must be a signed integer type.
   */
  struct SimplexKey {};
- 
-\ No newline at end of file
+ 
diff --git a/src/Simplex_tree/concept/SimplexTreeOptions.h b/src/Simplex_tree/concept/SimplexTreeOptions.h
new file mode 100644
index 00000000..add3ebdd
--- /dev/null
+++ b/src/Simplex_tree/concept/SimplexTreeOptions.h
@@ -0,0 +1,41 @@
+ /*    This file is part of the Gudhi Library. The Gudhi library 
+  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+  *    library for computational topology.
+  *
+  *    Author(s):       Marc Glisse
+  *
+  *    Copyright (C) 2015  INRIA Saclay - Ile-de-France (France)
+  *
+  *    This program is free software: you can redistribute it and/or modify
+  *    it under the terms of the GNU General Public License as published by
+  *    the Free Software Foundation, either version 3 of the License, or
+  *    (at your option) any later version.
+  *
+  *    This program is distributed in the hope that it will be useful,
+  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  *    GNU General Public License for more details.
+  *
+  *    You should have received a copy of the GNU General Public License
+  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+  */
+  
+/** \brief Concept of the template parameter for the class `Gudhi::Simplex_tree<SimplexTreeOptions>`.
+ *
+ * One model for this is `Gudhi::Simplex_tree_options_full_featured`. If you want to provide your own, it is recommended that you derive from it and override some parts instead of writing a class from scratch.
+ */
+struct SimplexTreeOptions {
+  /// Forced for now.
+  typedef IndexingTag Indexing_tag;
+  /// Must be a signed integer type. It admits a total order <.
+  typedef VertexHandle Vertex_handle;
+  /// Must be comparable with operator<.
+  typedef FiltrationValue Filtration_value;
+  /// Must be a signed integer type.
+  typedef SimplexKey Simplex_key;
+  /// If true, each simplex has extra storage for one `Simplex_key`. Necessary for `Persistent_cohomology`.
+  static const bool store_key;
+  /// If true, each simplex has extra storage for one `Filtration_value`, and this value is propagated by operations like `Gudhi::Simplex_tree::expansion`. Without it, `Persistent_cohomology` degenerates to computing usual (non-persistent) cohomology.
+  static const bool store_filtration;
+};
+
diff --git a/src/Simplex_tree/concept/VertexHandle.h b/src/Simplex_tree/concept/VertexHandle.h
index 491f0f56..3efbba61 100644
--- a/src/Simplex_tree/concept/VertexHandle.h
+++ b/src/Simplex_tree/concept/VertexHandle.h
@@ -22,5 +22,6 @@
   
 /** \brief Handle type for the vertices of a cell complex.
   * 
-  * Must be int.*/
+  * Must be a signed integer type. <code>operator&lt;</code> defines a total order on it.
+  */
 struct VertexHandle {};
diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt
index 1a3cdfbf..c70cfe35 100644
--- a/src/Simplex_tree/example/CMakeLists.txt
+++ b/src/Simplex_tree/example/CMakeLists.txt
@@ -1,21 +1,24 @@
 cmake_minimum_required(VERSION 2.6)
 project(GUDHISimplexTreeFromFile)
 
-add_executable ( simplex_tree_from_file simplex_tree_from_file.cpp )
-add_test(simplex_tree_from_file_2 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_file ${CMAKE_SOURCE_DIR}/data/points/Klein_bottle_complex.txt 2)
-add_test(simplex_tree_from_file_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_file ${CMAKE_SOURCE_DIR}/data/points/Klein_bottle_complex.txt 3)
+add_executable ( simplex_tree_from_cliques_of_graph simplex_tree_from_cliques_of_graph.cpp )
+add_test(simplex_tree_from_cliques_of_graph_2 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_cliques_of_graph ${CMAKE_SOURCE_DIR}/data/points/Klein_bottle_complex.txt 2)
+add_test(simplex_tree_from_cliques_of_graph_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_cliques_of_graph ${CMAKE_SOURCE_DIR}/data/points/Klein_bottle_complex.txt 3)
 
 add_executable ( simple_simplex_tree simple_simplex_tree.cpp )
 add_test(simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/simple_simplex_tree)
-   
+
+add_executable ( mini_simplex_tree mini_simplex_tree.cpp )
+add_test(mini_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/mini_simplex_tree)
+
 
 # An example with Simplex-tree using CGAL alpha_shapes_3
 if(GMP_FOUND AND CGAL_FOUND)
    message("CGAL_lib = ${CGAL_LIBRARIES_DIR}")
-   message("GMP_LIBRARIES = ${GMP_LIBRARIES}")   
+   message("GMP_LIBRARIES = ${GMP_LIBRARIES}")
    INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
    INCLUDE_DIRECTORIES(${CGAL_INCLUDE_DIRS})
    add_executable ( simplex_tree_from_alpha_shapes_3 simplex_tree_from_alpha_shapes_3.cpp )
    target_link_libraries(simplex_tree_from_alpha_shapes_3 ${GMP_LIBRARIES} ${CGAL_LIBRARY})
    add_test(simplex_tree_from_alpha_shapes_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_alpha_shapes_3 ${CMAKE_SOURCE_DIR}/data/points/bunny_5000)
-endif()  
+endif()
diff --git a/src/Simplex_tree/example/mini_simplex_tree.cpp b/src/Simplex_tree/example/mini_simplex_tree.cpp
new file mode 100644
index 00000000..7e48aaaf
--- /dev/null
+++ b/src/Simplex_tree/example/mini_simplex_tree.cpp
@@ -0,0 +1,69 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Marc Glisse
+ *
+ *    Copyright (C) 2015  INRIA Saclay - Ile-de-France (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <gudhi/Simplex_tree.h>
+#include <iostream>
+#include <initializer_list>
+
+using namespace Gudhi;
+
+struct MyOptions : Simplex_tree_options_full_featured {
+  // Not doing persistence, so we don't need those
+  static const bool store_key = false;
+  static const bool store_filtration = false;
+  // I have few vertices
+  typedef short Vertex_handle;
+};
+typedef Simplex_tree<MyOptions> ST;
+
+// Dictionary should be private, but for now this is the easiest way.
+static_assert(sizeof(ST::Dictionary::value_type) < sizeof(Simplex_tree<>::Dictionary::value_type),
+    "Not storing the filtration and key should save some space");
+
+int main() {
+  ST st;
+
+  /* Complex to build. */
+  /*    1              */
+  /*    o              */
+  /*   /X\             */
+  /*  o---o---o        */
+  /*  2   0   3        */
+
+  auto triangle012 = {0, 1, 2};
+  auto edge03 = {0, 3};
+  st.insert_simplex_and_subfaces(triangle012);
+  st.insert_simplex_and_subfaces(edge03);
+  // FIXME: Remove this line
+  st.set_dimension(2);
+
+  auto edge02 = {0, 2};
+  ST::Simplex_handle e = st.find(edge02);
+  // We are not using filtrations so everything has value 0
+  assert(st.filtration(e) == 0);
+  for (ST::Simplex_handle t : st.cofaces_simplex_range(e, 1)) {
+    // Only coface is 012
+    for (ST::Vertex_handle v : st.simplex_vertex_range(t))  // v in { 0, 1, 2 }
+        std::cout << v;
+      std::cout << '\n';
+  }
+}
diff --git a/src/Simplex_tree/example/simple_simplex_tree.cpp b/src/Simplex_tree/example/simple_simplex_tree.cpp
index 6d20e43e..5146b906 100644
--- a/src/Simplex_tree/example/simple_simplex_tree.cpp
+++ b/src/Simplex_tree/example/simple_simplex_tree.cpp
@@ -20,10 +20,12 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
+#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/Simplex_tree.h>
+
 #include <iostream>
-#include <ctime>
-#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Simplex_tree.h"
+#include <utility>  // for pair
+#include <vector>
 
 using namespace Gudhi;
 
@@ -35,15 +37,11 @@ int main(int argc, char * const argv[]) {
   const Filtration_value SECOND_FILTRATION_VALUE = 0.2;
   const Filtration_value THIRD_FILTRATION_VALUE = 0.3;
   const Filtration_value FOURTH_FILTRATION_VALUE = 0.4;
-  Vertex_handle FIRST_VERTEX_HANDLE = (Vertex_handle) 0;
-  Vertex_handle SECOND_VERTEX_HANDLE = (Vertex_handle) 1;
-  Vertex_handle THIRD_VERTEX_HANDLE = (Vertex_handle) 2;
-  Vertex_handle FOURTH_VERTEX_HANDLE = (Vertex_handle) 3;
 
   // TEST OF INSERTION
   std::cout << "********************************************************************" << std::endl;
   std::cout << "EXAMPLE OF SIMPLE INSERTION" << std::endl;
-  //Construct the Simplex Tree
+  // Construct the Simplex Tree
   Simplex_tree<> simplexTree;
 
   /* Simplex to be inserted:  */
@@ -55,190 +53,149 @@ int main(int argc, char * const argv[]) {
 
   // ++ FIRST
   std::cout << "   * INSERT 0" << std::endl;
-  typeVectorVertex firstSimplexVector;
-  firstSimplexVector.push_back(FIRST_VERTEX_HANDLE);
+  typeVectorVertex firstSimplexVector = { 0 };
   typePairSimplexBool returnValue =
       simplexTree.insert_simplex(firstSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE));
 
   if (returnValue.second == true) {
     std::cout << "   + 0 INSERTED" << std::endl;
-    int nb_simplices = simplexTree.num_simplices() + 1;
-    simplexTree.set_num_simplices(nb_simplices);
   } else {
     std::cout << "   - 0 NOT INSERTED" << std::endl;
   }
 
   // ++ SECOND
   std::cout << "   * INSERT 1" << std::endl;
-  typeVectorVertex secondSimplexVector;
-  secondSimplexVector.push_back(SECOND_VERTEX_HANDLE);
+  typeVectorVertex secondSimplexVector = { 1 };
   returnValue =
       simplexTree.insert_simplex(secondSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE));
 
   if (returnValue.second == true) {
     std::cout << "   + 1 INSERTED" << std::endl;
-    int nb_simplices = simplexTree.num_simplices() + 1;
-    simplexTree.set_num_simplices(nb_simplices);
   } else {
     std::cout << "   - 1 NOT INSERTED" << std::endl;
   }
 
   // ++ THIRD
   std::cout << "   * INSERT (0,1)" << std::endl;
-  typeVectorVertex thirdSimplexVector;
-  thirdSimplexVector.push_back(FIRST_VERTEX_HANDLE);
-  thirdSimplexVector.push_back(SECOND_VERTEX_HANDLE);
+  typeVectorVertex thirdSimplexVector = { 0, 1 };
   returnValue =
       simplexTree.insert_simplex(thirdSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE));
 
   if (returnValue.second == true) {
     std::cout << "   + (0,1) INSERTED" << std::endl;
-    int nb_simplices = simplexTree.num_simplices() + 1;
-    simplexTree.set_num_simplices(nb_simplices);
   } else {
     std::cout << "   - (0,1) NOT INSERTED" << std::endl;
   }
 
   // ++ FOURTH
   std::cout << "   * INSERT 2" << std::endl;
-  typeVectorVertex fourthSimplexVector;
-  fourthSimplexVector.push_back(THIRD_VERTEX_HANDLE);
+  typeVectorVertex fourthSimplexVector = { 2 };
   returnValue =
       simplexTree.insert_simplex(fourthSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE));
 
   if (returnValue.second == true) {
     std::cout << "   + 2 INSERTED" << std::endl;
-    int nb_simplices = simplexTree.num_simplices() + 1;
-    simplexTree.set_num_simplices(nb_simplices);
   } else {
     std::cout << "   - 2 NOT INSERTED" << std::endl;
   }
 
   // ++ FIFTH
   std::cout << "   * INSERT (2,0)" << std::endl;
-  typeVectorVertex fifthSimplexVector;
-  fifthSimplexVector.push_back(THIRD_VERTEX_HANDLE);
-  fifthSimplexVector.push_back(FIRST_VERTEX_HANDLE);
+  typeVectorVertex fifthSimplexVector = { 2, 0 };
   returnValue =
       simplexTree.insert_simplex(fifthSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE));
 
   if (returnValue.second == true) {
     std::cout << "   + (2,0) INSERTED" << std::endl;
-    int nb_simplices = simplexTree.num_simplices() + 1;
-    simplexTree.set_num_simplices(nb_simplices);
   } else {
     std::cout << "   - (2,0) NOT INSERTED" << std::endl;
   }
 
   // ++ SIXTH
   std::cout << "   * INSERT (2,1)" << std::endl;
-  typeVectorVertex sixthSimplexVector;
-  sixthSimplexVector.push_back(THIRD_VERTEX_HANDLE);
-  sixthSimplexVector.push_back(SECOND_VERTEX_HANDLE);
+  typeVectorVertex sixthSimplexVector = { 2, 1 };
   returnValue =
       simplexTree.insert_simplex(sixthSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE));
 
   if (returnValue.second == true) {
     std::cout << "   + (2,1) INSERTED" << std::endl;
-    int nb_simplices = simplexTree.num_simplices() + 1;
-    simplexTree.set_num_simplices(nb_simplices);
   } else {
     std::cout << "   - (2,1) NOT INSERTED" << std::endl;
   }
 
   // ++ SEVENTH
   std::cout << "   * INSERT (2,1,0)" << std::endl;
-  typeVectorVertex seventhSimplexVector;
-  seventhSimplexVector.push_back(THIRD_VERTEX_HANDLE);
-  seventhSimplexVector.push_back(SECOND_VERTEX_HANDLE);
-  seventhSimplexVector.push_back(FIRST_VERTEX_HANDLE);
+  typeVectorVertex seventhSimplexVector = { 2, 1, 0 };
   returnValue =
       simplexTree.insert_simplex(seventhSimplexVector, Filtration_value(THIRD_FILTRATION_VALUE));
 
   if (returnValue.second == true) {
     std::cout << "   + (2,1,0) INSERTED" << std::endl;
-    int nb_simplices = simplexTree.num_simplices() + 1;
-    simplexTree.set_num_simplices(nb_simplices);
   } else {
     std::cout << "   - (2,1,0) NOT INSERTED" << std::endl;
   }
 
   // ++ EIGHTH
   std::cout << "   * INSERT 3" << std::endl;
-  typeVectorVertex eighthSimplexVector;
-  eighthSimplexVector.push_back(FOURTH_VERTEX_HANDLE);
+  typeVectorVertex eighthSimplexVector = { 3 };
   returnValue =
       simplexTree.insert_simplex(eighthSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE));
 
   if (returnValue.second == true) {
     std::cout << "   + 3 INSERTED" << std::endl;
-    int nb_simplices = simplexTree.num_simplices() + 1;
-    simplexTree.set_num_simplices(nb_simplices);
   } else {
     std::cout << "   - 3 NOT INSERTED" << std::endl;
   }
 
   // ++ NINETH
   std::cout << "   * INSERT (3,0)" << std::endl;
-  typeVectorVertex ninethSimplexVector;
-  ninethSimplexVector.push_back(FOURTH_VERTEX_HANDLE);
-  ninethSimplexVector.push_back(FIRST_VERTEX_HANDLE);
+  typeVectorVertex ninethSimplexVector = { 3, 0 };
   returnValue =
       simplexTree.insert_simplex(ninethSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE));
 
   if (returnValue.second == true) {
     std::cout << "   + (3,0) INSERTED" << std::endl;
-    int nb_simplices = simplexTree.num_simplices() + 1;
-    simplexTree.set_num_simplices(nb_simplices);
   } else {
     std::cout << "   - (3,0) NOT INSERTED" << std::endl;
   }
 
   // ++ TENTH
   std::cout << "   * INSERT 0 (already inserted)" << std::endl;
-  typeVectorVertex tenthSimplexVector;
-  tenthSimplexVector.push_back(FIRST_VERTEX_HANDLE);
-  returnValue =
-      simplexTree.insert_simplex(tenthSimplexVector, Filtration_value(FOURTH_FILTRATION_VALUE)); // With a different filtration value
+  typeVectorVertex tenthSimplexVector = { 0 };
+  // With a different filtration value
+  returnValue = simplexTree.insert_simplex(tenthSimplexVector, Filtration_value(FOURTH_FILTRATION_VALUE));
 
   if (returnValue.second == true) {
     std::cout << "   + 0 INSERTED" << std::endl;
-    int nb_simplices = simplexTree.num_simplices() + 1;
-    simplexTree.set_num_simplices(nb_simplices);
   } else {
     std::cout << "   - 0 NOT INSERTED" << std::endl;
   }
 
   // ++ ELEVENTH
   std::cout << "   * INSERT (2,1,0) (already inserted)" << std::endl;
-  typeVectorVertex eleventhSimplexVector;
-  eleventhSimplexVector.push_back(THIRD_VERTEX_HANDLE);
-  eleventhSimplexVector.push_back(SECOND_VERTEX_HANDLE);
-  eleventhSimplexVector.push_back(FIRST_VERTEX_HANDLE);
+  typeVectorVertex eleventhSimplexVector = { 2, 1, 0 };
   returnValue =
       simplexTree.insert_simplex(eleventhSimplexVector, Filtration_value(FOURTH_FILTRATION_VALUE));
 
   if (returnValue.second == true) {
     std::cout << "   + (2,1,0) INSERTED" << std::endl;
-    int nb_simplices = simplexTree.num_simplices() + 1;
-    simplexTree.set_num_simplices(nb_simplices);
   } else {
     std::cout << "   - (2,1,0) NOT INSERTED" << std::endl;
   }
 
   // ++ GENERAL VARIABLE SET
-  simplexTree.set_filtration(FOURTH_FILTRATION_VALUE); // Max filtration value
-  simplexTree.set_dimension(2); // Max dimension = 2 -> (2,1,0)
+  simplexTree.set_filtration(FOURTH_FILTRATION_VALUE);  // Max filtration value
+  simplexTree.set_dimension(2);  // Max dimension = 2 -> (2,1,0)
 
-  std::cout << "********************************************************************" << std::endl;
+  std::cout << "********************************************************************\n";
   // Display the Simplex_tree - Can not be done in the middle of 2 inserts
-  std::cout << "* The complex contains " << simplexTree.num_simplices() << " simplices" << std::endl;
-  std::cout << "   - dimension " << simplexTree.dimension() << "   - filtration " << simplexTree.filtration() << std::endl;
-  std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
+  std::cout << "* The complex contains " << simplexTree.num_simplices() << " simplices\n";
+  std::cout << "   - dimension " << simplexTree.dimension() << "   - filtration " << simplexTree.filtration() << "\n";
+  std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n";
   for (auto f_simplex : simplexTree.filtration_simplex_range()) {
     std::cout << "   " << "[" << simplexTree.filtration(f_simplex) << "] ";
     for (auto vertex : simplexTree.simplex_vertex_range(f_simplex)) {
-      std::cout << (int) vertex << " ";
+      std::cout << static_cast<int>(vertex) << " ";
     }
     std::cout << std::endl;
   }
@@ -262,9 +219,7 @@ int main(int argc, char * const argv[]) {
   else
     std::cout << "***- NO IT ISN'T\n";
 
-  Vertex_handle UNKNOWN_VERTEX_HANDLE = (Vertex_handle) 15;
-  typeVectorVertex unknownSimplexVector;
-  unknownSimplexVector.push_back(UNKNOWN_VERTEX_HANDLE);
+  typeVectorVertex unknownSimplexVector = { 15 };
   simplexFound = simplexTree.find(unknownSimplexVector);
   std::cout << "**************IS THE SIMPLEX {15} IN THE SIMPLEX TREE ?\n";
   if (simplexFound != simplexTree.null_simplex())
@@ -279,9 +234,7 @@ int main(int argc, char * const argv[]) {
   else
     std::cout << "***- NO IT ISN'T\n";
 
-  typeVectorVertex otherSimplexVector;
-  otherSimplexVector.push_back(UNKNOWN_VERTEX_HANDLE);
-  otherSimplexVector.push_back(SECOND_VERTEX_HANDLE);
+  typeVectorVertex otherSimplexVector = { 1, 15 };
   simplexFound = simplexTree.find(otherSimplexVector);
   std::cout << "**************IS THE SIMPLEX {15,1} IN THE SIMPLEX TREE ?\n";
   if (simplexFound != simplexTree.null_simplex())
@@ -289,10 +242,7 @@ int main(int argc, char * const argv[]) {
   else
     std::cout << "***- NO IT ISN'T\n";
 
-  typeVectorVertex invSimplexVector;
-  invSimplexVector.push_back(SECOND_VERTEX_HANDLE);
-  invSimplexVector.push_back(THIRD_VERTEX_HANDLE);
-  invSimplexVector.push_back(FIRST_VERTEX_HANDLE);
+  typeVectorVertex invSimplexVector = { 1, 2, 0 };
   simplexFound = simplexTree.find(invSimplexVector);
   std::cout << "**************IS THE SIMPLEX {1,2,0} IN THE SIMPLEX TREE ?\n";
   if (simplexFound != simplexTree.null_simplex())
diff --git a/src/Simplex_tree/example/simplex_tree_from_alpha_shapes_3.cpp b/src/Simplex_tree/example/simplex_tree_from_alpha_shapes_3.cpp
index 5f797e93..45efe3ed 100644
--- a/src/Simplex_tree/example/simplex_tree_from_alpha_shapes_3.cpp
+++ b/src/Simplex_tree/example/simplex_tree_from_alpha_shapes_3.cpp
@@ -1,24 +1,28 @@
- /*    This file is part of the Gudhi Library. The Gudhi library
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++
-  *    library for computational topology.
-  *
-  *    Author(s):       Vincent Rouvreau
-  *
-  *    Copyright (C) 2014  INRIA Saclay (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2014  INRIA Saclay (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/Simplex_tree.h>
+#include <boost/variant.hpp>
 
 #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
 #include <CGAL/Delaunay_triangulation_3.h>
@@ -27,32 +31,34 @@
 
 #include <fstream>
 #include <cmath>
-
-#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Simplex_tree.h"
-#include <boost/variant.hpp>
+#include <string>
+#include <tuple>  // for tuple<>
+#include <map>
+#include <utility>  // for pair<>
+#include <list>
+#include <vector>
 
 // Alpha_shape_3 templates type definitions
 typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel;
-typedef CGAL::Alpha_shape_vertex_base_3<Kernel>             Vb;
-typedef CGAL::Alpha_shape_cell_base_3<Kernel>               Fb;
-typedef CGAL::Triangulation_data_structure_3<Vb,Fb>         Tds;
-typedef CGAL::Delaunay_triangulation_3<Kernel,Tds>          Triangulation_3;
-typedef CGAL::Alpha_shape_3<Triangulation_3>                Alpha_shape_3;
+typedef CGAL::Alpha_shape_vertex_base_3<Kernel> Vb;
+typedef CGAL::Alpha_shape_cell_base_3<Kernel> Fb;
+typedef CGAL::Triangulation_data_structure_3<Vb, Fb> Tds;
+typedef CGAL::Delaunay_triangulation_3<Kernel, Tds> Triangulation_3;
+typedef CGAL::Alpha_shape_3<Triangulation_3> Alpha_shape_3;
 
 // From file type definition
-typedef Kernel::Point_3                                     Point;
+typedef Kernel::Point_3 Point;
 
 // filtration with alpha values needed type definition
 typedef Alpha_shape_3::FT Alpha_value_type;
-typedef CGAL::Object      Object;
+typedef CGAL::Object Object;
 typedef CGAL::Dispatch_output_iterator<
-  CGAL::cpp11::tuple<Object, Alpha_value_type>,
-  CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >, std::back_insert_iterator< std::vector<Alpha_value_type> >
-                     > > Dispatch;
-typedef Alpha_shape_3::Cell_handle   Cell_handle;
-typedef Alpha_shape_3::Facet         Facet;
-typedef Alpha_shape_3::Edge          Edge;
+CGAL::cpp11::tuple<Object, Alpha_value_type>,
+CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >,
+    std::back_insert_iterator< std::vector<Alpha_value_type> > > > Dispatch;
+typedef Alpha_shape_3::Cell_handle Cell_handle;
+typedef Alpha_shape_3::Facet Facet;
+typedef Alpha_shape_3::Edge Edge;
 typedef std::list<Alpha_shape_3::Vertex_handle> Vertex_list;
 
 // gudhi type definition
@@ -61,225 +67,209 @@ typedef std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex > Alpha_shape
 typedef std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex> Alpha_shape_simplex_tree_pair;
 typedef std::vector< Simplex_tree_vertex > Simplex_tree_vector_vertex;
 
-//#define DEBUG_TRACES
-
-Vertex_list from (const Cell_handle& ch)
-{
-	Vertex_list the_list;
-	for (auto i = 0; i < 4; i++)
-	{
+Vertex_list from(const Cell_handle& ch) {
+  Vertex_list the_list;
+  for (auto i = 0; i < 4; i++) {
 #ifdef DEBUG_TRACES
-		std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl;
-#endif // DEBUG_TRACES
-		the_list.push_back(ch->vertex(i));
-	}
-	return the_list;
+    std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl;
+#endif  // DEBUG_TRACES
+    the_list.push_back(ch->vertex(i));
+  }
+  return the_list;
 }
-Vertex_list from (const Facet& fct)
-{
-	Vertex_list the_list;
-	for (auto i = 0; i < 4; i++)
-	{
-		if (fct.second != i)
-		{
+
+Vertex_list from(const Facet& fct) {
+  Vertex_list the_list;
+  for (auto i = 0; i < 4; i++) {
+    if (fct.second != i) {
 #ifdef DEBUG_TRACES
-			std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl;
-#endif // DEBUG_TRACES
-			the_list.push_back(fct.first->vertex(i));
-		}
-	}
-	return the_list;
+      std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl;
+#endif  // DEBUG_TRACES
+      the_list.push_back(fct.first->vertex(i));
+    }
+  }
+  return the_list;
 }
-Vertex_list from (const Edge& edg)
-{
-	Vertex_list the_list;
-	for (auto i = 0; i < 4; i++)
-	{
-		if ((edg.second == i) ||(edg.third == i))
-		{
+
+Vertex_list from(const Edge& edg) {
+  Vertex_list the_list;
+  for (auto i = 0; i < 4; i++) {
+    if ((edg.second == i) || (edg.third == i)) {
 #ifdef DEBUG_TRACES
-			std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl;
-#endif // DEBUG_TRACES
-			the_list.push_back(edg.first->vertex(i));
-		}
-	}
-	return the_list;
+      std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl;
+#endif  // DEBUG_TRACES
+      the_list.push_back(edg.first->vertex(i));
+    }
+  }
+  return the_list;
 }
-Vertex_list from (const Alpha_shape_3::Vertex_handle& vh)
-{
-	Vertex_list the_list;
+
+Vertex_list from(const Alpha_shape_3::Vertex_handle& vh) {
+  Vertex_list the_list;
 #ifdef DEBUG_TRACES
-	std::cout << "from vertex=" << vh->point() << std::endl;
-#endif // DEBUG_TRACES
-	the_list.push_back(vh);
-	return the_list;
+  std::cout << "from vertex=" << vh->point() << std::endl;
+#endif  // DEBUG_TRACES
+  the_list.push_back(vh);
+  return the_list;
 }
 
+int main(int argc, char * const argv[]) {
+  // program args management
+  if (argc != 2) {
+    std::cerr << "Usage: " << argv[0]
+        << " path_to_file_graph \n";
+    return 0;
+  }
 
-int main (int argc, char * const argv[])
-{
-	// program args management
-	if (argc != 2) {
-		std::cerr << "Usage: " << argv[0]
-		                               << " path_to_file_graph \n";
-		return 0; // ----- >>
-	}
-
-	// Read points from file
-	std::string filegraph   = argv[1];
-	std::list<Point> lp;
-	std::ifstream is(filegraph.c_str());
-	int n;
-	is >> n;
+  // Read points from file
+  std::string filegraph = argv[1];
+  std::list<Point> lp;
+  std::ifstream is(filegraph.c_str());
+  int n;
+  is >> n;
 #ifdef DEBUG_TRACES
-	std::cout << "Reading " << n << " points " << std::endl;
-#endif // DEBUG_TRACES
-	Point p;
-	for( ; n>0 ; n--)    {
-		is >> p;
-		lp.push_back(p);
-	}
+  std::cout << "Reading " << n << " points " << std::endl;
+#endif  // DEBUG_TRACES
+  Point p;
+  for (; n > 0; n--) {
+    is >> p;
+    lp.push_back(p);
+  }
 
-	// alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode.
-	Alpha_shape_3 as(lp.begin(),lp.end(),0,Alpha_shape_3::GENERAL);
+  // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode.
+  Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL);
 #ifdef DEBUG_TRACES
-	std::cout << "Alpha shape computed in GENERAL mode" << std::endl;
-#endif // DEBUG_TRACES
+  std::cout << "Alpha shape computed in GENERAL mode" << std::endl;
+#endif  // DEBUG_TRACES
 
-	// filtration with alpha values from alpha shape
-	std::vector<Object> the_objects;
-	std::vector<Alpha_value_type> the_alpha_values;
+  // filtration with alpha values from alpha shape
+  std::vector<Object> the_objects;
+  std::vector<Alpha_value_type> the_alpha_values;
 
-	Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>( std::back_inserter(the_objects), std::back_inserter(the_alpha_values));
+  Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>(std::back_inserter(the_objects),
+      std::back_inserter(the_alpha_values));
 
-	as.filtration_with_alpha_values(disp);
+  as.filtration_with_alpha_values(disp);
 #ifdef DEBUG_TRACES
-	std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl;
-#endif // DEBUG_TRACES
+  std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl;
+#endif  // DEBUG_TRACES
 
-	Alpha_shape_3::size_type count_vertices = 0;
-	Alpha_shape_3::size_type count_edges    = 0;
-	Alpha_shape_3::size_type count_facets   = 0;
-	Alpha_shape_3::size_type count_cells    = 0;
+  Alpha_shape_3::size_type count_vertices = 0;
+  Alpha_shape_3::size_type count_edges = 0;
+  Alpha_shape_3::size_type count_facets = 0;
+  Alpha_shape_3::size_type count_cells = 0;
 
-	// Loop on objects vector
-	Vertex_list vertex_list;
-	Gudhi::Simplex_tree<> simplex_tree;
-	Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
-	std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
-	for(auto object_iterator: the_objects)
-	{
-		// Retrieve Alpha shape vertex list from object
-		if (const Cell_handle* cell = CGAL::object_cast<Cell_handle>(&object_iterator))
-		{
-			vertex_list = from(*cell);
-			count_cells++;
-		}
-		else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator))
-		{
-			vertex_list = from(*facet);
-			count_facets++;
-		}
-		else if (const Edge* edge = CGAL::object_cast<Edge>(&object_iterator))
-		{
-			vertex_list = from(*edge);
-			count_edges++;
-		}
-		else if (const Alpha_shape_3::Vertex_handle* vertex = CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator))
-		{
-			count_vertices++;
-			vertex_list = from(*vertex);
-		}
-		// Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
-		Simplex_tree_vector_vertex the_simplex_tree;
-		for (auto the_alpha_shape_vertex:vertex_list)
-		{
-			Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
-			if (the_map_iterator == map_cgal_simplex_tree.end())
-			{
-				// alpha shape not found
-				Simplex_tree_vertex vertex = map_cgal_simplex_tree.size();
+  // Loop on objects vector
+  Vertex_list vertex_list;
+  Gudhi::Simplex_tree<> simplex_tree;
+  Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
+  std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
+  for (auto object_iterator : the_objects) {
+    // Retrieve Alpha shape vertex list from object
+    if (const Cell_handle * cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
+      vertex_list = from(*cell);
+      count_cells++;
+    } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) {
+      vertex_list = from(*facet);
+      count_facets++;
+    } else if (const Edge * edge = CGAL::object_cast<Edge>(&object_iterator)) {
+      vertex_list = from(*edge);
+      count_edges++;
+    } else if (const Alpha_shape_3::Vertex_handle * vertex =
+              CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator)) {
+      count_vertices++;
+      vertex_list = from(*vertex);
+    }
+    // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
+    Simplex_tree_vector_vertex the_simplex_tree;
+    for (auto the_alpha_shape_vertex : vertex_list) {
+      Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
+      if (the_map_iterator == map_cgal_simplex_tree.end()) {
+        // alpha shape not found
+        Simplex_tree_vertex vertex = map_cgal_simplex_tree.size();
 #ifdef DEBUG_TRACES
-				std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert_simplex " << vertex << std::endl;
-#endif // DEBUG_TRACES
-				the_simplex_tree.push_back(vertex);
-				map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex,vertex));
-			} else
-			{
-				// alpha shape found
-				Simplex_tree_vertex vertex = the_map_iterator->second;
+        std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert_simplex " << vertex << "\n";
+#endif  // DEBUG_TRACES
+        the_simplex_tree.push_back(vertex);
+        map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex));
+      } else {
+        // alpha shape found
+        Simplex_tree_vertex vertex = the_map_iterator->second;
 #ifdef DEBUG_TRACES
-				std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
-#endif // DEBUG_TRACES
-				the_simplex_tree.push_back(vertex);
-			}
-		}
-		// Construction of the simplex_tree
+        std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
+#endif  // DEBUG_TRACES
+        the_simplex_tree.push_back(vertex);
+      }
+    }
+    // Construction of the simplex_tree
 #ifdef DEBUG_TRACES
-		std::cout << "filtration = " << *the_alpha_value_iterator << std::endl;
-#endif // DEBUG_TRACES
-		simplex_tree.insert_simplex(the_simplex_tree, std::sqrt(*the_alpha_value_iterator));
-		if (the_alpha_value_iterator != the_alpha_values.end())
-			++the_alpha_value_iterator;
-		else
-			std::cout << "This shall not happen" << std::endl;
-	}
+    std::cout << "filtration = " << *the_alpha_value_iterator << std::endl;
+#endif  // DEBUG_TRACES
+    simplex_tree.insert_simplex(the_simplex_tree, std::sqrt(*the_alpha_value_iterator));
+    if (the_alpha_value_iterator != the_alpha_values.end())
+      ++the_alpha_value_iterator;
+    else
+      std::cerr << "This shall not happen" << std::endl;
+  }
 #ifdef DEBUG_TRACES
-	std::cout << "vertices \t\t" << count_vertices << std::endl;
-	std::cout << "edges \t\t"    << count_edges << std::endl;
-	std::cout << "facets \t\t"   << count_facets << std::endl;
-	std::cout << "cells \t\t"    << count_cells << std::endl;
+  std::cout << "vertices \t\t" << count_vertices << std::endl;
+  std::cout << "edges \t\t" << count_edges << std::endl;
+  std::cout << "facets \t\t" << count_facets << std::endl;
+  std::cout << "cells \t\t" << count_cells << std::endl;
 
 
-	std::cout << "Information of the Simplex Tree: " << std::endl;
-	std::cout << "  Number of vertices = " << simplex_tree.num_vertices() << " ";
-	std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
-#endif // DEBUG_TRACES
+  std::cout << "Information of the Simplex Tree:\n";
+  std::cout << "  Number of vertices = " << simplex_tree.num_vertices() << " ";
+  std::cout << "  Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
+#endif  // DEBUG_TRACES
 
 #ifdef DEBUG_TRACES
-	std::cout << "Iterator on vertices: " << std::endl;
-	for( auto vertex : simplex_tree.complex_vertex_range() )
-	{ std::cout << vertex << " "; }
-#endif // DEBUG_TRACES
+  std::cout << "Iterator on vertices: \n";
+  for (auto vertex : simplex_tree.complex_vertex_range()) {
+    std::cout << vertex << " ";
+  }
+#endif  // DEBUG_TRACES
 
-	std::cout << simplex_tree << std::endl;
+  std::cout << simplex_tree << std::endl;
 
 #ifdef DEBUG_TRACES
-	std::cout << std::endl << std::endl << "Iterator on simplices: " << std::endl;
-	for( auto simplex : simplex_tree.complex_simplex_range() )
-	{
-		std::cout << "   ";
-		for( auto vertex : simplex_tree.simplex_vertex_range(simplex) ) { std::cout << vertex << " "; }
-		std::cout << std::endl;
-	}
-#endif // DEBUG_TRACES
+  std::cout << std::endl << std::endl << "Iterator on simplices:\n";
+  for (auto simplex : simplex_tree.complex_simplex_range()) {
+    std::cout << "   ";
+    for (auto vertex : simplex_tree.simplex_vertex_range(simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << std::endl;
+  }
+#endif  // DEBUG_TRACES
 #ifdef DEBUG_TRACES
-	std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
-	for( auto f_simplex : simplex_tree.filtration_simplex_range() )
-	{ std::cout << "   " << "[" << simplex_tree.filtration(f_simplex) << "] ";
-	for( auto vertex : simplex_tree.simplex_vertex_range(f_simplex) )
-	{ std::cout << vertex << " "; }
-	std::cout << std::endl;
-	}
-#endif // DEBUG_TRACES
+  std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:\n";
+  for (auto f_simplex : simplex_tree.filtration_simplex_range()) {
+    std::cout << "   " << "[" << simplex_tree.filtration(f_simplex) << "] ";
+    for (auto vertex : simplex_tree.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << std::endl;
+  }
+#endif  // DEBUG_TRACES
 #ifdef DEBUG_TRACES
-	std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, and their boundary simplices:" << std::endl;
-	for( auto f_simplex : simplex_tree.filtration_simplex_range() )
-	{
-		std::cout << "   " << "[" << simplex_tree.filtration(f_simplex) << "] ";
-		for( auto vertex : simplex_tree.simplex_vertex_range(f_simplex) )
-		{ std::cout << vertex << " "; }
-		std::cout << std::endl;
+  std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, and their boundary simplices:\n";
+  for (auto f_simplex : simplex_tree.filtration_simplex_range()) {
+    std::cout << "   " << "[" << simplex_tree.filtration(f_simplex) << "] ";
+    for (auto vertex : simplex_tree.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << std::endl;
 
-		for( auto b_simplex : simplex_tree.boundary_simplex_range(f_simplex) )
-		{
-			std::cout << "      " << "[" << simplex_tree.filtration(b_simplex) << "] ";
-			for( auto vertex : simplex_tree.simplex_vertex_range(b_simplex) )
-			{ std::cout << vertex << " "; }
-			std::cout << std::endl;
-		}
-	}
-#endif // DEBUG_TRACES
+    for (auto b_simplex : simplex_tree.boundary_simplex_range(f_simplex)) {
+      std::cout << "      " << "[" << simplex_tree.filtration(b_simplex) << "] ";
+      for (auto vertex : simplex_tree.simplex_vertex_range(b_simplex)) {
+        std::cout << vertex << " ";
+      }
+      std::cout << std::endl;
+    }
+  }
+#endif  // DEBUG_TRACES
 
-	return 0;
+  return 0;
 }
diff --git a/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp b/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp
new file mode 100644
index 00000000..58085014
--- /dev/null
+++ b/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp
@@ -0,0 +1,114 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Clément Maria
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <gudhi/reader_utils.h>
+#include <gudhi/Simplex_tree.h>
+
+#include <iostream>
+#include <ctime>
+#include <string>
+
+using namespace Gudhi;
+
+int main(int argc, char * const argv[]) {
+  if (argc != 3) {
+    std::cerr << "Usage: " << argv[0]
+        << " path_to_file_graph max_dim \n";
+    return 0;
+  }
+  std::string filegraph = argv[1];
+  int max_dim = atoi(argv[2]);
+
+  clock_t start, end;
+  // Construct the Simplex Tree
+  Simplex_tree<> st;
+
+  start = clock();
+  auto g = read_graph(filegraph);
+  // insert the graph in the simplex tree as 1-skeleton
+  st.insert_graph(g);
+  end = clock();
+  std::cout << "Insert the 1-skeleton in the simplex tree in "
+      << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
+
+  start = clock();
+  // expand the 1-skeleton until dimension max_dim
+  st.expansion(max_dim);
+  end = clock();
+  std::cout << "max_dim = " << max_dim << "\n";
+  std::cout << "Expand the simplex tree in "
+      << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
+
+  std::cout << "Information of the Simplex Tree: " << std::endl;
+  std::cout << "  Number of vertices = " << st.num_vertices() << " ";
+  std::cout << "  Number of simplices = " << st.num_simplices() << std::endl;
+  std::cout << std::endl << std::endl;
+
+  std::cout << "Iterator on vertices: ";
+  for (auto vertex : st.complex_vertex_range()) {
+    std::cout << vertex << " ";
+  }
+
+  std::cout << std::endl;
+
+  std::cout << std::endl << std::endl;
+
+  std::cout << "Iterator on simplices: " << std::endl;
+  for (auto simplex : st.complex_simplex_range()) {
+    std::cout << "   ";
+    for (auto vertex : st.simplex_vertex_range(simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << std::endl;
+  }
+
+  std::cout << std::endl << std::endl;
+
+  std::cout << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
+  for (auto f_simplex : st.filtration_simplex_range()) {
+    std::cout << "   " << "[" << st.filtration(f_simplex) << "] ";
+    for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << std::endl;
+  }
+
+  std::cout << std::endl << std::endl;
+
+  std::cout << "Iterator on Simplices in the filtration, and their boundary simplices:" << std::endl;
+  for (auto f_simplex : st.filtration_simplex_range()) {
+    std::cout << "   " << "[" << st.filtration(f_simplex) << "] ";
+    for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << std::endl;
+
+    for (auto b_simplex : st.boundary_simplex_range(f_simplex)) {
+      std::cout << "      " << "[" << st.filtration(b_simplex) << "] ";
+      for (auto vertex : st.simplex_vertex_range(b_simplex)) {
+        std::cout << vertex << " ";
+      }
+      std::cout << std::endl;
+    }
+  }
+  return 0;
+}
diff --git a/src/Simplex_tree/example/simplex_tree_from_file.cpp b/src/Simplex_tree/example/simplex_tree_from_file.cpp
deleted file mode 100644
index 20e8f067..00000000
--- a/src/Simplex_tree/example/simplex_tree_from_file.cpp
+++ /dev/null
@@ -1,104 +0,0 @@
- /*    This file is part of the Gudhi Library. The Gudhi library
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++
-  *    library for computational topology.
-  *
-  *    Author(s):       Clément Maria
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-
-#include <iostream>
-#include <ctime>
-#include "gudhi/reader_utils.h"
-#include "gudhi/Simplex_tree.h"
-
-using namespace Gudhi;
-
-int main (int argc, char * const argv[])
-{
-  if (argc != 3) {
-    std::cerr << "Usage: " << argv[0]
-      << " path_to_file_graph max_dim \n";
-    return 0;
-  }
-  std::string filegraph   = argv[1];
-  int max_dim       = atoi(argv[2]);
-
-  clock_t start, end;
-  //Construct the Simplex Tree
-  Simplex_tree<> st;
-
-  start = clock();
-  auto g = read_graph(filegraph);
-  st.insert_graph (g); //insert the graph in the simplex tree as 1-skeleton
-  end = clock();
-  std::cout << "Insert the 1-skeleton in the simplex tree in "
-       << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
-
-  start = clock();
-  st.expansion ( max_dim ); //expand the 1-skeleton until dimension max_dim
-  end = clock();
-  std::cout << "max_dim = " << max_dim << "\n";
-  std::cout << "Expand the simplex tree in "
-       << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
-
-  std::cout << "Information of the Simplex Tree: " << std::endl;
-  std::cout << "  Number of vertices = " << st.num_vertices() << " ";
-  std::cout << "  Number of simplices = " << st.num_simplices() << std::endl;
-  std::cout << std::endl << std::endl;
-
-  std::cout << "Iterator on vertices: ";
-    for( auto vertex : st.complex_vertex_range() ) { std::cout << vertex << " "; }
-
-  std::cout << std::endl;
-
-  std::cout << std::endl << std::endl;
-
-  std::cout << "Iterator on simplices: " << std::endl;
-  for( auto simplex : st.complex_simplex_range() )
-  {
-    std::cout << "   ";
-    for( auto vertex : st.simplex_vertex_range(simplex) ) { std::cout << vertex << " "; }
-    std::cout << std::endl;
-  }
-
-  std::cout << std::endl << std::endl;
-
-  std::cout << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
-  for( auto f_simplex : st.filtration_simplex_range() )
-  { std::cout << "   " << "[" << st.filtration(f_simplex) << "] ";
-    for( auto vertex : st.simplex_vertex_range(f_simplex) )
-      { std::cout << vertex << " "; } std::cout << std::endl;
-  }
-
-  std::cout << std::endl << std::endl;
-
-  std::cout << "Iterator on Simplices in the filtration, and their boundary simplices:" << std::endl;
-  for( auto f_simplex : st.filtration_simplex_range() )
-  {
-    std::cout << "   " << "[" << st.filtration(f_simplex) << "] ";
-    for( auto vertex : st.simplex_vertex_range(f_simplex) )
-      { std::cout << vertex << " "; } std::cout << std::endl;
-
-    for( auto b_simplex : st.boundary_simplex_range(f_simplex) )
-    {
-      std::cout << "      " << "[" << st.filtration(b_simplex) << "] ";
-    for( auto vertex : st.simplex_vertex_range(b_simplex) )
-      { std::cout << vertex << " "; } std::cout << std::endl;
-    }
-  }
-  return 0;
-}
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 5d3753ca..ea61fa2e 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -20,14 +20,17 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_H_
-#define SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_H_
+#ifndef SIMPLEX_TREE_H_
+#define SIMPLEX_TREE_H_
 
 #include <gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h>
 #include <gudhi/Simplex_tree/Simplex_tree_siblings.h>
 #include <gudhi/Simplex_tree/Simplex_tree_iterators.h>
 #include <gudhi/Simplex_tree/indexing_tag.h>
 
+#include <gudhi/reader_utils.h>
+#include <gudhi/graph_simplicial_complex.h>
+
 #include <boost/container/flat_map.hpp>
 #include <boost/iterator/transform_iterator.hpp>
 #include <boost/graph/adjacency_list.hpp>
@@ -35,10 +38,11 @@
 #include <algorithm>
 #include <utility>
 #include <vector>
-#include <iostream>
+#include <functional>  // for greater<>
+#include <initializer_list>
 
 namespace Gudhi {
-  
+
 /** \defgroup simplex_tree Filtered Complexes
  *
  * A simplicial complex \f$\mathbf{K}\f$
@@ -73,6 +77,17 @@ namespace Gudhi {
  * \copyright GNU General Public License v3.
  * @{
  */
+
+/// Model of SimplexTreeOptions.
+struct Simplex_tree_options_full_featured {
+  typedef linear_indexing_tag Indexing_tag;
+  typedef int Vertex_handle;
+  typedef double Filtration_value;
+  typedef int Simplex_key;
+  static const bool store_key = true;
+  static const bool store_filtration = true;
+};
+
 /**
  * \brief Simplex Tree data structure for representing simplicial complexes.
  *
@@ -84,46 +99,69 @@ namespace Gudhi {
  * \implements FilteredComplex
  *
  */
-template<typename IndexingTag = linear_indexing_tag,
-    typename FiltrationValue = double, typename SimplexKey = int  // must be a signed integer type
-    , typename VertexHandle = int  // must be a signed integer type, int convertible to it
-//         , bool ContiguousVertexHandles = true   //true is Vertex_handles are exactly the set [0;n)
->
+
+template<typename SimplexTreeOptions = Simplex_tree_options_full_featured>
 class Simplex_tree {
  public:
-  typedef IndexingTag Indexing_tag;
+  typedef SimplexTreeOptions Options;
+  typedef typename Options::Indexing_tag Indexing_tag;
   /** \brief Type for the value of the filtration function.
    *
    * Must be comparable with <. */
-  typedef FiltrationValue Filtration_value;
+  typedef typename Options::Filtration_value Filtration_value;
   /** \brief Key associated to each simplex.
    *
    * Must be a signed integer type. */
-  typedef SimplexKey Simplex_key;
+  typedef typename Options::Simplex_key Simplex_key;
   /** \brief Type for the vertex handle.
    *
    * Must be a signed integer type. It admits a total order <. */
-  typedef VertexHandle Vertex_handle;
+  typedef typename Options::Vertex_handle Vertex_handle;
 
   /* Type of node in the simplex tree. */
   typedef Simplex_tree_node_explicit_storage<Simplex_tree> Node;
   /* Type of dictionary Vertex_handle -> Node for traversing the simplex tree. */
+  // Note: this wastes space when Vertex_handle is 32 bits and Node is aligned on 64 bits. It would be better to use a
+  // flat_set (with our own comparator) where we can control the layout of the struct (put Vertex_handle and
+  // Simplex_key next to each other).
   typedef typename boost::container::flat_map<Vertex_handle, Node> Dictionary;
 
-  friend class Simplex_tree_node_explicit_storage< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> >;
-  friend class Simplex_tree_siblings< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle>, Dictionary>;
-  friend class Simplex_tree_simplex_vertex_iterator< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> >;
-  friend class Simplex_tree_boundary_simplex_iterator< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> >;
-  friend class Simplex_tree_complex_simplex_iterator< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> >;
-  friend class Simplex_tree_skeleton_simplex_iterator< Simplex_tree<FiltrationValue, SimplexKey, VertexHandle> >;
-
   /* \brief Set of nodes sharing a same parent in the simplex tree. */
   /* \brief Set of nodes sharing a same parent in the simplex tree. */
   typedef Simplex_tree_siblings<Simplex_tree, Dictionary> Siblings;
 
+  struct Key_simplex_base_real {
+    Key_simplex_base_real() : key_(-1) {}
+    void assign_key(Simplex_key k) { key_ = k; }
+    Simplex_key key() const { return key_; }
+   private:
+    Simplex_key key_;
+  };
+  struct Key_simplex_base_dummy {
+    Key_simplex_base_dummy() {}
+    void assign_key(Simplex_key) { }
+    Simplex_key key() const { assert(false); return -1; }
+  };
+  typedef typename std::conditional<Options::store_key, Key_simplex_base_real, Key_simplex_base_dummy>::type Key_simplex_base;
+
+  struct Filtration_simplex_base_real {
+    Filtration_simplex_base_real() : filt_(0) {}
+    void assign_filtration(Filtration_value f) { filt_ = f; }
+    Filtration_value filtration() const { return filt_; }
+   private:
+    Filtration_value filt_;
+  };
+  struct Filtration_simplex_base_dummy {
+    Filtration_simplex_base_dummy() {}
+    void assign_filtration(Filtration_value f) { assert(f == 0); }
+    Filtration_value filtration() const { return 0; }
+  };
+  typedef typename std::conditional<Options::store_filtration, Filtration_simplex_base_real,
+    Filtration_simplex_base_dummy>::type Filtration_simplex_base;
+
  public:
   /** \brief Handle type to a simplex contained in the simplicial complex represented
-   * byt he simplex tree. */
+   * by the simplex tree. */
   typedef typename Dictionary::iterator Simplex_handle;
 
  private:
@@ -157,6 +195,8 @@ class Simplex_tree {
   typedef Simplex_tree_simplex_vertex_iterator<Simplex_tree> Simplex_vertex_iterator;
   /** \brief Range over the vertices of a simplex. */
   typedef boost::iterator_range<Simplex_vertex_iterator> Simplex_vertex_range;
+  /** \brief Range over the cofaces of a simplex. */
+  typedef std::vector<Simplex_handle> Cofaces_simplex_range;
   /** \brief Iterator over the simplices of the boundary of a simplex.
    *
    * 'value_type' is Simplex_handle. */
@@ -177,24 +217,23 @@ class Simplex_tree {
   /** \brief Range over the simplices of the skeleton of the simplicial complex, for a given 
    * dimension. */
   typedef boost::iterator_range<Skeleton_simplex_iterator> Skeleton_simplex_range;
+  /** \brief Range over the simplices of the simplicial complex, ordered by the filtration. */
+  typedef std::vector<Simplex_handle> Filtration_simplex_range;
   /** \brief Iterator over the simplices of the simplicial complex, ordered by the filtration.
    *
    * 'value_type' is Simplex_handle. */
-  typedef typename std::vector<Simplex_handle>::iterator Filtration_simplex_iterator;
-  /** \brief Range over the simplices of the simplicial complex, ordered by the filtration. */
-  typedef boost::iterator_range<Filtration_simplex_iterator> Filtration_simplex_range;
+  typedef typename Filtration_simplex_range::const_iterator Filtration_simplex_iterator;
 
   /* @} */  // end name range and iterator types
   /** \name Range and iterator methods
    * @{ */
 
-  /** \brief Returns a range over the vertices of the simplicial complex.
-   *
+  /** \brief Returns a range over the vertices of the simplicial complex. 
    * The order is increasing according to < on Vertex_handles.*/
   Complex_vertex_range complex_vertex_range() {
     return Complex_vertex_range(
-        boost::make_transform_iterator(root_.members_.begin(), return_first()),
-        boost::make_transform_iterator(root_.members_.end(), return_first()));
+                                boost::make_transform_iterator(root_.members_.begin(), return_first()),
+                                boost::make_transform_iterator(root_.members_.end(), return_first()));
   }
 
   /** \brief Returns a range over the simplices of the simplicial complex.
@@ -234,18 +273,15 @@ class Simplex_tree {
    * order is used.
    *
    * The filtration must be valid. If the filtration has not been initialized yet, the
-   * method initializes it (i.e. order the simplices). */
-  Filtration_simplex_range filtration_simplex_range(Indexing_tag) {
+   * method initializes it (i.e. order the simplices). If the complex has changed since the last time the filtration
+   * was initialized, please call `initialize_filtration()` to recompute it. */
+  Filtration_simplex_range const& filtration_simplex_range(Indexing_tag = Indexing_tag()) {
     if (filtration_vect_.empty()) {
       initialize_filtration();
     }
-    return Filtration_simplex_range(filtration_vect_.begin(),
-                                    filtration_vect_.end());
+    return filtration_vect_;
   }
 
-  Filtration_simplex_range filtration_simplex_range() {
-    return filtration_simplex_range(Indexing_tag());
-  }
   /** \brief Returns a range over the vertices of a simplex.
    *
    * The order in which the vertices are visited is the decreasing order for < on Vertex_handles,
@@ -253,6 +289,7 @@ class Simplex_tree {
    * equal to \f$(-1)^{\text{dim} \sigma}\f$ the canonical orientation on the simplex.
    */
   Simplex_vertex_range simplex_vertex_range(Simplex_handle sh) {
+    assert(sh != null_simplex());  // Empty simplex
     return Simplex_vertex_range(Simplex_vertex_iterator(this, sh),
                                 Simplex_vertex_iterator(this));
   }
@@ -283,11 +320,48 @@ class Simplex_tree {
   /** \brief Constructs an empty simplex tree. */
   Simplex_tree()
       : null_vertex_(-1),
-        threshold_(0),
-        num_simplices_(0),
-        root_(NULL, null_vertex_),
-        filtration_vect_(),
-        dimension_(-1) {
+      threshold_(0),
+      root_(nullptr, null_vertex_),
+      filtration_vect_(),
+      dimension_(-1) { }
+
+  /** \brief User-defined copy constructor reproduces the whole tree structure. */
+  Simplex_tree(const Simplex_tree& simplex_source)
+      : null_vertex_(simplex_source.null_vertex_),
+      threshold_(simplex_source.threshold_),
+      filtration_vect_(),
+      dimension_(simplex_source.dimension_) {
+    auto root_source = simplex_source.root_;
+    auto memb_source = root_source.members();
+    root_ = Siblings(nullptr, null_vertex_, memb_source);
+    rec_copy(&root_, &root_source);
+  }
+
+  /** \brief depth first search, inserts simplices when reaching a leaf. */
+  void rec_copy(Siblings *sib, Siblings *sib_source) {
+    for (auto sh = sib->members().begin(), sh_source = sib_source->members().begin();
+         sh != sib->members().end(); ++sh, ++sh_source) {
+      if (has_children(sh_source)) {
+        Siblings * newsib = new Siblings(sib, sh_source->first);
+        newsib->members_.reserve(sh_source->second.children()->members().size());
+        for (auto & child : sh_source->second.children()->members())
+          newsib->members_.emplace_hint(newsib->members_.end(), child.first, Node(sib, child.second.filtration()));
+        rec_copy(newsib, sh_source->second.children());
+        sh->second.assign_children(newsib);
+      }
+    }
+  }
+
+  /** \brief User-defined move constructor moves the whole tree structure. */
+  Simplex_tree(Simplex_tree && old)
+      : null_vertex_(std::move(old.null_vertex_)),
+      threshold_(std::move(old.threshold_)),
+      root_(std::move(old.root_)),
+      filtration_vect_(std::move(old.filtration_vect_)),
+      dimension_(std::move(old.dimension_)) {
+    old.dimension_ = -1;
+    old.threshold_ = 0;
+    old.root_ = Siblings(nullptr, null_vertex_);
   }
 
   /** \brief Destructor; deallocates the whole tree structure. */
@@ -300,7 +374,7 @@ class Simplex_tree {
   }
   /** @} */  // end constructor/destructor
  private:
-  /** Recursive deletion. */
+  // Recursive deletion
   void rec_delete(Siblings * sib) {
     for (auto sh = sib->members().begin(); sh != sib->members().end(); ++sh) {
       if (has_children(sh)) {
@@ -311,72 +385,135 @@ class Simplex_tree {
   }
 
  public:
+  /** \brief Checks if two simplex trees are equal. */
+  bool operator==(Simplex_tree& st2) {
+    if ((null_vertex_ != st2.null_vertex_) ||
+        (threshold_ != st2.threshold_) ||
+        (dimension_ != st2.dimension_))
+      return false;
+    return rec_equal(&root_, &st2.root_);
+  }
+
+  /** \brief Checks if two simplex trees are different. */
+  bool operator!=(Simplex_tree& st2) {
+    return (!(*this == st2));
+  }
+
+ private:
+  /** rec_equal: Checks recursively whether or not two simplex trees are equal, using depth first search. */
+  bool rec_equal(Siblings* s1, Siblings* s2) {
+    if (s1->members().size() != s2->members().size())
+      return false;
+    for (auto sh1 = s1->members().begin(), sh2 = s2->members().begin();
+         (sh1 != s1->members().end() && sh2 != s2->members().end()); ++sh1, ++sh2) {
+      if (sh1->first != sh2->first || sh1->second.filtration() != sh2->second.filtration())
+        return false;
+      if (has_children(sh1) != has_children(sh2))
+        return false;
+      // Recursivity on children only if both have children
+      else if (has_children(sh1))
+        if (!rec_equal(sh1->second.children(), sh2->second.children()))
+          return false;
+    }
+    return true;
+  }
+
+ public:
   /** \brief Returns the key associated to a simplex.
    *
-   * The filtration must be initialized. */
-  Simplex_key key(Simplex_handle sh) {
+   * The filtration must be initialized.
+   * \pre SimplexTreeOptions::store_key
+   */
+  static Simplex_key key(Simplex_handle sh) {
     return sh->second.key();
   }
+
   /** \brief Returns the simplex associated to a key.
    *
-   * The filtration must be initialized. */
-  Simplex_handle simplex(Simplex_key key) {
+   * The filtration must be initialized.
+   * \pre SimplexTreeOptions::store_key
+   */
+  Simplex_handle simplex(Simplex_key key) const {
     return filtration_vect_[key];
   }
+
   /** \brief Returns the filtration value of a simplex.
    *
-   * Called on the null_simplex, returns INFINITY. */
-  Filtration_value filtration(Simplex_handle sh) const {
+   * Called on the null_simplex, returns INFINITY.
+   * If SimplexTreeOptions::store_filtration is false, returns 0.
+   */
+  static Filtration_value filtration(Simplex_handle sh) {
     if (sh != null_simplex()) {
       return sh->second.filtration();
     } else {
       return INFINITY;
-    }  // filtration(); }
+    }
   }
+
   /** \brief Returns an upper bound of the filtration values of the simplices. */
   Filtration_value filtration() const {
     return threshold_;
   }
+
   /** \brief Returns a Simplex_handle different from all Simplex_handles
    * associated to the simplices in the simplicial complex.
    *
    * One can call filtration(null_simplex()). */
-  Simplex_handle null_simplex() const {
-    return Dictionary_it(NULL);
+  static Simplex_handle null_simplex() {
+    return Dictionary_it(nullptr);
   }
+
   /** \brief Returns a key different for all keys associated to the
    * simplices of the simplicial complex. */
-  Simplex_key null_key() const {
+  static Simplex_key null_key() {
     return -1;
   }
+
   /** \brief Returns a Vertex_handle different from all Vertex_handles associated
    * to the vertices of the simplicial complex. */
   Vertex_handle null_vertex() const {
     return null_vertex_;
   }
+
   /** \brief Returns the number of vertices in the complex. */
   size_t num_vertices() const {
     return root_.members_.size();
   }
-  /** \brief Returns the number of simplices in the complex.
-   *
-   * Does not count the empty simplex. */
-  unsigned int num_simplices() const {
-    return num_simplices_;
+
+ public:
+  /** \brief returns the number of simplices in the simplex_tree. */
+  size_t num_simplices() {
+    return num_simplices(&root_);
   }
 
+ private:
+  /** \brief returns the number of simplices in the simplex_tree. */
+  size_t num_simplices(Siblings * sib) {
+    auto sib_begin = sib->members().begin();
+    auto sib_end = sib->members().end();
+    size_t simplices_number = sib_end - sib_begin;
+    for (auto sh = sib_begin; sh != sib_end; ++sh) {
+      if (has_children(sh)) {
+        simplices_number += num_simplices(sh->second.children());
+      }
+    }
+    return simplices_number;
+  }
+
+ public:
   /** \brief Returns the dimension of a simplex.
    *
    * Must be different from null_simplex().*/
   int dimension(Simplex_handle sh) {
     Siblings * curr_sib = self_siblings(sh);
     int dim = 0;
-    while (curr_sib != NULL) {
+    while (curr_sib != nullptr) {
       ++dim;
       curr_sib = curr_sib->oncles();
     }
     return dim - 1;
   }
+
   /** \brief Returns an upper bound on the dimension of the simplicial complex. */
   int dimension() const {
     return dimension_;
@@ -388,25 +525,34 @@ class Simplex_tree {
     return (sh->second.children()->parent() == sh->first);
   }
 
-  /** \brief Given a range of Vertex_handles, returns the Simplex_handle
+    /** \brief Given a range of Vertex_handles, returns the Simplex_handle
    * of the simplex in the simplicial complex containing the corresponding
    * vertices. Return null_simplex() if the simplex is not in the complex.
    *
-   * The type RandomAccessVertexRange must be a range for which .begin() and
-   * .end() return random access iterators, with <CODE>value_type</CODE>
-   * <CODE>Vertex_handle</CODE>.
+   * The type InputVertexRange must be a range of <CODE>Vertex_handle</CODE>
+   * on which we can call std::begin() function
    */
-  template<class RandomAccessVertexRange>
-  Simplex_handle find(RandomAccessVertexRange & s) {
-    if (s.begin() == s.end())
-      std::cerr << "Empty simplex \n";
-
-    sort(s.begin(), s.end());
+  template<class InputVertexRange=std::initializer_list<Vertex_handle>>
+  Simplex_handle find(const InputVertexRange & s) {
+    auto first = std::begin(s);
+    auto last = std::end(s);
+
+    if (first == last)
+      return null_simplex();  // ----->>
+
+    // Copy before sorting
+    std::vector<Vertex_handle> copy(first, last);
+    std::sort(std::begin(copy), std::end(copy));
+    return find_simplex(copy);
+  }
 
+ private:
+  /** Find function, with a sorted range of vertices. */
+  Simplex_handle find_simplex(const std::vector<Vertex_handle> & simplex) {
     Siblings * tmp_sib = &root_;
     Dictionary_it tmp_dit;
-    Vertex_handle last = s[s.size() - 1];
-    for (auto v : s) {
+    Vertex_handle last = simplex.back();
+    for (auto v : simplex) {
       tmp_dit = tmp_sib->members_.find(v);
       if (tmp_dit == tmp_sib->members_.end()) {
         return null_simplex();
@@ -424,8 +570,39 @@ class Simplex_tree {
   Simplex_handle find_vertex(Vertex_handle v) {
     return root_.members_.begin() + v;
   }
-//{ return root_.members_.find(v); }
+  //{ return root_.members_.find(v); }
+
+ private:
+  /** \brief Inserts a simplex represented by a vector of vertex.
+   \warning the vector must be sorted by increasing vertex handle order */
+  std::pair<Simplex_handle, bool> insert_vertex_vector(const std::vector<Vertex_handle>& simplex,
+                                                     Filtration_value filtration) {
+    Siblings * curr_sib = &root_;
+    std::pair<Simplex_handle, bool> res_insert;
+    auto vi = simplex.begin();
+    for (; vi != simplex.end() - 1; ++vi) {
+      res_insert = curr_sib->members_.emplace(*vi, Node(curr_sib, filtration));
+      if (!(has_children(res_insert.first))) {
+        res_insert.first->second.assign_children(new Siblings(curr_sib, *vi));
+      }
+      curr_sib = res_insert.first->second.children();
+    }
+    res_insert = curr_sib->members_.emplace(*vi, Node(curr_sib, filtration));
+    if (!res_insert.second) {
+      // if already in the complex
+      if (res_insert.first->second.filtration() > filtration) {
+        // if filtration value modified
+        res_insert.first->second.assign_filtration(filtration);
+        return res_insert;
+      }
+      // if filtration value unchanged
+      return std::pair<Simplex_handle, bool>(null_simplex(), false);
+    }
+    // otherwise the insertion has succeeded
+    return res_insert;
+  }
 
+ public:
   /** \brief Insert a simplex, represented by a range of Vertex_handles, in the simplicial complex.
    *
    * @param[in]  simplex    range of Vertex_handles, representing the vertices of the new simplex
@@ -435,7 +612,7 @@ class Simplex_tree {
    * to the new simplex.
    * If the insertion fails (the simplex is already there), the bool is set to false. If the insertion
    * fails and the simplex already in the complex has a filtration value strictly bigger than 'filtration',
-   * we assign this simplex with the new value 'filtration', and set the Simplex_handle filed of the
+   * we assign this simplex with the new value 'filtration', and set the Simplex_handle field of the
    * output pair to the Simplex_handle of the simplex. Otherwise, we set the Simplex_handle part to
    * null_simplex.
    *
@@ -447,76 +624,107 @@ class Simplex_tree {
    * The filtration value
    * assigned to the new simplex must preserve the monotonicity of the filtration.
    *
-   * The type RandomAccessVertexRange must be a range for which .begin() and
-   * .end() return random access iterators, with 'value_type' Vertex_handle. */
-  template<class RandomAccessVertexRange>
-  std::pair<Simplex_handle, bool> insert_simplex(RandomAccessVertexRange & simplex,
-                                         Filtration_value filtration) {
-    if (simplex.empty()) {
-      return std::pair<Simplex_handle, bool>(null_simplex(), true);
-    }
-
-    sort(simplex.begin(), simplex.end());  // must be sorted in increasing order
-
-    Siblings * curr_sib = &root_;
-    std::pair<Simplex_handle, bool> res_insert;
-    typename RandomAccessVertexRange::iterator vi;
-    for (vi = simplex.begin(); vi != simplex.end() - 1; ++vi) {
-      res_insert = curr_sib->members_.emplace(*vi, Node(curr_sib, filtration));
-      if (!(has_children(res_insert.first))) {
-        res_insert.first->second.assign_children(new Siblings(curr_sib, *vi));
-      }
-      curr_sib = res_insert.first->second.children();
-    }
-    res_insert = curr_sib->members_.emplace(*vi, Node(curr_sib, filtration));
-    if (!res_insert.second) {  // if already in the complex
-      if (res_insert.first->second.filtration() > filtration) {  // if filtration value modified
-        res_insert.first->second.assign_filtration(filtration);
-        return res_insert;
-      }
-      return std::pair<Simplex_handle, bool>(null_simplex(), false);  // if filtration value unchanged
-    }
-    // otherwise the insertion has succeeded
-    return res_insert;
+   * The type InputVertexRange must be a range for which .begin() and
+   * .end() return input iterators, with 'value_type' Vertex_handle. */
+  template<class InputVertexRange=std::initializer_list<Vertex_handle>>
+  std::pair<Simplex_handle, bool> insert_simplex(const InputVertexRange & simplex,
+                                                 Filtration_value filtration = 0) {
+    auto first = std::begin(simplex);
+    auto last = std::end(simplex);
+
+    if (first == last)
+      return std::pair<Simplex_handle, bool>(null_simplex(), true);  // ----->>
+
+    // Copy before sorting
+    std::vector<Vertex_handle> copy(first, last);
+    std::sort(std::begin(copy), std::end(copy));
+    return insert_vertex_vector(copy, filtration);
   }
 
-
-  /** \brief Insert a N-simplex and all his subfaces, from a N-simplex represented by a range of
+    /** \brief Insert a N-simplex and all his subfaces, from a N-simplex represented by a range of
    * Vertex_handles, in the simplicial complex.
    *
    * @param[in]  Nsimplex   range of Vertex_handles, representing the vertices of the new N-simplex
    * @param[in]  filtration the filtration value assigned to the new N-simplex.
-  */
-  template<class RandomAccessVertexRange>
-  void insert_simplex_and_subfaces(RandomAccessVertexRange& Nsimplex,
-                                         Filtration_value filtration = 0.0) {
-    if (Nsimplex.size() > 1) {
-      for (unsigned int NIndex = 0; NIndex < Nsimplex.size(); NIndex++) {
-        // insert N (N-1)-Simplex
-        RandomAccessVertexRange NsimplexMinusOne;
-        for (unsigned int NListIter = 0; NListIter < Nsimplex.size() - 1; NListIter++) {
-          // (N-1)-Simplex creation
-          NsimplexMinusOne.push_back( Nsimplex[(NIndex + NListIter) % Nsimplex.size()]);
-        }
-        // (N-1)-Simplex recursive call
-        insert_simplex_and_subfaces(NsimplexMinusOne, filtration);
+   * The return type is a pair. If the new simplex is inserted successfully (i.e. it was not in the
+   * simplicial complex yet) the bool is set to true and the Simplex_handle is the handle assigned
+   * to the new simplex.
+   * If the insertion fails (the simplex is already there), the bool is set to false. If the insertion
+   * fails and the simplex already in the complex has a filtration value strictly bigger than 'filtration',
+   * we assign this simplex with the new value 'filtration', and set the Simplex_handle field of the
+   * output pair to the Simplex_handle of the simplex. Otherwise, we set the Simplex_handle part to
+   * null_simplex.
+   */
+  template<class InputVertexRange=std::initializer_list<Vertex_handle>>
+  std::pair<Simplex_handle, bool> insert_simplex_and_subfaces(const InputVertexRange& Nsimplex,
+                                   Filtration_value filtration = 0) {
+    auto first = std::begin(Nsimplex);
+    auto last = std::end(Nsimplex);
+
+    if (first == last)
+      return std::pair<Simplex_handle, bool>(null_simplex(), true);  // ----->>
+
+    // Copy before sorting
+    std::vector<Vertex_handle> copy(first, last);
+    std::sort(std::begin(copy), std::end(copy));
+
+    std::vector<std::vector<Vertex_handle>> to_be_inserted;
+    std::vector<std::vector<Vertex_handle>> to_be_propagated;
+    return rec_insert_simplex_and_subfaces(copy, to_be_inserted, to_be_propagated, filtration);
+  }
+
+ private:
+  std::pair<Simplex_handle, bool> rec_insert_simplex_and_subfaces(std::vector<Vertex_handle>& the_simplex,
+                                                             std::vector<std::vector<Vertex_handle>>& to_be_inserted,
+                                                             std::vector<std::vector<Vertex_handle>>& to_be_propagated,
+                                                             Filtration_value filtration = 0.0) {
+    std::pair<Simplex_handle, bool> insert_result;
+    if (the_simplex.size() > 1) {
+      // Get and remove last vertex
+      Vertex_handle last_vertex = the_simplex.back();
+      the_simplex.pop_back();
+      // Recursive call after last vertex removal
+      insert_result = rec_insert_simplex_and_subfaces(the_simplex, to_be_inserted, to_be_propagated, filtration);
+
+      // Concatenation of to_be_inserted and to_be_propagated
+      to_be_inserted.insert(to_be_inserted.begin(), to_be_propagated.begin(), to_be_propagated.end());
+      to_be_propagated = to_be_inserted;
+
+      // to_be_inserted treatment
+      for (auto& simplex_tbi : to_be_inserted) {
+        simplex_tbi.push_back(last_vertex);
       }
-      // N-Simplex insert
-      std::pair<Simplex_handle, bool> returned = insert_simplex(Nsimplex, filtration);
-      if (returned.second == true) {
-        num_simplices_++;
+      std::vector<Vertex_handle> last_simplex(1, last_vertex);
+      to_be_inserted.insert(to_be_inserted.begin(), last_simplex);
+      // i.e. (0,1,2) =>
+      // [to_be_inserted | to_be_propagated] = [(1) (0,1) | (0)]
+      // [to_be_inserted | to_be_propagated] = [(2) (0,2) (1,2) (0,1,2) | (0) (1) (0,1)]
+      // N.B. : it is important the last inserted to be the highest in dimension
+      // in order to return the "last" insert_simplex result
+
+      // insert all to_be_inserted
+      for (auto& simplex_tbi : to_be_inserted) {
+        insert_result = insert_vertex_vector(simplex_tbi, filtration);
       }
-    } else if (Nsimplex.size() == 1) {
-      // 1-Simplex insert - End of recursivity
-      std::pair<Simplex_handle, bool> returned = insert_simplex(Nsimplex, filtration);
-      if (returned.second == true) {
-        num_simplices_++;
+    } else if (the_simplex.size() == 1) {
+      // When reaching the end of recursivity, vector of simplices shall be empty and filled on back recursive
+      if ((to_be_inserted.size() != 0) || (to_be_propagated.size() != 0)) {
+        std::cerr << "Simplex_tree::rec_insert_simplex_and_subfaces - Error vector not empty" << std::endl;
+        exit(-1);
       }
+      std::vector<Vertex_handle> first_simplex(1, the_simplex.back());
+      // i.e. (0,1,2) => [to_be_inserted | to_be_propagated] = [(0) | ]
+      to_be_inserted.push_back(first_simplex);
+
+      insert_result = insert_vertex_vector(first_simplex, filtration);
     } else {
-      // Nothing to insert - empty vector
+        std::cerr << "Simplex_tree::rec_insert_simplex_and_subfaces - Recursivity error" << std::endl;
+        exit(-1);
     }
+    return insert_result;
   }
 
+ public:
   /** \brief Assign a value 'key' to the key of the simplex
    * represented by the Simplex_handle 'sh'. */
   void assign_key(Simplex_handle sh, Simplex_key key) {
@@ -528,9 +736,8 @@ class Simplex_tree {
    * and edge. sh must point to a 1-dimensional simplex. This is an
    * optimized version of the boundary computation. */
   std::pair<Simplex_handle, Simplex_handle> endpoints(Simplex_handle sh) {
-    return std::pair<Simplex_handle, Simplex_handle>(
-        root_.members_.find(sh->first),
-        root_.members_.find(self_siblings(sh)->parent()));
+    assert(dimension(sh) == 1);
+    return { find_vertex(sh->first), find_vertex(self_siblings(sh)->parent()) };
   }
 
   /** Returns the Siblings containing a simplex.*/
@@ -541,32 +748,17 @@ class Simplex_tree {
       return sh->second.children();
   }
 
-// void display_simplex(Simplex_handle sh)
-// {
-//   std::cout << "   " << "[" << filtration(sh) << "] ";
-//   for( auto vertex : simplex_vertex_range(sh) )
-//     { std::cout << vertex << " "; }
-// }
-
-  // void print(Simplex_handle sh, std::ostream& os = std::cout)
-  // {  for(auto v : simplex_vertex_range(sh)) {os << v << " ";}
-  //    os << std::endl; }
-
  public:
   /** Returns a pointer to the root nodes of the simplex tree. */
   Siblings * root() {
     return &root_;
   }
 
- public:
   /** Set an upper bound for the filtration values. */
   void set_filtration(Filtration_value fil) {
     threshold_ = fil;
   }
-  /** Set a number of simplices for the simplicial complex. */
-  void set_num_simplices(unsigned int num_simplices) {
-    num_simplices_ = num_simplices;
-  }
+
   /** Set a dimension for the simplicial complex. */
   void set_dimension(int dimension) {
     dimension_ = dimension;
@@ -580,28 +772,114 @@ class Simplex_tree {
    * assigned a Simplex_key corresponding to its order in the filtration (from 0 to m-1 for a
    * simplicial complex with m simplices).
    *
-   * The use of a depth-first traversal of the simplex tree, provided by
-   * complex_simplex_range(), combined with
-   * a stable sort is meant to optimize the order of simplices with same
-   * filtration value. The heuristic consists in inserting the cofaces of a
-   * simplex as soon as possible.
-   *
    * Will be automatically called when calling filtration_simplex_range()
    * if the filtration has never been initialized yet. */
   void initialize_filtration() {
     filtration_vect_.clear();
     filtration_vect_.reserve(num_simplices());
-    for (auto cpx_it = complex_simplex_range().begin();
-        cpx_it != complex_simplex_range().end(); ++cpx_it) {
-      filtration_vect_.push_back(*cpx_it);
-    }
-
-    // the stable sort ensures the ordering heuristic
+    for (Simplex_handle sh : complex_simplex_range())
+      filtration_vect_.push_back(sh);
+
+    /* We use stable_sort here because with libstdc++ it is faster than sort.
+     * is_before_in_filtration is now a total order, but we used to call
+     * stable_sort for the following heuristic:
+     * The use of a depth-first traversal of the simplex tree, provided by
+     * complex_simplex_range(), combined with a stable sort is meant to
+     * optimize the order of simplices with same filtration value. The
+     * heuristic consists in inserting the cofaces of a simplex as soon as
+     * possible.
+     */
     std::stable_sort(filtration_vect_.begin(), filtration_vect_.end(),
                      is_before_in_filtration(this));
   }
 
  private:
+  /** Recursive search of cofaces
+   * This function uses DFS
+   *\param vertices contains a list of vertices, which represent the vertices of the simplex not found yet.
+   *\param curr_nbVertices represents the number of vertices of the simplex we reached by going through the tree.
+   *\param cofaces contains a list of Simplex_handle, representing all the cofaces asked.
+   *\param star true if we need the star of the simplex
+   *\param nbVertices number of vertices of the cofaces we search
+   * Prefix actions : When the bottom vertex matches with the current vertex in the tree, we remove the bottom vertex from vertices.
+   * Infix actions : Then we call or not the recursion.
+   * Postfix actions : Finally, we add back the removed vertex into vertices, and remove this vertex from curr_nbVertices so that we didn't change the parameters.
+   * If the vertices list is empty, we need to check if curr_nbVertices matches with the dimension of the cofaces asked.
+   */
+  void rec_coface(std::vector<Vertex_handle> &vertices, Siblings *curr_sib, int curr_nbVertices,
+                  std::vector<Simplex_handle>& cofaces, bool star, int nbVertices) {
+    if (!(star || curr_nbVertices <= nbVertices))  // dimension of actual simplex <= nbVertices
+      return;
+    for (Simplex_handle simplex = curr_sib->members().begin(); simplex != curr_sib->members().end(); ++simplex) {
+      if (vertices.empty()) {
+        // If we reached the end of the vertices, and the simplex has more vertices than the given simplex
+        // => we found a coface
+
+        // Add a coface if we wan't the star or if the number of vertices of the current simplex matches with nbVertices
+        bool addCoface = (star || curr_nbVertices == nbVertices);
+        if (addCoface)
+          cofaces.push_back(simplex);
+        if ((!addCoface || star) && has_children(simplex))  // Rec call
+          rec_coface(vertices, simplex->second.children(), curr_nbVertices + 1, cofaces, star, nbVertices);
+      } else {
+        if (simplex->first == vertices.back()) {
+          // If curr_sib matches with the top vertex
+          bool equalDim = (star || curr_nbVertices == nbVertices);  // dimension of actual simplex == nbVertices
+          bool addCoface = vertices.size() == 1 && equalDim;
+          if (addCoface)
+            cofaces.push_back(simplex);
+          if ((!addCoface || star) && has_children(simplex)) {
+            // Rec call
+            Vertex_handle tmp = vertices.back();
+            vertices.pop_back();
+            rec_coface(vertices, simplex->second.children(), curr_nbVertices + 1, cofaces, star, nbVertices);
+            vertices.push_back(tmp);
+          }
+        } else if (simplex->first > vertices.back()) {
+          return;
+        } else {
+          // (simplex->first < vertices.back()
+          if (has_children(simplex))
+            rec_coface(vertices, simplex->second.children(), curr_nbVertices + 1, cofaces, star, nbVertices);
+        }
+      }
+    }
+  }
+
+ public:
+  /** \brief Compute the star of a n simplex
+   * \param simplex represent the simplex of which we search the star
+   * \return Vector of Simplex_handle, empty vector if no cofaces found.
+   */
+
+  Cofaces_simplex_range star_simplex_range(const Simplex_handle simplex) {
+    return cofaces_simplex_range(simplex, 0);
+  }
+
+  /** \brief Compute the cofaces of a n simplex
+   * \param simplex represent the n-simplex of which we search the n+codimension cofaces
+   * \param codimension The function returns the n+codimension-cofaces of the n-simplex. If codimension = 0, 
+   * return all cofaces (equivalent of star function)
+   * \return Vector of Simplex_handle, empty vector if no cofaces found.
+   */
+
+  Cofaces_simplex_range cofaces_simplex_range(const Simplex_handle simplex, int codimension) {
+    Cofaces_simplex_range cofaces;
+    // codimension must be positive or null integer
+    assert(codimension >= 0);
+    Simplex_vertex_range rg = simplex_vertex_range(simplex);
+    std::vector<Vertex_handle> copy(rg.begin(), rg.end());
+    if (codimension + static_cast<int>(copy.size()) > dimension_ + 1 ||
+        (codimension == 0 && static_cast<int>(copy.size()) > dimension_))  // n+codimension greater than dimension_
+      return cofaces;
+    // must be sorted in decreasing order
+    assert(std::is_sorted(copy.begin(), copy.end(), std::greater<Vertex_handle>()));
+    bool star = codimension == 0;
+    rec_coface(copy, &root_, 1, cofaces, star, codimension + static_cast<int>(copy.size()));
+    return cofaces;
+  }
+
+ private:
   /** \brief Returns true iff the list of vertices of sh1
    * is smaller than the list of vertices of sh2 w.r.t.
    * lexicographic order on the lists read in reverse.
@@ -624,6 +902,7 @@ class Simplex_tree {
     }
     return ((it1 == rg1.end()) && (it2 != rg2.end()));
   }
+
   /** \brief StrictWeakOrdering, for the simplices, defined by the filtration.
    *
    * It corresponds to the partial order
@@ -632,15 +911,15 @@ class Simplex_tree {
    * to be smaller. The filtration function must be monotonic. */
   struct is_before_in_filtration {
     explicit is_before_in_filtration(Simplex_tree * st)
-        : st_(st) {
-    }
+        : st_(st) { }
 
     bool operator()(const Simplex_handle sh1, const Simplex_handle sh2) const {
-      if (st_->filtration(sh1) != st_->filtration(sh2)) {
-        return st_->filtration(sh1) < st_->filtration(sh2);
+      // Not using st_->filtration(sh1) because it uselessly tests for null_simplex.
+      if (sh1->second.filtration() != sh2->second.filtration()) {
+	return sh1->second.filtration() < sh2->second.filtration();
       }
-
-      return st_->reverse_lexicographic_order(sh1, sh2);  // is sh1 a proper subface of sh2
+      // is sh1 a proper subface of sh2
+      return st_->reverse_lexicographic_order(sh1, sh2);
     }
 
     Simplex_tree * st_;
@@ -667,7 +946,8 @@ class Simplex_tree {
    *                                    must be undirected_tag. */
   template<class OneSkeletonGraph>
   void insert_graph(const OneSkeletonGraph& skel_graph) {
-    assert(num_simplices() == 0);  // the simplex tree must be empty
+    // the simplex tree must be empty
+    assert(num_simplices() == 0);
 
     if (boost::num_vertices(skel_graph) == 0) {
       return;
@@ -678,37 +958,37 @@ class Simplex_tree {
       dimension_ = 1;
     }
 
-    num_simplices_ = boost::num_vertices(skel_graph)
-        + boost::num_edges(skel_graph);
     root_.members_.reserve(boost::num_vertices(skel_graph));
 
     typename boost::graph_traits<OneSkeletonGraph>::vertex_iterator v_it,
         v_it_end;
     for (std::tie(v_it, v_it_end) = boost::vertices(skel_graph); v_it != v_it_end;
-        ++v_it) {
+         ++v_it) {
       root_.members_.emplace_hint(
-          root_.members_.end(), *v_it,
-          Node(&root_, boost::get(vertex_filtration_t(), skel_graph, *v_it)));
+                                  root_.members_.end(), *v_it,
+                                  Node(&root_, boost::get(vertex_filtration_t(), skel_graph, *v_it)));
     }
     typename boost::graph_traits<OneSkeletonGraph>::edge_iterator e_it,
         e_it_end;
     for (std::tie(e_it, e_it_end) = boost::edges(skel_graph); e_it != e_it_end;
-        ++e_it) {
+         ++e_it) {
       auto u = source(*e_it, skel_graph);
       auto v = target(*e_it, skel_graph);
-      if (u < v) {  // count edges only once { std::swap(u,v); } // u < v
+      if (u < v) {
+        // count edges only once { std::swap(u,v); } // u < v
         auto sh = find_vertex(u);
         if (!has_children(sh)) {
           sh->second.assign_children(new Siblings(&root_, sh->first));
         }
 
         sh->second.children()->members().emplace(
-            v,
-            Node(sh->second.children(),
-                 boost::get(edge_filtration_t(), skel_graph, *e_it)));
+                                                 v,
+                                                 Node(sh->second.children(),
+                                                      boost::get(edge_filtration_t(), skel_graph, *e_it)));
       }
     }
   }
+
   /** \brief Expands the Simplex_tree containing only its one skeleton
    * until dimension max_dim.
    *
@@ -723,7 +1003,7 @@ class Simplex_tree {
   void expansion(int max_dim) {
     dimension_ = max_dim;
     for (Dictionary_it root_it = root_.members_.begin();
-        root_it != root_.members_.end(); ++root_it) {
+         root_it != root_.members_.end(); ++root_it) {
       if (has_children(root_it)) {
         siblings_expansion(root_it->second.children(), max_dim - 1);
       }
@@ -734,7 +1014,7 @@ class Simplex_tree {
  private:
   /** \brief Recursive expansion of the simplex tree.*/
   void siblings_expansion(Siblings * siblings,  // must contain elements
-      int k) {
+                          int k) {
     if (dimension_ > k) {
       dimension_ = k;
     }
@@ -745,68 +1025,55 @@ class Simplex_tree {
 
     static std::vector<std::pair<Vertex_handle, Node> > inter;  // static, not thread-safe.
     for (Dictionary_it s_h = siblings->members().begin();
-        s_h != siblings->members().end(); ++s_h, ++next) {
+         s_h != siblings->members().end(); ++s_h, ++next) {
       Simplex_handle root_sh = find_vertex(s_h->first);
       if (has_children(root_sh)) {
         intersection(
-            inter,                      // output intersection
-            next,                       // begin
-            siblings->members().end(),  // end
-            root_sh->second.children()->members().begin(),
-            root_sh->second.children()->members().end(),
-            s_h->second.filtration());
+                     inter,  // output intersection
+                     next,  // begin
+                     siblings->members().end(),  // end
+                     root_sh->second.children()->members().begin(),
+                     root_sh->second.children()->members().end(),
+                     s_h->second.filtration());
         if (inter.size() != 0) {
-          this->num_simplices_ += inter.size();
           Siblings * new_sib = new Siblings(siblings,  // oncles
-              s_h->first,  // parent
-              inter);      // boost::container::ordered_unique_range_t
+                                            s_h->first,  // parent
+                                            inter);  // boost::container::ordered_unique_range_t
           inter.clear();
           s_h->second.assign_children(new_sib);
           siblings_expansion(new_sib, k - 1);
         } else {
-          s_h->second.assign_children(siblings);  // ensure the children property
+          // ensure the children property
+          s_h->second.assign_children(siblings);
           inter.clear();
         }
       }
     }
   }
+
   /** \brief Intersects Dictionary 1 [begin1;end1) with Dictionary 2 [begin2,end2)
    * and assigns the maximal possible Filtration_value to the Nodes. */
   static void intersection(std::vector<std::pair<Vertex_handle, Node> >& intersection,
                            Dictionary_it begin1, Dictionary_it end1,
                            Dictionary_it begin2, Dictionary_it end2,
-                           Filtration_value filtration) {
+                           Filtration_value filtration_) {
     if (begin1 == end1 || begin2 == end2)
       return;  // ----->>
     while (true) {
       if (begin1->first == begin2->first) {
-        intersection.push_back(
-            std::pair<Vertex_handle, Node>(
-                begin1->first,
-                Node(NULL, maximum(begin1->second.filtration(), begin2->second.filtration(), filtration))));
-        ++begin1;
-        ++begin2;
-        if (begin1 == end1 || begin2 == end2)
+        Filtration_value filt = (std::max)({begin1->second.filtration(), begin2->second.filtration(), filtration_});
+        intersection.emplace_back(begin1->first, Node(nullptr, filt));
+        if (++begin1 == end1 || ++begin2 == end2)
+          return;  // ----->>
+      } else if (begin1->first < begin2->first) {
+        if (++begin1 == end1)
+          return;
+      } else /* begin1->first > begin2->first */ {
+        if (++begin2 == end2)
           return;  // ----->>
-      } else {
-        if (begin1->first < begin2->first) {
-          ++begin1;
-          if (begin1 == end1)
-            return;
-        } else {
-          ++begin2;
-          if (begin2 == end2)
-            return;  // ----->>
-        }
       }
     }
   }
-  /** Maximum over 3 values.*/
-  static Filtration_value maximum(Filtration_value a, Filtration_value b,
-                                  Filtration_value c) {
-    Filtration_value max = (a < b) ? b : a;
-    return ((max < c) ? c : max);
-  }
 
  public:
   /** \brief Write the hasse diagram of the simplicial complex in os.
@@ -817,7 +1084,7 @@ class Simplex_tree {
    * of the simplex, and fil is its filtration value. */
   void print_hasse(std::ostream& os) {
     os << num_simplices() << " " << std::endl;
-    for (auto sh : filtration_simplex_range(Indexing_tag())) {
+    for (auto sh : filtration_simplex_range()) {
       os << dimension(sh) << " ";
       for (auto b_sh : boundary_simplex_range(sh)) {
         os << key(b_sh) << " ";
@@ -831,7 +1098,6 @@ class Simplex_tree {
   /** \brief Upper bound on the filtration values of the simplices.*/
   Filtration_value threshold_;
   /** \brief Total number of simplices in the complex, without the empty simplex.*/
-  unsigned int num_simplices_;
   /** \brief Set of simplex tree Nodes representing the vertices.*/
   Siblings root_;
   /** \brief Simplices ordered according to a filtration.*/
@@ -841,8 +1107,9 @@ class Simplex_tree {
 };
 
 // Print a Simplex_tree in os.
-template<typename T1, typename T2, typename T3>
-std::ostream& operator<<(std::ostream & os, Simplex_tree<T1, T2, T3> & st) {
+
+template<typename...T>
+std::ostream& operator<<(std::ostream & os, Simplex_tree<T...> & st) {
   for (auto sh : st.filtration_simplex_range()) {
     os << st.dimension(sh) << " ";
     for (auto v : st.simplex_vertex_range(sh)) {
@@ -852,35 +1119,35 @@ std::ostream& operator<<(std::ostream & os, Simplex_tree<T1, T2, T3> & st) {
   }
   return os;
 }
-template<typename T1, typename T2, typename T3>
-std::istream& operator>>(std::istream & is, Simplex_tree<T1, T2, T3> & st) {
-  // assert(st.num_simplices() == 0);
 
-  std::vector<typename Simplex_tree<T1, T2, T3>::Vertex_handle> simplex;
-  typename Simplex_tree<T1, T2, T3>::Filtration_value fil;
-  typename Simplex_tree<T1, T2, T3>::Filtration_value max_fil = 0;
+template<typename...T>
+std::istream& operator>>(std::istream & is, Simplex_tree<T...> & st) {
+  typedef Simplex_tree<T...> ST;
+  std::vector<typename ST::Vertex_handle> simplex;
+  typename ST::Filtration_value fil;
+  typename ST::Filtration_value max_fil = 0;
   int max_dim = -1;
-  size_t num_simplices = 0;
-  while (read_simplex(is, simplex, fil)) {  // read all simplices in the file as a list of vertices
-    ++num_simplices;
-    int dim = static_cast<int>(simplex.size() - 1);  // Warning : simplex_size needs to be casted in int - Can be 0
+  while (read_simplex(is, simplex, fil)) {
+    // read all simplices in the file as a list of vertices
+    // Warning : simplex_size needs to be casted in int - Can be 0
+    int dim = static_cast<int> (simplex.size() - 1);
     if (max_dim < dim) {
       max_dim = dim;
     }
     if (max_fil < fil) {
       max_fil = fil;
     }
-    st.insert_simplex(simplex, fil);  // insert every simplex in the simplex tree
+    // insert every simplex in the simplex tree
+    st.insert_simplex(simplex, fil);
     simplex.clear();
   }
-  st.set_num_simplices(num_simplices);
   st.set_dimension(max_dim);
   st.set_filtration(max_fil);
 
   return is;
 }
-
 /** @} */  // end defgroup simplex_tree
+
 }  // namespace Gudhi
 
-#endif  // SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_H_
+#endif  // SIMPLEX_TREE_H_
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h
index 06462c88..372ef329 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h
@@ -20,10 +20,14 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_
-#define SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_
+#ifndef SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_
+#define SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_
 
 #include <boost/iterator/iterator_facade.hpp>
+#include <boost/version.hpp>
+#if BOOST_VERSION >= 105600
+# include <boost/container/static_vector.hpp>
+#endif
 
 #include <vector>
 
@@ -131,8 +135,7 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade<
     }
 
     Siblings * for_sib = sib_;
-    for (typename std::vector<Vertex_handle>::reverse_iterator rit = suffix_
-        .rbegin(); rit != suffix_.rend(); ++rit) {
+    for (auto rit = suffix_.rbegin(); rit != suffix_.rend(); ++rit) {
       sh_ = for_sib->find(*rit);
       for_sib = sh_->second.children();
     }
@@ -142,9 +145,18 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade<
     sib_ = sib_->oncles();
   }
 
+  // Most of the storage should be moved to the range, iterators should be light.
   Vertex_handle last_;  // last vertex of the simplex
   Vertex_handle next_;  // next vertex to push in suffix_
+#if BOOST_VERSION >= 105600
+  // 40 seems a conservative bound on the dimension of a Simplex_tree for now,
+  // as it would not fit on the biggest hard-drive.
+  boost::container::static_vector<Vertex_handle, 40> suffix_;
+  // static_vector still has some overhead compared to a trivial hand-made
+  // version using std::aligned_storage, or compared to making suffix_ static.
+#else
   std::vector<Vertex_handle> suffix_;
+#endif
   Siblings * sib_;  // where the next search will start from
   Simplex_handle sh_;  // current Simplex_handle in the boundary
   SimplexTree * st_;  // simplex containing the simplicial complex
@@ -303,4 +315,4 @@ class Simplex_tree_skeleton_simplex_iterator : public boost::iterator_facade<
 /* @} */  // end addtogroup simplex_tree
 }  // namespace Gudhi
 
-#endif  // SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_
+#endif  // SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h
index 1f1a34cc..25d4888a 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H_
-#define SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H_
+#ifndef SIMPLEX_TREE_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H_
+#define SIMPLEX_TREE_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H_
 
 #include <vector>
 
@@ -39,65 +39,34 @@ namespace Gudhi {
  * It stores explicitely its own filtration value and its own Simplex_key.
  */
 template<class SimplexTree>
-class Simplex_tree_node_explicit_storage {
- public:
+struct Simplex_tree_node_explicit_storage : SimplexTree::Filtration_simplex_base, SimplexTree::Key_simplex_base {
   typedef typename SimplexTree::Siblings Siblings;
   typedef typename SimplexTree::Filtration_value Filtration_value;
   typedef typename SimplexTree::Simplex_key Simplex_key;
 
-  // Default constructor.
-  Simplex_tree_node_explicit_storage()
-      : children_(NULL),
-        simplex_key_(-1),
-        filtration_(0) {
-  }
-
-  Simplex_tree_node_explicit_storage(Siblings * sib,
-                                     Filtration_value filtration)
-      : children_(sib),
-        simplex_key_(-1),
-        filtration_(filtration) {
-  }
-
-  void assign_key(Simplex_key key) {
-    simplex_key_ = key;
+  Simplex_tree_node_explicit_storage(Siblings * sib = nullptr,
+                                     Filtration_value filtration = 0)
+      : children_(sib) {
+    this->assign_filtration(filtration);
   }
 
   /*
-   * Assign a children to the node
+   * Assign children to the node
    */
   void assign_children(Siblings * children) {
     children_ = children;
   }
-  /*
-   *
-   */
-  void assign_filtration(double filtration_value) {
-    filtration_ = filtration_value;
-  }
-
-  Filtration_value filtration() {
-    return filtration_;
-  }
 
   /* Careful -> children_ can be NULL*/
   Siblings * children() {
     return children_;
   }
 
-  Simplex_key key() {
-    return simplex_key_;
-  }
-
  private:
   Siblings * children_;
-
-  // Data attached to simplex, explicit storage
-  Simplex_key simplex_key_;
-  Filtration_value filtration_;   // value in the filtration
 };
 
 /* @} */  // end addtogroup simplex_tree
 }  // namespace Gudhi
 
-#endif  // SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H_
+#endif  // SIMPLEX_TREE_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H_
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h
index 977fafa1..158ee1f7 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h
@@ -20,11 +20,12 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_SIMPLEX_TREE_SIBLINGS_H_
-#define SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_SIMPLEX_TREE_SIBLINGS_H_
+#ifndef SIMPLEX_TREE_SIMPLEX_TREE_SIBLINGS_H_
+#define SIMPLEX_TREE_SIMPLEX_TREE_SIBLINGS_H_
 
-#include "boost/container/flat_map.hpp"
-#include "Simplex_tree_node_explicit_storage.h"
+#include <gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h>
+
+#include <boost/container/flat_map.hpp>
 
 #include <utility>
 #include <vector>
@@ -71,14 +72,14 @@ class Simplex_tree_siblings {
   /* \brief Constructor with initialized set of members.
    *
    * 'members' must be sorted and unique.*/
-  Simplex_tree_siblings(Simplex_tree_siblings * oncles, Vertex_handle parent,
-                        const std::vector<std::pair<Vertex_handle, Node> > & members)
+  template<typename RandomAccessVertexRange>
+  Simplex_tree_siblings(Simplex_tree_siblings * oncles, Vertex_handle parent, const RandomAccessVertexRange & members)
       : oncles_(oncles),
         parent_(parent),
         members_(boost::container::ordered_unique_range, members.begin(),
                  members.end()) {
-    for (auto map_it = members_.begin(); map_it != members_.end(); map_it++) {
-      map_it->second.assign_children(this);
+    for (auto& map_el : members_) {
+      map_el.second.assign_children(this);
     }
   }
 
@@ -90,19 +91,12 @@ class Simplex_tree_siblings {
    * present in the node.
    */
   void insert(Vertex_handle v, Filtration_value filtration_value) {
-    typename Dictionary::iterator sh = members_.find(v);
-    if (sh != members_.end() && sh->second.filtration() > filtration_value) {
-      sh->second.assign_filtration(filtration_value);
-      return;
-    }
-    if (sh == members_.end()) {
-      members_.insert(
-          std::pair<Vertex_handle, Node>(v, Node(this, filtration_value)));
-      return;
-    }
+    auto ins = members_.emplace(v, Node(this, filtration_value));
+    if (!ins.second && filtration(ins.first) > filtration_value)
+      ins.first->second.assign_filtration(filtration_value);
   }
 
-  typename Dictionary::iterator find(Vertex_handle v) {
+  Dictionary_it find(Vertex_handle v) {
     return members_.find(v);
   }
 
@@ -110,7 +104,7 @@ class Simplex_tree_siblings {
     return oncles_;
   }
 
-  Vertex_handle parent() {
+  Vertex_handle parent() const {
     return parent_;
   }
 
@@ -118,7 +112,7 @@ class Simplex_tree_siblings {
     return members_;
   }
 
-  size_t size() {
+  size_t size() const {
     return members_.size();
   }
 
@@ -130,4 +124,4 @@ class Simplex_tree_siblings {
 /* @} */  // end addtogroup simplex_tree
 }  // namespace Gudhi
 
-#endif  // SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_SIMPLEX_TREE_SIBLINGS_H_
+#endif  // SIMPLEX_TREE_SIMPLEX_TREE_SIBLINGS_H_
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h b/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h
index 69ffa44b..0adeb46d 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_INDEXING_TAG_H_
-#define SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_INDEXING_TAG_H_
+#ifndef SIMPLEX_TREE_INDEXING_TAG_H_
+#define SIMPLEX_TREE_INDEXING_TAG_H_
 
 namespace Gudhi {
 
@@ -36,4 +36,4 @@ struct linear_indexing_tag {
 //  struct zigzag_indexing_tag {};
 }  // namespace Gudhi
 
-#endif  // SRC_SIMPLEX_TREE_INCLUDE_GUDHI_SIMPLEX_TREE_INDEXING_TAG_H_
+#endif  // SIMPLEX_TREE_INDEXING_TAG_H_
diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt
index b6a1c0b6..c9eae163 100644
--- a/src/Simplex_tree/test/CMakeLists.txt
+++ b/src/Simplex_tree/test/CMakeLists.txt
@@ -17,6 +17,9 @@ endif()
 add_executable ( SimplexTreeUT simplex_tree_unit_test.cpp )
 target_link_libraries(SimplexTreeUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
+# Do not forget to copy test files in current binary dir
+file(COPY "simplex_tree_for_unit_test.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+
 # Unitary tests
 add_test(NAME SimplexTreeUT
   COMMAND ${CMAKE_CURRENT_BINARY_DIR}/SimplexTreeUT 
diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
index 6b0a1f3d..fff00d77 100644
--- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp
+++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
@@ -1,17 +1,16 @@
-#define BOOST_TEST_MODULE simplex_tree test
-#include <boost/test/included/unit_test.hpp>
-#include <boost/system/error_code.hpp>
-#include <boost/chrono/thread_clock.hpp>
 #include <iostream>
 #include <string>
-
+#include <algorithm>
 #include <utility> // std::pair, std::make_pair
-
 #include <cmath> // float comparison
 #include <limits>
 
-#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/reader_utils.h"
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "simplex_tree"
+#include <boost/test/unit_test.hpp>
+
+//  ^
+// /!\ Nothing else from Simplex_tree shall be included to test includes are well defined.
 #include "gudhi/Simplex_tree.h"
 
 using namespace Gudhi;
@@ -21,7 +20,7 @@ typedef std::pair<typeST::Simplex_handle, bool> typePairSimplexBool;
 typedef std::vector<Vertex_handle> typeVectorVertex;
 typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
 
-const Vertex_handle DEFAULT_VERTEX_HANDLE = (const Vertex_handle) -1;
+const Vertex_handle DEFAULT_VERTEX_HANDLE = (const Vertex_handle) - 1;
 const Filtration_value DEFAULT_FILTRATION_VALUE = (const Filtration_value) 0.0;
 
 void test_empty_simplex_tree(typeST& tst) {
@@ -40,55 +39,52 @@ void test_iterators_on_empty_simplex_tree(typeST& tst) {
   std::cout << "Iterator on vertices: " << std::endl;
   for (auto vertex : tst.complex_vertex_range()) {
     std::cout << "vertice:" << vertex << std::endl;
-    BOOST_CHECK(false);  // shall be empty
+    BOOST_CHECK(false); // shall be empty
   }
   std::cout << "Iterator on simplices: " << std::endl;
   for (auto simplex : tst.complex_simplex_range()) {
-    BOOST_CHECK(simplex != simplex);  // shall be empty - to remove warning of non-used simplex
+    BOOST_CHECK(simplex != simplex); // shall be empty - to remove warning of non-used simplex
   }
 
   std::cout
       << "Iterator on Simplices in the filtration, with [filtration value]:"
       << std::endl;
   for (auto f_simplex : tst.filtration_simplex_range()) {
-    BOOST_CHECK(false);  // shall be empty
+    BOOST_CHECK(false); // shall be empty
     std::cout << "test_iterators_on_empty_simplex_tree - filtration="
         << tst.filtration(f_simplex) << std::endl;
   }
 }
 
-BOOST_AUTO_TEST_CASE( simplex_tree_when_empty )
-{
+BOOST_AUTO_TEST_CASE(simplex_tree_when_empty) {
   const Filtration_value DEFAULT_FILTRATION_VALUE = 0;
 
-  // TEST OF DEFAULT CONSTRUCTOR
   std::cout << "********************************************************************" << std::endl;
   std::cout << "TEST OF DEFAULT CONSTRUCTOR" << std::endl;
   typeST st;
 
-  test_empty_simplex_tree (st);
+  test_empty_simplex_tree(st);
 
-  test_iterators_on_empty_simplex_tree (st);
+  test_iterators_on_empty_simplex_tree(st);
   // TEST OF EMPTY INSERTION
   std::cout << "TEST OF EMPTY INSERTION" << std::endl;
   typeVectorVertex simplexVectorEmpty;
   BOOST_CHECK(simplexVectorEmpty.empty() == true);
   typePairSimplexBool returnEmptyValue = st.insert_simplex(simplexVectorEmpty,
-                                                   DEFAULT_FILTRATION_VALUE);
+                                                           DEFAULT_FILTRATION_VALUE);
   BOOST_CHECK(returnEmptyValue.first == typeST::Simplex_handle(NULL));
   BOOST_CHECK(returnEmptyValue.second == true);
 
-  test_empty_simplex_tree (st);
+  test_empty_simplex_tree(st);
 
-  test_iterators_on_empty_simplex_tree (st);
+  test_iterators_on_empty_simplex_tree(st);
 }
 
 bool AreAlmostTheSame(float a, float b) {
   return std::fabs(a - b) < std::numeric_limits<float>::epsilon();
 }
 
-BOOST_AUTO_TEST_CASE( simplex_tree_from_file )
-{
+BOOST_AUTO_TEST_CASE(simplex_tree_from_file) {
   // TEST OF INSERTION
   std::cout << "********************************************************************" << std::endl;
   std::cout << "TEST OF SIMPLEX TREE FROM A FILE" << std::endl;
@@ -108,16 +104,16 @@ BOOST_AUTO_TEST_CASE( simplex_tree_from_file )
   BOOST_CHECK(st.filtration() == 0.4);
 
   int previous_size = 0;
-  for( auto f_simplex : st.filtration_simplex_range() )
-  {
+  for (auto f_simplex : st.filtration_simplex_range()) {
     // Size of simplex
     int size = 0;
-    for( auto vertex : st.simplex_vertex_range(f_simplex) )
-    {
+    for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+      // Remove warning
+      (void) vertex;
       size++;
     }
-    BOOST_CHECK(AreAlmostTheSame(st.filtration(f_simplex),(0.1* size)));  // Specific test: filtration = 0.1 * simplex_size
-    BOOST_CHECK(previous_size <= size);// Check list is sorted (because of sorted filtrations in simplex_tree.txt)
+    BOOST_CHECK(AreAlmostTheSame(st.filtration(f_simplex), (0.1 * size))); // Specific test: filtration = 0.1 * simplex_size
+    BOOST_CHECK(previous_size <= size); // Check list is sorted (because of sorted filtrations in simplex_tree.txt)
     previous_size = size;
   }
   simplex_tree_stream.close();
@@ -127,13 +123,13 @@ void test_simplex_tree_contains(typeST& simplexTree, typeSimplex& simplex, int p
   auto f_simplex = simplexTree.filtration_simplex_range().begin() + pos;
 
   std::cout << "test_simplex_tree_contains - filtration=" << simplexTree.filtration(*f_simplex) << "||" << simplex.second << std::endl;
-  BOOST_CHECK( AreAlmostTheSame(simplexTree.filtration(*f_simplex),simplex.second) );
+  BOOST_CHECK(AreAlmostTheSame(simplexTree.filtration(*f_simplex), simplex.second));
 
-  int simplexIndex=simplex.first.size()-1;
-  for( auto vertex : simplexTree.simplex_vertex_range(*f_simplex) )
-  {
+  int simplexIndex = simplex.first.size() - 1;
+  std::sort(simplex.first.begin(), simplex.first.end()); // if the simplex wasn't sorted, the next test could fail
+  for (auto vertex : simplexTree.simplex_vertex_range(*f_simplex)) {
     std::cout << "test_simplex_tree_contains - vertex=" << vertex << "||" << simplex.first.at(simplexIndex) << std::endl;
-    BOOST_CHECK(vertex ==  simplex.first.at(simplexIndex));
+    BOOST_CHECK(vertex == simplex.first.at(simplexIndex));
     BOOST_CHECK(simplexIndex >= 0);
     simplexIndex--;
   }
@@ -141,7 +137,7 @@ void test_simplex_tree_contains(typeST& simplexTree, typeSimplex& simplex, int p
 
 void test_simplex_tree_insert_returns_true(const typePairSimplexBool& returnValue) {
   BOOST_CHECK(returnValue.second == true);
-  typeST::Simplex_handle shReturned = returnValue.first;  // Simplex_handle = boost::container::flat_map< Vertex_handle, Node >::iterator
+  typeST::Simplex_handle shReturned = returnValue.first; // Simplex_handle = boost::container::flat_map< Vertex_handle, Node >::iterator
   BOOST_CHECK(shReturned != typeST::Simplex_handle(NULL));
 }
 
@@ -162,24 +158,26 @@ void set_and_test_simplex_tree_dim_fil(typeST& simplexTree, int vectorSize, cons
     std::cout << "   set_and_test_simplex_tree_dim_fil - max_fil=" << max_fil
         << std::endl;
   }
-  unsigned int nb_simplices = simplexTree.num_simplices() + 1;
-  simplexTree.set_num_simplices(nb_simplices);
 
   BOOST_CHECK(simplexTree.dimension() == dim_max);
   BOOST_CHECK(AreAlmostTheSame(simplexTree.filtration(), max_fil));
-  BOOST_CHECK(simplexTree.num_simplices() == nb_simplices);
+
+  // Another way to count simplices:
+  size_t num_simp = 0;
+  for (auto f_simplex : simplexTree.complex_simplex_range()) {
+    // Remove warning
+    (void) f_simplex;
+    num_simp++;
+  }
+
+  BOOST_CHECK(simplexTree.num_simplices() == num_simp);
 }
 
-BOOST_AUTO_TEST_CASE( simplex_tree_insertion )
-{
+BOOST_AUTO_TEST_CASE(simplex_tree_insertion) {
   const Filtration_value FIRST_FILTRATION_VALUE = 0.1;
   const Filtration_value SECOND_FILTRATION_VALUE = 0.2;
   const Filtration_value THIRD_FILTRATION_VALUE = 0.3;
   const Filtration_value FOURTH_FILTRATION_VALUE = 0.4;
-  Vertex_handle FIRST_VERTEX_HANDLE = (Vertex_handle) 0;
-  Vertex_handle SECOND_VERTEX_HANDLE = (Vertex_handle) 1;
-  Vertex_handle THIRD_VERTEX_HANDLE = (Vertex_handle) 2;
-  Vertex_handle FOURTH_VERTEX_HANDLE = (Vertex_handle) 3;
 
   // TEST OF INSERTION
   std::cout << "********************************************************************" << std::endl;
@@ -188,171 +186,131 @@ BOOST_AUTO_TEST_CASE( simplex_tree_insertion )
 
   // ++ FIRST
   std::cout << "   - INSERT 0" << std::endl;
-  typeVectorVertex firstSimplexVector;
-  firstSimplexVector.push_back(FIRST_VERTEX_HANDLE);
-  BOOST_CHECK( firstSimplexVector.size() == 1 );
-  typeSimplex firstSimplex = std::make_pair(
-      firstSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE));
-  typePairSimplexBool returnValue = st.insert_simplex(firstSimplex.first,
-                                              firstSimplex.second);
-
-  test_simplex_tree_insert_returns_true (returnValue);
+  typeVectorVertex firstSimplexVector{0};
+  BOOST_CHECK(firstSimplexVector.size() == 1);
+  typeSimplex firstSimplex = std::make_pair(firstSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE));
+  typePairSimplexBool returnValue = st.insert_simplex(firstSimplex.first, firstSimplex.second);
+
+  test_simplex_tree_insert_returns_true(returnValue);
   set_and_test_simplex_tree_dim_fil(st, firstSimplexVector.size(), firstSimplex.second);
-  BOOST_CHECK( st.num_vertices() == (size_t)1 );
+  BOOST_CHECK(st.num_vertices() == (size_t) 1);
 
   // ++ SECOND
   std::cout << "   - INSERT 1" << std::endl;
-  typeVectorVertex secondSimplexVector;
-  secondSimplexVector.push_back(SECOND_VERTEX_HANDLE);
-  BOOST_CHECK( secondSimplexVector.size() == 1 );
-  typeSimplex secondSimplex = std::make_pair(
-      secondSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE));
-  returnValue =
-  st.insert_simplex ( secondSimplex.first, secondSimplex.second );
-
-  test_simplex_tree_insert_returns_true (returnValue);
+  typeVectorVertex secondSimplexVector{1};
+  BOOST_CHECK(secondSimplexVector.size() == 1);
+  typeSimplex secondSimplex = std::make_pair(secondSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE));
+  returnValue = st.insert_simplex(secondSimplex.first, secondSimplex.second);
+
+  test_simplex_tree_insert_returns_true(returnValue);
   set_and_test_simplex_tree_dim_fil(st, secondSimplexVector.size(), secondSimplex.second);
-  BOOST_CHECK( st.num_vertices() == (size_t)2 );
+  BOOST_CHECK(st.num_vertices() == (size_t) 2);
 
   // ++ THIRD
   std::cout << "   - INSERT (0,1)" << std::endl;
-  typeVectorVertex thirdSimplexVector;
-  thirdSimplexVector.push_back(FIRST_VERTEX_HANDLE);
-  thirdSimplexVector.push_back(SECOND_VERTEX_HANDLE);
-  BOOST_CHECK( thirdSimplexVector.size() == 2 );
-  typeSimplex thirdSimplex = std::make_pair(
-      thirdSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE));
-  returnValue =
-  st.insert_simplex ( thirdSimplex.first, thirdSimplex.second );
-
-  test_simplex_tree_insert_returns_true (returnValue);
+  typeVectorVertex thirdSimplexVector{0, 1};
+  BOOST_CHECK(thirdSimplexVector.size() == 2);
+  typeSimplex thirdSimplex = std::make_pair(thirdSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE));
+  returnValue = st.insert_simplex(thirdSimplex.first, thirdSimplex.second);
+
+  test_simplex_tree_insert_returns_true(returnValue);
   set_and_test_simplex_tree_dim_fil(st, thirdSimplexVector.size(), thirdSimplex.second);
-  BOOST_CHECK( st.num_vertices() == (size_t)2 );  // Not incremented !!
+  BOOST_CHECK(st.num_vertices() == (size_t) 2); // Not incremented !!
 
   // ++ FOURTH
   std::cout << "   - INSERT 2" << std::endl;
-  typeVectorVertex fourthSimplexVector;
-  fourthSimplexVector.push_back(THIRD_VERTEX_HANDLE);
-  BOOST_CHECK( fourthSimplexVector.size() == 1 );
-  typeSimplex fourthSimplex = std::make_pair(
-      fourthSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE));
-  returnValue =
-  st.insert_simplex ( fourthSimplex.first, fourthSimplex.second );
-
-  test_simplex_tree_insert_returns_true (returnValue);
+  typeVectorVertex fourthSimplexVector{2};
+  BOOST_CHECK(fourthSimplexVector.size() == 1);
+  typeSimplex fourthSimplex = std::make_pair(fourthSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE));
+  returnValue = st.insert_simplex(fourthSimplex.first, fourthSimplex.second);
+
+  test_simplex_tree_insert_returns_true(returnValue);
   set_and_test_simplex_tree_dim_fil(st, fourthSimplexVector.size(), fourthSimplex.second);
-  BOOST_CHECK( st.num_vertices() == (size_t)3 );
+  BOOST_CHECK(st.num_vertices() == (size_t) 3);
 
   // ++ FIFTH
   std::cout << "   - INSERT (2,0)" << std::endl;
-  typeVectorVertex fifthSimplexVector;
-  fifthSimplexVector.push_back(THIRD_VERTEX_HANDLE);
-  fifthSimplexVector.push_back(FIRST_VERTEX_HANDLE);
-  BOOST_CHECK( fifthSimplexVector.size() == 2 );
-  typeSimplex fifthSimplex = std::make_pair(
-      fifthSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE));
-  returnValue =
-  st.insert_simplex ( fifthSimplex.first, fifthSimplex.second );
-
-  test_simplex_tree_insert_returns_true (returnValue);
+  typeVectorVertex fifthSimplexVector{2, 0};
+  BOOST_CHECK(fifthSimplexVector.size() == 2);
+  typeSimplex fifthSimplex = std::make_pair(fifthSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE));
+  returnValue = st.insert_simplex(fifthSimplex.first, fifthSimplex.second);
+
+  test_simplex_tree_insert_returns_true(returnValue);
   set_and_test_simplex_tree_dim_fil(st, fifthSimplexVector.size(), fifthSimplex.second);
-  BOOST_CHECK( st.num_vertices() == (size_t)3 );  // Not incremented !!
+  BOOST_CHECK(st.num_vertices() == (size_t) 3); // Not incremented !!
 
   // ++ SIXTH
   std::cout << "   - INSERT (2,1)" << std::endl;
-  typeVectorVertex sixthSimplexVector;
-  sixthSimplexVector.push_back(THIRD_VERTEX_HANDLE);
-  sixthSimplexVector.push_back(SECOND_VERTEX_HANDLE);
-  BOOST_CHECK( sixthSimplexVector.size() == 2 );
-  typeSimplex sixthSimplex = std::make_pair(
-      sixthSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE));
-  returnValue =
-  st.insert_simplex ( sixthSimplex.first, sixthSimplex.second );
-
-  test_simplex_tree_insert_returns_true (returnValue);
+  typeVectorVertex sixthSimplexVector{2, 1};
+  BOOST_CHECK(sixthSimplexVector.size() == 2);
+  typeSimplex sixthSimplex = std::make_pair(sixthSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE));
+  returnValue = st.insert_simplex(sixthSimplex.first, sixthSimplex.second);
+
+  test_simplex_tree_insert_returns_true(returnValue);
   set_and_test_simplex_tree_dim_fil(st, sixthSimplexVector.size(), sixthSimplex.second);
-  BOOST_CHECK( st.num_vertices() == (size_t)3 );  // Not incremented !!
+  BOOST_CHECK(st.num_vertices() == (size_t) 3); // Not incremented !!
 
   // ++ SEVENTH
   std::cout << "   - INSERT (2,1,0)" << std::endl;
-  typeVectorVertex seventhSimplexVector;
-  seventhSimplexVector.push_back(THIRD_VERTEX_HANDLE);
-  seventhSimplexVector.push_back(SECOND_VERTEX_HANDLE);
-  seventhSimplexVector.push_back(FIRST_VERTEX_HANDLE);
-  BOOST_CHECK( seventhSimplexVector.size() == 3 );
-  typeSimplex seventhSimplex = std::make_pair(
-      seventhSimplexVector, Filtration_value(THIRD_FILTRATION_VALUE));
-  returnValue =
-  st.insert_simplex ( seventhSimplex.first, seventhSimplex.second );
-
-  test_simplex_tree_insert_returns_true (returnValue);
+  typeVectorVertex seventhSimplexVector{2, 1, 0};
+  BOOST_CHECK(seventhSimplexVector.size() == 3);
+  typeSimplex seventhSimplex = std::make_pair(seventhSimplexVector, Filtration_value(THIRD_FILTRATION_VALUE));
+  returnValue = st.insert_simplex(seventhSimplex.first, seventhSimplex.second);
+
+  test_simplex_tree_insert_returns_true(returnValue);
   set_and_test_simplex_tree_dim_fil(st, seventhSimplexVector.size(), seventhSimplex.second);
-  BOOST_CHECK( st.num_vertices() == (size_t)3 );  // Not incremented !!
+  BOOST_CHECK(st.num_vertices() == (size_t) 3); // Not incremented !!
 
   // ++ EIGHTH
   std::cout << "   - INSERT 3" << std::endl;
-  typeVectorVertex eighthSimplexVector;
-  eighthSimplexVector.push_back(FOURTH_VERTEX_HANDLE);
-  BOOST_CHECK( eighthSimplexVector.size() == 1 );
-  typeSimplex eighthSimplex = std::make_pair(
-      eighthSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE));
-  returnValue =
-  st.insert_simplex ( eighthSimplex.first, eighthSimplex.second );
-
-  test_simplex_tree_insert_returns_true (returnValue);
+  typeVectorVertex eighthSimplexVector{3};
+  BOOST_CHECK(eighthSimplexVector.size() == 1);
+  typeSimplex eighthSimplex = std::make_pair(eighthSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE));
+  returnValue = st.insert_simplex(eighthSimplex.first, eighthSimplex.second);
+
+  test_simplex_tree_insert_returns_true(returnValue);
   set_and_test_simplex_tree_dim_fil(st, eighthSimplexVector.size(), eighthSimplex.second);
-  BOOST_CHECK( st.num_vertices() == (size_t)4 );
+  BOOST_CHECK(st.num_vertices() == (size_t) 4);
 
   // ++ NINETH
   std::cout << "   - INSERT (3,0)" << std::endl;
-  typeVectorVertex ninethSimplexVector;
-  ninethSimplexVector.push_back(FOURTH_VERTEX_HANDLE);
-  ninethSimplexVector.push_back(FIRST_VERTEX_HANDLE);
-  BOOST_CHECK( ninethSimplexVector.size() == 2 );
-  typeSimplex ninethSimplex = std::make_pair(
-      ninethSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE));
-  returnValue =
-  st.insert_simplex ( ninethSimplex.first, ninethSimplex.second );
-
-  test_simplex_tree_insert_returns_true (returnValue);
+  typeVectorVertex ninethSimplexVector{3, 0};
+  BOOST_CHECK(ninethSimplexVector.size() == 2);
+  typeSimplex ninethSimplex = std::make_pair(ninethSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE));
+  returnValue = st.insert_simplex(ninethSimplex.first, ninethSimplex.second);
+
+  test_simplex_tree_insert_returns_true(returnValue);
   set_and_test_simplex_tree_dim_fil(st, ninethSimplexVector.size(), ninethSimplex.second);
-  BOOST_CHECK( st.num_vertices() == (size_t)4 );  // Not incremented !!
+  BOOST_CHECK(st.num_vertices() == (size_t) 4); // Not incremented !!
 
   // ++ TENTH
   std::cout << "   - INSERT 0 (already inserted)" << std::endl;
-  typeVectorVertex tenthSimplexVector;
-  tenthSimplexVector.push_back(FIRST_VERTEX_HANDLE);
-  BOOST_CHECK( tenthSimplexVector.size() == 1 );
-  typeSimplex tenthSimplex = std::make_pair(
-      tenthSimplexVector, Filtration_value(FOURTH_FILTRATION_VALUE));  // With a different filtration value
-  returnValue =
-  st.insert_simplex ( tenthSimplex.first, tenthSimplex.second );
+  typeVectorVertex tenthSimplexVector{0};
+  BOOST_CHECK(tenthSimplexVector.size() == 1);
+  // With a different filtration value
+  typeSimplex tenthSimplex = std::make_pair(tenthSimplexVector, Filtration_value(FOURTH_FILTRATION_VALUE));
+  returnValue = st.insert_simplex(tenthSimplex.first, tenthSimplex.second);
 
   BOOST_CHECK(returnValue.second == false);
-  typeST::Simplex_handle shReturned = returnValue.first;  // Simplex_handle = boost::container::flat_map< Vertex_handle, Node >::iterator
+  typeST::Simplex_handle shReturned = returnValue.first; // Simplex_handle = boost::container::flat_map< Vertex_handle, Node >::iterator
   BOOST_CHECK(shReturned == typeST::Simplex_handle(NULL));
-  BOOST_CHECK( st.num_vertices() == (size_t)4 );  // Not incremented !!
-  BOOST_CHECK( st.dimension() == dim_max );
-  BOOST_CHECK( AreAlmostTheSame(st.filtration(), max_fil) );
+  BOOST_CHECK(st.num_vertices() == (size_t) 4); // Not incremented !!
+  BOOST_CHECK(st.dimension() == dim_max);
+  BOOST_CHECK(AreAlmostTheSame(st.filtration(), max_fil));
 
   // ++ ELEVENTH
   std::cout << "   - INSERT (2,1,0) (already inserted)" << std::endl;
-  typeVectorVertex eleventhSimplexVector;
-  eleventhSimplexVector.push_back(THIRD_VERTEX_HANDLE);
-  eleventhSimplexVector.push_back(SECOND_VERTEX_HANDLE);
-  eleventhSimplexVector.push_back(FIRST_VERTEX_HANDLE);
-  BOOST_CHECK( eleventhSimplexVector.size() == 3 );
-  typeSimplex eleventhSimplex = std::make_pair(
-      eleventhSimplexVector, Filtration_value(FOURTH_FILTRATION_VALUE));
-  returnValue =
-  st.insert_simplex ( eleventhSimplex.first, eleventhSimplex.second );
+  typeVectorVertex eleventhSimplexVector{2, 1, 0};
+  BOOST_CHECK(eleventhSimplexVector.size() == 3);
+  typeSimplex eleventhSimplex = std::make_pair(eleventhSimplexVector, Filtration_value(FOURTH_FILTRATION_VALUE));
+  returnValue = st.insert_simplex(eleventhSimplex.first, eleventhSimplex.second);
 
   BOOST_CHECK(returnValue.second == false);
-  shReturned = returnValue.first;  // Simplex_handle = boost::container::flat_map< Vertex_handle, Node >::iterator
+  shReturned = returnValue.first; // Simplex_handle = boost::container::flat_map< Vertex_handle, Node >::iterator
   BOOST_CHECK(shReturned == typeST::Simplex_handle(NULL));
-  BOOST_CHECK( st.num_vertices() == (size_t)4 );// Not incremented !!
-  BOOST_CHECK( st.dimension() == dim_max );
-  BOOST_CHECK( AreAlmostTheSame(st.filtration(), max_fil) );
+  BOOST_CHECK(st.num_vertices() == (size_t) 4); // Not incremented !!
+  BOOST_CHECK(st.dimension() == dim_max);
+  BOOST_CHECK(AreAlmostTheSame(st.filtration(), max_fil));
 
   /* Inserted simplex:        */
   /*    1                     */
@@ -372,119 +330,153 @@ BOOST_AUTO_TEST_CASE( simplex_tree_insertion )
   //   [0.3] 2 1 0
   //  !! Be careful, simplex are sorted by filtration value on insertion !!
   std::cout << "simplex_tree_insertion - first - 0" << std::endl;
-  test_simplex_tree_contains(st, firstSimplex, 0);// (0) -> 0
+  test_simplex_tree_contains(st, firstSimplex, 0); // (0) -> 0
   std::cout << "simplex_tree_insertion - second - 1" << std::endl;
-  test_simplex_tree_contains(st, secondSimplex, 1);// (1) -> 1
+  test_simplex_tree_contains(st, secondSimplex, 1); // (1) -> 1
   std::cout << "simplex_tree_insertion - third - 4" << std::endl;
-  test_simplex_tree_contains(st, thirdSimplex, 4);// (0,1) -> 4
+  test_simplex_tree_contains(st, thirdSimplex, 4); // (0,1) -> 4
   std::cout << "simplex_tree_insertion - fourth - 2" << std::endl;
-  test_simplex_tree_contains(st, fourthSimplex, 2);// (2) -> 2
+  test_simplex_tree_contains(st, fourthSimplex, 2); // (2) -> 2
   std::cout << "simplex_tree_insertion - fifth - 5" << std::endl;
-  test_simplex_tree_contains(st, fifthSimplex, 5);// (2,0) -> 5
+  test_simplex_tree_contains(st, fifthSimplex, 5); // (2,0) -> 5
   std::cout << "simplex_tree_insertion - sixth - 6" << std::endl;
-  test_simplex_tree_contains(st, sixthSimplex, 6);//(2,1) -> 6
+  test_simplex_tree_contains(st, sixthSimplex, 6); //(2,1) -> 6
   std::cout << "simplex_tree_insertion - seventh - 8" << std::endl;
-  test_simplex_tree_contains(st, seventhSimplex, 8);// (2,1,0) -> 8
+  test_simplex_tree_contains(st, seventhSimplex, 8); // (2,1,0) -> 8
   std::cout << "simplex_tree_insertion - eighth - 3" << std::endl;
-  test_simplex_tree_contains(st, eighthSimplex, 3);// (3) -> 3
+  test_simplex_tree_contains(st, eighthSimplex, 3); // (3) -> 3
   std::cout << "simplex_tree_insertion - nineth - 7" << std::endl;
-  test_simplex_tree_contains(st, ninethSimplex, 7);// (3,0) -> 7
+  test_simplex_tree_contains(st, ninethSimplex, 7); // (3,0) -> 7
 
   // Display the Simplex_tree - Can not be done in the middle of 2 inserts
   std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl;
   std::cout << "   - dimension " << st.dimension() << "   - filtration " << st.filtration() << std::endl;
   std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
-  for( auto f_simplex : st.filtration_simplex_range() )
-  {
+  for (auto f_simplex : st.filtration_simplex_range()) {
     std::cout << "   " << "[" << st.filtration(f_simplex) << "] ";
-    for( auto vertex : st.simplex_vertex_range(f_simplex) )
-    {
-      std::cout << (int)vertex << " ";
+    for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+      std::cout << (int) vertex << " ";
     }
     std::cout << std::endl;
   }
 
 }
 
-BOOST_AUTO_TEST_CASE( NSimplexAndSubfaces_tree_insertion )
-{
-  Vertex_handle FIRST_VERTEX_HANDLE = (Vertex_handle)0;
-  Vertex_handle SECOND_VERTEX_HANDLE = (Vertex_handle) 1;
-  Vertex_handle THIRD_VERTEX_HANDLE = (Vertex_handle) 2;
-  Vertex_handle FOURTH_VERTEX_HANDLE = (Vertex_handle) 3;
-  Vertex_handle FIFTH_VERTEX_HANDLE = (Vertex_handle) 4;
-  Vertex_handle SIXTH_VERTEX_HANDLE = (Vertex_handle) 5;
-  Vertex_handle SEVENTH_VERTEX_HANDLE = (Vertex_handle) 6;
-  Vertex_handle EIGHTH_VERTEX_HANDLE = (Vertex_handle) 7;
+bool sort_in_decr_order (Vertex_handle i,Vertex_handle j) { return (i>j); }
 
-  // TEST OF INSERTION
+BOOST_AUTO_TEST_CASE(NSimplexAndSubfaces_tree_insertion) {
   std::cout << "********************************************************************" << std::endl;
-  std::cout << "TEST OF INSERTION" << std::endl;
+  std::cout << "TEST OF RECURSIVE INSERTION" << std::endl;
   typeST st;
+  typePairSimplexBool returnValue;
+  int position = 0;
 
   // ++ FIRST
   std::cout << "   - INSERT (2,1,0)" << std::endl;
-  typeVectorVertex SimplexVector1;
-  SimplexVector1.push_back(THIRD_VERTEX_HANDLE);
-  SimplexVector1.push_back(SECOND_VERTEX_HANDLE);
-  SimplexVector1.push_back(FIRST_VERTEX_HANDLE);
-  BOOST_CHECK( SimplexVector1.size() == 3 );
-  st.insert_simplex_and_subfaces ( SimplexVector1 );
-
-  BOOST_CHECK( st.num_vertices() == (size_t)3 ); // +3 (2, 1 and 0 are not existing)
+  typeVectorVertex SimplexVector1{2, 1, 0};
+  BOOST_CHECK(SimplexVector1.size() == 3);
+  returnValue = st.insert_simplex_and_subfaces(SimplexVector1);
+
+  BOOST_CHECK(st.num_vertices() == (size_t) 3); // +3 (2, 1 and 0 are not existing)
+
+  // Check it is well inserted
+  BOOST_CHECK(true == returnValue.second);
+  position = 0;
+  std::sort(SimplexVector1.begin(), SimplexVector1.end(), sort_in_decr_order);
+  for (auto vertex : st.simplex_vertex_range(returnValue.first)) {
+    // Check returned Simplex_handle
+    std::cout << "vertex = " << vertex << " | vector[" << position << "] = " << SimplexVector1[position] << std::endl;
+    BOOST_CHECK(vertex == SimplexVector1[position]);
+    position++;
+  }
 
   // ++ SECOND
   std::cout << "   - INSERT 3" << std::endl;
-  typeVectorVertex SimplexVector2;
-  SimplexVector2.push_back(FOURTH_VERTEX_HANDLE);
-  BOOST_CHECK( SimplexVector2.size() == 1 );
-  st.insert_simplex_and_subfaces ( SimplexVector2 );
-
-  BOOST_CHECK( st.num_vertices() == (size_t)4 ); // +1 (3 is not existing)
+  typeVectorVertex SimplexVector2{3};
+  BOOST_CHECK(SimplexVector2.size() == 1);
+  returnValue = st.insert_simplex_and_subfaces(SimplexVector2);
+
+  BOOST_CHECK(st.num_vertices() == (size_t) 4); // +1 (3 is not existing)
+
+  // Check it is well inserted
+  BOOST_CHECK(true == returnValue.second);
+  position = 0;
+  std::sort(SimplexVector2.begin(), SimplexVector2.end(), sort_in_decr_order);
+  for (auto vertex : st.simplex_vertex_range(returnValue.first)) {
+    // Check returned Simplex_handle
+    std::cout << "vertex = " << vertex << " | vector[" << position << "] = " << SimplexVector2[position] << std::endl;
+    BOOST_CHECK(vertex == SimplexVector2[position]);
+    position++;
+  }
 
   // ++ THIRD
   std::cout << "   - INSERT (0,3)" << std::endl;
-  typeVectorVertex SimplexVector3;
-  SimplexVector3.push_back(FOURTH_VERTEX_HANDLE);
-  SimplexVector3.push_back(FIRST_VERTEX_HANDLE);
-  BOOST_CHECK( SimplexVector3.size() == 2 );
-  st.insert_simplex_and_subfaces ( SimplexVector3 );
-
-  BOOST_CHECK( st.num_vertices() == (size_t)4 );  // Not incremented (all are existing)
+  typeVectorVertex SimplexVector3{3, 0};
+  BOOST_CHECK(SimplexVector3.size() == 2);
+  returnValue = st.insert_simplex_and_subfaces(SimplexVector3);
+
+  BOOST_CHECK(st.num_vertices() == (size_t) 4); // Not incremented (all are existing)
+
+  // Check it is well inserted
+  BOOST_CHECK(true == returnValue.second);
+  position = 0;
+  std::sort(SimplexVector3.begin(), SimplexVector3.end(), sort_in_decr_order);
+  for (auto vertex : st.simplex_vertex_range(returnValue.first)) {
+    // Check returned Simplex_handle
+    std::cout << "vertex = " << vertex << " | vector[" << position << "] = " << SimplexVector3[position] << std::endl;
+    BOOST_CHECK(vertex == SimplexVector3[position]);
+    position++;
+  }
 
   // ++ FOURTH
   std::cout << "   - INSERT (1,0) (already inserted)" << std::endl;
-  typeVectorVertex SimplexVector4;
-  SimplexVector4.push_back(SECOND_VERTEX_HANDLE);
-  SimplexVector4.push_back(FIRST_VERTEX_HANDLE);
-  BOOST_CHECK( SimplexVector4.size() == 2 );
-  st.insert_simplex_and_subfaces ( SimplexVector4 );
+  typeVectorVertex SimplexVector4{1, 0};
+  BOOST_CHECK(SimplexVector4.size() == 2);
+  returnValue = st.insert_simplex_and_subfaces(SimplexVector4);
 
-  BOOST_CHECK( st.num_vertices() == (size_t)4 );  // Not incremented (all are existing)
+  BOOST_CHECK(st.num_vertices() == (size_t) 4); // Not incremented (all are existing)
+
+  // Check it was not inserted (already there from {2,1,0} insertion)
+  BOOST_CHECK(false == returnValue.second);
 
   // ++ FIFTH
   std::cout << "   - INSERT (3,4,5)" << std::endl;
-  typeVectorVertex SimplexVector5;
-  SimplexVector5.push_back(FOURTH_VERTEX_HANDLE);
-  SimplexVector5.push_back(FIFTH_VERTEX_HANDLE);
-  SimplexVector5.push_back(SIXTH_VERTEX_HANDLE);
-  BOOST_CHECK( SimplexVector5.size() == 3 );
-  st.insert_simplex_and_subfaces ( SimplexVector5 );
-
-  BOOST_CHECK( st.num_vertices() == (size_t)6 );
+  typeVectorVertex SimplexVector5{3, 4, 5};
+  BOOST_CHECK(SimplexVector5.size() == 3);
+  returnValue = st.insert_simplex_and_subfaces(SimplexVector5);
+
+  BOOST_CHECK(st.num_vertices() == (size_t) 6);
+
+  // Check it is well inserted
+  BOOST_CHECK(true == returnValue.second);
+  position = 0;
+  std::sort(SimplexVector5.begin(), SimplexVector5.end(), sort_in_decr_order);
+  for (auto vertex : st.simplex_vertex_range(returnValue.first)) {
+    // Check returned Simplex_handle
+    std::cout << "vertex = " << vertex << " | vector[" << position << "] = " << SimplexVector5[position] << std::endl;
+    BOOST_CHECK(vertex == SimplexVector5[position]);
+    position++;
+  }
 
   // ++ SIXTH
   std::cout << "   - INSERT (0,1,6,7)" << std::endl;
-  typeVectorVertex SimplexVector6;
-  SimplexVector6.push_back(FIRST_VERTEX_HANDLE);
-  SimplexVector6.push_back(SECOND_VERTEX_HANDLE);
-  SimplexVector6.push_back(SEVENTH_VERTEX_HANDLE);
-  SimplexVector6.push_back(EIGHTH_VERTEX_HANDLE);
-  BOOST_CHECK( SimplexVector6.size() == 4 );
-  st.insert_simplex_and_subfaces ( SimplexVector6 );
-
-  BOOST_CHECK( st.num_vertices() == (size_t)8 ); // +2 (6 and 7 are not existing - 0 and 1 are already existing)
-
+  typeVectorVertex SimplexVector6{0, 1, 6, 7};
+  BOOST_CHECK(SimplexVector6.size() == 4);
+  returnValue = st.insert_simplex_and_subfaces(SimplexVector6);
+
+  BOOST_CHECK(st.num_vertices() == (size_t) 8); // +2 (6 and 7 are not existing - 0 and 1 are already existing)
+
+  // Check it is well inserted
+  BOOST_CHECK(true == returnValue.second);
+  position = 0;
+  std::sort(SimplexVector6.begin(), SimplexVector6.end(), sort_in_decr_order);
+  for (auto vertex : st.simplex_vertex_range(returnValue.first)) {
+    // Check returned Simplex_handle
+    std::cout << "vertex = " << vertex << " | vector[" << position << "] = " << SimplexVector6[position] << std::endl;
+    BOOST_CHECK(vertex == SimplexVector6[position]);
+    position++;
+  }
+  
   /* Inserted simplex:        */
   /*    1   6                 */
   /*    o---o                 */
@@ -506,18 +498,17 @@ BOOST_AUTO_TEST_CASE( NSimplexAndSubfaces_tree_insertion )
   typeSimplex simplexPair4 = std::make_pair(SimplexVector4, DEFAULT_FILTRATION_VALUE);
   typeSimplex simplexPair5 = std::make_pair(SimplexVector5, DEFAULT_FILTRATION_VALUE);
   typeSimplex simplexPair6 = std::make_pair(SimplexVector6, DEFAULT_FILTRATION_VALUE);
-  test_simplex_tree_contains(st,simplexPair1,6);  // (2,1,0) is in position 6
-  test_simplex_tree_contains(st,simplexPair2,7);  // (3) is in position 7
-  test_simplex_tree_contains(st,simplexPair3,8);  // (3,0) is in position 8
-  test_simplex_tree_contains(st,simplexPair4,2);  // (1,0) is in position 2
-  test_simplex_tree_contains(st,simplexPair5,14);  // (3,4,5) is in position 14
-  test_simplex_tree_contains(st,simplexPair6,26);  // (7,6,1,0) is in position 26
-  
+  test_simplex_tree_contains(st, simplexPair1, 6); // (2,1,0) is in position 6
+  test_simplex_tree_contains(st, simplexPair2, 7); // (3) is in position 7
+  test_simplex_tree_contains(st, simplexPair3, 8); // (3,0) is in position 8
+  test_simplex_tree_contains(st, simplexPair4, 2); // (1,0) is in position 2
+  test_simplex_tree_contains(st, simplexPair5, 14); // (3,4,5) is in position 14
+  test_simplex_tree_contains(st, simplexPair6, 26); // (7,6,1,0) is in position 26
+
   // ------------------------------------------------------------------------------------------------------------------
   // Find in the simplex_tree
   // ------------------------------------------------------------------------------------------------------------------
-  typeVectorVertex simpleSimplexVector;
-  simpleSimplexVector.push_back(SECOND_VERTEX_HANDLE);
+  typeVectorVertex simpleSimplexVector{1};
   Simplex_tree<>::Simplex_handle simplexFound = st.find(simpleSimplexVector);
   std::cout << "**************IS THE SIMPLEX {1} IN THE SIMPLEX TREE ?\n";
   if (simplexFound != st.null_simplex())
@@ -527,9 +518,7 @@ BOOST_AUTO_TEST_CASE( NSimplexAndSubfaces_tree_insertion )
   // Check it is found
   BOOST_CHECK(simplexFound != st.null_simplex());
 
-  Vertex_handle UNKNOWN_VERTEX_HANDLE = (Vertex_handle) 15;
-  typeVectorVertex unknownSimplexVector;
-  unknownSimplexVector.push_back(UNKNOWN_VERTEX_HANDLE);
+  typeVectorVertex unknownSimplexVector{15};
   simplexFound = st.find(unknownSimplexVector);
   std::cout << "**************IS THE SIMPLEX {15} IN THE SIMPLEX TREE ?\n";
   if (simplexFound != st.null_simplex())
@@ -547,10 +536,8 @@ BOOST_AUTO_TEST_CASE( NSimplexAndSubfaces_tree_insertion )
     std::cout << "***- NO IT ISN'T\n";
   // Check it is found
   BOOST_CHECK(simplexFound != st.null_simplex());
-      
-  typeVectorVertex otherSimplexVector;
-  otherSimplexVector.push_back(UNKNOWN_VERTEX_HANDLE);
-  otherSimplexVector.push_back(SECOND_VERTEX_HANDLE);
+
+  typeVectorVertex otherSimplexVector{1, 15};
   simplexFound = st.find(otherSimplexVector);
   std::cout << "**************IS THE SIMPLEX {15,1} IN THE SIMPLEX TREE ?\n";
   if (simplexFound != st.null_simplex())
@@ -560,10 +547,7 @@ BOOST_AUTO_TEST_CASE( NSimplexAndSubfaces_tree_insertion )
   // Check it is NOT found
   BOOST_CHECK(simplexFound == st.null_simplex());
 
-  typeVectorVertex invSimplexVector;
-  invSimplexVector.push_back(SECOND_VERTEX_HANDLE);
-  invSimplexVector.push_back(THIRD_VERTEX_HANDLE);
-  invSimplexVector.push_back(FIRST_VERTEX_HANDLE);
+  typeVectorVertex invSimplexVector{1, 2, 0};
   simplexFound = st.find(invSimplexVector);
   std::cout << "**************IS THE SIMPLEX {1,2,0} IN THE SIMPLEX TREE ?\n";
   if (simplexFound != st.null_simplex())
@@ -572,19 +556,191 @@ BOOST_AUTO_TEST_CASE( NSimplexAndSubfaces_tree_insertion )
     std::cout << "***- NO IT ISN'T\n";
   // Check it is found
   BOOST_CHECK(simplexFound != st.null_simplex());
-  
+
   // Display the Simplex_tree - Can not be done in the middle of 2 inserts
   std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl;
   std::cout << "   - dimension " << st.dimension() << "   - filtration " << st.filtration() << std::endl;
   std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
-  for( auto f_simplex : st.filtration_simplex_range() )
-  {
+  for (auto f_simplex : st.filtration_simplex_range()) {
     std::cout << "   " << "[" << st.filtration(f_simplex) << "] ";
-    for( auto vertex : st.simplex_vertex_range(f_simplex) )
-    {
-      std::cout << (int)vertex << " ";
+    for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+      std::cout << (int) vertex << " ";
+    }
+    std::cout << std::endl;
+  }
+}
+
+void test_cofaces(typeST& st, std::vector<Vertex_handle> expected, int dim, std::vector<typeST::Simplex_handle> res) {
+  typeST::Cofaces_simplex_range cofaces;
+  if (dim == 0)
+    cofaces = st.star_simplex_range(st.find(expected));
+  else
+    cofaces = st.cofaces_simplex_range(st.find(expected), dim);
+  for (auto simplex = cofaces.begin(); simplex != cofaces.end(); ++simplex) {
+    typeST::Simplex_vertex_range rg = st.simplex_vertex_range(*simplex);
+    for (auto vertex = rg.begin(); vertex != rg.end(); ++vertex) {
+      std::cout << "(" << *vertex << ")";
     }
     std::cout << std::endl;
+    BOOST_CHECK(std::find(res.begin(), res.end(), *simplex) != res.end());
   }
+}
+
+BOOST_AUTO_TEST_CASE(coface_on_simplex_tree) {
+  std::cout << "********************************************************************" << std::endl;
+  std::cout << "TEST COFACE ALGORITHM" << std::endl;
+  typeST st;
+
+  typeVectorVertex SimplexVector{2, 1, 0};
+  st.insert_simplex_and_subfaces(SimplexVector);
 
+  SimplexVector = {3, 0};
+  st.insert_simplex_and_subfaces(SimplexVector);
+
+  SimplexVector = {3, 4, 5};
+  st.insert_simplex_and_subfaces(SimplexVector);
+
+  SimplexVector = {0, 1, 6, 7};
+  st.insert_simplex_and_subfaces(SimplexVector);
+
+  /* Inserted simplex:        */
+  /*    1   6                 */
+  /*    o---o                 */
+  /*   /X\7/                  */
+  /*  o---o---o---o           */
+  /*  2   0   3\X/4           */
+  /*            o             */
+  /*            5             */
+
+  // FIXME
+  st.set_dimension(3);
+
+  std::vector<Vertex_handle> simplex_result;
+  std::vector<typeST::Simplex_handle> result;
+  std::cout << "First test - Star of (3):" << std::endl;
+
+  simplex_result = {3};
+  result.push_back(st.find(simplex_result));
+
+  simplex_result = {3, 0};
+  result.push_back(st.find(simplex_result));
+
+  simplex_result = {4, 3};
+  result.push_back(st.find(simplex_result));
+
+  simplex_result = {5, 4, 3};
+  result.push_back(st.find(simplex_result));
+
+  simplex_result = {5, 3};
+  result.push_back(st.find(simplex_result));
+  simplex_result.clear();
+
+  std::vector<Vertex_handle> vertex = {3};
+  test_cofaces(st, vertex, 0, result);
+  vertex.clear();
+  result.clear();
+
+  vertex.push_back(1);
+  vertex.push_back(7);
+  std::cout << "Second test - Star of (1,7): " << std::endl;
+
+  simplex_result = {7, 1};
+  result.push_back(st.find(simplex_result));
+
+  simplex_result = {7, 6, 1, 0};
+  result.push_back(st.find(simplex_result));
+
+  simplex_result = {7, 1, 0};
+  result.push_back(st.find(simplex_result));
+
+  simplex_result = {7, 6, 1};
+  result.push_back(st.find(simplex_result));
+
+  test_cofaces(st, vertex, 0, result);
+  result.clear();
+
+  std::cout << "Third test - 2-dimension Cofaces of simplex(1,7) : " << std::endl;
+
+  simplex_result = {7, 1, 0};
+  result.push_back(st.find(simplex_result));
+
+  simplex_result = {7, 6, 1};
+  result.push_back(st.find(simplex_result));
+
+  test_cofaces(st, vertex, 1, result);
+  result.clear();
+
+  std::cout << "Cofaces with a codimension too high (codimension + vetices > tree.dimension) :" << std::endl;
+  test_cofaces(st, vertex, 5, result);
+
+  //std::cout << "Cofaces with an empty codimension" << std::endl;
+  //test_cofaces(st, vertex, -1, result);
+  //    std::cout << "Cofaces in an empty simplex tree" << std::endl;
+  //   typeST empty_tree;
+  //    test_cofaces(empty_tree, vertex, 1, result);
+  //std::cout << "Cofaces of an empty simplex" << std::endl;
+  //vertex.clear();
+  // test_cofaces(st, vertex, 1, result);
+
+}
+
+BOOST_AUTO_TEST_CASE(copy_move_on_simplex_tree) {
+  std::cout << "********************************************************************" << std::endl;
+  std::cout << "TEST COPY MOVE CONSTRUCTORS" << std::endl;
+  typeST st;
+
+  typeVectorVertex SimplexVector{2, 1, 0};
+  st.insert_simplex_and_subfaces(SimplexVector);
+
+  SimplexVector = {3, 0};
+  st.insert_simplex_and_subfaces(SimplexVector);
+
+  SimplexVector = {3, 4, 5};
+  st.insert_simplex_and_subfaces(SimplexVector);
+
+  SimplexVector = {0, 1, 6, 7};
+  st.insert_simplex_and_subfaces(SimplexVector);
+
+  /* Inserted simplex:        */
+  /*    1   6                 */
+  /*    o---o                 */
+  /*   /X\7/                  */
+  /*  o---o---o---o           */
+  /*  2   0   3\X/4           */
+  /*            o             */
+  /*            5             */
+
+  // FIXME
+  st.set_dimension(3);
+
+  std::cout << "Printing st - address = " << &st << std::endl;
+
+  // Copy constructor  
+  typeST st_copy = st;
+  std::cout << "Printing a copy of st - address = " << &st_copy << std::endl;
+
+  // Check the data are the same
+  BOOST_CHECK(st == st_copy);
+  // Check there is a new simplex tree reference
+  BOOST_CHECK(&st != &st_copy);
+
+  // Move constructor  
+  typeST st_move = std::move(st);
+  std::cout << "Printing a move of st - address = " << &st_move << std::endl;
+
+  // Check the data are the same
+  BOOST_CHECK(st_move == st_copy);
+  // Check there is a new simplex tree reference
+  BOOST_CHECK(&st_move != &st_copy);
+  BOOST_CHECK(&st_move != &st);
+  
+  typeST st_empty;
+  // Check st has been emptied by the move
+  BOOST_CHECK(st == st_empty);
+  BOOST_CHECK(st.filtration() == 0);
+  BOOST_CHECK(st.dimension() == -1);
+  BOOST_CHECK(st.num_simplices() == 0);
+  BOOST_CHECK(st.num_vertices() == (size_t)0);
+  
+  std::cout << "Printing st once again- address = " << &st << std::endl;
 }
diff --git a/src/Skeleton_blocker/example/CMakeLists.txt b/src/Skeleton_blocker/example/CMakeLists.txt
index d1228526..de0c7bba 100644
--- a/src/Skeleton_blocker/example/CMakeLists.txt
+++ b/src/Skeleton_blocker/example/CMakeLists.txt
@@ -1,10 +1,12 @@
 cmake_minimum_required(VERSION 2.6)
 project(GUDHIskbl)
 
-
 add_executable(SkeletonBlockerFromSimplices Skeleton_blocker_from_simplices.cpp)
 add_executable(SkeletonBlockerIteration Skeleton_blocker_iteration.cpp)
 add_executable(SkeletonBlockerLink Skeleton_blocker_link.cpp)
 
+target_link_libraries(SkeletonBlockerIteration ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBRARY})
 
-target_link_libraries(SkeletonBlockerIteration ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBRARY})	
+add_test(SkeletonBlockerFromSimplices ${CMAKE_CURRENT_BINARY_DIR}/SkeletonBlockerFromSimplices)
+add_test(SkeletonBlockerIteration ${CMAKE_CURRENT_BINARY_DIR}/SkeletonBlockerIteration)
+add_test(SkeletonBlockerLink ${CMAKE_CURRENT_BINARY_DIR}/SkeletonBlockerLink)
diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp
index 9f9b3d52..5935a56d 100644
--- a/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp
+++ b/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp
@@ -1,34 +1,33 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <gudhi/Skeleton_blocker.h>
 
 #include <stdio.h>
 #include <stdlib.h>
 #include <string>
 #include <fstream>
 #include <sstream>
-
-
-#include "gudhi/Skeleton_blocker.h"
+#include <vector>
 
 using namespace std;
 using namespace Gudhi;
@@ -36,48 +35,46 @@ using namespace skbl;
 
 typedef Skeleton_blocker_complex<Skeleton_blocker_simple_traits> Complex;
 typedef Complex::Vertex_handle Vertex_handle;
-typedef Complex::Simplex_handle Simplex_handle;
-typedef Complex::Simplex_handle Simplex;
+typedef Complex::Simplex Simplex;
 
-int main (int argc, char *argv[]){
-	std::vector<Simplex_handle> simplices;
+int main(int argc, char *argv[]) {
+  std::vector<Simplex> simplices;
 
-	//add 4 triangles of a tetrahedron 0123
-	simplices.push_back(Simplex_handle(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2)));
-	simplices.push_back(Simplex_handle(Vertex_handle(1),Vertex_handle(2),Vertex_handle(3)));
-	simplices.push_back(Simplex_handle(Vertex_handle(3),Vertex_handle(0),Vertex_handle(2)));
-	simplices.push_back(Simplex_handle(Vertex_handle(3),Vertex_handle(0),Vertex_handle(1)));
+  // add 4 triangles of a tetrahedron 0123
+  simplices.push_back(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2)));
+  simplices.push_back(Simplex(Vertex_handle(1), Vertex_handle(2), Vertex_handle(3)));
+  simplices.push_back(Simplex(Vertex_handle(3), Vertex_handle(0), Vertex_handle(2)));
+  simplices.push_back(Simplex(Vertex_handle(3), Vertex_handle(0), Vertex_handle(1)));
 
-	//get complex from top faces
-	Complex complex(make_complex_from_top_faces<Complex>(simplices.begin(),simplices.end()));
+  // get complex from top faces
+  Complex complex(make_complex_from_top_faces<Complex>(simplices.begin(), simplices.end()));
 
 
-	std::cout << "Simplices:"<<std::endl;
-	for(const Simplex & s : complex.simplex_range())
-		std::cout << s << " ";
-	std::cout << std::endl;
+  std::cout << "Simplices:" << std::endl;
+  for (const Simplex & s : complex.complex_simplex_range())
+    std::cout << s << " ";
+  std::cout << std::endl;
 
-	//One blocker as simplex 0123 is not in the complex but all its proper faces are.
-	std::cout << "Blockers: "<<complex.blockers_to_string()<<std::endl;
+  // One blocker as simplex 0123 is not in the complex but all its proper faces are.
+  std::cout << "Blockers: " << complex.blockers_to_string() << std::endl;
 
-	//now build a complex from its full list of simplices
-	simplices.clear();
-	simplices.push_back(Simplex_handle(Vertex_handle(0)));
-	simplices.push_back(Simplex_handle(Vertex_handle(1)));
-	simplices.push_back(Simplex_handle(Vertex_handle(2)));
-	simplices.push_back(Simplex_handle(Vertex_handle(0),Vertex_handle(1)));
-	simplices.push_back(Simplex_handle(Vertex_handle(1),Vertex_handle(2)));
-	simplices.push_back(Simplex_handle(Vertex_handle(2),Vertex_handle(0)));
-	complex = Complex(simplices.begin(),simplices.end());
+  // now build a complex from its full list of simplices
+  simplices.clear();
+  simplices.push_back(Simplex(Vertex_handle(0)));
+  simplices.push_back(Simplex(Vertex_handle(1)));
+  simplices.push_back(Simplex(Vertex_handle(2)));
+  simplices.push_back(Simplex(Vertex_handle(0), Vertex_handle(1)));
+  simplices.push_back(Simplex(Vertex_handle(1), Vertex_handle(2)));
+  simplices.push_back(Simplex(Vertex_handle(2), Vertex_handle(0)));
+  complex = Complex(simplices.begin(), simplices.end());
 
-	std::cout << "Simplices:"<<std::endl;
-	for(const Simplex & s : complex.simplex_range())
-		std::cout << s << " ";
-	std::cout << std::endl;
+  std::cout << "Simplices:" << std::endl;
+  for (const Simplex & s : complex.complex_simplex_range())
+    std::cout << s << " ";
+  std::cout << std::endl;
 
-	//One blocker as simplex 012 is not in the complex but all its proper faces are.
-	std::cout << "Blockers: "<<complex.blockers_to_string()<<std::endl;
+  // One blocker as simplex 012 is not in the complex but all its proper faces are.
+  std::cout << "Blockers: " << complex.blockers_to_string() << std::endl;
 
-	return EXIT_SUCCESS;
+  return EXIT_SUCCESS;
 }
-
diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp
index 126e32ec..41b5ee00 100644
--- a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp
+++ b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp
@@ -1,24 +1,26 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <gudhi/Skeleton_blocker.h>
 
 #include <boost/timer/timer.hpp>
 
@@ -29,64 +31,60 @@
 #include <sstream>
 
 
-#include "gudhi/Skeleton_blocker.h"
-
 using namespace std;
 using namespace Gudhi;
 using namespace skbl;
 
 typedef Skeleton_blocker_complex<Skeleton_blocker_simple_traits> Complex;
 typedef Complex::Vertex_handle Vertex_handle;
-typedef Complex::Simplex_handle Simplex;
+typedef Complex::Simplex Simplex;
 
-
-Complex build_complete_complex(int n){
-	// build a full complex with n vertices and 2^n-1 simplices
-		Complex complex;
-		for(int i=0;i<n;i++)
-			complex.add_vertex();
-		for(int i=0;i<n;i++)
-			for(int j=0;j<i;j++)
-				//note that add_edge, add the edge and all its cofaces
-				complex.add_edge(Vertex_handle(i),Vertex_handle(j));
-		return complex;
+Complex build_complete_complex(int n) {
+  // build a full complex with n vertices and 2^n-1 simplices
+  Complex complex;
+  for (int i = 0; i < n; i++)
+    complex.add_vertex();
+  for (int i = 0; i < n; i++)
+    for (int j = 0; j < i; j++)
+      complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(j));
+  return complex;
 }
 
-int main (int argc, char *argv[]){
-	boost::timer::auto_cpu_timer t;
+int main(int argc, char *argv[]) {
+  boost::timer::auto_cpu_timer t;
 
-	const int n = 15;
+  const int n = 15;
 
-	// build a full complex with n vertices and 2^n-1 simplices
-	Complex complex(build_complete_complex(n));
+  // build a full complex with n vertices and 2^n-1 simplices
+  Complex complex(build_complete_complex(n));
 
-	// this is just to illustrate iterators, to count number of vertices
-	// or edges, complex.num_vertices() and complex.num_edges() are
-	// more appropriated!
-	unsigned num_vertices = 0;
-	for(auto v : complex.vertex_range()) {
-	  std::cout << "Vertex " << v <<std::endl;
-	  ++num_vertices;
-        }
+  // this is just to illustrate iterators, to count number of vertices
+  // or edges, complex.num_vertices() and complex.num_edges() are
+  // more appropriated!
+  unsigned num_vertices = 0;
+  for (auto v : complex.vertex_range()) {
+    std::cout << "Vertex " << v << std::endl;
+    ++num_vertices;
+  }
 
-	// such loop can also be done directly with distance as iterators are STL compliant
-	auto edges = complex.edge_range();
-	unsigned num_edges = std::distance(edges.begin(), edges.end());
+  // such loop can also be done directly with distance as iterators are STL compliant
+  auto edges = complex.edge_range();
+  unsigned num_edges = std::distance(edges.begin(), edges.end());
 
-	unsigned euler = 0;
-	unsigned num_simplices = 0;
-	// we use a reference to a simplex instead of a copy
-	// value here because a simplex is a set of integers
-	// and copying it cost time
-	for(const Simplex & s : complex.simplex_range()){
-		++num_simplices;
-		if(s.dimension()%2 == 0) 
-			euler += 1;
-		else 
-			euler -= 1;
-	}
-	std::cout << "Saw "<<num_vertices<<" vertices, "<<num_edges<<" edges and "<<num_simplices<<" simplices"<<std::endl;
-	std::cout << "The Euler Characteristic is "<<euler<<std::endl;
-	return EXIT_SUCCESS;
+  unsigned euler = 0;
+  unsigned num_simplices = 0;
+  // we use a reference to a simplex instead of a copy
+  // value here because a simplex is a set of integers
+  // and copying it cost time
+  for (const Simplex & s : complex.complex_simplex_range()) {
+    ++num_simplices;
+    if (s.dimension() % 2 == 0)
+      euler += 1;
+    else
+      euler -= 1;
+  }
+  std::cout << "Saw " << num_vertices << " vertices, " << num_edges << " edges and " << num_simplices << " simplices"
+      << std::endl;
+  std::cout << "The Euler Characteristic is " << euler << std::endl;
+  return EXIT_SUCCESS;
 }
-
diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp
index 0987cc89..698a8106 100644
--- a/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp
+++ b/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp
@@ -1,25 +1,26 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
 
+#include <gudhi/Skeleton_blocker.h>
 
 #include <stdio.h>
 #include <stdlib.h>
@@ -27,9 +28,6 @@
 #include <fstream>
 #include <sstream>
 
-
-#include "gudhi/Skeleton_blocker.h"
-
 using namespace std;
 using namespace Gudhi;
 using namespace skbl;
@@ -37,35 +35,37 @@ using namespace skbl;
 typedef Skeleton_blocker_complex<Skeleton_blocker_simple_traits> Complex;
 typedef Complex::Vertex_handle Vertex_handle;
 typedef Complex::Root_vertex_handle Root_vertex_handle;
-typedef Complex::Simplex_handle Simplex;
+typedef Complex::Simplex Simplex;
 
+int main(int argc, char *argv[]) {
+  // build a full complex with 4 vertices and 2^4-1 simplices
 
-int main (int argc, char *argv[]){
-	// build a full complex with 4 vertices and 2^4-1 simplices
-	// Initial vertices are (0,1,2,3,4)
-	Simplex tetrahedron(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2),Vertex_handle(3));
-	Complex complex;
-	complex.add_simplex(tetrahedron);
+  // Create a complex with four vertices (0,1,2,3)
+  Complex complex;
 
-	cout<<"complex:"<<complex.to_string()<<endl;
+  // Add a tetrahedron to this complex
+  Simplex tetrahedron(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2), Vertex_handle(3));
+  complex.add_simplex(tetrahedron);
 
-	//build the link of vertex 1, eg a triangle {0,2,3}
-	auto link = complex.link(Vertex_handle(1));
-	cout<<"link:"<<link.to_string()<<endl;
+  cout << "complex:" << complex.to_string() << endl;
 
-	//Internally link is a subcomplex of 'complex' and its vertices are stored in a vector.
-	//They can be accessed via Vertex_handle(x) where x is an index of the vector.
-	//In that example, link has three vertices and thus it contains only
-	// Vertex_handle(0),Vertex_handle(1) and Vertex_handle(2) are).
-	for(int i = 0; i<5; ++i)
-		cout << "link.contains_vertex(Vertex_handle("<<i<<")):"<<link.contains_vertex(Vertex_handle(i))<<endl;
-	cout<<endl;
+  // build the link of vertex 1, eg a triangle {0,2,3}
+  auto link = complex.link(Vertex_handle(1));
+  cout << "link:" << link.to_string() << endl;
 
-	//To access to the initial vertices eg (0,1,2,3,4),  Root_vertex_handle must be used.
-	//For instance, to test if the link contains the vertex that was labeled i:
-	for(int i = 0; i<5; ++i)
-		cout << "link.contains_vertex(Root_vertex_handle("<<i<<")):"<<link.contains_vertex(Root_vertex_handle(i))<<endl;
+  // Internally link is a subcomplex of 'complex' and its vertices are stored in a vector.
+  // They can be accessed via Vertex_handle(x) where x is an index of the vector.
+  // In that example, link has three vertices and thus it contains only
+  // Vertex_handle(0),Vertex_handle(1) and Vertex_handle(2) are).
+  for (int i = 0; i < 5; ++i)
+    cout << "link.contains_vertex(Vertex_handle(" << i << ")):" << link.contains_vertex(Vertex_handle(i)) << endl;
+  cout << endl;
 
-	return EXIT_SUCCESS;
-}
+  // To access to the initial vertices eg (0,1,2,3,4),  Root_vertex_handle must be used.
+  // For instance, to test if the link contains the vertex that was labeled i:
+  for (int i = 0; i < 5; ++i)
+    cout << "link.contains_vertex(Root_vertex_handle(" << i << ")):" <<
+        link.contains_vertex(Root_vertex_handle(i)) << endl;
 
+  return EXIT_SUCCESS;
+}
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
index 289819b5..615b3a81 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
@@ -19,23 +19,24 @@
   *    You should have received a copy of the GNU General Public License
   *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
   */
-#ifndef SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_H_
-#define SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_H_
 
-#include "gudhi/Skeleton_blocker_complex.h"
-#include "gudhi/Skeleton_blocker_geometric_complex.h"
-#include "gudhi/Skeleton_blocker_simplifiable_complex.h"
-#include "gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h"
+#ifndef SKELETON_BLOCKER_H_
+#define SKELETON_BLOCKER_H_
 
-#include "gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h"
-#include "gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h"
+#include <gudhi/Skeleton_blocker_complex.h>
+#include <gudhi/Skeleton_blocker_geometric_complex.h>
+#include <gudhi/Skeleton_blocker_simplifiable_complex.h>
+#include <gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h>
 
+#include <gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h>
+#include <gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h>
 
-#include "gudhi/Utils.h"  // xxx
-
+#include <gudhi/Utils.h>  // xxx
 
 namespace Gudhi {
+
 namespace skbl {
+
 /** \defgroup skbl Skeleton-Blocker 
 
 \author David Salinas
@@ -128,7 +129,7 @@ of a simplicial complex.
   \code{.cpp}
 	typedef Skeleton_blocker_complex<Skeleton_blocker_simple_traits> Complex;
 	typedef Complex::Vertex_handle Vertex_handle;
-	typedef Complex::Simplex_handle Simplex;
+	typedef Complex::Simplex Simplex;
 
   	const int n = 15;
 
@@ -138,8 +139,7 @@ of a simplicial complex.
 		complex.add_vertex();
 	for(int i=0;i<n;i++)
 		for(int j=0;j<i;j++)
-			//note that add_edge adds the edge and all its cofaces
-			complex.add_edge(Vertex_handle(i),Vertex_handle(j));
+			complex.add_edge_without_blockers(Vertex_handle(i),Vertex_handle(j));
 
 	// this is just to illustrate iterators, to count number of vertices
 	// or edges, complex.num_vertices() and complex.num_edges() are
@@ -158,7 +158,7 @@ of a simplicial complex.
 	// we use a reference to a simplex instead of a copy
 	// value here because a simplex is a set of integers
 	// and copying it cost time
-	for(const Simplex & s : complex.simplex_range()){
+	for(const Simplex & s : complex.star_simplex_range()){
 		++num_simplices;
 		if(s.dimension()%2 == 0) 
 			euler += 1;
@@ -181,20 +181,20 @@ The Euler Characteristic is 1
 \subsection s Constructing a skeleton-blockers from a list of maximal faces or from a list of faces
 
   \code{.cpp}
-	std::vector<Simplex_handle> simplices;
+	std::vector<Simplex> simplices;
 
 	//add 4 triangles of a tetrahedron 0123
-	simplices.push_back(Simplex_handle(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2)));
-	simplices.push_back(Simplex_handle(Vertex_handle(1),Vertex_handle(2),Vertex_handle(3)));
-	simplices.push_back(Simplex_handle(Vertex_handle(3),Vertex_handle(0),Vertex_handle(2)));
-	simplices.push_back(Simplex_handle(Vertex_handle(3),Vertex_handle(0),Vertex_handle(1)));
+	simplices.push_back(Simplex(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2)));
+	simplices.push_back(Simplex(Vertex_handle(1),Vertex_handle(2),Vertex_handle(3)));
+	simplices.push_back(Simplex(Vertex_handle(3),Vertex_handle(0),Vertex_handle(2)));
+	simplices.push_back(Simplex(Vertex_handle(3),Vertex_handle(0),Vertex_handle(1)));
 
 	Complex complex;
 	//get complex from top faces
 	make_complex_from_top_faces(complex,simplices.begin(),simplices.end());
 
 	std::cout << "Simplices:"<<std::endl;
-	for(const Simplex & s : complex.simplex_range())
+	for(const Simplex & s : complex.star_simplex_range())
 		std::cout << s << " ";
 	std::cout << std::endl;
 
@@ -203,16 +203,16 @@ The Euler Characteristic is 1
 
 	//now build a complex from its full list of simplices
 	simplices.clear();
-	simplices.push_back(Simplex_handle(Vertex_handle(0)));
-	simplices.push_back(Simplex_handle(Vertex_handle(1)));
-	simplices.push_back(Simplex_handle(Vertex_handle(2)));
-	simplices.push_back(Simplex_handle(Vertex_handle(0),Vertex_handle(1)));
-	simplices.push_back(Simplex_handle(Vertex_handle(1),Vertex_handle(2)));
-	simplices.push_back(Simplex_handle(Vertex_handle(2),Vertex_handle(0)));
+	simplices.push_back(Simplex(Vertex_handle(0)));
+	simplices.push_back(Simplex(Vertex_handle(1)));
+	simplices.push_back(Simplex(Vertex_handle(2)));
+	simplices.push_back(Simplex(Vertex_handle(0),Vertex_handle(1)));
+	simplices.push_back(Simplex(Vertex_handle(1),Vertex_handle(2)));
+	simplices.push_back(Simplex(Vertex_handle(2),Vertex_handle(0)));
 	complex = Complex(simplices.begin(),simplices.end());
 
 	std::cout << "Simplices:"<<std::endl;
-	for(const Simplex & s : complex.simplex_range())
+	for(const Simplex & s : complex.star_simplex_range())
 		std::cout << s << " ";
 	std::cout << std::endl;
 
@@ -240,14 +240,12 @@ their collaboration to write the two initial papers
 
 
 \copyright GNU General Public License v3.                         
-\verbatim  Contact: David Salinas,     david.salinas@inria.fr \endverbatim
+\verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
 */
 /** @} */  // end defgroup
-}  // namespace skbl
-}  // namespace Gudhi
-
-
-#endif  // SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_H_
 
+}  // namespace skbl
 
+}  // namespace Gudhi
 
+#endif  // SKELETON_BLOCKER_H_
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h
index 829ab1e8..4ade68e7 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h
@@ -19,10 +19,10 @@
  *    You should have received a copy of the GNU General Public License
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-#ifndef SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_COMPLEX_VISITOR_H_
-#define SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_COMPLEX_VISITOR_H_
+#ifndef SKELETON_BLOCKER_SKELETON_BLOCKER_COMPLEX_VISITOR_H_
+#define SKELETON_BLOCKER_SKELETON_BLOCKER_COMPLEX_VISITOR_H_
 
-#include "gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h"
+#include <gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h>
 
 namespace Gudhi {
 
@@ -41,7 +41,7 @@ class Skeleton_blocker_complex_visitor {
   virtual void on_add_vertex(Vertex_handle) = 0;
   virtual void on_remove_vertex(Vertex_handle) = 0;
 
-  virtual void on_add_edge(Vertex_handle a, Vertex_handle b) = 0;
+  virtual void on_add_edge_without_blockers(Vertex_handle a, Vertex_handle b) = 0;
   virtual void on_remove_edge(Vertex_handle a, Vertex_handle b) = 0;
 
   /**
@@ -54,12 +54,12 @@ class Skeleton_blocker_complex_visitor {
    * @brief Called when performing an edge contraction when
    * an edge bx is replaced by an edge ax (not already present).
    * Precisely, this methods is called this way in contract_edge :
-   * add_edge(a,x)
+   * add_edge_without_blockers(a,x)
    * on_swaped_edge(a,b,x)
    * remove_edge(b,x)
    */
   virtual void on_swaped_edge(Vertex_handle a, Vertex_handle b,
-                              Vertex_handle x)=0;
+                              Vertex_handle x) = 0;
   virtual void on_add_blocker(
       const Skeleton_blocker_simplex<Vertex_handle>&) = 0;
   virtual void on_delete_blocker(
@@ -79,7 +79,7 @@ class Dummy_complex_visitor : public Skeleton_blocker_complex_visitor<
   }
   void on_remove_vertex(Vertex_handle) {
   }
-  void on_add_edge(Vertex_handle a, Vertex_handle b) {
+  void on_add_edge_without_blockers(Vertex_handle a, Vertex_handle b) {
   }
   void on_remove_edge(Vertex_handle a, Vertex_handle b) {
   }
@@ -108,8 +108,8 @@ class Print_complex_visitor : public Skeleton_blocker_complex_visitor<
   void on_remove_vertex(Vertex_handle v) {
     std::cerr << "on_remove_vertex:" << v << std::endl;
   }
-  void on_add_edge(Vertex_handle a, Vertex_handle b) {
-    std::cerr << "on_add_edge:" << a << "," << b << std::endl;
+  void on_add_edge_without_blockers(Vertex_handle a, Vertex_handle b) {
+    std::cerr << "on_add_edge_without_blockers:" << a << "," << b << std::endl;
   }
   void on_remove_edge(Vertex_handle a, Vertex_handle b) {
     std::cerr << "on_remove_edge:" << a << "," << b << std::endl;
@@ -132,4 +132,4 @@ class Print_complex_visitor : public Skeleton_blocker_complex_visitor<
 
 }  // namespace Gudhi
 
-#endif  // SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_COMPLEX_VISITOR_H_
+#endif  // SKELETON_BLOCKER_SKELETON_BLOCKER_COMPLEX_VISITOR_H_
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h
index 17d58956..876bdba9 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h
@@ -19,10 +19,10 @@
  *    You should have received a copy of the GNU General Public License
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-#ifndef SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_LINK_SUPERIOR_H_
-#define SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_LINK_SUPERIOR_H_
+#ifndef SKELETON_BLOCKER_SKELETON_BLOCKER_LINK_SUPERIOR_H_
+#define SKELETON_BLOCKER_SKELETON_BLOCKER_LINK_SUPERIOR_H_
 
-#include "gudhi/Skeleton_blocker_link_complex.h"
+#include <gudhi/Skeleton_blocker_link_complex.h>
 
 namespace Gudhi {
 
@@ -44,13 +44,13 @@ class Skeleton_blocker_link_superior : public Skeleton_blocker_link_complex<
  public:
   typedef typename ComplexType::Vertex_handle Vertex_handle;
   typedef typename ComplexType::Root_vertex_handle Root_vertex_handle;
-  typedef typename ComplexType::Simplex_handle Simplex_handle;
+  typedef typename ComplexType::Simplex Simplex;
   typedef typename ComplexType::Root_simplex_handle Root_simplex_handle;
   typedef typename ComplexType::BlockerMap BlockerMap;
   typedef typename ComplexType::BlockerPair BlockerPair;
   typedef typename ComplexType::BlockerMapIterator BlockerMapIterator;
   typedef typename ComplexType::BlockerMapConstIterator BlockerMapConstIterator;
-  typedef typename ComplexType::Simplex_handle::Simplex_vertex_const_iterator AddressSimplexConstIterator;
+  typedef typename ComplexType::Simplex::Simplex_vertex_const_iterator AddressSimplexConstIterator;
   typedef typename ComplexType::Root_simplex_handle::Simplex_vertex_const_iterator IdSimplexConstIterator;
 
   Skeleton_blocker_link_superior()
@@ -58,7 +58,7 @@ class Skeleton_blocker_link_superior : public Skeleton_blocker_link_complex<
   }
 
   Skeleton_blocker_link_superior(const ComplexType & parent_complex,
-                                 Simplex_handle& alpha_parent_adress)
+                                 Simplex& alpha_parent_adress)
       : Skeleton_blocker_link_complex<ComplexType>(parent_complex,
                                                    alpha_parent_adress, true) {
   }
@@ -74,4 +74,4 @@ class Skeleton_blocker_link_superior : public Skeleton_blocker_link_complex<
 
 }  // namespace Gudhi
 
-#endif  // SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_LINK_SUPERIOR_H_
+#endif  // SKELETON_BLOCKER_SKELETON_BLOCKER_LINK_SUPERIOR_H_
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h
index aaaab8b0..ad2d2f85 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h
@@ -19,15 +19,15 @@
  *    You should have received a copy of the GNU General Public License
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-#ifndef SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_OFF_IO_H_
-#define SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_OFF_IO_H_
+#ifndef SKELETON_BLOCKER_SKELETON_BLOCKER_OFF_IO_H_
+#define SKELETON_BLOCKER_SKELETON_BLOCKER_OFF_IO_H_
+
+#include <gudhi/Off_reader.h>
 
 #include <string>
 #include <vector>
 #include <map>
 
-#include "gudhi/Off_reader.h"
-
 namespace Gudhi {
 
 namespace skbl {
@@ -61,7 +61,7 @@ class Skeleton_blocker_off_flag_visitor_reader {
     if (!load_only_points_) {
       for (size_t i = 0; i < face.size(); ++i)
         for (size_t j = i + 1; j < face.size(); ++j) {
-          complex_.add_edge(Vertex_handle(face[i]), Vertex_handle(face[j]));
+          complex_.add_edge_without_blockers(Vertex_handle(face[i]), Vertex_handle(face[j]));
         }
     }
   }
@@ -76,12 +76,12 @@ template<typename Complex>
 class Skeleton_blocker_off_visitor_reader {
   Complex& complex_;
   typedef typename Complex::Vertex_handle Vertex_handle;
-  typedef typename Complex::Simplex_handle Simplex_handle;
+  typedef typename Complex::Simplex Simplex;
   typedef typename Complex::Point Point;
 
   const bool load_only_points_;
   std::vector<Point> points_;
-  std::vector<Simplex_handle> maximal_faces_;
+  std::vector<Simplex> maximal_faces_;
 
  public:
   explicit Skeleton_blocker_off_visitor_reader(Complex& complex, bool load_only_points = false) :
@@ -99,7 +99,7 @@ class Skeleton_blocker_off_visitor_reader {
 
   void maximal_face(const std::vector<int>& face) {
     if (!load_only_points_) {
-      Simplex_handle s;
+      Simplex s;
       for (auto x : face)
         s.add_vertex(Vertex_handle(x));
       maximal_faces_.emplace_back(s);
@@ -107,7 +107,7 @@ class Skeleton_blocker_off_visitor_reader {
   }
 
   void done() {
-    complex_ = make_complex_from_top_faces(maximal_faces_.begin(), maximal_faces_.end(),
+    complex_ = make_complex_from_top_faces<Complex>(maximal_faces_.begin(), maximal_faces_.end(),
                                            points_.begin(), points_.end() );
   }
 };
@@ -197,4 +197,4 @@ class Skeleton_blocker_off_writer {
 
 }  // namespace Gudhi
 
-#endif  // SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_OFF_IO_H_
+#endif  // SKELETON_BLOCKER_SKELETON_BLOCKER_OFF_IO_H_
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h
index d3a5b9d8..8508d9a5 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h
@@ -19,14 +19,14 @@
  *    You should have received a copy of the GNU General Public License
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-#ifndef SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLE_GEOMETRIC_TRAITS_H_
-#define SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLE_GEOMETRIC_TRAITS_H_
+#ifndef SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLE_GEOMETRIC_TRAITS_H_
+#define SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLE_GEOMETRIC_TRAITS_H_
+
+#include <gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h>
 
 #include <string>
 #include <sstream>
 
-#include "gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h"
-
 namespace Gudhi {
 
 namespace skbl {
@@ -91,4 +91,4 @@ struct Skeleton_blocker_simple_geometric_traits :
 
 }  // namespace Gudhi
 
-#endif  // SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLE_GEOMETRIC_TRAITS_H_
+#endif  // SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLE_GEOMETRIC_TRAITS_H_
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h
index 52e454ea..0d2de767 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h
@@ -19,12 +19,13 @@
  *    You should have received a copy of the GNU General Public License
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-#ifndef SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLE_TRAITS_H_
-#define SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLE_TRAITS_H_
+#ifndef SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLE_TRAITS_H_
+#define SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLE_TRAITS_H_
+
+#include <gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h>
 
 #include <string>
 #include <sstream>
-#include "Skeleton_blocker_simplex.h"
 
 namespace Gudhi {
 
@@ -77,7 +78,7 @@ struct Skeleton_blocker_simple_traits {
         : vertex(val) {
     }
 
-    operator int() const { return (int)vertex; }
+    operator int() const { return static_cast<int>(vertex); }
 
     boost_vertex_handle vertex;
 
@@ -178,4 +179,4 @@ struct Skeleton_blocker_simple_traits {
 
 }  // namespace Gudhi
 
-#endif  // SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLE_TRAITS_H_
+#endif  // SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLE_TRAITS_H_
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h
index 10d64e98..714bf23c 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLEX_H_
-#define SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLEX_H_
+#ifndef SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLEX_H_
+#define SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLEX_H_
 
 #include <cassert>
 #include <iostream>
@@ -69,7 +69,9 @@ class Skeleton_blocker_simplex {
   }
 
   Skeleton_blocker_simplex(std::initializer_list<T>& list) {
-    for_each(list.begin(), list.end(), add_vertex);
+    std::for_each(list.begin(), list.end(), [&] (T const& elt) {
+      add_vertex(elt);
+    });
   }
 
   template<typename ... Args>
@@ -216,7 +218,7 @@ class Skeleton_blocker_simplex {
   }
 
   /**
-   * Returns the first vertex of the (oriented) simplex.
+   * Returns the first and smallest vertex of the simplex.
    *
    * Be careful : assumes the simplex is non-empty.
    */
@@ -226,7 +228,7 @@ class Skeleton_blocker_simplex {
   }
 
   /**
-   * Returns the last vertex of the (oriented) simplex.
+   * Returns the last and greatest vertex of the simplex.
    *
    * Be careful : assumes the simplex is non-empty.
    */
@@ -369,5 +371,4 @@ class Skeleton_blocker_simplex {
 
 }  // namespace Gudhi
 
-#endif  // SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLEX_H_
-
+#endif  // SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLEX_H_
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h
index e906df75..50a83345 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h
@@ -20,16 +20,16 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_SUB_COMPLEX_H_
-#define SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_SUB_COMPLEX_H_
+#ifndef SKELETON_BLOCKER_SKELETON_BLOCKER_SUB_COMPLEX_H_
+#define SKELETON_BLOCKER_SKELETON_BLOCKER_SUB_COMPLEX_H_
+
+#include <gudhi/Skeleton_blocker_complex.h>
+#include <gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h>
+#include <gudhi/Utils.h>
 
 #include <map>
 #include <vector>
 
-#include "gudhi/Skeleton_blocker_complex.h"
-#include "gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h"
-#include "gudhi/Utils.h"
-
 namespace Gudhi {
 
 namespace skbl {
@@ -66,34 +66,19 @@ class Skeleton_blocker_sub_complex : public ComplexType {
 
  public:
   using ComplexType::add_vertex;
-  using ComplexType::add_edge;
+  using ComplexType::add_edge_without_blockers;
   using ComplexType::add_blocker;
 
   typedef typename ComplexType::Vertex_handle Vertex_handle;
   typedef typename ComplexType::Root_vertex_handle Root_vertex_handle;
-  typedef typename ComplexType::Simplex_handle Simplex_handle;
+  typedef typename ComplexType::Simplex Simplex;
   typedef typename ComplexType::Root_simplex_handle Root_simplex_handle;
 
  protected:
-  ///**
-  //* @brief Returns true iff the simplex formed by all vertices contained in 'addresses_sigma_in_link'
-  //* but 'vertex_to_be_ignored' is in 'link'
-  //*/
-  /*
-   template<typename T> friend bool
-   proper_face_in_union(
-   Skeleton_blocker_sub_complex<T> & link,
-   std::vector<boost::optional<typename T::Vertex_handle> > & addresses_sigma_in_link,
-   int vertex_to_be_ignored);*/
-
   /**
    * @brief Determines whether all proper faces of simplex 'sigma' belong to 'link1' \cup 'link2'
    * where 'link1' and 'link2' are subcomplexes of the same complex of type ComplexType
    */
-  // template<typename T> friend bool
-  // proper_faces_in_union(Skeleton_blocker_simplex<typename T::Root_vertex_handle> & sigma, Skeleton_blocker_sub_complex<T> & link1, Skeleton_blocker_sub_complex<T> & link2){
-  // template<typename T> friend bool
-  // proper_faces_in_union(Skeleton_blocker_simplex<typename T::Root_vertex_handle> & sigma, Skeleton_blocker_sub_complex<T> & link1, Skeleton_blocker_sub_complex<T> & link2);
   typedef std::map<Root_vertex_handle, Vertex_handle> IdAddressMap;
   typedef typename IdAddressMap::value_type AddressPair;
   typedef typename IdAddressMap::iterator IdAddressMapIterator;
@@ -124,11 +109,11 @@ class Skeleton_blocker_sub_complex : public ComplexType {
    * It assumes that both vertices corresponding to v1_root and v2_root are present
    * in the sub-complex.
    */
-  void add_edge(Root_vertex_handle v1_root, Root_vertex_handle v2_root) {
+  void add_edge_without_blockers(Root_vertex_handle v1_root, Root_vertex_handle v2_root) {
     auto v1_sub(this->get_address(v1_root));
     auto v2_sub(this->get_address(v2_root));
     assert(v1_sub && v2_sub);
-    this->ComplexType::add_edge(*v1_sub, *v2_sub);
+    this->ComplexType::add_edge_without_blockers(*v1_sub, *v2_sub);
   }
 
   /**
@@ -139,7 +124,7 @@ class Skeleton_blocker_sub_complex : public ComplexType {
   void add_blocker(const Root_simplex_handle& blocker_root) {
     auto blocker_sub = this->get_address(blocker_root);
     assert(blocker_sub);
-    this->add_blocker(new Simplex_handle(*blocker_sub));
+    this->add_blocker(new Simplex(*blocker_sub));
   }
 
  public:
@@ -148,7 +133,7 @@ class Skeleton_blocker_sub_complex : public ComplexType {
    * vertices of 'simplex'.
    */
   void make_restricted_complex(const ComplexType & parent_complex,
-                               const Simplex_handle& simplex) {
+                               const Simplex& simplex) {
     this->clear();
     // add vertices to the sub complex
     for (auto x : simplex) {
@@ -160,11 +145,11 @@ class Skeleton_blocker_sub_complex : public ComplexType {
     // add edges to the sub complex
     for (auto x : simplex) {
       // x_neigh is the neighbor of x intersected with vertices_simplex
-      Simplex_handle x_neigh;
+      Simplex x_neigh;
       parent_complex.add_neighbours(x, x_neigh, true);
       x_neigh.intersection(simplex);
       for (auto y : x_neigh) {
-        this->add_edge(parent_complex[x].get_id(), parent_complex[y].get_id());
+        this->add_edge_without_blockers(parent_complex[x].get_id(), parent_complex[y].get_id());
       }
     }
 
@@ -173,9 +158,9 @@ class Skeleton_blocker_sub_complex : public ComplexType {
       // check if it is the first time we encounter the blocker
       if (simplex.contains(*blocker)) {
         Root_simplex_handle blocker_root(parent_complex.get_id(*(blocker)));
-        Simplex_handle blocker_restr(
+        Simplex blocker_restr(
             *(this->get_simplex_address(blocker_root)));
-        this->add_blocker(new Simplex_handle(blocker_restr));
+        this->add_blocker(new Simplex(blocker_restr));
       }
     }
   }
@@ -203,7 +188,7 @@ class Skeleton_blocker_sub_complex : public ComplexType {
   //  * Allocates a simplex in L corresponding to the simplex s in K
   //  * with its local adresses and returns an AddressSimplex.
   //  */
-  // boost::optional<Simplex_handle> get_address(const Root_simplex_handle & s) const;
+  // boost::optional<Simplex> get_address(const Root_simplex_handle & s) const;
 
 // private:
   /**
@@ -235,7 +220,7 @@ bool proper_face_in_union(
   // we test that all vertices of 'addresses_sigma_in_link' but 'vertex_to_be_ignored'
   // are in link1 if it is the case we construct the corresponding simplex
   bool vertices_sigma_are_in_link = true;
-  typename ComplexType::Simplex_handle sigma_in_link;
+  typename ComplexType::Simplex sigma_in_link;
   for (int i = 0; i < addresses_sigma_in_link.size(); ++i) {
     if (i != vertex_to_be_ignored) {
       if (!addresses_sigma_in_link[i]) {
@@ -301,5 +286,5 @@ bool proper_faces_in_union(
 
 }  // namespace Gudhi
 
-#endif  // SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_SUB_COMPLEX_H_
+#endif  // SKELETON_BLOCKER_SKELETON_BLOCKER_SUB_COMPLEX_H_
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Top_faces.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Top_faces.h
index 32538f38..eb970195 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Top_faces.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Top_faces.h
@@ -1,67 +1,70 @@
- /*    This file is part of the Gudhi Library. The Gudhi library
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-#ifndef TOP_FACES_H_
-#define TOP_FACES_H_
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+#ifndef SKELETON_BLOCKER_INTERNAL_TOP_FACES_H_
+#define SKELETON_BLOCKER_INTERNAL_TOP_FACES_H_
 
 #include <list>
 #include <vector>
 #include <set>
 
+namespace Gudhi {
+
+namespace skbl {
+
 template<typename SimplexHandle>
-std::list<SimplexHandle> subfaces(SimplexHandle top_face){
-	std::list<SimplexHandle> res;
-	if(top_face.dimension()==-1) return res;
-	if(top_face.dimension()==0) {
-		res.push_back(top_face);
-		return res;
-	}
-	else{
-		auto first_vertex = top_face.first_vertex();
-		top_face.remove_vertex(first_vertex);
-		res = subfaces(top_face);
-		std::list<SimplexHandle> copy = res;
-		for(auto& simplex : copy){
-			simplex.add_vertex(first_vertex);
-		}
-		res.push_back(SimplexHandle(first_vertex));
-		res.splice(res.end(),copy);
-		return res;
-	}
+std::list<SimplexHandle> subfaces(SimplexHandle top_face) {
+  std::list<SimplexHandle> res;
+  if (top_face.dimension() == -1) return res;
+  if (top_face.dimension() == 0) {
+    res.push_back(top_face);
+    return res;
+  } else {
+    auto first_vertex = top_face.first_vertex();
+    top_face.remove_vertex(first_vertex);
+    res = subfaces(top_face);
+    std::list<SimplexHandle> copy = res;
+    for (auto& simplex : copy) {
+      simplex.add_vertex(first_vertex);
+    }
+    res.push_back(SimplexHandle(first_vertex));
+    res.splice(res.end(), copy);
+    return res;
+  }
 }
 
 /**
  * add all faces of top_face in simplices_per_dimension
  */
 template<typename SimplexHandle>
-void register_faces(
-		std::vector< std::set<SimplexHandle> >& simplices_per_dimension,
-		const SimplexHandle& top_face){
-	std::list<SimplexHandle> subfaces_list = subfaces(top_face);
-	for(auto& simplex : subfaces_list ){
-		simplices_per_dimension[simplex.dimension()].insert(simplex);
-	}
+void register_faces(std::vector< std::set<SimplexHandle> >& simplices_per_dimension,
+                    const SimplexHandle& top_face) {
+  std::list<SimplexHandle> subfaces_list = subfaces(top_face);
+  for (auto& simplex : subfaces_list) {
+    simplices_per_dimension[simplex.dimension()].insert(simplex);
+  }
 }
 
+}  // namespace skbl
 
+}  // namespace Gudhi
 
-
-#endif /* TOP_FACES_H_ */
+#endif  // SKELETON_BLOCKER_INTERNAL_TOP_FACES_H_
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Trie.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Trie.h
index f2a443dc..499980c4 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Trie.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Trie.h
@@ -1,13 +1,10 @@
-/*
- * Trie.h
- *  Created on: Jan 29, 2015
- * This file is part of the Gudhi Library. The Gudhi library 
+/* This file is part of the Gudhi Library. The Gudhi library 
  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
  *    library for computational topology.
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-M�diterran�e (France)
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
@@ -25,8 +22,8 @@
  */
 
 
-#ifndef TRIE_H_
-#define TRIE_H_
+#ifndef SKELETON_BLOCKER_INTERNAL_TRIE_H_
+#define SKELETON_BLOCKER_INTERNAL_TRIE_H_
 
 #include <memory>
 #include <vector>
@@ -35,242 +32,237 @@
 
 namespace Gudhi {
 
-
 namespace skbl {
 
-
 template<typename SimplexHandle>
-struct Trie{
-	typedef SimplexHandle Simplex_handle;
-	typedef typename SimplexHandle::Vertex_handle Vertex_handle;
-
-	Vertex_handle v;
-	std::vector<std::shared_ptr<Trie> > childs;
-	//std::vector<std::unique_ptr<Trie> > childs; -> use of deleted function
-private:
-	const Trie* parent_;
-public:
-	Trie():parent_(0){}
-	Trie(Vertex_handle v_):v(v_),parent_(0){}
-
-	Trie(Vertex_handle v_,Trie* parent):v(v_),parent_(parent){}
-
-
-	bool operator==(const Trie& other) const{
-		return (v == other.v) ;
-	}
-
-	void add_child(Trie* child){
-		if(child){
-			std::shared_ptr<Trie> ptr_to_add(child);
-			childs.push_back(ptr_to_add);
-			child->parent_ = this;
-		}
-	}
-
-	typedef typename Simplex_handle::Simplex_vertex_const_iterator Simplex_vertex_const_iterator;
-
-
-	Trie* make_trie(Simplex_vertex_const_iterator s_it,Simplex_vertex_const_iterator s_end){
-		if(s_it == s_end) return 0;
-		else{
-			Trie* res = new Trie(*s_it);
-			Trie* child = make_trie(++s_it,s_end);
-			res->add_child(child);
-			return res;
-		}
-	}
-private:
-	//go down recursively in the tree while advancing the simplex iterator.
-	//when it reaches a leaf, it inserts the remaining that is not present
-	void add_simplex_helper(Simplex_vertex_const_iterator s_it,Simplex_vertex_const_iterator s_end){
-		assert(*s_it == v);
-		++s_it;
-		if(s_it==s_end) return ;
-		if(!is_leaf()){
-			for(auto child : childs){
-				if(child->v == *s_it)
-					return child->add_simplex_helper(s_it,s_end);
-			}
-			//s_it is not found and needs to be inserted
-		}
-		//not leaf -> remaining of s needs to be inserted
-		Trie* son_with_what_remains_of_s(make_trie(s_it,s_end));
-		add_child(son_with_what_remains_of_s);
-		return;
-	}
-
-	void maximal_faces_helper(std::vector<Simplex_handle>& res) const{
-		if(is_leaf()) res.push_back(simplex());
-		else
-			for(auto child : childs)
-				child->maximal_faces_helper(res);
-	}
-
-public:
-	/**
-	 * adds the simplex to the trie
-	 */
-	void add_simplex(const Simplex_handle& s){
-		if(s.empty()) return;
-		assert(v==s.first_vertex());
-		add_simplex_helper(s.begin(),s.end());
-	}
-
-	std::vector<Simplex_handle> maximal_faces() const{
-		std::vector<Simplex_handle> res;
-		maximal_faces_helper(res);
-		return res;
-	}
-
-	/**
-	 * Goes to the root in the trie to consitute simplex
-	 */
-	void add_vertices_up_to_the_root(Simplex_handle& res) const{
-		res.add_vertex(v);
-		if(parent_)
-			parent_->add_vertices_up_to_the_root(res);
-	}
-
-	Simplex_handle simplex() const{
-		Simplex_handle res;
-		add_vertices_up_to_the_root(res);
-		return res;
-	}
-
-	bool is_leaf() const{
-		return childs.empty();
-	}
-
-	bool is_root() const{
-		return parent_==0;
-	}
-
-	const Trie* parent() {
-		return parent_;
-	}
-
-	void remove_leaf() {
-		assert(is_leaf);
-		if(!is_root())
-			parent_->childs.erase(this);
-	}
-
-	/**
-	 * true iff the simplex corresponds to one node in the trie
-	 */
-	bool contains(const Simplex_handle& s) const{
-		Trie const* current = this;
-		if(s.empty()) return true;
-		if(current->v != s.first_vertex()) return false;
-		auto s_pos = s.begin();
-		++s_pos;
-		while(s_pos != s.end() && current != 0){
-			bool found = false;
-			for(const auto child : current->childs){
-				if(child->v == *s_pos) {
-					++s_pos;
-					current = child.get();
-					found = true;
-					break;
-				}
-			}
-			if(!found) return false;
-		}
-		return current!=0;
-	}
-
-	Trie* go_bottom_left(){
-		if(is_leaf())
-			return this;
-		else
-			return (*childs.begin())->go_bottom_left();
-	}
-
-	friend std::ostream& operator<<(std::ostream& stream, const Trie& trie){
-		stream<< "T( "<< trie.v<< " ";
-		for(auto t : trie.childs)
-			stream << *t ;
-		stream<<")";
-		return stream;
-	}
+struct Trie {
+  typedef SimplexHandle Simplex;
+  typedef typename SimplexHandle::Vertex_handle Vertex_handle;
+
+  Vertex_handle v;
+  std::vector<std::shared_ptr<Trie> > childs;
+  // std::vector<std::unique_ptr<Trie> > childs; -> use of deleted function
+ private:
+  const Trie* parent_;
+
+ public:
+  Trie() : parent_(0) { }
+
+  Trie(Vertex_handle v_) : v(v_), parent_(0) { }
+
+  Trie(Vertex_handle v_, Trie* parent) : v(v_), parent_(parent) { }
+
+  bool operator==(const Trie& other) const {
+    return (v == other.v);
+  }
+
+  void add_child(Trie* child) {
+    if (child) {
+      std::shared_ptr<Trie> ptr_to_add(child);
+      childs.push_back(ptr_to_add);
+      child->parent_ = this;
+    }
+  }
+
+  typedef typename Simplex::Simplex_vertex_const_iterator Simplex_vertex_const_iterator;
+
+  Trie* make_trie(Simplex_vertex_const_iterator s_it, Simplex_vertex_const_iterator s_end) {
+    if (s_it == s_end) {
+      return 0;
+    } else {
+      Trie* res = new Trie(*s_it);
+      Trie* child = make_trie(++s_it, s_end);
+      res->add_child(child);
+      return res;
+    }
+  }
+
+ private:
+  // go down recursively in the tree while advancing the simplex iterator.
+  // when it reaches a leaf, it inserts the remaining that is not present
+  void add_simplex_helper(Simplex_vertex_const_iterator s_it, Simplex_vertex_const_iterator s_end) {
+    assert(*s_it == v);
+    ++s_it;
+    if (s_it == s_end) return;
+    if (!is_leaf()) {
+      for (auto child : childs) {
+        if (child->v == *s_it)
+          return child->add_simplex_helper(s_it, s_end);
+      }
+      // s_it is not found and needs to be inserted
+    }
+    // not leaf -> remaining of s needs to be inserted
+    Trie * son_with_what_remains_of_s(make_trie(s_it, s_end));
+    add_child(son_with_what_remains_of_s);
+    return;
+  }
+
+  void maximal_faces_helper(std::vector<Simplex>& res) const {
+    if (is_leaf()) res.push_back(simplex());
+    else
+      for (auto child : childs)
+        child->maximal_faces_helper(res);
+  }
+
+ public:
+  /**
+   * adds the simplex to the trie
+   */
+  void add_simplex(const Simplex& s) {
+    if (s.empty()) return;
+    assert(v == s.first_vertex());
+    add_simplex_helper(s.begin(), s.end());
+  }
+
+  std::vector<Simplex> maximal_faces() const {
+    std::vector<Simplex> res;
+    maximal_faces_helper(res);
+    return res;
+  }
+
+  /**
+   * Goes to the root in the trie to consitute simplex
+   */
+  void add_vertices_up_to_the_root(Simplex& res) const {
+    res.add_vertex(v);
+    if (parent_)
+      parent_->add_vertices_up_to_the_root(res);
+  }
+
+  Simplex simplex() const {
+    Simplex res;
+    add_vertices_up_to_the_root(res);
+    return res;
+  }
+
+  bool is_leaf() const {
+    return childs.empty();
+  }
+
+  bool is_root() const {
+    return parent_ == 0;
+  }
+
+  const Trie* parent() {
+    return parent_;
+  }
+
+  void remove_leaf() {
+    assert(is_leaf);
+    if (!is_root())
+      parent_->childs.erase(this);
+  }
+
+  /**
+   * true iff the simplex corresponds to one node in the trie
+   */
+  bool contains(const Simplex& s) const {
+    Trie const* current = this;
+    if (s.empty()) return true;
+    if (current->v != s.first_vertex()) return false;
+    auto s_pos = s.begin();
+    ++s_pos;
+    while (s_pos != s.end() && current != 0) {
+      bool found = false;
+      for (const auto child : current->childs) {
+        if (child->v == *s_pos) {
+          ++s_pos;
+          current = child.get();
+          found = true;
+          break;
+        }
+      }
+      if (!found) return false;
+    }
+    return current != 0;
+  }
+
+  Trie* go_bottom_left() {
+    if (is_leaf())
+      return this;
+    else
+      return (*childs.begin())->go_bottom_left();
+  }
+
+  friend std::ostream& operator<<(std::ostream& stream, const Trie& trie) {
+    stream << "T( " << trie.v << " ";
+    for (auto t : trie.childs)
+      stream << *t;
+    stream << ")";
+    return stream;
+  }
 };
 
-
 template<typename SimplexHandle>
-struct Tries{
-	typedef typename SimplexHandle::Vertex_handle Vertex_handle;
-	typedef SimplexHandle Simplex_handle;
-
-	typedef Trie<Simplex_handle> STrie;
-
-
-	template<typename SimpleHandleOutputIterator>
-	Tries(unsigned num_vertices,SimpleHandleOutputIterator simplex_begin, SimpleHandleOutputIterator simplex_end):
-	cofaces_(num_vertices,0){
-		for (auto i = 0u; i < num_vertices; ++i)
-			cofaces_[i] = new STrie(Vertex_handle(i));
-		for (auto s_it = simplex_begin; s_it != simplex_end; ++s_it) {
-			if (s_it->dimension() >= 1)
-				cofaces_[s_it->first_vertex()]->add_simplex(*s_it);
-		}
-	}
-
-	~Tries(){
-		for(STrie* t : cofaces_)
-			delete t;
-	}
-
-	//return a simplex that consists in all u such uv is an edge and u>v
-	Simplex_handle positive_neighbors(Vertex_handle v) const{
-		Simplex_handle res;
-		for(auto child : cofaces_[v]->childs)
-			res.add_vertex(child->v);
-		return res;
-	}
-
-	bool contains(const Simplex_handle& s) const{
-		auto first_v = s.first_vertex();
-		return cofaces_[first_v]->contains(s);
-	}
-
-	friend std::ostream& operator<<(std::ostream& stream, const Tries& tries){
-		for(auto trie : tries.cofaces_)
-			stream<<*trie<<std::endl;
-		return stream;
-	}
-
-	//init_next_dimension must be called first
-	std::vector<Simplex_handle> next_dimension_simplices() const{
-		std::vector<Simplex_handle> res;
-		while(!to_see_.empty() && to_see_.front()->simplex().dimension()==current_dimension_){
-			res.emplace_back(to_see_.front()->simplex());
-			for(auto child : to_see_.front()->childs)
-				to_see_.push_back(child.get());
-			to_see_.pop_front();
-		}
-		++current_dimension_;
-		return res;
-	}
-
-	void init_next_dimension() const{
-		for(auto trie : cofaces_)
-			to_see_.push_back(trie);
-	}
-
-private:
-	mutable std::deque<STrie*> to_see_;
-	mutable unsigned current_dimension_=0;
-
-
-	std::vector<STrie*> cofaces_;
-
+struct Tries {
+  typedef typename SimplexHandle::Vertex_handle Vertex_handle;
+  typedef SimplexHandle Simplex;
+
+  typedef Trie<Simplex> STrie;
+
+  template<typename SimpleHandleOutputIterator>
+  Tries(unsigned num_vertices, SimpleHandleOutputIterator simplex_begin, SimpleHandleOutputIterator simplex_end) :
+      cofaces_(num_vertices, 0) {
+    for (auto i = 0u; i < num_vertices; ++i)
+      cofaces_[i] = new STrie(Vertex_handle(i));
+    for (auto s_it = simplex_begin; s_it != simplex_end; ++s_it) {
+      if (s_it->dimension() >= 1)
+        cofaces_[s_it->first_vertex()]->add_simplex(*s_it);
+    }
+  }
+
+  ~Tries() {
+    for (STrie* t : cofaces_)
+      delete t;
+  }
+
+  // return a simplex that consists in all u such uv is an edge and u>v
+
+  Simplex positive_neighbors(Vertex_handle v) const {
+    Simplex res;
+    for (auto child : cofaces_[v]->childs)
+      res.add_vertex(child->v);
+    return res;
+  }
+
+  bool contains(const Simplex& s) const {
+    auto first_v = s.first_vertex();
+    return cofaces_[first_v]->contains(s);
+  }
+
+  friend std::ostream& operator<<(std::ostream& stream, const Tries& tries) {
+    for (auto trie : tries.cofaces_)
+      stream << *trie << std::endl;
+    return stream;
+  }
+
+  // init_next_dimension must be called first
+
+  std::vector<Simplex> next_dimension_simplices() const {
+    std::vector<Simplex> res;
+    while (!to_see_.empty() && to_see_.front()->simplex().dimension() == current_dimension_) {
+      res.emplace_back(to_see_.front()->simplex());
+      for (auto child : to_see_.front()->childs)
+        to_see_.push_back(child.get());
+      to_see_.pop_front();
+    }
+    ++current_dimension_;
+    return res;
+  }
+
+  void init_next_dimension() const {
+    for (auto trie : cofaces_)
+      to_see_.push_back(trie);
+  }
+
+ private:
+  mutable std::deque<STrie*> to_see_;
+  mutable unsigned current_dimension_ = 0;
+  std::vector<STrie*> cofaces_;
 };
 
+}  // namespace skbl
 
+}  // namespace Gudhi
 
-}
-
-}
-
-#endif /* TRIE_H_ */
+#endif  // SKELETON_BLOCKER_INTERNAL_TRIE_H_
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_blockers_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_blockers_iterators.h
index f6f2c955..4a437ac6 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_blockers_iterators.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_blockers_iterators.h
@@ -1,134 +1,131 @@
- /*    This file is part of the Gudhi Library. The Gudhi library
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-#ifndef GUDHI_SKELETON_BLOCKERS_BLOCKERS_ITERATORS_H_
-#define GUDHI_SKELETON_BLOCKERS_BLOCKERS_ITERATORS_H_
-
-#include "boost/iterator/iterator_facade.hpp"
-
-namespace Gudhi{
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+#ifndef SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_BLOCKERS_ITERATORS_H_
+#define SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_BLOCKERS_ITERATORS_H_
+
+#include <boost/iterator/iterator_facade.hpp>
+
+namespace Gudhi {
 
 namespace skbl {
 
 /**
  * @brief Iterator through the blockers of a vertex.
-  */
-// ReturnType = const Simplex_handle* or Simplex_handle*
+ */
+// ReturnType = const Simplex* or Simplex*
 // MapIteratorType = BlockerMapConstIterator or BlockerMapIterator
+
 template<typename MapIteratorType, typename ReturnType>
 class Blocker_iterator_internal : public boost::iterator_facade<
-  Blocker_iterator_internal<MapIteratorType,ReturnType>,
-  ReturnType,
-  boost::forward_traversal_tag,
-  ReturnType
-  >{
-private:
-	MapIteratorType current_position;
-	MapIteratorType end_of_map;
-public:
-
-	Blocker_iterator_internal():current_position(){}
-
-	Blocker_iterator_internal(MapIteratorType position,MapIteratorType end_of_map_ ):
-		current_position(position), end_of_map(end_of_map_)
-	{	}
-
-	bool equal(const Blocker_iterator_internal& other) const{
-		return current_position == other.current_position;
-	}
-
-	void increment(){
-		goto_next_blocker();
-	}
-
-	ReturnType dereference() const	{
-		return(current_position->second);
-	}
-
-private:
-	/**
-	 * Let the current pair be (v,sigma) where v is a vertex and sigma is a blocker.
-	 * If v is not the first vertex of sigma then we already have seen sigma as a blocker
-	 * and we look for the next one.
-	 */
-	void goto_next_blocker(){
-		do {
-			++current_position;
-		} while (!(current_position == end_of_map) && !first_time_blocker_is_seen());
-	}
-
-	bool first_time_blocker_is_seen() const{
-		return current_position->first  == current_position->second->first_vertex();
-	}
+Blocker_iterator_internal<MapIteratorType, ReturnType>,
+ReturnType,
+boost::forward_traversal_tag,
+ReturnType
+> {
+ private:
+  MapIteratorType current_position;
+  MapIteratorType end_of_map;
+
+ public:
+  Blocker_iterator_internal() : current_position() { }
+
+  Blocker_iterator_internal(MapIteratorType position, MapIteratorType end_of_map_) :
+      current_position(position), end_of_map(end_of_map_) { }
+
+  bool equal(const Blocker_iterator_internal& other) const {
+    return current_position == other.current_position;
+  }
+
+  void increment() {
+    goto_next_blocker();
+  }
+
+  ReturnType dereference() const {
+    return (current_position->second);
+  }
+
+ private:
+  /**
+   * Let the current pair be (v,sigma) where v is a vertex and sigma is a blocker.
+   * If v is not the first vertex of sigma then we already have seen sigma as a blocker
+   * and we look for the next one.
+   */
+  void goto_next_blocker() {
+    do {
+      ++current_position;
+    } while (!(current_position == end_of_map) && !first_time_blocker_is_seen());
+  }
+
+  bool first_time_blocker_is_seen() const {
+    return current_position->first == current_position->second->first_vertex();
+  }
 };
 
-
-
 /**
  * @brief Iterator through the blockers of a vertex
  */
-// ReturnType = const Simplex_handle* or Simplex_handle*
+// ReturnType = const Simplex* or Simplex*
 // MapIteratorType = BlockerMapConstIterator or BlockerMapIterator
+
 template<typename MapIteratorType, typename ReturnType>
 class Blocker_iterator_around_vertex_internal : public boost::iterator_facade<
-	Blocker_iterator_around_vertex_internal<MapIteratorType,ReturnType>,
-	ReturnType,
-	boost::forward_traversal_tag,
-	ReturnType
->{
-private:
-	MapIteratorType current_position_;
-public:
-
-	Blocker_iterator_around_vertex_internal():current_position_(){}
-
-	Blocker_iterator_around_vertex_internal(MapIteratorType position):
-		current_position_(position)
-	{}
-
-	Blocker_iterator_around_vertex_internal& operator=(Blocker_iterator_around_vertex_internal other){
-		this->current_position_ = other.current_position_;
-		return *this;
-	}
-
-	bool equal(const Blocker_iterator_around_vertex_internal& other) const{
-		return current_position_ == other.current_position_;
-	}
-
-	void increment(){
-		current_position_++;
-	}
-
-	ReturnType dereference() const{
-		return(current_position_->second);
-	}
-
-
-	MapIteratorType current_position(){
-		return this->current_position_;
-	}
+Blocker_iterator_around_vertex_internal<MapIteratorType, ReturnType>,
+ReturnType,
+boost::forward_traversal_tag,
+ReturnType
+> {
+ private:
+  MapIteratorType current_position_;
+
+ public:
+  Blocker_iterator_around_vertex_internal() : current_position_() { }
+
+  Blocker_iterator_around_vertex_internal(MapIteratorType position) :
+      current_position_(position) { }
+
+  Blocker_iterator_around_vertex_internal& operator=(Blocker_iterator_around_vertex_internal other) {
+    this->current_position_ = other.current_position_;
+    return *this;
+  }
+
+  bool equal(const Blocker_iterator_around_vertex_internal& other) const {
+    return current_position_ == other.current_position_;
+  }
+
+  void increment() {
+    current_position_++;
+  }
+
+  ReturnType dereference() const {
+    return (current_position_->second);
+  }
+
+  MapIteratorType current_position() {
+    return this->current_position_;
+  }
 };
 
-}
+}  // namespace skbl
 
-} // namespace GUDHI
+}  // namespace Gudhi
 
-#endif /* GUDHI_SKELETON_BLOCKERS_BLOCKERS_ITERATORS_H_ */
+#endif  // SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_BLOCKERS_ITERATORS_H_
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_edges_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_edges_iterators.h
index 0be6c74d..ef4c7970 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_edges_iterators.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_edges_iterators.h
@@ -1,167 +1,144 @@
- /*    This file is part of the Gudhi Library. The Gudhi library
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-#ifndef GUDHI_SKELETON_BLOCKERS_ITERATORS_EDGES_H_
-#define GUDHI_SKELETON_BLOCKERS_ITERATORS_EDGES_H_
-
-#include "boost/iterator/iterator_facade.hpp"
-
-
-namespace Gudhi{
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+#ifndef SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_EDGES_ITERATORS_H_
+#define SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_EDGES_ITERATORS_H_
+
+#include <boost/iterator/iterator_facade.hpp>
+#include <boost/graph/adjacency_list.hpp>
+
+#include <utility>  // for pair<>
+
+namespace Gudhi {
 
 namespace skbl {
 
 template<typename SkeletonBlockerComplex>
-class Edge_around_vertex_iterator :
- public boost::iterator_facade < Edge_around_vertex_iterator<SkeletonBlockerComplex>
-		, typename SkeletonBlockerComplex::Edge_handle const
-		, boost::forward_traversal_tag
-		, typename SkeletonBlockerComplex::Edge_handle const
-		>
-{
-	friend class boost::iterator_core_access;
-
-	typedef SkeletonBlockerComplex Complex;
-	typedef typename Complex::boost_adjacency_iterator boost_adjacency_iterator;
-	typedef typename Complex::Vertex_handle Vertex_handle;
-	typedef typename Complex::Edge_handle Edge_handle;
-
-private:
-
-	const Complex* complex;
-	Vertex_handle v;
-
-	boost_adjacency_iterator current_;
-	boost_adjacency_iterator end_;
-
-public:
-
-	Edge_around_vertex_iterator():complex(NULL){
-	}
-
-	Edge_around_vertex_iterator(const Complex* complex_,Vertex_handle v_):
-		complex(complex_),
-		v(v_)
-	{
-		tie(current_,end_) = adjacent_vertices(v.vertex, complex->skeleton);
-	}
-
-	/**
-	 * returns an iterator to the end
-	 */
-	Edge_around_vertex_iterator(const Complex* complex_,Vertex_handle v_,int end):
-		complex(complex_),
-		v(v_)
-	{
-		tie(current_,end_) = adjacent_vertices(v.vertex, complex->skeleton);
-		set_end();
-	}
-
-	bool equal(const Edge_around_vertex_iterator& other) const{
-		return (complex== other.complex) && (v == other.v) && (current_ == other.current_) && (end_ == other.end_);
-	}
-
-	void increment(){
-		if(current_ != end_)
-			++current_;
-	}
-
-	Edge_handle dereference() const{
-		return *(*complex)[std::make_pair(v,static_cast<Vertex_handle>(*current_))];
-	}
-
-private:
-	//remove this ugly hack
-	void set_end(){
-		current_ = end_;
-	}
+class Edge_around_vertex_iterator : public boost::iterator_facade <Edge_around_vertex_iterator<SkeletonBlockerComplex>
+, typename SkeletonBlockerComplex::Edge_handle const, boost::forward_traversal_tag
+, typename SkeletonBlockerComplex::Edge_handle const> {
+  friend class boost::iterator_core_access;
+
+  typedef SkeletonBlockerComplex Complex;
+  typedef typename Complex::boost_adjacency_iterator boost_adjacency_iterator;
+  typedef typename Complex::Vertex_handle Vertex_handle;
+  typedef typename Complex::Edge_handle Edge_handle;
+
+ private:
+  const Complex* complex;
+  Vertex_handle v;
+
+  boost_adjacency_iterator current_;
+  boost_adjacency_iterator end_;
+
+ public:
+  Edge_around_vertex_iterator() : complex(NULL) { }
+
+  Edge_around_vertex_iterator(const Complex* complex_, Vertex_handle v_) :
+      complex(complex_),
+      v(v_) {
+    tie(current_, end_) = adjacent_vertices(v.vertex, complex->skeleton);
+  }
+
+  /**
+   * returns an iterator to the end
+   */
+  Edge_around_vertex_iterator(const Complex* complex_, Vertex_handle v_, int end) :
+      complex(complex_),
+      v(v_) {
+    tie(current_, end_) = adjacent_vertices(v.vertex, complex->skeleton);
+    set_end();
+  }
+
+  bool equal(const Edge_around_vertex_iterator& other) const {
+    return (complex == other.complex) && (v == other.v) && (current_ == other.current_) && (end_ == other.end_);
+  }
+
+  void increment() {
+    if (current_ != end_)
+      ++current_;
+  }
+
+  Edge_handle dereference() const {
+    return *(*complex)[std::make_pair(v, static_cast<Vertex_handle> (*current_))];
+  }
+
+ private:
+  // remove this ugly hack
+  void set_end() {
+    current_ = end_;
+  }
 };
 
-
-
 /**
  *@brief Iterator on the edges of a simplicial complex.
  *
  */
 template<typename SkeletonBlockerComplex>
-class Edge_iterator :
-public boost::iterator_facade < Edge_iterator<SkeletonBlockerComplex>
+class Edge_iterator : public boost::iterator_facade <Edge_iterator<SkeletonBlockerComplex>
 , typename SkeletonBlockerComplex::Edge_handle const
 , boost::forward_traversal_tag
-, typename SkeletonBlockerComplex::Edge_handle const
->
-
-{
-	friend class boost::iterator_core_access;
-public:
-	typedef SkeletonBlockerComplex Complex;
-	typedef typename Complex::boost_edge_iterator boost_edge_iterator;
-	typedef typename Complex::Edge_handle Edge_handle;
-
-
-	const Complex* complex;
-	std::pair<boost_edge_iterator,boost_edge_iterator> edge_iterator ;
-
-	Edge_iterator():complex(NULL){
-	}
-
-	Edge_iterator(const SkeletonBlockerComplex* complex_):
-		complex(complex_),
-		edge_iterator(boost::edges(complex_->skeleton))
-	{
-	}
-
-	/**
-	 * return an iterator to the end
-	 */
-	Edge_iterator(const SkeletonBlockerComplex* complex_,int end):
-		complex(complex_),
-		edge_iterator(boost::edges(complex_->skeleton))
-	{
-		edge_iterator.first = edge_iterator.second;
-	}
-
-
-	bool equal(const Edge_iterator& other) const{
-		return (complex == other.complex) && (edge_iterator == other.edge_iterator);
-	}
-
-	void increment(){
-		if(edge_iterator.first != edge_iterator.second){
-			++(edge_iterator.first);
-		}
-	}
-
-	Edge_handle dereference() const{
-		return(*(edge_iterator.first));
-	}
+, typename SkeletonBlockerComplex::Edge_handle const> {
+  friend class boost::iterator_core_access;
+
+ public:
+  typedef SkeletonBlockerComplex Complex;
+  typedef typename Complex::boost_edge_iterator boost_edge_iterator;
+  typedef typename Complex::Edge_handle Edge_handle;
+
+  const Complex* complex;
+  std::pair<boost_edge_iterator, boost_edge_iterator> edge_iterator;
+
+  Edge_iterator() : complex(NULL) { }
+
+  Edge_iterator(const SkeletonBlockerComplex* complex_) :
+      complex(complex_),
+      edge_iterator(boost::edges(complex_->skeleton)) { }
+
+  /**
+   * return an iterator to the end
+   */
+  Edge_iterator(const SkeletonBlockerComplex* complex_, int end) :
+      complex(complex_),
+      edge_iterator(boost::edges(complex_->skeleton)) {
+    edge_iterator.first = edge_iterator.second;
+  }
+
+  bool equal(const Edge_iterator& other) const {
+    return (complex == other.complex) && (edge_iterator == other.edge_iterator);
+  }
+
+  void increment() {
+    if (edge_iterator.first != edge_iterator.second) {
+      ++(edge_iterator.first);
+    }
+  }
+
+  Edge_handle dereference() const {
+    return (*(edge_iterator.first));
+  }
 };
 
+}  // namespace skbl
 
+}  // namespace Gudhi
 
-}
-
-} // namespace GUDHI
-
-
-#endif /* GUDHI_SKELETON_BLOCKERS_ITERATORS_EDGES_H_ */
-
-
+#endif  // SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_EDGES_ITERATORS_H_
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_iterators.h
index 20a94734..cc3ed276 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_iterators.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_iterators.h
@@ -19,17 +19,14 @@
   *    You should have received a copy of the GNU General Public License
   *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
   */
-#ifndef GUDHI_SKELETON_BLOCKERS_ITERATORS_H_
-#define GUDHI_SKELETON_BLOCKERS_ITERATORS_H_
 
+#ifndef SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_ITERATORS_H_
+#define SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_ITERATORS_H_
 
-#include "Skeleton_blockers_vertices_iterators.h"
-#include "Skeleton_blockers_edges_iterators.h"
-#include "Skeleton_blockers_blockers_iterators.h"
-#include "Skeleton_blockers_triangles_iterators.h"
-#include "Skeleton_blockers_simplices_iterators.h"
+#include <gudhi/Skeleton_blocker/iterators/Skeleton_blockers_vertices_iterators.h>
+#include <gudhi/Skeleton_blocker/iterators/Skeleton_blockers_edges_iterators.h>
+#include <gudhi/Skeleton_blocker/iterators/Skeleton_blockers_blockers_iterators.h>
+#include <gudhi/Skeleton_blocker/iterators/Skeleton_blockers_triangles_iterators.h>
+#include <gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h>
 
-
-
-
-#endif /* GUDHI_SKELETON_BLOCKERS_ITERATORS_H_ */
+#endif  // SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_ITERATORS_H_
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h
index 666ce430..ce565166 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h
@@ -1,46 +1,42 @@
- /*    This file is part of the Gudhi Library. The Gudhi library
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-#ifndef GUDHI_KELETON_BLOCKERS_SIMPLICES_ITERATORS_H_
-#define GUDHI_SKELETON_BLOCKERS_SIMPLICES_ITERATORS_H_
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+#ifndef SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_SIMPLICES_ITERATORS_H_
+#define SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_SIMPLICES_ITERATORS_H_
+
+#include <gudhi/Skeleton_blocker_link_complex.h>
+#include <gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h>
+#include <gudhi/Skeleton_blocker/internal/Trie.h>
+#include <gudhi/Utils.h>
+
+#include <boost/iterator/iterator_facade.hpp>
 
 #include <memory>
 #include <list>
 #include <iostream>
-#include "gudhi/Utils.h"
-#include "boost/iterator/iterator_facade.hpp"
-
-
-#include "gudhi/Skeleton_blocker_link_complex.h"
-#include "gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h"
-
-#include "gudhi/Skeleton_blocker/internal/Trie.h"
-
 
 namespace Gudhi {
 
-
 namespace skbl {
 
-
 /**
  * Link may be Skeleton_blocker_link_complex<SkeletonBlockerComplex> to iterate over all
  * simplices around a vertex OR
@@ -49,299 +45,354 @@ namespace skbl {
  * The iteration is done by computing a trie with the link and doing a breadth-first traversal
  * of the trie.
  */
-template<typename SkeletonBlockerComplex,typename Link>
+template<typename SkeletonBlockerComplex, typename Link>
 class Simplex_around_vertex_iterator :
-		public boost::iterator_facade < Simplex_around_vertex_iterator<SkeletonBlockerComplex,Link>
-, typename SkeletonBlockerComplex::Simplex_handle
+public boost::iterator_facade < Simplex_around_vertex_iterator<SkeletonBlockerComplex, Link>
+, typename SkeletonBlockerComplex::Simplex
 , boost::forward_traversal_tag
-, typename SkeletonBlockerComplex::Simplex_handle
->
-{
-	friend class boost::iterator_core_access;
-	typedef SkeletonBlockerComplex Complex;
-	typedef typename Complex::Vertex_handle Vertex_handle;
-	typedef typename Complex::Edge_handle Edge_handle;
-	typedef typename Complex::Simplex_handle Simplex_handle;
-
-
-	typedef typename Link::Vertex_handle Link_vertex_handle;
-	// Link_vertex_handle == Complex_Vertex_handle but this renaming helps avoiding confusion
-
-	typedef typename Gudhi::skbl::Trie<Simplex_handle> Trie;
-
-
-private:
-	const Complex* complex;
-	Vertex_handle v;
-	std::shared_ptr<Link> link_v;
-	std::shared_ptr<Trie> trie;
-	std::list<Trie*> nodes_to_be_seen; // todo deque
-
-public:
-	Simplex_around_vertex_iterator():complex(0){
-	}
-
-	Simplex_around_vertex_iterator(const Complex* complex_,Vertex_handle v_):
-		complex(complex_),
-		v(v_),
-		link_v(new Link(*complex_,v_)),
-		trie(new Trie(v_)){
-		compute_trie_and_nodes_to_be_seen();
-	}
-
-	// todo avoid useless copy
-	// todo currently just work if copy begin iterator
-	Simplex_around_vertex_iterator(const Simplex_around_vertex_iterator& other):
-		complex(other.complex),
-		v(other.v),
-		link_v(other.link_v),
-		trie(other.trie),
-		nodes_to_be_seen(other.nodes_to_be_seen){
-		if(!other.is_end()){
-		}
-	}
-
-	/**
-	 * returns an iterator to the end
-	 */
-	Simplex_around_vertex_iterator(const Complex* complex_,Vertex_handle v_,bool end):
-		complex(complex_),
-		v(v_){
-		set_end();
-	}
-
-private:
-
-
-	void compute_trie_and_nodes_to_be_seen(){
-		// once we go through every simplices passing through v0
-		// we remove v0. That way, it prevents from passing a lot of times
-		// though edges leaving v0.
-		// another solution would have been to provides an adjacency iterator
-		// to superior vertices that avoids lower ones.
-		while(!link_v->empty()){
-			auto v0 = *(link_v->vertex_range().begin());
-			trie->add_child(build_trie(v0,trie.get()));
-			link_v->remove_vertex(v0);
-		}
-		nodes_to_be_seen.push_back(trie.get());
-	}
-
-	Trie* build_trie(Link_vertex_handle link_vh,Trie* parent){
-		Trie* res = new Trie(parent_vertex(link_vh),parent);
-		for(Link_vertex_handle nv : link_v->vertex_range(link_vh)) {
-			if(link_vh < nv){
-				Simplex_handle simplex_node_plus_nv(res->simplex());
-				simplex_node_plus_nv.add_vertex(parent_vertex(nv));
-				if(complex->contains(simplex_node_plus_nv)){
-					res->add_child(build_trie(nv,res));
-				}
-			}
-		}
-		return res;
-	}
-
-	bool is_node_in_complex(Trie* trie){
-		return true;
-	}
-
-	Vertex_handle parent_vertex(Link_vertex_handle link_vh) const{
-		return complex->convert_handle_from_another_complex(*link_v,link_vh);
-	}
-
-
-
-public:
-
-	friend std::ostream& operator<<(std::ostream& stream, const Simplex_around_vertex_iterator& savi){
-		stream<< savi.trie<< std::endl; ;
-		stream << "("<<savi.nodes_to_be_seen.size()<<") nodes to see\n";
-		return stream;
-	}
-
-	bool equal(const Simplex_around_vertex_iterator& other) const{
-		bool same_complex = (complex == other.complex);
-		if(!same_complex)
-			return false;
-
-		if(!(v == other.v))
-			return false;
-
-		bool both_empty = nodes_to_be_seen.empty() && other.nodes_to_be_seen.empty();
-		if(both_empty)
-			return true;
-
-		bool both_non_empty = !nodes_to_be_seen.empty() && !other.nodes_to_be_seen.empty();
-
-		if(!both_non_empty) return false; //one is empty the other is not
-
-		bool same_node = (**(nodes_to_be_seen.begin()) == **(other.nodes_to_be_seen.begin()));
-		return same_node;
-	}
-
-	void increment(){
-		assert(!is_end());
-		Trie* first_node = nodes_to_be_seen.front();
-
-		nodes_to_be_seen.pop_front();
-
-		for(auto childs : first_node->childs){
-			nodes_to_be_seen.push_back(childs.get());
-		}
-
-	}
-
-	Simplex_handle dereference() const{
-		assert(!nodes_to_be_seen.empty());
-		Trie* first_node = nodes_to_be_seen.front();
-		return first_node->simplex();
-	}
-
-//private:
-	Simplex_handle get_trie_address() const{
-		assert(!nodes_to_be_seen.empty());
-		return nodes_to_be_seen.front();
-	}
-
-private:
-	void set_end(){
-		nodes_to_be_seen.clear();
-	}
-
-	bool is_end() const{
-		return nodes_to_be_seen.empty();
-	}
+, typename SkeletonBlockerComplex::Simplex
+> {
+  friend class boost::iterator_core_access;
+  typedef SkeletonBlockerComplex Complex;
+  typedef typename Complex::Vertex_handle Vertex_handle;
+  typedef typename Complex::Edge_handle Edge_handle;
+  typedef typename Complex::Simplex Simplex;
+
+  // Link_vertex_handle == Complex_Vertex_handle but this renaming helps avoiding confusion
+  typedef typename Link::Vertex_handle Link_vertex_handle;
+
+  typedef typename Gudhi::skbl::Trie<Simplex> Trie;
+
+ private:
+  const Complex* complex;
+  Vertex_handle v;
+  std::shared_ptr<Link> link_v;
+  std::shared_ptr<Trie> trie;
+  std::list<Trie*> nodes_to_be_seen;  // todo deque
+
+ public:
+  Simplex_around_vertex_iterator() : complex(0) {}
+
+  Simplex_around_vertex_iterator(const Complex* complex_, Vertex_handle v_) :
+      complex(complex_),
+      v(v_),
+      link_v(new Link(*complex_, v_)),
+      trie(new Trie(v_)) {
+    compute_trie_and_nodes_to_be_seen();
+  }
+
+  // todo avoid useless copy
+  // todo currently just work if copy begin iterator
+  Simplex_around_vertex_iterator(const Simplex_around_vertex_iterator& other) :
+      complex(other.complex),
+      v(other.v),
+      link_v(other.link_v),
+      trie(other.trie),
+      nodes_to_be_seen(other.nodes_to_be_seen) {
+    if (!other.is_end()) {}
+  }
+
+  /**
+   * returns an iterator to the end
+   */
+  Simplex_around_vertex_iterator(const Complex* complex_, Vertex_handle v_, bool end) :
+      complex(complex_),
+      v(v_) {
+    set_end();
+  }
+
+ private:
+  void compute_trie_and_nodes_to_be_seen() {
+    // once we go through every simplices passing through v0
+    // we remove v0. That way, it prevents from passing a lot of times
+    // though edges leaving v0.
+    // another solution would have been to provides an adjacency iterator
+    // to superior vertices that avoids lower ones.
+    while (!link_v->empty()) {
+      auto v0 = *(link_v->vertex_range().begin());
+      trie->add_child(build_trie(v0, trie.get()));
+      link_v->remove_vertex(v0);
+    }
+    nodes_to_be_seen.push_back(trie.get());
+  }
+
+  Trie* build_trie(Link_vertex_handle link_vh, Trie* parent) {
+    Trie* res = new Trie(parent_vertex(link_vh), parent);
+    for (Link_vertex_handle nv : link_v->vertex_range(link_vh)) {
+      if (link_vh < nv) {
+        Simplex simplex_node_plus_nv(res->simplex());
+        simplex_node_plus_nv.add_vertex(parent_vertex(nv));
+        if (complex->contains(simplex_node_plus_nv)) {
+          res->add_child(build_trie(nv, res));
+        }
+      }
+    }
+    return res;
+  }
+
+  bool is_node_in_complex(Trie* trie) {
+    return true;
+  }
+
+  Vertex_handle parent_vertex(Link_vertex_handle link_vh) const {
+    return complex->convert_handle_from_another_complex(*link_v, link_vh);
+  }
+
+ public:
+  friend std::ostream& operator<<(std::ostream& stream, const Simplex_around_vertex_iterator& savi) {
+    stream << savi.trie << std::endl;
+    stream << "(" << savi.nodes_to_be_seen.size() << ") nodes to see\n";
+    return stream;
+  }
+
+  bool equal(const Simplex_around_vertex_iterator& other) const {
+    bool same_complex = (complex == other.complex);
+    if (!same_complex)
+      return false;
+
+    if (!(v == other.v))
+      return false;
+
+    bool both_empty = nodes_to_be_seen.empty() && other.nodes_to_be_seen.empty();
+    if (both_empty)
+      return true;
+
+    bool both_non_empty = !nodes_to_be_seen.empty() && !other.nodes_to_be_seen.empty();
+
+    if (!both_non_empty) return false;  // one is empty the other is not
+
+    bool same_node = (**(nodes_to_be_seen.begin()) == **(other.nodes_to_be_seen.begin()));
+    return same_node;
+  }
+
+  void increment() {
+    assert(!is_end());
+    Trie* first_node = nodes_to_be_seen.front();
+
+    nodes_to_be_seen.pop_front();
+
+    for (auto childs : first_node->childs) {
+      nodes_to_be_seen.push_back(childs.get());
+    }
+  }
+
+  Simplex dereference() const {
+    assert(!nodes_to_be_seen.empty());
+    Trie* first_node = nodes_to_be_seen.front();
+    return first_node->simplex();
+  }
+
+  Simplex get_trie_address() const {
+    assert(!nodes_to_be_seen.empty());
+    return nodes_to_be_seen.front();
+  }
+
+ private:
+  void set_end() {
+    nodes_to_be_seen.clear();
+  }
+
+  bool is_end() const {
+    return nodes_to_be_seen.empty();
+  }
 };
 
-
-
 template<typename SkeletonBlockerComplex>
 class Simplex_iterator :
-		public boost::iterator_facade < Simplex_iterator<SkeletonBlockerComplex>
-, typename SkeletonBlockerComplex::Simplex_handle
+public boost::iterator_facade < Simplex_iterator<SkeletonBlockerComplex>
+, typename SkeletonBlockerComplex::Simplex
 , boost::forward_traversal_tag
-, typename SkeletonBlockerComplex::Simplex_handle
->
-{
-	typedef Skeleton_blocker_link_superior<SkeletonBlockerComplex> Link;
-
-	friend class boost::iterator_core_access;
-
-	template<class SkBlDS> friend class Skeleton_blocker_complex;
-
-
-	typedef SkeletonBlockerComplex Complex;
-	typedef typename Complex::Vertex_handle Vertex_handle;
-	typedef typename Complex::Edge_handle Edge_handle;
-	typedef typename Complex::Simplex_handle Simplex_handle;
-
-	typedef typename Complex::Complex_vertex_iterator Complex_vertex_iterator;
-
-
-	typedef typename Link::Vertex_handle Link_vertex_handle;
-
-private:
-
-	const Complex* complex_;
-	Complex_vertex_iterator current_vertex_;
-
-	typedef Simplex_around_vertex_iterator<SkeletonBlockerComplex,Link> SAVI;
-	SAVI current_simplex_around_current_vertex_;
-	SAVI simplices_around_current_vertex_end_;
-
-
-public:
-	Simplex_iterator():complex_(0){}
-
-	// should not be called if the complex is empty
-	Simplex_iterator(const Complex* complex):
-		complex_(complex),
-		current_vertex_(complex->vertex_range().begin()),
-		current_simplex_around_current_vertex_(complex,*current_vertex_),
-		simplices_around_current_vertex_end_(complex,*current_vertex_,true)
-	{
-		assert(!complex->empty());
-	}
+, typename SkeletonBlockerComplex::Simplex
+> {
+  typedef Skeleton_blocker_link_superior<SkeletonBlockerComplex> Link;
+
+  friend class boost::iterator_core_access;
+
+  template<class SkBlDS> friend class Skeleton_blocker_complex;
+
+  typedef SkeletonBlockerComplex Complex;
+  typedef typename Complex::Vertex_handle Vertex_handle;
+  typedef typename Complex::Edge_handle Edge_handle;
+  typedef typename Complex::Simplex Simplex;
+  typedef typename Complex::Complex_vertex_iterator Complex_vertex_iterator;
+  typedef typename Link::Vertex_handle Link_vertex_handle;
+
+ private:
+  const Complex* complex_;
+  Complex_vertex_iterator current_vertex_;
+
+  typedef Simplex_around_vertex_iterator<SkeletonBlockerComplex, Link> SAVI;
+  SAVI current_simplex_around_current_vertex_;
+  SAVI simplices_around_current_vertex_end_;
+
+ public:
+  Simplex_iterator() : complex_(0) { }
+
+  Simplex_iterator(const Complex* complex) :
+      complex_(complex),
+      current_vertex_(complex->vertex_range().begin()),
+      current_simplex_around_current_vertex_(complex, *current_vertex_),
+      simplices_around_current_vertex_end_(complex, *current_vertex_, true) {
+    // should not be called if the complex is empty
+    assert(!complex->empty());
+  }
+
+ private:
+  // todo return to private
+  Simplex_iterator(const Complex* complex, bool end) :
+      complex_(complex) {
+    set_end();
+  }
+
+ public:
+  Simplex_iterator(const Simplex_iterator& other)
+      :
+      complex_(other.complex_),
+      current_vertex_(other.current_vertex_),
+      current_simplex_around_current_vertex_(other.current_simplex_around_current_vertex_),
+      simplices_around_current_vertex_end_(other.simplices_around_current_vertex_end_) { }
+
+  friend Simplex_iterator make_begin_iterator(const Complex* complex) {
+    if (complex->empty())
+      return make_end_simplex_iterator(complex);
+    else
+      return Simplex_iterator(complex);
+  }
+
+  friend Simplex_iterator make_end_simplex_iterator(const Complex* complex) {
+    return Simplex_iterator(complex, true);
+  }
+
+  bool equal(const Simplex_iterator& other) const {
+    if (complex_ != other.complex_) return false;
+    if (current_vertex_ != other.current_vertex_) return false;
+    if (is_end() && other.is_end()) return true;
+    if (current_simplex_around_current_vertex_ != other.current_simplex_around_current_vertex_)
+      return false;
+    return true;
+  }
+
+  void increment() {
+    if (current_simplex_around_current_vertex_ != simplices_around_current_vertex_end_) {
+      current_simplex_around_current_vertex_.increment();
+      if (current_simplex_around_current_vertex_ == simplices_around_current_vertex_end_)
+        goto_next_vertex();
+    } else {
+      goto_next_vertex();
+    }
+  }
+
+  void goto_next_vertex() {
+    current_vertex_.increment();
+    if (!is_end()) {
+      current_simplex_around_current_vertex_ = SAVI(complex_, *current_vertex_);
+      simplices_around_current_vertex_end_ = SAVI(complex_, *current_vertex_, true);
+    }
+  }
+
+  Simplex dereference() const {
+    return current_simplex_around_current_vertex_.dereference();
+  }
+
+ private:
+  void set_end() {
+    current_vertex_ = complex_->vertex_range().end();
+  }
+
+  bool is_end() const {
+    return (current_vertex_ == complex_->vertex_range().end());
+  }
+};
 
-private:
-	// todo return to private
-	Simplex_iterator(const Complex* complex,bool end):
-		complex_(complex)
-	{
-		set_end();
-	}
+/**
+ * Iterator through the maximal faces of the coboundary of a simplex.
+ */ 
+template<typename SkeletonBlockerComplex, typename Link>
+class Simplex_coboundary_iterator :
+public boost::iterator_facade < Simplex_coboundary_iterator<SkeletonBlockerComplex, Link>
+, typename SkeletonBlockerComplex::Simplex, boost::forward_traversal_tag, typename SkeletonBlockerComplex::Simplex> {
+  friend class boost::iterator_core_access;
+  typedef SkeletonBlockerComplex Complex;
+  typedef typename Complex::Vertex_handle Vertex_handle;
+  typedef typename Complex::Edge_handle Edge_handle;
+  typedef typename Complex::Simplex Simplex;
+  typedef typename Complex::Complex_vertex_iterator Complex_vertex_iterator;
+
+  // Link_vertex_handle == Complex_Vertex_handle but this renaming helps avoiding confusion
+  typedef typename Link::Vertex_handle Link_vertex_handle;
+
+ private:
+  const Complex* complex;
+  const Simplex& sigma;
+  std::shared_ptr<Link> link;
+  Complex_vertex_iterator current_vertex;
+  Complex_vertex_iterator link_vertex_end;
+
+ public:
+  Simplex_coboundary_iterator() : complex(0) {}
+
+  Simplex_coboundary_iterator(const Complex* complex_, const Simplex& sigma_) :
+      complex(complex_),
+      sigma(sigma_),
+      //need only vertices of the link hence the true flag
+      link(new Link(*complex_, sigma_, false, true)) {
+    auto link_vertex_range = link->vertex_range();
+    current_vertex = link_vertex_range.begin();
+    link_vertex_end = link_vertex_range.end();
+  }
+
+  Simplex_coboundary_iterator(const Simplex_coboundary_iterator& other) :
+      complex(other.complex),
+      sigma(other.sigma),
+      link(other.link),
+      current_vertex(other.current_vertex),
+      link_vertex_end(other.link_vertex_end) { }
+  
+  // returns an iterator to the end
+  Simplex_coboundary_iterator(const Complex* complex_,const Simplex& sigma_, bool end) :
+      complex(complex_),
+      sigma(sigma_) {
+    // to represent an end iterator without having to build a useless link, we use
+    // the convection that link is not initialized.
+  }
+
+ private:
+  Vertex_handle parent_vertex(Link_vertex_handle link_vh) const {
+    return complex->convert_handle_from_another_complex(*link, link_vh);
+  }
 
 public:
-
-	Simplex_iterator(const Simplex_iterator& other)
-	:
-		complex_(other.complex_),
-		current_vertex_(other.current_vertex_),
-		current_simplex_around_current_vertex_(other.current_simplex_around_current_vertex_),
-		simplices_around_current_vertex_end_(other.simplices_around_current_vertex_end_)
-	{
-	}
-
-	friend Simplex_iterator make_begin_iterator(const Complex* complex){
-		if(complex->empty())
-			return make_end_simplex_iterator(complex);
-		else
-			return Simplex_iterator(complex);
-	}
-
-	friend Simplex_iterator make_end_simplex_iterator(const Complex* complex){
-		return Simplex_iterator(complex,true);
-	}
-
-	bool equal(const Simplex_iterator& other) const{
-		if(complex_!=other.complex_) return false;
-		if(current_vertex_!=other.current_vertex_) return false;
-		if(is_end() && other.is_end()) return true;
-		if(current_simplex_around_current_vertex_ != other.current_simplex_around_current_vertex_)
-			return false;
-		return true;
-	}
-
-	void increment(){
-		if(current_simplex_around_current_vertex_!= simplices_around_current_vertex_end_){
-			current_simplex_around_current_vertex_.increment();
-			if( current_simplex_around_current_vertex_== simplices_around_current_vertex_end_)
-				goto_next_vertex();
-		}
-		else{
-			goto_next_vertex();
-		}
-	}
-
-	void goto_next_vertex(){
-		current_vertex_.increment();
-		if(!is_end()){
-			current_simplex_around_current_vertex_= SAVI(complex_,*current_vertex_);
-			simplices_around_current_vertex_end_ = SAVI(complex_,*current_vertex_,true);
-		}
-	}
-
-	Simplex_handle dereference() const{
-		return current_simplex_around_current_vertex_.dereference();
-	}
+  friend std::ostream& operator<<(std::ostream& stream, const Simplex_coboundary_iterator& sci) {
+    return stream;
+  }
+
+  // assume that iterator points to the same complex and comes from the same simplex
+  bool equal(const Simplex_coboundary_iterator& other) const {
+    assert(complex == other.complex && sigma == other.sigma);
+    if(is_end()) return other.is_end();
+    if(other.is_end()) return is_end();
+    return *current_vertex == *(other.current_vertex);
+  }
+
+  void increment() {
+    ++current_vertex;
+  }
+
+  Simplex dereference() const {
+    Simplex res(sigma);
+    res.add_vertex(parent_vertex(*current_vertex));
+    return res;
+  }
 
 private:
-	void set_end(){
-		current_vertex_ = complex_->vertex_range().end();
-	}
-
-	bool is_end() const{
-		return (current_vertex_ == complex_->vertex_range().end());
-	}
+  bool is_end() const {
+    return !link || current_vertex == link_vertex_end;
+  }
 };
 
 
-}
-
-} // namespace GUDHI
-
-
-
+}  // namespace skbl
 
+}  // namespace Gudhi
 
-#endif /* SKELETON_BLOCKERS_SIMPLICES_ITERATORS_H_ */
+#endif  // SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_SIMPLICES_ITERATORS_H_
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_triangles_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_triangles_iterators.h
index e137d1ea..116023d7 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_triangles_iterators.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_triangles_iterators.h
@@ -1,117 +1,108 @@
- /*    This file is part of the Gudhi Library. The Gudhi library
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-#ifndef GUDHI_SKELETON_BLOCKERS_TRIANGLES_ITERATORS_H_
-#define GUDHI_SKELETON_BLOCKERS_TRIANGLES_ITERATORS_H_
-
-#include "boost/iterator/iterator_facade.hpp"
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+#ifndef SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_TRIANGLES_ITERATORS_H_
+#define SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_TRIANGLES_ITERATORS_H_
+
+#include <boost/iterator/iterator_facade.hpp>
 #include <memory>
 
-namespace Gudhi{
+namespace Gudhi {
 
 namespace skbl {
 
-//////////////////////////////////////////////////////////////////////
 /**
  * \brief Iterator over the triangles that are
  * adjacent to a vertex of the simplicial complex.
  * \remark Will be removed soon -> dont look
  */
-template<typename Complex,typename LinkType>
+template<typename Complex, typename LinkType>
 class Triangle_around_vertex_iterator : public boost::iterator_facade
-< Triangle_around_vertex_iterator <Complex,LinkType>
-, typename Complex::Simplex_handle const
+< Triangle_around_vertex_iterator <Complex, LinkType>
+, typename Complex::Simplex const
 , boost::forward_traversal_tag
-, typename Complex::Simplex_handle const
->
-{
-	friend class boost::iterator_core_access;
-	template<typename T> friend class Triangle_iterator;
-private:
-	typedef typename LinkType::Vertex_handle Vertex_handle;
-	typedef typename LinkType::Root_vertex_handle Root_vertex_handle;
-	typedef typename LinkType::Simplex_handle Simplex_handle;
-	typedef typename Complex::Complex_edge_iterator Complex_edge_iterator_;
-
-	const Complex* complex_;
-	Vertex_handle v_;
-	std::shared_ptr<LinkType> link_;
-	Complex_edge_iterator_ current_edge_;
-	bool is_end_;
-public:
-	Triangle_around_vertex_iterator(const Complex* complex,Vertex_handle v):
-		complex_(complex),v_(v),link_(new LinkType(*complex,v_)),
-		current_edge_(link_->edge_range().begin()),
-		is_end_(current_edge_ == link_->edge_range().end()){
-	}
-
-	/**
-	 * @brief ugly hack to get an iterator to the end
-	 */
-	Triangle_around_vertex_iterator(const Complex* complex,Vertex_handle v,bool is_end):
-		complex_(complex),v_(v),link_(0),is_end_(true){
-	}
-
-	/**
-	 * @brief ugly hack to get an iterator to the end
-	 */
-	Triangle_around_vertex_iterator():
-		complex_(0),v_(-1),link_(0),is_end_(true){
-	}
-
-
-	Triangle_around_vertex_iterator(const Triangle_around_vertex_iterator& other){
-		v_ = other.v_;
-		complex_ = other.complex_;
-		is_end_ = other.is_end_;
-
-		if(!is_end_){
-			link_ = other.link_;
-			current_edge_= other.current_edge_;
-		}
-	}
-
-	bool equal(const Triangle_around_vertex_iterator& other) const{
-		return (complex_==other.complex_) && ((finished() &&other.finished()) || current_edge_ == other.current_edge_);
-	}
-
-	Simplex_handle dereference() const{
-		Root_vertex_handle v1 = (*link_)[*current_edge_].first();
-		Root_vertex_handle v2 = (*link_)[*current_edge_].second();
-		return Simplex_handle(v_,*(complex_->get_address(v1)),*(complex_->get_address(v2)));
-	}
-
-	void increment(){
-		++current_edge_;
-	}
-
-private:
-	bool finished() const{
-		return is_end_ || (current_edge_ == link_->edge_range().end());
-	}
-
+, typename Complex::Simplex const> {
+  friend class boost::iterator_core_access;
+  template<typename T> friend class Triangle_iterator;
+ private:
+  typedef typename LinkType::Vertex_handle Vertex_handle;
+  typedef typename LinkType::Root_vertex_handle Root_vertex_handle;
+  typedef typename LinkType::Simplex Simplex;
+  typedef typename Complex::Complex_edge_iterator Complex_edge_iterator_;
+
+  const Complex* complex_;
+  Vertex_handle v_;
+  std::shared_ptr<LinkType> link_;
+  Complex_edge_iterator_ current_edge_;
+  bool is_end_;
+
+ public:
+  Triangle_around_vertex_iterator(const Complex* complex, Vertex_handle v) :
+      complex_(complex), v_(v), link_(new LinkType(*complex, v_)),
+      current_edge_(link_->edge_range().begin()),
+      is_end_(current_edge_ == link_->edge_range().end()) { }
+
+  /**
+   * @brief ugly hack to get an iterator to the end
+   */
+  Triangle_around_vertex_iterator(const Complex* complex, Vertex_handle v, bool is_end) :
+      complex_(complex), v_(v), link_(0), is_end_(true) { }
+
+  /**
+   * @brief ugly hack to get an iterator to the end
+   */
+  Triangle_around_vertex_iterator() :
+      complex_(0), v_(-1), link_(0), is_end_(true) { }
+
+  Triangle_around_vertex_iterator(const Triangle_around_vertex_iterator& other) {
+    v_ = other.v_;
+    complex_ = other.complex_;
+    is_end_ = other.is_end_;
+
+    if (!is_end_) {
+      link_ = other.link_;
+      current_edge_ = other.current_edge_;
+    }
+  }
+
+  bool equal(const Triangle_around_vertex_iterator& other) const {
+    return (complex_ == other.complex_) && ((finished() && other.finished()) || current_edge_ == other.current_edge_);
+  }
+
+  Simplex dereference() const {
+    Root_vertex_handle v1 = (*link_)[*current_edge_].first();
+    Root_vertex_handle v2 = (*link_)[*current_edge_].second();
+    return Simplex(v_, *(complex_->get_address(v1)), *(complex_->get_address(v2)));
+  }
+
+  void increment() {
+    ++current_edge_;
+  }
+
+ private:
+  bool finished() const {
+    return is_end_ || (current_edge_ == link_->edge_range().end());
+  }
 };
 
-
-
 /**
  * \brief Iterator over the triangles of the
  * simplicial complex.
@@ -119,121 +110,111 @@ private:
  *
  */
 template<typename SkeletonBlockerComplex>
-class Triangle_iterator :
-		public boost::iterator_facade<
-		Triangle_iterator <SkeletonBlockerComplex>,
-		typename SkeletonBlockerComplex::Simplex_handle const
-		, boost::forward_traversal_tag
-		, typename SkeletonBlockerComplex::Simplex_handle const
-		>
-{
-	friend class boost::iterator_core_access;
-private:
-	typedef typename SkeletonBlockerComplex::Vertex_handle Vertex_handle;
-	typedef typename SkeletonBlockerComplex::Root_vertex_handle Root_vertex_handle;
-	typedef typename SkeletonBlockerComplex::Simplex_handle Simplex_handle;
-	typedef typename SkeletonBlockerComplex::Superior_triangle_around_vertex_iterator STAVI;
-	typedef typename SkeletonBlockerComplex::Complex_vertex_iterator Complex_vertex_iterator;
-
-	const SkeletonBlockerComplex* complex_;
-	Complex_vertex_iterator current_vertex_;
-	STAVI current_triangle_;
-	bool is_end_;
-public:
-
-	/*
-	 * @remark  assume that the complex is non-empty
-	 */
-	Triangle_iterator(const SkeletonBlockerComplex* complex):
-		complex_(complex),
-		current_vertex_(complex->vertex_range().begin()),
-		current_triangle_(complex,*current_vertex_), // xxx this line is problematic is the complex is empty
-		is_end_(false){
-
-		assert(!complex->empty());
-		gotoFirstTriangle();
-	}
-
-private:
-	//goto to the first triangle or to the end if none
-	void gotoFirstTriangle(){
-		if(!is_finished() && current_triangle_.finished()){
-			goto_next_vertex();
-		}
-	}
-public:
-
-	/**
-	 * @brief ugly hack to get an iterator to the end
-	 * @remark  assume that the complex is non-empty
-	 */
-	Triangle_iterator(const SkeletonBlockerComplex* complex,bool is_end):
-		complex_(complex),
-		current_vertex_(complex->vertex_range().end()),
-		current_triangle_(), // xxx this line is problematic is the complex is empty
-		is_end_(true){
-	}
-
-
-	Triangle_iterator& operator=(const Triangle_iterator & other){
-		complex_ = other.complex_;
-		Complex_vertex_iterator current_vertex_;
-		STAVI current_triangle_;
-		return *this;
-	}
-
-
-	bool equal(const Triangle_iterator& other) const{
-		bool both_are_finished = is_finished() && other.is_finished();
-		bool both_arent_finished = !is_finished() && !other.is_finished();
-		// if the two iterators are not finished, they must have the same state
-		return (complex_==other.complex_) &&
-				(both_are_finished	||
-						( (both_arent_finished) && current_vertex_ == other.current_vertex_ && current_triangle_ == other.current_triangle_));
-
-	}
-
-	Simplex_handle dereference() const{
-		return *current_triangle_;
-	}
-
-private:
-
-	// goto the next vertex that has a triangle pending or the
-	// end vertex iterator if none exists
-	void goto_next_vertex(){
-		assert(current_triangle_.finished()); //we mush have consume all triangles passing through the vertex
-		assert(!is_finished()); // we must not be done
-
-		++current_vertex_;
-
-		if(!is_finished()){
-			current_triangle_ = STAVI(complex_, *current_vertex_);
-			if(current_triangle_.finished())
-				goto_next_vertex();
-		}
-	}
-public:
-	void increment(){
-		if(!current_triangle_.finished()){
-			++current_triangle_; // problem here
-			if(current_triangle_.finished())
-				goto_next_vertex();
-		}
-		else{
-			assert(!is_finished());
-			goto_next_vertex();
-		}
-	}
-
-private:
-	bool is_finished() const{
-		return is_end_ || current_vertex_ == complex_->vertex_range().end();
-	}
+class Triangle_iterator : public boost::iterator_facade<
+Triangle_iterator <SkeletonBlockerComplex>,
+typename SkeletonBlockerComplex::Simplex const
+, boost::forward_traversal_tag
+, typename SkeletonBlockerComplex::Simplex const> {
+  friend class boost::iterator_core_access;
+ private:
+  typedef typename SkeletonBlockerComplex::Vertex_handle Vertex_handle;
+  typedef typename SkeletonBlockerComplex::Root_vertex_handle Root_vertex_handle;
+  typedef typename SkeletonBlockerComplex::Simplex Simplex;
+  typedef typename SkeletonBlockerComplex::Superior_triangle_around_vertex_iterator STAVI;
+  typedef typename SkeletonBlockerComplex::Complex_vertex_iterator Complex_vertex_iterator;
+
+  const SkeletonBlockerComplex* complex_;
+  Complex_vertex_iterator current_vertex_;
+  STAVI current_triangle_;
+  bool is_end_;
+
+ public:
+  /*
+   * @remark  assume that the complex is non-empty
+   */
+  Triangle_iterator(const SkeletonBlockerComplex* complex) :
+      complex_(complex),
+      current_vertex_(complex->vertex_range().begin()),
+      current_triangle_(complex, *current_vertex_),  // xxx this line is problematic is the complex is empty
+      is_end_(false) {
+    assert(!complex->empty());
+    gotoFirstTriangle();
+  }
+
+ private:
+  // goto to the first triangle or to the end if none
+  void gotoFirstTriangle() {
+    if (!is_finished() && current_triangle_.finished()) {
+      goto_next_vertex();
+    }
+  }
+
+ public:
+  /**
+   * @brief ugly hack to get an iterator to the end
+   * @remark  assume that the complex is non-empty
+   */
+  Triangle_iterator(const SkeletonBlockerComplex* complex, bool is_end) :
+      complex_(complex),
+      current_vertex_(complex->vertex_range().end()),
+      current_triangle_(),  // xxx this line is problematic is the complex is empty
+      is_end_(true) { }
+
+  Triangle_iterator& operator=(const Triangle_iterator & other) {
+    complex_ = other.complex_;
+    Complex_vertex_iterator current_vertex_;
+    STAVI current_triangle_;
+    return *this;
+  }
+
+  bool equal(const Triangle_iterator& other) const {
+    bool both_are_finished = is_finished() && other.is_finished();
+    bool both_arent_finished = !is_finished() && !other.is_finished();
+    // if the two iterators are not finished, they must have the same state
+    return (complex_ == other.complex_) && (both_are_finished || ((both_arent_finished) &&
+        current_vertex_ == other.current_vertex_ && current_triangle_ == other.current_triangle_));
+  }
+
+  Simplex dereference() const {
+    return *current_triangle_;
+  }
+
+ private:
+  // goto the next vertex that has a triangle pending or the
+  // end vertex iterator if none exists
+  void goto_next_vertex() {
+    assert(current_triangle_.finished());  // we mush have consume all triangles passing through the vertex
+    assert(!is_finished());  // we must not be done
+
+    ++current_vertex_;
+
+    if (!is_finished()) {
+      current_triangle_ = STAVI(complex_, *current_vertex_);
+      if (current_triangle_.finished())
+        goto_next_vertex();
+    }
+  }
+
+ public:
+  void increment() {
+    if (!current_triangle_.finished()) {
+      ++current_triangle_;  // problem here
+      if (current_triangle_.finished())
+        goto_next_vertex();
+    } else {
+      assert(!is_finished());
+      goto_next_vertex();
+    }
+  }
+
+ private:
+  bool is_finished() const {
+    return is_end_ || current_vertex_ == complex_->vertex_range().end();
+  }
 };
 
-}
+}  // namespace skbl
 
-} // namespace GUDHI
+}  // namespace Gudhi
 
-#endif /* GUDHI_SKELETON_BLOCKERS_TRIANGLES_ITERATORS_H_ */
+#endif  // SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_TRIANGLES_ITERATORS_H_
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_vertices_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_vertices_iterators.h
index a9d4e373..14ae136a 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_vertices_iterators.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_vertices_iterators.h
@@ -1,31 +1,32 @@
- /*    This file is part of the Gudhi Library. The Gudhi library
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-#ifndef GUDHI_SKELETON_BLOCKERS_VERTICES_ITERATORS_H_
-#define GUDHI_SKELETON_BLOCKERS_VERTICES_ITERATORS_H_
-
-#include "boost/iterator/iterator_facade.hpp"
-
-
-namespace Gudhi{
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+#ifndef SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_VERTICES_ITERATORS_H_
+#define SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_VERTICES_ITERATORS_H_
+
+#include <boost/iterator/iterator_facade.hpp>
+
+#include <utility>  // for pair<>
+
+namespace Gudhi {
 
 namespace skbl {
 
@@ -35,148 +36,137 @@ namespace skbl {
  *@remark Incrementation increases Vertex_handle.
  */
 template<typename SkeletonBlockerComplex>
-class Vertex_iterator : public boost::iterator_facade
-< Vertex_iterator <SkeletonBlockerComplex>
-  , typename SkeletonBlockerComplex::Vertex_handle const
-  , boost::forward_traversal_tag
-  , typename SkeletonBlockerComplex::Vertex_handle const
-  >
-{
-	friend class boost::iterator_core_access;
-
-	typedef typename SkeletonBlockerComplex::boost_vertex_iterator boost_vertex_iterator;
-	typedef typename SkeletonBlockerComplex::Vertex_handle Vertex_handle;
-private:
-	const SkeletonBlockerComplex* complex;
-	std::pair<boost_vertex_iterator,boost_vertex_iterator> vertexIterator;
-
-
-public:
-	Vertex_iterator():complex(NULL){
-	}
-
-	Vertex_iterator(const SkeletonBlockerComplex* complex_):
-		complex(complex_),
-		vertexIterator(vertices(complex_->skeleton)){
-		if(!finished() && !is_active()) {
-			goto_next_valid();
-		}
-	}
-
-	/**
-	 * return an iterator to the end.
-	 */
-	Vertex_iterator(const SkeletonBlockerComplex* complex_,int end):
-		complex(complex_),vertexIterator(vertices(complex_->skeleton)){
-		vertexIterator.first = vertexIterator.second ;
-	}
-
-public:
-	void increment () {goto_next_valid();}
-	Vertex_handle  dereference() const	{
-		return(Vertex_handle(*(vertexIterator.first)));
-	}
-
-	bool equal(const Vertex_iterator& other) const{
-		return vertexIterator == other.vertexIterator &&  complex == other.complex;
-	}
-
-	bool operator<(const Vertex_iterator& other) const{
-		return dereference()<other.dereference();
-	}
-
-private:
-	bool finished() const{
-		return vertexIterator.first == vertexIterator.second;
-	}
-
-	void goto_next_valid(){
-		++vertexIterator.first;
-		if(!finished() && !is_active()){
-			goto_next_valid();
-		}
-	}
-
-	bool is_active() const{
-		return ((*complex)[Vertex_handle(*vertexIterator.first)]).is_active();
-	}
-
+class Vertex_iterator : public boost::iterator_facade< Vertex_iterator <SkeletonBlockerComplex>
+, typename SkeletonBlockerComplex::Vertex_handle const
+, boost::forward_traversal_tag
+, typename SkeletonBlockerComplex::Vertex_handle const> {
+  friend class boost::iterator_core_access;
+
+  typedef typename SkeletonBlockerComplex::boost_vertex_iterator boost_vertex_iterator;
+  typedef typename SkeletonBlockerComplex::Vertex_handle Vertex_handle;
+ private:
+  const SkeletonBlockerComplex* complex;
+  std::pair<boost_vertex_iterator, boost_vertex_iterator> vertexIterator;
+
+
+ public:
+  Vertex_iterator() : complex(NULL) { }
+
+  Vertex_iterator(const SkeletonBlockerComplex* complex_) :
+      complex(complex_),
+      vertexIterator(vertices(complex_->skeleton)) {
+    if (!finished() && !is_active()) {
+      goto_next_valid();
+    }
+  }
+
+  /**
+   * return an iterator to the end.
+   */
+  Vertex_iterator(const SkeletonBlockerComplex* complex_, int end) :
+      complex(complex_), vertexIterator(vertices(complex_->skeleton)) {
+    vertexIterator.first = vertexIterator.second;
+  }
+
+ public:
+  void increment() {
+    goto_next_valid();
+  }
+
+  Vertex_handle dereference() const {
+    return (Vertex_handle(*(vertexIterator.first)));
+  }
+
+  bool equal(const Vertex_iterator& other) const {
+    return vertexIterator == other.vertexIterator && complex == other.complex;
+  }
+
+  bool operator<(const Vertex_iterator& other) const {
+    return dereference() < other.dereference();
+  }
+
+ private:
+  bool finished() const {
+    return vertexIterator.first == vertexIterator.second;
+  }
+
+  void goto_next_valid() {
+    ++vertexIterator.first;
+    if (!finished() && !is_active()) {
+      goto_next_valid();
+    }
+  }
+
+  bool is_active() const {
+    return ((*complex)[Vertex_handle(*vertexIterator.first)]).is_active();
+  }
 };
 
-
-
-
 template<typename SkeletonBlockerComplex>
-class Neighbors_vertices_iterator
-: public boost::iterator_facade < Neighbors_vertices_iterator<SkeletonBlockerComplex>
-  , typename SkeletonBlockerComplex::Vertex_handle const
-  , boost::forward_traversal_tag
-  , typename SkeletonBlockerComplex::Vertex_handle const
-  >
-{
-	friend class boost::iterator_core_access;
-
-	typedef SkeletonBlockerComplex Complex;
-	typedef typename Complex::boost_adjacency_iterator boost_adjacency_iterator;
-	typedef typename Complex::Vertex_handle Vertex_handle;
-	typedef typename Complex::Edge_handle Edge_handle;
-
-private:
-
-	const Complex* complex;
-	Vertex_handle v;
-
-	boost_adjacency_iterator current_;
-	boost_adjacency_iterator end_;
-
-public:
-	//	boost_adjacency_iterator ai, ai_end;
-	//	for (tie(ai, ai_end) = adjacent_vertices(v.vertex, skeleton); ai != ai_end; ++ai){
-
-	Neighbors_vertices_iterator():complex(NULL){
-	}
-
-	Neighbors_vertices_iterator(const Complex* complex_,Vertex_handle v_):
-		complex(complex_),
-		v(v_){
-		tie(current_,end_) = adjacent_vertices(v.vertex, complex->skeleton);
-	}
-
-	/**
-	 * returns an iterator to the end
-	 */
-	Neighbors_vertices_iterator(const Complex* complex_,Vertex_handle v_,int end):
-		complex(complex_),
-		v(v_){
-		tie(current_,end_) = adjacent_vertices(v.vertex, complex->skeleton);
-		set_end();
-	}
-
-
-	void increment () {
-		if(current_ != end_)
-			++current_;
-	}
-
-	Vertex_handle  dereference() const	{
-		return(Vertex_handle(*current_));
-	}
-
-	bool equal(const Neighbors_vertices_iterator& other) const{
-		return (complex== other.complex) && (v == other.v) && (current_ == other.current_) && (end_ == other.end_);
-	}
-
-private:
-	//todo remove this ugly hack
-	void set_end(){
-		current_ = end_;
-	}
+class Neighbors_vertices_iterator: public boost::iterator_facade < Neighbors_vertices_iterator<SkeletonBlockerComplex>
+, typename SkeletonBlockerComplex::Vertex_handle const
+, boost::forward_traversal_tag
+, typename SkeletonBlockerComplex::Vertex_handle const> {
+  friend class boost::iterator_core_access;
+
+  typedef SkeletonBlockerComplex Complex;
+  typedef typename Complex::boost_adjacency_iterator boost_adjacency_iterator;
+  typedef typename Complex::Vertex_handle Vertex_handle;
+  typedef typename Complex::Edge_handle Edge_handle;
+
+ private:
+  const Complex* complex;
+  Vertex_handle v;
+
+  boost_adjacency_iterator current_;
+  boost_adjacency_iterator end_;
+
+ public:
+  // boost_adjacency_iterator ai, ai_end;
+  // for (tie(ai, ai_end) = adjacent_vertices(v.vertex, skeleton); ai != ai_end; ++ai) {
+
+  Neighbors_vertices_iterator() : complex(NULL) { }
+
+  Neighbors_vertices_iterator(const Complex* complex_, Vertex_handle v_) :
+      complex(complex_),
+      v(v_) {
+    tie(current_, end_) = adjacent_vertices(v.vertex, complex->skeleton);
+  }
+
+  /**
+   * returns an iterator to the end
+   */
+  Neighbors_vertices_iterator(const Complex* complex_, Vertex_handle v_, int end) :
+      complex(complex_),
+      v(v_) {
+    tie(current_, end_) = adjacent_vertices(v.vertex, complex->skeleton);
+    set_end();
+  }
+
+  void increment() {
+    if (current_ != end_)
+      ++current_;
+  }
+
+  Vertex_handle dereference() const {
+    return (Vertex_handle(*current_));
+  }
+
+  bool equal(const Neighbors_vertices_iterator& other) const {
+    return (complex == other.complex) && (v == other.v) && (current_ == other.current_) && (end_ == other.end_);
+  }
+
+ private:
+  // todo remove this ugly hack
+  void set_end() {
+    current_ = end_;
+  }
 };
 
-}
+}  // namespace skbl
 
-} // namespace GUDHI
+}  // namespace Gudhi
 
-#endif /* GUDHI_SKELETON_BLOCKERS_VERTICES_ITERATORS_H_ */
+#endif  // SKELETON_BLOCKER_ITERATORS_SKELETON_BLOCKERS_VERTICES_ITERATORS_H_
 
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
index 700830f2..5b774f25 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
@@ -20,8 +20,18 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_COMPLEX_H_
-#define SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_COMPLEX_H_
+#ifndef SKELETON_BLOCKER_COMPLEX_H_
+#define SKELETON_BLOCKER_COMPLEX_H_
+
+#include <gudhi/Skeleton_blocker/iterators/Skeleton_blockers_iterators.h>
+#include <gudhi/Skeleton_blocker_link_complex.h>
+#include <gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h>
+#include <gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h>
+#include <gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h>
+#include <gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h>
+#include <gudhi/Skeleton_blocker/internal/Top_faces.h>
+#include <gudhi/Skeleton_blocker/internal/Trie.h>
+#include <gudhi/Utils.h>
 
 #include <boost/graph/adjacency_list.hpp>
 #include <boost/graph/connected_components.hpp>
@@ -40,18 +50,6 @@
 #include <algorithm>
 #include <utility>
 
-#include "gudhi/Skeleton_blocker/iterators/Skeleton_blockers_iterators.h"
-#include "gudhi/Skeleton_blocker_link_complex.h"
-#include "gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h"
-#include "gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h"
-#include "gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h"
-
-#include "gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h"
-#include "gudhi/Skeleton_blocker/internal/Top_faces.h"
-#include "gudhi/Skeleton_blocker/internal/Trie.h"
-
-#include "gudhi/Utils.h"
-
 namespace Gudhi {
 
 namespace skbl {
@@ -94,16 +92,16 @@ class Skeleton_blocker_complex {
   /**
    * @brief A ordered set of integers that represents a simplex.
    */
-  typedef Skeleton_blocker_simplex<Vertex_handle> Simplex_handle;
+  typedef Skeleton_blocker_simplex<Vertex_handle> Simplex;
   typedef Skeleton_blocker_simplex<Root_vertex_handle> Root_simplex_handle;
 
   /**
    * @brief Handle to a blocker of the complex.
    */
-  typedef Simplex_handle* Blocker_handle;
+  typedef Simplex* Blocker_handle;
 
   typedef typename Root_simplex_handle::Simplex_vertex_const_iterator Root_simplex_iterator;
-  typedef typename Simplex_handle::Simplex_vertex_const_iterator Simplex_handle_iterator;
+  typedef typename Simplex::Simplex_vertex_const_iterator Simplex_handle_iterator;
 
  protected:
   typedef typename boost::adjacency_list<boost::setS,  // edges
@@ -128,14 +126,14 @@ class Skeleton_blocker_complex {
   typedef typename boost::graph_traits<Graph>::edge_descriptor Edge_handle;
 
  protected:
-  typedef std::multimap<Vertex_handle, Simplex_handle *> BlockerMap;
-  typedef typename std::multimap<Vertex_handle, Simplex_handle *>::value_type BlockerPair;
-  typedef typename std::multimap<Vertex_handle, Simplex_handle *>::iterator BlockerMapIterator;
-  typedef typename std::multimap<Vertex_handle, Simplex_handle *>::const_iterator BlockerMapConstIterator;
+  typedef std::multimap<Vertex_handle, Simplex *> BlockerMap;
+  typedef typename std::multimap<Vertex_handle, Simplex *>::value_type BlockerPair;
+  typedef typename std::multimap<Vertex_handle, Simplex *>::iterator BlockerMapIterator;
+  typedef typename std::multimap<Vertex_handle, Simplex *>::const_iterator BlockerMapConstIterator;
 
  protected:
-  int num_vertices_;
-  int num_blockers_;
+  size_t num_vertices_;
+  size_t num_blockers_;
 
   typedef Skeleton_blocker_complex_visitor<Vertex_handle> Visitor;
   // typedef Visitor* Visitor_ptr;
@@ -164,17 +162,17 @@ class Skeleton_blocker_complex {
   /**
    *@brief constructs a simplicial complex with a given number of vertices and a visitor.
    */
-  explicit Skeleton_blocker_complex(int num_vertices_ = 0, Visitor* visitor_ = NULL)
+  explicit Skeleton_blocker_complex(size_t num_vertices_ = 0, Visitor* visitor_ = NULL)
       : visitor(visitor_) {
     clear();
-    for (int i = 0; i < num_vertices_; ++i) {
+    for (size_t i = 0; i < num_vertices_; ++i) {
       add_vertex();
     }
   }
 
  private:
   // typedef Trie<Skeleton_blocker_complex<SkeletonBlockerDS>> STrie;
-  typedef Trie<Simplex_handle> STrie;
+  typedef Trie<Simplex> STrie;
 
  public:
   /**
@@ -182,37 +180,41 @@ class Skeleton_blocker_complex {
    * @details is_flag_complex indicates if the complex is a flag complex or not (to know if blockers have to be computed or not).
    */
   template<typename SimpleHandleOutputIterator>
-  Skeleton_blocker_complex(SimpleHandleOutputIterator simplex_begin, SimpleHandleOutputIterator simplex_end,
+  Skeleton_blocker_complex(SimpleHandleOutputIterator simplices_begin, SimpleHandleOutputIterator simplices_end,
                            bool is_flag_complex = false, Visitor* visitor_ = NULL)
       : num_vertices_(0),
       num_blockers_(0),
       visitor(visitor_) {
-    add_vertex_and_edges(simplex_begin, simplex_end);
+    add_vertices_and_edges(simplices_begin, simplices_end);
 
     if (!is_flag_complex)
       // need to compute blockers
-      add_blockers(simplex_begin, simplex_end);
+      add_blockers(simplices_begin, simplices_end);
   }
 
  private:
+  /**
+   * Add vertices and edges of a simplex in one pass
+   */
   template<typename SimpleHandleOutputIterator>
-  void add_vertex_and_edges(SimpleHandleOutputIterator simplex_begin, SimpleHandleOutputIterator simplex_end) {
+  void add_vertices_and_edges(SimpleHandleOutputIterator simplices_begin, SimpleHandleOutputIterator simplices_end) {
     std::vector<std::pair<Vertex_handle, Vertex_handle>> edges;
     // first pass to add vertices and edges
     int num_vertex = -1;
-    for (auto s_it = simplex_begin; s_it != simplex_end; ++s_it) {
+    for (auto s_it = simplices_begin; s_it != simplices_end; ++s_it) {
       if (s_it->dimension() == 0) num_vertex = (std::max)(num_vertex, s_it->first_vertex().vertex);
       if (s_it->dimension() == 1) edges.emplace_back(s_it->first_vertex(), s_it->last_vertex());
     }
     while (num_vertex-- >= 0) add_vertex();
 
     for (const auto& e : edges)
-      add_edge(e.first, e.second);
+      add_edge_without_blockers(e.first, e.second);
   }
 
+
   template<typename SimpleHandleOutputIterator>
-  void add_blockers(SimpleHandleOutputIterator simplex_begin, SimpleHandleOutputIterator simplex_end) {
-    Tries<Simplex_handle> tries(num_vertices(), simplex_begin, simplex_end);
+  void add_blockers(SimpleHandleOutputIterator simplices_begin, SimpleHandleOutputIterator simplices_end) {
+    Tries<Simplex> tries(num_vertices(), simplices_begin, simplices_end);
     tries.init_next_dimension();
     auto simplices(tries.next_dimension_simplices());
 
@@ -221,7 +223,7 @@ class Skeleton_blocker_complex {
       for (auto& sigma : simplices) {
         // common_positive_neighbors is the set of vertices u such that
         // for all s in sigma, us is an edge and u>s
-        Simplex_handle common_positive_neighbors(tries.positive_neighbors(sigma.last_vertex()));
+        Simplex common_positive_neighbors(tries.positive_neighbors(sigma.last_vertex()));
         for (auto sigma_it = sigma.rbegin(); sigma_it != sigma.rend(); ++sigma_it)
           if (sigma_it != sigma.rbegin())
             common_positive_neighbors.intersection(tries.positive_neighbors(*sigma_it));
@@ -378,6 +380,7 @@ class Skeleton_blocker_complex {
 
   /**
    * @brief Adds a vertex to the simplicial complex and returns its Vertex_handle.
+   * @remark Vertex representation is contiguous.
    */
   Vertex_handle add_vertex() {
     Vertex_handle address(boost::add_vertex(skeleton));
@@ -427,7 +430,7 @@ class Skeleton_blocker_complex {
    * @return true iff the simplicial complex contains all vertices
    * of simplex sigma
    */
-  bool contains_vertices(const Simplex_handle & sigma) const {
+  bool contains_vertices(const Simplex & sigma) const {
     for (auto vertex : sigma)
       if (!contains_vertex(vertex))
         return false;
@@ -535,41 +538,68 @@ class Skeleton_blocker_complex {
    * @details it assumes that the edge is present in the complex
 
    */
-  Simplex_handle get_vertices(Edge_handle edge_handle) const {
+  Simplex get_vertices(Edge_handle edge_handle) const {
     auto edge((*this)[edge_handle]);
-    return Simplex_handle((*this)[edge.first()], (*this)[edge.second()]);
+    return Simplex((*this)[edge.first()], (*this)[edge.second()]);
   }
 
   /**
-   * @brief Adds an edge between vertices a and b and all its cofaces.
+   * @brief Adds an edge between vertices a and b.
+   * @details For instance, the complex contains edge 01 and 12, then calling
+   * add_edge with vertex 0 and 2 will create a complex containing
+   * the edges 01, 12, 20 but not the triangle 012 (and hence this complex
+   * will contains a blocker 012).
    */
   Edge_handle add_edge(Vertex_handle a, Vertex_handle b) {
+    // if the edge is already there we musnt go further
+    // as we may add blockers that should not be here
+    if (contains_edge(a, b))
+      return *((*this)[std::make_pair(a, b)]);
+    auto res = add_edge_without_blockers(a, b);
+    add_blockers_after_simplex_insertion(Simplex(a, b));
+    return res;
+  }
+
+    /**
+   * @brief Adds all edges of s in the complex.
+   */
+  void add_edge(const Simplex& s) {
+    for (auto i = s.begin(); i != s.end(); ++i)
+      for (auto j = i; ++j != s.end(); /**/)
+        add_edge(*i, *j);
+  }
+
+  /**
+   * @brief Adds an edge between vertices a and b without blockers.
+   * @details For instance, the complex contains edge 01 and 12, then calling
+   * add_edge with vertex 0 and 2 will create a complex containing
+   * the triangle 012.
+   */
+  Edge_handle add_edge_without_blockers(Vertex_handle a, Vertex_handle b) {
     assert(contains_vertex(a) && contains_vertex(b));
     assert(a != b);
 
     auto edge_handle((*this)[std::make_pair(a, b)]);
-    // std::pair<Edge_handle,bool> pair_descr_bool = (*this)[std::make_pair(a,b)];
-    // Edge_handle edge_descr;
-    // bool edge_present = pair_descr_bool.second;
     if (!edge_handle) {
       edge_handle = boost::add_edge(a.vertex, b.vertex, skeleton).first;
       (*this)[*edge_handle].setId(get_id(a), get_id(b));
       degree_[a.vertex]++;
       degree_[b.vertex]++;
       if (visitor)
-        visitor->on_add_edge(a, b);
+        visitor->on_add_edge_without_blockers(a, b);
     }
     return *edge_handle;
   }
 
+
   /**
-   * @brief Adds all edges and their cofaces of a simplex to the simplicial complex.
+   * @brief Adds all edges of s in the complex without adding blockers.
    */
-  void add_edges(const Simplex_handle & sigma) {
-    Simplex_handle_iterator i, j;
-    for (i = sigma.begin(); i != sigma.end(); ++i)
-      for (j = i, j++; j != sigma.end(); ++j)
-        add_edge(*i, *j);
+  void add_edge_without_blockers(Simplex s) {
+    for (auto i = s.begin(); i != s.end(); ++i) {
+      for (auto j = i; ++j != s.end(); /**/)
+        add_edge_without_blockers(*i, *j);
+    }
   }
 
   /**
@@ -627,7 +657,7 @@ class Skeleton_blocker_complex {
    * @return true iff the simplicial complex contains all vertices
    * and all edges of simplex sigma
    */
-  bool contains_edges(const Simplex_handle & sigma) const {
+  bool contains_edges(const Simplex & sigma) const {
     for (auto i = sigma.begin(); i != sigma.end(); ++i) {
       if (!contains_vertex(*i))
         return false;
@@ -649,15 +679,14 @@ class Skeleton_blocker_complex {
    * @brief Adds the simplex to the set of blockers and
    * returns a Blocker_handle toward it if was not present before and 0 otherwise.
    */
-  Blocker_handle add_blocker(const Simplex_handle& blocker) {
+  Blocker_handle add_blocker(const Simplex& blocker) {
     assert(blocker.dimension() > 1);
     if (contains_blocker(blocker)) {
-      // std::cerr << "ATTEMPT TO ADD A BLOCKER ALREADY THERE ---> BLOCKER IGNORED" << endl;
       return 0;
     } else {
       if (visitor)
         visitor->on_add_blocker(blocker);
-      Blocker_handle blocker_pt = new Simplex_handle(blocker);
+      Blocker_handle blocker_pt = new Simplex(blocker);
       num_blockers_++;
       auto vertex = blocker_pt->begin();
       while (vertex != blocker_pt->end()) {
@@ -739,7 +768,7 @@ class Skeleton_blocker_complex {
    *
    * @remark contrarily to delete_blockers does not call the destructor
    */
-  void remove_blocker(const Simplex_handle& sigma) {
+  void remove_blocker(const Simplex& sigma) {
     assert(contains_blocker(sigma));
     for (auto vertex : sigma)
       remove_blocker(sigma, vertex);
@@ -777,7 +806,7 @@ class Skeleton_blocker_complex {
   /**
    * @return true iff s is a blocker of the simplicial complex
    */
-  bool contains_blocker(const Simplex_handle & s) const {
+  bool contains_blocker(const Simplex & s) const {
     if (s.dimension() < 2)
       return false;
 
@@ -795,7 +824,7 @@ class Skeleton_blocker_complex {
    * @return true iff a blocker of the simplicial complex
    * is a face of sigma.
    */
-  bool blocks(const Simplex_handle & sigma) const {
+  bool blocks(const Simplex & sigma) const {
     for (auto s : sigma)
       for (auto blocker : const_blocker_range(s))
         if (sigma.contains(*blocker))
@@ -810,7 +839,7 @@ class Skeleton_blocker_complex {
    * @details Adds to simplex the neighbours of v e.g. \f$ n \leftarrow n \cup N(v) \f$.
    * If keep_only_superior is true then only vertices that are greater than v are added.
    */
-  virtual void add_neighbours(Vertex_handle v, Simplex_handle & n,
+  virtual void add_neighbours(Vertex_handle v, Simplex & n,
                               bool keep_only_superior = false) const {
     boost_adjacency_iterator ai, ai_end;
     for (tie(ai, ai_end) = adjacent_vertices(v.vertex, skeleton); ai != ai_end;
@@ -833,7 +862,7 @@ class Skeleton_blocker_complex {
    * todo revoir
    *
    */
-  virtual void add_neighbours(const Simplex_handle &alpha, Simplex_handle & res,
+  virtual void add_neighbours(const Simplex &alpha, Simplex & res,
                               bool keep_only_superior = false) const {
     res.clear();
     auto alpha_vertex = alpha.begin();
@@ -848,9 +877,9 @@ class Skeleton_blocker_complex {
    * not neighbours of v e.g. \f$ res \leftarrow res \cap N(v) \f$.
    * If 'keep_only_superior' is true then only vertices that are greater than v are keeped.
    */
-  virtual void keep_neighbours(Vertex_handle v, Simplex_handle& res,
+  virtual void keep_neighbours(Vertex_handle v, Simplex& res,
                                bool keep_only_superior = false) const {
-    Simplex_handle nv;
+    Simplex nv;
     add_neighbours(v, nv, keep_only_superior);
     res.intersection(nv);
   }
@@ -860,9 +889,9 @@ class Skeleton_blocker_complex {
    * neighbours of v eg \f$ res \leftarrow res \setminus N(v) \f$.
    * If 'keep_only_superior' is true then only vertices that are greater than v are added.
    */
-  virtual void remove_neighbours(Vertex_handle v, Simplex_handle & res,
+  virtual void remove_neighbours(Vertex_handle v, Simplex & res,
                                  bool keep_only_superior = false) const {
-    Simplex_handle nv;
+    Simplex nv;
     add_neighbours(v, nv, keep_only_superior);
     res.difference(nv);
   }
@@ -874,7 +903,7 @@ class Skeleton_blocker_complex {
    * Constructs the link of 'simplex' with points coordinates.
    */
   Link_complex link(Vertex_handle v) const {
-    return Link_complex(*this, Simplex_handle(v));
+    return Link_complex(*this, Simplex(v));
   }
 
   /**
@@ -887,7 +916,7 @@ class Skeleton_blocker_complex {
   /**
    * Constructs the link of 'simplex' with points coordinates.
    */
-  Link_complex link(const Simplex_handle& simplex) const {
+  Link_complex link(const Simplex& simplex) const {
     return Link_complex(*this, simplex);
   }
 
@@ -899,11 +928,11 @@ class Skeleton_blocker_complex {
    */
   // xxx rename get_address et place un using dans sub_complex
 
-  boost::optional<Simplex_handle> get_simplex_address(
+  boost::optional<Simplex> get_simplex_address(
                                                       const Root_simplex_handle& s) const {
-    boost::optional<Simplex_handle> res;
+    boost::optional<Simplex> res;
 
-    Simplex_handle s_address;
+    Simplex s_address;
     // Root_simplex_const_iterator i;
     for (auto i = s.begin(); i != s.end(); ++i) {
       boost::optional<Vertex_handle> address = get_address(*i);
@@ -920,7 +949,7 @@ class Skeleton_blocker_complex {
    * @brief returns a simplex with vertices which are the id of vertices of the
    * argument.
    */
-  Root_simplex_handle get_id(const Simplex_handle& local_simplex) const {
+  Root_simplex_handle get_id(const Simplex& local_simplex) const {
     Root_simplex_handle global_simplex;
     for (auto x = local_simplex.begin(); x != local_simplex.end(); ++x) {
       global_simplex.add_vertex(get_id(*x));
@@ -932,7 +961,7 @@ class Skeleton_blocker_complex {
    * @brief returns true iff the simplex s belongs to the simplicial
    * complex.
    */
-  virtual bool contains(const Simplex_handle & s) const {
+  virtual bool contains(const Simplex & s) const {
     if (s.dimension() == -1) {
       return false;
     } else if (s.dimension() == 0) {
@@ -972,10 +1001,31 @@ class Skeleton_blocker_complex {
     return std::distance(triangles.begin(), triangles.end());
   }
 
+
+  /*
+   * @brief returns the number of simplices of a given dimension in the complex.
+   */  
+  size_t num_simplices() const {
+    auto simplices = complex_simplex_range();
+    return std::distance(simplices.begin(), simplices.end());
+  }
+
+  /*
+   * @brief returns the number of simplices of a given dimension in the complex.
+   */  
+  size_t num_simplices(unsigned dimension) const {
+    // TODO(DS): iterator on k-simplices
+    size_t res = 0;
+    for (const auto& s : complex_simplex_range())
+      if (s.dimension() == dimension)
+        ++res;
+    return res;
+  }
+
   /*
    * @brief returns the number of blockers in the complex.
    */
-  int num_blockers() const {
+  size_t num_blockers() const {
     return num_blockers_;
   }
 
@@ -1018,7 +1068,7 @@ class Skeleton_blocker_complex {
   }
 
   //@}
-  /** @Simplification operations
+  /** @name Simplification operations
    */
   //@{
 
@@ -1061,7 +1111,7 @@ class Skeleton_blocker_complex {
    * Furthermore, all simplices tau of the form sigma \setminus simplex_to_be_removed must be added
    * whenever the dimension of tau is at least 2.
    */
-  void update_blockers_after_remove_star_of_vertex_or_edge(const Simplex_handle& simplex_to_be_removed);
+  void update_blockers_after_remove_star_of_vertex_or_edge(const Simplex& simplex_to_be_removed);
 
  public:
   /**
@@ -1078,31 +1128,33 @@ class Skeleton_blocker_complex {
   /**
    * Remove the star of the simplex 'sigma' which needs to belong to the complex
    */
-  void remove_star(const Simplex_handle& sigma);
+  void remove_star(const Simplex& sigma);
 
   /**
-   * @brief add a maximal simplex plus all its cofaces.
-   * @details the simplex must have dimension greater than one (otherwise use add_vertex or add_edge).
+   * @brief add a simplex and all its faces.
+   * @details the simplex must have dimension greater than one (otherwise use add_vertex or add_edge_without_blockers).   
    */
-  void add_simplex(const Simplex_handle& sigma);
+  void add_simplex(const Simplex& sigma);
 
  private:
+  void add_blockers_after_simplex_insertion(Simplex s);
+
   /**
    * remove all blockers that contains sigma
    */
-  void remove_blocker_containing_simplex(const Simplex_handle& sigma);
+  void remove_blocker_containing_simplex(const Simplex& sigma);
 
   /**
    * remove all blockers that contains sigma
    */
-  void remove_blocker_include_in_simplex(const Simplex_handle& sigma);
+  void remove_blocker_include_in_simplex(const Simplex& sigma);
 
  public:
   enum simplifiable_status {
     NOT_HOMOTOPY_EQ, MAYBE_HOMOTOPY_EQ, HOMOTOPY_EQ
   };
 
-  simplifiable_status is_remove_star_homotopy_preserving(const Simplex_handle& simplex) {
+  simplifiable_status is_remove_star_homotopy_preserving(const Simplex& simplex) {
     // todo write a virtual method 'link' in Skeleton_blocker_complex which will be overloaded by the current one of
     // Skeleton_blocker_geometric_complex
     // then call it there to build the link and return the value of link.is_contractible()
@@ -1131,7 +1183,7 @@ class Skeleton_blocker_complex {
   }
   //@}
 
-  /** @Edge contraction operations
+  /** @name Edge contraction operations
    */
   //@{
 
@@ -1174,7 +1226,7 @@ class Skeleton_blocker_complex {
    * that may be used to construct a new blocker after contracting ab.
    * It requires that the link condition is satisfied.
    */
-  void tip_blockers(Vertex_handle a, Vertex_handle b, std::vector<Simplex_handle> & buffer) const;
+  void tip_blockers(Vertex_handle a, Vertex_handle b, std::vector<Simplex> & buffer) const;
 
  private:
   /**
@@ -1217,7 +1269,7 @@ class Skeleton_blocker_complex {
 
  private:
   void get_blockers_to_be_added_after_contraction(Vertex_handle a, Vertex_handle b,
-                                                  std::set<Simplex_handle>& blockers_to_add);
+                                                  std::set<Simplex>& blockers_to_add);
   /**
    * delete all blockers that passes through a or b
    */
@@ -1358,12 +1410,28 @@ class Skeleton_blocker_complex {
   /**
    * @brief Returns a Complex_simplex_around_vertex_range over all the simplices around a vertex of the complex
    */
-  Complex_simplex_around_vertex_range simplex_range(Vertex_handle v) const {
+  Complex_simplex_around_vertex_range star_simplex_range(Vertex_handle v) const {
     assert(contains_vertex(v));
     return Complex_simplex_around_vertex_range(
                                                Complex_simplex_around_vertex_iterator(this, v),
                                                Complex_simplex_around_vertex_iterator(this, v, true));
   }
+  typedef Simplex_coboundary_iterator<Skeleton_blocker_complex, Link> Complex_simplex_coboundary_iterator;
+
+  /**
+   * @brief Range over the simplices of the coboundary of a simplex.
+   * Methods .begin() and .end() return a Complex_simplex_coboundary_iterator.
+   */
+  typedef boost::iterator_range < Complex_simplex_coboundary_iterator > Complex_coboundary_range;
+
+  /**
+   * @brief Returns a Complex_simplex_coboundary_iterator over the simplices of the coboundary of a simplex.
+   */
+  Complex_coboundary_range coboundary_range(const Simplex& s) const {
+    assert(contains(s));
+    return Complex_coboundary_range(Complex_simplex_coboundary_iterator(this, s),
+                                    Complex_simplex_coboundary_iterator(this, s, true));
+  }
 
   // typedef Simplex_iterator<Skeleton_blocker_complex,Superior_link> Complex_simplex_iterator;
   typedef Simplex_iterator<Skeleton_blocker_complex> Complex_simplex_iterator;
@@ -1373,7 +1441,7 @@ class Skeleton_blocker_complex {
   /**
    * @brief Returns a Complex_simplex_range over all the simplices of the complex
    */
-  Complex_simplex_range simplex_range() const {
+  Complex_simplex_range complex_simplex_range() const {
     Complex_simplex_iterator end(this, true);
     if (empty()) {
       return Complex_simplex_range(end, end);
@@ -1393,7 +1461,7 @@ class Skeleton_blocker_complex {
    * @brief Iterator over the blockers adjacent to a vertex
    */
   typedef Blocker_iterator_around_vertex_internal<
-  typename std::multimap<Vertex_handle, Simplex_handle *>::iterator,
+  typename std::multimap<Vertex_handle, Simplex *>::iterator,
   Blocker_handle>
   Complex_blocker_around_vertex_iterator;
 
@@ -1401,12 +1469,13 @@ class Skeleton_blocker_complex {
    * @brief Iterator over (constant) blockers adjacent to a vertex
    */
   typedef Blocker_iterator_around_vertex_internal<
-  typename std::multimap<Vertex_handle, Simplex_handle *>::const_iterator,
+  typename std::multimap<Vertex_handle, Simplex *>::const_iterator,
   const Blocker_handle>
   Const_complex_blocker_around_vertex_iterator;
 
   typedef boost::iterator_range <Complex_blocker_around_vertex_iterator> Complex_blocker_around_vertex_range;
-  typedef boost::iterator_range <Const_complex_blocker_around_vertex_iterator> Const_complex_blocker_around_vertex_range;
+  typedef boost::iterator_range <Const_complex_blocker_around_vertex_iterator>
+  Const_complex_blocker_around_vertex_range;
 
  public:
   /**
@@ -1432,7 +1501,7 @@ class Skeleton_blocker_complex {
    * @brief Iterator over the blockers.
    */
   typedef Blocker_iterator_internal<
-  typename std::multimap<Vertex_handle, Simplex_handle *>::iterator,
+  typename std::multimap<Vertex_handle, Simplex *>::iterator,
   Blocker_handle>
   Complex_blocker_iterator;
 
@@ -1440,7 +1509,7 @@ class Skeleton_blocker_complex {
    * @brief Iterator over the (constant) blockers.
    */
   typedef Blocker_iterator_internal<
-  typename std::multimap<Vertex_handle, Simplex_handle *>::const_iterator,
+  typename std::multimap<Vertex_handle, Simplex *>::const_iterator,
   const Blocker_handle>
   Const_complex_blocker_iterator;
 
@@ -1514,11 +1583,12 @@ class Skeleton_blocker_complex {
  * return the total number of simplices
  */
 template<typename Complex, typename SimplexHandleIterator>
-Complex make_complex_from_top_faces(SimplexHandleIterator simplex_begin, SimplexHandleIterator simplex_end, 
+Complex make_complex_from_top_faces(SimplexHandleIterator simplices_begin, SimplexHandleIterator simplices_end,
                                     bool is_flag_complex = false) {
-  typedef typename Complex::Simplex_handle Simplex_handle;
-  std::vector<Simplex_handle> simplices;
-  for (auto top_face = simplex_begin; top_face != simplex_end; ++top_face) {
+  // TODO(DS): use add_simplex instead! should be more efficient and more elegant :)
+  typedef typename Complex::Simplex Simplex;
+  std::vector<Simplex> simplices;
+  for (auto top_face = simplices_begin; top_face != simplices_end; ++top_face) {
     auto subfaces_topface = subfaces(*top_face);
     simplices.insert(simplices.end(), subfaces_topface.begin(), subfaces_topface.end());
   }
@@ -1531,6 +1601,4 @@ Complex make_complex_from_top_faces(SimplexHandleIterator simplex_begin, Simplex
 
 #include "Skeleton_blocker_simplifiable_complex.h"
 
-
-#endif  // SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_COMPLEX_H_
-
+#endif  // SKELETON_BLOCKER_COMPLEX_H_
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h
index 437482cb..5c898152 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h
@@ -19,12 +19,12 @@
  *    You should have received a copy of the GNU General Public License
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-#ifndef SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_GEOMETRIC_COMPLEX_H_
-#define SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_GEOMETRIC_COMPLEX_H_
+#ifndef SKELETON_BLOCKER_GEOMETRIC_COMPLEX_H_
+#define SKELETON_BLOCKER_GEOMETRIC_COMPLEX_H_
 
-#include "gudhi/Utils.h"
-#include "gudhi/Skeleton_blocker_complex.h"
-#include "gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h"
+#include <gudhi/Utils.h>
+#include <gudhi/Skeleton_blocker_complex.h>
+#include <gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h>
 
 namespace Gudhi {
 
@@ -46,7 +46,7 @@ public Skeleton_blocker_complex<SkeletonBlockerGeometricDS> {
   typedef typename SimplifiableSkeletonblocker::Vertex_handle Vertex_handle;
   typedef typename SimplifiableSkeletonblocker::Root_vertex_handle Root_vertex_handle;
   typedef typename SimplifiableSkeletonblocker::Edge_handle Edge_handle;
-  typedef typename SimplifiableSkeletonblocker::Simplex_handle Simplex_handle;
+  typedef typename SimplifiableSkeletonblocker::Simplex Simplex;
 
   typedef typename SimplifiableSkeletonblocker::Graph_vertex Graph_vertex;
 
@@ -79,23 +79,6 @@ public Skeleton_blocker_complex<SkeletonBlockerGeometricDS> {
       (*this)[Vertex_handle(current++)].point() = Point(point->begin(), point->end());
   }
 
-  template<typename SimpleHandleOutputIterator, typename PointIterator>
-  friend Skeleton_blocker_geometric_complex make_complex_from_top_faces(
-                                                                        SimpleHandleOutputIterator simplex_begin,
-                                                                        SimpleHandleOutputIterator simplex_end,
-                                                                        PointIterator points_begin,
-                                                                        PointIterator points_end,
-                                                                        bool is_flag_complex = false) {
-    Skeleton_blocker_geometric_complex complex;
-    unsigned current = 0;
-    complex =
-        make_complex_from_top_faces<Skeleton_blocker_geometric_complex>(simplex_begin, simplex_end, is_flag_complex);
-    for (auto point = points_begin; point != points_end; ++point)
-      // complex.point(Vertex_handle(current++)) = Point(point->begin(),point->end());
-      complex.point(Vertex_handle(current++)) = Point(*point);
-    return complex;
-  }
-
   /**
    * @brief Constructor with a list of simplices.
    * Points of every vertex are the point constructed with default constructor.
@@ -157,7 +140,7 @@ public Skeleton_blocker_complex<SkeletonBlockerGeometricDS> {
    * Constructs the link of 'simplex' with points coordinates.
    */
   Geometric_link link(Vertex_handle v) const {
-    Geometric_link link(*this, Simplex_handle(v));
+    Geometric_link link(*this, Simplex(v));
     // we now add the point info
     add_points_to_link(link);
     return link;
@@ -166,7 +149,7 @@ public Skeleton_blocker_complex<SkeletonBlockerGeometricDS> {
   /**
    * Constructs the link of 'simplex' with points coordinates.
    */
-  Geometric_link link(const Simplex_handle& simplex) const {
+  Geometric_link link(const Simplex& simplex) const {
     Geometric_link link(*this, simplex);
     // we now add the point info
     add_points_to_link(link);
@@ -189,13 +172,13 @@ public Skeleton_blocker_complex<SkeletonBlockerGeometricDS> {
    * Constructs the abstract link of v (without points coordinates).
    */
   Abstract_link abstract_link(Vertex_handle v) const {
-    return Abstract_link(*this, Simplex_handle(v));
+    return Abstract_link(*this, Simplex(v));
   }
 
   /**
    * Constructs the link of 'simplex' with points coordinates.
    */
-  Abstract_link abstract_link(const Simplex_handle& simplex) const {
+  Abstract_link abstract_link(const Simplex& simplex) const {
     return Abstract_link(*this, simplex);
   }
 
@@ -215,8 +198,27 @@ public Skeleton_blocker_complex<SkeletonBlockerGeometricDS> {
   }
 };
 
+
+template<typename SkeletonBlockerGeometricComplex, typename SimpleHandleOutputIterator, typename PointIterator>
+SkeletonBlockerGeometricComplex make_complex_from_top_faces(
+        SimpleHandleOutputIterator simplex_begin,
+        SimpleHandleOutputIterator simplex_end,
+        PointIterator points_begin,
+        PointIterator points_end,
+        bool is_flag_complex = false) {
+  typedef SkeletonBlockerGeometricComplex SBGC;
+  SkeletonBlockerGeometricComplex complex;
+  unsigned current = 0;
+  complex =
+    make_complex_from_top_faces<SBGC>(simplex_begin, simplex_end, is_flag_complex);
+  for (auto point = points_begin; point != points_end; ++point)
+    // complex.point(Vertex_handle(current++)) = Point(point->begin(),point->end());
+    complex.point(typename SBGC::Vertex_handle(current++)) = typename SBGC::Point(*point);
+  return complex;
+}
+
 }  // namespace skbl
 
 }  // namespace Gudhi
 
-#endif  // SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_GEOMETRIC_COMPLEX_H_
+#endif  // SKELETON_BLOCKER_GEOMETRIC_COMPLEX_H_
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h
index 725ecce5..85a6b0b5 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h
@@ -19,11 +19,11 @@
  *    You should have received a copy of the GNU General Public License
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-#ifndef SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_LINK_COMPLEX_H_
-#define SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_LINK_COMPLEX_H_
+#ifndef SKELETON_BLOCKER_LINK_COMPLEX_H_
+#define SKELETON_BLOCKER_LINK_COMPLEX_H_
 
-#include "gudhi/Utils.h"
-#include "gudhi/Skeleton_blocker_complex.h"
+#include <gudhi/Utils.h>
+#include <gudhi/Skeleton_blocker_complex.h>
 
 namespace Gudhi {
 
@@ -52,12 +52,11 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
   typedef typename ComplexType::Vertex_handle Vertex_handle;
   typedef typename ComplexType::Root_vertex_handle Root_vertex_handle;
 
-  typedef typename ComplexType::Simplex_handle Simplex_handle;
+  typedef typename ComplexType::Simplex Simplex;
   typedef typename ComplexType::Root_simplex_handle Root_simplex_handle;
 
   typedef typename ComplexType::Blocker_handle Blocker_handle;
 
-  typedef typename ComplexType::Simplex_handle::Simplex_vertex_const_iterator Simplex_handle_iterator;
   typedef typename ComplexType::Root_simplex_handle::Simplex_vertex_const_iterator Root_simplex_handle_iterator;
 
   explicit Skeleton_blocker_link_complex(bool only_superior_vertices = false)
@@ -67,13 +66,15 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
   /**
    * If the parameter only_superior_vertices is true,
    * only vertices greater than the one of alpha are added.
+   * Only vertices are computed if only_vertices is true.
    */
   Skeleton_blocker_link_complex(const ComplexType & parent_complex,
-                                const Simplex_handle& alpha_parent_adress,
-                                bool only_superior_vertices = false)
+                                const Simplex& alpha_parent_adress,
+                                bool only_superior_vertices = false,
+                                bool only_vertices = false)
       : only_superior_vertices_(only_superior_vertices) {
     if (!alpha_parent_adress.empty())
-      build_link(parent_complex, alpha_parent_adress);
+      build_link(parent_complex, alpha_parent_adress, only_vertices);
   }
 
   /**
@@ -84,7 +85,7 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
                                 Vertex_handle a_parent_adress,
                                 bool only_superior_vertices = false)
       : only_superior_vertices_(only_superior_vertices) {
-    Simplex_handle alpha_simplex(a_parent_adress);
+    Simplex alpha_simplex(a_parent_adress);
     build_link(parent_complex, alpha_simplex);
   }
 
@@ -96,7 +97,7 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
                                 Edge_handle edge, bool only_superior_vertices =
                                     false)
       : only_superior_vertices_(only_superior_vertices) {
-    Simplex_handle alpha_simplex(parent_complex.first_vertex(edge),
+    Simplex alpha_simplex(parent_complex.first_vertex(edge),
                                  parent_complex.second_vertex(edge));
     build_link(parent_complex, alpha_simplex);
   }
@@ -108,7 +109,7 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
    * are greater than  vertices of alpha_parent_adress are added.
    */
   void compute_link_vertices(const ComplexType & parent_complex,
-                             const Simplex_handle& alpha_parent_adress,
+                             const Simplex& alpha_parent_adress,
                              bool only_superior_vertices,
                              bool is_alpha_blocker = false) {
     if (alpha_parent_adress.dimension() == 0) {
@@ -119,7 +120,7 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
                                   only_superior_vertices_);
     } else {
       // we compute the intersection of neighbors of alpha and store it in link_vertices
-      Simplex_handle link_vertices_parent;
+      Simplex link_vertices_parent;
       parent_complex.add_neighbours(alpha_parent_adress, link_vertices_parent,
                                     only_superior_vertices);
       // For all vertex 'v' in this intersection, we go through all its adjacent blockers.
@@ -162,13 +163,8 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
   }
 
   void compute_link_edges(const ComplexType & parent_complex,
-                          const Simplex_handle& alpha_parent_adress,
+                          const Simplex& alpha_parent_adress,
                           bool is_alpha_blocker = false) {
-    Simplex_handle_iterator y_link, x_parent, y_parent;
-    // ----------------------------
-    // Compute edges in the link
-    // -------------------------
-
     if (this->num_vertices() <= 1)
       return;
 
@@ -194,7 +190,7 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
             }
           }
           if (new_edge)
-            this->add_edge(*x_link, *y_link);
+            this->add_edge_without_blockers(*x_link, *y_link);
         }
       }
     }
@@ -217,7 +213,7 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
    * the blocker is anticollapsed.
    */
   void compute_link_blockers(const ComplexType & parent_complex,
-                             const Simplex_handle& alpha_parent,
+                             const Simplex& alpha_parent,
                              bool is_alpha_blocker = false) {
     for (auto x_link : this->vertex_range()) {
       Vertex_handle x_parent = *this->give_equivalent_vertex(parent_complex,
@@ -225,7 +221,7 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
 
       for (auto blocker_parent : parent_complex.const_blocker_range(x_parent)) {
         if (!is_alpha_blocker || *blocker_parent != alpha_parent) {
-          Simplex_handle sigma_parent(*blocker_parent);
+          Simplex sigma_parent(*blocker_parent);
 
           sigma_parent.difference(alpha_parent);
 
@@ -239,7 +235,7 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
               for (auto a : alpha_parent) {
                 for (auto eta_parent : parent_complex.const_blocker_range(a)) {
                   if (!is_alpha_blocker || *eta_parent != alpha_parent) {
-                    Simplex_handle eta_minus_alpha(*eta_parent);
+                    Simplex eta_minus_alpha(*eta_parent);
                     eta_minus_alpha.difference(alpha_parent);
                     if (eta_minus_alpha != sigma_parent
                         && sigma_parent.contains_difference(*eta_parent,
@@ -253,7 +249,7 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
                   break;
               }
               if (is_new_blocker)
-                this->add_blocker(new Simplex_handle(*sigma_link));
+                this->add_blocker(new Simplex(*sigma_link));
             }
           }
         }
@@ -268,14 +264,15 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
    * with vertices that are greater than  vertices of alpha_parent_adress.
    */
   void build_link(const ComplexType & parent_complex,
-                  const Simplex_handle& alpha_parent_adress,
-                  bool is_alpha_blocker = false) {
+                  const Simplex& alpha_parent_adress,
+                  bool is_alpha_blocker = false,
+                  bool only_vertices = false) {
     assert(is_alpha_blocker || parent_complex.contains(alpha_parent_adress));
-    compute_link_vertices(parent_complex, alpha_parent_adress,
-                          only_superior_vertices_);
-    compute_link_edges(parent_complex, alpha_parent_adress, is_alpha_blocker);
-    compute_link_blockers(parent_complex, alpha_parent_adress,
-                          is_alpha_blocker);
+    compute_link_vertices(parent_complex, alpha_parent_adress, only_superior_vertices_);
+    if(!only_vertices) {
+      compute_link_edges(parent_complex, alpha_parent_adress, is_alpha_blocker);
+      compute_link_blockers(parent_complex, alpha_parent_adress, is_alpha_blocker);
+    }
   }
 
   /**
@@ -284,7 +281,7 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
    * removed from the blockers of the complex.
    */
   friend void build_link_of_blocker(const ComplexType & parent_complex,
-                                    Simplex_handle& blocker,
+                                    Simplex& blocker,
                                     Skeleton_blocker_link_complex & result) {
     assert(blocker.dimension() >= 2);
     assert(parent_complex.contains_blocker(blocker));
@@ -297,4 +294,4 @@ class Skeleton_blocker_link_complex : public Skeleton_blocker_sub_complex<
 
 }  // namespace Gudhi
 
-#endif  // SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_LINK_COMPLEX_H_
+#endif  // SKELETON_BLOCKER_LINK_COMPLEX_H_
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h
index dd8d898e..94a125c1 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h
@@ -19,15 +19,15 @@
  *    You should have received a copy of the GNU General Public License
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-#ifndef SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SIMPLIFIABLE_COMPLEX_H_
-#define SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SIMPLIFIABLE_COMPLEX_H_
+#ifndef SKELETON_BLOCKER_SIMPLIFIABLE_COMPLEX_H_
+#define SKELETON_BLOCKER_SIMPLIFIABLE_COMPLEX_H_
+
+#include <gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h>
 
 #include <list>
 #include <vector>
 #include <set>
 
-#include "gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h"
-
 namespace Gudhi {
 
 namespace skbl {
@@ -45,9 +45,7 @@ bool Skeleton_blocker_complex<SkeletonBlockerDS>::is_popable_blocker(Blocker_han
   assert(this->contains_blocker(*sigma));
   Skeleton_blocker_link_complex<Skeleton_blocker_complex> link_blocker_sigma;
   build_link_of_blocker(*this, *sigma, link_blocker_sigma);
-
-  bool res = link_blocker_sigma.is_contractible() == CONTRACTIBLE;
-  return res;
+  return link_blocker_sigma.is_contractible() == CONTRACTIBLE;
 }
 
 /**
@@ -133,7 +131,7 @@ void Skeleton_blocker_complex<SkeletonBlockerDS>::remove_all_popable_blockers(Ve
 template<typename SkeletonBlockerDS>
 void Skeleton_blocker_complex<SkeletonBlockerDS>::remove_star(Vertex_handle v) {
   // we remove the blockers that are not consistent anymore
-  update_blockers_after_remove_star_of_vertex_or_edge(Simplex_handle(v));
+  update_blockers_after_remove_star_of_vertex_or_edge(Simplex(v));
   while (this->degree(v) > 0) {
     Vertex_handle w(* (adjacent_vertices(v.vertex, this->skeleton).first));
     this->remove_edge(v, w);
@@ -148,7 +146,7 @@ void Skeleton_blocker_complex<SkeletonBlockerDS>::remove_star(Vertex_handle v) {
  */
 template<typename SkeletonBlockerDS>
 void Skeleton_blocker_complex<SkeletonBlockerDS>::update_blockers_after_remove_star_of_vertex_or_edge(
-    const Simplex_handle& simplex_to_be_removed) {
+    const Simplex& simplex_to_be_removed) {
   std::list <Blocker_handle> blockers_to_update;
   if (simplex_to_be_removed.empty()) return;
 
@@ -159,7 +157,7 @@ void Skeleton_blocker_complex<SkeletonBlockerDS>::update_blockers_after_remove_s
   }
 
   for (auto blocker_to_update : blockers_to_update) {
-    Simplex_handle sub_blocker_to_be_added;
+    Simplex sub_blocker_to_be_added;
     bool sub_blocker_need_to_be_added =
         (blocker_to_update->dimension() - simplex_to_be_removed.dimension()) >= 2;
     if (sub_blocker_need_to_be_added) {
@@ -178,7 +176,7 @@ void Skeleton_blocker_complex<SkeletonBlockerDS>::update_blockers_after_remove_s
  */
 template<typename SkeletonBlockerDS>
 void Skeleton_blocker_complex<SkeletonBlockerDS>::remove_star(Vertex_handle a, Vertex_handle b) {
-  update_blockers_after_remove_star_of_vertex_or_edge(Simplex_handle(a, b));
+  update_blockers_after_remove_star_of_vertex_or_edge(Simplex(a, b));
   // we remove the edge
   this->remove_edge(a, b);
 }
@@ -195,7 +193,7 @@ void Skeleton_blocker_complex<SkeletonBlockerDS>::remove_star(Edge_handle e) {
  * Remove the star of the simplex 'sigma' which needs to belong to the complex
  */
 template<typename SkeletonBlockerDS>
-void Skeleton_blocker_complex<SkeletonBlockerDS>::remove_star(const Simplex_handle& sigma) {
+void Skeleton_blocker_complex<SkeletonBlockerDS>::remove_star(const Simplex& sigma) {
   assert(this->contains(sigma));
   if (sigma.dimension() == 0) {
     remove_star(sigma.first_vertex());
@@ -207,33 +205,41 @@ void Skeleton_blocker_complex<SkeletonBlockerDS>::remove_star(const Simplex_hand
   }
 }
 
-/**
- * @brief add a maximal simplex plus all its cofaces.
- * @details the simplex must have dimension greater than one (otherwise use add_vertex or add_edge).
- */
 template<typename SkeletonBlockerDS>
-void Skeleton_blocker_complex<SkeletonBlockerDS>::add_simplex(const Simplex_handle& sigma) {
+void Skeleton_blocker_complex<SkeletonBlockerDS>::add_simplex(const Simplex& sigma) {
+  // to add a simplex s, all blockers included in s are first removed
+  // and then all simplex in the coboundary of s are added as blockers
   assert(!this->contains(sigma));
   assert(sigma.dimension() > 1);
+  if (!contains_vertices(sigma)) {
+    std::cerr << "add_simplex: Some vertices were not present in the complex, adding them" << std::endl;
+    size_t num_vertices_to_add = sigma.last_vertex() - this->num_vertices() + 1;
+    for (size_t i = 0; i < num_vertices_to_add; ++i)
+      this->add_vertex();
+  }
+  assert(contains_vertices(sigma));
+  if (!contains_edges(sigma))
+    add_edge(sigma);
+  remove_blocker_include_in_simplex(sigma);
+  add_blockers_after_simplex_insertion(sigma);
+}
 
-  int num_vertex_to_add = 0;
-  for (auto v : sigma)
-    if (!contains_vertex(v)) ++num_vertex_to_add;
-  while (num_vertex_to_add--) add_vertex();
 
-  for (auto u_it = sigma.begin(); u_it != sigma.end(); ++u_it)
-    for (auto v_it = u_it; ++v_it != sigma.end(); /**/) {
-      // std::cout << "add edge" << *u_it << " " << *v_it << std::endl;
-      add_edge(*u_it, *v_it);
-    }
-  remove_blocker_include_in_simplex(sigma);
+
+template<typename SkeletonBlockerDS>
+void Skeleton_blocker_complex<SkeletonBlockerDS>::add_blockers_after_simplex_insertion(Simplex sigma) {
+  if (sigma.dimension() < 1) return;
+
+  for (auto s : coboundary_range(sigma)) {
+    this->add_blocker(s);
+  }
 }
 
 /**
  * remove all blockers that contains sigma
  */
 template<typename SkeletonBlockerDS>
-void Skeleton_blocker_complex<SkeletonBlockerDS>::remove_blocker_containing_simplex(const Simplex_handle& sigma) {
+void Skeleton_blocker_complex<SkeletonBlockerDS>::remove_blocker_containing_simplex(const Simplex& sigma) {
   std::vector <Blocker_handle> blockers_to_remove;
   for (auto blocker : this->blocker_range(sigma.first_vertex())) {
     if (blocker->contains(sigma))
@@ -247,14 +253,26 @@ void Skeleton_blocker_complex<SkeletonBlockerDS>::remove_blocker_containing_simp
  * remove all blockers that contains sigma
  */
 template<typename SkeletonBlockerDS>
-void Skeleton_blocker_complex<SkeletonBlockerDS>::remove_blocker_include_in_simplex(const Simplex_handle& sigma) {
-  std::vector <Blocker_handle> blockers_to_remove;
-  for (auto blocker : this->blocker_range(sigma.first_vertex())) {
-    if (sigma.contains(*blocker))
-      blockers_to_remove.push_back(blocker);
+void Skeleton_blocker_complex<SkeletonBlockerDS>::remove_blocker_include_in_simplex(const Simplex& sigma) {
+  // TODO(DS): write efficiently by using only superior blockers
+  // eg for all s, check blockers whose vertices are all greater than s
+  std::set <Blocker_handle> blockers_to_remove;
+  for (auto s : sigma) {
+    for (auto blocker : this->blocker_range(s)) {
+      if (sigma.contains(*blocker))
+        blockers_to_remove.insert(blocker);
+    }
   }
-  for (auto blocker_to_update : blockers_to_remove)
+  for (auto blocker_to_update : blockers_to_remove) {
+    auto s = *blocker_to_update;
     this->delete_blocker(blocker_to_update);
+    // now if there is a vertex v in the link of s
+    // and v is not included in sigma then v.s is a blocker
+    // (all faces of v.s are there since v belongs to the link of s)
+    for (const auto& b : coboundary_range(s))
+      if (!sigma.contains(b))
+        this->add_blocker(b);
+  }
 }
 
 /**
@@ -264,21 +282,21 @@ void Skeleton_blocker_complex<SkeletonBlockerDS>::remove_blocker_include_in_simp
  */
 template<typename SkeletonBlockerDS>
 void Skeleton_blocker_complex<SkeletonBlockerDS>::tip_blockers(Vertex_handle a, Vertex_handle b,
-                                                               std::vector<Simplex_handle> & buffer) const {
+                                                               std::vector<Simplex> & buffer) const {
   for (auto const & blocker : this->const_blocker_range(a)) {
-    Simplex_handle beta = (*blocker);
+    Simplex beta = (*blocker);
     beta.remove_vertex(a);
     buffer.push_back(beta);
   }
 
-  Simplex_handle n;
+  Simplex n;
   this->add_neighbours(b, n);
   this->remove_neighbours(a, n);
   n.remove_vertex(a);
 
 
   for (Vertex_handle y : n) {
-    Simplex_handle beta;
+    Simplex beta;
     beta.add_vertex(y);
     buffer.push_back(beta);
   }
@@ -295,7 +313,7 @@ void Skeleton_blocker_complex<SkeletonBlockerDS>::tip_blockers(Vertex_handle a,
 template<typename SkeletonBlockerDS>
 void
 Skeleton_blocker_complex<SkeletonBlockerDS>::swap_edge(Vertex_handle a, Vertex_handle b, Vertex_handle x) {
-  this->add_edge(a, x);
+  this->add_edge_without_blockers(a, x);
   if (this->visitor) this->visitor->on_swaped_edge(a, b, x);
   this->remove_edge(b, x);
 }
@@ -338,13 +356,15 @@ void
 Skeleton_blocker_complex<SkeletonBlockerDS>::contract_edge(Vertex_handle a, Vertex_handle b) {
   assert(this->contains_vertex(a));
   assert(this->contains_vertex(b));
-  assert(this->contains_edge(a, b));
 
-  // if some blockers passes through 'ab', we remove them.
+  if (this->contains_edge(a, b))
+    this->add_edge_without_blockers(a, b);
+
+  // if some blockers passes through 'ab', we need to remove them.
   if (!link_condition(a, b))
     delete_blockers_around_edge(a, b);
 
-  std::set<Simplex_handle> blockers_to_add;
+  std::set<Simplex> blockers_to_add;
 
   get_blockers_to_be_added_after_contraction(a, b, blockers_to_add);
 
@@ -364,9 +384,8 @@ Skeleton_blocker_complex<SkeletonBlockerDS>::contract_edge(Vertex_handle a, Vert
 }
 
 template<typename SkeletonBlockerDS>
-void
-Skeleton_blocker_complex<SkeletonBlockerDS>::get_blockers_to_be_added_after_contraction(Vertex_handle a, Vertex_handle b, 
-    std::set<Simplex_handle>& blockers_to_add) {
+void Skeleton_blocker_complex<SkeletonBlockerDS>::get_blockers_to_be_added_after_contraction(Vertex_handle a,
+    Vertex_handle b, std::set<Simplex>& blockers_to_add) {
   blockers_to_add.clear();
 
   typedef Skeleton_blocker_link_complex<Skeleton_blocker_complex<SkeletonBlockerDS> > LinkComplexType;
@@ -374,19 +393,19 @@ Skeleton_blocker_complex<SkeletonBlockerDS>::get_blockers_to_be_added_after_cont
   LinkComplexType link_a(*this, a);
   LinkComplexType link_b(*this, b);
 
-  std::vector<Simplex_handle> vector_alpha, vector_beta;
+  std::vector<Simplex> vector_alpha, vector_beta;
 
   tip_blockers(a, b, vector_alpha);
   tip_blockers(b, a, vector_beta);
 
   for (auto alpha = vector_alpha.begin(); alpha != vector_alpha.end(); ++alpha) {
     for (auto beta = vector_beta.begin(); beta != vector_beta.end(); ++beta) {
-      Simplex_handle sigma = *alpha;
+      Simplex sigma = *alpha;
       sigma.union_vertices(*beta);
       Root_simplex_handle sigma_id = this->get_id(sigma);
       if (this->contains(sigma) &&
           proper_faces_in_union<Skeleton_blocker_complex < SkeletonBlockerDS >> (sigma_id, link_a, link_b)) {
-        // Blocker_handle blocker = new Simplex_handle(sigma);
+        // Blocker_handle blocker = new Simplex(sigma);
         sigma.add_vertex(a);
         blockers_to_add.insert(sigma);
       }
@@ -444,4 +463,4 @@ Skeleton_blocker_complex<SkeletonBlockerDS>::notify_changed_edges(Vertex_handle
 
 }  // namespace Gudhi
 
-#endif  // SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SIMPLIFIABLE_COMPLEX_H_
+#endif  // SKELETON_BLOCKER_SIMPLIFIABLE_COMPLEX_H_
diff --git a/src/Skeleton_blocker/test/CMakeLists.txt b/src/Skeleton_blocker/test/CMakeLists.txt
index e62600a2..8b6fb672 100644
--- a/src/Skeleton_blocker/test/CMakeLists.txt
+++ b/src/Skeleton_blocker/test/CMakeLists.txt
@@ -18,6 +18,10 @@ add_executable(TestSkeletonBlockerComplex TestSkeletonBlockerComplex.cpp)
 add_executable(TestSimplifiable TestSimplifiable.cpp)
 add_executable(TestGeometricComplex TestGeometricComplex.cpp)
 
+# Do not forget to copy test files in current binary dir
+file(COPY "test.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+file(COPY "test2.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+
 add_test(TestSkeletonBlockerComplex ${CMAKE_CURRENT_BINARY_DIR}/TestSkeletonBlockerComplex)
 add_test(TestSimplifiable ${CMAKE_CURRENT_BINARY_DIR}/TestSimplifiable)
 add_test(TestGeometricComplex ${CMAKE_CURRENT_BINARY_DIR}/TestGeometricComplex)
diff --git a/src/Skeleton_blocker/test/TestGeometricComplex.cpp b/src/Skeleton_blocker/test/TestGeometricComplex.cpp
index bd7af89b..084e2b6b 100644
--- a/src/Skeleton_blocker/test/TestGeometricComplex.cpp
+++ b/src/Skeleton_blocker/test/TestGeometricComplex.cpp
@@ -1,24 +1,24 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
 
 #include <stdio.h>
 #include <stdlib.h>
@@ -33,8 +33,8 @@ using namespace std;
 using namespace Gudhi;
 using namespace skbl;
 
-struct Geometry_trait{
-	typedef std::vector<double> Point;
+struct Geometry_trait {
+  typedef std::vector<double> Point;
 };
 
 typedef Geometry_trait::Point Point;
@@ -42,79 +42,77 @@ typedef Skeleton_blocker_simple_geometric_traits<Geometry_trait> Complex_geometr
 typedef Skeleton_blocker_geometric_complex< Complex_geometric_traits > Complex;
 typedef Complex::Vertex_handle Vertex_handle;
 
+bool test_constructor1() {
+  Complex complex;
+  Skeleton_blocker_off_reader<Complex> off_reader("test2.off", complex);
+  if (!off_reader.is_valid()) {
+    std::cerr << "Unable to read file" << std::endl;
+    return false;
+  }
 
-bool test_constructor1(){
-	Complex complex;
-	Skeleton_blocker_off_reader<Complex> off_reader("test2.off",complex);
-	if(!off_reader.is_valid()){
-		std::cerr << "Unable to read file"<<std::endl;
-		return false;
-	}
 
+  std::cout << "complex has " <<
+      complex.num_vertices() << " vertices, " <<
+      complex.num_blockers() << " blockers, " <<
+      complex.num_edges() << " edges and" <<
+      complex.num_triangles() << " triangles.";
 
-	std::cout << "complex has "<<
-			complex.num_vertices()<<" vertices, "<<
-			complex.num_blockers()<<" blockers, "<<
-			complex.num_edges()<<" edges and" <<
-			complex.num_triangles()<<" triangles.";
+  if (complex.num_vertices() != 7 || complex.num_edges() != 12 || complex.num_triangles() != 6)
+    return false;
 
-	if(complex.num_vertices()!=7 || complex.num_edges()!=12 || complex.num_triangles() !=6)
-		return false;
+  Skeleton_blocker_off_writer<Complex> off_writer("tmp.off", complex);
+  Complex same;
+  Skeleton_blocker_off_reader<Complex> off_reader2("tmp.off", same);
 
-	Skeleton_blocker_off_writer<Complex> off_writer("tmp.off",complex);
-	Complex same;
-	Skeleton_blocker_off_reader<Complex> off_reader2("tmp.off",same);
+  std::cout << "\ncomplex:" << complex.to_string() << endl;
+  std::cout << "\nsame:" << same.to_string() << endl;
 
-	std::cout<<"\ncomplex:"<<complex.to_string()<<endl;
-	std::cout<<"\nsame:"<<same.to_string()<<endl;
-
-	return (complex==same);
+  return (complex == same);
 }
 
-bool test_constructor2(){
-	Complex complex;
-	Skeleton_blocker_off_reader<Complex> off_reader("test2.off",complex);
-	if(!off_reader.is_valid()){
-		std::cerr << "Unable to read file"<<std::endl;
-		return false;
-	}
-	std::cout << "complex has "<<
-			complex.num_vertices()<<" vertices, "<<
-			complex.num_blockers()<<" blockers, "<<
-			complex.num_edges()<<" edges and" <<
-			complex.num_triangles()<<" triangles.";
+bool test_constructor2() {
+  Complex complex;
+  Skeleton_blocker_off_reader<Complex> off_reader("test2.off", complex);
+  if (!off_reader.is_valid()) {
+    std::cerr << "Unable to read file" << std::endl;
+    return false;
+  }
+  std::cout << "complex has " <<
+      complex.num_vertices() << " vertices, " <<
+      complex.num_blockers() << " blockers, " <<
+      complex.num_edges() << " edges and" <<
+      complex.num_triangles() << " triangles.";
 
-	if(complex.num_vertices()!=7 || complex.num_edges()!=12 || complex.num_triangles() !=6)
-		return false;
+  if (complex.num_vertices() != 7 || complex.num_edges() != 12 || complex.num_triangles() != 6)
+    return false;
 
-	auto link_0 = complex.abstract_link(Vertex_handle(0));
+  auto link_0 = complex.abstract_link(Vertex_handle(0));
 
 
-	std::cout<<"\n link(0):"<<link_0.to_string()<<endl;
+  std::cout << "\n link(0):" << link_0.to_string() << endl;
 
-	auto link_geometric_0 = complex.link(Vertex_handle(0));
+  auto link_geometric_0 = complex.link(Vertex_handle(0));
 
-	auto print_point = [&](Vertex_handle v){for(auto x : link_geometric_0.point(v)) std::cout <<x<<" "; std::cout<<std::endl;};
+  auto print_point = [&](Vertex_handle v) {
+    for (auto x : link_geometric_0.point(v)) std::cout << x << " ";
+    std::cout << std::endl;
+  };
 
-	std::for_each(link_geometric_0.vertex_range().begin(),link_geometric_0.vertex_range().end(),print_point);
+  std::for_each(link_geometric_0.vertex_range().begin(), link_geometric_0.vertex_range().end(), print_point);
 
-//	for(auto v : link_geometric_0.vertex_range())
-//		std::cout<<"point("<<v<<"):"<<link_geometric_0.point(v)<<std::endl;
+  //	for(auto v : link_geometric_0.vertex_range())
+  //		std::cout<<"point("<<v<<"):"<<link_geometric_0.point(v)<<std::endl;
 
-	return link_0.num_vertices()==2;
+  return link_0.num_vertices() == 2;
 }
 
+int main(int argc, char *argv[]) {
+  Tests tests_geometric_complex;
+  tests_geometric_complex.add("Test constructor 1", test_constructor1);
+  tests_geometric_complex.add("Test constructor 2", test_constructor2);
 
-
-
-int main (int argc, char *argv[])
-{
-	Tests tests_geometric_complex;
-	tests_geometric_complex.add("Test constructor 1",test_constructor1);
-	tests_geometric_complex.add("Test constructor 2",test_constructor2);
-
-	if(tests_geometric_complex.run())
-		return EXIT_SUCCESS;
-	else
-		return EXIT_FAILURE;
+  if (tests_geometric_complex.run())
+    return EXIT_SUCCESS;
+  else
+    return EXIT_FAILURE;
 }
diff --git a/src/Skeleton_blocker/test/TestSimplifiable.cpp b/src/Skeleton_blocker/test/TestSimplifiable.cpp
index 09176934..b0855ce9 100644
--- a/src/Skeleton_blocker/test/TestSimplifiable.cpp
+++ b/src/Skeleton_blocker/test/TestSimplifiable.cpp
@@ -1,24 +1,24 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
 
 
 #include <stdio.h>
@@ -41,316 +41,382 @@ template<typename ComplexType> class Skeleton_blocker_sub_complex;
 typedef Skeleton_blocker_complex<Skeleton_blocker_simple_traits> Complex;
 typedef Complex::Vertex_handle Vertex_handle;
 typedef Complex::Root_vertex_handle Root_vertex_handle;
-typedef Skeleton_blocker_simplex<Vertex_handle> Simplex_handle;
+typedef Skeleton_blocker_simplex<Vertex_handle> Simplex;
 // true iff v \in complex
-bool assert_vertex(Complex &complex,Vertex_handle v){
-	Simplex_handle simplex(v);
-	bool test = complex.contains(simplex);
-	assert(test);
-	return test;
+
+bool assert_vertex(Complex &complex, Vertex_handle v) {
+  Simplex simplex(v);
+  bool test = complex.contains(simplex);
+  assert(test);
+  return test;
 }
 
 // true iff the blocker (a,b,c) is in complex
-bool assert_blocker(Complex &complex,Root_vertex_handle a,Root_vertex_handle b,Root_vertex_handle c){
 
-	return complex.contains_blocker(Simplex_handle(*complex.get_address(a),*complex.get_address(b),*complex.get_address(c)));
-	//return complex.contains_blocker((a),(b),(c));
+bool assert_blocker(Complex &complex, Root_vertex_handle a, Root_vertex_handle b, Root_vertex_handle c) {
+
+  return complex.contains_blocker(Simplex(*complex.get_address(a), *complex.get_address(b), *complex.get_address(c)));
+  //return complex.contains_blocker((a),(b),(c));
 }
 
-void build_complete(int n,Complex& complex){
-	complex.clear();
-	for(int i=0;i<n;i++)
-		complex.add_vertex();
-	for(int i=0;i<n;i++)
-		for(int j=0;j<i;j++)
-			complex.add_edge(Vertex_handle(i),Vertex_handle(j));
+void build_complete(int n, Complex& complex) {
+  complex.clear();
+  for (int i = 0; i < n; i++)
+    complex.add_vertex();
+  for (int i = 0; i < n; i++)
+    for (int j = 0; j < i; j++)
+      complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(j));
 }
 
-bool test_contraction1(){
-	enum { a, b, x, y, z, n };
-	Complex complex(n);
-	build_complete(n,complex);
-	complex.remove_edge(static_cast<Vertex_handle>(b), static_cast<Vertex_handle>(z));
-	complex.add_blocker(Simplex_handle(static_cast<Vertex_handle>(a), static_cast<Vertex_handle>(x),
-	                                   static_cast<Vertex_handle>(y)));
-	complex.add_blocker(Simplex_handle(static_cast<Vertex_handle>(b), static_cast<Vertex_handle>(x),
-	                                   static_cast<Vertex_handle>(y)));
-
-	// Print result
-	cerr << "complex before complex"<< complex.to_string()<<endl;
-
-	cerr <<endl<<endl;
-	complex.contract_edge(static_cast<Vertex_handle>(a),static_cast<Vertex_handle>(b));
-	// Print result
-	cerr << "ContractEdge(0,1)\n";
-	PRINT(complex.to_string());
-
-	// verification
-	for (int i=0;i<5;i++)
-		if (i!=1) assert_vertex(complex, static_cast<Vertex_handle>(i));
-	bool test1 = !complex.contains_edge(static_cast<Vertex_handle>(a),static_cast<Vertex_handle>(b));
-	bool test2 = assert_blocker(complex,Root_vertex_handle(a),Root_vertex_handle(x),Root_vertex_handle(y));
-	bool test3 = complex.num_edges()==6;
-	bool test4 = complex.num_blockers()==1;
-	Simplex_handle sigma;
-	sigma.add_vertex(static_cast<Vertex_handle>(a));
-	sigma.add_vertex(static_cast<Vertex_handle>(x));
-	sigma.add_vertex(static_cast<Vertex_handle>(y));
-	sigma.add_vertex(static_cast<Vertex_handle>(z));
-	bool test5 = !(complex.contains(sigma));
-	return test1&&test2&&test3&&test4&&test5;
+bool test_contraction1() {
+
+  enum {
+    a, b, x, y, z, n
+  };
+  Complex complex(n);
+  build_complete(n, complex);
+  complex.remove_edge(static_cast<Vertex_handle> (b), static_cast<Vertex_handle> (z));
+  complex.add_blocker(Simplex(static_cast<Vertex_handle> (a), static_cast<Vertex_handle> (x),
+                              static_cast<Vertex_handle> (y)));
+  complex.add_blocker(Simplex(static_cast<Vertex_handle> (b), static_cast<Vertex_handle> (x),
+                              static_cast<Vertex_handle> (y)));
+
+  // Print result
+  cerr << "complex before complex" << complex.to_string() << endl;
+
+  cerr << endl << endl;
+  complex.contract_edge(static_cast<Vertex_handle> (a), static_cast<Vertex_handle> (b));
+  // Print result
+  cerr << "ContractEdge(0,1)\n";
+  PRINT(complex.to_string());
+
+  // verification
+  for (int i = 0; i < 5; i++)
+    if (i != 1) assert_vertex(complex, static_cast<Vertex_handle> (i));
+  bool test1 = !complex.contains_edge(static_cast<Vertex_handle> (a), static_cast<Vertex_handle> (b));
+  bool test2 = assert_blocker(complex, Root_vertex_handle(a), Root_vertex_handle(x), Root_vertex_handle(y));
+  bool test3 = complex.num_edges() == 6;
+  bool test4 = complex.num_blockers() == 1;
+  Simplex sigma;
+  sigma.add_vertex(static_cast<Vertex_handle> (a));
+  sigma.add_vertex(static_cast<Vertex_handle> (x));
+  sigma.add_vertex(static_cast<Vertex_handle> (y));
+  sigma.add_vertex(static_cast<Vertex_handle> (z));
+  bool test5 = !(complex.contains(sigma));
+  return test1 && test2 && test3 && test4&&test5;
 }
 
+bool test_contraction2() {
 
-bool test_contraction2(){
-	enum { a, b, x, y, z, n };
-	Complex complex(n);
-	build_complete(n,complex);
-	complex.remove_edge(static_cast<Vertex_handle>(b),static_cast<Vertex_handle>(x));
-	Simplex_handle blocker;
-	blocker.add_vertex(static_cast<Vertex_handle>(a));
-	blocker.add_vertex(static_cast<Vertex_handle>(y));
-	blocker.add_vertex(static_cast<Vertex_handle>(z));
+  enum {
+    a, b, x, y, z, n
+  };
+  Complex complex(n);
+  build_complete(n, complex);
+  complex.remove_edge(static_cast<Vertex_handle> (b), static_cast<Vertex_handle> (x));
+  Simplex blocker;
+  blocker.add_vertex(static_cast<Vertex_handle> (a));
+  blocker.add_vertex(static_cast<Vertex_handle> (y));
+  blocker.add_vertex(static_cast<Vertex_handle> (z));
 
-	complex.add_blocker(blocker);
+  complex.add_blocker(blocker);
 
-	// Print result
-	cerr << "complex complex"<< complex.to_string();
-	cerr <<endl<<endl;
-	complex.contract_edge(static_cast<Vertex_handle>(a),static_cast<Vertex_handle>(b));
+  // Print result
+  cerr << "complex complex" << complex.to_string();
+  cerr << endl << endl;
+  complex.contract_edge(static_cast<Vertex_handle> (a), static_cast<Vertex_handle> (b));
 
-	cerr << "complex.ContractEdge(a,b)"<< complex.to_string();
+  cerr << "complex.ContractEdge(a,b)" << complex.to_string();
 
-	cerr <<endl<<endl;
+  cerr << endl << endl;
 
-	// there should be one blocker (a,c,d,e) in the complex
-	bool test ;
-	test = complex.contains_blocker(Simplex_handle(static_cast<Vertex_handle>(a), static_cast<Vertex_handle>(x),
-	                                               static_cast<Vertex_handle>(y),static_cast<Vertex_handle>(z)));
-	test = test && complex.num_blockers()==1;
-	return test;
+  // there should be one blocker (a,c,d,e) in the complex
+  bool test;
+  test = complex.contains_blocker(Simplex(static_cast<Vertex_handle> (a), static_cast<Vertex_handle> (x),
+                                          static_cast<Vertex_handle> (y), static_cast<Vertex_handle> (z)));
+  test = test && complex.num_blockers() == 1;
+  return test;
 }
 
-bool test_link_condition1(){
+bool test_link_condition1() {
 
-	Complex complex(0);
-	// Build the complexes
-	build_complete(4,complex);
-	complex.add_blocker(Simplex_handle(static_cast<Vertex_handle>(0), static_cast<Vertex_handle>(1), static_cast<Vertex_handle>(2)));
+  Complex complex(0);
+  // Build the complexes
+  build_complete(4, complex);
+  complex.add_blocker(Simplex(static_cast<Vertex_handle> (0), static_cast<Vertex_handle> (1), static_cast<Vertex_handle> (2)));
 
 
-	// Print result
-	cerr << "complex complex"<< complex.to_string();
-	cerr <<endl<<endl;
+  // Print result
+  cerr << "complex complex" << complex.to_string();
+  cerr << endl << endl;
 
-	bool weak_link_condition = complex.link_condition(Vertex_handle(1),Vertex_handle(2),true);
+  bool weak_link_condition = complex.link_condition(Vertex_handle(1), Vertex_handle(2), true);
 
-	bool strong_link_condition = complex.link_condition(Vertex_handle(1),Vertex_handle(2),false);
+  bool strong_link_condition = complex.link_condition(Vertex_handle(1), Vertex_handle(2), false);
 
-	return weak_link_condition && !strong_link_condition;
+  return weak_link_condition && !strong_link_condition;
 }
 
-
-bool test_collapse0(){
-	Complex complex(5);
-	build_complete(4,complex);
-	complex.add_vertex();
-	complex.add_edge(static_cast<Vertex_handle>(2), static_cast<Vertex_handle>(4));
-	complex.add_edge(static_cast<Vertex_handle>(3), static_cast<Vertex_handle>(4));
-	// Print result
-	cerr << "initial complex :\n"<< complex.to_string();
-	cerr <<endl<<endl;
-
-	Simplex_handle simplex_123(static_cast<Vertex_handle>(1), static_cast<Vertex_handle>(2), static_cast<Vertex_handle>(3));
-	complex.remove_star(simplex_123);
-	cerr << "complex.remove_star(1,2,3):\n"<< complex.to_string();
-	cerr <<endl<<endl;
-
-	// verification
-	bool blocker123_here = complex.contains_blocker(simplex_123);
-	cerr <<"----> Ocomplex \n";
-	return blocker123_here;
+bool test_collapse0() {
+  Complex complex(5);
+  build_complete(4, complex);
+  complex.add_vertex();
+  complex.add_edge_without_blockers(static_cast<Vertex_handle> (2), static_cast<Vertex_handle> (4));
+  complex.add_edge_without_blockers(static_cast<Vertex_handle> (3), static_cast<Vertex_handle> (4));
+  // Print result
+  cerr << "initial complex :\n" << complex.to_string();
+  cerr << endl << endl;
+
+  Simplex simplex_123(static_cast<Vertex_handle> (1), static_cast<Vertex_handle> (2), static_cast<Vertex_handle> (3));
+  complex.remove_star(simplex_123);
+  cerr << "complex.remove_star(1,2,3):\n" << complex.to_string();
+  cerr << endl << endl;
+
+  // verification
+  bool blocker123_here = complex.contains_blocker(simplex_123);
+  cerr << "----> Ocomplex \n";
+  return blocker123_here;
 }
 
-
-bool test_collapse1(){
-	Complex complex(5);
-	build_complete(4,complex);
-	complex.add_blocker(Simplex_handle(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2),Vertex_handle(3)));
-	// Print result
-	cerr << "initial complex :\n"<< complex.to_string();
-	cerr <<endl<<endl;
-
-	Simplex_handle simplex_123(Vertex_handle(1),Vertex_handle(2),Vertex_handle(3));
-	complex.remove_star(simplex_123);
-	cerr << "complex.remove_star(1,2,3):\n"<< complex.to_string();
-	cerr <<endl<<endl;
-
-	// verification
-	bool res = complex.contains_blocker(simplex_123);
-	res = res && complex.num_blockers()==1;
-	cerr <<"----> Ocomplex \n";
-	return res;
+bool test_collapse1() {
+  Complex complex(5);
+  build_complete(4, complex);
+  complex.add_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2), Vertex_handle(3)));
+  // Print result
+  cerr << "initial complex :\n" << complex.to_string();
+  cerr << endl << endl;
+
+  Simplex simplex_123(Vertex_handle(1), Vertex_handle(2), Vertex_handle(3));
+  complex.remove_star(simplex_123);
+  cerr << "complex.remove_star(1,2,3):\n" << complex.to_string();
+  cerr << endl << endl;
+
+  // verification
+  bool res = complex.contains_blocker(simplex_123);
+  res = res && complex.num_blockers() == 1;
+  cerr << "----> Ocomplex \n";
+  return res;
 }
 
-bool test_collapse2(){
-	Complex complex(5);
-	build_complete(4,complex);
-	complex.add_vertex();
-	complex.add_edge(Vertex_handle(1),Vertex_handle(4));
-	complex.add_edge(Vertex_handle(2),Vertex_handle(4));
-	complex.add_edge(Vertex_handle(3),Vertex_handle(4));
-	complex.add_blocker(Simplex_handle(Vertex_handle(1),Vertex_handle(2),Vertex_handle(3),Vertex_handle(4)));
-	// Print result
-	cerr << "initial complex :\n"<< complex.to_string();
-	cerr <<endl<<endl;
-
-	Simplex_handle sigma(Vertex_handle(1),Vertex_handle(2),Vertex_handle(3));
-	complex.remove_star(sigma);
-	cerr << "complex.remove_star(1,2,3):\n"<< complex.to_string();
-	cerr <<endl<<endl;
-
-	// verification
-	bool blocker_removed = !complex.contains_blocker(Simplex_handle(Vertex_handle(1),Vertex_handle(2),Vertex_handle(3),Vertex_handle(4)));
-	bool blocker123_here = complex.contains_blocker(sigma);
-	return blocker_removed && blocker123_here;
+bool test_collapse2() {
+  Complex complex(5);
+  build_complete(4, complex);
+  complex.add_vertex();
+  complex.add_edge_without_blockers(Vertex_handle(1), Vertex_handle(4));
+  complex.add_edge_without_blockers(Vertex_handle(2), Vertex_handle(4));
+  complex.add_edge_without_blockers(Vertex_handle(3), Vertex_handle(4));
+  complex.add_blocker(Simplex(Vertex_handle(1), Vertex_handle(2), Vertex_handle(3), Vertex_handle(4)));
+  // Print result
+  cerr << "initial complex :\n" << complex.to_string();
+  cerr << endl << endl;
+
+  Simplex sigma(Vertex_handle(1), Vertex_handle(2), Vertex_handle(3));
+  complex.remove_star(sigma);
+  cerr << "complex.remove_star(1,2,3):\n" << complex.to_string();
+  cerr << endl << endl;
+
+  // verification
+  bool blocker_removed = !complex.contains_blocker(Simplex(Vertex_handle(1), Vertex_handle(2), Vertex_handle(3), Vertex_handle(4)));
+  bool blocker123_here = complex.contains_blocker(sigma);
+  return blocker_removed && blocker123_here;
 }
 
-bool test_collapse3(){
-	Complex complex(5);
-	build_complete(4,complex);
-	complex.add_vertex();
-	complex.add_edge(Vertex_handle(1),Vertex_handle(4));
-	complex.add_edge(Vertex_handle(2),Vertex_handle(4));
-	complex.add_edge(Vertex_handle(3),Vertex_handle(4));
-	complex.add_blocker(Simplex_handle(Vertex_handle(1),Vertex_handle(2),Vertex_handle(3),Vertex_handle(4)));
-	// Print result
-	cerr << "initial complex:\n"<< complex.to_string();
-	cerr <<endl<<endl;
-
-	complex.remove_star(static_cast<Vertex_handle>(2));
-	cerr << "complex after remove star of 2:\n"<< complex.to_string();
-
-	bool blocker134_here = complex.contains_blocker(Simplex_handle(Vertex_handle(1),Vertex_handle(3),Vertex_handle(4)));
-	bool blocker1234_here = complex.contains_blocker(Simplex_handle(Vertex_handle(1),Vertex_handle(2),Vertex_handle(3),Vertex_handle(4)));
-	return blocker134_here && !blocker1234_here;
+bool test_collapse3() {
+  Complex complex(5);
+  build_complete(4, complex);
+  complex.add_vertex();
+  complex.add_edge_without_blockers(Vertex_handle(1), Vertex_handle(4));
+  complex.add_edge_without_blockers(Vertex_handle(2), Vertex_handle(4));
+  complex.add_edge_without_blockers(Vertex_handle(3), Vertex_handle(4));
+  complex.add_blocker(Simplex(Vertex_handle(1), Vertex_handle(2), Vertex_handle(3), Vertex_handle(4)));
+  // Print result
+  cerr << "initial complex:\n" << complex.to_string();
+  cerr << endl << endl;
+
+  complex.remove_star(static_cast<Vertex_handle> (2));
+  cerr << "complex after remove star of 2:\n" << complex.to_string();
+
+  bool blocker134_here = complex.contains_blocker(Simplex(Vertex_handle(1), Vertex_handle(3), Vertex_handle(4)));
+  bool blocker1234_here = complex.contains_blocker(Simplex(Vertex_handle(1), Vertex_handle(2), Vertex_handle(3), Vertex_handle(4)));
+  return blocker134_here && !blocker1234_here;
 }
 
-bool test_add_simplex(){
-	Complex complex(5);
-	build_complete(4,complex);
-	complex.add_blocker(Simplex_handle(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2)));
-	// Print result
-	cerr << "initial complex:\n"<< complex.to_string();
-	cerr <<endl<<endl;
-
-	complex.add_simplex(Simplex_handle(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2),Vertex_handle(3)));
-	cerr << "complex after add_simplex:\n"<< complex.to_string();
-
-	return complex.num_blockers()==0;
+bool test_add_simplex() {
+  Complex complex(4);
+  build_complete(4, complex);
+  complex.add_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(3)));
+  cerr << "initial complex:\n" << complex.to_string();
+  cerr << endl << endl;
+
+  complex.add_simplex(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(3)));
+  cerr << "complex after add_simplex:\n" << complex.to_string();
+  return complex.num_blockers() == 1
+      && complex.contains_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2), Vertex_handle(3)));
 }
 
-bool test_add_simplex2(){
-	Complex complex;
-	build_complete(4,complex);
-	// Print result
-	cerr << "initial complex:\n"<< complex.to_string();
-	cerr <<endl<<endl;
+bool test_add_simplex2() {
+  Complex complex;
+  build_complete(4, complex);
+  // Print result
+  cerr << "initial complex:\n" << complex.to_string();
+  cerr << endl << endl;
 
-	Complex copy(complex.num_vertices());
+  Complex copy(complex.num_vertices());
 
-	std::vector<Simplex_handle> simplices(complex.simplex_range().begin(),complex.simplex_range().end());
-	sort(simplices.begin(),simplices.end(),[&](const Simplex_handle& s1,const Simplex_handle& s2){
-		return s1.dimension()<s2.dimension();
-	});
-	for(const auto & simplex : simplices){
-		if(!copy.contains(simplex) && simplex.dimension()==1)
-			copy.add_edge(simplex.first_vertex(),simplex.last_vertex());
-		if(!copy.contains(simplex) && simplex.dimension()>1)
-			copy.add_simplex(simplex);
-	}
+  std::vector<Simplex> simplices(complex.complex_simplex_range().begin(), complex.complex_simplex_range().end());
+  sort(simplices.begin(), simplices.end(), [&](const Simplex& s1, const Simplex & s2) {
+    return s1.dimension() < s2.dimension();
+  });
+  for (const auto & simplex : simplices) {
+    if (!copy.contains(simplex) && simplex.dimension() == 1)
+      copy.add_edge_without_blockers(simplex.first_vertex(), simplex.last_vertex());
+    if (!copy.contains(simplex) && simplex.dimension() > 1)
+      copy.add_simplex(simplex);
+  }
 
 
-	cerr << "complex after add_simplex:\n"<< copy.to_string();
+  cerr << "complex after add_simplex:\n" << copy.to_string();
 
 
-	return complex.num_blockers()==copy.num_blockers() &&
-			complex.num_edges()==copy.num_edges() &&
-			complex.num_vertices()==copy.num_vertices();
+  return complex.num_blockers() == copy.num_blockers() &&
+      complex.num_edges() == copy.num_edges() &&
+      complex.num_vertices() == copy.num_vertices();
 }
 
+bool test_add_simplex3() {
+  Complex complex(5);
+  build_complete(5, complex);
+  complex.remove_edge(Vertex_handle(3), Vertex_handle(4));
+  Simplex sigma(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2));
+  complex.add_blocker(sigma);
+  // Print result
+  cerr << "initial complex:\n" << complex.to_string();
+  cerr << endl << endl;
+  complex.add_simplex(sigma);
+  //should create two blockers 0123 and 0124
+  cerr << "complex after adding simplex 012:\n" << complex.to_string();
+  return complex.num_blockers() == 2
+      && complex.contains_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2), Vertex_handle(3)))
+      && complex.contains_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2), Vertex_handle(4)));
+}
 
-
-bool test_remove_popable_blockers(){
-	Complex complex;
-	build_complete(4,complex);
-	complex.add_vertex();
-	complex.add_edge(Vertex_handle(3),Vertex_handle(4));
-	complex.add_edge(Vertex_handle(2),Vertex_handle(4));
-	Simplex_handle sigma1=Simplex_handle(Vertex_handle(1),Vertex_handle(2),Vertex_handle(3));
-	Simplex_handle sigma2=Simplex_handle(Vertex_handle(2),Vertex_handle(3),Vertex_handle(4));
-
-	complex.add_blocker(sigma1);
-	complex.add_blocker(sigma2);
-	cerr << "complex complex"<< complex.to_string();
-	cerr <<endl<<endl;
-	cerr << "complex.RemovePopableBlockers();"<<endl;
-	complex.remove_popable_blockers();
-	cerr << "complex complex"<< complex.to_string();
-	cerr <<endl<<endl;
-
-	bool test1 = (complex.num_blockers()==1);
-
-
-	// test 2
-	complex.clear();
-	build_complete(4,complex);
-	complex.add_vertex();
-	complex.add_vertex();
-	complex.add_edge(Vertex_handle(3),Vertex_handle(4));
-	complex.add_edge(Vertex_handle(2),Vertex_handle(4));
-	complex.add_edge(Vertex_handle(2),Vertex_handle(5));
-	complex.add_edge(Vertex_handle(3),Vertex_handle(5));
-	complex.add_edge(Vertex_handle(4),Vertex_handle(5));
-	sigma1=Simplex_handle(Vertex_handle(1),Vertex_handle(2),Vertex_handle(3));
-	sigma2=Simplex_handle(Vertex_handle(2),Vertex_handle(3),Vertex_handle(4));
-
-	complex.add_blocker(sigma1);
-	complex.add_blocker(sigma2);
-	cerr << "complex complex"<< complex.to_string();
-	cerr <<endl<<endl;	cerr << "complex.RemovePopableBlockers();"<<endl;
-	complex.remove_popable_blockers();
-	cerr << "complex complex"<< complex.to_string();
-
-	cerr <<endl<<endl;
-	bool test2 = (complex.num_blockers()==0);
-	return test1&&test2;
+bool test_add_simplex4() {
+  int n = 6;
+  Complex complex(n);
+
+  // add all simplex 0..n without i
+  for (int i = 0; i < n; i++) {
+    Simplex s;
+    for (int k = 0; k < n; k++)
+      s.add_vertex(Vertex_handle(k));
+    s.remove_vertex(Vertex_handle(i));
+    complex.add_simplex(s);
+
+    //at step i there is only blocker 0..i
+    if (i < 2 && complex.num_blockers() > 0)
+      return false;
+    if (i >= 2 && complex.num_blockers() != 1) {
+      Simplex b;
+      for (int k = 0; k < i; k++)
+        b.add_vertex(Vertex_handle(i));
+      if (!complex.contains_blocker(b))
+        return false;
+    }
+    TESTVALUE(complex.blockers_to_string());
+  }
+  Simplex s;
+  for (int k = 0; k < n; k++)
+    s.add_vertex(Vertex_handle(k));
+  return complex.num_blockers() == 1 && complex.contains_blocker(s);
 }
 
+bool test_add_edge() {
+  Complex complex(4);
+  for (unsigned i = 0u; i < 4; i++)
+    complex.add_edge(Vertex_handle(i), Vertex_handle((i + 1) % 4));
+
+  // Print result
+  cerr << "initial complex:\n" << complex.to_string();
+  cerr << endl << endl;
+  complex.add_edge(Vertex_handle(1), Vertex_handle(3));
+  //should create two blockers 013 and 012
+  cerr << "complex after adding edge 13:\n" << complex.to_string();
+  return complex.num_blockers() == 2
+      && complex.contains_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(3)))
+      && complex.contains_blocker(Simplex(Vertex_handle(1), Vertex_handle(2), Vertex_handle(3)));
+}
 
+bool test_remove_popable_blockers() {
+  Complex complex;
+  build_complete(4, complex);
+  complex.add_vertex();
+  complex.add_edge_without_blockers(Vertex_handle(3), Vertex_handle(4));
+  complex.add_edge_without_blockers(Vertex_handle(2), Vertex_handle(4));
+  Simplex sigma1 = Simplex(Vertex_handle(1), Vertex_handle(2), Vertex_handle(3));
+  Simplex sigma2 = Simplex(Vertex_handle(2), Vertex_handle(3), Vertex_handle(4));
+
+  complex.add_blocker(sigma1);
+  complex.add_blocker(sigma2);
+  cerr << "complex complex" << complex.to_string();
+  cerr << endl << endl;
+  cerr << "complex.RemovePopableBlockers();" << endl;
+  complex.remove_popable_blockers();
+  cerr << "complex complex" << complex.to_string();
+  cerr << endl << endl;
+
+  bool test1 = (complex.num_blockers() == 1);
+
+
+  // test 2
+  complex.clear();
+  build_complete(4, complex);
+  complex.add_vertex();
+  complex.add_vertex();
+  complex.add_edge_without_blockers(Vertex_handle(3), Vertex_handle(4));
+  complex.add_edge_without_blockers(Vertex_handle(2), Vertex_handle(4));
+  complex.add_edge_without_blockers(Vertex_handle(2), Vertex_handle(5));
+  complex.add_edge_without_blockers(Vertex_handle(3), Vertex_handle(5));
+  complex.add_edge_without_blockers(Vertex_handle(4), Vertex_handle(5));
+  sigma1 = Simplex(Vertex_handle(1), Vertex_handle(2), Vertex_handle(3));
+  sigma2 = Simplex(Vertex_handle(2), Vertex_handle(3), Vertex_handle(4));
+
+  complex.add_blocker(sigma1);
+  complex.add_blocker(sigma2);
+  cerr << "complex complex" << complex.to_string();
+  cerr << endl << endl;
+  cerr << "complex.RemovePopableBlockers();" << endl;
+  complex.remove_popable_blockers();
+  cerr << "complex complex" << complex.to_string();
+
+  cerr << endl << endl;
+  bool test2 = (complex.num_blockers() == 0);
+  return test1&&test2;
+}
 
-int main (int argc, char *argv[])
-{
-	Tests tests_simplifiable_complex;
-	tests_simplifiable_complex.add("Test contraction 1",test_contraction1);
-	tests_simplifiable_complex.add("Test contraction 2",test_contraction2);
-	tests_simplifiable_complex.add("Test Link condition 1",test_link_condition1);
-	tests_simplifiable_complex.add("Test remove popable blockers",test_remove_popable_blockers);
+int main(int argc, char *argv[]) {
+  Tests tests_simplifiable_complex;
+  tests_simplifiable_complex.add("Test contraction 1", test_contraction1);
+  tests_simplifiable_complex.add("Test contraction 2", test_contraction2);
+  tests_simplifiable_complex.add("Test Link condition 1", test_link_condition1);
+  tests_simplifiable_complex.add("Test remove popable blockers", test_remove_popable_blockers);
 
 
-	tests_simplifiable_complex.add("Test collapse 0",test_collapse0);
-	tests_simplifiable_complex.add("Test collapse 1",test_collapse1);
-	tests_simplifiable_complex.add("Test collapse 2",test_collapse2);
-	tests_simplifiable_complex.add("Test collapse 3",test_collapse3);
+  tests_simplifiable_complex.add("Test collapse 0", test_collapse0);
+  tests_simplifiable_complex.add("Test collapse 1", test_collapse1);
+  tests_simplifiable_complex.add("Test collapse 2", test_collapse2);
+  tests_simplifiable_complex.add("Test collapse 3", test_collapse3);
 
-	tests_simplifiable_complex.add("Test add simplex",test_add_simplex);
-	tests_simplifiable_complex.add("Test add simplex2",test_add_simplex2);
+  tests_simplifiable_complex.add("Test add edge",test_add_edge);
+  tests_simplifiable_complex.add("Test add simplex", test_add_simplex);
+  tests_simplifiable_complex.add("Test add simplex2", test_add_simplex2);
+  tests_simplifiable_complex.add("Test add simplex3",test_add_simplex3);
+  tests_simplifiable_complex.add("Test add simplex4",test_add_simplex4);
 
 
-	tests_simplifiable_complex.run();
+  tests_simplifiable_complex.run();
 
-	if(tests_simplifiable_complex.run())
-		return EXIT_SUCCESS;
-	else
-		return EXIT_FAILURE;
+  if (tests_simplifiable_complex.run())
+    return EXIT_SUCCESS;
+  else
+    return EXIT_FAILURE;
 }
diff --git a/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp b/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp
index 3dc38572..42482e23 100644
--- a/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp
+++ b/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp
@@ -42,911 +42,911 @@ using namespace skbl;
 typedef Skeleton_blocker_complex<Skeleton_blocker_simple_traits> Complex;
 typedef Complex::Vertex_handle Vertex_handle;
 typedef Complex::Root_vertex_handle Root_vertex_handle;
-typedef Complex::Simplex_handle Simplex_handle;
+typedef Complex::Simplex Simplex;
 typedef Complex::Root_simplex_handle Root_simplex_handle;
-typedef Simplex_handle::Simplex_vertex_const_iterator Simplex_vertex_const_iterator;
+typedef Simplex::Simplex_vertex_const_iterator Simplex_vertex_const_iterator;
 typedef Complex::Edge_handle Edge_handle;
 
 // true if v in complex
-bool assert_vertex(Complex &complex,Vertex_handle v){
-	//assert(complex.contains(v));
-	return complex.contains(static_cast<Simplex_handle>(v));
-}
-
-bool assert_simplex(Complex &complex,Root_vertex_handle a,Root_vertex_handle b,Root_vertex_handle c){
-	return true;
-	//	AddressSimplex simplex((a),(b),(c));
-	//	return complex.contains(&simplex);
-}
 
-// true iff the blocker (a,b,c) is in complex
-bool assert_blocker(Complex &complex,Root_vertex_handle a,Root_vertex_handle b,Root_vertex_handle c){
-	return true;
-	//return complex.contains_blocker((a),(b),(c));
+bool assert_vertex(Complex &complex, Vertex_handle v) {
+  //assert(complex.contains(v));
+  return complex.contains(static_cast<Simplex> (v));
 }
 
-// true iff the blocker (a,b,c,d) is in complex
-bool assert_blocker(Complex &complex,Root_vertex_handle a,Root_vertex_handle b,Root_vertex_handle c,Root_vertex_handle d){
-	return true;
-	//Simplex blocker (a,b,c,d);
-	//return complex.contains_blocker(&blocker);
-}
-
-
-
-void build_complete(int n,Complex& complex){
-	complex.clear();
-	for(int i=0;i<n;i++)
-		complex.add_vertex();
-
-	//	for(int i=n-1;i>=0;i--)
-	//		for(int j=i-1;j>=0;j--)
-	//			complex.add_edge(Vertex_handle(i),Vertex_handle(j));
-
-	for(int i=0;i<n;i++)
-		for(int j=0;j<i;j++)
-			complex.add_edge(Vertex_handle(i),Vertex_handle(j));
-}
-
-
-bool test_simplex(){
-	//	PRINT("test simplex");
-	Simplex_handle simplex(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2),Vertex_handle(3));
-	for (auto i = simplex.begin() ; i != simplex.end() ; ++i){
-		PRINT(*i);
-		auto j = i;
-		for (++j ;
-				j != simplex.end() ;
-				++j){
-			PRINT(*j);
-		}
-	}
-	return simplex.dimension()==3;
-}
-
-
-bool test_iterator_vertices1(){
-	int n = 10;
-	Complex complex(10);
-	cerr << "complex.num_vertices():"<<complex.num_vertices()<<endl;
-	int num_vertex_seen = 0;
-	for(auto vi :complex.vertex_range()){
-		cerr << "vertex:"<<vi<<endl;
-		++num_vertex_seen;
-	}
-	return num_vertex_seen == n;
-}
-
-bool test_iterator_vertices2(){
-	int n = 10;
-	Complex complex(10);
-	build_complete(10,complex);
-	cerr << "complex.num_vertices():"<<complex.num_vertices()<<endl;
-	cerr << "complex.num_edges():"<<complex.num_edges()<<endl;
-	int num_vertex_seen = 0;
-	for(auto vi :complex.vertex_range(Vertex_handle(2))){
-		cerr << "vertex:"<<vi<<endl;
-		++num_vertex_seen;
-	}
-	std::cerr<<"num_vertex_seen:"<<num_vertex_seen<<std::endl;
-	return num_vertex_seen == (n-1);
-}
-
-
-
-bool test_iterator_edge(){
-	const int n = 10;
-	Complex complex(n);
-	for(int i=0;i<n;i++)
-		for(int j=0;j<i;j++)
-			complex.add_edge(Vertex_handle(i),Vertex_handle(j));
-	complex.remove_edge(Vertex_handle(2),Vertex_handle(3));
-	complex.remove_edge(Vertex_handle(3),Vertex_handle(5));
-	cerr << "complex.num_edges():"<<complex.num_edges()<<endl;
-	int num_edges_seen = 0;
-	for(auto edge : complex.edge_range()){
-		cerr << "edge :"<<complex[edge]<<endl;
-		++num_edges_seen;
-	}
-
-	return num_edges_seen == n*(n-1)/2-2;
-}
-
-bool test_iterator_edge2(){
-	const int n = 10;
-	Complex complex(n);
-	for(int i=0;i<n;i++)
-		for(int j=0;j<i;j++)
-			complex.add_edge(Vertex_handle(i),Vertex_handle(j));
-	complex.remove_edge(Vertex_handle(2),Vertex_handle(3));
-	complex.remove_edge(Vertex_handle(3),Vertex_handle(5));
-	cerr << "complex.num_edges():"<<complex.num_edges()<<endl;
-	int num_neigbors_seen = 0;
-	for(auto neighbor : complex.vertex_range(Vertex_handle(2))){
-		cerr << "neighbor"<<neighbor<<endl;
-		++num_neigbors_seen;
-	}
-	return num_neigbors_seen==8;
-}
-
-
-
-bool test_iterator_edge3(){
-	const int n = 10;
-	Complex complex(n);
-	for(int i=0;i<n;i++)
-		for(int j=0;j<i;j++)
-			complex.add_edge(Vertex_handle(i),Vertex_handle(j));
-	complex.remove_edge(Vertex_handle(2),Vertex_handle(3));
-	complex.remove_edge(Vertex_handle(3),Vertex_handle(5));
-	cerr << "complex.num_edges():"<<complex.num_edges()<<endl;
-	int num_neigbors_seen = 0;
-	for(auto edge : complex.edge_range(Vertex_handle(2))){
-		std::cerr << edge<< std::endl;
-		++num_neigbors_seen;
-	}
-	return num_neigbors_seen==8;
-}
-
-
-
-bool test_iterator_triangles(){
-	const int n = 7;
-	Complex complex(n);
-	//create a "ring" around '0'
-	for(int i=1;i<n;i++)
-		complex.add_edge(Vertex_handle(0),Vertex_handle(i));
-	for(int i=1;i<n-1;i++)
-		complex.add_edge(Vertex_handle(i),Vertex_handle(i+1));
-	complex.add_edge(Vertex_handle(1),Vertex_handle(6));
-
-	PRINT(complex.to_string());
-
-	int num_triangles_seen=0;
-	//for (auto t : complex.triangle_range(5)){
-	TEST("triangles around 5 (should be 2 of them):");
-	for (auto t : complex.triangle_range(Vertex_handle(5))){
-		PRINT(t);
-		++num_triangles_seen;
-	}
-	bool test = (num_triangles_seen==2);
-
-	num_triangles_seen=0;
-	TEST("triangles around 0 (should be 6 of them):");
-	for (auto t : complex.triangle_range(Vertex_handle(0))){
-		PRINT(t);
-		++num_triangles_seen;
-	}
-	test = test&&(num_triangles_seen==6);
-
-	// we now add another triangle
-	complex.add_vertex();
-	complex.add_edge(Vertex_handle(4),Vertex_handle(7));
-	complex.add_edge(Vertex_handle(3),Vertex_handle(7));
-	complex.add_blocker(Simplex_handle(Vertex_handle(0),Vertex_handle(1),Vertex_handle(6)));
-	num_triangles_seen=0;
-
-	TEST("triangles (should be 6 of them):");
-	num_triangles_seen=0;
-	for (auto t : complex.triangle_range()){
-		PRINT(t);
-		++num_triangles_seen;
-	}
-	test = test&&(num_triangles_seen==6);
-	PRINT(num_triangles_seen);
-
-	return test;
+bool assert_simplex(Complex &complex, Root_vertex_handle a, Root_vertex_handle b, Root_vertex_handle c) {
+  return true;
+  //	AddressSimplex simplex((a),(b),(c));
+  //	return complex.contains(&simplex);
 }
 
+// true iff the blocker (a,b,c) is in complex
 
-//#include "combinatorics/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h"
-
-bool test_iterator_simplices(){
-	Complex complex(6);
-	complex.add_edge(Vertex_handle(0),Vertex_handle(1));
-	complex.add_edge(Vertex_handle(1),Vertex_handle(2));
-	complex.add_edge(Vertex_handle(2),Vertex_handle(0));
-	complex.add_edge(Vertex_handle(1),Vertex_handle(3));
-	complex.add_edge(Vertex_handle(2),Vertex_handle(3));
-	complex.add_edge(Vertex_handle(2),Vertex_handle(5));
-	complex.add_edge(Vertex_handle(3),Vertex_handle(5));
-	complex.add_edge(Vertex_handle(2),Vertex_handle(4));
-	complex.add_edge(Vertex_handle(4),Vertex_handle(5));
-	complex.add_edge(Vertex_handle(3),Vertex_handle(4));
-
-	complex.add_blocker(Simplex_handle(Vertex_handle(2),Vertex_handle(3),Vertex_handle(4),Vertex_handle(5)));
-
-	bool correct_number_simplices = true;
-
-	std::map<Vertex_handle,unsigned> expected_num_simplices;
-
-	expected_num_simplices[Vertex_handle(0)] = 4;
-	expected_num_simplices[Vertex_handle(1)] = 6;
-	expected_num_simplices[Vertex_handle(2)] = 11;
-	expected_num_simplices[Vertex_handle(3)] = 9;
-	expected_num_simplices[Vertex_handle(4)] = 7;
-	expected_num_simplices[Vertex_handle(5)] = 7;
-
-	for(auto pair : expected_num_simplices){
-		unsigned num_simplices_around = 0;
-		for(const auto& simplex : complex.simplex_range(pair.first)){
-			simplex.dimension();
-			DBGVALUE(simplex);
-			++num_simplices_around;
-		}
-
-		correct_number_simplices = correct_number_simplices && (num_simplices_around == pair.second);
-
-		DBGMSG("current vertex:",pair.first);
-		DBGMSG("expected_num_simplices:",pair.second);
-		DBGMSG("found:",num_simplices_around);
-	}
-	return correct_number_simplices;
+bool assert_blocker(Complex &complex, Root_vertex_handle a, Root_vertex_handle b, Root_vertex_handle c) {
+  return true;
+  //return complex.contains_blocker((a),(b),(c));
 }
 
+// true iff the blocker (a,b,c,d) is in complex
 
-
-bool test_iterator_simplices2(){
-	Complex complex(2);
-	complex.add_edge(Vertex_handle(0),Vertex_handle(1));
-
-	for(const auto& s:complex.triangle_range()){
-		s.dimension();
-		return false; // there are no triangles
-	}
-
-	unsigned num_simplices = 0 ;
-
-
-	DBGVALUE(complex.to_string());
-
-	for(const auto& simplex : complex.simplex_range(Vertex_handle(0))){
-		simplex.dimension();
-		DBGVALUE(simplex);
-	}
-
-
-	for(const auto& simplex : complex.simplex_range()){
-		DBGVALUE(simplex);
-		simplex.dimension();
-		++num_simplices;
-	}
-	bool correct_number_simplices = (num_simplices == 3);
-	return correct_number_simplices;
+bool assert_blocker(Complex &complex, Root_vertex_handle a, Root_vertex_handle b, Root_vertex_handle c, Root_vertex_handle d) {
+  return true;
+  //Simplex blocker (a,b,c,d);
+  //return complex.contains_blocker(&blocker);
+}
+
+void build_complete(int n, Complex& complex) {
+  complex.clear();
+  for (int i = 0; i < n; i++)
+    complex.add_vertex();
+
+  //	for(int i=n-1;i>=0;i--)
+  //		for(int j=i-1;j>=0;j--)
+  //			complex.add_edge_without_blockers(Vertex_handle(i),Vertex_handle(j));
+
+  for (int i = 0; i < n; i++)
+    for (int j = 0; j < i; j++)
+      complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(j));
+}
+
+bool test_simplex() {
+  //	PRINT("test simplex");
+  Simplex simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2), Vertex_handle(3));
+  for (auto i = simplex.begin(); i != simplex.end(); ++i) {
+    PRINT(*i);
+    auto j = i;
+    for (++j;
+         j != simplex.end();
+         ++j) {
+      PRINT(*j);
+    }
+  }
+  return simplex.dimension() == 3;
+}
+
+bool test_num_simplices() {
+  int n = 4;
+  Complex complex;
+  build_complete(n, complex);
+  size_t sum = 0;
+  for (int i = 0; i < n; i++) {
+    PRINT(complex.num_simplices(i));
+    sum += complex.num_simplices(i);
+  }
+  return 
+    complex.num_vertices() == n && 
+    complex.num_edges() == 6 && 
+    sum == 15 && 
+    complex.num_simplices() == 15;
+}
+
+
+bool test_iterator_vertices1() {
+  int n = 10;
+  Complex complex(10);
+  cerr << "complex.num_vertices():" << complex.num_vertices() << endl;
+  int num_vertex_seen = 0;
+  for (auto vi : complex.vertex_range()) {
+    cerr << "vertex:" << vi << endl;
+    ++num_vertex_seen;
+  }
+  return num_vertex_seen == n;
+}
+
+bool test_iterator_vertices2() {
+  int n = 10;
+  Complex complex;
+  build_complete(10, complex);
+  cerr << "complex.num_vertices():" << complex.num_vertices() << endl;
+  cerr << "complex.num_edges():" << complex.num_edges() << endl;
+  int num_vertex_seen = 0;
+  for (auto vi : complex.vertex_range(Vertex_handle(2))) {
+    cerr << "vertex:" << vi << endl;
+    ++num_vertex_seen;
+  }
+  std::cerr << "num_vertex_seen:" << num_vertex_seen << std::endl;
+  return num_vertex_seen == (n - 1);
+}
+
+bool test_iterator_edge() {
+  const int n = 10;
+  Complex complex(n);
+  for (int i = 0; i < n; i++)
+    for (int j = 0; j < i; j++)
+      complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(j));
+  complex.remove_edge(Vertex_handle(2), Vertex_handle(3));
+  complex.remove_edge(Vertex_handle(3), Vertex_handle(5));
+  cerr << "complex.num_edges():" << complex.num_edges() << endl;
+  int num_edges_seen = 0;
+  for (auto edge : complex.edge_range()) {
+    cerr << "edge :" << complex[edge] << endl;
+    ++num_edges_seen;
+  }
+
+  return num_edges_seen == n * (n - 1) / 2 - 2;
+}
+
+bool test_iterator_edge2() {
+  const int n = 10;
+  Complex complex(n);
+  for (int i = 0; i < n; i++)
+    for (int j = 0; j < i; j++)
+      complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(j));
+  complex.remove_edge(Vertex_handle(2), Vertex_handle(3));
+  complex.remove_edge(Vertex_handle(3), Vertex_handle(5));
+  cerr << "complex.num_edges():" << complex.num_edges() << endl;
+  int num_neigbors_seen = 0;
+  for (auto neighbor : complex.vertex_range(Vertex_handle(2))) {
+    cerr << "neighbor" << neighbor << endl;
+    ++num_neigbors_seen;
+  }
+  return num_neigbors_seen == 8;
+}
+
+bool test_iterator_edge3() {
+  const int n = 10;
+  Complex complex(n);
+  for (int i = 0; i < n; i++)
+    for (int j = 0; j < i; j++)
+      complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(j));
+  complex.remove_edge(Vertex_handle(2), Vertex_handle(3));
+  complex.remove_edge(Vertex_handle(3), Vertex_handle(5));
+  cerr << "complex.num_edges():" << complex.num_edges() << endl;
+  int num_neigbors_seen = 0;
+  for (auto edge : complex.edge_range(Vertex_handle(2))) {
+    std::cerr << edge << std::endl;
+    ++num_neigbors_seen;
+  }
+  return num_neigbors_seen == 8;
+}
+
+bool test_iterator_triangles() {
+  const int n = 7;
+  Complex complex(n);
+  //create a "ring" around '0'
+  for (int i = 1; i < n; i++)
+    complex.add_edge_without_blockers(Vertex_handle(0), Vertex_handle(i));
+  for (int i = 1; i < n - 1; i++)
+    complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(i + 1));
+  complex.add_edge_without_blockers(Vertex_handle(1), Vertex_handle(6));
+
+  PRINT(complex.to_string());
+
+  int num_triangles_seen = 0;
+  //for (auto t : complex.triangle_range(5)){
+  TEST("triangles around 5 (should be 2 of them):");
+  for (auto t : complex.triangle_range(Vertex_handle(5))) {
+    PRINT(t);
+    ++num_triangles_seen;
+  }
+  bool test = (num_triangles_seen == 2);
+
+  num_triangles_seen = 0;
+  TEST("triangles around 0 (should be 6 of them):");
+  for (auto t : complex.triangle_range(Vertex_handle(0))) {
+    PRINT(t);
+    ++num_triangles_seen;
+  }
+  test = test && (num_triangles_seen == 6);
+
+  // we now add another triangle
+  complex.add_vertex();
+  complex.add_edge_without_blockers(Vertex_handle(4), Vertex_handle(7));
+  complex.add_edge_without_blockers(Vertex_handle(3), Vertex_handle(7));
+  complex.add_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(6)));
+  num_triangles_seen = 0;
+
+  TEST("triangles (should be 6 of them):");
+  num_triangles_seen = 0;
+  for (auto t : complex.triangle_range()) {
+    PRINT(t);
+    ++num_triangles_seen;
+  }
+  test = test && (num_triangles_seen == 6);
+  PRINT(num_triangles_seen);
+
+  return test;
 }
 
 
-bool test_iterator_simplices3(){
-	Complex complex(3);
-	complex.add_edge(Vertex_handle(0),Vertex_handle(1));
-	complex.add_edge(Vertex_handle(1),Vertex_handle(2));
-	complex.add_edge(Vertex_handle(2),Vertex_handle(0));
-	complex.add_blocker(Simplex_handle(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2)));
-
-	unsigned num_simplices = 0 ;
-
-	for(const auto& simplex : complex.simplex_range(Vertex_handle(0))){
-		simplex.dimension();
-		DBGVALUE(simplex);
-	}
-
+//#include "combinatorics/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h"
 
-	for(const auto& simplex : complex.simplex_range()){
-		DBGVALUE(simplex);
-		simplex.dimension();
-		++num_simplices;
-	}
-	bool correct_number_simplices = (num_simplices == 6);
-	return correct_number_simplices;
+bool test_iterator_simplices() {
+  Complex complex(6);
+  complex.add_edge_without_blockers(Vertex_handle(0), Vertex_handle(1));
+  complex.add_edge_without_blockers(Vertex_handle(1), Vertex_handle(2));
+  complex.add_edge_without_blockers(Vertex_handle(2), Vertex_handle(0));
+  complex.add_edge_without_blockers(Vertex_handle(1), Vertex_handle(3));
+  complex.add_edge_without_blockers(Vertex_handle(2), Vertex_handle(3));
+  complex.add_edge_without_blockers(Vertex_handle(2), Vertex_handle(5));
+  complex.add_edge_without_blockers(Vertex_handle(3), Vertex_handle(5));
+  complex.add_edge_without_blockers(Vertex_handle(2), Vertex_handle(4));
+  complex.add_edge_without_blockers(Vertex_handle(4), Vertex_handle(5));
+  complex.add_edge_without_blockers(Vertex_handle(3), Vertex_handle(4));
+
+  complex.add_blocker(Simplex(Vertex_handle(2), Vertex_handle(3), Vertex_handle(4), Vertex_handle(5)));
+
+  bool correct_number_simplices = true;
+
+  std::map<Vertex_handle, unsigned> expected_num_simplices;
+
+  expected_num_simplices[Vertex_handle(0)] = 4;
+  expected_num_simplices[Vertex_handle(1)] = 6;
+  expected_num_simplices[Vertex_handle(2)] = 11;
+  expected_num_simplices[Vertex_handle(3)] = 9;
+  expected_num_simplices[Vertex_handle(4)] = 7;
+  expected_num_simplices[Vertex_handle(5)] = 7;
+
+  for (auto pair : expected_num_simplices) {
+    unsigned num_simplices_around = 0;
+    for (const auto& simplex : complex.star_simplex_range(pair.first)) {
+      simplex.dimension();
+      DBGVALUE(simplex);
+      ++num_simplices_around;
+    }
+
+    correct_number_simplices = correct_number_simplices && (num_simplices_around == pair.second);
+
+    DBGMSG("current vertex:", pair.first);
+    DBGMSG("expected_num_simplices:", pair.second);
+    DBGMSG("found:", num_simplices_around);
+  }
+  return correct_number_simplices;
+}
+
+bool test_iterator_simplices2() {
+  Complex complex(2);
+  complex.add_edge_without_blockers(Vertex_handle(0), Vertex_handle(1));
+
+  for (const auto& s : complex.triangle_range()) {
+    s.dimension();
+    return false; // there are no triangles
+  }
+
+  unsigned num_simplices = 0;
+
+
+  DBGVALUE(complex.to_string());
+
+  for (const auto& simplex : complex.star_simplex_range(Vertex_handle(0))) {
+    simplex.dimension();
+    DBGVALUE(simplex);
+  }
+
+
+  for (const auto& simplex : complex.complex_simplex_range()) {
+    DBGVALUE(simplex);
+    simplex.dimension();
+    ++num_simplices;
+  }
+  bool correct_number_simplices = (num_simplices == 3);
+  return correct_number_simplices;
+}
+
+bool test_iterator_simplices3() {
+  Complex complex(3);
+  complex.add_edge_without_blockers(Vertex_handle(0), Vertex_handle(1));
+  complex.add_edge_without_blockers(Vertex_handle(1), Vertex_handle(2));
+  complex.add_edge_without_blockers(Vertex_handle(2), Vertex_handle(0));
+  complex.add_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2)));
+
+  unsigned num_simplices = 0;
+
+  for (const auto& simplex : complex.star_simplex_range(Vertex_handle(0))) {
+    simplex.dimension();
+    DBGVALUE(simplex);
+  }
+
+
+  for (const auto& simplex : complex.complex_simplex_range()) {
+    DBGVALUE(simplex);
+    simplex.dimension();
+    ++num_simplices;
+  }
+  bool correct_number_simplices = (num_simplices == 6);
+  return correct_number_simplices;
+}
+
+bool test_iterator_simplices4() {
+  Complex empty_complex;
+  for (auto v : empty_complex.vertex_range()) {
+    (void) v;
+  }
+  for (auto e : empty_complex.edge_range()) {
+    empty_complex[e];
+  }
+  for (auto t : empty_complex.triangle_range()) {
+    t.dimension();
+  }
+  for (auto s : empty_complex.complex_simplex_range()) {
+    s.dimension();
+  }
+  return true;
 }
 
-bool test_iterator_simplices4(){
-	Complex empty_complex;
-	for(auto v : empty_complex.vertex_range()){
-		v;
-	}
-	for(auto e : empty_complex.edge_range()){
-		empty_complex[e];
-	}
-	for(auto t : empty_complex.triangle_range()){
-		t.dimension();
-	}
-	for(auto s : empty_complex.simplex_range()){
-		s.dimension();
-	}
-	return true;
+bool test_iterator_coboundary() {
+  Complex c;
+  build_complete(4, c);
+  c.remove_edge(Vertex_handle(1), Vertex_handle(3));
+  PRINT(c.to_string());
+  Simplex s02(Vertex_handle(0), Vertex_handle(2));
+  int n = 0;
+  std::set<Simplex> expected;
+  expected.insert(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2)));
+  expected.insert(Simplex(Vertex_handle(0), Vertex_handle(2), Vertex_handle(3)));
+  for (const auto & s : c.coboundary_range(s02)) {
+    PRINT(s);
+    if (expected.find(s) == expected.end())
+      return false;
+    ++n;
+  }
+  return n == 2;
 }
 
 
 
 
-
 template<typename Map>
-auto blocker_range(Map map) -> decltype( map | boost::adaptors::map_values){
-	return map| boost::adaptors::map_values ;
-}
-
-
-bool test_iterator_blockers(){
-	Complex complex;
-	Simplex_handle alpha;
-	Simplex_handle vertex_set_expected;
-	// Build the complexes
-	for (int i=0;i<20;i++){
-		complex.add_vertex();
-	}
-	for (int i=10;i<15;i++){
-		for (int j=i+1;j<15;j++)
-			complex.add_edge(Vertex_handle(i),Vertex_handle(j));
-	}
-
-	complex.add_blocker(Simplex_handle(Vertex_handle(10),Vertex_handle(11),Vertex_handle(12)));
-	complex.add_blocker(Simplex_handle(Vertex_handle(2),Vertex_handle(1),Vertex_handle(10)));
-	complex.add_blocker(Simplex_handle(Vertex_handle(10),Vertex_handle(9),Vertex_handle(15)));
-	complex.add_blocker(Simplex_handle(Vertex_handle(1),Vertex_handle(9),Vertex_handle(8)));
-
-	// Print result
-	int num_blockers=0;
-	for(auto blockers : complex.blocker_range(Vertex_handle(10))){
-		TESTVALUE(*blockers) ;
-		num_blockers++;
-	}
-	bool test = (num_blockers==3);
-
-	num_blockers=0;
-	for (auto blockers : complex.blocker_range()){
-		TESTVALUE(*blockers) ;
-		num_blockers++;
-	}
-	test = test && (num_blockers==4) ;
-
-	return test;
-}
-
-
-bool test_link0(){
-
-	enum { a, b, c, d, n };
-	Complex complex(n);
-	complex.add_edge(Vertex_handle(b),Vertex_handle(c));complex.add_edge(Vertex_handle(c),Vertex_handle(d));
-	Simplex_handle alpha = Simplex_handle(Vertex_handle(c));
-	Skeleton_blocker_link_complex<Complex> L(complex,alpha);
-
-	auto L2 = complex.link(alpha);
-	if(L!=L2) return false;
-
-	PRINT(L.num_vertices());
-	PRINT(L.to_string());
-
-	bool test1 = L.contains_vertex(*L.get_address(Root_vertex_handle(b)));
-	bool test2 = L.contains_vertex(*L.get_address(Root_vertex_handle(d)));
-	bool test3 = L.num_edges()==0;
-	bool test4 = L.num_blockers()==0;
-	return test1&&test2&&test3&&test4;
-
-}
-
-bool test_link1(){
-	Complex complex;
-
-
-	// Build the complexes
-	for (int i=0;i<20;i++){
-		complex.add_vertex();
-	}
-	for (int i=10;i<15;i++){
-		for (int j=i+1;j<15;j++)
-			complex.add_edge(Vertex_handle(i),Vertex_handle(j));
-	}
-	Simplex_handle alpha(Vertex_handle(12),Vertex_handle(14));
-	Skeleton_blocker_link_complex<Complex> L(complex,alpha);
-	// Complexes built
-
-	auto L2 = complex.link(alpha);
-	if(L!=L2) return false;
-
-	// verification
-	bool test1 = L.contains_vertex(*L.get_address(Root_vertex_handle(10)));
-	bool test2 = L.contains_vertex(*L.get_address(Root_vertex_handle(11)));
-	bool test3 = L.contains_vertex(*L.get_address(Root_vertex_handle(13)));
-	bool test4 = L.num_edges()==3;
-	bool test5 = L.num_blockers()==0;
-	Root_simplex_handle simplex;
-	simplex.add_vertex(Root_vertex_handle(10));
-	simplex.add_vertex(Root_vertex_handle(11));
-	simplex.add_vertex(Root_vertex_handle(13));
-	bool test6(L.get_simplex_address(simplex));
-	bool test7 = L.contains(*(L.get_simplex_address(simplex)));
-	cerr <<"----> Ocomplex \n";
-	return test1&&test2&&test3&&test4&&test5&&test6&&test7 ;
-
-}
-
-
-bool test_link2(){
-	Complex complex;
-
-	Simplex_handle alpha;
-	Simplex_handle vertex_set_expected;
-	// Build the complexes
-	for (int i=0;i<20;i++){
-		complex.add_vertex();
-	}
-	for (int i=10;i<15;i++){
-		for (int j=i+1;j<15;j++)
-			complex.add_edge(Vertex_handle(i),Vertex_handle(j));
-	}
-	complex.add_blocker(Simplex_handle(Vertex_handle(10),Vertex_handle(11),Vertex_handle(13)));
-	alpha = Simplex_handle(Vertex_handle(12),Vertex_handle(14));
-	Skeleton_blocker_link_complex<Complex> L(complex,alpha);
-	// Complexes built
-
-	// Print result
-	cerr << "complex complex"<< complex.to_string();
-	cerr <<endl<<endl;
-	cerr << "L= Link_complex("<<alpha<<") : \n"<<L.to_string();
-
-	auto L2 = complex.link(alpha);
-	if(L!=L2) return false;
-
-
-	// verification
-	bool test1 = L.contains_vertex(*L.get_address(Root_vertex_handle(10)));
-	bool test2 = L.contains_vertex(*L.get_address(Root_vertex_handle(11)));
-	bool test3 = L.contains_vertex(*L.get_address(Root_vertex_handle(13)));
-	bool test4 = L.num_edges()==3;
-	bool test5 = L.num_blockers()==1;
-	Root_simplex_handle simplex;
-	simplex.add_vertex(Root_vertex_handle(10));
-	simplex.add_vertex(Root_vertex_handle(11));
-	simplex.add_vertex(Root_vertex_handle(13));
-	bool test6 = L.contains_blocker(*(L.get_simplex_address(simplex)));
-	cerr <<"----> Ocomplex \n";
-	return test1&&test2&&test3&&test4&&test5&&test6 ;
-}
-
-bool test_link3(){
-	Complex complex;
-
-	Simplex_handle alpha;
-	Simplex_handle vertex_set_expected;
-	// Build the complexes
-	for (int i=0;i<20;i++){
-		complex.add_vertex();
-	}
-	for (int i=10;i<15;i++){
-		for (int j=i+1;j<15;j++)
-			complex.add_edge(Vertex_handle(i),Vertex_handle(j));
-	}
-	complex.add_blocker(Simplex_handle(Vertex_handle(10),Vertex_handle(11),Vertex_handle(12)));
-	alpha = Simplex_handle(Vertex_handle(12),Vertex_handle(14));
-	Skeleton_blocker_link_complex<Complex> L(complex,alpha);
-	// Complexes built
-
-	// Print result
-	cerr << "complex complex"<< complex.to_string();
-	cerr <<endl<<endl;
-	cerr << "L= Link_complex("<<alpha<<") : \n"<<L.to_string();
-
-	auto L2 = complex.link(alpha);
-	if(L!=L2) return false;
-
-
-	// verification
-	bool test = assert_vertex(L,*L.get_address(Root_vertex_handle(10)));
-	test = test&& assert_vertex(L,*L.get_address(Root_vertex_handle(11)));
-	test = test&& assert_vertex(L,*L.get_address(Root_vertex_handle(13)));
-	test = test&& L.num_edges()==2;
-	test = test&&L.contains_edge(*L.get_address(Root_vertex_handle(10)),*L.get_address(Root_vertex_handle(13)));
-	test=test&&L.contains_edge(*L.get_address(Root_vertex_handle(13)),*L.get_address(Root_vertex_handle(11)));
-	test=test&&L.num_blockers()==0;
-	return test;
-}
-
-bool test_link4(){
-	Complex complex;
-
-	// Build the complexes
-	for (int i=0;i<20;i++){
-		complex.add_vertex();
-	}
-	for (int i=10;i<15;i++){
-		for (int j=i+1;j<15;j++)
-			complex.add_edge(Vertex_handle(i),Vertex_handle(j));
-	}
-	complex.add_blocker(Simplex_handle(Vertex_handle(10),Vertex_handle(11),Vertex_handle(12),Vertex_handle(13)));
-	Simplex_handle alpha(Vertex_handle(12),Vertex_handle(14));
-	Skeleton_blocker_link_complex<Complex> L(complex,alpha);
-	// Complexes built
-
-	// verification
-	bool test1 = L.contains_vertex(*L.get_address(Root_vertex_handle(10)));
-	bool test2 = L.contains_vertex(*L.get_address(Root_vertex_handle(11)));
-	bool test3 = L.contains_vertex(*L.get_address(Root_vertex_handle(13)));
-	bool test4 = L.num_edges()==3;
-	bool test5 = L.num_blockers()==1;
-	Root_simplex_handle simplex;
-	simplex.add_vertex(Root_vertex_handle(10));
-	simplex.add_vertex(Root_vertex_handle(11));
-	simplex.add_vertex(Root_vertex_handle(13));
-	bool test6 = L.contains_blocker(*(L.get_simplex_address(simplex)));
-	cerr <<"----> Ocomplex \n";
-	return test1&&test2&&test3&&test4&&test5&&test6 ;
-
-}
-
-bool test_link5(){
-	Complex complex(0,new Print_complex_visitor<Vertex_handle>());
-	// Build the complexes
-	build_complete(4,complex);
-	complex.add_blocker(Simplex_handle(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2),Vertex_handle(3)));
-
-	Simplex_handle alpha(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2));
+auto blocker_range(Map map) -> decltype(map | boost::adaptors::map_values) {
+  return map | boost::adaptors::map_values;
+}
+
+bool test_iterator_blockers() {
+  Complex complex;
+  Simplex alpha;
+  Simplex vertex_set_expected;
+  // Build the complexes
+  for (int i = 0; i < 20; i++) {
+    complex.add_vertex();
+  }
+  for (int i = 10; i < 15; i++) {
+    for (int j = i + 1; j < 15; j++)
+      complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(j));
+  }
+
+  complex.add_blocker(Simplex(Vertex_handle(10), Vertex_handle(11), Vertex_handle(12)));
+  complex.add_blocker(Simplex(Vertex_handle(2), Vertex_handle(1), Vertex_handle(10)));
+  complex.add_blocker(Simplex(Vertex_handle(10), Vertex_handle(9), Vertex_handle(15)));
+  complex.add_blocker(Simplex(Vertex_handle(1), Vertex_handle(9), Vertex_handle(8)));
+
+  // Print result
+  int num_blockers = 0;
+  for (auto blockers : complex.blocker_range(Vertex_handle(10))) {
+    TESTVALUE(*blockers);
+    num_blockers++;
+  }
+  bool test = (num_blockers == 3);
+
+  num_blockers = 0;
+  for (auto blockers : complex.blocker_range()) {
+    TESTVALUE(*blockers);
+    num_blockers++;
+  }
+  test = test && (num_blockers == 4);
+
+  return test;
+}
+
+bool test_link0() {
+
+  enum {
+    a, b, c, d, n
+  };
+  Complex complex(n);
+  complex.add_edge_without_blockers(Vertex_handle(b), Vertex_handle(c));
+  complex.add_edge_without_blockers(Vertex_handle(c), Vertex_handle(d));
+  Simplex alpha = Simplex(Vertex_handle(c));
+  Skeleton_blocker_link_complex<Complex> L(complex, alpha);
+
+  auto L2 = complex.link(alpha);
+  if (L != L2) return false;
+
+  PRINT(L.num_vertices());
+  PRINT(L.to_string());
+
+  bool test1 = L.contains_vertex(*L.get_address(Root_vertex_handle(b)));
+  bool test2 = L.contains_vertex(*L.get_address(Root_vertex_handle(d)));
+  bool test3 = L.num_edges() == 0;
+  bool test4 = L.num_blockers() == 0;
+  return test1 && test2 && test3&&test4;
+
+}
+
+bool test_link1() {
+  Complex complex;
+
+
+  // Build the complexes
+  for (int i = 0; i < 20; i++) {
+    complex.add_vertex();
+  }
+  for (int i = 10; i < 15; i++) {
+    for (int j = i + 1; j < 15; j++)
+      complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(j));
+  }
+  Simplex alpha(Vertex_handle(12), Vertex_handle(14));
+  Skeleton_blocker_link_complex<Complex> L(complex, alpha);
+  // Complexes built
+
+  auto L2 = complex.link(alpha);
+  if (L != L2) return false;
+
+  // verification
+  bool test1 = L.contains_vertex(*L.get_address(Root_vertex_handle(10)));
+  bool test2 = L.contains_vertex(*L.get_address(Root_vertex_handle(11)));
+  bool test3 = L.contains_vertex(*L.get_address(Root_vertex_handle(13)));
+  bool test4 = L.num_edges() == 3;
+  bool test5 = L.num_blockers() == 0;
+  Root_simplex_handle simplex;
+  simplex.add_vertex(Root_vertex_handle(10));
+  simplex.add_vertex(Root_vertex_handle(11));
+  simplex.add_vertex(Root_vertex_handle(13));
+  bool test6(L.get_simplex_address(simplex));
+  bool test7 = L.contains(*(L.get_simplex_address(simplex)));
+  cerr << "----> Ocomplex \n";
+  return test1 && test2 && test3 && test4 && test5 && test6&&test7;
+
+}
+
+bool test_link2() {
+  Complex complex;
+
+  Simplex alpha;
+  Simplex vertex_set_expected;
+  // Build the complexes
+  for (int i = 0; i < 20; i++) {
+    complex.add_vertex();
+  }
+  for (int i = 10; i < 15; i++) {
+    for (int j = i + 1; j < 15; j++)
+      complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(j));
+  }
+  complex.add_blocker(Simplex(Vertex_handle(10), Vertex_handle(11), Vertex_handle(13)));
+  alpha = Simplex(Vertex_handle(12), Vertex_handle(14));
+  Skeleton_blocker_link_complex<Complex> L(complex, alpha);
+  // Complexes built
+
+  // Print result
+  cerr << "complex complex" << complex.to_string();
+  cerr << endl << endl;
+  cerr << "L= Link_complex(" << alpha << ") : \n" << L.to_string();
+
+  auto L2 = complex.link(alpha);
+  if (L != L2) return false;
+
+
+  // verification
+  bool test1 = L.contains_vertex(*L.get_address(Root_vertex_handle(10)));
+  bool test2 = L.contains_vertex(*L.get_address(Root_vertex_handle(11)));
+  bool test3 = L.contains_vertex(*L.get_address(Root_vertex_handle(13)));
+  bool test4 = L.num_edges() == 3;
+  bool test5 = L.num_blockers() == 1;
+  Root_simplex_handle simplex;
+  simplex.add_vertex(Root_vertex_handle(10));
+  simplex.add_vertex(Root_vertex_handle(11));
+  simplex.add_vertex(Root_vertex_handle(13));
+  bool test6 = L.contains_blocker(*(L.get_simplex_address(simplex)));
+  cerr << "----> Ocomplex \n";
+  return test1 && test2 && test3 && test4 && test5&&test6;
+}
+
+bool test_link3() {
+  Complex complex;
+
+  Simplex alpha;
+  Simplex vertex_set_expected;
+  // Build the complexes
+  for (int i = 0; i < 20; i++) {
+    complex.add_vertex();
+  }
+  for (int i = 10; i < 15; i++) {
+    for (int j = i + 1; j < 15; j++)
+      complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(j));
+  }
+  complex.add_blocker(Simplex(Vertex_handle(10), Vertex_handle(11), Vertex_handle(12)));
+  alpha = Simplex(Vertex_handle(12), Vertex_handle(14));
+  Skeleton_blocker_link_complex<Complex> L(complex, alpha);
+  // Complexes built
+
+  // Print result
+  cerr << "complex complex" << complex.to_string();
+  cerr << endl << endl;
+  cerr << "L= Link_complex(" << alpha << ") : \n" << L.to_string();
+
+  auto L2 = complex.link(alpha);
+  if (L != L2) return false;
+
+
+  // verification
+  bool test = assert_vertex(L, *L.get_address(Root_vertex_handle(10)));
+  test = test && assert_vertex(L, *L.get_address(Root_vertex_handle(11)));
+  test = test && assert_vertex(L, *L.get_address(Root_vertex_handle(13)));
+  test = test && L.num_edges() == 2;
+  test = test && L.contains_edge(*L.get_address(Root_vertex_handle(10)), *L.get_address(Root_vertex_handle(13)));
+  test = test && L.contains_edge(*L.get_address(Root_vertex_handle(13)), *L.get_address(Root_vertex_handle(11)));
+  test = test && L.num_blockers() == 0;
+  return test;
+}
+
+bool test_link4() {
+  Complex complex;
+
+  // Build the complexes
+  for (int i = 0; i < 20; i++) {
+    complex.add_vertex();
+  }
+  for (int i = 10; i < 15; i++) {
+    for (int j = i + 1; j < 15; j++)
+      complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(j));
+  }
+  complex.add_blocker(Simplex(Vertex_handle(10), Vertex_handle(11), Vertex_handle(12), Vertex_handle(13)));
+  Simplex alpha(Vertex_handle(12), Vertex_handle(14));
+  Skeleton_blocker_link_complex<Complex> L(complex, alpha);
+  // Complexes built
+
+  // verification
+  bool test1 = L.contains_vertex(*L.get_address(Root_vertex_handle(10)));
+  bool test2 = L.contains_vertex(*L.get_address(Root_vertex_handle(11)));
+  bool test3 = L.contains_vertex(*L.get_address(Root_vertex_handle(13)));
+  bool test4 = L.num_edges() == 3;
+  bool test5 = L.num_blockers() == 1;
+  Root_simplex_handle simplex;
+  simplex.add_vertex(Root_vertex_handle(10));
+  simplex.add_vertex(Root_vertex_handle(11));
+  simplex.add_vertex(Root_vertex_handle(13));
+  bool test6 = L.contains_blocker(*(L.get_simplex_address(simplex)));
+  cerr << "----> Ocomplex \n";
+  return test1 && test2 && test3 && test4 && test5&&test6;
+
+}
+
+bool test_link5() {
+  Complex complex(0, new Print_complex_visitor<Vertex_handle>());
+  // Build the complexes
+  build_complete(4, complex);
+  complex.add_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2), Vertex_handle(3)));
+
+  Simplex alpha(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2));
+
+
+  Skeleton_blocker_link_complex<Complex> L(complex, alpha); // Complexes built
+
+  // Print result
+  PRINT(complex.to_string());
+  cerr << endl << endl;
+  PRINT(L.to_string());
+
+  // verification
+  return L.num_vertices() == 0;
+}
+
+bool test_link6() {
+  Complex complex(0, new Print_complex_visitor<Vertex_handle>());
+  // Build the complexes
+  build_complete(4, complex);
+  complex.add_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2)));
 
+  Simplex alpha(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2));
 
-	Skeleton_blocker_link_complex<Complex> L(complex,alpha);	// Complexes built
+  Skeleton_blocker_link_complex<Complex> link_blocker_alpha;
 
-	// Print result
-	PRINT(complex.to_string());
-	cerr <<endl<<endl;
-	PRINT(L.to_string());
+  build_link_of_blocker(complex, alpha, link_blocker_alpha);
+
+  // Print result
+  PRINT(complex.to_string());
+  cerr << endl << endl;
+  PRINT(link_blocker_alpha.to_string());
 
-	// verification
-	return L.num_vertices()==0;
+  // verification
+  return link_blocker_alpha.num_vertices() == 1;
 }
 
-bool test_link6(){
-	Complex complex(0,new Print_complex_visitor<Vertex_handle>());
-	// Build the complexes
-	build_complete(4,complex);
-	complex.add_blocker(Simplex_handle(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2)));
+bool test_link7() {
+  Complex complex(0, new Print_complex_visitor<Vertex_handle>());
+  // Build the complexes
+  build_complete(6, complex);
+  complex.add_vertex();
+  complex.add_vertex();
+  for (int i = 3; i < 6; ++i) {
+    complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(6));
+    complex.add_edge_without_blockers(Vertex_handle(i), Vertex_handle(7));
+  }
+  complex.add_edge_without_blockers(Vertex_handle(6), Vertex_handle(7));
+  complex.add_blocker(Simplex(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2)));
+  complex.add_blocker(Simplex(Vertex_handle(3), Vertex_handle(4), Vertex_handle(5)));
 
-	Simplex_handle alpha(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2));
+  Simplex alpha(Vertex_handle(3), Vertex_handle(4), Vertex_handle(5));
 
-	Skeleton_blocker_link_complex<Complex> link_blocker_alpha;
+  Skeleton_blocker_link_complex<Complex> link_blocker_alpha;
 
-	build_link_of_blocker(complex,alpha,link_blocker_alpha);
+  build_link_of_blocker(complex, alpha, link_blocker_alpha);
 
-	// Print result
-	PRINT(complex.to_string());
-	cerr <<endl<<endl;
-	PRINT(link_blocker_alpha.to_string());
+  //the result should be the edge {6,7} plus the blocker {0,1,2}
 
-	// verification
-	return link_blocker_alpha.num_vertices()==1;
-}
-
-
-bool test_link7(){
-	Complex complex(0,new Print_complex_visitor<Vertex_handle>());
-	// Build the complexes
-	build_complete(6,complex);
-	complex.add_vertex();
-	complex.add_vertex();
-	for(int i = 3; i<6; ++i){
-		complex.add_edge(Vertex_handle(i),Vertex_handle(6));
-		complex.add_edge(Vertex_handle(i),Vertex_handle(7));
-	}
-	complex.add_edge(Vertex_handle(6),Vertex_handle(7));
-	complex.add_blocker(Simplex_handle(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2)));
-	complex.add_blocker(Simplex_handle(Vertex_handle(3),Vertex_handle(4),Vertex_handle(5)));
-
-	Simplex_handle alpha(Vertex_handle(3),Vertex_handle(4),Vertex_handle(5));
-
-	Skeleton_blocker_link_complex<Complex> link_blocker_alpha;
-
-	build_link_of_blocker(complex,alpha,link_blocker_alpha);
+  // Print result
+  PRINT(complex.to_string());
+  cerr << endl << endl;
+  DBGVALUE(link_blocker_alpha.to_string());
 
-	//the result should be the edge {6,7} plus the blocker {0,1,2}
+  Skeleton_blocker_link_complex<Complex> link_blocker_alpha_cpy = link_blocker_alpha;
 
-	// Print result
-	PRINT(complex.to_string());
-	cerr <<endl<<endl;
-	DBGVALUE(link_blocker_alpha.to_string());
+  DBGVALUE(link_blocker_alpha_cpy.to_string());
 
-	Skeleton_blocker_link_complex<Complex> link_blocker_alpha_cpy = link_blocker_alpha;
+  bool equal_complexes =
+      (link_blocker_alpha.num_vertices() == link_blocker_alpha_cpy.num_vertices())
+      &&(link_blocker_alpha.num_blockers() == link_blocker_alpha_cpy.num_blockers())
+      &&(link_blocker_alpha.num_edges() == link_blocker_alpha_cpy.num_edges())
+      ;
+  DBGVALUE((link_blocker_alpha.num_blockers() == link_blocker_alpha_cpy.num_blockers()));
+  DBGVALUE((link_blocker_alpha.num_blockers()));
+  DBGVALUE((link_blocker_alpha_cpy.num_blockers()));
 
-	DBGVALUE(link_blocker_alpha_cpy.to_string());
+  DBGVALUE(equal_complexes);
 
-	bool equal_complexes =
-			(link_blocker_alpha.num_vertices() == link_blocker_alpha_cpy.num_vertices())
-			&&(link_blocker_alpha.num_blockers() == link_blocker_alpha_cpy.num_blockers())
-			&&(link_blocker_alpha.num_edges() == link_blocker_alpha_cpy.num_edges())
-			;
-	DBGVALUE((link_blocker_alpha.num_blockers() == link_blocker_alpha_cpy.num_blockers()));
-	DBGVALUE((link_blocker_alpha.num_blockers() ));
-	DBGVALUE(( link_blocker_alpha_cpy.num_blockers()));
-
-	DBGVALUE(equal_complexes);
-
-	// verification
-	return link_blocker_alpha.num_vertices()==5 && link_blocker_alpha.num_edges()==4 && link_blocker_alpha.num_blockers()==1 && equal_complexes;
+  // verification
+  return link_blocker_alpha.num_vertices() == 5 && link_blocker_alpha.num_edges() == 4 && link_blocker_alpha.num_blockers() == 1 && equal_complexes;
 }
 
-
-
-
-
-
-
-
 template<typename SimplexHandle>
-void add_triangle_edges(int a,int b,int c,list<SimplexHandle>& simplices){
-	typedef SimplexHandle Simplex_handle;
-	typedef typename SimplexHandle::Vertex_handle Vertex_handle;
+void add_triangle_edges(int a, int b, int c, list<SimplexHandle>& simplices) {
+  typedef SimplexHandle Simplex;
+  typedef typename SimplexHandle::Vertex_handle Vertex_handle;
 
-	simplices.push_back(Simplex_handle(Vertex_handle(a),Vertex_handle(b) ));
-	simplices.push_back(Simplex_handle(Vertex_handle(b),Vertex_handle(c) ));
-	simplices.push_back(Simplex_handle(Vertex_handle(c),Vertex_handle(a) ));
+  simplices.push_back(Simplex(Vertex_handle(a), Vertex_handle(b)));
+  simplices.push_back(Simplex(Vertex_handle(b), Vertex_handle(c)));
+  simplices.push_back(Simplex(Vertex_handle(c), Vertex_handle(a)));
 }
 
 template<typename SimplexHandle>
-void add_triangle(int a,int b,int c,list<SimplexHandle>& simplices){
-	typedef SimplexHandle Simplex_handle;
-	typedef typename SimplexHandle::Vertex_handle Vertex_handle;
-	simplices.push_back(Simplex_handle(Vertex_handle(a),Vertex_handle(b),Vertex_handle(c)));
-}
-
-bool test_constructor(){
-	list <Simplex_handle> simplices;
-
-	simplices.push_back(Simplex_handle(Vertex_handle(0)));
-	simplices.push_back(Simplex_handle(Vertex_handle(1)));
-	simplices.push_back(Simplex_handle(Vertex_handle(2)));
-	simplices.push_back(Simplex_handle(Vertex_handle(3)));
-	simplices.push_back(Simplex_handle(Vertex_handle(4)));
-	simplices.push_back(Simplex_handle(Vertex_handle(5)));
-
-	simplices.push_back(Simplex_handle(Vertex_handle(3),Vertex_handle(5) ));
-
-	add_triangle_edges(0,1,5,simplices);
-	add_triangle_edges(1,2,3,simplices);
-	add_triangle_edges(2,3,4,simplices);
-	add_triangle_edges(1,3,4,simplices);
-	add_triangle_edges(1,2,4,simplices);
-
-
-	add_triangle(0,1,5,simplices);
-	add_triangle(1,2,3,simplices);
-	add_triangle(1,3,4,simplices);
-	add_triangle(1,2,4,simplices);
-	add_triangle(2,3,4,simplices);
-
-	Complex complex(simplices.begin(),simplices.end());
-
-	PRINT(complex.to_string());
-
-	return ( complex.num_vertices()==6&&complex.num_edges()==10&&  complex.num_blockers()==2);
-}
-
-
-list<Simplex_handle> subfaces(Simplex_handle top_face){
-	list<Simplex_handle> res;
-	if(top_face.dimension()==-1) return res;
-	if(top_face.dimension()==0) {
-		res.push_back(top_face);
-		return res;
-	}
-	else{
-		Vertex_handle first_vertex = top_face.first_vertex();
-		top_face.remove_vertex(first_vertex);
-		res = subfaces(top_face);
-		list<Simplex_handle> copy = res;
-		for(auto& simplex : copy){
-			simplex.add_vertex(first_vertex);
-		}
-		res.push_back(Simplex_handle(first_vertex));
-		res.splice(res.end(),copy);
-		return res;
-	}
-}
-
-
-bool test_constructor2(){
-	Simplex_handle simplex;
-	for(int i =0 ; i < 5;++i)
-		simplex.add_vertex(static_cast<Vertex_handle>(i));
-
-	list <Simplex_handle> simplices(subfaces(simplex));
-	simplices.remove(simplex);
-
-	Complex complex(simplices.begin(),simplices.end());
-
-	PRINT(complex.to_string());
-
-	for(auto b : complex.const_blocker_range()){
-		cout << "b:"<<b<<endl;
-	}
-
-	return ( complex.num_vertices()==5&&complex.num_edges()==10&&  complex.num_blockers()==1);
+void add_triangle(int a, int b, int c, list<SimplexHandle>& simplices) {
+  typedef SimplexHandle Simplex;
+  typedef typename SimplexHandle::Vertex_handle Vertex_handle;
+  simplices.push_back(Simplex(Vertex_handle(a), Vertex_handle(b), Vertex_handle(c)));
 }
 
+bool test_constructor() {
+  list <Simplex> simplices;
 
-bool test_constructor3(){
-	typedef Vertex_handle Vh;
-	typedef Simplex_handle Sh;
-	std::vector<Simplex_handle> simplices;
-	auto subf(subfaces(Sh(Vh(0),Vh(1),Vh(2))));
-	subf.pop_back(); //remove max face -> now a blocker 012
-	simplices.insert(simplices.begin(),subf.begin(),subf.end());
-	DBGCONT(simplices);
-	Complex complex(simplices.begin(),simplices.end());
-
-	DBGVALUE(complex.to_string());
+  simplices.push_back(Simplex(Vertex_handle(0)));
+  simplices.push_back(Simplex(Vertex_handle(1)));
+  simplices.push_back(Simplex(Vertex_handle(2)));
+  simplices.push_back(Simplex(Vertex_handle(3)));
+  simplices.push_back(Simplex(Vertex_handle(4)));
+  simplices.push_back(Simplex(Vertex_handle(5)));
 
-	if(complex.num_blockers()!=1) return false;
-		Sh expected_blocker(Vh(0),Vh(1),Vh(2));
-		for(auto b : complex.const_blocker_range())
-			if(*b!=expected_blocker) return false;
+  simplices.push_back(Simplex(Vertex_handle(3), Vertex_handle(5)));
 
+  add_triangle_edges(0, 1, 5, simplices);
+  add_triangle_edges(1, 2, 3, simplices);
+  add_triangle_edges(2, 3, 4, simplices);
+  add_triangle_edges(1, 3, 4, simplices);
+  add_triangle_edges(1, 2, 4, simplices);
 
-	return complex.num_vertices()==3 && complex.num_blockers()==1;
-}
-
-bool test_constructor4(){
-	typedef Vertex_handle Vh;
-	typedef Simplex_handle Sh;
-	std::vector<Simplex_handle> simplices;
-	auto subf(subfaces(Sh(Vh(0),Vh(1),Vh(2),Vh(3))));
-	simplices.insert(simplices.begin(),subf.begin(),subf.end());
 
-	simplices.push_back(Sh(Vh(4)));
-	simplices.push_back(Sh(Vh(4),Vh(1)));
-	simplices.push_back(Sh(Vh(4),Vh(0)));
+  add_triangle(0, 1, 5, simplices);
+  add_triangle(1, 2, 3, simplices);
+  add_triangle(1, 3, 4, simplices);
+  add_triangle(1, 2, 4, simplices);
+  add_triangle(2, 3, 4, simplices);
 
-	DBGCONT(simplices);
-	Complex complex(simplices.begin(),simplices.end());
+  Complex complex(simplices.begin(), simplices.end());
 
-	DBGVALUE(complex.to_string());
-	if(complex.num_blockers()!=1) return false;
-		Sh expected_blocker(Vh(0),Vh(1),Vh(4));
-		for(auto b : complex.const_blocker_range())
-			if(*b!=expected_blocker) return false;
+  PRINT(complex.to_string());
 
-	return complex.num_vertices()==5 && complex.num_blockers()==1 && complex.num_edges()==8;
+  return ( complex.num_vertices() == 6 && complex.num_edges() == 10 && complex.num_blockers() == 2);
 }
 
-
-
-bool test_constructor5(){
-	typedef Vertex_handle Vh;
-	typedef Simplex_handle Sh;
-	std::vector<Simplex_handle> simplices;
-	auto subf(subfaces(Sh(Vh(0),Vh(1),Vh(2))));
-	simplices.insert(simplices.begin(),subf.begin(),subf.end());
-
-	simplices.push_back(Sh(Vh(3)));
-	simplices.push_back(Sh(Vh(3),Vh(1)));
-	simplices.push_back(Sh(Vh(3),Vh(2)));
-	simplices.push_back(Sh(Vh(4)));
-	simplices.push_back(Sh(Vh(4),Vh(1)));
-	simplices.push_back(Sh(Vh(4),Vh(0)));
-	simplices.push_back(Sh(Vh(5)));
-	simplices.push_back(Sh(Vh(5),Vh(2)));
-	simplices.push_back(Sh(Vh(5),Vh(0)));
-
-	DBGCONT(simplices);
-	Complex complex(simplices.begin(),simplices.end());
-
-	DBGVALUE(complex.to_string());
-
-	return complex.num_vertices()==6 && complex.num_blockers()==3 && complex.num_edges()==9;
+list<Simplex> subfaces(Simplex top_face) {
+  list<Simplex> res;
+  if (top_face.dimension() == -1) return res;
+  if (top_face.dimension() == 0) {
+    res.push_back(top_face);
+    return res;
+  } else {
+    Vertex_handle first_vertex = top_face.first_vertex();
+    top_face.remove_vertex(first_vertex);
+    res = subfaces(top_face);
+    list<Simplex> copy = res;
+    for (auto& simplex : copy) {
+      simplex.add_vertex(first_vertex);
+    }
+    res.push_back(Simplex(first_vertex));
+    res.splice(res.end(), copy);
+    return res;
+  }
 }
 
+bool test_constructor2() {
+  Simplex simplex;
+  for (int i = 0; i < 5; ++i)
+    simplex.add_vertex(static_cast<Vertex_handle> (i));
 
-bool test_constructor6(){
-	typedef Vertex_handle Vh;
-	typedef Simplex_handle Sh;
-	std::vector<Simplex_handle> simplices;
-	auto subf(subfaces(Sh(Vh(0),Vh(1),Vh(2),Vh(3))));
-	for(auto s:subf){
-		Sh s1(Vh(0),Vh(1),Vh(2),Vh(3));
-		Sh s2(Vh(1),Vh(2),Vh(3));
-		if(s!=s1 && s!=s2) simplices.push_back(s);
-	}
+  list <Simplex> simplices(subfaces(simplex));
+  simplices.remove(simplex);
 
-	DBGCONT(simplices);
-	Complex complex(simplices.begin(),simplices.end());
+  Complex complex(simplices.begin(), simplices.end());
 
-	DBGVALUE(complex.to_string());
+  PRINT(complex.to_string());
 
-	if(complex.num_blockers()!=1) return false;
-	Sh expected_blocker(Vh(1),Vh(2),Vh(3));
-	for(auto b : complex.const_blocker_range())
-		if(*b!=expected_blocker) return false;
-	return complex.num_vertices()==4 && complex.num_blockers()==1 && complex.num_edges()==6;
-}
+  for (auto b : complex.const_blocker_range()) {
+    cout << "b:" << b << endl;
+  }
 
-
-bool test_constructor7(){
-	typedef Vertex_handle Vh;
-	typedef Simplex_handle Sh;
-	std::vector<Simplex_handle> simplices;
-	simplices.push_back(Sh(Vh(0),Vh(1),Vh(2)));
-	simplices.push_back(Sh(Vh(1),Vh(2),Vh(3)));
-	simplices.push_back(Sh(Vh(3),Vh(0),Vh(2)));
-	simplices.push_back(Sh(Vh(3),Vh(0),Vh(1)));
-
-	//get complex from top faces
-	Complex complex(make_complex_from_top_faces<Complex>(simplices.begin(),simplices.end()));
-
-	DBGVALUE(complex.to_string());
-
-	if(complex.num_blockers()!=1) return false;
-	Sh expected_blocker(Vh(0),Vh(1),Vh(2),Vh(3));
-	for(auto b : complex.const_blocker_range())
-		if(*b!=expected_blocker) return false;
-	return complex.num_vertices()==4 && complex.num_blockers()==1 && complex.num_edges()==6;
+  return ( complex.num_vertices() == 5 && complex.num_edges() == 10 && complex.num_blockers() == 1);
 }
 
+bool test_constructor3() {
+  typedef Vertex_handle Vh;
+  typedef Simplex Sh;
+  std::vector<Simplex> simplices;
+  auto subf(subfaces(Sh(Vh(0), Vh(1), Vh(2))));
+  subf.pop_back(); //remove max face -> now a blocker 012
+  simplices.insert(simplices.begin(), subf.begin(), subf.end());
+  DBGCONT(simplices);
+  Complex complex(simplices.begin(), simplices.end());
 
-bool test_constructor8(){
-	typedef Vertex_handle Vh;
-	typedef Simplex_handle Sh;
-	std::vector<Simplex_handle> simplices;
-	simplices.push_back(Sh(Vh(0),Vh(1)));
-	simplices.push_back(Sh(Vh(2),Vh(1)));
-	simplices.push_back(Sh(Vh(0),Vh(2)));
-	simplices.push_back(Sh(Vh(3),Vh(1)));
-	simplices.push_back(Sh(Vh(2),Vh(3)));
+  DBGVALUE(complex.to_string());
 
-	//get complex from top faces
-	Complex complex(make_complex_from_top_faces<Complex>(simplices.begin(),simplices.end()));
+  if (complex.num_blockers() != 1) return false;
+  Sh expected_blocker(Vh(0), Vh(1), Vh(2));
+  for (auto b : complex.const_blocker_range())
+    if (*b != expected_blocker) return false;
 
-	DBGVALUE(complex.to_string());
 
-	return complex.num_vertices()==4 && complex.num_blockers()==2 && complex.num_edges()==5;
+  return complex.num_vertices() == 3 && complex.num_blockers() == 1;
 }
 
+bool test_constructor4() {
+  typedef Vertex_handle Vh;
+  typedef Simplex Sh;
+  std::vector<Simplex> simplices;
+  auto subf(subfaces(Sh(Vh(0), Vh(1), Vh(2), Vh(3))));
+  simplices.insert(simplices.begin(), subf.begin(), subf.end());
 
+  simplices.push_back(Sh(Vh(4)));
+  simplices.push_back(Sh(Vh(4), Vh(1)));
+  simplices.push_back(Sh(Vh(4), Vh(0)));
 
+  DBGCONT(simplices);
+  Complex complex(simplices.begin(), simplices.end());
 
+  DBGVALUE(complex.to_string());
+  if (complex.num_blockers() != 1) return false;
+  Sh expected_blocker(Vh(0), Vh(1), Vh(4));
+  for (auto b : complex.const_blocker_range())
+    if (*b != expected_blocker) return false;
 
-int main (int argc, char *argv[])
-{
-	Tests tests_complex;
-	tests_complex.add("test simplex",test_simplex);
-	tests_complex.add("test_link0",test_link0);
-	tests_complex.add("test_link1",test_link1);
-	tests_complex.add("test_link2",test_link2);
-	tests_complex.add("test_link3",test_link3);
-	tests_complex.add("test_link4",test_link4);
-	tests_complex.add("test_link5",test_link5);
-	tests_complex.add("test_link6",test_link6);
-	tests_complex.add("test_link7",test_link7);
-
-	tests_complex.add("test iterator vertices 1",test_iterator_vertices1);
-	tests_complex.add("test iterator vertices 2",test_iterator_vertices2);
-	tests_complex.add("test iterator edges",test_iterator_edge);
-	tests_complex.add("test iterator edges 2",test_iterator_edge2);
-	tests_complex.add("test iterator edges 3",test_iterator_edge3);
-
-	tests_complex.add("test iterator simplices",test_iterator_simplices);
-	tests_complex.add("test iterator simplices2",test_iterator_simplices2);
-	tests_complex.add("test iterator simplices3",test_iterator_simplices3);
-	tests_complex.add("test iterator simplices4",test_iterator_simplices4);
-
-
-	tests_complex.add("test iterator blockers",test_iterator_blockers);
-	tests_complex.add("test_iterator_triangles",test_iterator_triangles);
-
-	tests_complex.add("test_constructor_list_simplices",test_constructor);
-	tests_complex.add("test_constructor_list_simplices2",test_constructor2);
-	tests_complex.add("test_constructor_list_simplices3",test_constructor3);
-	tests_complex.add("test_constructor_list_simplices4",test_constructor4);
-	tests_complex.add("test_constructor_list_simplices5",test_constructor5);
-	tests_complex.add("test_constructor_list_simplices6",test_constructor6);
-	tests_complex.add("test_constructor_list_simplices7",test_constructor7);
-	tests_complex.add("test_constructor_list_simplices8",test_constructor8);
-
-
-	if(tests_complex.run()){
-		return EXIT_SUCCESS;
-	}
-	else{
-		return EXIT_FAILURE;
-	}
+  return complex.num_vertices() == 5 && complex.num_blockers() == 1 && complex.num_edges() == 8;
+}
 
-	//	test_iterator_simplices();
+bool test_constructor5() {
+  typedef Vertex_handle Vh;
+  typedef Simplex Sh;
+  std::vector<Simplex> simplices;
+  auto subf(subfaces(Sh(Vh(0), Vh(1), Vh(2))));
+  simplices.insert(simplices.begin(), subf.begin(), subf.end());
+
+  simplices.push_back(Sh(Vh(3)));
+  simplices.push_back(Sh(Vh(3), Vh(1)));
+  simplices.push_back(Sh(Vh(3), Vh(2)));
+  simplices.push_back(Sh(Vh(4)));
+  simplices.push_back(Sh(Vh(4), Vh(1)));
+  simplices.push_back(Sh(Vh(4), Vh(0)));
+  simplices.push_back(Sh(Vh(5)));
+  simplices.push_back(Sh(Vh(5), Vh(2)));
+  simplices.push_back(Sh(Vh(5), Vh(0)));
+
+  DBGCONT(simplices);
+  Complex complex(simplices.begin(), simplices.end());
+
+  DBGVALUE(complex.to_string());
+
+  return complex.num_vertices() == 6 && complex.num_blockers() == 3 && complex.num_edges() == 9;
+}
+
+bool test_constructor6() {
+  typedef Vertex_handle Vh;
+  typedef Simplex Sh;
+  std::vector<Simplex> simplices;
+  auto subf(subfaces(Sh(Vh(0), Vh(1), Vh(2), Vh(3))));
+  for (auto s : subf) {
+    Sh s1(Vh(0), Vh(1), Vh(2), Vh(3));
+    Sh s2(Vh(1), Vh(2), Vh(3));
+    if (s != s1 && s != s2) simplices.push_back(s);
+  }
+
+  DBGCONT(simplices);
+  Complex complex(simplices.begin(), simplices.end());
+
+  DBGVALUE(complex.to_string());
+
+  if (complex.num_blockers() != 1) return false;
+  Sh expected_blocker(Vh(1), Vh(2), Vh(3));
+  for (auto b : complex.const_blocker_range())
+    if (*b != expected_blocker) return false;
+  return complex.num_vertices() == 4 && complex.num_blockers() == 1 && complex.num_edges() == 6;
+}
+
+bool test_constructor7() {
+  typedef Vertex_handle Vh;
+  typedef Simplex Sh;
+  std::vector<Simplex> simplices;
+  simplices.push_back(Sh(Vh(0), Vh(1), Vh(2)));
+  simplices.push_back(Sh(Vh(1), Vh(2), Vh(3)));
+  simplices.push_back(Sh(Vh(3), Vh(0), Vh(2)));
+  simplices.push_back(Sh(Vh(3), Vh(0), Vh(1)));
+
+  //get complex from top faces
+  Complex complex(make_complex_from_top_faces<Complex>(simplices.begin(), simplices.end()));
+
+  DBGVALUE(complex.to_string());
+
+  if (complex.num_blockers() != 1) return false;
+  Sh expected_blocker(Vh(0), Vh(1), Vh(2), Vh(3));
+  for (auto b : complex.const_blocker_range())
+    if (*b != expected_blocker) return false;
+  return complex.num_vertices() == 4 && complex.num_blockers() == 1 && complex.num_edges() == 6;
+}
+
+bool test_constructor8() {
+  typedef Vertex_handle Vh;
+  typedef Simplex Sh;
+  std::vector<Simplex> simplices;
+  simplices.push_back(Sh(Vh(0), Vh(1)));
+  simplices.push_back(Sh(Vh(2), Vh(1)));
+  simplices.push_back(Sh(Vh(0), Vh(2)));
+  simplices.push_back(Sh(Vh(3), Vh(1)));
+  simplices.push_back(Sh(Vh(2), Vh(3)));
+
+  //get complex from top faces
+  Complex complex(make_complex_from_top_faces<Complex>(simplices.begin(), simplices.end()));
+
+  DBGVALUE(complex.to_string());
+
+  return complex.num_vertices() == 4 && complex.num_blockers() == 2 && complex.num_edges() == 5;
+}
+
+int main(int argc, char *argv[]) {
+  Tests tests_complex;
+  tests_complex.add("test simplex", test_simplex);
+  tests_complex.add("test_num_simplices", test_num_simplices);
+  tests_complex.add("test_link0", test_link0);
+  tests_complex.add("test_link1", test_link1);
+  tests_complex.add("test_link2", test_link2);
+  tests_complex.add("test_link3", test_link3);
+  tests_complex.add("test_link4", test_link4);
+  tests_complex.add("test_link5", test_link5);
+  tests_complex.add("test_link6", test_link6);
+  tests_complex.add("test_link7", test_link7);
+
+  tests_complex.add("test_constructor_list_simplices", test_constructor);
+  tests_complex.add("test_constructor_list_simplices2", test_constructor2);
+  tests_complex.add("test_constructor_list_simplices3", test_constructor3);
+  tests_complex.add("test_constructor_list_simplices4", test_constructor4);
+  tests_complex.add("test_constructor_list_simplices5", test_constructor5);
+  tests_complex.add("test_constructor_list_simplices6", test_constructor6);
+  tests_complex.add("test_constructor_list_simplices7", test_constructor7);
+  tests_complex.add("test_constructor_list_simplices8", test_constructor8);
+
+  tests_complex.add("test iterator vertices 1", test_iterator_vertices1);
+  tests_complex.add("test iterator vertices 2", test_iterator_vertices2);
+  tests_complex.add("test iterator edges", test_iterator_edge);
+  tests_complex.add("test iterator edges 2", test_iterator_edge2);
+  tests_complex.add("test iterator edges 3", test_iterator_edge3);
+  tests_complex.add("test iterator blockers", test_iterator_blockers);
+  tests_complex.add("test_iterator_triangles", test_iterator_triangles);
+  tests_complex.add("test iterator simplices", test_iterator_simplices);
+  tests_complex.add("test iterator simplices2", test_iterator_simplices2);
+  tests_complex.add("test iterator simplices3", test_iterator_simplices3);
+  tests_complex.add("test iterator simplices4", test_iterator_simplices4);
+  tests_complex.add("test iterator coboundary", test_iterator_coboundary);
+
+  if (tests_complex.run()) {
+    return EXIT_SUCCESS;
+  } else {
+    return EXIT_FAILURE;
+  }
+
+  //	test_iterator_simplices();
 }
 
diff --git a/src/Witness_complex/example/Torus_distance.h b/src/Witness_complex/example/Torus_distance.h
deleted file mode 100644
index 5ae127df..00000000
--- a/src/Witness_complex/example/Torus_distance.h
+++ /dev/null
@@ -1,209 +0,0 @@
-#ifndef GUDHI_TORUS_DISTANCE_H_
-#define GUDHI_TORUS_DISTANCE_H_
-
-#include <math.h>
-
-#include <CGAL/Search_traits.h>
-#include <CGAL/Search_traits_adapter.h>
-#include <CGAL/Epick_d.h>
-
-typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
-typedef K::Point_d Point_d;
-typedef K::FT FT;
-typedef CGAL::Search_traits<
-  FT, Point_d,
-  typename K::Cartesian_const_iterator_d,
-  typename K::Construct_cartesian_const_iterator_d> Traits_base;
-
-/**
- * \brief Class of distance in a flat torus in dimension D
- *
- */
-class Torus_distance {
-
-public:
-    typedef K::FT    FT;
-    typedef K::Point_d Point_d;
-    typedef Point_d Query_item;
-    typedef typename CGAL::Dynamic_dimension_tag D;
-
-  double box_length = 2;
-
-  FT transformed_distance(Query_item q, Point_d p) const
-  {
-    FT distance = FT(0);
-    FT coord = FT(0);
-    //std::cout << "Hello skitty!\n";
-    typename K::Construct_cartesian_const_iterator_d construct_it=Traits_base().construct_cartesian_const_iterator_d_object();
-    typename K::Cartesian_const_iterator_d qit = construct_it(q),
-	qe = construct_it(q,1), pit = construct_it(p);
-	for(; qit != qe; qit++, pit++)
-          {
-            coord = sqrt(((*qit)-(*pit))*((*qit)-(*pit)));
-            if (coord*coord <= (box_length-coord)*(box_length-coord))
-              distance += coord*coord;
-            else
-              distance += (box_length-coord)*(box_length-coord);
-          }
-        return distance;
-  }
-
-  FT min_distance_to_rectangle(const Query_item& q,
-                               const CGAL::Kd_tree_rectangle<FT,D>& r) const {
-    FT distance = FT(0);
-    FT dist1, dist2;
-    typename K::Construct_cartesian_const_iterator_d construct_it=Traits_base().construct_cartesian_const_iterator_d_object();
-    typename K::Cartesian_const_iterator_d qit = construct_it(q),
-                                           qe = construct_it(q,1);
-    for(unsigned int i = 0;qit != qe; i++, qit++)
-      {
-        if((*qit) < r.min_coord(i))
-          {
-            dist1 = (r.min_coord(i)-(*qit));
-            dist2 = (box_length - r.max_coord(i)+(*qit));
-            if (dist1 < dist2)
-              distance += dist1*dist1;
-            else
-              distance += dist2*dist2;
-          }
-        else if ((*qit) > r.max_coord(i))
-          {
-            dist1 = (box_length - (*qit)+r.min_coord(i));
-            dist2 = ((*qit) - r.max_coord(i));
-            if (dist1 < dist2)
-              distance += dist1*dist1;
-            else
-              distance += dist2*dist2;
-          }
-      }
-    return distance;
-  }
-
-  FT min_distance_to_rectangle(const Query_item& q,
-                               const CGAL::Kd_tree_rectangle<FT,D>& r,
-                               std::vector<FT>& dists) const {
-    FT distance = FT(0);
-    FT dist1, dist2;
-    typename K::Construct_cartesian_const_iterator_d construct_it=Traits_base().construct_cartesian_const_iterator_d_object();
-    typename K::Cartesian_const_iterator_d qit = construct_it(q),
-	                  	           qe = construct_it(q,1);
-    //std::cout << r.max_coord(0) << std::endl;
-    for(unsigned int i = 0;qit != qe; i++, qit++)
-      {
-        if((*qit) < r.min_coord(i))
-          {
-            dist1 = (r.min_coord(i)-(*qit));
-            dist2 = (box_length - r.max_coord(i)+(*qit));
-            if (dist1 < dist2)
-              {
-                dists[i] = dist1;
-                distance += dist1*dist1;
-              }
-            else
-              {
-                dists[i] = dist2;
-                distance += dist2*dist2;
-                //std::cout << "Good stuff1\n";
-              }
-          }
-        else if ((*qit) > r.max_coord(i))
-          {
-            dist1 = (box_length - (*qit)+r.min_coord(i));
-            dist2 = ((*qit) - r.max_coord(i));
-            if (dist1 < dist2)
-              {
-                dists[i] = dist1;
-                distance += dist1*dist1;
-                //std::cout << "Good stuff2\n";
-              }
-            else
-              {
-                dists[i] = dist2;
-                distance += dist2*dist2;
-              }
-          }
-      };
-    return distance;
-  }
-    
-  FT max_distance_to_rectangle(const Query_item& q,
-                               const CGAL::Kd_tree_rectangle<FT,D>& r) const {
-    FT distance=FT(0);
-    typename K::Construct_cartesian_const_iterator_d construct_it=Traits_base().construct_cartesian_const_iterator_d_object();
-    typename K::Cartesian_const_iterator_d qit = construct_it(q),
-		                           qe = construct_it(q,1);
-    for(unsigned int i = 0;qit != qe; i++, qit++)
-      {
-        if (box_length <= (r.min_coord(i)+r.max_coord(i)))
-          if ((r.max_coord(i)+r.min_coord(i)-box_length)/FT(2.0) <= (*qit) &&
-              (*qit) <= (r.min_coord(i)+r.max_coord(i))/FT(2.0))
-            distance += (r.max_coord(i)-(*qit))*(r.max_coord(i)-(*qit));
-          else
-            distance += ((*qit)-r.min_coord(i))*((*qit)-r.min_coord(i));
-        else
-          if ((box_length-r.max_coord(i)-r.min_coord(i))/FT(2.0) <= (*qit) ||
-              (*qit) <= (r.min_coord(i)+r.max_coord(i))/FT(2.0))
-            distance += (r.max_coord(i)-(*qit))*(r.max_coord(i)-(*qit));
-          else
-            distance += ((*qit)-r.min_coord(i))*((*qit)-r.min_coord(i));
-      }
-    return distance;
-  }
-
-  
-  FT max_distance_to_rectangle(const Query_item& q,
-                               const CGAL::Kd_tree_rectangle<FT,D>& r,
-                               std::vector<FT>& dists) const {
-    FT distance=FT(0);
-    typename K::Construct_cartesian_const_iterator_d construct_it=Traits_base().construct_cartesian_const_iterator_d_object();
-    typename K::Cartesian_const_iterator_d qit = construct_it(q),
-		                           qe = construct_it(q,1);
-    for(unsigned int i = 0;qit != qe; i++, qit++)
-      {
-        if (box_length <= (r.min_coord(i)+r.max_coord(i)))
-          if ((r.max_coord(i)+r.min_coord(i)-box_length)/FT(2.0) <= (*qit) &&
-              (*qit) <= (r.min_coord(i)+r.max_coord(i))/FT(2.0))
-            {
-              dists[i] = r.max_coord(i)-(*qit);
-              distance += (r.max_coord(i)-(*qit))*(r.max_coord(i)-(*qit));
-            }
-          else
-            {
-              dists[i] = sqrt(((*qit)-r.min_coord(i))*((*qit)-r.min_coord(i)));
-              distance += ((*qit)-r.min_coord(i))*((*qit)-r.min_coord(i));
-            }
-        else
-          if ((box_length-r.max_coord(i)-r.min_coord(i))/FT(2.0) <= (*qit) ||
-              (*qit) <= (r.min_coord(i)+r.max_coord(i))/FT(2.0))
-            {
-              dists[i] = sqrt((r.max_coord(i)-(*qit))*(r.max_coord(i)-(*qit)));
-              distance += (r.max_coord(i)-(*qit))*(r.max_coord(i)-(*qit));
-              
-            }
-          else
-            {
-              dists[i] = (*qit)-r.min_coord(i);
-              distance += ((*qit)-r.min_coord(i))*((*qit)-r.min_coord(i));
-            }
-      }
-    return distance;
-  }
-
-    inline FT new_distance(FT dist, FT old_off, FT new_off,
-                           int )  const {
-      
-      FT new_dist = dist + (new_off*new_off - old_off*old_off);
-      return new_dist;
-    }
-    
-  inline FT transformed_distance(FT d) const {
-    return d*d;
-  }
-
-  inline FT inverse_of_transformed_distance(FT d) const {
-    return sqrt(d);
-  }
-  
-};
-
-#endif
diff --git a/src/Witness_complex/example/protected_sets/output_tikz.h b/src/Witness_complex/example/protected_sets/output_tikz.h
deleted file mode 100644
index edfd9a5f..00000000
--- a/src/Witness_complex/example/protected_sets/output_tikz.h
+++ /dev/null
@@ -1,67 +0,0 @@
-#ifndef OUTPUT_TIKZ_H
-#define OUTPUT_TIKZ_H
-
-#include <vector>
-#include <string>
-#include <algorithm>
-#include <fstream>
-#include <cmath>
-
-void write_tikz_plot(std::vector<FT> data, std::string filename)
-{
-  int n = data.size();
-  FT vmax = *(std::max_element(data.begin(), data.end()));
-  //std::cout << std::log10(vmax) << " " << std::floor(std::log10(vmax));
-  
-  FT order10 = pow(10,std::floor(std::log10(vmax)));
-  int digit = std::floor( vmax / order10) + 1;
-  if (digit == 4 || digit == 6) digit = 5;
-  if (digit > 6) digit = 10;
-  FT plot_max = digit*order10;
-  std::cout << plot_max << " " << vmax;
-  FT hstep = 10.0/(n-1);
-  FT wstep = 10.0 / plot_max;
-
-  std::cout << "(eps_max-eps_min)/(N-48) = " << (vmax-*data.begin())/(data.size()-48) << "\n";
-  std::ofstream ofs(filename, std::ofstream::out);
-
-  ofs <<
-    "\\documentclass{standalone}\n" <<
-    "\\usepackage[utf8]{inputenc}\n" <<
-    "\\usepackage{amsmath}\n" <<
-    "\\usepackage{tikz}\n\n" <<
-    "\\begin{document}\n" <<
-    "\\begin{tikzpicture}\n";
-  
-  ofs <<  "\\draw[->] (0,0) -- (0,11);" << std::endl <<
-    "\\draw[->] (0,0) -- (11,0);" << std::endl <<
-    "\\foreach \\i in {1,...,10}" << std::endl <<
-    "\\draw (0,\\i) -- (-0.05,\\i);" << std::endl <<
-    "\\foreach \\i in {1,...,10}" << std::endl <<
-    "\\draw (\\i,0) -- (\\i,-0.05);" << std::endl << std::endl <<
-
-    "\\foreach \\i in {1,...,10}" << std::endl <<
-    "\\draw[dashed] (-0.05,\\i) -- (11,\\i);" << std::endl << std::endl <<
-    
-    "\\node at (-0.5,11) {$*$}; " << std::endl <<
-    "\\node at (11,-0.5) {$*$}; " << std::endl <<
-    "\\node at (-0.5,-0.5) {0}; " << std::endl <<
-    "\\node at (-0.5,10) {" << plot_max << "}; " << std::endl <<
-    "%\\node at (10,-0.5) {2}; " << std::endl;
-
-  ofs << "\\draw[red] (0," << wstep*data[0] << ")";
-  for (int i = 1; i < n; ++i)
-    ofs << " -- (" << hstep*i << "," << wstep*data[i] << ")";
-  ofs << ";\n";
-
-  ofs <<
-    "\\end{tikzpicture}\n" <<
-    "\\end{document}";
-  
-  ofs.close();
-
-
-  
-}
-
-#endif
diff --git a/src/Witness_complex/example/protected_sets/protected_sets.h b/src/Witness_complex/example/protected_sets/protected_sets.h
deleted file mode 100644
index ec627808..00000000
--- a/src/Witness_complex/example/protected_sets/protected_sets.h
+++ /dev/null
@@ -1,597 +0,0 @@
-#ifndef PROTECTED_SETS_H
-#define PROTECTED_SETS_H
-
-#include <algorithm>
-#include <CGAL/Cartesian_d.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/Euclidean_distance.h>
-#include <CGAL/Kernel_d/Sphere_d.h>
-#include <CGAL/Kernel_d/Hyperplane_d.h>
-#include <CGAL/Kernel_d/Vector_d.h>
-
-#include <CGAL/point_generators_d.h>
-#include <CGAL/constructions_d.h>
-
-
-typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
-typedef K::Point_d Point_d;
-typedef K::Vector_d Vector_d;
-typedef K::Oriented_side_d Oriented_side_d;
-typedef K::Has_on_positive_side_d Has_on_positive_side_d;
-typedef K::Sphere_d Sphere_d;
-typedef K::Hyperplane_d Hyperplane_d;
-
-typedef CGAL::Delaunay_triangulation<K> Delaunay_triangulation;
-typedef Delaunay_triangulation::Facet Facet;
-typedef Delaunay_triangulation::Vertex_handle Delaunay_vertex;
-typedef Delaunay_triangulation::Full_cell_handle Full_cell_handle;
-
-typedef std::vector<Point_d> Point_Vector;
-typedef CGAL::Euclidean_distance<Traits_base> Euclidean_distance;
-
-FT  _sfty = pow(10,-14);
-
-///////////////////////////////////////////////////////////////////////////////////////////////////////////
-// AUXILLARY FUNCTIONS
-///////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-/** Insert a point in Delaunay triangulation. If you are working in a flat torus, the procedure adds all the 3^d copies in adjacent cubes as well 
- *  
- *  W is the initial point vector
- *  chosen_landmark is the index of the chosen point in W
- *  landmarks_ind is the vector of indices of already chosen points in W
- *  delaunay is the Delaunay triangulation
- *  landmark_count is the current number of chosen vertices
- *  torus is true iff you are working on a flat torus [-1,1]^d
- *  OUT: Vertex handle to the newly inserted point
- */
-Delaunay_vertex insert_delaunay_landmark_with_copies(Point_Vector& W, int chosen_landmark, std::vector<int>& landmarks_ind, Delaunay_triangulation& delaunay, int& landmark_count, bool torus)
-{
-  if (!torus)
-    {
-      Delaunay_vertex v =delaunay.insert(W[chosen_landmark]);
-      landmarks_ind.push_back(chosen_landmark);
-      landmark_count++;
-      return v;
-    }
-  else
-    {
-      int D = W[0].size();
-      int nb_cells = pow(3, D);
-      Delaunay_vertex v;
-      for (int i = 0; i < nb_cells; ++i)
-        {
-          std::vector<FT> point;
-          int cell_i = i;
-          for (int l = 0; l < D; ++l)
-            {
-              point.push_back(W[chosen_landmark][l] + 2.0*(cell_i%3-1));
-              cell_i /= 3;
-            }
-          v = delaunay.insert(point);
-        }
-      landmarks_ind.push_back(chosen_landmark);
-      landmark_count++;
-      return v;
-    }
-}
-
-/** Small check if the vertex v is in the full cell fc
- */
-
-bool vertex_is_in_full_cell(Delaunay_triangulation::Vertex_handle v, Full_cell_handle fc)
-{
-  for (auto v_it = fc->vertices_begin(); v_it != fc->vertices_end(); ++v_it)
-    if (*v_it == v)
-      return true;
-  return false;
-}
-
-/** Fill chosen point vector from indices with copies if you are working on a flat torus
- *  
- *  IN:  W is the point vector
- *  OUT: landmarks is the output vector
- *  IN:  landmarks_ind is the vector of indices
- *  IN:  torus is true iff you are working on a flat torus [-1,1]^d
- */
-
-void fill_landmarks(Point_Vector& W, Point_Vector& landmarks, std::vector<int>& landmarks_ind, bool torus)
-{
-  if (!torus)
-    for (unsigned j = 0; j < landmarks_ind.size(); ++j)
-      landmarks.push_back(W[landmarks_ind[j]]);
-  else
-    {
-      int D = W[0].size();
-      int nb_cells = pow(3, D);
-      int nbL = landmarks_ind.size();
-      // Fill landmarks
-      for (int i = 0; i < nb_cells-1; ++i)
-        for (int j = 0; j < nbL; ++j)
-          {
-            int cell_i = i;
-            Point_d point;
-            for (int l = 0; l < D; ++l)
-              {
-                point.push_back(W[landmarks_ind[j]][l] + 2.0*(cell_i-1));
-                cell_i /= 3;
-              }
-            landmarks.push_back(point);
-          }
-    }
-}
-
-/** Fill a vector of all simplices in the Delaunay triangulation giving integer indices to vertices
- *
- *  IN: t is the Delaunay triangulation
- *  OUT: full_cells is the output vector
- */
-
-void fill_full_cell_vector(Delaunay_triangulation& t, std::vector<std::vector<int>>& full_cells)
-{
-  // Store vertex indices in a map
-  int ind = 0; //index of a vertex
-  std::map<Delaunay_triangulation::Vertex_handle, int> index_of_vertex;
-  for (auto v_it = t.vertices_begin(); v_it != t.vertices_end(); ++v_it)
-    if (t.is_infinite(v_it))
-      continue;
-    else
-      index_of_vertex[v_it] = ind++;
-  // Write full cells as vectors in full_cells
-  for (auto fc_it = t.full_cells_begin(); fc_it != t.full_cells_end(); ++fc_it)
-    {
-      if (t.is_infinite(fc_it))
-        continue;
-      Point_Vector vertices;
-      for (auto fc_v_it = fc_it->vertices_begin(); fc_v_it != fc_it->vertices_end(); ++fc_v_it)
-        vertices.push_back((*fc_v_it)->point());
-      Sphere_d cs( vertices.begin(), vertices.end());
-      Point_d csc = cs.center();
-      bool in_cube = true; 
-      for (auto xi = csc.cartesian_begin(); xi != csc.cartesian_end(); ++xi)
-        if (*xi > 1.0 || *xi < -1.0)
-          {
-            in_cube = false; break;
-          }
-      if (!in_cube)
-        continue;
-      std::vector<int> cell;
-      for (auto v_it = fc_it->vertices_begin(); v_it != fc_it->vertices_end(); ++v_it)
-        cell.push_back(index_of_vertex[*v_it]);
-      full_cells.push_back(cell);
-    }
-}
-
-////////////////////////////////////////////////////////////////////////////////////////////////////////////
-// IS VIOLATED TEST
-////////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-/** Check if a newly created cell is protected from old vertices
- *  
- *  t is the Delaunay triangulation
- *  vertices is the vector containing the point to insert and a facet f in t
- *  v1 is the vertex of t, such that f and v1 form a simplex
- *  v2 is the vertex of t, such that f and v2 form another simplex
- *  delta is the protection constant
- *  power_protection is true iff the delta-power protection is used
- */
-
-bool new_cell_is_violated(Delaunay_triangulation& t, std::vector<Point_d>& vertices, const Delaunay_vertex& v1, const Delaunay_vertex v2, FT delta, bool power_protection, FT theta0)
-{
-  assert(vertices.size() == vertices[0].size() ||
-         vertices.size() == vertices[0].size() + 1); //simplex size = d | d+1
-  assert(v1 != v2);
-  if (vertices.size() == vertices[0].size() + 1)
-  // FINITE CASE
-    {
-      Sphere_d cs(vertices.begin(), vertices.end());
-      Point_d center_cs = cs.center();
-      FT r = sqrt(Euclidean_distance().transformed_distance(center_cs, vertices[0]));
-      /*
-      for (auto v_it = t.vertices_begin(); v_it != t.vertices_end(); ++v_it)
-        if (!t.is_infinite(v_it)) 
-          {
-            //CGAL::Oriented_side side = Oriented_side_d()(cs, (v_it)->point()); 
-            if (std::find(vertices.begin(), vertices.end(), v_it->point()) == vertices.end())
-              {
-                FT dist2 = Euclidean_distance().transformed_distance(center_cs, (v_it)->point());
-                if (!power_protection)
-                  if (dist2 >= r*r-_sfty && dist2 <= (r+delta)*(r+delta))
-                    return true;
-                if (power_protection)
-                  if (dist2 >= r*r-_sfty && dist2 <= r*r+delta*delta) 
-                    return true;                 
-              }
-          }
-      */
-      // Check if the simplex is thick enough
-      Hyperplane_d tau_h(vertices.begin()+1, vertices.end());
-      Vector_d orth_tau = tau_h.orthogonal_vector();
-      /*
-               p_s1 = Vector_d(*(vertices.begin()), *(vertices.begin()+1));
-      */
-      //std::cout << "||orth_tau|| = " << sqrt(orth_tau.squared_length()) << "\n";
-      FT orth_length = sqrt(orth_tau.squared_length());
-      K::Cartesian_const_iterator_d o_it, p_it, s_it, c_it;
-      // Compute the altitude
-      FT h = 0;
-      for (o_it = orth_tau.cartesian_begin(),
-           p_it = vertices.begin()->cartesian_begin(),
-           s_it = (vertices.begin()+1)->cartesian_begin();
-           o_it != orth_tau.cartesian_end();
-           ++o_it, ++p_it, ++s_it)
-        h += (*o_it)*(*p_it - *s_it)/orth_length;
-      h = fabs(h);
-      // Is the center inside the box?
-      bool inside_the_box = true;
-      for (c_it = center_cs.cartesian_begin(); c_it != center_cs.cartesian_end(); ++c_it)
-        if (*c_it > 1.0 || *c_it < -1.0)
-          {
-            inside_the_box = false; break;
-          }
-      if (inside_the_box && h/r < theta0)
-        return true;
-      if (!t.is_infinite(v1))
-        {
-          FT dist2 = Euclidean_distance().transformed_distance(center_cs, v1->point());
-          if (!power_protection)
-            if (dist2 >= r*r-_sfty && dist2 <= (r+delta)*(r+delta))
-              return true;
-          if (power_protection)
-            if (dist2 >= r*r-_sfty && dist2 <= r*r+delta*delta) 
-              return true;
-        }
-      if (!t.is_infinite(v2))
-        {
-          FT dist2 = Euclidean_distance().transformed_distance(center_cs, v2->point());
-          if (!power_protection)
-            if (dist2 >= r*r-_sfty && dist2 <= (r+delta)*(r+delta))
-              return true;
-          if (power_protection)
-            if (dist2 >= r*r-_sfty && dist2 <= r*r+delta*delta) 
-              return true;
-        }
-    }
-  else
-  // INFINITE CASE
-    {
-      Delaunay_triangulation::Vertex_iterator v = t.vertices_begin();
-      while (t.is_infinite(v) || std::find(vertices.begin(), vertices.end(), v->point()) == vertices.end())
-        v++;
-      Hyperplane_d facet_plane(vertices.begin(), vertices.end(), v->point(), CGAL::ON_POSITIVE_SIDE);
-      Vector_d orth_v = facet_plane.orthogonal_vector();
-      /*
-      for (auto v_it = t.vertices_begin(); v_it != t.vertices_end(); ++v_it)
-        if (!t.is_infinite(v_it))
-          if (std::find(vertices.begin(), vertices.end(), v_it->point()) == vertices.end())
-            {
-              std::vector<FT> coords;
-              Point_d p = v_it->point();
-              auto orth_i = orth_v.cartesian_begin(), p_i = p.cartesian_begin();
-              for (; orth_i != orth_v.cartesian_end(); ++orth_i, ++p_i)
-                coords.push_back((*p_i) - (*orth_i) * delta / sqrt(orth_v.squared_length()));
-              Point_d p_delta = Point_d(coords);
-              bool p_is_inside = !Has_on_positive_side_d()(facet_plane, p);
-              bool p_delta_is_inside = !Has_on_positive_side_d()(facet_plane, p_delta);
-              if (!p_is_inside && p_delta_is_inside)
-                return true;
-            }
-      */
-      if (!t.is_infinite(v1))
-        {
-          std::vector<FT> coords;
-          Point_d p = v1->point();
-          auto orth_i = orth_v.cartesian_begin(), p_i = p.cartesian_begin();
-          for (; orth_i != orth_v.cartesian_end(); ++orth_i, ++p_i)
-            coords.push_back((*p_i) - (*orth_i) * delta / sqrt(orth_v.squared_length()));
-          Point_d p_delta = Point_d(coords);
-          bool p_is_inside = !Has_on_positive_side_d()(facet_plane, p);
-          bool p_delta_is_inside = !Has_on_positive_side_d()(facet_plane, p_delta);
-          if (!power_protection && !p_is_inside && p_delta_is_inside)
-            return true;
-        }
-      if (!t.is_infinite(v2))
-        {
-          std::vector<FT> coords;
-          Point_d p = v2->point();
-          auto orth_i = orth_v.cartesian_begin(), p_i = p.cartesian_begin();
-          for (; orth_i != orth_v.cartesian_end(); ++orth_i, ++p_i)
-            coords.push_back((*p_i) - (*orth_i) * delta / sqrt(orth_v.squared_length()));
-          Point_d p_delta = Point_d(coords);
-          bool p_is_inside = !Has_on_positive_side_d()(facet_plane, p);
-          bool p_delta_is_inside = !Has_on_positive_side_d()(facet_plane, p_delta);
-          if (!power_protection && !p_is_inside && p_delta_is_inside)
-            return true;
-        }
-    }
-  return false;
-}
-  
-/** Auxillary recursive function to check if the point p violates the protection of the cell c and
- *  if there is a violation of an eventual new cell
- *
- *  p is the point to insert
- *  t is the current triangulation
- *  c is the current cell (simplex)
- *  parent_cell is the parent cell (simplex)
- *  index is the index of the facet between c and parent_cell from parent_cell's point of view
- *  D is the dimension of the triangulation
- *  delta is the protection constant
- *  marked_cells is the vector of all visited cells containing p in their circumscribed ball
- *  power_protection is true iff you are working with delta-power protection
- *
- *  OUT: true iff inserting p hasn't produced any violation so far
- */
-
-bool is_violating_protection(Point_d& p, Delaunay_triangulation& t, Full_cell_handle c, Full_cell_handle parent_cell, int index, int D, FT delta, std::vector<Full_cell_handle>& marked_cells, bool power_protection, FT theta0)
-{
-  Euclidean_distance ed;
-  std::vector<Point_d> vertices;
-  if (!t.is_infinite(c))
-    {
-      // if the cell is finite, we look if the protection is violated
-      for (auto v_it = c->vertices_begin(); v_it != c->vertices_end(); ++v_it)
-        vertices.push_back((*v_it)->point());
-      Sphere_d cs( vertices.begin(), vertices.end());
-      Point_d center_cs = cs.center();
-      FT r = sqrt(ed.transformed_distance(center_cs, vertices[0]));
-      FT dist2 = ed.transformed_distance(center_cs, p);
-      // if the new point is inside the protection ball of a non conflicting simplex
-      if (!power_protection)
-        if (dist2 >= r*r-_sfty && dist2 <= (r+delta)*(r+delta))
-          return true;
-      if (power_protection)
-        if (dist2 >= r*r-_sfty && dist2 <= r*r+delta*delta) 
-          return true;    
-      // if the new point is inside the circumscribing ball : continue violation searching on neighbours
-      //if (dist2 < r*r)
-      //if (dist2 < (5*r+delta)*(5*r+delta))
-      if (dist2 < r*r)
-        {
-          c->tds_data().mark_visited();
-          marked_cells.push_back(c);
-          for (int i = 0; i < D+1; ++i)
-            {
-              Full_cell_handle next_c = c->neighbor(i);
-              if (next_c->tds_data().is_clear() &&
-                  is_violating_protection(p, t, next_c, c, i, D, delta, marked_cells, power_protection, theta0))
-                return true;
-            }
-        }
-      // if the new point is outside the protection sphere
-      else
-        {
-          // facet f is on the border of the conflict zone : check protection of simplex {p,f}
-          // the new simplex is guaranteed to be finite
-          vertices.clear(); vertices.push_back(p);
-          for (int i = 0; i < D+1; ++i)
-            if (i != index)
-              vertices.push_back(parent_cell->vertex(i)->point());
-          Delaunay_vertex vertex_to_check = t.infinite_vertex();
-          for (auto vh_it = c->vertices_begin(); vh_it != c->vertices_end(); ++vh_it)
-            if (!vertex_is_in_full_cell(*vh_it, parent_cell))
-              {
-                vertex_to_check = *vh_it; break;
-              }
-          if (new_cell_is_violated(t, vertices, vertex_to_check, parent_cell->vertex(index), delta, power_protection, theta0)) 
-          //if (new_cell_is_violated(t, vertices, vertex_to_check->point(), delta)) 
-            return true;            
-        }
-    } 
-  else
-    {
-      // Inside of the convex hull is + side. Outside is - side.
-      for (auto vh_it = c->vertices_begin(); vh_it != c->vertices_end(); ++vh_it)
-        if (!t.is_infinite(*vh_it))
-          vertices.push_back((*vh_it)->point());
-      Delaunay_triangulation::Vertex_iterator v_it = t.vertices_begin();
-      while (t.is_infinite(v_it) || vertex_is_in_full_cell(v_it, c))
-        v_it++;
-      Hyperplane_d facet_plane(vertices.begin(), vertices.end(), v_it->point(), CGAL::ON_POSITIVE_SIDE);
-      //CGAL::Oriented_side outside = Oriented_side_d()(facet_plane, v_it->point());
-      Vector_d orth_v = facet_plane.orthogonal_vector();
-      std::vector<FT> coords;
-      auto orth_i = orth_v.cartesian_begin(), p_i = p.cartesian_begin();
-      for (; orth_i != orth_v.cartesian_end(); ++orth_i, ++p_i)
-        coords.push_back((*p_i) - (*orth_i) * delta / sqrt(orth_v.squared_length()));
-      Point_d p_delta = Point_d(coords);
-      bool p_is_inside = !Has_on_positive_side_d()(facet_plane, p) && (Oriented_side_d()(facet_plane, p) != CGAL::ZERO);
-      bool p_delta_is_inside = !Has_on_positive_side_d()(facet_plane, p_delta);
-
-      // If we work with power protection, we just ignore any conflicts
-      if (!power_protection && !p_is_inside && p_delta_is_inside)
-        return true;
-      //if the cell is infinite we look at the neighbours regardless
-      if (p_is_inside)
-        {
-          c->tds_data().mark_visited();
-          marked_cells.push_back(c);    
-          for (int i = 0; i < D+1; ++i)
-            {
-              Full_cell_handle next_c = c->neighbor(i);
-              if (next_c->tds_data().is_clear() &&
-                  is_violating_protection(p, t, next_c, c, i, D, delta, marked_cells, power_protection, theta0))
-                return true;
-            }
-        }
-      else
-        {
-          // facet f is on the border of the conflict zone : check protection of simplex {p,f}
-          // the new simplex is finite if the parent cell is finite
-          vertices.clear(); vertices.push_back(p);
-          for (int i = 0; i < D+1; ++i)
-            if (i != index)
-              if (!t.is_infinite(parent_cell->vertex(i)))
-                vertices.push_back(parent_cell->vertex(i)->point());
-          Delaunay_vertex vertex_to_check = t.infinite_vertex();
-          for (auto vh_it = c->vertices_begin(); vh_it != c->vertices_end(); ++vh_it)
-            if (!vertex_is_in_full_cell(*vh_it, parent_cell))
-              {
-                vertex_to_check = *vh_it; break;
-              }
-          if (new_cell_is_violated(t, vertices, vertex_to_check, parent_cell->vertex(index), delta, power_protection, theta0)) 
-          //if (new_cell_is_violated(t, vertices, vertex_to_check->point(), delta)) 
-            return true;
-        }
-    }
-  //c->tds_data().clear_visited();
-  //marked_cells.pop_back();
-  return false;
-}
-
-/** Checks if inserting the point p in t will make conflicts
- *
- *  p is the point to insert
- *  t is the current triangulation
- *  D is the dimension of triangulation
- *  delta is the protection constant
- *  power_protection is true iff you are working with delta-power protection
- *  OUT: true iff inserting p produces a violation of delta-protection.
- */
-
-bool is_violating_protection(Point_d& p, Delaunay_triangulation& t, int D, FT delta, bool power_protection, FT theta0)
-{
-  Euclidean_distance ed;
-  Delaunay_triangulation::Vertex_handle v;
-  Delaunay_triangulation::Face f(t.current_dimension()); 
-  Delaunay_triangulation::Facet ft; 
-  Delaunay_triangulation::Full_cell_handle c; 
-  Delaunay_triangulation::Locate_type lt;
-  std::vector<Full_cell_handle> marked_cells;
-  c = t.locate(p, lt, f, ft, v);
-  bool violation_existing_cells = is_violating_protection(p, t, c, c, 0, D, delta, marked_cells, power_protection, theta0);
-  for (Full_cell_handle fc : marked_cells)
-    fc->tds_data().clear();
-  return violation_existing_cells;
-}
-
-///////////////////////////////////////////////////////////////////////
-///////////////////////////////////////////////////////////////////////
-//!!!!!!!!!!!!! THE INTERFACE FOR LANDMARK CHOICE IS BELOW !!!!!!!!!!//
-///////////////////////////////////////////////////////////////////////
-///////////////////////////////////////////////////////////////////////
-
-///////////////////////////////////////////////////////////////////////
-// LANDMARK CHOICE PROCEDURE
-///////////////////////////////////////////////////////////////////////
-
-/** Procedure to compute a maximal protected subset from a point cloud. All OUTs should be empty at call.
- *
- *  IN:  W is the initial point cloud having type Epick_d<Dynamic_dimension_tag>::Point_d
- *  IN:  nbP is the size of W
- *  OUT: landmarks is the output vector for the points
- *  OUT: landmarks_ind is the output vector for the indices of the selected points in W
- *  IN:  delta is the constant of protection
- *  OUT: full_cells is the output vector of the simplices in the final Delaunay triangulation
- *  IN:  torus is true iff you are working on a flat torus [-1,1]^d
- */ 
-
-void landmark_choice_protected_delaunay(Point_Vector& W, int nbP, Point_Vector& landmarks, std::vector<int>& landmarks_ind, FT delta, std::vector<std::vector<int>>& full_cells, bool torus, bool power_protection, FT theta0)
-{
-  bool return_ = true;
-  unsigned D = W[0].size();
-  Torus_distance td;
-  Euclidean_distance ed;
-  Delaunay_triangulation t(D);
-  CGAL::Random rand;
-  int landmark_count = 0;
-  std::list<int> index_list;
-  //      shuffle the list of indexes (via a vector)
-  {
-    std::vector<int> temp_vector;
-    for (int i = 0; i < nbP; ++i)
-      temp_vector.push_back(i);
-    unsigned seed = std::chrono::system_clock::now().time_since_epoch().count();
-    std::shuffle(temp_vector.begin(), temp_vector.end(), std::default_random_engine(seed));
-    //CGAL::spatial_sort(temp_vector.begin(), temp_vector.end());
-    for (std::vector<int>::iterator it = temp_vector.begin(); it != temp_vector.end(); ++it)
-      index_list.push_front(*it);
-  }
-  if (!torus)
-    for (unsigned pos1 = 0; pos1 < D+1; ++pos1)
-      {
-        std::vector<FT> point;
-        for (unsigned i = 0; i < pos1; ++i)
-          point.push_back(-1);
-        if (pos1 != D)
-          point.push_back(1);
-        for (unsigned i = pos1+1; i < D; ++i)
-          point.push_back(0);
-        assert(point.size() == D);
-        W[index_list.front()] = Point_d(point);
-        insert_delaunay_landmark_with_copies(W, index_list.front(), landmarks_ind, t, landmark_count, torus);
-        index_list.pop_front();
-      }
-  else if (D == 2)
-    {
-      for (int i = 0; i < 4; ++i)
-        for (int j = 0; j < 2; ++j)
-          {
-            W[index_list.front()] = Point_d(std::vector<FT>{i*0.5, j*1.0});
-            insert_delaunay_landmark_with_copies(W, index_list.front(), landmarks_ind, t, landmark_count, torus);
-            index_list.pop_front();
-            W[index_list.front()] = Point_d(std::vector<FT>{0.25+i*0.5, 0.5+j});
-            insert_delaunay_landmark_with_copies(W, index_list.front(), landmarks_ind, t, landmark_count, torus);
-            index_list.pop_front();
-          }
-    }
-  else
-    std::cout << "No torus starter available for dim>2\n";
-  std::list<int>::iterator list_it = index_list.begin();
-  while (list_it != index_list.end())
-    {
-      if (!is_violating_protection(W[*list_it], t, D, delta, power_protection, theta0))
-        {
-          // If no conflicts then insert in every copy of T^3
-
-          insert_delaunay_landmark_with_copies(W, *list_it, landmarks_ind, t, landmark_count, torus);
-          if (return_)
-            {
-              index_list.erase(list_it);
-              list_it = index_list.begin();
-            }
-          else
-            index_list.erase(list_it++);
-          /*
-          // PIECE OF CODE FOR DEBUGGING PURPOSES
-          
-          Delaunay_vertex inserted_v = insert_delaunay_landmark_with_copies(W, *list_it, landmarks_ind, t, landmark_count);
-          if (triangulation_is_protected(t, delta))
-            {
-              index_list.erase(list_it);
-              list_it = index_list.begin();
-            }
-          else
-            { //THAT'S WHERE SOMETHING'S WRONG
-              t.remove(inserted_v);
-              landmarks_ind.pop_back();
-              landmark_count--;
-              write_delaunay_mesh(t, W[*list_it], is2d);
-              is_violating_protection(W[*list_it], t_old, D, delta); //Called for encore
-            }
-          */
-          //std::cout << "index_list_size() = " << index_list.size() << "\n";
-        }
-      else
-        {
-          list_it++;
-          //std::cout << "!!!!!WARNING!!!!! A POINT HAS BEEN OMITTED!!!\n";
-        }
-      //if (list_it != index_list.end())
-      //  write_delaunay_mesh(t, W[*list_it], is2d);
-    }
-  fill_landmarks(W, landmarks, landmarks_ind, torus);
-  fill_full_cell_vector(t, full_cells);
-  /*
-  if (triangulation_is_protected(t, delta))
-    std::cout << "Triangulation is ok\n";
-  else
-    {
-      std::cout << "Triangulation is BAD!! T_T しくしく!\n";
-    }
-  */
-  //write_delaunay_mesh(t, W[0], is2d);
-  //std::cout << t << std::endl;
-}
-
-#endif
diff --git a/src/Witness_complex/example/protected_sets/protected_sets_paper.cpp b/src/Witness_complex/example/protected_sets/protected_sets_paper.cpp
deleted file mode 100644
index f3df3f1e..00000000
--- a/src/Witness_complex/example/protected_sets/protected_sets_paper.cpp
+++ /dev/null
@@ -1,610 +0,0 @@
-#ifndef PROTECTED_SETS_H
-#define PROTECTED_SETS_H
-
-#include <algorithm>
-#include <CGAL/Cartesian_d.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/Euclidean_distance.h>
-#include <CGAL/Kernel_d/Sphere_d.h>
-#include <CGAL/Kernel_d/Hyperplane_d.h>
-#include <CGAL/Kernel_d/Vector_d.h>
-
-typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
-typedef K::Point_d Point_d;
-typedef K::Vector_d Vector_d;
-typedef K::Oriented_side_d Oriented_side_d;
-typedef K::Has_on_positive_side_d Has_on_positive_side_d;
-typedef K::Sphere_d Sphere_d;
-typedef K::Hyperplane_d Hyperplane_d;
-
-typedef CGAL::Delaunay_triangulation<K> Delaunay_triangulation;
-typedef Delaunay_triangulation::Facet Facet;
-typedef Delaunay_triangulation::Vertex_handle Delaunay_vertex;
-typedef Delaunay_triangulation::Full_cell_handle Full_cell_handle;
-
-typedef std::vector<Point_d> Point_Vector;
-typedef CGAL::Euclidean_distance<Traits_base> Euclidean_distance;
-
-FT  _sfty = pow(10,-14);
-
-///////////////////////////////////////////////////////////////////////////////////////////////////////////
-// AUXILLARY FUNCTIONS
-///////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-/** Insert a point in Delaunay triangulation. If you are working in a flat torus, the procedure adds all the 3^d copies in adjacent cubes as well 
- *  
- *  W is the initial point vector
- *  chosen_landmark is the index of the chosen point in W
- *  landmarks_ind is the vector of indices of already chosen points in W
- *  delaunay is the Delaunay triangulation
- *  landmark_count is the current number of chosen vertices
- *  torus is true iff you are working on a flat torus [-1,1]^d
- *  OUT: Vertex handle to the newly inserted point
- */
-Delaunay_vertex insert_delaunay_landmark_with_copies(Point_d& p, Delaunay_triangulation& delaunay, int& landmark_count, bool torus)
-{
-  if (!torus)
-    {
-      Delaunay_vertex v =delaunay.insert(p);
-      landmark_count++;
-      return v;
-    }
-  else
-    {
-      int D = W[0].size();
-      int nb_cells = pow(3, D);
-      Delaunay_vertex v;
-      for (int i = 0; i < nb_cells; ++i)
-        {
-          std::vector<FT> point;
-          int cell_i = i;
-          for (int l = 0; l < D; ++l)
-            {
-              point.push_back(p[l] + 2.0*(cell_i%3-1));
-              cell_i /= 3;
-            }
-          v = delaunay.insert(point);
-        }
-      landmark_count++;
-      return v;
-    }
-}
-
-/** Small check if the vertex v is in the full cell fc
- */
-
-bool vertex_is_in_full_cell(Delaunay_triangulation::Vertex_handle v, Full_cell_handle fc)
-{
-  for (auto v_it = fc->vertices_begin(); v_it != fc->vertices_end(); ++v_it)
-    if (*v_it == v)
-      return true;
-  return false;
-}
-
-/** Fill chosen point vector from indices with copies if you are working on a flat torus
- *  
- *  IN:  W is the point vector
- *  OUT: landmarks is the output vector
- *  IN:  landmarks_ind is the vector of indices
- *  IN:  torus is true iff you are working on a flat torus [-1,1]^d
- */
-
-void fill_landmarks(Point_Vector& W, Point_Vector& landmarks, std::vector<int>& landmarks_ind, bool torus)
-{
-  if (!torus)
-    for (unsigned j = 0; j < landmarks_ind.size(); ++j)
-      landmarks.push_back(W[landmarks_ind[j]]);
-  else
-    {
-      int D = W[0].size();
-      int nb_cells = pow(3, D);
-      int nbL = landmarks_ind.size();
-      // Fill landmarks
-      for (int i = 0; i < nb_cells-1; ++i)
-        for (int j = 0; j < nbL; ++j)
-          {
-            int cell_i = i;
-            Point_d point;
-            for (int l = 0; l < D; ++l)
-              {
-                point.push_back(W[landmarks_ind[j]][l] + 2.0*(cell_i-1));
-                cell_i /= 3;
-              }
-            landmarks.push_back(point);
-          }
-    }
-}
-
-/** Fill a vector of all simplices in the Delaunay triangulation giving integer indices to vertices
- *
- *  IN: t is the Delaunay triangulation
- *  OUT: full_cells is the output vector
- */
-
-void fill_full_cell_vector(Delaunay_triangulation& t, std::vector<std::vector<int>>& full_cells)
-{
-  // Store vertex indices in a map
-  int ind = 0; //index of a vertex
-  std::map<Delaunay_triangulation::Vertex_handle, int> index_of_vertex;
-  for (auto v_it = t.vertices_begin(); v_it != t.vertices_end(); ++v_it)
-    if (t.is_infinite(v_it))
-      continue;
-    else
-      index_of_vertex[v_it] = ind++;
-  // Write full cells as vectors in full_cells
-  for (auto fc_it = t.full_cells_begin(); fc_it != t.full_cells_end(); ++fc_it)
-    {
-      if (t.is_infinite(fc_it))
-        continue;
-      Point_Vector vertices;
-      for (auto fc_v_it = fc_it->vertices_begin(); fc_v_it != fc_it->vertices_end(); ++fc_v_it)
-        vertices.push_back((*fc_v_it)->point());
-      Sphere_d cs( vertices.begin(), vertices.end());
-      Point_d csc = cs.center();
-      bool in_cube = true; 
-      for (auto xi = csc.cartesian_begin(); xi != csc.cartesian_end(); ++xi)
-        if (*xi > 1.0 || *xi < -1.0)
-          {
-            in_cube = false; break;
-          }
-      if (!in_cube)
-        continue;
-      std::vector<int> cell;
-      for (auto v_it = fc_it->vertices_begin(); v_it != fc_it->vertices_end(); ++v_it)
-        cell.push_back(index_of_vertex[*v_it]);
-      full_cells.push_back(cell);
-    }
-}
-
-////////////////////////////////////////////////////////////////////////////////////////////////////////////
-// IS VIOLATED TEST
-////////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-/** Check if a newly created cell is protected from old vertices
- *  
- *  t is the Delaunay triangulation
- *  vertices is the vector containing the point to insert and a facet f in t
- *  v1 is the vertex of t, such that f and v1 form a simplex
- *  v2 is the vertex of t, such that f and v2 form another simplex
- *  delta is the protection constant
- *  power_protection is true iff the delta-power protection is used
- */
-
-bool new_cell_is_violated(Delaunay_triangulation& t, std::vector<Point_d>& vertices, const Delaunay_vertex& v1, const Delaunay_vertex v2, FT delta, bool power_protection, FT theta0)
-{
-  assert(vertices.size() == vertices[0].size() ||
-         vertices.size() == vertices[0].size() + 1); //simplex size = d | d+1
-  assert(v1 != v2);
-  if (vertices.size() == vertices[0].size() + 1)
-  // FINITE CASE
-    {
-      Sphere_d cs(vertices.begin(), vertices.end());
-      Point_d center_cs = cs.center();
-      FT r = sqrt(Euclidean_distance().transformed_distance(center_cs, vertices[0]));
-      /*
-      for (auto v_it = t.vertices_begin(); v_it != t.vertices_end(); ++v_it)
-        if (!t.is_infinite(v_it)) 
-          {
-            //CGAL::Oriented_side side = Oriented_side_d()(cs, (v_it)->point()); 
-            if (std::find(vertices.begin(), vertices.end(), v_it->point()) == vertices.end())
-              {
-                FT dist2 = Euclidean_distance().transformed_distance(center_cs, (v_it)->point());
-                if (!power_protection)
-                  if (dist2 >= r*r-_sfty && dist2 <= (r+delta)*(r+delta))
-                    return true;
-                if (power_protection)
-                  if (dist2 >= r*r-_sfty && dist2 <= r*r+delta*delta) 
-                    return true;                 
-              }
-          }
-      */
-      // Check if the simplex is thick enough
-      Hyperplane_d tau_h(vertices.begin()+1, vertices.end());
-      Vector_d orth_tau = tau_h.orthogonal_vector();
-      /*
-               p_s1 = Vector_d(*(vertices.begin()), *(vertices.begin()+1));
-      */
-      //std::cout << "||orth_tau|| = " << sqrt(orth_tau.squared_length()) << "\n";
-      FT orth_length = sqrt(orth_tau.squared_length());
-      K::Cartesian_const_iterator_d o_it, p_it, s_it, c_it;
-      // Compute the altitude
-      FT h = 0;
-      for (o_it = orth_tau.cartesian_begin(),
-           p_it = vertices.begin()->cartesian_begin(),
-           s_it = (vertices.begin()+1)->cartesian_begin();
-           o_it != orth_tau.cartesian_end();
-           ++o_it, ++p_it, ++s_it)
-        h += (*o_it)*(*p_it - *s_it)/orth_length;
-      h = fabs(h);
-      // Is the center inside the box?
-      bool inside_the_box = true;
-      for (c_it = center_cs.cartesian_begin(); c_it != center_cs.cartesian_end(); ++c_it)
-        if (*c_it > 1.0 || *c_it < -1.0)
-          {
-            inside_the_box = false; break;
-          }
-      if (inside_the_box && h/r < theta0)
-        return true;
-      if (!t.is_infinite(v1))
-        {
-          FT dist2 = Euclidean_distance().transformed_distance(center_cs, v1->point());
-          if (!power_protection)
-            if (dist2 >= r*r-_sfty && dist2 <= (r+delta)*(r+delta))
-              return true;
-          if (power_protection)
-            if (dist2 >= r*r-_sfty && dist2 <= r*r+delta*delta) 
-              return true;
-        }
-      if (!t.is_infinite(v2))
-        {
-          FT dist2 = Euclidean_distance().transformed_distance(center_cs, v2->point());
-          if (!power_protection)
-            if (dist2 >= r*r-_sfty && dist2 <= (r+delta)*(r+delta))
-              return true;
-          if (power_protection)
-            if (dist2 >= r*r-_sfty && dist2 <= r*r+delta*delta) 
-              return true;
-        }
-    }
-  else
-  // INFINITE CASE
-    {
-      Delaunay_triangulation::Vertex_iterator v = t.vertices_begin();
-      while (t.is_infinite(v) || std::find(vertices.begin(), vertices.end(), v->point()) == vertices.end())
-        v++;
-      Hyperplane_d facet_plane(vertices.begin(), vertices.end(), v->point(), CGAL::ON_POSITIVE_SIDE);
-      Vector_d orth_v = facet_plane.orthogonal_vector();
-      /*
-      for (auto v_it = t.vertices_begin(); v_it != t.vertices_end(); ++v_it)
-        if (!t.is_infinite(v_it))
-          if (std::find(vertices.begin(), vertices.end(), v_it->point()) == vertices.end())
-            {
-              std::vector<FT> coords;
-              Point_d p = v_it->point();
-              auto orth_i = orth_v.cartesian_begin(), p_i = p.cartesian_begin();
-              for (; orth_i != orth_v.cartesian_end(); ++orth_i, ++p_i)
-                coords.push_back((*p_i) - (*orth_i) * delta / sqrt(orth_v.squared_length()));
-              Point_d p_delta = Point_d(coords);
-              bool p_is_inside = !Has_on_positive_side_d()(facet_plane, p);
-              bool p_delta_is_inside = !Has_on_positive_side_d()(facet_plane, p_delta);
-              if (!p_is_inside && p_delta_is_inside)
-                return true;
-            }
-      */
-      if (!t.is_infinite(v1))
-        {
-          std::vector<FT> coords;
-          Point_d p = v1->point();
-          auto orth_i = orth_v.cartesian_begin(), p_i = p.cartesian_begin();
-          for (; orth_i != orth_v.cartesian_end(); ++orth_i, ++p_i)
-            coords.push_back((*p_i) - (*orth_i) * delta / sqrt(orth_v.squared_length()));
-          Point_d p_delta = Point_d(coords);
-          bool p_is_inside = !Has_on_positive_side_d()(facet_plane, p);
-          bool p_delta_is_inside = !Has_on_positive_side_d()(facet_plane, p_delta);
-          if (!power_protection && !p_is_inside && p_delta_is_inside)
-            return true;
-        }
-      if (!t.is_infinite(v2))
-        {
-          std::vector<FT> coords;
-          Point_d p = v2->point();
-          auto orth_i = orth_v.cartesian_begin(), p_i = p.cartesian_begin();
-          for (; orth_i != orth_v.cartesian_end(); ++orth_i, ++p_i)
-            coords.push_back((*p_i) - (*orth_i) * delta / sqrt(orth_v.squared_length()));
-          Point_d p_delta = Point_d(coords);
-          bool p_is_inside = !Has_on_positive_side_d()(facet_plane, p);
-          bool p_delta_is_inside = !Has_on_positive_side_d()(facet_plane, p_delta);
-          if (!power_protection && !p_is_inside && p_delta_is_inside)
-            return true;
-        }
-    }
-  return false;
-}
-  
-/** Auxillary recursive function to check if the point p violates the protection of the cell c and
- *  if there is a violation of an eventual new cell
- *
- *  p is the point to insert
- *  t is the current triangulation
- *  c is the current cell (simplex)
- *  parent_cell is the parent cell (simplex)
- *  index is the index of the facet between c and parent_cell from parent_cell's point of view
- *  D is the dimension of the triangulation
- *  delta is the protection constant
- *  marked_cells is the vector of all visited cells containing p in their circumscribed ball
- *  power_protection is true iff you are working with delta-power protection
- *
- *  OUT: true iff inserting p hasn't produced any violation so far
- */
-
-bool is_violating_protection(Point_d& p, Delaunay_triangulation& t, Full_cell_handle c, Full_cell_handle parent_cell, int index, int D, FT delta, std::vector<Full_cell_handle>& marked_cells, bool power_protection, FT theta0)
-{
-  Euclidean_distance ed;
-  std::vector<Point_d> vertices;
-  if (!t.is_infinite(c))
-    {
-      // if the cell is finite, we look if the protection is violated
-      for (auto v_it = c->vertices_begin(); v_it != c->vertices_end(); ++v_it)
-        vertices.push_back((*v_it)->point());
-      Sphere_d cs( vertices.begin(), vertices.end());
-      Point_d center_cs = cs.center();
-      FT r = sqrt(ed.transformed_distance(center_cs, vertices[0]));
-      FT dist2 = ed.transformed_distance(center_cs, p);
-      // if the new point is inside the protection ball of a non conflicting simplex
-      if (!power_protection)
-        if (dist2 >= r*r-_sfty && dist2 <= (r+delta)*(r+delta))
-          return true;
-      if (power_protection)
-        if (dist2 >= r*r-_sfty && dist2 <= r*r+delta*delta) 
-          return true;    
-      // if the new point is inside the circumscribing ball : continue violation searching on neighbours
-      //if (dist2 < r*r)
-      //if (dist2 < (5*r+delta)*(5*r+delta))
-      if (dist2 < r*r)
-        {
-          c->tds_data().mark_visited();
-          marked_cells.push_back(c);
-          for (int i = 0; i < D+1; ++i)
-            {
-              Full_cell_handle next_c = c->neighbor(i);
-              if (next_c->tds_data().is_clear() &&
-                  is_violating_protection(p, t, next_c, c, i, D, delta, marked_cells, power_protection, theta0))
-                return true;
-            }
-        }
-      // if the new point is outside the protection sphere
-      else
-        {
-          // facet f is on the border of the conflict zone : check protection of simplex {p,f}
-          // the new simplex is guaranteed to be finite
-          vertices.clear(); vertices.push_back(p);
-          for (int i = 0; i < D+1; ++i)
-            if (i != index)
-              vertices.push_back(parent_cell->vertex(i)->point());
-          Delaunay_vertex vertex_to_check = t.infinite_vertex();
-          for (auto vh_it = c->vertices_begin(); vh_it != c->vertices_end(); ++vh_it)
-            if (!vertex_is_in_full_cell(*vh_it, parent_cell))
-              {
-                vertex_to_check = *vh_it; break;
-              }
-          if (new_cell_is_violated(t, vertices, vertex_to_check, parent_cell->vertex(index), delta, power_protection, theta0)) 
-          //if (new_cell_is_violated(t, vertices, vertex_to_check->point(), delta)) 
-            return true;            
-        }
-    } 
-  else
-    {
-      // Inside of the convex hull is + side. Outside is - side.
-      for (auto vh_it = c->vertices_begin(); vh_it != c->vertices_end(); ++vh_it)
-        if (!t.is_infinite(*vh_it))
-          vertices.push_back((*vh_it)->point());
-      Delaunay_triangulation::Vertex_iterator v_it = t.vertices_begin();
-      while (t.is_infinite(v_it) || vertex_is_in_full_cell(v_it, c))
-        v_it++;
-      Hyperplane_d facet_plane(vertices.begin(), vertices.end(), v_it->point(), CGAL::ON_POSITIVE_SIDE);
-      //CGAL::Oriented_side outside = Oriented_side_d()(facet_plane, v_it->point());
-      Vector_d orth_v = facet_plane.orthogonal_vector();
-      std::vector<FT> coords;
-      auto orth_i = orth_v.cartesian_begin(), p_i = p.cartesian_begin();
-      for (; orth_i != orth_v.cartesian_end(); ++orth_i, ++p_i)
-        coords.push_back((*p_i) - (*orth_i) * delta / sqrt(orth_v.squared_length()));
-      Point_d p_delta = Point_d(coords);
-      bool p_is_inside = !Has_on_positive_side_d()(facet_plane, p) && (Oriented_side_d()(facet_plane, p) != CGAL::ZERO);
-      bool p_delta_is_inside = !Has_on_positive_side_d()(facet_plane, p_delta);
-
-      // If we work with power protection, we just ignore any conflicts
-      if (!power_protection && !p_is_inside && p_delta_is_inside)
-        return true;
-      //if the cell is infinite we look at the neighbours regardless
-      if (p_is_inside)
-        {
-          c->tds_data().mark_visited();
-          marked_cells.push_back(c);    
-          for (int i = 0; i < D+1; ++i)
-            {
-              Full_cell_handle next_c = c->neighbor(i);
-              if (next_c->tds_data().is_clear() &&
-                  is_violating_protection(p, t, next_c, c, i, D, delta, marked_cells, power_protection, theta0))
-                return true;
-            }
-        }
-      else
-        {
-          // facet f is on the border of the conflict zone : check protection of simplex {p,f}
-          // the new simplex is finite if the parent cell is finite
-          vertices.clear(); vertices.push_back(p);
-          for (int i = 0; i < D+1; ++i)
-            if (i != index)
-              if (!t.is_infinite(parent_cell->vertex(i)))
-                vertices.push_back(parent_cell->vertex(i)->point());
-          Delaunay_vertex vertex_to_check = t.infinite_vertex();
-          for (auto vh_it = c->vertices_begin(); vh_it != c->vertices_end(); ++vh_it)
-            if (!vertex_is_in_full_cell(*vh_it, parent_cell))
-              {
-                vertex_to_check = *vh_it; break;
-              }
-          if (new_cell_is_violated(t, vertices, vertex_to_check, parent_cell->vertex(index), delta, power_protection, theta0)) 
-          //if (new_cell_is_violated(t, vertices, vertex_to_check->point(), delta)) 
-            return true;
-        }
-    }
-  //c->tds_data().clear_visited();
-  //marked_cells.pop_back();
-  return false;
-}
-
-/** Checks if inserting the point p in t will make conflicts
- *
- *  p is the point to insert
- *  t is the current triangulation
- *  D is the dimension of triangulation
- *  delta is the protection constant
- *  power_protection is true iff you are working with delta-power protection
- *  OUT: true iff inserting p produces a violation of delta-protection.
- */
-
-bool is_violating_protection(Point_d& p, Delaunay_triangulation& t, int D, FT delta, bool power_protection, FT theta0)
-{
-  Euclidean_distance ed;
-  Delaunay_triangulation::Vertex_handle v;
-  Delaunay_triangulation::Face f(t.current_dimension()); 
-  Delaunay_triangulation::Facet ft; 
-  Delaunay_triangulation::Full_cell_handle c; 
-  Delaunay_triangulation::Locate_type lt;
-  std::vector<Full_cell_handle> marked_cells;
-  c = t.locate(p, lt, f, ft, v);
-  bool violation_existing_cells = is_violating_protection(p, t, c, c, 0, D, delta, marked_cells, power_protection, theta0);
-  for (Full_cell_handle fc : marked_cells)
-    fc->tds_data().clear();
-  return violation_existing_cells;
-}
-
-//////////////////////////////////////////////////////////////////////
-// INITIALIZATION
-//////////////////////////////////////////////////////////////////////
-
-void initialize(Search_Tree& W, Delaunay& t, int D, int width, bool torus)
-{
-  if (!torus)
-    std::cout << "Non-toric case is not supported\n";
-  else
-    {
-      if (D == 2)
-        {
-          FT stepx = 2.0/width;
-          FT stepy = sqrt(3)/width;
-          for (int i = 0; i < width; ++i)
-            for (int j = 0; j < floor(2*width/sqrt(3)); ++j)
-              {
-                insert_delaunay_landmark_with_copies(Point_d(step*i,))
-              }
-        }
-      else (D == 3)
-        {
-          
-        }
-      else std::cout << "T^d with d>3 not supported";
-    }
-}
-  
-///////////////////////////////////////////////////////////////////////
-///////////////////////////////////////////////////////////////////////
-//!!!!!!!!!!!!! THE INTERFACE FOR LANDMARK CHOICE IS BELOW !!!!!!!!!!//
-///////////////////////////////////////////////////////////////////////
-///////////////////////////////////////////////////////////////////////
-
-///////////////////////////////////////////////////////////////////////
-// LANDMARK CHOICE PROCEDURE AS IN PAPER
-///////////////////////////////////////////////////////////////////////
-
-/** Procedure to compute a maximal protected subset from a point cloud. All OUTs should be empty at call.
- *
- *  IN:  W is the initial point cloud having type Epick_d<Dynamic_dimension_tag>::Point_d
- *  IN:  nbP is the size of W
- *  OUT: landmarks is the output vector for the points
- *  OUT: landmarks_ind is the output vector for the indices of the selected points in W
- *  IN:  delta is the constant of protection
- *  OUT: full_cells is the output vector of the simplices in the final Delaunay triangulation
- *  IN:  torus is true iff you are working on a flat torus [-1,1]^d
- */ 
-
-template<class Search_Tree>
-void protected_delaunay_refinement(Search_Tree& W, int nbP, Point_Vector& landmarks, FT delta, bool torus, bool power_protection, FT theta0)
-{
-  bool return_ = true;
-  unsigned D = W[0].size();
-  Torus_distance td;
-  Euclidean_distance ed;
-  Delaunay_triangulation t(D);
-  CGAL::Random rand;
-  int landmark_count = 0;
-  //std::list<int> index_list;
-  //      shuffle the list of indexes (via a vector)
-  // {
-  //   std::vector<int> temp_vector;
-  //   for (int i = 0; i < nbP; ++i)
-  //     temp_vector.push_back(i);
-  //   unsigned seed = std::chrono::system_clock::now().time_since_epoch().count();
-  //   std::shuffle(temp_vector.begin(), temp_vector.end(), std::default_random_engine(seed));
-  //   //CGAL::spatial_sort(temp_vector.begin(), temp_vector.end());
-  //   for (std::vector<int>::iterator it = temp_vector.begin(); it != temp_vector.end(); ++it)
-  //     index_list.push_front(*it);
-  // }
-  if (torus)
-  if (D == 2)
-    // \T^2
-    {
-      for (int i = 0; i < 4; ++i)
-        for (int j = 0; j < 2; ++j)
-          {
-            W[index_list.front()] = Point_d(std::vector<FT>{i*0.5, j*1.0});
-            insert_delaunay_landmark_with_copies(W, index_list.front(), landmarks_ind, t, landmark_count, torus);
-            index_list.pop_front();
-            W[index_list.front()] = Point_d(std::vector<FT>{0.25+i*0.5, 0.5+j});
-            insert_delaunay_landmark_with_copies(W, index_list.front(), landmarks_ind, t, landmark_count, torus);
-            index_list.pop_front();
-          }
-    }
-  else if (D == 3)
-    {
-      
-    }
-    //std::cout << "No torus starter available for dim>2\n";
-  std::list<int>::iterator list_it = index_list.begin();
-  while (list_it != index_list.end())
-    {
-      if (!is_violating_protection(W[*list_it], t, D, delta, power_protection, theta0))
-        {
-          // If no conflicts then insert in every copy of T^3
-
-          insert_delaunay_landmark_with_copies(W, *list_it, landmarks_ind, t, landmark_count, torus);
-          if (return_)
-            {
-              index_list.erase(list_it);
-              list_it = index_list.begin();
-            }
-          else
-            index_list.erase(list_it++);
-          /*
-          // PIECE OF CODE FOR DEBUGGING PURPOSES
-          
-          Delaunay_vertex inserted_v = insert_delaunay_landmark_with_copies(W, *list_it, landmarks_ind, t, landmark_count);
-          if (triangulation_is_protected(t, delta))
-            {
-              index_list.erase(list_it);
-              list_it = index_list.begin();
-            }
-          else
-            { //THAT'S WHERE SOMETHING'S WRONG
-              t.remove(inserted_v);
-              landmarks_ind.pop_back();
-              landmark_count--;
-              write_delaunay_mesh(t, W[*list_it], is2d);
-              is_violating_protection(W[*list_it], t_old, D, delta); //Called for encore
-            }
-          */
-          //std::cout << "index_list_size() = " << index_list.size() << "\n";
-        }
-      else
-        {
-          list_it++;
-          //std::cout << "!!!!!WARNING!!!!! A POINT HAS BEEN OMITTED!!!\n";
-        }
-      //if (list_it != index_list.end())
-      //  write_delaunay_mesh(t, W[*list_it], is2d);
-    }
-  fill_landmarks(W, landmarks, landmarks_ind, torus);
-  fill_full_cell_vector(t, full_cells);
-  /*
-  if (triangulation_is_protected(t, delta))
-    std::cout << "Triangulation is ok\n";
-  else
-    {
-      std::cout << "Triangulation is BAD!! T_T しくしく!\n";
-    }
-  */
-  //write_delaunay_mesh(t, W[0], is2d);
-  //std::cout << t << std::endl;
-}
-
-#endif
diff --git a/src/Witness_complex/example/protected_sets/protected_sets_paper.h b/src/Witness_complex/example/protected_sets/protected_sets_paper.h
deleted file mode 100644
index 61fcc75b..00000000
--- a/src/Witness_complex/example/protected_sets/protected_sets_paper.h
+++ /dev/null
@@ -1,917 +0,0 @@
-#ifndef PROTECTED_SETS_H
-#define PROTECTED_SETS_H
-
-#include <algorithm>
-#include <CGAL/Cartesian_d.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/Euclidean_distance.h>
-#include <CGAL/Kernel_d/Sphere_d.h>
-#include <CGAL/Kernel_d/Hyperplane_d.h>
-#include <CGAL/Kernel_d/Vector_d.h>
-
-#include <CGAL/Orthogonal_k_neighbor_search.h>
-#include <CGAL/Kd_tree.h>
-#include <CGAL/Fuzzy_sphere.h>
-
-#include <boost/heap/fibonacci_heap.hpp>
-#include <boost/heap/policies.hpp>
-
-#include "output_tikz.h"
-
-typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
-typedef K::Point_d Point_d;
-typedef K::Line_d Line_d;
-typedef K::Vector_d Vector_d;
-typedef K::Oriented_side_d Oriented_side_d;
-typedef K::Has_on_positive_side_d Has_on_positive_side_d;
-typedef K::Sphere_d Sphere_d;
-typedef K::Hyperplane_d Hyperplane_d;
-
-typedef CGAL::Delaunay_triangulation<K> Delaunay_triangulation;
-typedef Delaunay_triangulation::Facet Facet;
-typedef Delaunay_triangulation::Vertex_handle Delaunay_vertex;
-typedef Delaunay_triangulation::Full_cell_handle Full_cell_handle;
-
-typedef std::vector<Point_d> Point_Vector;
-typedef CGAL::Euclidean_distance<Traits_base> Euclidean_distance;
-
-typedef CGAL::Search_traits_adapter<
-  std::ptrdiff_t, Point_d*, Traits_base> STraits;
-//typedef K TreeTraits;
-//typedef CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance > Euclidean_adapter;
-//typedef CGAL::Kd_tree<STraits> Kd_tree;
-typedef CGAL::Orthogonal_k_neighbor_search<STraits, CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance>> K_neighbor_search;
-typedef K_neighbor_search::Tree Tree;
-typedef K_neighbor_search::Distance Distance;
-typedef K_neighbor_search::iterator KNS_iterator;
-typedef K_neighbor_search::iterator KNS_range;
-typedef CGAL::Fuzzy_sphere<STraits> Fuzzy_sphere;
-
-
-FT  _sfty = pow(10,-14);
-
-bool experiment1, experiment2 = false;
-
-/* Experiment 1: epsilon as function on time **********************/
-std::vector<FT> eps_vector;
-
-/* Experiment 2: R/epsilon on delta *******************************/
-std::vector<FT> epsratio_vector;
-
-///////////////////////////////////////////////////////////////////////////////////////////////////////////
-// AUXILLARY FUNCTIONS
-///////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-/** Insert a point in Delaunay triangulation. If you are working in a flat torus, the procedure adds all the 3^d copies in adjacent cubes as well 
- *  
- *  W is the initial point vector
- *  chosen_landmark is the index of the chosen point in W
- *  landmarks_ind is the vector of indices of already chosen points in W
- *  delaunay is the Delaunay triangulation
- *  landmark_count is the current number of chosen vertices
- *  torus is true iff you are working on a flat torus [-1,1]^d
- *  OUT: Vertex handle to the newly inserted point
- */
-Delaunay_vertex insert_delaunay_landmark_with_copies(Point_Vector& W, int chosen_landmark, std::vector<int>& landmarks_ind, Delaunay_triangulation& delaunay, int& landmark_count, bool torus)
-{
-  if (!torus)
-    {
-      Delaunay_vertex v =delaunay.insert(W[chosen_landmark]);
-      landmarks_ind.push_back(chosen_landmark);
-      landmark_count++;
-      return v;
-    }
-  else
-    {
-      int D = W[0].size();
-      int nb_cells = pow(3, D);
-      Delaunay_vertex v;
-      for (int i = 0; i < nb_cells; ++i)
-        {
-          std::vector<FT> point;
-          int cell_i = i;
-          for (int l = 0; l < D; ++l)
-            {
-              point.push_back(W[chosen_landmark][l] + 2.0*(cell_i%3-1));
-              cell_i /= 3;
-            }
-          if (i == nb_cells/2)
-            v = delaunay.insert(point); //v = center point
-          else
-            delaunay.insert(point);
-        }
-      landmarks_ind.push_back(chosen_landmark);
-      landmark_count++;
-      return v;
-    }
-}
-
-/** Small check if the vertex v is in the full cell fc
- */
-
-bool vertex_is_in_full_cell(Delaunay_triangulation::Vertex_handle v, Full_cell_handle fc)
-{
-  for (auto v_it = fc->vertices_begin(); v_it != fc->vertices_end(); ++v_it)
-    if (*v_it == v)
-      return true;
-  return false;
-}
-
-/** Fill chosen point vector from indices with copies if you are working on a flat torus
- *  
- *  IN:  W is the point vector
- *  OUT: landmarks is the output vector
- *  IN:  landmarks_ind is the vector of indices
- *  IN:  torus is true iff you are working on a flat torus [-1,1]^d
- */
-
-void fill_landmarks(Point_Vector& W, Point_Vector& landmarks, std::vector<int>& landmarks_ind, bool torus)
-{
-  if (!torus)
-    for (unsigned j = 0; j < landmarks_ind.size(); ++j)
-      landmarks.push_back(W[landmarks_ind[j]]);
-  else
-    {
-      int D = W[0].size();
-      int nb_cells = pow(3, D);
-      int nbL = landmarks_ind.size();
-      // Fill landmarks
-      for (int i = 0; i < nb_cells-1; ++i)
-        for (int j = 0; j < nbL; ++j)
-          {
-            int cell_i = i;
-            Point_d point;
-            for (int l = 0; l < D; ++l)
-              {
-                point.push_back(W[landmarks_ind[j]][l] + 2.0*(cell_i-1));
-                cell_i /= 3;
-              }
-            landmarks.push_back(point);
-          }
-    }
-}
-
-/** Fill a vector of all simplices in the Delaunay triangulation giving integer indices to vertices
- *
- *  IN: t is the Delaunay triangulation
- *  OUT: full_cells is the output vector
- */
-
-void fill_full_cell_vector(Delaunay_triangulation& t, std::vector<std::vector<int>>& full_cells)
-{
-  // Store vertex indices in a map
-  int ind = 0; //index of a vertex
-  std::map<Delaunay_triangulation::Vertex_handle, int> index_of_vertex;
-  for (auto v_it = t.vertices_begin(); v_it != t.vertices_end(); ++v_it)
-    if (t.is_infinite(v_it))
-      continue;
-    else
-      index_of_vertex[v_it] = ind++;
-  // Write full cells as vectors in full_cells
-  for (auto fc_it = t.full_cells_begin(); fc_it != t.full_cells_end(); ++fc_it)
-    {
-      if (t.is_infinite(fc_it))
-        continue;
-      Point_Vector vertices;
-      for (auto fc_v_it = fc_it->vertices_begin(); fc_v_it != fc_it->vertices_end(); ++fc_v_it)
-        vertices.push_back((*fc_v_it)->point());
-      Sphere_d cs( vertices.begin(), vertices.end());
-      Point_d csc = cs.center();
-      bool in_cube = true; 
-      for (auto xi = csc.cartesian_begin(); xi != csc.cartesian_end(); ++xi)
-        if (*xi > 1.0 || *xi < -1.0)
-          {
-            in_cube = false; break;
-          }
-      if (!in_cube)
-        continue;
-      std::vector<int> cell;
-      for (auto v_it = fc_it->vertices_begin(); v_it != fc_it->vertices_end(); ++v_it)
-        cell.push_back(index_of_vertex[*v_it]);
-      full_cells.push_back(cell);
-    }
-}
-
-bool sphere_intersects_cube(Point_d& c, FT r)
-{
-  bool in_cube = true;
-  //  int i = 0, D = p.size();
-  for (auto xi = c.cartesian_begin(); xi != c.cartesian_end(); ++xi)
-    // if ((*xi < 1.0 || *xi > -1.0) &&
-    //     (*xi-r < 1.0 || *xi-r > -1.0) &&
-    //     (*xi+r < 1.0 || *xi+r > -1.0))
-
-    if ((*xi-r < -1.0 && *xi+r < -1.0) ||
-        (*xi-r > 1.0  && *xi+r >  1.0 ))
-      {
-        in_cube = false; break;
-      }
-  return in_cube;
-}
-
-/** Recursive function for checking if the simplex is good,
- *  meaning it does not contain a k-face, which is not theta0^(k-1) thick 
- */
-
-bool is_theta0_good(std::vector<Point_d>& vertices, FT theta0)
-{
-  if (theta0 > 1)
-    {
-      std::cout << "Warning! theta0 is set > 1\n";
-      return false;
-    }
-  int D = vertices.size()-1;
-  if (D <= 1)
-    return true; // Edges are always good
-  //******** Circumscribed sphere
-  Euclidean_distance ed;
-  Sphere_d cs(vertices.begin(), vertices.end());
-  FT r = sqrt(cs.squared_radius());
-  for (std::vector<Point_d>::iterator v_it = vertices.begin(); v_it != vertices.end(); ++v_it)
-    {
-      std::vector<Point_d> facet;
-      for (std::vector<Point_d>::iterator f_it = vertices.begin(); f_it != vertices.end(); ++f_it)
-        if (f_it != v_it)
-          facet.push_back(*f_it);
-      // Compute the altitude
-
-      if (vertices[0].size() == 3 && D == 2)
-        {
-          //Vector_d l = facet[0] - facet[1];
-          FT orth_length2 = ed.transformed_distance(facet[0],facet[1]);
-          K::Cartesian_const_iterator_d l_it, p_it, s_it, c_it;
-          FT h = 0;
-          // Scalar product = <sp,l>
-          FT scalar = 0;
-          for (p_it = v_it->cartesian_begin(),
-               s_it = facet[0].cartesian_begin(),
-               l_it = facet[1].cartesian_begin();
-               p_it != v_it->cartesian_end();
-               ++l_it, ++p_it, ++s_it)
-            scalar += (*l_it - *s_it)*(*p_it - *s_it);
-          // Gram-Schmidt for one vector
-          for (p_it = v_it->cartesian_begin(),
-               s_it = facet[0].cartesian_begin(),
-               l_it = facet[1].cartesian_begin();
-               p_it != v_it->cartesian_end();
-               ++l_it, ++p_it, ++s_it)
-            {
-              FT hx = (*p_it - *s_it) - scalar*(*l_it - *s_it)/orth_length2;
-              h += hx*hx;
-            }
-          h = sqrt(h);
-      
-          if (h/(2*r) < pow(theta0, D-1))
-            return false;
-          if (!is_theta0_good(facet, theta0))
-            return false;
-        }
-      else
-        {
-      Hyperplane_d tau_h(facet.begin(), facet.end(), *v_it);
-      Vector_d orth_tau = tau_h.orthogonal_vector();
-      FT orth_length = sqrt(orth_tau.squared_length());
-      K::Cartesian_const_iterator_d o_it, p_it, s_it, c_it;
-      FT h = 0;
-      for (o_it = orth_tau.cartesian_begin(),
-           p_it = v_it->cartesian_begin(),
-           s_it = (facet.begin())->cartesian_begin();
-           o_it != orth_tau.cartesian_end();
-           ++o_it, ++p_it, ++s_it)
-        h += (*o_it)*(*p_it - *s_it)/orth_length;
-      h = fabs(h);
-      if (h/(2*r) < pow(theta0, D-1))
-        return false;
-      if (!is_theta0_good(facet, theta0))
-        return false;
-        }
-    }
-  return true;
-}
-
-
-////////////////////////////////////////////////////////////////////////////////////////////////////////////
-// IS VIOLATED TEST
-////////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-/** Check if a newly created cell is protected from old vertices
- *  
- *  t is the Delaunay triangulation
- *  vertices is the vector containing the point to insert and a facet f in t
- *  v1 is the vertex of t, such that f and v1 form a simplex
- *  v2 is the vertex of t, such that f and v2 form another simplex
- *  delta is the protection constant
- *  power_protection is true iff the delta-power protection is used
- */
-
-bool new_cell_is_violated(Delaunay_triangulation& t, std::vector<Point_d>& vertices, const Delaunay_vertex& v1, const Delaunay_vertex v2, FT delta, bool power_protection, FT theta0)
-{
-  assert(vertices.size() == vertices[0].size() ||
-         vertices.size() == vertices[0].size() + 1); //simplex size = d | d+1
-  assert(v1 != v2);
-  if (vertices.size() == vertices[0].size() + 1)
-  // FINITE CASE
-    {
-      Sphere_d cs(vertices.begin(), vertices.end());
-      Point_d center_cs = cs.center();
-      FT r = sqrt(Euclidean_distance().transformed_distance(center_cs, vertices[0]));
-      /*
-      for (auto v_it = t.vertices_begin(); v_it != t.vertices_end(); ++v_it)
-        if (!t.is_infinite(v_it)) 
-          {
-            //CGAL::Oriented_side side = Oriented_side_d()(cs, (v_it)->point()); 
-            if (std::find(vertices.begin(), vertices.end(), v_it->point()) == vertices.end())
-              {
-                FT dist2 = Euclidean_distance().transformed_distance(center_cs, (v_it)->point());
-                if (!power_protection)
-                  if (dist2 >= r*r-_sfty && dist2 <= (r+delta)*(r+delta))
-                    return true;
-                if (power_protection)
-                  if (dist2 >= r*r-_sfty && dist2 <= r*r+delta*delta) 
-                    return true;                 
-              }
-          }
-      */
-      // Check if the simplex is theta0-good
-      if (!is_theta0_good(vertices, theta0))
-        return true;
-      // Is the center inside the box? (only Euclidean case)
-      // if (!torus)
-      //   {
-      //     bool inside_the_box = true;
-      //     for (c_it = center_cs.cartesian_begin(); c_it != center_cs.cartesian_end(); ++c_it)
-      //       if (*c_it > 1.0 || *c_it < -1.0)
-      //         {
-      //           inside_the_box = false; break;
-      //         }
-      //     if (inside_the_box && h/r < theta0)
-      //       return true;
-      //   }
-      // Check the two vertices (if not infinite)
-      if (!t.is_infinite(v1))
-        {
-          FT dist2 = Euclidean_distance().transformed_distance(center_cs, v1->point());
-          if (!power_protection)
-            if (dist2 >= r*r-_sfty && dist2 <= (r+delta)*(r+delta))
-              return true;
-          if (power_protection)
-            if (dist2 >= r*r-_sfty && dist2 <= r*r+delta*delta) 
-              return true;
-        }
-      if (!t.is_infinite(v2))
-        {
-          FT dist2 = Euclidean_distance().transformed_distance(center_cs, v2->point());
-          if (!power_protection)
-            if (dist2 >= r*r-_sfty && dist2 <= (r+delta)*(r+delta))
-              return true;
-          if (power_protection)
-            if (dist2 >= r*r-_sfty && dist2 <= r*r+delta*delta) 
-              return true;
-        }
-    }
-  else
-  // INFINITE CASE
-    {
-      Delaunay_triangulation::Vertex_iterator v = t.vertices_begin();
-      while (t.is_infinite(v) || std::find(vertices.begin(), vertices.end(), v->point()) == vertices.end())
-        v++;
-      Hyperplane_d facet_plane(vertices.begin(), vertices.end(), v->point(), CGAL::ON_POSITIVE_SIDE);
-      Vector_d orth_v = facet_plane.orthogonal_vector();
-      /*
-      for (auto v_it = t.vertices_begin(); v_it != t.vertices_end(); ++v_it)
-        if (!t.is_infinite(v_it))
-          if (std::find(vertices.begin(), vertices.end(), v_it->point()) == vertices.end())
-            {
-              std::vector<FT> coords;
-              Point_d p = v_it->point();
-              auto orth_i = orth_v.cartesian_begin(), p_i = p.cartesian_begin();
-              for (; orth_i != orth_v.cartesian_end(); ++orth_i, ++p_i)
-                coords.push_back((*p_i) - (*orth_i) * delta / sqrt(orth_v.squared_length()));
-              Point_d p_delta = Point_d(coords);
-              bool p_is_inside = !Has_on_positive_side_d()(facet_plane, p);
-              bool p_delta_is_inside = !Has_on_positive_side_d()(facet_plane, p_delta);
-              if (!p_is_inside && p_delta_is_inside)
-                return true;
-            }
-      */
-      if (!t.is_infinite(v1))
-        {
-          std::vector<FT> coords;
-          Point_d p = v1->point();
-          auto orth_i = orth_v.cartesian_begin(), p_i = p.cartesian_begin();
-          for (; orth_i != orth_v.cartesian_end(); ++orth_i, ++p_i)
-            coords.push_back((*p_i) - (*orth_i) * delta / sqrt(orth_v.squared_length()));
-          Point_d p_delta = Point_d(coords);
-          bool p_is_inside = !Has_on_positive_side_d()(facet_plane, p);
-          bool p_delta_is_inside = !Has_on_positive_side_d()(facet_plane, p_delta);
-          if (!power_protection && !p_is_inside && p_delta_is_inside)
-            return true;
-        }
-      if (!t.is_infinite(v2))
-        {
-          std::vector<FT> coords;
-          Point_d p = v2->point();
-          auto orth_i = orth_v.cartesian_begin(), p_i = p.cartesian_begin();
-          for (; orth_i != orth_v.cartesian_end(); ++orth_i, ++p_i)
-            coords.push_back((*p_i) - (*orth_i) * delta / sqrt(orth_v.squared_length()));
-          Point_d p_delta = Point_d(coords);
-          bool p_is_inside = !Has_on_positive_side_d()(facet_plane, p);
-          bool p_delta_is_inside = !Has_on_positive_side_d()(facet_plane, p_delta);
-          if (!power_protection && !p_is_inside && p_delta_is_inside)
-            return true;
-        }
-    }
-  return false;
-}
-  
-/** Auxillary recursive function to check if the point p violates the protection of the cell c and
- *  if there is a violation of an eventual new cell
- *
- *  p is the point to insert
- *  t is the current triangulation
- *  c is the current cell (simplex)
- *  parent_cell is the parent cell (simplex)
- *  index is the index of the facet between c and parent_cell from parent_cell's point of view
- *  D is the dimension of the triangulation
- *  delta is the protection constant
- *  marked_cells is the vector of all visited cells containing p in their circumscribed ball
- *  power_protection is true iff you are working with delta-power protection
- *
- *  OUT: true iff inserting p hasn't produced any violation so far
- */
-
-bool is_violating_protection(Point_d& p, Delaunay_triangulation& t, Full_cell_handle c, Full_cell_handle parent_cell, int index, int D, FT delta, std::vector<Full_cell_handle>& marked_cells, bool power_protection, FT theta0)
-{
-  Euclidean_distance ed;
-  std::vector<Point_d> vertices;
-  if (!t.is_infinite(c))
-    {
-      // if the cell is finite, we look if the protection is violated
-      for (auto v_it = c->vertices_begin(); v_it != c->vertices_end(); ++v_it)
-        vertices.push_back((*v_it)->point());
-      Sphere_d cs( vertices.begin(), vertices.end());
-      Point_d center_cs = cs.center();
-      FT r = sqrt(ed.transformed_distance(center_cs, vertices[0]));
-      FT dist2 = ed.transformed_distance(center_cs, p);
-      // if the new point is inside the protection ball of a non conflicting simplex
-      if (!power_protection)
-        if (dist2 >= r*r-_sfty && dist2 <= (r+delta)*(r+delta))
-          return true;
-      if (power_protection)
-        if (dist2 >= r*r-_sfty && dist2 <= r*r+delta*delta) 
-          return true;    
-      // if the new point is inside the circumscribing ball : continue violation searching on neighbours
-      //if (dist2 < r*r)
-      //if (dist2 < (5*r+delta)*(5*r+delta))
-      if (dist2 < r*r)
-        {
-          c->tds_data().mark_visited();
-          marked_cells.push_back(c);
-          for (int i = 0; i < D+1; ++i)
-            {
-              Full_cell_handle next_c = c->neighbor(i);
-              if (next_c->tds_data().is_clear() &&
-                  is_violating_protection(p, t, next_c, c, i, D, delta, marked_cells, power_protection, theta0))
-                return true;
-            }
-        }
-      // if the new point is outside the protection sphere
-      else
-        {
-          // facet f is on the border of the conflict zone : check protection of simplex {p,f}
-          // the new simplex is guaranteed to be finite
-          vertices.clear(); vertices.push_back(p);
-          for (int i = 0; i < D+1; ++i)
-            if (i != index)
-              vertices.push_back(parent_cell->vertex(i)->point());
-          Delaunay_vertex vertex_to_check = t.infinite_vertex();
-          for (auto vh_it = c->vertices_begin(); vh_it != c->vertices_end(); ++vh_it)
-            if (!vertex_is_in_full_cell(*vh_it, parent_cell))
-              {
-                vertex_to_check = *vh_it; break;
-              }
-          if (new_cell_is_violated(t, vertices, vertex_to_check, parent_cell->vertex(index), delta, power_protection, theta0)) 
-          //if (new_cell_is_violated(t, vertices, vertex_to_check->point(), delta)) 
-            return true;            
-        }
-    } 
-  else
-    {
-      // Inside of the convex hull is + side. Outside is - side.
-      for (auto vh_it = c->vertices_begin(); vh_it != c->vertices_end(); ++vh_it)
-        if (!t.is_infinite(*vh_it))
-          vertices.push_back((*vh_it)->point());
-      Delaunay_triangulation::Vertex_iterator v_it = t.vertices_begin();
-      while (t.is_infinite(v_it) || vertex_is_in_full_cell(v_it, c))
-        v_it++;
-      Hyperplane_d facet_plane(vertices.begin(), vertices.end(), v_it->point(), CGAL::ON_POSITIVE_SIDE);
-      //CGAL::Oriented_side outside = Oriented_side_d()(facet_plane, v_it->point());
-      Vector_d orth_v = facet_plane.orthogonal_vector();
-      std::vector<FT> coords;
-      auto orth_i = orth_v.cartesian_begin(), p_i = p.cartesian_begin();
-      for (; orth_i != orth_v.cartesian_end(); ++orth_i, ++p_i)
-        coords.push_back((*p_i) - (*orth_i) * delta / sqrt(orth_v.squared_length()));
-      Point_d p_delta = Point_d(coords);
-      bool p_is_inside = !Has_on_positive_side_d()(facet_plane, p) && (Oriented_side_d()(facet_plane, p) != CGAL::ZERO);
-      bool p_delta_is_inside = !Has_on_positive_side_d()(facet_plane, p_delta);
-
-      // If we work with power protection, we just ignore any conflicts
-      if (!power_protection && !p_is_inside && p_delta_is_inside)
-        return true;
-      //if the cell is infinite we look at the neighbours regardless
-      if (p_is_inside)
-        {
-          c->tds_data().mark_visited();
-          marked_cells.push_back(c);    
-          for (int i = 0; i < D+1; ++i)
-            {
-              Full_cell_handle next_c = c->neighbor(i);
-              if (next_c->tds_data().is_clear() &&
-                  is_violating_protection(p, t, next_c, c, i, D, delta, marked_cells, power_protection, theta0))
-                return true;
-            }
-        }
-      else
-        {
-          // facet f is on the border of the conflict zone : check protection of simplex {p,f}
-          // the new simplex is finite if the parent cell is finite
-          vertices.clear(); vertices.push_back(p);
-          for (int i = 0; i < D+1; ++i)
-            if (i != index)
-              if (!t.is_infinite(parent_cell->vertex(i)))
-                vertices.push_back(parent_cell->vertex(i)->point());
-          Delaunay_vertex vertex_to_check = t.infinite_vertex();
-          for (auto vh_it = c->vertices_begin(); vh_it != c->vertices_end(); ++vh_it)
-            if (!vertex_is_in_full_cell(*vh_it, parent_cell))
-              {
-                vertex_to_check = *vh_it; break;
-              }
-          if (new_cell_is_violated(t, vertices, vertex_to_check, parent_cell->vertex(index), delta, power_protection, theta0)) 
-          //if (new_cell_is_violated(t, vertices, vertex_to_check->point(), delta)) 
-            return true;
-        }
-    }
-  //c->tds_data().clear_visited();
-  //marked_cells.pop_back();
-  return false;
-}
-
-/** Checks if inserting the point p in t will make conflicts
- *
- *  p is the point to insert
- *  t is the current triangulation
- *  D is the dimension of triangulation
- *  delta is the protection constant
- *  power_protection is true iff you are working with delta-power protection
- *  OUT: true iff inserting p produces a violation of delta-protection.
- */
-
-bool is_violating_protection(Point_d& p, Delaunay_triangulation& t, int D, FT delta, bool power_protection, FT theta0)
-{
-  Euclidean_distance ed;
-  Delaunay_triangulation::Vertex_handle v;
-  Delaunay_triangulation::Face f(t.current_dimension()); 
-  Delaunay_triangulation::Facet ft; 
-  Delaunay_triangulation::Full_cell_handle c; 
-  Delaunay_triangulation::Locate_type lt;
-  std::vector<Full_cell_handle> marked_cells;
-  //c = t.locate(p, lt, f, ft, v);
-  c = t.locate(p);
-  bool violation_existing_cells = is_violating_protection(p, t, c, c, 0, D, delta, marked_cells, power_protection, theta0);
-  for (Full_cell_handle fc : marked_cells)
-    fc->tds_data().clear();
-  return violation_existing_cells;
-}
-
-
-////////////////////////////////////////////////////////////////////////
-// INITIALIZATION
-////////////////////////////////////////////////////////////////////////
-
-// Query for a sphere near a cite in all copies of a torus
-// OUT points_inside
-void torus_search(Tree& treeW, int D, Point_d cite, FT r, std::vector<int>& points_inside)
-{
-  int nb_cells = pow(3, D);
-  Delaunay_vertex v;
-  for (int i = 0; i < nb_cells; ++i)
-    {
-      std::vector<FT> cite_copy;
-      int cell_i = i;
-      for (int l = 0; l < D; ++l)
-        {
-          cite_copy.push_back(cite[l] + 2.0*(cell_i%3-1));
-          cell_i /= 3;
-        }
-      Fuzzy_sphere fs(cite_copy, r, 0, treeW.traits());
-      treeW.search(std::insert_iterator<std::vector<int>>(points_inside, points_inside.end()), fs);
-    }
-}
-
-  
-void initialize_torus(Point_Vector& W, Tree& treeW, Delaunay_triangulation& t, FT epsilon, std::vector<int>& landmarks_ind, int& landmark_count)
-{
-  int D = W[0].size();
-  if (D == 2)
-    {
-      int xw = 6, yw = 4;
-      // Triangular lattice close to regular triangles h=0.866a ~ 0.875a   : 48p
-      for (int i = 0; i < xw; ++i)
-        for (int j = 0; j < yw; ++j)
-          {
-            Point_d cite1(std::vector<FT>{2.0/xw*i, 1.0/yw*j});
-            std::vector<int> points_inside;
-            torus_search(treeW, D, cite1, epsilon, points_inside);
-            assert(points_inside.size() > 0);
-            insert_delaunay_landmark_with_copies(W, *(points_inside.begin()),
-                                                 landmarks_ind, t, landmark_count, true);
-            Point_d cite2(std::vector<FT>{2.0/xw*(i+0.5), 1.0/yw*(j+0.5)});
-            points_inside.clear();
-            torus_search(treeW, D, cite2, epsilon, points_inside);
-            assert(points_inside.size() > 0);
-            insert_delaunay_landmark_with_copies(W, *(points_inside.begin()),
-                                                 landmarks_ind, t, landmark_count, true);            
-          }
-    }
-  else if (D == 3)
-    {
-      int wd = 3;
-      // Body-centered cubic lattice : 54p
-      for (int i = 0; i < wd; ++i)
-        for (int j = 0; j < wd; ++j)
-          for (int k = 0; k < wd; ++k)
-            {
-              Point_d cite1(std::vector<FT>{2.0/wd*i, 2.0/wd*j, 2.0/wd*k});
-              std::vector<int> points_inside;
-              torus_search(treeW, D, cite1, epsilon, points_inside);
-              assert(points_inside.size() > 0);
-              insert_delaunay_landmark_with_copies(W, *(points_inside.begin()),
-                                                   landmarks_ind, t, landmark_count, true);
-              Point_d cite2(std::vector<FT>{2.0/wd*(i+0.5), 2.0/wd*(j+0.5), 2.0/wd*(k+0.5)});
-              points_inside.clear();
-              torus_search(treeW, D, cite2, epsilon, points_inside);
-              assert(points_inside.size() > 0);
-              insert_delaunay_landmark_with_copies(W, *(points_inside.begin()),
-                                                   landmarks_ind, t, landmark_count, true);
-            }
-    }
-}
-  
-///////////////////////////////////////////////////////////////////////
-///////////////////////////////////////////////////////////////////////
-//!!!!!!!!!!!!! THE INTERFACE FOR LANDMARK CHOICE IS BELOW !!!!!!!!!!//
-///////////////////////////////////////////////////////////////////////
-///////////////////////////////////////////////////////////////////////
-
-// Struct for R_max_heap elements
-
-struct R_max_handle
-{
-  FT value;
-  Point_d center;
-  
-  R_max_handle(FT value_, Point_d c): value(value_), center(c)
-  {}
-};
-
-struct R_max_compare
-{
-  bool operator()(const R_max_handle& rmh1, const R_max_handle& rmh2) const
-  {
-    return rmh1.value < rmh2.value;
-  }
-};
-
-// typedef boost::heap::fibonacci_heap<R_max_handle, boost::heap::compare<R_max_compare>> Heap;
-
-// void make_heap(Delaunay_triangulation& t, Heap& R_max_heap)
-// {
-//   R_max_heap.clear();
-//   for (auto fc_it = t.full_cells_begin(); fc_it != t.full_cells_end(); ++fc_it) 
-//     {
-//       if (t.is_infinite(fc_it))
-//         continue;
-//       Point_Vector vertices;
-//       for (auto fc_v_it = fc_it->vertices_begin(); fc_v_it != fc_it->vertices_end(); ++fc_v_it)
-//         vertices.push_back((*fc_v_it)->point());
-//       Sphere_d cs( vertices.begin(), vertices.end());
-//       Point_d csc = cs.center();
-//       FT r = sqrt(cs.squared_radius());
-//       // A ball is in the heap, if it intersects the cube
-//       bool accepted = sphere_intersects_cube(csc, sqrt(r)); 
-//       if (!accepted)
-//         continue;
-//       R_max_heap.push(R_max_handle(r, fc_it, csc));
-//     }
-// }
-
-//////////////////////////////////////////////////////////////////////////////////////////////////////////
-// SAMPLING RADIUS 
-//////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-R_max_handle sampling_radius(Delaunay_triangulation& t)
-{
-  FT epsilon2 = 0;
-  Point_d final_center;
-  Point_d control_point;
-  for (auto fc_it = t.full_cells_begin(); fc_it != t.full_cells_end(); ++fc_it)
-    {
-      if (t.is_infinite(fc_it))
-        continue;
-      Point_Vector vertices;
-      for (auto fc_v_it = fc_it->vertices_begin(); fc_v_it != fc_it->vertices_end(); ++fc_v_it)
-        vertices.push_back((*fc_v_it)->point());
-      Sphere_d cs( vertices.begin(), vertices.end());
-      Point_d csc = cs.center();
-      bool in_cube = true; 
-      for (auto xi = csc.cartesian_begin(); xi != csc.cartesian_end(); ++xi)
-        if (*xi > 1.0 || *xi < -1.0)
-          {
-            in_cube = false; break;
-          }
-      if (!in_cube)
-        continue;
-      FT r2 = Euclidean_distance().transformed_distance(cs.center(), *(vertices.begin()));
-      if (epsilon2 < r2)
-        {
-          epsilon2 = r2;
-          final_center = csc;         
-          control_point = (*vertices.begin());
-        }
-    }
-  return R_max_handle(sqrt(epsilon2), final_center);
-}
-
-///////////////////////////////////////////////////////////////////////
-// LANDMARK CHOICE PROCEDURE
-///////////////////////////////////////////////////////////////////////
-
-/** Procedure to compute a maximal protected subset from a point cloud. All OUTs should be empty at call.
- *
- *  IN:  W is the initial point cloud having type Epick_d<Dynamic_dimension_tag>::Point_d
- *  IN:  nbP is the size of W
- *  OUT: landmarks is the output vector for the points
- *  OUT: landmarks_ind is the output vector for the indices of the selected points in W
- *  IN:  delta is the constant of protection
- *  OUT: full_cells is the output vector of the simplices in the final Delaunay triangulation
- *  IN:  torus is true iff you are working on a flat torus [-1,1]^d
- */ 
-
-void protected_delaunay(Point_Vector& W,
-                        //Point_Vector& landmarks,
-                        std::vector<int>& landmarks_ind,
-                        FT delta,
-                        FT epsilon,
-                        FT alpha,
-                        FT theta0,
-                        //std::vector<std::vector<int>>& full_cells,
-                        bool torus,
-                        bool power_protection
-                        )
-{
-  //bool return_ = true;
-  unsigned D = W[0].size();
-  int nbP = W.size();
-  Torus_distance td;
-  Euclidean_distance ed;
-  Delaunay_triangulation t(D);
-  CGAL::Random rand;
-  int landmark_count = 0;
-  std::list<int> index_list;
-  //****************** Kd Tree W
-  STraits traits(&(W[0]));
-  Tree treeW(boost::counting_iterator<std::ptrdiff_t>(0),
-         boost::counting_iterator<std::ptrdiff_t>(nbP),
-         typename Tree::Splitter(),
-         traits);
-  //      shuffle the list of indexes (via a vector)
-  {
-    std::vector<int> temp_vector;
-    for (int i = 0; i < nbP; ++i)
-      temp_vector.push_back(i);
-    unsigned seed = std::chrono::system_clock::now().time_since_epoch().count();
-    std::shuffle(temp_vector.begin(), temp_vector.end(), std::default_random_engine(seed));
-    //CGAL::spatial_sort(temp_vector.begin(), temp_vector.end());
-    for (std::vector<int>::iterator it = temp_vector.begin(); it != temp_vector.end(); ++it)
-      index_list.push_front(*it);
-  }
-  //******************** Initialize point set
-  if (!torus)
-    for (unsigned pos1 = 0; pos1 < D+1; ++pos1)
-      {
-        std::vector<FT> point;
-        for (unsigned i = 0; i < pos1; ++i)
-          point.push_back(-1);
-        if (pos1 != D)
-          point.push_back(1);
-        for (unsigned i = pos1+1; i < D; ++i)
-          point.push_back(0);
-        assert(point.size() == D);
-        W[index_list.front()] = Point_d(point);
-        insert_delaunay_landmark_with_copies(W, index_list.front(), landmarks_ind, t, landmark_count, torus);
-        index_list.pop_front();
-      }
-  else
-    initialize_torus(W, treeW, t, epsilon, landmarks_ind, landmark_count);
-  //std::cout << "Size of treeW: " << treeW.size() << "\n";
-  //std::cout << "Size of t: " << t.number_of_vertices() << "\n";
-  //******************* Initialize heap for R_max
-  //Heap R_max_heap;
-  //make_heap(t, R_max_heap);
-
-  
-  R_max_handle rh = sampling_radius(t);
-  FT epsilon0 = rh.value; 
-  if (experiment1) eps_vector.push_back(pow(1/rh.value,D));
-  //******************** Iterative algorithm
-  std::vector<int> candidate_points;
-  torus_search(treeW, D,
-               rh.center,
-               alpha*rh.value,
-               candidate_points);
-  std::list<int>::iterator list_it;
-  std::vector<int>::iterator cp_it = candidate_points.begin();
-  while (cp_it != candidate_points.end())
-    {
-      if (!is_violating_protection(W[*cp_it], t, D, delta, power_protection, theta0))
-        {
-          insert_delaunay_landmark_with_copies(W, *cp_it, landmarks_ind, t, landmark_count, torus);
-          //make_heap(t, R_max_heap);
-          rh = sampling_radius(t);
-          if (experiment1) eps_vector.push_back(pow(1/rh.value,D));
-          //std::cout << "rhvalue = " << rh.value << "\n";
-          //std::cout << "D = " << 
-          candidate_points.clear();
-          torus_search(treeW, D,
-                       rh.center,
-                       alpha*rh.value,
-                       candidate_points);
-          /*
-          // PIECE OF CODE FOR DEBUGGING PURPOSES
-          
-          Delaunay_vertex inserted_v = insert_delaunay_landmark_with_copies(W, *list_it, landmarks_ind, t, landmark_count);
-          if (triangulation_is_protected(t, delta))
-            {
-              index_list.erase(list_it);
-              list_it = index_list.begin();
-            }
-          else
-            { //THAT'S WHERE SOMETHING'S WRONG
-              t.remove(inserted_v);
-              landmarks_ind.pop_back();
-              landmark_count--;
-              write_delaunay_mesh(t, W[*list_it], is2d);
-              is_violating_protection(W[*list_it], t_old, D, delta); //Called for encore
-            }
-          */
-          //std::cout << "index_list_size() = " << index_list.size() << "\n";
-        }
-      else
-        {
-          cp_it++;
-          //std::cout << "!!!!!WARNING!!!!! A POINT HAS BEEN OMITTED!!!\n";
-        }
-      //if (list_it != index_list.end())
-      //  write_delaunay_mesh(t, W[*list_it], is2d);
-    }
-  if (experiment2) epsratio_vector.push_back(rh.value/epsilon0);
-  std::cout << "The iteration ended when cp_count = " << candidate_points.size() << "\n";
-  std::cout << "alphaRmax = " << alpha*rh.value << "\n";
-  std::cout << "epsilon' = " << rh.value << "\n";
-  std::cout << "nbL = " << landmarks_ind.size() << "\n";
-  //fill_landmarks(W, landmarks, landmarks_ind, torus);
-  //fill_full_cell_vector(t, full_cells);
-  /*
-  if (triangulation_is_protected(t, delta))
-    std::cout << "Triangulation is ok\n";
-  else
-    {
-      std::cout << "Triangulation is BAD!! T_T しくしく!\n";
-    }
-  */
-  //write_delaunay_mesh(t, W[0], is2d);
-  //std::cout << t << std::endl;
-}
-
-///////////////////////////////////////////////////////////////////////////////////////////////////////////
-// Series of experiments
-///////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-void start_experiments(Point_Vector& W, FT theta0, std::vector<int>& landmarks_ind, FT epsilon)
-{
-  // Experiment 1
-  experiment1 = true;
-  protected_delaunay(W, landmarks_ind, 0.1*epsilon, epsilon, 0.5, 0, true, true);
-  write_tikz_plot(eps_vector,"epstime.tikz");
-  experiment1 = false;
-
-  // Experiment 2
-  // experiment2 = true;
-  // for (FT delta = 0; delta < epsilon; delta += 0.1*epsilon)
-  //   protected_delaunay(W, landmarks_ind, delta, epsilon, 0.5, 0, true, true);
-  // write_tikz_plot(epsratio_vector,"epsratio_delta.tikz");
-  // experiment2 = false;
-
-}
-  
-#endif
diff --git a/src/Witness_complex/example/protected_sets/protected_sets_paper2.h b/src/Witness_complex/example/protected_sets/protected_sets_paper2.h
deleted file mode 100644
index 04b5e3bc..00000000
--- a/src/Witness_complex/example/protected_sets/protected_sets_paper2.h
+++ /dev/null
@@ -1,1384 +0,0 @@
-#ifndef PROTECTED_SETS_H
-#define PROTECTED_SETS_H
-
-#include <algorithm>
-#include <CGAL/Cartesian_d.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/Euclidean_distance.h>
-#include <CGAL/Kernel_d/Sphere_d.h>
-#include <CGAL/Kernel_d/Hyperplane_d.h>
-#include <CGAL/Kernel_d/Vector_d.h>
-
-#include <CGAL/Orthogonal_k_neighbor_search.h>
-#include <CGAL/Kd_tree.h>
-#include <CGAL/Fuzzy_sphere.h>
-
-#include <boost/heap/fibonacci_heap.hpp>
-#include <boost/heap/policies.hpp>
-
-#include "output_tikz.h"
-#include "../output.h"
-#include "../generators.h"
-
-#include <CGAL/point_generators_d.h>
-
-
-typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
-typedef K::Point_d Point_d;
-typedef K::Line_d Line_d;
-typedef K::Vector_d Vector_d;
-typedef K::Oriented_side_d Oriented_side_d;
-typedef K::Has_on_positive_side_d Has_on_positive_side_d;
-typedef K::Sphere_d Sphere_d;
-typedef K::Hyperplane_d Hyperplane_d;
-
-typedef CGAL::Delaunay_triangulation<K> Delaunay_triangulation;
-typedef Delaunay_triangulation::Facet Facet;
-typedef Delaunay_triangulation::Vertex_handle Delaunay_vertex;
-typedef Delaunay_triangulation::Full_cell_handle Full_cell_handle;
-
-typedef std::vector<Point_d> Point_Vector;
-typedef CGAL::Euclidean_distance<Traits_base> Euclidean_distance;
-
-typedef CGAL::Search_traits_adapter<
-  std::ptrdiff_t, Point_d*, Traits_base> STraits;
-//typedef K TreeTraits;
-//typedef CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance > Euclidean_adapter;
-//typedef CGAL::Kd_tree<STraits> Kd_tree;
-typedef CGAL::Orthogonal_k_neighbor_search<STraits, CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance>> K_neighbor_search;
-typedef K_neighbor_search::Tree Tree;
-typedef K_neighbor_search::Distance Distance;
-typedef K_neighbor_search::iterator KNS_iterator;
-typedef K_neighbor_search::iterator KNS_range;
-typedef CGAL::Fuzzy_sphere<STraits> Fuzzy_sphere;
-
-typedef CGAL::Random_points_in_ball_d<Point_d> Random_point_iterator;
-
-
-FT  _sfty = pow(10,-14);
-
-bool experiment1, experiment2, experiment3, experiment5 = false;
-
-/* Experiment 1: epsilon as function on time **********************/
-std::vector<FT> eps_vector;
-
-/* Experiment 2: R/epsilon on alpha *******************************/
-std::vector<FT> epsratio_vector;
-std::vector<FT> epsslope_vector;
-
-/* Experiment 3: theta on delta ***********************************/
-std::vector<FT> thetamin_vector; FT curr_theta;
-std::vector<FT> gammamin_vector;
-
-/* Statistical data ***********************************************/
-int refused_case1, refused_case2, refused_bad, refused_centers1, refused_centers2;
-
-void initialize_statistics()
-{
-  refused_case1 = 0;
-  refused_case2 = 0;
-  refused_bad   = 0;
-  refused_centers1 = 0;
-  refused_centers2 = 0;
-}
-
-void print_statistics()
-{
-  std::cout << " * Old simplex not protected: " << refused_case1 << "\n";
-  std::cout << " * New simplex not protected: " << refused_case2 << "\n";
-  std::cout << " * New simplex not good:      " << refused_bad << "\n";
-  std::cout << " * New-old centers too close:      " << refused_centers1 << "\n";
-  std::cout << " * New-new centers too close:      " << refused_centers2 << "\n";
-}
-
-///////////////////////////////////////////////////////////////////////////////////////////////////////////
-// AUXILLARY FUNCTIONS
-///////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-/** Insert a point in Delaunay triangulation. If you are working in a flat torus, the procedure adds all the 3^d copies in adjacent cubes as well 
- *  
- *  W is the initial point vector
- *  chosen_landmark is the index of the chosen point in W
- *  landmarks_ind is the vector of indices of already chosen points in W
- *  delaunay is the Delaunay triangulation
- *  landmark_count is the current number of chosen vertices
- *  torus is true iff you are working on a flat torus [-1,1]^d
- *  OUT: Vertex handle to the newly inserted point
- */
-Delaunay_vertex insert_delaunay_landmark_with_copies(Point_Vector& W, int chosen_landmark, std::vector<int>& landmarks_ind, Delaunay_triangulation& delaunay, int& landmark_count, bool torus)
-{
-  if (!torus)
-    {
-      Delaunay_vertex v =delaunay.insert(W[chosen_landmark]);
-      landmarks_ind.push_back(chosen_landmark);
-      landmark_count++;
-      return v;
-    }
-  else
-    {
-      int D = W[0].size();
-      int nb_cells = pow(3, D);
-      Delaunay_vertex v;
-      for (int i = 0; i < nb_cells; ++i)
-        {
-          std::vector<FT> point;
-          int cell_i = i;
-          for (int l = 0; l < D; ++l)
-            {
-              point.push_back(W[chosen_landmark][l] + 2.0*(cell_i%3-1));
-              cell_i /= 3;
-            }
-          if (i == nb_cells/2)
-            v = delaunay.insert(point); //v = center point
-          else
-            delaunay.insert(point);
-        }
-      landmarks_ind.push_back(chosen_landmark);
-      landmark_count++;
-      return v;
-    }
-}
-
-/** Small check if the vertex v is in the full cell fc
- */
-
-bool vertex_is_in_full_cell(Delaunay_triangulation::Vertex_handle v, Full_cell_handle fc)
-{
-  for (auto v_it = fc->vertices_begin(); v_it != fc->vertices_end(); ++v_it)
-    if (*v_it == v)
-      return true;
-  return false;
-}
-
-/** Fill chosen point vector from indices with copies if you are working on a flat torus
- *  
- *  IN:  W is the point vector
- *  OUT: landmarks is the output vector
- *  IN:  landmarks_ind is the vector of indices
- *  IN:  torus is true iff you are working on a flat torus [-1,1]^d
- */
-
-void fill_landmarks(Point_Vector& W, Point_Vector& landmarks, std::vector<int>& landmarks_ind, bool torus)
-{
-  if (!torus)
-    for (unsigned j = 0; j < landmarks_ind.size(); ++j)
-      landmarks.push_back(W[landmarks_ind[j]]);
-  else
-    {
-      int D = W[0].size();
-      int nb_cells = pow(3, D);
-      int nbL = landmarks_ind.size();
-      // Fill landmarks
-      for (int i = 0; i < nb_cells-1; ++i)
-        for (int j = 0; j < nbL; ++j)
-          {
-            int cell_i = i;
-            Point_d point;
-            for (int l = 0; l < D; ++l)
-              {
-                point.push_back(W[landmarks_ind[j]][l] + 2.0*(cell_i-1));
-                cell_i /= 3;
-              }
-            landmarks.push_back(point);
-          }
-    }
-}
-
-/** Fill a vector of all simplices in the Delaunay triangulation giving integer indices to vertices
- *
- *  IN: t is the Delaunay triangulation
- *  OUT: full_cells is the output vector
- */
-
-void fill_full_cell_vector(Delaunay_triangulation& t, std::vector<std::vector<int>>& full_cells)
-{
-  // Store vertex indices in a map
-  int ind = 0; //index of a vertex
-  std::map<Delaunay_triangulation::Vertex_handle, int> index_of_vertex;
-  for (auto v_it = t.vertices_begin(); v_it != t.vertices_end(); ++v_it)
-    if (t.is_infinite(v_it))
-      continue;
-    else
-      index_of_vertex[v_it] = ind++;
-  // Write full cells as vectors in full_cells
-  for (auto fc_it = t.full_cells_begin(); fc_it != t.full_cells_end(); ++fc_it)
-    {
-      if (t.is_infinite(fc_it))
-        continue;
-      Point_Vector vertices;
-      for (auto fc_v_it = fc_it->vertices_begin(); fc_v_it != fc_it->vertices_end(); ++fc_v_it)
-        vertices.push_back((*fc_v_it)->point());
-      Sphere_d cs( vertices.begin(), vertices.end());
-      Point_d csc = cs.center();
-      bool in_cube = true; 
-      for (auto xi = csc.cartesian_begin(); xi != csc.cartesian_end(); ++xi)
-        if (*xi > 1.0 || *xi < -1.0)
-          {
-            in_cube = false; break;
-          }
-      if (!in_cube)
-        continue;
-      std::vector<int> cell;
-      for (auto v_it = fc_it->vertices_begin(); v_it != fc_it->vertices_end(); ++v_it)
-        cell.push_back(index_of_vertex[*v_it]);
-      full_cells.push_back(cell);
-    }
-}
-
-bool sphere_intersects_cube(Point_d& c, FT r)
-{
-  bool in_cube = true;
-  //  int i = 0, D = p.size();
-  for (auto xi = c.cartesian_begin(); xi != c.cartesian_end(); ++xi)
-    // if ((*xi < 1.0 || *xi > -1.0) &&
-    //     (*xi-r < 1.0 || *xi-r > -1.0) &&
-    //     (*xi+r < 1.0 || *xi+r > -1.0))
-
-    if ((*xi-r < -1.0 && *xi+r < -1.0) ||
-        (*xi-r > 1.0  && *xi+r >  1.0 ))
-      {
-        in_cube = false; break;
-      }
-  return in_cube;
-}
-
-/** Recursive function for checking if the simplex is good,
- *  meaning it does not contain a k-face, which is not theta0^(k-1) thick 
- */
-
-bool is_theta0_good(std::vector<Point_d>& vertices, FT theta0)
-{
-  if (theta0 > 1)
-    {
-      std::cout << "Warning! theta0 is set > 1\n";
-      return false;
-    }
-  int D = vertices.size()-1;
-  if (D <= 1)
-    return true; // Edges are always good
-  //******** Circumscribed sphere
-  Euclidean_distance ed;
-  Sphere_d cs(vertices.begin(), vertices.end());
-  FT r = sqrt(cs.squared_radius());
-  for (std::vector<Point_d>::iterator v_it = vertices.begin(); v_it != vertices.end(); ++v_it)
-    {
-      std::vector<Point_d> facet;
-      for (std::vector<Point_d>::iterator f_it = vertices.begin(); f_it != vertices.end(); ++f_it)
-        if (f_it != v_it)
-          facet.push_back(*f_it);
-      // Compute the altitude
-
-      if (vertices[0].size() == 3 && D == 2)
-        {
-          //Vector_d l = facet[0] - facet[1];
-          FT orth_length2 = ed.transformed_distance(facet[0],facet[1]);
-          K::Cartesian_const_iterator_d l_it, p_it, s_it, c_it;
-          FT h = 0;
-          // Scalar product = <sp,l>
-          FT scalar = 0;
-          for (p_it = v_it->cartesian_begin(),
-               s_it = facet[0].cartesian_begin(),
-               l_it = facet[1].cartesian_begin();
-               p_it != v_it->cartesian_end();
-               ++l_it, ++p_it, ++s_it)
-            scalar += (*l_it - *s_it)*(*p_it - *s_it);
-          // Gram-Schmidt for one vector
-          for (p_it = v_it->cartesian_begin(),
-               s_it = facet[0].cartesian_begin(),
-               l_it = facet[1].cartesian_begin();
-               p_it != v_it->cartesian_end();
-               ++l_it, ++p_it, ++s_it)
-            {
-              FT hx = (*p_it - *s_it) - scalar*(*l_it - *s_it)/orth_length2;
-              h += hx*hx;
-            }
-          h = sqrt(h);
-      
-          if (h/(2*r) < pow(theta0, D-1))
-            return false;
-          if (!is_theta0_good(facet, theta0))
-            return false;
-        }
-      else
-        {
-          Hyperplane_d tau_h(facet.begin(), facet.end(), *v_it);
-          Vector_d orth_tau = tau_h.orthogonal_vector();
-          FT orth_length = sqrt(orth_tau.squared_length());
-          K::Cartesian_const_iterator_d o_it, p_it, s_it, c_it;
-          FT h = 0;
-          for (o_it = orth_tau.cartesian_begin(),
-                 p_it = v_it->cartesian_begin(),
-                 s_it = (facet.begin())->cartesian_begin();
-               o_it != orth_tau.cartesian_end();
-               ++o_it, ++p_it, ++s_it)
-            h += (*o_it)*(*p_it - *s_it)/orth_length;
-          h = fabs(h);
-          if (experiment3 && thetamin_vector[thetamin_vector.size()-1] > pow(h/(2*r), 1.0/(D-1)))
-            {
-              thetamin_vector[thetamin_vector.size()-1] = pow(h/(2*r), 1.0/(D-1));
-              //std::cout << "theta=" << h/(2*r) << ", ";
-            }
-          if (h/(2*r) < pow(theta0, D-1))
-              return false;
-          if (!is_theta0_good(facet, theta0))
-            return false;
-        }
-    }
-  return true;
-}
-
-/** Recursive function for checking the goodness of a simplex,
- *  meaning it does not contain a k-face, which is not theta0^(k-1) thick 
- */
-
-FT theta(std::vector<Point_d>& vertices)
-{
-  FT curr_value = 1.0;
-  int D = vertices.size()-1;
-  if (D <= 1)
-    return 1; // Edges are always good
-  //******** Circumscribed sphere
-  Euclidean_distance ed;
-  Sphere_d cs(vertices.begin(), vertices.end());
-  FT r = sqrt(cs.squared_radius());
-  for (std::vector<Point_d>::iterator v_it = vertices.begin(); v_it != vertices.end(); ++v_it)
-    {
-      std::vector<Point_d> facet;
-      for (std::vector<Point_d>::iterator f_it = vertices.begin(); f_it != vertices.end(); ++f_it)
-        if (f_it != v_it)
-          facet.push_back(*f_it);
-      // Compute the altitude
-      curr_value = std::min(curr_value, theta(facet)); // Check the corresponding facet
-      if (vertices[0].size() == 3 && D == 2)
-        {
-          //Vector_d l = facet[0] - facet[1];
-          FT orth_length2 = ed.transformed_distance(facet[0],facet[1]);
-          K::Cartesian_const_iterator_d l_it, p_it, s_it, c_it;
-          FT h = 0;
-          // Scalar product = <sp,l>
-          FT scalar = 0;
-          for (p_it = v_it->cartesian_begin(),
-               s_it = facet[0].cartesian_begin(),
-               l_it = facet[1].cartesian_begin();
-               p_it != v_it->cartesian_end();
-               ++l_it, ++p_it, ++s_it)
-            scalar += (*l_it - *s_it)*(*p_it - *s_it);
-          // Gram-Schmidt for one vector
-          for (p_it = v_it->cartesian_begin(),
-               s_it = facet[0].cartesian_begin(),
-               l_it = facet[1].cartesian_begin();
-               p_it != v_it->cartesian_end();
-               ++l_it, ++p_it, ++s_it)
-            {
-              FT hx = (*p_it - *s_it) - scalar*(*l_it - *s_it)/orth_length2;
-              h += hx*hx;
-            }
-          h = sqrt(h);
-          curr_value = std::min(curr_value, std::pow(h/(2*r), 1.0/(D-1)));
-        }
-      else
-        {
-          Hyperplane_d tau_h(facet.begin(), facet.end(), *v_it);
-          Vector_d orth_tau = tau_h.orthogonal_vector();
-          FT orth_length = sqrt(orth_tau.squared_length());
-          K::Cartesian_const_iterator_d o_it, p_it, s_it, c_it;
-          FT h = 0;
-          for (o_it = orth_tau.cartesian_begin(),
-                 p_it = v_it->cartesian_begin(),
-                 s_it = (facet.begin())->cartesian_begin();
-               o_it != orth_tau.cartesian_end();
-               ++o_it, ++p_it, ++s_it)
-            h += (*o_it)*(*p_it - *s_it)/orth_length;
-          h = fabs(h);
-          curr_value = std::min(curr_value, pow(h/(2*r), 1.0/(D-1)));
-        }
-    }
-  return curr_value;
-}
-
-// Doubling in a way 1->2->5->10
-void double_round(int& i)
-{
-  FT order10 = pow(10,std::floor(std::log10(i)));
-  int digit = std::floor( i / order10);
-  std::cout << digit;
-  if (digit == 1)
-    i *= 2;
-  else if (digit == 2)
-    i = 5*i/2;
-  else if (digit == 5)
-    i *= 2;
-  else
-    std::cout << "digit not correct. digit = " << digit << std::endl;
-}
-
-////////////////////////////////////////////////////////////////////////////////////////////////////////////
-// IS VIOLATED TEST
-////////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-/** Check if a newly created cell is protected from old vertices
- *  
- *  t is the Delaunay triangulation
- *  vertices is the vector containing the point to insert and a facet f in t
- *  v1 is the vertex of t, such that f and v1 form a simplex
- *  v2 is the vertex of t, such that f and v2 form another simplex
- *  delta is the protection constant
- *  power_protection is true iff the delta-power protection is used
- */
-
-bool new_cell_is_violated(Delaunay_triangulation& t, std::vector<Point_d>& vertices, const Delaunay_vertex& v1, const Delaunay_vertex v2, FT delta0, bool power_protection, FT theta0, FT gamma0)
-{
-  assert(vertices.size() == vertices[0].size() ||
-         vertices.size() == vertices[0].size() + 1); //simplex size = d | d+1
-  assert(v1 != v2);
-  if (vertices.size() == vertices[0].size() + 1)
-  // FINITE CASE
-    {
-      Sphere_d cs(vertices.begin(), vertices.end());
-      Point_d center_cs = cs.center();
-      FT r = sqrt(Euclidean_distance().transformed_distance(center_cs, vertices[0]));
-      /*
-      for (auto v_it = t.vertices_begin(); v_it != t.vertices_end(); ++v_it)
-        if (!t.is_infinite(v_it)) 
-          {
-            //CGAL::Oriented_side side = Oriented_side_d()(cs, (v_it)->point()); 
-            if (std::find(vertices.begin(), vertices.end(), v_it->point()) == vertices.end())
-              {
-                FT dist2 = Euclidean_distance().transformed_distance(center_cs, (v_it)->point());
-                if (!power_protection)
-                  if (dist2 >= r*r-_sfty && dist2 <= (r+delta)*(r+delta))
-                    return true;
-                if (power_protection)
-                  if (dist2 >= r*r-_sfty && dist2 <= r*r+delta*delta) 
-                    return true;                 
-              }
-          }
-      */
-      // Is the center inside the box? (only Euclidean case)
-      // if (!torus)
-      //   {
-      //     bool inside_the_box = true;
-      //     for (c_it = center_cs.cartesian_begin(); c_it != center_cs.cartesian_end(); ++c_it)
-      //       if (*c_it > 1.0 || *c_it < -1.0)
-      //         {
-      //           inside_the_box = false; break;
-      //         }
-      //     if (inside_the_box && h/r < theta0)
-      //       return true;
-      //   }
-      // Check the two vertices (if not infinite)
-      if (!t.is_infinite(v1))
-        {
-          FT dist2 = Euclidean_distance().transformed_distance(center_cs, v1->point());
-          if (!power_protection)
-            if (dist2 >= r*r-_sfty && dist2 <= (r+r*delta0)*(r+r*delta0))
-              { refused_case2++; return true;}
-          if (power_protection)
-            if (dist2 >= r*r-_sfty && dist2 <= r*r+r*r*delta0*delta0) 
-              { refused_case2++; return true;}
-          // Check if the centers are not too close
-          std::vector<Point_d> sigma(vertices);
-          sigma[0] = v1->point();
-          Sphere_d cs_sigma(sigma.begin(), sigma.end());
-          Point_d csc_sigma = cs_sigma.center();
-          FT r_sigma = sqrt(cs_sigma.squared_radius());
-          FT dcc = sqrt(Euclidean_distance().transformed_distance(center_cs, csc_sigma));
-          if (experiment3 && dcc/r < gammamin_vector[gammamin_vector.size()-1])
-            gammamin_vector[gammamin_vector.size()-1] = dcc/r;
-          if (experiment3 && dcc/r_sigma < gammamin_vector[gammamin_vector.size()-1])
-            gammamin_vector[gammamin_vector.size()-1] = dcc/r_sigma;
-          if (dcc < r*gamma0 || dcc < r_sigma*gamma0)
-            { refused_centers1++; return true; }
-        }
-      if (!t.is_infinite(v2))
-        {
-          FT dist2 = Euclidean_distance().transformed_distance(center_cs, v2->point());
-          if (!power_protection)
-            if (dist2 >= r*r-_sfty && dist2 <= (r+r*delta0)*(r+r*delta0))
-              { refused_case2++; return true;}
-          if (power_protection)
-            if (dist2 >= r*r-_sfty && dist2 <= r*r+r*r*delta0*delta0) 
-              { refused_case2++; return true;}
-          // Check if the centers are not too close
-          std::vector<Point_d> sigma(vertices);
-          sigma[0] = v2->point();
-          Sphere_d cs_sigma(sigma.begin(), sigma.end());
-          Point_d csc_sigma = cs_sigma.center();
-          FT r_sigma = sqrt(cs_sigma.squared_radius());
-          FT dcc = sqrt(Euclidean_distance().transformed_distance(center_cs, csc_sigma));
-          if (experiment3 && dcc/r < gammamin_vector[gammamin_vector.size()-1])
-            gammamin_vector[gammamin_vector.size()-1] = dcc/r;
-          if (experiment3 && dcc/r_sigma < gammamin_vector[gammamin_vector.size()-1])
-            gammamin_vector[gammamin_vector.size()-1] = dcc/r_sigma;
-          if (dcc < r*gamma0 || dcc < r_sigma*gamma0)
-            { refused_centers1++; return true; }
-        }
-      // Check if the simplex is theta0-good
-      if (!is_theta0_good(vertices, theta0))
-        { refused_bad++; return true;}
-      
-    }
-  else
-  // INFINITE CASE
-    {
-      Delaunay_triangulation::Vertex_iterator v = t.vertices_begin();
-      while (t.is_infinite(v) || std::find(vertices.begin(), vertices.end(), v->point()) == vertices.end())
-        v++;
-      Hyperplane_d facet_plane(vertices.begin(), vertices.end(), v->point(), CGAL::ON_POSITIVE_SIDE);
-      Vector_d orth_v = facet_plane.orthogonal_vector();
-      /*
-      for (auto v_it = t.vertices_begin(); v_it != t.vertices_end(); ++v_it)
-        if (!t.is_infinite(v_it))
-          if (std::find(vertices.begin(), vertices.end(), v_it->point()) == vertices.end())
-            {
-              std::vector<FT> coords;
-              Point_d p = v_it->point();
-              auto orth_i = orth_v.cartesian_begin(), p_i = p.cartesian_begin();
-              for (; orth_i != orth_v.cartesian_end(); ++orth_i, ++p_i)
-                coords.push_back((*p_i) - (*orth_i) * delta / sqrt(orth_v.squared_length()));
-              Point_d p_delta = Point_d(coords);
-              bool p_is_inside = !Has_on_positive_side_d()(facet_plane, p);
-              bool p_delta_is_inside = !Has_on_positive_side_d()(facet_plane, p_delta);
-              if (!p_is_inside && p_delta_is_inside)
-                return true;
-            }
-      */
-      if (!t.is_infinite(v1))
-        {
-          std::vector<FT> coords;
-          Point_d p = v1->point();
-          auto orth_i = orth_v.cartesian_begin(), p_i = p.cartesian_begin();
-          for (; orth_i != orth_v.cartesian_end(); ++orth_i, ++p_i)
-            coords.push_back((*p_i) - (*orth_i) * delta0 / sqrt(orth_v.squared_length()));
-          Point_d p_delta = Point_d(coords);
-          bool p_is_inside = !Has_on_positive_side_d()(facet_plane, p);
-          bool p_delta_is_inside = !Has_on_positive_side_d()(facet_plane, p_delta);
-          if (!power_protection && !p_is_inside && p_delta_is_inside)
-            return true;
-        }
-      if (!t.is_infinite(v2))
-        {
-          std::vector<FT> coords;
-          Point_d p = v2->point();
-          auto orth_i = orth_v.cartesian_begin(), p_i = p.cartesian_begin();
-          for (; orth_i != orth_v.cartesian_end(); ++orth_i, ++p_i)
-            coords.push_back((*p_i) - (*orth_i) * delta0 / sqrt(orth_v.squared_length()));
-          Point_d p_delta = Point_d(coords);
-          bool p_is_inside = !Has_on_positive_side_d()(facet_plane, p);
-          bool p_delta_is_inside = !Has_on_positive_side_d()(facet_plane, p_delta);
-          if (!power_protection && !p_is_inside && p_delta_is_inside)
-            return true;
-        }
-    }
-  return false;
-}
-  
-/** Auxillary recursive function to check if the point p violates the protection of the cell c and
- *  if there is a violation of an eventual new cell
- *
- *  p is the point to insert
- *  t is the current triangulation
- *  c is the current cell (simplex)
- *  parent_cell is the parent cell (simplex)
- *  index is the index of the facet between c and parent_cell from parent_cell's point of view
- *  D is the dimension of the triangulation
- *  delta is the protection constant
- *  marked_cells is the vector of all visited cells containing p in their circumscribed ball
- *  power_protection is true iff you are working with delta-power protection
- *
- *  OUT: true iff inserting p hasn't produced any violation so far
- */
-
-bool is_violating_protection(Point_d& p, Delaunay_triangulation& t, Full_cell_handle c, Full_cell_handle parent_cell, int index, int D, FT delta0, std::vector<Full_cell_handle>& marked_cells, bool power_protection, FT theta0, FT gamma0)
-{
-  Euclidean_distance ed;
-  std::vector<Point_d> vertices;
-  if (!t.is_infinite(c))
-    {
-      // if the cell is finite, we look if the protection is violated
-      for (auto v_it = c->vertices_begin(); v_it != c->vertices_end(); ++v_it)
-        vertices.push_back((*v_it)->point());
-      Sphere_d cs( vertices.begin(), vertices.end());
-      Point_d center_cs = cs.center();
-      FT r = sqrt(ed.transformed_distance(center_cs, vertices[0]));
-      FT dist2 = ed.transformed_distance(center_cs, p);
-      // if the new point is inside the protection ball of a non conflicting simplex
-      if (!power_protection)
-        if (dist2 >= r*r-_sfty && dist2 <= (r+r*delta0)*(r+r*delta0))
-          { refused_case1++; return true;}
-      if (power_protection)
-        if (dist2 >= r*r-_sfty && dist2 <= r*r+delta0*delta0*r*r) 
-          { refused_case1++; return true;}    
-      // if the new point is inside the circumscribing ball : continue violation searching on neighbours
-      //if (dist2 < r*r)
-      //if (dist2 < (5*r+delta)*(5*r+delta))
-      if (dist2 < r*r)
-        {
-          c->tds_data().mark_visited();
-          marked_cells.push_back(c);
-          for (int i = 0; i < D+1; ++i)
-            {
-              Full_cell_handle next_c = c->neighbor(i);
-              if (next_c->tds_data().is_clear() &&
-                  is_violating_protection(p, t, next_c, c, i, D, delta0, marked_cells, power_protection, theta0, gamma0))
-                return true;
-            }
-        }
-      // if the new point is outside the protection sphere
-      else
-        {
-          // facet f is on the border of the conflict zone : check protection of simplex {p,f}
-          // the new simplex is guaranteed to be finite
-          vertices.clear(); vertices.push_back(p);
-          for (int i = 0; i < D+1; ++i)
-            if (i != index)
-              vertices.push_back(parent_cell->vertex(i)->point());
-          Delaunay_vertex vertex_to_check = t.infinite_vertex();
-          for (auto vh_it = c->vertices_begin(); vh_it != c->vertices_end(); ++vh_it)
-            if (!vertex_is_in_full_cell(*vh_it, parent_cell))
-              {
-                vertex_to_check = *vh_it; break;
-              }
-          if (new_cell_is_violated(t, vertices, vertex_to_check, parent_cell->vertex(index), delta0, power_protection, theta0, gamma0)) 
-          //if (new_cell_is_violated(t, vertices, vertex_to_check->point(), delta)) 
-            return true;            
-        }
-    } 
-  else
-    {
-      // Inside of the convex hull is + side. Outside is - side.
-      for (auto vh_it = c->vertices_begin(); vh_it != c->vertices_end(); ++vh_it)
-        if (!t.is_infinite(*vh_it))
-          vertices.push_back((*vh_it)->point());
-      Delaunay_triangulation::Vertex_iterator v_it = t.vertices_begin();
-      while (t.is_infinite(v_it) || vertex_is_in_full_cell(v_it, c))
-        v_it++;
-      Hyperplane_d facet_plane(vertices.begin(), vertices.end(), v_it->point(), CGAL::ON_POSITIVE_SIDE);
-      //CGAL::Oriented_side outside = Oriented_side_d()(facet_plane, v_it->point());
-      Vector_d orth_v = facet_plane.orthogonal_vector();
-      std::vector<FT> coords;
-      auto orth_i = orth_v.cartesian_begin(), p_i = p.cartesian_begin();
-      for (; orth_i != orth_v.cartesian_end(); ++orth_i, ++p_i)
-        coords.push_back((*p_i) - (*orth_i) * delta0 / sqrt(orth_v.squared_length()));
-      Point_d p_delta = Point_d(coords);
-      bool p_is_inside = !Has_on_positive_side_d()(facet_plane, p) && (Oriented_side_d()(facet_plane, p) != CGAL::ZERO);
-      bool p_delta_is_inside = !Has_on_positive_side_d()(facet_plane, p_delta);
-
-      // If we work with power protection, we just ignore any conflicts
-      if (!power_protection && !p_is_inside && p_delta_is_inside)
-        return true;
-      //if the cell is infinite we look at the neighbours regardless
-      if (p_is_inside)
-        {
-          c->tds_data().mark_visited();
-          marked_cells.push_back(c);    
-          for (int i = 0; i < D+1; ++i)
-            {
-              Full_cell_handle next_c = c->neighbor(i);
-              if (next_c->tds_data().is_clear() &&
-                  is_violating_protection(p, t, next_c, c, i, D, delta0, marked_cells, power_protection, theta0, gamma0))
-                return true;
-            }
-        }
-      else
-        {
-          // facet f is on the border of the conflict zone : check protection of simplex {p,f}
-          // the new simplex is finite if the parent cell is finite
-          vertices.clear(); vertices.push_back(p);
-          for (int i = 0; i < D+1; ++i)
-            if (i != index)
-              if (!t.is_infinite(parent_cell->vertex(i)))
-                vertices.push_back(parent_cell->vertex(i)->point());
-          Delaunay_vertex vertex_to_check = t.infinite_vertex();
-          for (auto vh_it = c->vertices_begin(); vh_it != c->vertices_end(); ++vh_it)
-            if (!vertex_is_in_full_cell(*vh_it, parent_cell))
-              {
-                vertex_to_check = *vh_it; break;
-              }
-          if (new_cell_is_violated(t, vertices, vertex_to_check, parent_cell->vertex(index), delta0, power_protection, theta0, gamma0)) 
-          //if (new_cell_is_violated(t, vertices, vertex_to_check->point(), delta)) 
-            return true;
-        }
-    }
-  //c->tds_data().clear_visited();
-  //marked_cells.pop_back();
-  return false;
-}
-
-/** Checks if inserting the point p in t will make conflicts
- *
- *  p is the point to insert
- *  t is the current triangulation
- *  D is the dimension of triangulation
- *  delta is the protection constant
- *  power_protection is true iff you are working with delta-power protection
- *  OUT: true iff inserting p produces a violation of delta-protection.
- */
-
-bool is_violating_protection(Point_d& p, Delaunay_triangulation& t, int D, FT delta0, bool power_protection, FT theta0, FT gamma0)
-{
-  Euclidean_distance ed;
-  Delaunay_triangulation::Vertex_handle v;
-  Delaunay_triangulation::Face f(t.current_dimension()); 
-  Delaunay_triangulation::Facet ft; 
-  Delaunay_triangulation::Full_cell_handle c; 
-  Delaunay_triangulation::Locate_type lt;
-  std::vector<Full_cell_handle> marked_cells;
-  //c = t.locate(p, lt, f, ft, v);
-  c = t.locate(p);
-  bool violation_existing_cells = is_violating_protection(p, t, c, c, 0, D, delta0, marked_cells, power_protection, theta0, gamma0);
-  for (Full_cell_handle fc : marked_cells)
-    fc->tds_data().clear();
-  return violation_existing_cells;
-}
-
-
-////////////////////////////////////////////////////////////////////////
-// INITIALIZATION
-////////////////////////////////////////////////////////////////////////
-
-// Query for a sphere near a cite in all copies of a torus
-// OUT points_inside
-void torus_search(Tree& treeW, int D, Point_d cite, FT r, std::vector<int>& points_inside)
-{
-  int nb_cells = pow(3, D);
-  Delaunay_vertex v;
-  for (int i = 0; i < nb_cells; ++i)
-    {
-      std::vector<FT> cite_copy;
-      int cell_i = i;
-      for (int l = 0; l < D; ++l)
-        {
-          cite_copy.push_back(cite[l] + 2.0*(cell_i%3-1));
-          cell_i /= 3;
-        }
-      Fuzzy_sphere fs(cite_copy, r, 0, treeW.traits());
-      treeW.search(std::insert_iterator<std::vector<int>>(points_inside, points_inside.end()), fs);
-    }
-}
-
-  
-void initialize_torus(Point_Vector& W, Tree& treeW, Delaunay_triangulation& t, FT epsilon, std::vector<int>& landmarks_ind, int& landmark_count, std::vector<bool>& point_taken)
-{
-  initialize_statistics();
-  int D = W[0].size();
-  if (D == 2)
-    {
-      int xw = 6, yw = 4;
-      // Triangular lattice close to regular triangles h=0.866a ~ 0.875a   : 48p
-      for (int i = 0; i < xw; ++i)
-        for (int j = 0; j < yw; ++j)
-          {
-            Point_d cite1(std::vector<FT>{2.0/xw*i, 2.0/yw*j});
-            std::vector<int> points_inside;
-            torus_search(treeW, D, cite1, epsilon, points_inside);
-            //std::cout << "i=" << i << ", j=" << j << " "; print_vector(points_inside); std::cout << "\n";
-            std::vector<int>::iterator p_it = points_inside.begin();
-            while (p_it != points_inside.end() && point_taken[*p_it])
-              ++p_it;
-            assert(p_it != points_inside.end());
-            //W[*p_it] = cite1;  // debug purpose
-            insert_delaunay_landmark_with_copies(W, *p_it,
-                                                 landmarks_ind, t, landmark_count, true);
-            point_taken[*p_it] = true;
-
-            Point_d cite2(std::vector<FT>{2.0/xw*(i+0.5), 2.0/yw*(j+0.5)});
-            points_inside.clear();
-            torus_search(treeW, D, cite2, epsilon, points_inside);
-            //std::cout << "i=" << i << ", j=" << j << " "; print_vector(points_inside); std::cout << "\n";
-            p_it = points_inside.begin();
-            while (p_it != points_inside.end() && point_taken[*p_it])
-              ++p_it;
-            assert(p_it != points_inside.end());
-            //W[*p_it] = cite2;  // debug purpose
-            insert_delaunay_landmark_with_copies(W, *p_it,
-                                                 landmarks_ind, t, landmark_count, true);
-            point_taken[*p_it] = true;            
-          }
-    }
-  else if (D == 3)
-    {
-      int wd = 3;
-      // Body-centered cubic lattice : 54p
-      for (int i = 0; i < wd; ++i)
-        for (int j = 0; j < wd; ++j)
-          for (int k = 0; k < wd; ++k)
-            {
-              Point_d cite1(std::vector<FT>{2.0/wd*i, 2.0/wd*j, 2.0/wd*k});
-              std::vector<int> points_inside;
-              torus_search(treeW, D, cite1, epsilon, points_inside);
-              std::vector<int>::iterator p_it = points_inside.begin();
-              while (p_it != points_inside.end() && point_taken[*p_it])
-                ++p_it;
-              assert(p_it != points_inside.end());
-              insert_delaunay_landmark_with_copies(W, *(points_inside.begin()),
-                                                   landmarks_ind, t, landmark_count, true);
-              point_taken[*p_it] = true;
-              
-              Point_d cite2(std::vector<FT>{2.0/wd*(i+0.5), 2.0/wd*(j+0.5), 2.0/wd*(k+0.5)});
-              points_inside.clear();
-              torus_search(treeW, D, cite2, epsilon, points_inside);
-              p_it = points_inside.begin();
-              while (p_it != points_inside.end() && point_taken[*p_it])
-                ++p_it;
-              assert(p_it != points_inside.end());
-              insert_delaunay_landmark_with_copies(W, *(points_inside.begin()),
-                                                   landmarks_ind, t, landmark_count, true);
-              point_taken[*p_it] = true;
-            }
-    }
-  //write_mesh
-}
-  
-///////////////////////////////////////////////////////////////////////
-///////////////////////////////////////////////////////////////////////
-//!!!!!!!!!!!!! THE INTERFACE FOR LANDMARK CHOICE IS BELOW !!!!!!!!!!//
-///////////////////////////////////////////////////////////////////////
-///////////////////////////////////////////////////////////////////////
-
-// Struct for R_max_heap elements
-
-struct R_max_handle
-{
-  FT value;
-  Point_d center;
-  
-  R_max_handle(FT value_, Point_d c): value(value_), center(c)
-  {}
-};
-
-struct R_max_compare
-{
-  bool operator()(const R_max_handle& rmh1, const R_max_handle& rmh2) const
-  {
-    return rmh1.value < rmh2.value;
-  }
-};
-
-// typedef boost::heap::fibonacci_heap<R_max_handle, boost::heap::compare<R_max_compare>> Heap;
-
-// void make_heap(Delaunay_triangulation& t, Heap& R_max_heap)
-// {
-//   R_max_heap.clear();
-//   for (auto fc_it = t.full_cells_begin(); fc_it != t.full_cells_end(); ++fc_it) 
-//     {
-//       if (t.is_infinite(fc_it))
-//         continue;
-//       Point_Vector vertices;
-//       for (auto fc_v_it = fc_it->vertices_begin(); fc_v_it != fc_it->vertices_end(); ++fc_v_it)
-//         vertices.push_back((*fc_v_it)->point());
-//       Sphere_d cs( vertices.begin(), vertices.end());
-//       Point_d csc = cs.center();
-//       FT r = sqrt(cs.squared_radius());
-//       // A ball is in the heap, if it intersects the cube
-//       bool accepted = sphere_intersects_cube(csc, sqrt(r)); 
-//       if (!accepted)
-//         continue;
-//       R_max_heap.push(R_max_handle(r, fc_it, csc));
-//     }
-// }
-
-//////////////////////////////////////////////////////////////////////////////////////////////////////////
-// SAMPLING RADIUS 
-//////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-R_max_handle sampling_radius(Delaunay_triangulation& t)
-{
-  FT epsilon2 = 0;
-  Point_d final_center;
-  Point_d control_point;
-  for (auto fc_it = t.full_cells_begin(); fc_it != t.full_cells_end(); ++fc_it)
-    {
-      if (t.is_infinite(fc_it))
-        continue;
-      Point_Vector vertices;
-      for (auto fc_v_it = fc_it->vertices_begin(); fc_v_it != fc_it->vertices_end(); ++fc_v_it)
-        vertices.push_back((*fc_v_it)->point());
-      Sphere_d cs( vertices.begin(), vertices.end());
-      Point_d csc = cs.center();
-      bool in_cube = true; 
-      for (auto xi = csc.cartesian_begin(); xi != csc.cartesian_end(); ++xi)
-        if (*xi > 1.0 || *xi < -1.0)
-          {
-            in_cube = false; break;
-          }
-      if (!in_cube)
-        continue;
-      FT r2 = Euclidean_distance().transformed_distance(cs.center(), *(vertices.begin()));
-      if (epsilon2 < r2)
-        {
-          epsilon2 = r2;
-          final_center = csc;         
-          control_point = (*vertices.begin());
-        }
-    }
-  return R_max_handle(sqrt(epsilon2), final_center);
-}
-
-FT sampling_fatness(Delaunay_triangulation& t)
-{
-  FT curr_theta = 1.0;
-  for (auto fc_it = t.full_cells_begin(); fc_it != t.full_cells_end(); ++fc_it)
-    {
-      if (t.is_infinite(fc_it))
-        continue;
-      Point_Vector vertices;
-      for (auto fc_v_it = fc_it->vertices_begin(); fc_v_it != fc_it->vertices_end(); ++fc_v_it)
-        vertices.push_back((*fc_v_it)->point());
-      Sphere_d cs( vertices.begin(), vertices.end());
-      Point_d csc = cs.center();
-      bool in_cube = true; 
-      for (auto xi = csc.cartesian_begin(); xi != csc.cartesian_end(); ++xi)
-        if (*xi > 1.0 || *xi < -1.0)
-          {
-            in_cube = false; break;
-          }
-      if (!in_cube)
-        continue;
-      FT theta_f = theta(vertices);
-      curr_theta = std::min(curr_theta, theta_f);
-      //std::cout << "theta(sigma) = " << theta_f << "\n";
-    }
-  return curr_theta;
-}
-
-// Generate an epsilon sample for a given epsilon
-void generate_epsilon_sample_torus(Point_Vector& W, FT epsilon, int dim, Delaunay_triangulation& t)
-{
-  W.clear();
-  t.clear();
-  int point_count = 0;
-  std::vector<int> point_ind;
-  // std::vector<FT> coords;
-  FT curr_eps = 2*dim;
-  // Initialize
-  // for (int i = 0; i < dim; ++i)
-  //   coords.push_back(-1);
-  // R_max_handle rmh(2*sqrt(dim), Point_d(coords));
-  // int N = dim; std::floor(std::pow(1/epsilon,dim));
-  // std::cout << N << "\n";
-  typedef CGAL::Random_points_in_cube_d<Point_d> Random_cube_iterator;
-  Random_cube_iterator rp(dim, 1.0);
-  W.push_back(*rp++);
-  insert_delaunay_landmark_with_copies(W, W.size()-1, point_ind, t, point_count, true);
-  curr_eps = sampling_radius(t).value;      
-  while (curr_eps > epsilon)
-    {
-      
-      W.push_back(*rp++);
-      insert_delaunay_landmark_with_copies(W, W.size()-1, point_ind, t, point_count, true);
-      
-      Point_d c = sampling_radius(t).center;
-      W.push_back(c);
-      insert_delaunay_landmark_with_copies(W, W.size()-1, point_ind, t, point_count, true);
-      curr_eps = sampling_radius(t).value;
-      
-      std::cout << "curr_eps = " << curr_eps << "\n";
-    }
-  // Iterate and insert in a torus
-  // while (rmh.value > epsilon)
-  //   {
-  //     W.push_back(rmh.center);
-  //     insert_delaunay_landmark_with_copies(W, W.size()-1, point_ind, t, point_count, true);
-  //     rmh = sampling_radius(t);
-  //     //std::cout << rmh.value;
-  //   }
-}
-
-///////////////////////////////////////////////////////////////////////
-// LANDMARK CHOICE PROCEDURE
-///////////////////////////////////////////////////////////////////////
-
-/** Procedure to compute a maximal protected subset from a point cloud. All OUTs should be empty at call.
- *
- *  IN:  W is the initial point cloud having type Epick_d<Dynamic_dimension_tag>::Point_d
- *  IN:  nbP is the size of W
- *  OUT: landmarks is the output vector for the points
- *  OUT: landmarks_ind is the output vector for the indices of the selected points in W
- *  IN:  delta is the constant of protection
- *  OUT: full_cells is the output vector of the simplices in the final Delaunay triangulation
- *  IN:  torus is true iff you are working on a flat torus [-1,1]^d
- */ 
-
-void protected_delaunay(Point_Vector& W,
-                        //Point_Vector& landmarks,
-                        std::vector<int>& landmarks_ind,
-                        FT alpha,
-                        FT epsilon,
-                        FT delta0,
-                        FT theta0,
-                        FT gamma0,
-                        //std::vector<std::vector<int>>& full_cells,
-                        bool torus,
-                        bool power_protection
-                        )
-{
-  //bool return_ = true;
-  unsigned D = W[0].size();
-  int nbP = W.size();
-  //FT beta = 1/(1-alpha);
-  //FT Ad = pow((4*alpha + 8*beta)/alpha, D);
-  //FT theta0 = 1/Ad;
-  //FT delta0 = pow(1/Ad,D);
-  Torus_distance td;
-  Euclidean_distance ed;
-  Delaunay_triangulation t(D);
-  std::vector<bool> point_taken(nbP,false);
-  CGAL::Random rand;
-  int landmark_count = 0;
-  std::list<int> index_list;
-  //****************** Kd Tree W
-  STraits traits(&(W[0]));
-  Tree treeW(boost::counting_iterator<std::ptrdiff_t>(0),
-         boost::counting_iterator<std::ptrdiff_t>(nbP),
-         typename Tree::Splitter(),
-         traits);
-  //      shuffle the list of indexes (via a vector)
-  {
-    std::vector<int> temp_vector;
-    for (int i = 0; i < nbP; ++i)
-      temp_vector.push_back(i);
-    unsigned seed = std::chrono::system_clock::now().time_since_epoch().count();
-    std::shuffle(temp_vector.begin(), temp_vector.end(), std::default_random_engine(seed));
-    //CGAL::spatial_sort(temp_vector.begin(), temp_vector.end());
-    for (std::vector<int>::iterator it = temp_vector.begin(); it != temp_vector.end(); ++it)
-      index_list.push_front(*it);
-  }
-  //******************** Initialize point set
-  if (!torus)
-    for (unsigned pos1 = 0; pos1 < D+1; ++pos1)
-      {
-        std::vector<FT> point;
-        for (unsigned i = 0; i < pos1; ++i)
-          point.push_back(-1);
-        if (pos1 != D)
-          point.push_back(1);
-        for (unsigned i = pos1+1; i < D; ++i)
-          point.push_back(0);
-        assert(point.size() == D);
-        W[index_list.front()] = Point_d(point);
-        insert_delaunay_landmark_with_copies(W, index_list.front(), landmarks_ind, t, landmark_count, torus);
-        index_list.pop_front();
-      }
-  else
-    initialize_torus(W, treeW, t, epsilon, landmarks_ind, landmark_count, point_taken);
-  //std::cout << "Size of treeW: " << treeW.size() << "\n";
-  //std::cout << "Size of t: " << t.number_of_vertices() << "\n";
-  //******************* Initialize heap for R_max
-  //Heap R_max_heap;
-  //make_heap(t, R_max_heap);
-
-  
-  R_max_handle rh = sampling_radius(t);
-  FT epsilon0 = rh.value; 
-  if (experiment1) eps_vector.push_back(pow(1/rh.value,D));
-  //******************** Iterative algorithm
-  std::vector<int> candidate_points;
-  torus_search(treeW, D,
-               rh.center,
-               alpha*rh.value,
-               candidate_points);
-  std::list<int>::iterator list_it;
-  std::vector<int>::iterator cp_it = candidate_points.begin();
-  while (cp_it != candidate_points.end())
-    {
-      if (!point_taken[*cp_it] && !is_violating_protection(W[*cp_it], t, D, delta0, power_protection, theta0, gamma0))
-        {
-          Delaunay_vertex v = insert_delaunay_landmark_with_copies(W, *cp_it, landmarks_ind, t, landmark_count, torus);
-          {
-            // Simple check if the new cells don't have centers too close one to another
-            std::vector<Full_cell_handle> inc_cells;
-            std::back_insert_iterator<std::vector<Full_cell_handle>> out(inc_cells);
-            t.tds().incident_full_cells(v, out);
-
-            std::vector<Sphere_d> spheres;
-            for (auto i_it = inc_cells.begin(); i_it != inc_cells.end(); ++i_it)
-              {
-                std::vector<Point_d> vertices;
-                for (auto v_it = (*i_it)->vertices_begin(); v_it != (*i_it)->vertices_end(); ++v_it)
-                  vertices.push_back((*v_it)->point());
-                spheres.push_back(Sphere_d(vertices.begin(), vertices.end()));
-              }
-            for (auto s_it = spheres.begin(); s_it != spheres.end(); ++s_it)
-              for (auto t_it = s_it+1; t_it != spheres.end(); ++t_it)
-                {
-                  FT ddc2 = ed.transformed_distance(s_it->center(),t_it->center());
-                  if (ddc2 < gamma0*gamma0*s_it->squared_radius() ||
-                      ddc2 < gamma0*gamma0*t_it->squared_radius())
-                    { refused_centers2++; }
-                }
-          }
-            
-          //std::cout << *cp_it << ",\n";
-          //make_heap(t, R_max_heap);
-          point_taken[*cp_it] = true;
-          rh = sampling_radius(t);
-          if (experiment1) eps_vector.push_back(pow(1/rh.value,D));
-          //std::cout << "rhvalue = " << rh.value << "\n";
-          //std::cout << "D = " << 
-          candidate_points.clear();
-          torus_search(treeW, D,
-                       rh.center,
-                       alpha*rh.value,
-                       candidate_points);
-          cp_it = candidate_points.begin();
-          /*
-          // PIECE OF CODE FOR DEBUGGING PURPOSES
-          
-          Delaunay_vertex inserted_v = insert_delaunay_landmark_with_copies(W, *list_it, landmarks_ind, t, landmark_count);
-          if (triangulation_is_protected(t, delta))
-            {
-              index_list.erase(list_it);
-              list_it = index_list.begin();
-            }
-          else
-            { //THAT'S WHERE SOMETHING'S WRONG
-              t.remove(inserted_v);
-              landmarks_ind.pop_back();
-              landmark_count--;
-              write_delaunay_mesh(t, W[*list_it], is2d);
-              is_violating_protection(W[*list_it], t_old, D, delta); //Called for encore
-            }
-          */
-          //std::cout << "index_list_size() = " << index_list.size() << "\n";
-        }
-      else
-        {
-          cp_it++;
-          //std::cout << "!!!!!WARNING!!!!! A POINT HAS BEEN OMITTED!!!\n";
-        }
-      //if (list_it != index_list.end())
-      //  write_delaunay_mesh(t, W[*list_it], is2d);
-    }
-  
-  if (experiment2) epsratio_vector.push_back(rh.value/epsilon0);
-  if (experiment2) epsslope_vector.push_back( (pow(1/rh.value,D)-pow(1/epsilon0,D))/(landmarks_ind.size() - 48) );
-  std::cout << "The iteration ended when cp_count = " << candidate_points.size() << "\n";
-  std::cout << "alphaRmax = " << alpha*rh.value << "\n";
-  std::cout << "epsilon' = " << rh.value << "\n";
-  std::cout << "nbL = " << landmarks_ind.size() << "\n";
-  print_statistics();
-  //print_vector(landmarks_ind); std::cout << std::endl;
-  //std::sort(landmarks_ind.begin(), landmarks_ind.end());
-  print_vector(landmarks_ind); std::cout << std::endl;
-  if (experiment3) thetamin_vector[thetamin_vector.size()-1] = sampling_fatness(t);
-  std::cout << "theta = " << sampling_fatness(t) << "\n";
-  //fill_landmarks(W, landmarks, landmarks_ind, torus);
-  //fill_full_cell_vector(t, full_cells);
-  /*
-  if (triangulation_is_protected(t, delta))
-    std::cout << "Triangulation is ok\n";
-  else
-    {
-      std::cout << "Triangulation is BAD!! T_T しくしく!\n";
-    }
-  */
-  write_delaunay_mesh(t, W[0], true);
-  //std::cout << t << std::endl;
-}
-
-void run_experiment5(Point_Vector& W,
-                     int D,
-                     FT alpha,
-                     FT epsilon,
-                     FT delta0,
-                     FT theta0,
-                     FT gamma0,
-                     //std::vector<std::vector<int>>& full_cells,
-                     bool torus,
-                     bool power_protection
-                     )
-{
-  // INITIALIZATION
-  Delaunay_triangulation t(D);
-  std::vector<int> landmarks_ind;
-  int landmark_count = 0;
-  initialize_statistics();
-  if (D == 2)
-    {
-      int xw = 6, yw = 4;
-      // Triangular lattice close to regular triangles h=0.866a ~ 0.875a   : 48p
-      for (int i = 0; i < xw; ++i)
-        for (int j = 0; j < yw; ++j)
-          {
-            Point_d cite1(std::vector<FT>{2.0/xw*i, 2.0/yw*j});
-            W.push_back(cite1);  // debug purpose
-            insert_delaunay_landmark_with_copies(W, W.size()-1,
-                                                 landmarks_ind, t, landmark_count, true);
-
-            Point_d cite2(std::vector<FT>{2.0/xw*(i+0.5), 2.0/yw*(j+0.5)});
-            W.push_back(cite2);  // debug purpose
-            insert_delaunay_landmark_with_copies(W, W.size()-1,
-                                                 landmarks_ind, t, landmark_count, true);
-          }
-    }
-  else if (D == 3)
-    {
-      int wd = 3;
-      // Body-centered cubic lattice : 54p
-      for (int i = 0; i < wd; ++i)
-        for (int j = 0; j < wd; ++j)
-          for (int k = 0; k < wd; ++k)
-            {
-              Point_d cite1(std::vector<FT>{2.0/wd*i, 2.0/wd*j, 2.0/wd*k});
-              W.push_back(cite1);  // debug purpose
-              insert_delaunay_landmark_with_copies(W, W.size()-1,
-                                                   landmarks_ind, t, landmark_count, true);
-
-              Point_d cite2(std::vector<FT>{2.0/wd*(i+0.5), 2.0/wd*(j+0.5), 2.0/wd*(k+0.5)});
-              W.push_back(cite2);  // debug purpose
-              insert_delaunay_landmark_with_copies(W, W.size()-1,
-                                                   landmarks_ind, t, landmark_count, true);
-            }
-    }
-
-  // ITERATIONS
-  R_max_handle rh = sampling_radius(t);
-  Point_d rp = *(Random_point_iterator(D, alpha*rh.value));
-  int death_count = 0;
-  std::cout << "death count " << death_count << " rp = " << rp << "\n";
-  while (death_count < 100)
-    {
-      std::vector<FT> coords;
-      for (auto c_it = rh.center.cartesian_begin(),
-           r_it = rp.cartesian_begin();
-           c_it != rh.center.cartesian_end();
-           ++c_it, ++r_it)
-        coords.push_back(*c_it + *r_it);
-      Point_d new_p(coords);
-      if (!is_violating_protection(new_p, t, D, delta0, power_protection, theta0, gamma0))
-        {
-          W.push_back(new_p);
-          insert_delaunay_landmark_with_copies(W, W.size()-1, landmarks_ind, t, landmark_count, torus);
-          rh = sampling_radius(t);
-          rp = *(Random_point_iterator(D, alpha*rh.value));
-          death_count = 0;
-          std::cout << "death count " << death_count << " rp = " << rp << "\n";
-        }
-      else
-        {
-          rp = *(Random_point_iterator(D, alpha*rh.value));
-          death_count++;
-          std::cout << "death count " << death_count << " rp = " << rp << "\n";
-        }
-      //Point_d new_p = (*rp++) + Vector_d;
-    }
-}
-
-///////////////////////////////////////////////////////////////////////////////////////////////////////////
-// Series of experiments
-///////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-void start_experiments(Point_Vector& W, FT alpha, std::vector<int>& landmarks_ind, FT epsilon)
-{
-  int experiment_no = 1;
-  FT delta0 = 0.1;
-  FT theta0 = 0.1;
-  FT gamma0 = 0.01;
-  std::string suffix;
-  //std::cout << "ようこそジプシー我が神秘の部屋へ:\n";
-  while (experiment_no != 0)
-    {
-      std::cout << "Enter experiment no (0 to exit): ";
-      std::cin >> experiment_no;
-      switch (experiment_no)
-        {
-        case 1:
-          // Experiment 1
-          experiment1 = true;         
-          eps_vector = {};
-          std::cout << "Enter delta0: "; std::cin >> delta0;
-          std::cout << "Enter theta0: "; std::cin >> theta0;
-          std::cout << "Enter gamma0: "; std::cin >> gamma0;
-          protected_delaunay(W, landmarks_ind, alpha, epsilon, delta0, theta0, gamma0, true, true);
-          write_tikz_plot(eps_vector,"epstime.tikz");
-          experiment1 = false;
-          break;
-          
-        case 2:
-          // Experiment 2
-          suffix = "";
-          experiment2 = true;
-          epsratio_vector = {0};
-          epsslope_vector = {0};
-          std::cout << "File name suffix: ";
-          std::cin >> suffix;
-          for (FT alpha = 0.01; alpha < 0.999; alpha += 0.01)
-            {
-              landmarks_ind.clear();
-              std::cout << "Test for alpha = " << alpha << "\n";
-              protected_delaunay(W, landmarks_ind, alpha, epsilon, delta0, theta0, gamma0, true, true);
-            }
-          write_tikz_plot(epsratio_vector,"epsratio_alpha." + suffix + ".tex");
-          write_tikz_plot(epsslope_vector,"epsslope_alpha." + suffix + ".tex");
-          experiment2 = false;
-          break;
-
-        case 3:
-          // Experiment 3
-          experiment3 = true;
-          thetamin_vector = {};
-          gammamin_vector = {};
-          theta0 = 0;
-          gamma0 = 0;
-          for (FT delta0 = 0; delta0 < 0.999; delta0 += 0.05)
-            {
-              landmarks_ind.clear();
-              thetamin_vector.push_back(1.0); //0.7489 fatness of the initialization
-              gammamin_vector.push_back(10);
-              std::cout << "Test for delta0 = " << delta0 << "\n";
-              protected_delaunay(W, landmarks_ind, alpha, epsilon, delta0, theta0, gamma0, true, true);
-            }
-          write_tikz_plot(thetamin_vector,"thetamin_delta.tex");
-          write_tikz_plot(gammamin_vector,"gammamin_delta.tex");
-          experiment3 = false;
-          break;
-
-        // case 4:
-        //   // Experiment 4
-        //   {
-        //     int dim;
-        //     std::cout << "Enter dimension: ";
-        //     std::cin >> dim;
-        //     Delaunay_triangulation t(dim);
-        //     // for (FT eps = 0.7; eps < 1.1; eps += 0.1)
-        //   //     {
-        //   //       generate_epsilon_sample_torus(W, eps, dim, t);
-        //   //       for (auto v_it = t.vertices_begin(); v_it != t.vertices_end(); ++v_it)
-        //   //         {
-        //   //           if (t.is_infinite(v_it))
-        //   //             continue;
-        //   //           bool in_cube = true; 
-        //   //           for (auto xi = v_it->cartesian_begin(); xi != v_it->cartesian_end(); ++xi)
-        //   //             if (*xi > 1.0 || *xi < -1.0)
-        //   //               {
-        //   //                 in_cube = false; break;
-        //   //               }
-        //   //           if (!in_cube)
-        //   //             continue;
-        //   //           for (auto t.tds().incident_full_cells())
-        //   //         }
-        //   //       std::cout << "eps = " << eps << ", real epsilon = " << sampling_radius(t).value << "\n";
-        //   //     }
-        //   // }
-        //   break;
-
-
-        case 5:
-          // Experiment 5
-          experiment5 = true;
-          //     std::cout << "Enter dimension: ";
-          //     std::cin >> dim;
-
-          landmarks_ind.clear();
-          W.clear();
-          run_experiment5(W,  alpha, epsilon, delta0, theta0, gamma0, true, true);
-          experiment5 = false;
-          break;
-        }
-
-    }
-
-}
-  
-#endif
diff --git a/src/Witness_complex/example/witness_complex_cube.cpp b/src/Witness_complex/example/witness_complex_cube.cpp
deleted file mode 100644
index e448c55d..00000000
--- a/src/Witness_complex/example/witness_complex_cube.cpp
+++ /dev/null
@@ -1,590 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Siargey Kachanovich
- *
- *    Copyright (C) 2015  INRIA Sophia Antipolis-Méditerranée (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-// Avoiding the max arity issue with CGAL
-#ifndef BOOST_PARAMETER_MAX_ARITY
-# define BOOST_PARAMETER_MAX_ARITY 12
-#endif
-
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#include <utility>
-#include <algorithm>
-#include <set>
-#include <iterator>
-#include <chrono>
-
-#include <sys/types.h>
-#include <sys/stat.h>
-//#include <stdlib.h>
-
-//#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Witness_complex.h"
-#include "gudhi/reader_utils.h"
-#include "Torus_distance.h" 
-#include "generators.h"
-#include "output.h"
-//#include "protected_sets/protected_sets.h"
-#include "protected_sets/protected_sets_paper2.h"
-
-#include <CGAL/Cartesian_d.h>
-#include <CGAL/Search_traits.h>
-#include <CGAL/Search_traits_adapter.h>
-#include <CGAL/property_map.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/Orthogonal_k_neighbor_search.h>
-#include <CGAL/Kd_tree.h>
-#include <CGAL/Euclidean_distance.h>
-#include <CGAL/Kernel_d/Sphere_d.h>
-#include <CGAL/Kernel_d/Hyperplane_d.h>
-#include <CGAL/enum.h>
-
-#include <CGAL/Kernel_d/Vector_d.h>
-#include <CGAL/point_generators_d.h>
-#include <CGAL/constructions_d.h>
-#include <CGAL/Fuzzy_sphere.h>
-#include <CGAL/Random.h>
-#include <CGAL/Timer.h>
-#include <CGAL/Delaunay_triangulation.h>
-
-
-#include <boost/tuple/tuple.hpp>
-#include <boost/iterator/zip_iterator.hpp>
-#include <boost/iterator/counting_iterator.hpp>
-#include <boost/range/iterator_range.hpp>
-
-using namespace Gudhi;
-//using namespace boost::filesystem;
-
-typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
-typedef K::Point_d Point_d;
-typedef K::Vector_d Vector_d;
-typedef K::Oriented_side_d Oriented_side_d;
-typedef K::Has_on_positive_side_d Has_on_positive_side_d;
-
-//typedef CGAL::Point_d<K> Point_d;
-typedef K::FT FT;
-typedef CGAL::Search_traits<
-  FT, Point_d,
-  typename K::Cartesian_const_iterator_d,
-  typename K::Construct_cartesian_const_iterator_d> Traits_base;
-typedef CGAL::Euclidean_distance<Traits_base> Euclidean_distance;
-
-
-typedef std::vector< Vertex_handle > typeVectorVertex;
-
-//typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
-//typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
-
-typedef CGAL::Search_traits_adapter<
-  std::ptrdiff_t, Point_d*, Traits_base> STraits;
-//typedef K TreeTraits;
-//typedef CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance > Euclidean_adapter;
-//typedef CGAL::Kd_tree<STraits> Kd_tree;
-typedef CGAL::Orthogonal_k_neighbor_search<STraits, CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance>> K_neighbor_search;
-typedef K_neighbor_search::Tree Tree;
-typedef K_neighbor_search::Distance Distance;
-typedef K_neighbor_search::iterator KNS_iterator;
-typedef K_neighbor_search::iterator KNS_range;
-typedef boost::container::flat_map<int, int> Point_etiquette_map;
-typedef CGAL::Kd_tree<STraits> Tree2;
-
-typedef CGAL::Fuzzy_sphere<STraits> Fuzzy_sphere;
-
-typedef std::vector<Point_d> Point_Vector;
-
-//typedef K::Equal_d Equal_d;
-//typedef CGAL::Random_points_in_cube_d<CGAL::Point_d<CGAL::Cartesian_d<FT> > > Random_cube_iterator;
-
-typedef CGAL::Delaunay_triangulation<K> Delaunay_triangulation;
-typedef Delaunay_triangulation::Facet Facet;
-typedef Delaunay_triangulation::Vertex_handle Delaunay_vertex;
-typedef Delaunay_triangulation::Full_cell_handle Full_cell_handle;
-//typedef CGAL::Sphere_d<K> Sphere_d;
-typedef K::Sphere_d Sphere_d;
-typedef K::Hyperplane_d Hyperplane_d;
-
-/*//////////////////////////////////////
- * GLOBAL VARIABLES ********************
- *//////////////////////////////////////
-
-//NA bool toric=false;
-bool power_protection = true;
-bool grid_points = true;
-bool is2d = true;
-//FT  _sfty = pow(10,-14);
-bool torus = false;
-
-
-bool triangulation_is_protected(Delaunay_triangulation& t, FT delta)
-{
-  std::cout << "Start protection verification\n";
-  Euclidean_distance ed;
-  // Fill the map Vertices -> Numbers
-  std::map<Delaunay_triangulation::Vertex_handle, int> index_of_vertex;
-  int ind = 0;
-  for (auto v_it = t.vertices_begin(); v_it != t.vertices_end(); ++v_it)
-    {
-      if (t.is_infinite(v_it))
-        continue;
-      index_of_vertex[v_it] = ind++;
-    }
-  for (auto fc_it = t.full_cells_begin(); fc_it != t.full_cells_end(); ++fc_it)
-    if (!t.is_infinite(fc_it))
-      {
-        std::vector<Point_d> vertices;
-        for (auto fc_v_it = fc_it->vertices_begin(); fc_v_it != fc_it->vertices_end(); ++fc_v_it)
-          vertices.push_back((*fc_v_it)->point());                
-        Sphere_d cs( vertices.begin(), vertices.end());
-        Point_d center_cs = cs.center();
-        FT r = sqrt(ed.transformed_distance(center_cs, fc_it->vertex(0)->point()));
-        for (auto v_it = t.vertices_begin(); v_it != t.vertices_end(); ++v_it)
-          if (!t.is_infinite(v_it))
-          //check if vertex belongs to the face
-            if (!vertex_is_in_full_cell(v_it, fc_it))
-              {
-                FT dist2 = ed.transformed_distance(center_cs, v_it->point());
-                //if the new point is inside the protection ball of a non conflicting simplex
-                //std::cout << "Dist^2 = " << dist2 << " (r+delta)*(r+delta) = " << (r+delta)*(r+delta) << " r^2 = " << r*r <<"\n";
-                if (!power_protection)
-                  if (dist2 <= (r+delta)*(r+delta) && dist2 >= r*r)
-                    {
-                      write_delaunay_mesh(t, v_it->point(), is2d);
-                      // Output the problems
-                      std::cout << "Problematic vertex " << index_of_vertex[v_it] << " ";
-                      std::cout << "Problematic cell ";
-                      for (auto vh_it = fc_it->vertices_begin(); vh_it != fc_it->vertices_end(); ++vh_it)
-                        if (!t.is_infinite(*vh_it))
-                          std::cout << index_of_vertex[*vh_it] << " ";
-                      std::cout << "\n";
-                      std::cout << "r^2 = " << r*r << ", d^2 = " << dist2 << ", (r+delta)^2 = " << (r+delta)*(r+delta) << "\n";
-                      return false;
-                    }
-                if (power_protection)
-                  if (dist2 <= r*r+delta*delta && dist2 >= r*r)
-                    {
-                      write_delaunay_mesh(t, v_it->point(), is2d);
-                      std::cout << "Problematic vertex " << *v_it << " ";
-                      std::cout << "Problematic cell " << *fc_it << "\n";
-                      std::cout << "r^2 = " << r*r << ", d^2 = " << dist2 << ", r^2+delta^2 = " << r*r+delta*delta << "\n";
-                      return false;
-                    }
-              }
-      } 
-  return true;
-}
-
-//////////////////////////////////////////////////////////////////////////////////////////////////////////
-// SAMPLING RADIUS 
-//////////////////////////////////////////////////////////////////////////////////////////////////////////
-
-FT sampling_radius(Delaunay_triangulation& t, FT epsilon0)
-{
-  FT epsilon2 = 0;
-  Point_d control_point;
-  for (auto fc_it = t.full_cells_begin(); fc_it != t.full_cells_end(); ++fc_it)
-    {
-      if (t.is_infinite(fc_it))
-        continue;
-      Point_Vector vertices;
-      for (auto fc_v_it = fc_it->vertices_begin(); fc_v_it != fc_it->vertices_end(); ++fc_v_it)
-        vertices.push_back((*fc_v_it)->point());
-      Sphere_d cs( vertices.begin(), vertices.end());
-      Point_d csc = cs.center();
-      bool in_cube = true; 
-      for (auto xi = csc.cartesian_begin(); xi != csc.cartesian_end(); ++xi)
-        if (*xi > 1.0 || *xi < -1.0)
-          {
-            in_cube = false; break;
-          }
-      if (!in_cube)
-        continue;
-      FT r2 = Euclidean_distance().transformed_distance(cs.center(), *(vertices.begin()));
-      if (epsilon2 < r2)
-        {
-          epsilon2 = r2;
-          control_point = (*vertices.begin());
-        }
-    }
-  if (epsilon2 < epsilon0*epsilon0)
-    {
-      std::cout << "ACHTUNG! E' < E\n";
-      std::cout << "eps = " << epsilon0 << " eps' = " << sqrt(epsilon2) << "\n";
-      write_delaunay_mesh(t, control_point, is2d);
-    }
-  return sqrt(epsilon2);
-}
-
-FT point_sampling_radius_by_delaunay(Point_Vector& points, FT epsilon0)
-{
-  Delaunay_triangulation t(points[0].size());
-  t.insert(points.begin(), points.end());
-  return sampling_radius(t, epsilon0);
-}
-
-// A little script to make a tikz histogram of epsilon distribution
-// Returns the average epsilon
-FT epsilon_histogram(Delaunay_triangulation& t, int n)
-{
-  FT epsilon_max = 0; //sampling_radius(t,0);
-  FT sum_epsilon = 0;
-  int count_simplices = 0;
-  std::vector<int> histo(n+1, 0);
-  for (auto fc_it = t.full_cells_begin(); fc_it != t.full_cells_end(); ++fc_it)
-    {
-      if (t.is_infinite(fc_it))
-        continue;
-      Point_Vector vertices;
-      for (auto fc_v_it = fc_it->vertices_begin(); fc_v_it != fc_it->vertices_end(); ++fc_v_it)
-        vertices.push_back((*fc_v_it)->point());
-      Sphere_d cs( vertices.begin(), vertices.end());
-      Point_d csc = cs.center();
-      bool in_cube = true; 
-      for (auto xi = csc.cartesian_begin(); xi != csc.cartesian_end(); ++xi)
-        if (*xi > 1.0 || *xi < -1.0)
-          {
-            in_cube = false; break;
-          }
-      if (!in_cube)
-        continue;
-      FT r = sqrt(Euclidean_distance().transformed_distance(cs.center(), *(vertices.begin())));
-      if (r > epsilon_max)
-        epsilon_max = r;
-      sum_epsilon += r;
-      count_simplices++;
-      histo[floor(r/epsilon_max*n)]++;
-    }
-  std::ofstream ofs ("histogram.tikz", std::ofstream::out);
-  FT barwidth = 20.0/n;
-  int max_value = *(std::max_element(histo.begin(), histo.end()));
-  std::cout << max_value << std::endl;
-  FT ten_power = pow(10, ceil(log10(max_value)));
-  FT max_histo = ten_power;
-  if (max_value/ten_power < 2)
-    max_histo = 0.2*ten_power;
-  if (max_value/ten_power < 5)
-    max_histo = 0.5*ten_power;  
-  std::cout << ceil(log10(max_value)) << std::endl << max_histo << std::endl;
-  FT unitht = max_histo/10.0;
-
-  ofs << "\\draw[->] (0,0) -- (0,11);\n" <<
-    "\\draw[->] (0,0) -- (21,0);\n" <<
-    "\\foreach \\i in {1,...,10}\n" <<
-    "\\draw (0,\\i) -- (-0.1,\\i);\n" <<
-    "\\foreach \\i in {1,...,20}\n" <<
-    "\\draw (\\i,0) -- (\\i,-0.1);\n" <<
- 
-    "\\node at (-1,11) {$\\epsilon$};\n" << 
-    "\\node at (22,-1) {$\\epsilon/\\epsilon_{max}$};\n" << 
-    "\\node at (-0.5,-0.5) {0};\n" << 
-    "\\node at (-0.5,10) {" << max_histo << "};\n" << 
-    "\\node at (20,-0.5) {1};\n";
-    
-
-  for (int i = 0; i < n; ++i)
-    ofs << "\\draw (" << barwidth*i << "," << histo[i]/unitht << ") -- ("
-        << barwidth*(i+1) << "," << histo[i]/unitht << ") -- ("
-  << barwidth*(i+1) << ",0) -- (" << barwidth*i << ",0) -- cycle;\n";
-  
-  ofs.close();
-
-  //return sum_epsilon/count_simplices;
-  return epsilon_max;
-}
-
-FT epsilon_histogram_by_delaunay(Point_Vector& points, int n)
-{
-  Delaunay_triangulation t(points[0].size());
-  t.insert(points.begin(), points.end());
-  return epsilon_histogram(t, n);
-}
-
-
-int landmark_perturbation(Point_Vector &W, int nbL, Point_Vector& landmarks, std::vector<int>& landmarks_ind, std::vector<std::vector<int>>& full_cells)
-{
-  //******************** Preface: origin point
-  int D = W[0].size();
-  std::vector<FT> orig_vector;
-  for (int i=0; i<D; i++)
-    orig_vector.push_back(0);
-  Point_d origin(orig_vector);
-
-  //******************** Constructing a WL matrix
-  int nbP = W.size();
-  Euclidean_distance ed;
-  FT lambda = ed.transformed_distance(landmarks[0],landmarks[1]);
-  std::vector<Point_d> landmarks_ext;
-  int nb_cells = 1;
-  for (int i = 0; i < D; ++i)
-    nb_cells *= 3;
-  for (int i = 0; i < nb_cells; ++i)
-      for (int k = 0; k < nbL; ++k)
-        {
-          std::vector<double> point;
-          int cell_i = i;
-          for (int l = 0; l < D; ++l)
-            {
-              point.push_back(landmarks[k][l] + 2.0*((cell_i%3)-1.0));
-              cell_i /= 3;
-            }
-          landmarks_ext.push_back(point);
-        }
-  write_points("landmarks/initial_landmarks",landmarks_ext);
-  STraits traits(&(landmarks_ext[0]));
-  std::vector< std::vector <int> > WL(nbP);
-
-  //********************** Neighbor search in a Kd tree
-  Tree L(boost::counting_iterator<std::ptrdiff_t>(0),
-         boost::counting_iterator<std::ptrdiff_t>(nb_cells*nbL),
-         typename Tree::Splitter(),
-         traits);
-  std::cout << "Enter (D+1) nearest landmarks\n";
-  for (int i = 0; i < nbP; i++)
-    {
-      Point_d& w = W[i];
-      ////Search D+1 nearest neighbours from the tree of landmarks L
-      K_neighbor_search search(L, w, D+1, FT(0), true,
-                               CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance>(&(landmarks_ext[0])) );
-      for(K_neighbor_search::iterator it = search.begin(); it != search.end(); ++it)
-        {
-          if (std::find(WL[i].begin(), WL[i].end(), (it->first)%nbL) == WL[i].end())
-            WL[i].push_back((it->first)%nbL);
-        }
-      if (i == landmarks_ind[WL[i][0]])
-        {
-          FT dist = ed.transformed_distance(W[i], landmarks[WL[i][1]]);
-          if (dist < lambda)
-            lambda = dist;
-        }
-    }
-  std::string out_file = "wl_result";
-  //write_wl(out_file,WL);
-  
-  //******************** Constructng a witness complex
-  std::cout << "Entered witness complex construction\n";
-  Witness_complex<> witnessComplex;
-  witnessComplex.setNbL(nbL);
-  witnessComplex.witness_complex(WL);
-
-  //******************** Verifying if all full cells are in the complex
-
-  int in=0, not_in=0;
-  for (auto cell : full_cells)
-    {
-      //print_vector(cell);
-      if (witnessComplex.find(cell) != witnessComplex.null_simplex())
-        in++;
-      else
-        not_in++;
-    }
-  std::cout << "Out of all the cells in Delaunay triangulation:\n" << in << " are in the witness complex\n" <<
-    not_in << " are not.\n";
-  
-  //******************** Making a set of bad link landmarks
-  
-  std::cout << "Entered bad links\n";
-  std::set< int > perturbL;
-  int count_badlinks = 0;
-  //std::cout << "Bad links around ";
-  std::vector< int > count_bad(D);
-  std::vector< int > count_good(D);
-  for (auto u: witnessComplex.complex_vertex_range())
-    {
-       if (!witnessComplex.has_good_link(u, count_bad, count_good))
-         {
-           count_badlinks++;
-           Point_d& l = landmarks[u];
-           Fuzzy_sphere fs(l, sqrt(lambda)*3, 0, traits);
-           std::vector<int> curr_perturb;
-           L.search(std::insert_iterator<std::vector<int>>(curr_perturb,curr_perturb.begin()),fs);
-           for (int i: curr_perturb)
-             perturbL.insert(i%nbL);
-       }
-    }
-  for (unsigned int i = 0; i != count_good.size(); i++)
-    if (count_good[i] != 0)
-      std::cout << "count_good[" << i << "] = " << count_good[i] << std::endl;
-  for (unsigned int i = 0; i != count_bad.size(); i++)
-    if (count_bad[i] != 0)
-      std::cout << "count_bad[" << i << "] = " << count_bad[i] << std::endl;
-  std::cout << "\nBad links total: " << count_badlinks << " Points to perturb: " << perturbL.size() << std::endl;
-  
-  //*********************** Perturb bad link landmarks  
-  /*
-  for (auto u: perturbL)
-    {
-      Random_point_iterator rp(D,sqrt(lambda)/8);
-      std::vector<FT> point;
-      for (int i = 0; i < D; i++)
-        {
-          while (K().squared_distance_d_object()(*rp,origin) < lambda/256)
-            rp++;
-          FT coord = landmarks[u][i] + (*rp)[i];
-          if (coord > 1)
-            point.push_back(coord-1);
-          else if (coord < -1)
-            point.push_back(coord+1);
-          else
-            point.push_back(coord);
-        }
-      landmarks[u] = Point_d(point);
-    }
-  std::cout << "lambda=" << lambda << std::endl;
-  */
-  char buffer[100];
-  int i = sprintf(buffer,"stree_result.txt");
-  
-  if (i >= 0)
-    {
-      std::string out_file = (std::string)buffer;
-      std::ofstream ofs (out_file, std::ofstream::out);
-      witnessComplex.st_to_file(ofs);
-      ofs.close();
-    }
-  
-  //write_edges("landmarks/edges", witnessComplex, landmarks);
-  /*
-  return count_badlinks;
-  */
-  return 0;
-}
-
-int main (int argc, char * const argv[])
-{
-  power_protection = true;//false;
-  grid_points = false;//true;
-  torus = true;
-  
-  if (argc != 4)
-    {
-      std::cerr << "Usage: " << argv[0]
-                << " nbP dim delta\n";
-      return 0;
-    }
-  int nbP       = atoi(argv[1]);
-  int dim       = atoi(argv[2]);
-  double theta0 = atof(argv[3]);
-  //double delta  = atof(argv[3]);
-
-  is2d = (dim == 2);
-  
-  std::cout << "Let the carnage begin!\n";
-  Point_Vector point_vector;
-  if (grid_points)
-    {
-      generate_points_grid(point_vector, (int)pow(nbP, 1.0/dim), dim, torus);
-      nbP = (int)pow((int)pow(nbP, 1.0/dim), dim);
-    }
-  else
-    generate_points_random_box(point_vector, nbP, dim);
-  FT epsilon = point_sampling_radius_by_delaunay(point_vector, 0);
-  //FT epsilon = epsilon_histogram_by_delaunay(point_vector,50);
-  std::cout << "Initial epsilon = " << epsilon << std::endl;
-  Point_Vector L;
-  std::vector<int> chosen_landmarks;
-  //write_points("landmarks/initial_pointset",point_vector);
-  //write_points("landmarks/initial_landmarks",L);
-  CGAL::Timer timer;
-
-  int n = 1;
-  std::vector<FT> values(n,0);
-  std::vector<FT> time(n,0);
-
-  //FT step = 0.001;
-  //FT delta = 0.01*epsilon;
-  //FT alpha = 0.5;
-  //FT step = atof(argv[3]);
-
-  start_experiments(point_vector, theta0, chosen_landmarks, epsilon);
-    
-  // for (int i = 0; i < n; i++)
-  // //for (int i = 0; bl > 0; i++)
-  //   {
-  //     //std::cout << "========== Start iteration " << i << "== curr_min(" << curr_min << ")========\n";
-  //     //double delta = pow(10, -(1.0*i)/2);
-  //     //delta = step*i*epsilon;
-  //     //theta0 = step*i;
-  //     std::cout << "delta/epsilon = " << delta/epsilon << std::endl;
-  //     std::cout << "theta0 = " << theta0 << std::endl;
-  //     // Averaging the result
-  //     int sum_values = 0;
-  //     int nb_iterations = 1;
-  //     std::vector<std::vector<int>> full_cells;
-  //     for (int i = 0; i < nb_iterations; ++i)
-  //       {
-  //         //L = {};
-  //         chosen_landmarks = {};
-  //         //full_cells = {};
-  //         //timer.start();
-  //         //protected_delaunay(point_vector, nbP, L, chosen_landmarks, delta, epsilon, alpha, theta0, full_cells, torus, power_protection);
-  //         protected_delaunay(point_vector, chosen_landmarks, delta, epsilon, alpha, theta0, torus, power_protection);
-  //         //timer.stop();
-  //         sum_values += chosen_landmarks.size();
-  //       }
-  //     //FT epsilon2 = point_sampling_radius_by_delaunay(L, epsilon);
-  //     //std::cout << "Final epsilon = " << epsilon2  << ". Ratio = " << epsilon2/epsilon << std::endl;
-  //     //write_points("landmarks/initial_landmarks",L);
-  //     //std::cout << "delta/epsilon' = " << delta/epsilon2 << std::endl;
-  //     FT nbL = (sum_values*1.0)/nb_iterations;
-  //     //values[i] = pow((1.0*nbL)/nbP, -1.0/dim);
-  //     values[i] = (1.0*nbL)/nbP;
-  //     std::cout << "Number of landmarks = " << nbL << ", time= " << timer.time() << "s"<< std::endl;
-  //     //landmark_perturbation(point_vector, nbL, L, chosen_landmarks, full_cells);
-  //     time[i] = timer.time();
-  //     timer.reset();
-  //     //write_points("landmarks/landmarks0",L);
-  //   }
-  
-  // // OUTPUT A PLOT
-  // FT hstep = 20.0/(n-1);
-  // FT wstep = 10.0;
-
-  // std::ofstream ofs("N'Nplot.tikz", std::ofstream::out);
-  // ofs << "\\draw[red] (0," << wstep*values[0] << ")";
-  // for (int i = 1; i < n; ++i)
-  //   ofs << " -- (" << hstep*i << "," << wstep*values[i] << ")";
-  // ofs << ";\n";
-  // ofs.close();
-  /*
-  wstep = 0.1;
-  ofs = std::ofstream("time.tikz", std::ofstream::out);
-  ofs << "\\draw[red] (0," << wstep*time[0] << ")";
-  for (int i = 1; i < n; ++i)
-    ofs << " -- (" << hstep*i << "," << wstep*time[i] << ")";
-  ofs << ";\n";
-  ofs.close();
-  
-  
-  std::vector<std::vector<int>> full_cells;
-  timer.start();
-  landmark_choice_protected_delaunay(point_vector, nbP, L, chosen_landmarks, delta, full_cells);
-  timer.stop();
-  FT epsilon2 = point_sampling_radius_by_delaunay(L);
-  std::cout << "Final epsilon = " << epsilon2  << ". Ratio = " << epsilon/epsilon2 << std::endl;
-  write_points("landmarks/initial_landmarks",L);
-  int nbL = chosen_landmarks.size();
-  std::cout << "Number of landmarks = " << nbL << ", time= " << timer.time() << "s"<< std::endl;
-  //landmark_perturbation(point_vector, nbL, L, chosen_landmarks, full_cells);
-  timer.reset();
-  */
-}
diff --git a/src/Witness_complex/example/witness_complex_cubic_systems.cpp b/src/Witness_complex/example/witness_complex_cubic_systems.cpp
deleted file mode 100644
index 2f4ee1cb..00000000
--- a/src/Witness_complex/example/witness_complex_cubic_systems.cpp
+++ /dev/null
@@ -1,547 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Siargey Kachanovich
- *
- *    Copyright (C) 2015  INRIA Sophia Antipolis-Méditerranée (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#include <utility>
-#include <algorithm>
-#include <set>
-#include <iterator>
-
-#include <sys/types.h>
-#include <sys/stat.h>
-#include <unistd.h>
-
-//#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Witness_complex.h"
-#include "gudhi/reader_utils.h"
-#include "Torus_distance.h" 
-
-#include <CGAL/Cartesian_d.h>
-#include <CGAL/Search_traits.h>
-#include <CGAL/Search_traits_adapter.h>
-#include <CGAL/property_map.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/Orthogonal_k_neighbor_search.h>
-#include <CGAL/Kd_tree.h>
-#include <CGAL/Euclidean_distance.h>
-#include <CGAL/Kernel_d/Sphere_d.h>
-
-#include <CGAL/Kernel_d/Vector_d.h>
-#include <CGAL/point_generators_d.h>
-#include <CGAL/constructions_d.h>
-#include <CGAL/Fuzzy_sphere.h>
-#include <CGAL/Random.h>
-#include <CGAL/Delaunay_triangulation.h>
-
-
-#include <boost/tuple/tuple.hpp>
-#include <boost/iterator/zip_iterator.hpp>
-#include <boost/iterator/counting_iterator.hpp>
-#include <boost/range/iterator_range.hpp>
-
-using namespace Gudhi;
-//using namespace boost::filesystem;
-
-typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
-typedef K::Point_d Point_d;
-//typedef CGAL::Cartesian_d<double> K;
-//typedef CGAL::Point_d<K> Point_d;
-typedef K::FT FT;
-typedef CGAL::Search_traits<
-  FT, Point_d,
-  typename K::Cartesian_const_iterator_d,
-  typename K::Construct_cartesian_const_iterator_d> Traits_base;
-typedef CGAL::Euclidean_distance<Traits_base> Euclidean_distance;
-
-
-typedef std::vector< Vertex_handle > typeVectorVertex;
-
-//typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
-//typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
-
-typedef CGAL::Search_traits_adapter<
-  std::ptrdiff_t, Point_d*, Traits_base> STraits;
-//typedef K TreeTraits;
-//typedef CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance > Euclidean_adapter;
-//typedef CGAL::Kd_tree<STraits> Kd_tree;
-typedef CGAL::Orthogonal_k_neighbor_search<STraits, CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance>> K_neighbor_search;
-typedef K_neighbor_search::Tree Tree;
-typedef K_neighbor_search::Distance Distance;
-typedef K_neighbor_search::iterator KNS_iterator;
-typedef K_neighbor_search::iterator KNS_range;
-typedef boost::container::flat_map<int, int> Point_etiquette_map;
-typedef CGAL::Kd_tree<STraits> Tree2;
-
-typedef CGAL::Fuzzy_sphere<STraits> Fuzzy_sphere;
-
-typedef std::vector<Point_d> Point_Vector;
-
-//typedef K::Equal_d Equal_d;
-//typedef CGAL::Random_points_in_cube_d<CGAL::Point_d<CGAL::Cartesian_d<FT> > > Random_cube_iterator;
-typedef CGAL::Random_points_in_cube_d<Point_d> Random_cube_iterator;
-typedef CGAL::Random_points_in_ball_d<Point_d> Random_point_iterator;
-
-typedef CGAL::Delaunay_triangulation<K> Delaunay_triangulation;
-typedef Delaunay_triangulation::Facet Facet;
-typedef CGAL::Sphere_d<K> Sphere_d;
-
-bool toric=false;
-
-
-/**
- * \brief Customized version of read_points
- * which takes into account a possible nbP first line
- *
- */
-inline void
-read_points_cust ( std::string file_name , Point_Vector & points)
-{  
-  std::ifstream in_file (file_name.c_str(),std::ios::in);
-  if(!in_file.is_open())
-    {
-      std::cerr << "Unable to open file " << file_name << std::endl;
-      return;
-    }
-  std::string line;
-  double x;
-  while( getline ( in_file , line ) )
-    {
-      std::vector< double > point;
-      std::istringstream iss( line );
-      while(iss >> x) { point.push_back(x); }
-      Point_d p(point.begin(), point.end());
-      if (point.size() != 1)
-        points.push_back(p);
-    }
-  in_file.close();
-}
-
-void generate_points_random_box(Point_Vector& W, int nbP, int dim)
-{
-  /*
-  Random_cube_iterator rp(dim, 1);
-  for (int i = 0; i < nbP; i++)
-    {
-      std::vector<double> point;
-      for (auto it = rp->cartesian_begin(); it != rp->cartesian_end(); ++it)
-        point.push_back(*it);
-      W.push_back(Point_d(point));
-      rp++;
-    }
-  */
-  Random_cube_iterator rp(dim, 1.0);
-  for (int i = 0; i < nbP; i++)
-    {
-      W.push_back(*rp++);
-    }
-}
-
-
-void write_wl( std::string file_name, std::vector< std::vector <int> > & WL)
-{
-  std::ofstream ofs (file_name, std::ofstream::out);
-  for (auto w : WL)
-    {
-      for (auto l: w)
-        ofs << l << " ";
-      ofs << "\n";
-    }
-  ofs.close();
-}
-
-
-void write_points( std::string file_name, std::vector< Point_d > & points)
-{
-  std::ofstream ofs (file_name, std::ofstream::out);
-  for (auto w : points)
-    {
-      for (auto it = w.cartesian_begin(); it != w.cartesian_end(); ++it)
-        ofs << *it << " ";
-      ofs << "\n";
-    }
-  ofs.close();
-}
-
-void write_edges(std::string file_name, Witness_complex<>& witness_complex, Point_Vector& landmarks)
-{
-  std::ofstream ofs (file_name, std::ofstream::out);
-  for (auto u: witness_complex.complex_vertex_range())
-    for (auto v: witness_complex.complex_vertex_range())
-      {
-        typeVectorVertex edge = {u,v};
-        if (u < v && witness_complex.find(edge) != witness_complex.null_simplex())   
-          {
-            for (auto it = landmarks[u].cartesian_begin(); it != landmarks[u].cartesian_end(); ++it)
-              ofs << *it << " ";
-            ofs << "\n";
-            for (auto it = landmarks[v].cartesian_begin(); it != landmarks[v].cartesian_end(); ++it)
-              ofs << *it << " ";
-            ofs << "\n\n\n";
-          }
-      }
-  ofs.close();
-}
-
-
-/** Function that chooses landmarks from W and place it in the kd-tree L.
- *  Note: nbL hould be removed if the code moves to Witness_complex
- */
-void landmark_choice(Point_Vector &W, int nbP, int nbL, Point_Vector& landmarks, std::vector<int>& landmarks_ind)
-{
-  std::cout << "Enter landmark choice to kd tree\n";
-  int chosen_landmark;
-  Point_d* p;
-  CGAL::Random rand;
-  for (int i = 0; i < nbL; i++)
-    {
-      //      while (!res.second)
-      //  {
-      do chosen_landmark = rand.get_int(0,nbP);
-      while (std::count(landmarks_ind.begin(),landmarks_ind.end(),chosen_landmark)!=0);
-      //rand++;
-      //std::cout << "Chose " << chosen_landmark << std::endl;
-      p = &W[chosen_landmark];
-      //L_i.emplace(chosen_landmark,i);
-      //  }
-      landmarks.push_back(*p);
-      landmarks_ind.push_back(chosen_landmark);
-      //std::cout << "Added landmark " << chosen_landmark << std::endl;
-    }
- }
-
-void aux_fill_grid(Point_Vector& W, int& width, Point_Vector& landmarks, std::vector<int>& landmarks_ind, std::vector<bool> & curr_pattern)
-{
-  int D = W[0].size();
-  int nb_points = 1;
-  for (int i = 0; i < D; ++i)
-    nb_points *= width;
-  for (int i = 0; i < nb_points; ++i)
-    {
-      std::vector<double> point;
-      int cell_i = i;
-      for (int l = 0; l < D; ++l)
-        {
-          if (curr_pattern[l])
-            point.push_back(-1.0+(2.0/width)*(cell_i%width)+(1.0/width));
-          else
-            point.push_back(-1.0+(2.0/width)*(cell_i%width));
-          cell_i /= width;
-        }
-      landmarks.push_back(Point_d(point));
-      landmarks_ind.push_back(0);//landmarks_ind.push_back(W.size());
-      //std::cout << "Added point " << W.size() << std::endl;;
-      //W.push_back(Point_d(point));
-    }
-}
-  
-void aux_put_halves(Point_Vector& W, int& width, Point_Vector& landmarks, std::vector<int>& landmarks_ind, std::vector<bool>& curr_pattern, std::vector<bool>::iterator curr_pattern_it, std::vector<bool>::iterator bool_it, std::vector<bool>::iterator bool_end)
-{
-  if (curr_pattern_it != curr_pattern.end())
-    {
-      if (bool_it != bool_end)
-        {
-          *curr_pattern_it = false;
-          aux_put_halves(W, width, landmarks, landmarks_ind, curr_pattern, curr_pattern_it+1, bool_it, bool_end);
-          *curr_pattern_it = true;
-          aux_put_halves(W, width, landmarks, landmarks_ind, curr_pattern, curr_pattern_it+1, bool_it+1, bool_end);
-        }
-    }
-  else
-    if (*bool_it)
-      {
-        std::cout << "Filling the pattern ";
-        for (bool b: curr_pattern)
-          if (b) std::cout << '1';
-          else   std::cout << '0';
-        std::cout << "\n";
-        aux_fill_grid(W, width, landmarks, landmarks_ind, curr_pattern);
-      }  
-}
-
-void landmark_choice_cs(Point_Vector& W, int width, Point_Vector& landmarks, std::vector<int>& landmarks_ind, std::vector<bool>& face_centers)
-{
-  std::cout << "Enter landmark choice to kd tree\n";
-  //int chosen_landmark;
-  CGAL::Random rand;
-  //To speed things up check the last true in the code and put it as the finishing condition
-  unsigned last_true = face_centers.size()-1;
-  while (!face_centers[last_true] && last_true != 0)
-    last_true--;
-  //Recursive procedure to understand where we put +1/2 in centers' coordinates
-  std::vector<bool> curr_pattern(W[0].size(), false);
-  aux_put_halves(W, width, landmarks, landmarks_ind, curr_pattern, curr_pattern.begin(), face_centers.begin(), face_centers.begin()+(last_true+1));
-  std::cout << "The number of landmarks is: " << landmarks.size() << std::endl;
-
- }
-
-int landmark_perturbation(Point_Vector &W, Point_Vector& landmarks, std::vector<int>& landmarks_ind)
-{
-  //******************** Preface: origin point
-  int D = W[0].size();
-  std::vector<FT> orig_vector;
-  for (int i=0; i<D; i++)
-    orig_vector.push_back(0);
-  Point_d origin(orig_vector);
-
-  //******************** Constructing a WL matrix
-  int nbP = W.size();
-  int nbL = landmarks.size();
-  Euclidean_distance ed;
-  FT lambda = ed.transformed_distance(landmarks[0],landmarks[1]);
-  std::vector<Point_d> landmarks_ext;
-  int nb_cells = 1;
-  for (int i = 0; i < D; ++i)
-    nb_cells *= 3;
-  for (int i = 0; i < nb_cells; ++i)
-      for (int k = 0; k < nbL; ++k)
-        {
-          std::vector<double> point;
-          int cell_i = i;
-          for (int l = 0; l < D; ++l)
-            {
-              point.push_back(landmarks[k][l] + 2.0*((cell_i%3)-1.0));
-              cell_i /= 3;
-            }
-          landmarks_ext.push_back(point);
-        }
-  write_points("landmarks/initial_landmarks",landmarks_ext);
-  STraits traits(&(landmarks_ext[0]));
-  std::vector< std::vector <int> > WL(nbP);
-
-  //********************** Neighbor search in a Kd tree
-  Tree L(boost::counting_iterator<std::ptrdiff_t>(0),
-         boost::counting_iterator<std::ptrdiff_t>(nb_cells*nbL),
-         typename Tree::Splitter(),
-         traits);
-  std::cout << "Enter (D+1) nearest landmarks\n";
-  for (int i = 0; i < nbP; i++)
-    {
-      Point_d& w = W[i];
-      ////Search D+1 nearest neighbours from the tree of landmarks L
-      K_neighbor_search search(L, w, D+1, FT(0), true,
-                               CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance>(&(landmarks_ext[0])) );
-      for(K_neighbor_search::iterator it = search.begin(); it != search.end(); ++it)
-        {
-          if (std::find(WL[i].begin(), WL[i].end(), (it->first)%nbL) == WL[i].end())
-            WL[i].push_back((it->first)%nbL);
-        }
-      if (i == landmarks_ind[WL[i][0]])
-        {
-          FT dist = ed.transformed_distance(W[i], landmarks[WL[i][1]]);
-          if (dist < lambda)
-            lambda = dist;
-        }
-    }
-  std::string out_file = "wl_result";
-  write_wl(out_file,WL);
-  
-  //******************** Constructng a witness complex
-  std::cout << "Entered witness complex construction\n";
-  Witness_complex<> witnessComplex;
-  witnessComplex.setNbL(nbL);
-  witnessComplex.witness_complex(WL);
-
-  //******************** Making a set of bad link landmarks
-  std::cout << "Entered bad links\n";
-  std::set< int > perturbL;
-  int count_badlinks = 0;
-  //std::cout << "Bad links around ";
-  std::vector< int > count_bad(D);
-  std::vector< int > count_good(D);
-  for (auto u: witnessComplex.complex_vertex_range())
-    {
-      if (!witnessComplex.has_good_link(u, count_bad, count_good, D))
-         {
-           count_badlinks++;
-           Point_d& l = landmarks[u];
-           Fuzzy_sphere fs(l, sqrt(lambda)*3, 0, traits);
-           std::vector<int> curr_perturb;
-           L.search(std::insert_iterator<std::vector<int>>(curr_perturb,curr_perturb.begin()),fs);
-           for (int i: curr_perturb)
-             perturbL.insert(i%nbL);
-       }
-    }
-  for (unsigned int i = 0; i != count_good.size(); i++)
-    if (count_good[i] != 0)
-      std::cout << "count_good[" << i << "] = " << count_good[i] << std::endl;
-  for (unsigned int i = 0; i != count_bad.size(); i++)
-    if (count_bad[i] != 0)
-      std::cout << "count_bad[" << i << "] = " << count_bad[i] << std::endl;
-  std::cout << "\nBad links total: " << count_badlinks << " Points to perturb: " << perturbL.size() << std::endl;
-  
-  //*********************** Perturb bad link landmarks  
-  for (auto u: perturbL)
-    {
-      Random_point_iterator rp(D,sqrt(lambda)/8);
-      std::vector<FT> point;
-      for (int i = 0; i < D; i++)
-        {
-          while (K().squared_distance_d_object()(*rp,origin) < lambda/256)
-            rp++;
-          FT coord = landmarks[u][i] + (*rp)[i];
-          if (coord > 1)
-            point.push_back(coord-1);
-          else if (coord < -1)
-            point.push_back(coord+1);
-          else
-            point.push_back(coord);
-        }
-      landmarks[u] = Point_d(point);
-    }
-  std::cout << "lambda=" << lambda << std::endl;
-  char buffer[100];
-  int i = sprintf(buffer,"stree_result.txt");
-  
-  if (i >= 0)
-    {
-      std::string out_file = (std::string)buffer;
-      std::ofstream ofs (out_file, std::ofstream::out);
-      witnessComplex.st_to_file(ofs);
-      ofs.close();
-    }
-  write_edges("landmarks/edges", witnessComplex, landmarks);
-  return count_badlinks;
-}
-
-void exaustive_search(Point_Vector& W, int width)
-{
-  int D = W[0].size()+1;
-  int nb_points = pow(2,D);
-  std::vector<bool> face_centers(D, false);
-  int bl = 0; //Bad links
-  std::vector<std::vector<bool>> good_patterns;
-  for (int i = 0; i < nb_points; ++i)
-    {
-      int cell_i = i;
-      for (int l = 0; l < D; ++l)
-        {
-          if (cell_i%2 == 0)
-            face_centers[l] = false;
-          else
-            face_centers[l] = true;
-          cell_i /= 2;
-        }
-      std::cout << "**Current pattern ";
-      for (bool b: face_centers)
-        if (b) std::cout << '1';
-        else   std::cout << '0';
-      std::cout << "\n";
-      Point_Vector landmarks;
-      std::vector<int> landmarks_ind;
-      Point_Vector W_copy(W);
-      landmark_choice_cs(W_copy, width, landmarks, landmarks_ind, face_centers);
-      if (landmarks.size() != 0)
-        {
-          bl = landmark_perturbation(W_copy, landmarks, landmarks_ind);
-          if ((1.0*bl)/landmarks.size() < 0.5)
-            good_patterns.push_back(face_centers);
-        }
-    }
-  std::cout << "The following patterns worked: ";
-  for (std::vector<bool> pattern : good_patterns)
-    {
-      std::cout << "[";
-      for (bool b: pattern)
-        if (b) std::cout << '1';
-        else   std::cout << '0';
-      std::cout << "] ";
-    }
-  std::cout << "\n";        
-}
-
-int main (int argc, char * const argv[])
-{
-  unsigned nbP       = atoi(argv[1]);
-  unsigned width     = atoi(argv[2]);
-  unsigned dim       = atoi(argv[3]);
-  std::string code   = (std::string) argv[4];
-  bool e_option = false;
-  int c;
-  if (argc != 5)
-    {
-      std::cerr << "Usage: " << argv[0]
-                << "witness_complex_cubic_systems nbP width dim code || witness_complex_systems -e nbP width dim\n"
-                << "where nbP stands for the number of witnesses, width for the width of the grid, dim for dimension "
-                << "and code is a sequence of (dim+1) symbols 0 and 1 representing if we take the centers of k-dimensional faces of the cubic system depending if it is 0 or 1."
-                << "-e stands for the 'exaustive' option";
-      return 0;
-    }
-  while ((c = getopt (argc, argv, "e::")) != -1)
-    switch(c)
-      {
-      case 'e' :
-        e_option  = true;
-        nbP       = atoi(argv[2]);
-        width     = atoi(argv[3]);
-        dim       = atoi(argv[4]);
-        break;
-      default  :
-        nbP       = atoi(argv[1]);
-        width     = atoi(argv[2]);
-        dim       = atoi(argv[3]);
-        code   = (std::string) argv[4];
-      }
-  Point_Vector point_vector;
-  generate_points_random_box(point_vector, nbP, dim);
-  
-  // Exaustive search
-  if (e_option)
-    {
-      std::cout << "Start exaustive search!\n";
-      exaustive_search(point_vector, width);
-      return 0;
-    }
-  // Search with a specific cubic system
-  std::vector<bool> face_centers;
-  if (code.size() != dim+1)
-    {
-      std::cerr << "The code should contain (dim+1) symbols";
-      return 1;
-    }
-  for (char c: code)
-    if (c == '0')
-      face_centers.push_back(false);
-    else
-      face_centers.push_back(true);
-  std::cout << "Let the carnage begin!\n";
-  Point_Vector L;
-  std::vector<int> chosen_landmarks;
-  
-  landmark_choice_cs(point_vector, width, L, chosen_landmarks, face_centers);
-  
-  int nbL = width; //!!!!!!!!!!!!!
-  int bl = nbL, curr_min = bl;
-  write_points("landmarks/initial_pointset",point_vector);
-  //write_points("landmarks/initial_landmarks",L);
-  //for (int i = 0; i < 1; i++)
-  for (int i = 0; bl > 0; i++)
-    {
-      std::cout << "========== Start iteration " << i << "== curr_min(" << curr_min << ")========\n";
-      bl=landmark_perturbation(point_vector, L, chosen_landmarks);
-      if (bl < curr_min)
-        curr_min=bl;
-      write_points("landmarks/landmarks0",L);
-    }
-  
-}
diff --git a/src/Witness_complex/example/witness_complex_epsilon.cpp b/src/Witness_complex/example/witness_complex_epsilon.cpp
deleted file mode 100644
index 7f8b985f..00000000
--- a/src/Witness_complex/example/witness_complex_epsilon.cpp
+++ /dev/null
@@ -1,55 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Siargey Kachanovich
- *
- *    Copyright (C) 2015  INRIA Sophia Antipolis-Méditerranée (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <iostream>
-#include <vector>
-
-#include <CGAL/Epick_d.h>
-#include <CGAL/enum.h>
-
-typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
-typedef K::Point_d                                 Point_d;
-typedef K::FT                                      FT;
-typedef K::Hyperplane_d                            Hyperplane_d;
-typedef K::Has_on_positive_side_d                  Has_on_positive_side_d;
-
-int main ()
-{
-  std::vector<Point_d> vertices;
-  Point_d v1(std::vector<FT>({-1,1}));
-  Point_d v2(std::vector<FT>({1,-1}));
-  vertices.push_back(v1);
-  vertices.push_back(v2);
-  Point_d p(std::vector<FT>({-1,-1}));
-  Hyperplane_d hp(vertices.begin(), vertices.end());
-  //Hyperplane_d hp(vertices.begin(), vertices.end(), p, CGAL::ON_POSITIVE_SIDE);
-  if (Has_on_positive_side_d()(hp, p))
-    std::cout << "OK\n";
-  else
-    std::cout << "NOK\n";
-  CGAL::Oriented_side side_p = K::Oriented_side_d()(hp, p);
-  if (side_p == CGAL::ZERO)
-    std::cout << "Point (-1,-1) is on the line passing through (-1,1) and (1,-1)";
-  CGAL::Oriented_side side_v2 = K::Oriented_side_d()(hp, v2);
-  if (side_v2 != CGAL::ZERO)
-    std::cout << "Point (1,-1) is not on the line passing through (-1,1) and (1,-1)";
-}
diff --git a/src/Witness_complex/example/witness_complex_flat_torus.cpp b/src/Witness_complex/example/witness_complex_flat_torus.cpp
deleted file mode 100644
index 49383154..00000000
--- a/src/Witness_complex/example/witness_complex_flat_torus.cpp
+++ /dev/null
@@ -1,851 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Siargey Kachanovich
- *
- *    Copyright (C) 2015  INRIA Sophia Antipolis-Méditerranée (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#include <utility>
-#include <algorithm>
-#include <set>
-#include <iterator>
-
-#include <sys/types.h>
-#include <sys/stat.h>
-//#include <stdlib.h>
-
-//#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Witness_complex.h"
-#include "gudhi/reader_utils.h"
-//#include <boost/filesystem.hpp> 
-
-//#include <CGAL/Delaunay_triangulation.h>
-#include <CGAL/Cartesian_d.h>
-#include <CGAL/Search_traits.h>
-#include <CGAL/Search_traits_adapter.h>
-#include <CGAL/property_map.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/Orthogonal_k_neighbor_search.h>
-#include <CGAL/Kd_tree.h>
-#include <CGAL/Euclidean_distance.h>
-
-#include <CGAL/Kernel_d/Vector_d.h>
-#include <CGAL/point_generators_d.h>
-#include <CGAL/constructions_d.h>
-#include <CGAL/Fuzzy_sphere.h>
-#include <CGAL/Random.h>
-
-
-#include <boost/tuple/tuple.hpp>
-#include <boost/iterator/zip_iterator.hpp>
-#include <boost/iterator/counting_iterator.hpp>
-#include <boost/range/iterator_range.hpp>
-
-using namespace Gudhi;
-//using namespace boost::filesystem;
-
-typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
-typedef K::Point_d Point_d;
-//typedef CGAL::Cartesian_d<double> K;
-//typedef CGAL::Point_d<K> Point_d;
-typedef K::FT FT;
-typedef CGAL::Search_traits<
-  FT, Point_d,
-  typename K::Cartesian_const_iterator_d,
-  typename K::Construct_cartesian_const_iterator_d> Traits_base;
-typedef CGAL::Euclidean_distance<Traits_base> Euclidean_distance;
-
-/**
- * \brief Class of distance in a flat torus in dimension D
- *
- */
-//class Torus_distance : public Euclidean_distance {
-/*
-  class Torus_distance {
-
-public:
-    typedef K::FT    FT;
-    typedef K::Point_d Point_d;
-    typedef Point_d Query_item;
-    typedef typename CGAL::Dynamic_dimension_tag D;
-
-  double box_length = 2;
-
-  FT transformed_distance(Query_item q, Point_d p) const
-  {
-    FT distance = FT(0);
-    FT coord = FT(0);
-    //std::cout << "Hello skitty!\n";
-    typename K::Construct_cartesian_const_iterator_d construct_it=Traits_base().construct_cartesian_const_iterator_d_object();
-    typename K::Cartesian_const_iterator_d qit = construct_it(q),
-	qe = construct_it(q,1), pit = construct_it(p);
-	for(; qit != qe; qit++, pit++)
-          {
-            coord = sqrt(((*qit)-(*pit))*((*qit)-(*pit)));
-            if (coord*coord <= (box_length-coord)*(box_length-coord))
-              distance += coord*coord;
-            else
-              distance += (box_length-coord)*(box_length-coord);
-          }
-        return distance;
-  }
-
-  FT min_distance_to_rectangle(const Query_item& q,
-                               const CGAL::Kd_tree_rectangle<FT,D>& r) const {
-    FT distance = FT(0);
-    FT dist1, dist2;
-    typename K::Construct_cartesian_const_iterator_d construct_it=Traits_base().construct_cartesian_const_iterator_d_object();
-    typename K::Cartesian_const_iterator_d qit = construct_it(q),
-                                           qe = construct_it(q,1);
-    for(unsigned int i = 0;qit != qe; i++, qit++)
-      {
-        if((*qit) < r.min_coord(i))
-          {
-            dist1 = (r.min_coord(i)-(*qit));
-            dist2 = (box_length - r.max_coord(i)+(*qit));
-            if (dist1 < dist2)
-              distance += dist1*dist1;
-            else
-              distance += dist2*dist2;
-          }
-        else if ((*qit) > r.max_coord(i))
-          {
-            dist1 = (box_length - (*qit)+r.min_coord(i));
-            dist2 = ((*qit) - r.max_coord(i));
-            if (dist1 < dist2)
-              distance += dist1*dist1;
-            else
-              distance += dist2*dist2;
-          }
-      }
-    return distance;
-  }
-
-  FT min_distance_to_rectangle(const Query_item& q,
-                               const CGAL::Kd_tree_rectangle<FT,D>& r,
-                               std::vector<FT>& dists) const {
-    FT distance = FT(0);
-    FT dist1, dist2;
-    typename K::Construct_cartesian_const_iterator_d construct_it=Traits_base().construct_cartesian_const_iterator_d_object();
-    typename K::Cartesian_const_iterator_d qit = construct_it(q),
-	                  	           qe = construct_it(q,1);
-    //std::cout << r.max_coord(0) << std::endl;
-    for(unsigned int i = 0;qit != qe; i++, qit++)
-      {
-        if((*qit) < r.min_coord(i))
-          {
-            dist1 = (r.min_coord(i)-(*qit));
-            dist2 = (box_length - r.max_coord(i)+(*qit));
-            if (dist1 < dist2)
-              {
-                dists[i] = dist1;
-                distance += dist1*dist1;
-              }
-            else
-              {
-                dists[i] = dist2;
-                distance += dist2*dist2;
-                //std::cout << "Good stuff1\n";
-              }
-          }
-        else if ((*qit) > r.max_coord(i))
-          {
-            dist1 = (box_length - (*qit)+r.min_coord(i));
-            dist2 = ((*qit) - r.max_coord(i));
-            if (dist1 < dist2)
-              {
-                dists[i] = dist1;
-                distance += dist1*dist1;
-                //std::cout << "Good stuff2\n";
-              }
-            else
-              {
-                dists[i] = dist2;
-                distance += dist2*dist2;
-              }
-          }
-      };
-    return distance;
-  }
-    
-  FT max_distance_to_rectangle(const Query_item& q,
-                               const CGAL::Kd_tree_rectangle<FT,D>& r) const {
-    FT distance=FT(0);
-    typename K::Construct_cartesian_const_iterator_d construct_it=Traits_base().construct_cartesian_const_iterator_d_object();
-    typename K::Cartesian_const_iterator_d qit = construct_it(q),
-		                           qe = construct_it(q,1);
-    for(unsigned int i = 0;qit != qe; i++, qit++)
-      {
-        if (box_length <= (r.min_coord(i)+r.max_coord(i)))
-          if ((r.max_coord(i)+r.min_coord(i)-box_length)/FT(2.0) <= (*qit) &&
-              (*qit) <= (r.min_coord(i)+r.max_coord(i))/FT(2.0))
-            distance += (r.max_coord(i)-(*qit))*(r.max_coord(i)-(*qit));
-          else
-            distance += ((*qit)-r.min_coord(i))*((*qit)-r.min_coord(i));
-        else
-          if ((box_length-r.max_coord(i)-r.min_coord(i))/FT(2.0) <= (*qit) ||
-              (*qit) <= (r.min_coord(i)+r.max_coord(i))/FT(2.0))
-            distance += (r.max_coord(i)-(*qit))*(r.max_coord(i)-(*qit));
-          else
-            distance += ((*qit)-r.min_coord(i))*((*qit)-r.min_coord(i));
-      }
-    return distance;
-  }
-
-  
-  FT max_distance_to_rectangle(const Query_item& q,
-                               const CGAL::Kd_tree_rectangle<FT,D>& r,
-                               std::vector<FT>& dists) const {
-    FT distance=FT(0);
-    typename K::Construct_cartesian_const_iterator_d construct_it=Traits_base().construct_cartesian_const_iterator_d_object();
-    typename K::Cartesian_const_iterator_d qit = construct_it(q),
-		                           qe = construct_it(q,1);
-    for(unsigned int i = 0;qit != qe; i++, qit++)
-      {
-        if (box_length <= (r.min_coord(i)+r.max_coord(i)))
-          if ((r.max_coord(i)+r.min_coord(i)-box_length)/FT(2.0) <= (*qit) &&
-              (*qit) <= (r.min_coord(i)+r.max_coord(i))/FT(2.0))
-            {
-              dists[i] = r.max_coord(i)-(*qit);
-              distance += (r.max_coord(i)-(*qit))*(r.max_coord(i)-(*qit));
-            }
-          else
-            {
-              dists[i] = sqrt(((*qit)-r.min_coord(i))*((*qit)-r.min_coord(i)));
-              distance += ((*qit)-r.min_coord(i))*((*qit)-r.min_coord(i));
-            }
-        else
-          if ((box_length-r.max_coord(i)-r.min_coord(i))/FT(2.0) <= (*qit) ||
-              (*qit) <= (r.min_coord(i)+r.max_coord(i))/FT(2.0))
-            {
-              dists[i] = sqrt((r.max_coord(i)-(*qit))*(r.max_coord(i)-(*qit)));
-              distance += (r.max_coord(i)-(*qit))*(r.max_coord(i)-(*qit));
-              
-            }
-          else
-            {
-              dists[i] = (*qit)-r.min_coord(i);
-              distance += ((*qit)-r.min_coord(i))*((*qit)-r.min_coord(i));
-            }
-      }
-    return distance;
-  }
-
-    inline FT new_distance(FT dist, FT old_off, FT new_off,
-                           int )  const {
-      
-      FT new_dist = dist + (new_off*new_off - old_off*old_off);
-      return new_dist;
-    }
-    
-  inline FT transformed_distance(FT d) const {
-    return d*d;
-  }
-
-  inline FT inverse_of_transformed_distance(FT d) const {
-    return sqrt(d);
-  }
-  
-};
-*/
-
-typedef std::vector< Vertex_handle > typeVectorVertex;
-
-//typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
-//typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
-
-typedef CGAL::Search_traits_adapter<
-  std::ptrdiff_t, Point_d*, Traits_base> STraits;
-//typedef K TreeTraits;
-//typedef CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance > Euclidean_adapter;
-//typedef CGAL::Kd_tree<STraits> Kd_tree;
-typedef CGAL::Orthogonal_k_neighbor_search<STraits, CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance>> K_neighbor_search;
-typedef K_neighbor_search::Tree Tree;
-typedef K_neighbor_search::Distance Distance;
-typedef K_neighbor_search::iterator KNS_iterator;
-typedef K_neighbor_search::iterator KNS_range;
-typedef boost::container::flat_map<int, int> Point_etiquette_map;
-typedef CGAL::Kd_tree<STraits> Tree2;
-
-typedef CGAL::Fuzzy_sphere<STraits> Fuzzy_sphere;
-
-typedef std::vector<Point_d> Point_Vector;
-
-//typedef K::Equal_d Equal_d;
-//typedef CGAL::Random_points_in_cube_d<CGAL::Point_d<CGAL::Cartesian_d<FT> > > Random_cube_iterator;
-typedef CGAL::Random_points_in_cube_d<Point_d> Random_cube_iterator;
-typedef CGAL::Random_points_in_ball_d<Point_d> Random_point_iterator;
-
-bool toric=false;
-
-/**
- * \brief Customized version of read_points
- * which takes into account a possible nbP first line
- *
- */
-inline void
-read_points_cust ( std::string file_name , Point_Vector & points)
-{  
-  std::ifstream in_file (file_name.c_str(),std::ios::in);
-  if(!in_file.is_open())
-    {
-      std::cerr << "Unable to open file " << file_name << std::endl;
-      return;
-    }
-  std::string line;
-  double x;
-  while( getline ( in_file , line ) )
-    {
-      std::vector< double > point;
-      std::istringstream iss( line );
-      while(iss >> x) { point.push_back(x); }
-      Point_d p(point.begin(), point.end());
-      if (point.size() != 1)
-        points.push_back(p);
-    }
-  in_file.close();
-}
-
-void generate_points_grid(Point_Vector& W, int width, int D)
-{
-  int nb_points = 1;
-  for (int i = 0; i < D; ++i)
-    nb_points *= width;
-  for (int i = 0; i < nb_points; ++i)
-    {
-      std::vector<double> point;
-      int cell_i = i;
-      for (int l = 0; l < D; ++l)
-        {
-          point.push_back((2.0/width)*(cell_i%width));
-          cell_i /= width;
-        }
-      W.push_back(point);
-    }
-}
-
-void generate_points_random_box(Point_Vector& W, int nbP, int dim)
-{
-  /*
-  Random_cube_iterator rp(dim, 1);
-  for (int i = 0; i < nbP; i++)
-    {
-      std::vector<double> point;
-      for (auto it = rp->cartesian_begin(); it != rp->cartesian_end(); ++it)
-        point.push_back(*it);
-      W.push_back(Point_d(point));
-      rp++;
-    }
-  */
-  Random_cube_iterator rp(dim, 1.0);
-  for (int i = 0; i < nbP; i++)
-    {
-      W.push_back(*rp++);
-    }
-}
-
-/* NOT TORUS RELATED
- */
-void generate_points_sphere(Point_Vector& W, int nbP, int dim)
-{
-  CGAL::Random_points_on_sphere_d<Point_d> rp(dim,1);
-  for (int i = 0; i < nbP; i++)
-    W.push_back(*rp++);
-}
-/*
-void read_points_to_tree (std::string file_name, Tree& tree)
-{
-  //I assume here that tree is empty
-  std::ifstream in_file (file_name.c_str(),std::ios::in);
-  if(!in_file.is_open())
-    {
-      std::cerr << "Unable to open file " << file_name << std::endl;
-      return;
-    }
-  std::string line;
-  double x;
-   while( getline ( in_file , line ) )
-    {
-      std::vector<double> coords;
-      std::istringstream iss( line );
-      while(iss >> x) { coords.push_back(x); }
-      if (coords.size() != 1)
-        {
-          Point_d point(coords.begin(), coords.end());
-          tree.insert(point);
-        }
-    }
-  in_file.close();
-}
-*/
-
-void write_wl( std::string file_name, std::vector< std::vector <int> > & WL)
-{
-  std::ofstream ofs (file_name, std::ofstream::out);
-  for (auto w : WL)
-    {
-      for (auto l: w)
-        ofs << l << " ";
-      ofs << "\n";
-    }
-  ofs.close();
-}
-
-
-std::vector<Point_d> convert_to_torus(std::vector< Point_d>& points)
-{
-  std::vector< Point_d > points_torus;
-  for (auto p: points)
-    {
-      FT theta = M_PI*p[0];
-      FT phi = M_PI*p[1];
-      std::vector<FT> p_torus;
-      p_torus.push_back((1+0.2*cos(theta))*cos(phi));
-      p_torus.push_back((1+0.2*cos(theta))*sin(phi));
-      p_torus.push_back(0.2*sin(theta));
-      points_torus.push_back(Point_d(p_torus));
-    }
-  return points_torus;
-}
-
-void write_points_torus( std::string file_name, std::vector< Point_d > & points)
-{
-  std::ofstream ofs (file_name, std::ofstream::out);
-  std::vector<Point_d> points_torus = convert_to_torus(points);
-  for (auto w : points_torus)
-    {
-      for (auto it = w.cartesian_begin(); it != w.cartesian_end(); ++it)
-        ofs << *it << " ";
-      ofs << "\n";
-    }
-  ofs.close();
-}
-
-void write_points( std::string file_name, std::vector< Point_d > & points)
-{
-  if (toric) write_points_torus(file_name, points);
-  else
-    {
-      std::ofstream ofs (file_name, std::ofstream::out);
-      for (auto w : points)
-        {
-          for (auto it = w.cartesian_begin(); it != w.cartesian_end(); ++it)
-            ofs << *it << " ";
-          ofs << "\n";
-        }
-      ofs.close();
-    }
-}
-
-
-void write_edges_torus(std::string file_name, Witness_complex<>& witness_complex, Point_Vector& landmarks)
-{
-  std::ofstream ofs (file_name, std::ofstream::out);
-  Point_Vector l_torus = convert_to_torus(landmarks);
-  for (auto u: witness_complex.complex_vertex_range())
-    for (auto v: witness_complex.complex_vertex_range())
-      {
-        typeVectorVertex edge = {u,v};
-        if (u < v && witness_complex.find(edge) != witness_complex.null_simplex())   
-          {
-            for (auto it = l_torus[u].cartesian_begin(); it != l_torus[u].cartesian_end(); ++it)
-              ofs << *it << " ";
-            ofs << "\n";
-            for (auto it = l_torus[v].cartesian_begin(); it != l_torus[v].cartesian_end(); ++it)
-              ofs << *it << " ";
-            ofs << "\n\n\n";
-          }
-    }
-  ofs.close();
-}
-
-void write_edges(std::string file_name, Witness_complex<>& witness_complex, Point_Vector& landmarks)
-{
-  std::ofstream ofs (file_name, std::ofstream::out);
-  if (toric) write_edges_torus(file_name, witness_complex, landmarks);
-  else
-    {
-      for (auto u: witness_complex.complex_vertex_range())
-        for (auto v: witness_complex.complex_vertex_range())
-          {
-            typeVectorVertex edge = {u,v};
-            if (u < v && witness_complex.find(edge) != witness_complex.null_simplex())   
-              {
-                for (auto it = landmarks[u].cartesian_begin(); it != landmarks[u].cartesian_end(); ++it)
-                  ofs << *it << " ";
-                ofs << "\n";
-                for (auto it = landmarks[v].cartesian_begin(); it != landmarks[v].cartesian_end(); ++it)
-                  ofs << *it << " ";
-                ofs << "\n\n\n";
-              }
-          }
-      ofs.close();
-    }
-}
-
-
-/** Function that chooses landmarks from W and place it in the kd-tree L.
- *  Note: nbL hould be removed if the code moves to Witness_complex
- */
-void landmark_choice(Point_Vector &W, int nbP, int nbL, Point_Vector& landmarks, std::vector<int>& landmarks_ind)
-{
-  std::cout << "Enter landmark choice to kd tree\n";
-  int chosen_landmark;
-  Point_d* p;
-  CGAL::Random rand;
-  for (int i = 0; i < nbL; i++)
-    {
-      //      while (!res.second)
-      //  {
-      do chosen_landmark = rand.get_int(0,nbP);
-      while (std::find(landmarks_ind.begin(),landmarks_ind.end(),chosen_landmark)!=landmarks_ind.end());
-      //rand++;
-      //std::cout << "Chose " << chosen_landmark << std::endl;
-      p = &W[chosen_landmark];
-      //L_i.emplace(chosen_landmark,i);
-      //  }
-      landmarks.push_back(*p);
-      landmarks_ind.push_back(chosen_landmark);
-      //std::cout << "Added landmark " << chosen_landmark << std::endl;
-    }
- }
-
-/** \brief Choose landmarks on a body-central cubic system
- */
-void landmark_choice_bcc(Point_Vector &W, int nbP, int width, Point_Vector& landmarks, std::vector<int>& landmarks_ind)
-{
-  int D = W[0].size();
-  int nb_points = 1;
-  for (int i = 0; i < D; ++i)
-    nb_points *= width;
-  for (int i = 0; i < nb_points; ++i)
-    {
-      std::vector<double> point;
-      std::vector<double> cpoint;
-      int cell_i = i;
-      for (int l = 0; l < D; ++l)
-        {
-          point.push_back(-1.0+(2.0/width)*(cell_i%width));
-          cpoint.push_back(-1.0+(2.0/width)*(cell_i%width)+(1.0/width));
-          cell_i /= width;
-        }
-      landmarks.push_back(point);
-      landmarks.push_back(cpoint);
-      landmarks_ind.push_back(2*i);
-      landmarks_ind.push_back(2*i+1);
-    }
-  std::cout << "The number of landmarks is: " << landmarks.size() << std::endl;
-}
-
-
-int landmark_perturbation(Point_Vector &W, Point_Vector& landmarks, std::vector<int>& landmarks_ind)
-{
-  //********************Preface: origin point
-  int D = W[0].size();
-  std::vector<FT> orig_vector;
-  for (int i=0; i<D; i++)
-    orig_vector.push_back(0);
-  Point_d origin(orig_vector);
-  //Distance dist;
-  //dist.transformed_distance(0,1);
-  //******************** Constructing a WL matrix
-  int nbP = W.size();
-  int nbL = landmarks.size();
-  //Point_Vector landmarks_ = landmarks;
-  Euclidean_distance ed;
-  //Equal_d ed;
-  //Point_d p1(std::vector<FT>({0.8,0.8})), p2(std::vector<FT>({0.1,0.1}));
-  FT lambda = ed.transformed_distance(landmarks[0],landmarks[1]);
-  //std::cout << "Lambda=" << lambda << std::endl;
-    //FT lambda = 0.1;//Euclidean_distance();
-  std::vector<Point_d> landmarks_ext;
-  int nb_cells = 1;
-  for (int i = 0; i < D; ++i)
-    nb_cells *= 3;
-  for (int i = 0; i < nb_cells; ++i)
-      for (int k = 0; k < nbL; ++k)
-        {
-          std::vector<double> point;
-          int cell_i = i;
-          for (int l = 0; l < D; ++l)
-            {
-              point.push_back(landmarks[k][l] + 2.0*((cell_i%3)-1.0));
-              cell_i /= 3;
-            }
-          landmarks_ext.push_back(point);
-        }
-  write_points("landmarks/initial_landmarks",landmarks_ext);
-  STraits traits(&(landmarks_ext[0]));
-  std::vector< std::vector <int> > WL(nbP);
-  Tree L(boost::counting_iterator<std::ptrdiff_t>(0),
-         boost::counting_iterator<std::ptrdiff_t>(nb_cells*nbL),
-         typename Tree::Splitter(),
-         traits);
-  /*Tree2 L2(boost::counting_iterator<std::ptrdiff_t>(0),
-           boost::counting_iterator<std::ptrdiff_t>(nbL),
-           typename Tree::Splitter(),
-           STraits(&(landmarks[0])));
-  */
-  std::cout << "Enter (D+1) nearest landmarks\n";
-  //std::cout << "Size of the tree is " << L.size() << std::endl;
-  for (int i = 0; i < nbP; i++)
-    {
-      //std::cout << "Entered witness number " << i << std::endl;
-      Point_d& w = W[i];
-      //std::cout << "Safely constructed a point\n";
-      ////Search D+1 nearest neighbours from the tree of landmarks L
-      /*
-      if (w[0]>0.95)
-        std::cout << i << std::endl;
-      */
-      K_neighbor_search search(L, w, D+1, FT(0), true,
-                               //CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance>(&(landmarks[0])) );
-                               CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance>(&(landmarks_ext[0])) );
-      //std::cout << "Safely found nearest landmarks\n";
-      for(K_neighbor_search::iterator it = search.begin(); it != search.end(); ++it)
-        {
-          //std::cout << "Entered KNN_it with point at distance " << it->second << "\n";
-          //Point_etiquette_map::iterator itm = L_i.find(it->first);
-          //assert(itm != L_i.end());
-          //std::cout << "Entered KNN_it with point at distance " << it->second << "\n";
-          if (std::find(WL[i].begin(), WL[i].end(), (it->first)%nbL) == WL[i].end())
-            WL[i].push_back((it->first)%nbL);
-          //std::cout << "ITFIRST " << it->first << std::endl;
-          //std::cout << i << " " << it->first << ": " << it->second << std::endl; 
-        }
-      if (i == landmarks_ind[WL[i][0]])
-        {
-          //std::cout << "'";
-          FT dist = ed.transformed_distance(W[i], landmarks[WL[i][1]]);
-          if (dist < lambda)
-            lambda = dist;
-        }
-    }
-  //std::cout << "\n";
-  
-  std::string out_file = "wl_result";
-  write_wl(out_file,WL);
-  
-  //******************** Constructng a witness complex
-  std::cout << "Entered witness complex construction\n";
-  Witness_complex<> witnessComplex;
-  witnessComplex.setNbL(nbL);
-  witnessComplex.witness_complex(WL);
-  /*
-  if (witnessComplex.is_witness_complex(WL))
-    std::cout << "!!YES. IT IS A WITNESS COMPLEX!!\n";
-  else
-    std::cout << "??NO. IT IS NOT A WITNESS COMPLEX??\n";    
-  */
-  //******************** Making a set of bad link landmarks
-  std::cout << "Entered bad links\n";
-  std::set< int > perturbL;
-  int count_badlinks = 0;
-  //std::cout << "Bad links around ";
-  std::vector< int > count_bad(D);
-  std::vector< int > count_good(D);
-  for (auto u: witnessComplex.complex_vertex_range())
-    {
-      //std::cout << "Vertex " << u << " ";
-      if (!witnessComplex.has_good_link(u, count_bad, count_good))
-      {
-        //std::cout << "Landmark " << u << " start!" << std::endl;
-        //perturbL.insert(u);
-        count_badlinks++;
-        //std::cout << u << " ";
-        Point_d& l = landmarks[u];
-        Fuzzy_sphere fs(l, sqrt(lambda), 0, traits);
-        std::vector<int> curr_perturb;
-        L.search(std::insert_iterator<std::vector<int>>(curr_perturb,curr_perturb.begin()),fs);
-        for (int i: curr_perturb)
-          perturbL.insert(i%nbL);
-        //L.search(std::inserter(perturbL,perturbL.begin()),fs);
-        //L.search(std::ostream_iterator<int>(std::cout,"\n"),fs);
-        //std::cout << "PerturbL size is " << perturbL.size() << std::endl;
-      }
-    }
-  for (unsigned int i = 0; i != count_good.size(); i++)
-    if (count_good[i] != 0)
-      std::cout << "count_good[" << i << "] = " << count_good[i] << std::endl;
-  for (unsigned int i = 0; i != count_bad.size(); i++)
-    if (count_bad[i] != 0)
-      std::cout << "count_bad[" << i << "] = " << count_bad[i] << std::endl;
-  std::cout << "\nBad links total: " << count_badlinks << " Points to perturb: " << perturbL.size() << std::endl;
-  //std::cout << "landmark[0][0] before" << landmarks[0][0] << std::endl;
-  //*********************** Perturb bad link landmarks
-  
-  for (auto u: perturbL)
-    {
-      Random_point_iterator rp(D,sqrt(lambda)/8);
-      //std::cout << landmarks[u] << std::endl;
-      
-      std::vector<FT> point;
-      for (int i = 0; i < D; i++)
-        {
-          while (K().squared_distance_d_object()(*rp,origin) < lambda/256)
-            rp++;
-          //FT coord = W[landmarks_ind[u]][i] + (*rp)[i];
-          FT coord = landmarks[u][i] + (*rp)[i];
-          if (coord > 1)
-            point.push_back(coord-1);
-          else if (coord < -1)
-            point.push_back(coord+1);
-          else
-            point.push_back(coord);
-        }
-      landmarks[u] = Point_d(point);
-      //std::cout << landmarks[u] << std::endl;
-    }
-  
-  //std::cout << "landmark[0][0] after" << landmarks[0][0] << std::endl;
-  std::cout << "lambda=" << lambda << std::endl;
-
-  //std::cout << "WL size" << WL.size() << std::endl;
-  /*
-  std::cout << "L:" << std::endl;
-  for (int i = 0; i < landmarks.size(); i++)
-      std::cout << landmarks[i] << std::endl;
-  */
-  
-  char buffer[100];
-  int i = sprintf(buffer,"stree_result.txt");
-  
-  if (i >= 0)
-    {
-      std::string out_file = (std::string)buffer;
-      std::ofstream ofs (out_file, std::ofstream::out);
-      witnessComplex.st_to_file(ofs);
-      ofs.close();
-    }
-  /*
-  i = sprintf(buffer,"badlinks.txt");
-  if (i >= 0)
-    {
-      std::string out_file = (std::string)buffer;
-      std::ofstream ofs (out_file, std::ofstream::out);
-      witnessComplex.write_bad_links(ofs);
-      ofs.close();
-    }
-  */
-  write_edges("landmarks/edges", witnessComplex, landmarks);
-  //std::cout << Distance().transformed_distance(Point_d(std::vector<double>({0.1,0.1})), Point_d(std::vector<double>({1.9,1.9}))) << std::endl;
-  return count_badlinks;
-}
-
-
-int main (int argc, char * const argv[])
-{
-  
-  if (argc != 4)
-    {
-      std::cerr << "Usage: " << argv[0]
-                << " nbP nbL dim\n";
-      return 0;
-    }
-  /*
-  boost::filesystem::path p;
-  for (; argc > 2; --argc, ++argv)
-    p /= argv[1];
-  */
-  
-  int nbP       = atoi(argv[1]);
-  int nbL       = atoi(argv[2]);
-  int dim       = atoi(argv[3]);
-  //clock_t start, end;
-  //Construct the Simplex Tree
-  //Witness_complex<> witnessComplex;
- 
-  std::cout << "Let the carnage begin!\n";
-  Point_Vector point_vector;
-  //read_points_cust(file_name, point_vector);
-  //generate_points_random_box(point_vector, nbP, dim);
-  generate_points_grid(point_vector, (int)pow(nbP, 1.0/dim), dim);
-  //nbP = (int)(pow((int)pow(nbP, 1.0/dim), dim));
-  /*
-  for (auto &p: point_vector)
-    {
-      assert(std::count(point_vector.begin(),point_vector.end(),p) == 1);
-    }
-  */
-  //std::cout << "Successfully read the points\n";
-  //witnessComplex.setNbL(nbL);
-  //  witnessComplex.witness_complex_from_points(point_vector);
-  //int nbP = point_vector.size();
-  //std::vector<std::vector< int > > WL(nbP);
-  //std::set<int> L;
-  Point_Vector L;
-  std::vector<int> chosen_landmarks;
-  //Point_etiquette_map L_i;
-  //start = clock();
-  //witnessComplex.landmark_choice_by_furthest_points(point_vector, point_vector.size(), WL);
-  bool ok=false;
-  while (!ok)
-    {
-      ok = true;
-      L = {};
-      chosen_landmarks = {};
-      landmark_choice(point_vector, nbP, nbL, L, chosen_landmarks);
-      
-      //int width = (int)pow(nbL, 1.0/dim); landmark_choice_bcc(point_vector, nbP, width, L, chosen_landmarks);
-      for (auto i: chosen_landmarks)
-        {
-          ok = ok && (std::count(chosen_landmarks.begin(),chosen_landmarks.end(),i) == 1);
-          if (!ok) break;
-        }
-      
-    }
-  int bl = nbL, curr_min = bl;
-  write_points("landmarks/initial_pointset",point_vector);
-  //write_points("landmarks/initial_landmarks",L);
-  for (int i = 0; i < 1; i++)
-    //for (int i = 0; bl > 0; i++)
-    {
-      std::cout << "========== Start iteration " << i << "== curr_min(" << curr_min << ")========\n";
-      bl=landmark_perturbation(point_vector, L, chosen_landmarks);
-      if (bl < curr_min)
-        curr_min=bl;
-      write_points("landmarks/landmarks0",L);
-    }
-  //end = clock();
-  
-  /*
-  std::cout << "Landmark choice took "
-            << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
-  start = clock();
-  witnessComplex.witness_complex(WL);
-  //
-  end = clock();
-  std::cout << "Howdy world! The process took "
-       << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
-  */
-  
-  /*
-  out_file = "output/"+file_name+"_"+argv[2]+".stree";
-  std::ofstream ofs (out_file, std::ofstream::out);
-  witnessComplex.st_to_file(ofs);
-  ofs.close();
-
-  out_file = "output/"+file_name+"_"+argv[2]+".badlinks";
-  std::ofstream ofs2(out_file, std::ofstream::out);
-  witnessComplex.write_bad_links(ofs2);
-  ofs2.close();
-  */
-}
diff --git a/src/Witness_complex/example/witness_complex_from_off.cpp b/src/Witness_complex/example/witness_complex_from_off.cpp
deleted file mode 100644
index 948f09a8..00000000
--- a/src/Witness_complex/example/witness_complex_from_off.cpp
+++ /dev/null
@@ -1,184 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Siargey Kachanovich
- *
- *    Copyright (C) 2015  INRIA Sophia Antipolis-Méditerranée (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#include <sys/types.h>
-#include <sys/stat.h>
-
-//#include <stdlib.h>
-
-//#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Witness_complex.h"
-#include "gudhi/reader_utils.h"
-
-using namespace Gudhi;
-
-typedef std::vector< Vertex_handle > typeVectorVertex;
-typedef std::vector< std::vector <double> > Point_Vector;
-//typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
-//typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
-
-
-/**
- * \brief Customized version of read_points
- * which takes into account a possible nbP first line
- *
- */
-inline void
-read_points_cust ( std::string file_name , std::vector< std::vector< double > > & points)
-{  
-  std::ifstream in_file (file_name.c_str(),std::ios::in);
-  if(!in_file.is_open())
-    {
-      std::cerr << "Unable to open file " << file_name << std::endl;
-      return;
-    }
-  std::string line;
-  double x;
-  while( getline ( in_file , line ) )
-    {
-      std::vector< double > point;
-      std::istringstream iss( line );
-      while(iss >> x) { point.push_back(x); }
-      if (point.size() != 1)
-        points.push_back(point);
-    }
-  in_file.close();
-}
-
-/**
- * \brief Rock age method of reading off file
- *
- */
-inline void
-off_reader_cust ( std::string file_name , std::vector< std::vector< double > > & points)
-{  
-  std::ifstream in_file (file_name.c_str(),std::ios::in);
-  if(!in_file.is_open())
-    {
-      std::cerr << "Unable to open file " << file_name << std::endl;
-      return;
-    }
-  std::string line;
-  double x;
-  // Line OFF. No need in it
-  if (!getline(in_file, line))
-    {
-      std::cerr << "No line OFF\n";
-      return;
-    }
-  // Line with 3 numbers. No need
-  if (!getline(in_file, line))
-    {
-      std::cerr << "No line with 3 numbers\n";
-      return;
-    }
-  // Reading points
-  while( getline ( in_file , line ) )
-    {
-      std::vector< double > point;
-      std::istringstream iss( line );
-      while(iss >> x) { point.push_back(x); }
-      points.push_back(point);
-    }
-  in_file.close();
-}
-
-int main (int argc, char * const argv[])
-{
-    if (argc != 3)
-      {
-          std::cerr << "Usage: " << argv[0]
-    << " path_to_point_file nbL \n";
-    return 0;
-  }
-  std::string file_name   = argv[1];
-  int nbL       = atoi(argv[2]);
-  
-  clock_t start, end;
-  //Construct the Simplex Tree
-  Witness_complex<> witnessComplex;
-
-  /*
-  std::cout << "Let the carnage begin!\n";
-  start = clock();
-  Point_Vector point_vector;
-  off_reader_cust(file_name, point_vector);
-  std::cout << "Successfully read the points\n";
-  witnessComplex.setNbL(nbL);
-  witnessComplex.witness_complex_from_points(point_vector);
-  end = clock();
-  std::cout << "Howdy world! The process took "
-       << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
-  char buffer[100];
-  int i = sprintf(buffer,"%s_%s_result.txt",argv[1],argv[2]);
-  if (i >= 0)
-    {
-      std::string out_file = (std::string)buffer;
-      std::ofstream ofs (out_file, std::ofstream::out);
-      witnessComplex.st_to_file(ofs);
-      ofs.close();
-    }
-  */
-  std::cout << "Let the carnage begin!\n";
-  Point_Vector point_vector;
-  off_reader_cust(file_name, point_vector);
-  //std::cout << "Successfully read the points\n";
-  witnessComplex.setNbL(nbL);
-  //  witnessComplex.witness_complex_from_points(point_vector);
-  std::vector<std::vector< int > > WL;
-  std::set<int> L;
-  start = clock();
-  //witnessComplex.landmark_choice_by_furthest_points(point_vector, point_vector.size(), WL);
-  witnessComplex.landmark_choice_by_random_points(point_vector, point_vector.size(), L);
-  witnessComplex.nearest_landmarks(point_vector,L,WL);
-  end = clock();
-  std::cout << "Landmark choice took "
-            << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
-  // Write the WL matrix in a file
-  mkdir("output", S_IRWXU);
-  const size_t last_slash_idx = file_name.find_last_of("/");
-  if (std::string::npos != last_slash_idx)
-    {
-      file_name.erase(0, last_slash_idx + 1);
-    }
-  std::string out_file = "output/"+file_name+"_"+argv[2]+".wl";
-  //write_wl(out_file,WL);
-  start = clock();
-  witnessComplex.witness_complex(WL);
-  //
-  end = clock();
-  std::cout << "Howdy world! The process took "
-       << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
-
-  out_file = "output/"+file_name+"_"+argv[2]+".stree";
-  std::ofstream ofs (out_file, std::ofstream::out);
-  witnessComplex.st_to_file(ofs);
-  ofs.close();
-
-  out_file = "output/"+file_name+"_"+argv[2]+".badlinks";
-  std::ofstream ofs2(out_file, std::ofstream::out);
-  witnessComplex.write_bad_links(ofs2);
-  ofs2.close();
-}
diff --git a/src/Witness_complex/example/witness_complex_from_wl_matrix.cpp b/src/Witness_complex/example/witness_complex_from_wl_matrix.cpp
deleted file mode 100644
index 614bb945..00000000
--- a/src/Witness_complex/example/witness_complex_from_wl_matrix.cpp
+++ /dev/null
@@ -1,148 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Siargey Kachanovich
- *
- *    Copyright (C) 2015  INRIA Sophia Antipolis-Méditerranée (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <iostream>
-#include <fstream>
-#include <ctime>
-
-#include <sys/types.h>
-#include <sys/stat.h>
-//#include <stdlib.h>
-
-//#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Witness_complex.h"
-#include "gudhi/reader_utils.h"
-//#include <boost/filesystem.hpp>
-
-using namespace Gudhi;
-//using namespace boost::filesystem;
-
-typedef std::vector< Vertex_handle > typeVectorVertex;
-typedef std::vector< std::vector <double> > Point_Vector;
-//typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
-//typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
-
-
-/**
- * \brief Customized version of read_points
- * which takes into account a possible nbP first line
- *
- */
-inline void
-read_points_cust ( std::string file_name , std::vector< std::vector< double > > & points)
-{  
-  std::ifstream in_file (file_name.c_str(),std::ios::in);
-  if(!in_file.is_open())
-    {
-      std::cerr << "Unable to open file " << file_name << std::endl;
-      return;
-    }
-  std::string line;
-  double x;
-  while( getline ( in_file , line ) )
-    {
-      std::vector< double > point;
-      std::istringstream iss( line );
-      while(iss >> x) { point.push_back(x); }
-      if (point.size() != 1)
-        points.push_back(point);
-    }
-  in_file.close();
-}
-
-void write_wl( std::string file_name, std::vector< std::vector <int> > & WL)
-{
-  std::ofstream ofs (file_name, std::ofstream::out);
-  for (auto w : WL)
-    {
-      for (auto l: w)
-        ofs << l << " ";
-      ofs << "\n";
-    }
-  ofs.close();
-}
-
-void read_wl( std::string file_name, std::vector< std::vector <int> > & WL)
-{
-  std::ifstream in_file (file_name.c_str(),std::ios::in);
-  if(!in_file.is_open())
-    {
-      std::cerr << "Unable to open file " << file_name << std::endl;
-      return;
-    }
-  std::string line;
-  int x;
-  while( getline ( in_file , line ) )
-    {
-      std::vector< int > witness;
-      std::istringstream iss( line );
-      while(iss >> x) { witness.push_back(x); }
-      WL.push_back(witness);
-    }
-  in_file.close();
-
-}
-
-int main (int argc, char * const argv[])
-{
-  if (argc != 2)
-    {
-      std::cerr << "Usage: " << argv[0]
-                << " path_to_point_file \n";
-      return 0;
-    }
-  /*
-  boost::filesystem::path p;
-
-  for (; argc > 2; --argc, ++argv)
-    p /= argv[1];
-  */
-  std::string file_name   = argv[1];
-  //int nbL       = atoi(argv[2]);
-  
-  clock_t start, end;
-  //Construct the Simplex Tree
-  Witness_complex<> witnessComplex;
- 
-  std::cout << "Let the carnage begin!\n";
-  Point_Vector point_vector;
-  read_points_cust(file_name, point_vector);
-  //std::cout << "Successfully read the points\n";
-  //  witnessComplex.witness_complex_from_points(point_vector);
-  std::vector<std::vector< int > > WL;
-  read_wl(file_name,WL);
-  witnessComplex.setNbL(WL[0].size());
-  // Write the WL matrix in a file
-  std::string out_file;
-  write_wl(out_file,WL);
-  start = clock();
-  witnessComplex.witness_complex(WL);
-  //
-  end = clock();
-  std::cout << "Howdy world! The process took "
-       << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
-  out_file = "output/"+file_name+"_"+argv[2]+".stree";
-  std::ofstream ofs (out_file, std::ofstream::out);
-  witnessComplex.st_to_file(ofs);
-  ofs.close();
-
-}
diff --git a/src/Witness_complex/example/witness_complex_knn_landmarks.cpp b/src/Witness_complex/example/witness_complex_knn_landmarks.cpp
deleted file mode 100644
index c45bc0c1..00000000
--- a/src/Witness_complex/example/witness_complex_knn_landmarks.cpp
+++ /dev/null
@@ -1,210 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Siargey Kachanovich
- *
- *    Copyright (C) 2015  INRIA Sophia Antipolis-Méditerranée (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#include <utility>
-
-#include <sys/types.h>
-#include <sys/stat.h>
-//#include <stdlib.h>
-
-//#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Witness_complex.h"
-#include "gudhi/reader_utils.h"
-#include "generators.h"
-#include "output.h"
-//#include <boost/filesystem.hpp>
-
-//#include <CGAL/Delaunay_triangulation.h>
-#include <CGAL/Cartesian_d.h>
-#include <CGAL/Search_traits.h>
-#include <CGAL/Search_traits_adapter.h>
-#include <CGAL/property_map.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/Orthogonal_k_neighbor_search.h>
-
-#include <boost/tuple/tuple.hpp>
-#include <boost/iterator/zip_iterator.hpp>
-#include <boost/iterator/counting_iterator.hpp>
-#include <boost/range/iterator_range.hpp>
-
-using namespace Gudhi;
-//using namespace boost::filesystem;
-
-typedef std::vector< Vertex_handle > typeVectorVertex;
-
-//typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
-//typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
-
-typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
-typedef K::FT FT;
-typedef K::Point_d Point_d;
-typedef CGAL::Search_traits<
-  FT, Point_d,
-  typename K::Cartesian_const_iterator_d,
-  typename K::Construct_cartesian_const_iterator_d> Traits_base;
-typedef CGAL::Search_traits_adapter<
-  std::ptrdiff_t, Point_d*, Traits_base> STraits;
-//typedef K TreeTraits;
-typedef CGAL::Orthogonal_k_neighbor_search<STraits> K_neighbor_search;
-typedef K_neighbor_search::Tree Tree;
-typedef K_neighbor_search::Distance Distance;
-typedef K_neighbor_search::iterator KNS_iterator;
-typedef K_neighbor_search::iterator KNS_range;
-typedef boost::container::flat_map<int, int> Point_etiquette_map;
-
-typedef std::vector<Point_d> Point_Vector;
-
-/** Function that chooses landmarks from W and place it in the kd-tree L.
- *  Note: nbL hould be removed if the code moves to Witness_complex
- */
-void landmark_choice_to_tree(Point_Vector &W, int nbP, Point_etiquette_map &L_i, int nbL, std::vector< std::vector <int> > &WL)
-{
-  std::cout << "Enter landmark choice to kd tree\n";
-  std::vector<Point_d> landmarks;
-  int chosen_landmark;
-  //std::pair<Point_etiquette_map::iterator,bool> res = std::make_pair(L_i.begin(),false);
-  Point_d* p;
-  srand(24660);
-  for (int i = 0; i < nbL; i++)
-    {
-      //      while (!res.second)
-      //  {
-          chosen_landmark = rand()%nbP;
-          p = &W[chosen_landmark];
-          //L_i.emplace(chosen_landmark,i);
-          //  }
-      landmarks.push_back(*p);
-      //std::cout << "Added landmark " << chosen_landmark << std::endl;
-    }
-  Tree L(boost::counting_iterator<std::ptrdiff_t>(0),
-         boost::counting_iterator<std::ptrdiff_t>(nbL),
-         typename Tree::Splitter(),
-         STraits((Point_d*)&(landmarks[0])));
-  /*}
-
-
-void d_nearest_landmarks(Point_Vector &W, Tree &L, Point_etiquette_map &L_i, std::vector< std::vector <int> > &WL)
-{*/
-  std::cout << "Enter (D+1) nearest landmarks\n";
-  std::cout << "Size of the tree is " << L.size() << std::endl;
-//int nbP = W.size();
-  int D = W[0].size();
-  for (int i = 0; i < nbP; i++)
-    {
-      //std::cout << "Entered witness number " << i << std::endl;
-      Point_d& w = W[i];
-      //std::cout << "Safely constructed a point\n";
-      //Search D+1 nearest neighbours from the tree of landmarks L 
-      K_neighbor_search search(L, w, D+1, FT(0), true,
-                               CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,CGAL::Euclidean_distance<Traits_base>>((Point_d*)&(landmarks[0])) );
-      //std::cout << "Safely found nearest landmarks\n";
-      for(K_neighbor_search::iterator it = search.begin(); it != search.end(); ++it)
-        {
-          //std::cout << "Entered KNN_it with point at distance " << it->second << "\n";
-          //Point_etiquette_map::iterator itm = L_i.find(it->first);
-          //assert(itm != L_i.end());
-          //std::cout << "Entered KNN_it with point at distance " << it->second << "\n";
-          WL[i].push_back(it->first);
-          //std::cout << i << " " << it->first << ": " << it->second << std::endl; 
-        }
-    }
-}
-
-int main (int argc, char * const argv[])
-{
-  if (argc != 3)
-    {
-      std::cerr << "Usage: " << argv[0]
-                << " path_to_point_file nbL \n";
-      return 0;
-    }
-  /*
-  boost::filesystem::path p;
-
-  for (; argc > 2; --argc, ++argv)
-    p /= argv[1];
-  */
-  std::string file_name   = argv[1];
-  int nbL       = atoi(argv[2]);
-  
-  clock_t start, end;
-  //Construct the Simplex Tree
-  Witness_complex<> witnessComplex;
- 
-  std::cout << "Let the carnage begin!\n";
-  Point_Vector point_vector;
-  read_points_cust(file_name, point_vector);
-  //std::cout << "Successfully read the points\n";
-  witnessComplex.setNbL(nbL);
-  //  witnessComplex.witness_complex_from_points(point_vector);
-  int nbP = point_vector.size();
-  std::vector<std::vector< int > > WL(nbP);
-  //std::set<int> L;
-  Tree L;
-  Point_etiquette_map L_i;
-  start = clock();
-  //witnessComplex.landmark_choice_by_furthest_points(point_vector, point_vector.size(), WL);
-  landmark_choice_to_tree(point_vector, nbP, L_i, nbL, WL);
-  //d_nearest_landmarks(point_vector, L, L_i, WL);
-  end = clock();
-  std::cout << "Landmark choice took "
-            << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
-  // Write the WL matrix in a file
-  mkdir("output", S_IRWXU);
-  const size_t last_slash_idx = file_name.find_last_of("/");
-  if (std::string::npos != last_slash_idx)
-    {
-      file_name.erase(0, last_slash_idx + 1);
-    }
-  std::string out_file = "output/"+file_name+"_"+argv[2]+".wl";
-  write_wl(out_file,WL);
-  start = clock();
-  witnessComplex.witness_complex(WL);
-  //
-  end = clock();
-  std::cout << "Howdy world! The process took "
-       << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
-  /*
-  char buffer[100];
-  int i = sprintf(buffer,"%s_%s_result.txt",argv[1],argv[2]);
-  if (i >= 0)
-    {
-      std::string out_file = (std::string)buffer;
-      std::ofstream ofs (out_file, std::ofstream::out);
-      witnessComplex.st_to_file(ofs);
-      ofs.close();
-    }
-  */
-
-  out_file = "output/"+file_name+"_"+argv[2]+".stree";
-  std::ofstream ofs (out_file, std::ofstream::out);
-  witnessComplex.st_to_file(ofs);
-  ofs.close();
-
-  out_file = "output/"+file_name+"_"+argv[2]+".badlinks";
-  std::ofstream ofs2(out_file, std::ofstream::out);
-  //witnessComplex.write_bad_links(ofs2);
-  ofs2.close();
-}
diff --git a/src/Witness_complex/example/witness_complex_perturbations.cpp b/src/Witness_complex/example/witness_complex_perturbations.cpp
deleted file mode 100644
index f78bcdab..00000000
--- a/src/Witness_complex/example/witness_complex_perturbations.cpp
+++ /dev/null
@@ -1,462 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Siargey Kachanovich
- *
- *    Copyright (C) 2015  INRIA Sophia Antipolis-Méditerranée (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#include <utility>
-#include <set>
-#include <iterator>
-
-#include <sys/types.h>
-#include <sys/stat.h>
-//#include <stdlib.h>
-
-//#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Witness_complex.h"
-#include "gudhi/reader_utils.h"
-//#include <boost/filesystem.hpp> 
-
-//#include <CGAL/Delaunay_triangulation.h>
-#include <CGAL/Cartesian_d.h>
-#include <CGAL/Search_traits.h>
-#include <CGAL/Search_traits_adapter.h>
-#include <CGAL/property_map.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/Orthogonal_k_neighbor_search.h>
-#include <CGAL/Kd_tree.h>
-#include <CGAL/Euclidean_distance.h>
-
-#include <CGAL/Kernel_d/Vector_d.h>
-#include <CGAL/point_generators_d.h>
-#include <CGAL/constructions_d.h>
-#include <CGAL/Fuzzy_sphere.h>
-#include <CGAL/Origin.h>
-
-#include <boost/tuple/tuple.hpp>
-#include <boost/iterator/zip_iterator.hpp>
-#include <boost/iterator/counting_iterator.hpp>
-#include <boost/range/iterator_range.hpp>
-
-using namespace Gudhi;
-//using namespace boost::filesystem;
-
-typedef std::vector< Vertex_handle > typeVectorVertex;
-
-//typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
-//typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
-
-typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
-typedef K::FT FT;
-typedef K::Point_d Point_d;
-typedef CGAL::Search_traits<
-  FT, Point_d,
-  typename K::Cartesian_const_iterator_d,
-  typename K::Construct_cartesian_const_iterator_d> Traits_base;
-typedef CGAL::Search_traits_adapter<
-  std::ptrdiff_t, Point_d*, Traits_base> STraits;
-//typedef K TreeTraits;
-typedef CGAL::Orthogonal_k_neighbor_search<STraits> K_neighbor_search;
-typedef K_neighbor_search::Tree Tree;
-typedef K_neighbor_search::Distance Distance;
-typedef K_neighbor_search::iterator KNS_iterator;
-typedef K_neighbor_search::iterator KNS_range;
-typedef boost::container::flat_map<int, int> Point_etiquette_map;
-typedef CGAL::Kd_tree<STraits> Tree2;
-
-typedef CGAL::Fuzzy_sphere<STraits> Fuzzy_sphere;
-
-typedef std::vector<Point_d> Point_Vector;
-
-typedef CGAL::Euclidean_distance<Traits_base> Euclidean_distance;
-//typedef K::Equal_d Equal_d;
-typedef CGAL::Random_points_in_ball_d<Point_d> Random_point_iterator;
-/**
- * \brief Customized version of read_points
- * which takes into account a possible nbP first line
- *
- */
-inline void
-read_points_cust ( std::string file_name , Point_Vector & points)
-{  
-  std::ifstream in_file (file_name.c_str(),std::ios::in);
-  if(!in_file.is_open())
-    {
-      std::cerr << "Unable to open file " << file_name << std::endl;
-      return;
-    }
-  std::string line;
-  double x;
-  while( getline ( in_file , line ) )
-    {
-      std::vector< double > point;
-      std::istringstream iss( line );
-      while(iss >> x) { point.push_back(x); }
-      Point_d p(point.begin(), point.end());
-      if (point.size() != 1)
-        points.push_back(p);
-    }
-  in_file.close();
-}
-
-/*
-void read_points_to_tree (std::string file_name, Tree& tree)
-{
-  //I assume here that tree is empty
-  std::ifstream in_file (file_name.c_str(),std::ios::in);
-  if(!in_file.is_open())
-    {
-      std::cerr << "Unable to open file " << file_name << std::endl;
-      return;
-    }
-  std::string line;
-  double x;
-   while( getline ( in_file , line ) )
-    {
-      std::vector<double> coords;
-      std::istringstream iss( line );
-      while(iss >> x) { coords.push_back(x); }
-      if (coords.size() != 1)
-        {
-          Point_d point(coords.begin(), coords.end());
-          tree.insert(point);
-        }
-    }
-  in_file.close();
-}
-*/
-
-void write_wl( std::string file_name, std::vector< std::vector <int> > & WL)
-{
-  std::ofstream ofs (file_name, std::ofstream::out);
-  for (auto w : WL)
-    {
-      for (auto l: w)
-        ofs << l << " ";
-      ofs << "\n";
-    }
-  ofs.close();
-}
-
-void write_points( std::string file_name, std::vector< Point_d > & WL)
-{
-  std::ofstream ofs (file_name, std::ofstream::out);
-  for (auto w : WL)
-    {
-      for (auto it = w.cartesian_begin(); it != w.cartesian_end(); ++it)
-        ofs << *it << " ";
-      ofs << "\n";
-    }
-  ofs.close();
-}
-
-void write_edges_gnuplot(std::string file_name, Witness_complex<>& witness_complex, Point_Vector& landmarks)
-{
-  std::ofstream ofs (file_name, std::ofstream::out);
-  for (auto u: witness_complex.complex_vertex_range())
-    for (auto v: witness_complex.complex_vertex_range())
-      {
-        typeVectorVertex edge = {u,v};
-        if (u < v && witness_complex.find(edge) != witness_complex.null_simplex())   
-          {
-            for (auto it = landmarks[u].cartesian_begin(); it != landmarks[u].cartesian_end(); ++it)
-              ofs << *it << " ";
-            ofs << "\n";
-            for (auto it = landmarks[v].cartesian_begin(); it != landmarks[v].cartesian_end(); ++it)
-              ofs << *it << " ";
-            ofs << "\n\n\n";
-          }
-    }
-  ofs.close();
-}
-    
-
-
-/** Function that chooses landmarks from W and place it in the kd-tree L.
- *  Note: nbL hould be removed if the code moves to Witness_complex
- */
-/*
-void landmark_choice(Point_Vector &W, int nbP, int nbL, Point_Vector& landmarks, std::vector<int>& landmarks_ind)
-{
-  std::cout << "Enter landmark choice to kd tree\n";
-  //std::vector<Point_d> landmarks;
-  int chosen_landmark;
-  //std::pair<Point_etiquette_map::iterator,bool> res = std::make_pair(L_i.begin(),false);
-  Point_d* p;
-  srand(24660);
-  for (int i = 0; i < nbL; i++)
-    {
-      //      while (!res.second)
-      //  {
-      chosen_landmark = rand()%nbP;
-      p = &W[chosen_landmark];
-      //L_i.emplace(chosen_landmark,i);
-      //  }
-      landmarks.push_back(*p);
-      landmarks_ind.push_back(chosen_landmark);
-      //std::cout << "Added landmark " << chosen_landmark << std::endl;
-    }
- }
-*/
-
-void landmark_choice(Point_Vector &W, int nbP, int nbL, Point_Vector& landmarks, std::vector<int>& landmarks_ind)
-{
-  std::cout << "Enter landmark choice to kd tree\n";
-  //std::vector<Point_d> landmarks;
-  int chosen_landmark = 0;
-  //std::pair<Point_etiquette_map::iterator,bool> res = std::make_pair(L_i.begin(),false);
-  Point_d* p;
-  CGAL::Random rand;
-  for (int i = 0; i < nbL; i++)
-    {
-      //      while (!res.second)
-      //  {
-      do chosen_landmark = rand.uniform_int(0,nbP);
-      while (std::find(landmarks_ind.begin(),landmarks_ind.end(),chosen_landmark) != landmarks_ind.end());
-          //rand++;
-      //std::cout << "Chose " << chosen_landmark << std::endl;
-      p = &W[chosen_landmark];
-      //L_i.emplace(chosen_landmark,i);
-      //  }
-      landmarks.push_back(*p);
-      landmarks_ind.push_back(chosen_landmark);
-      //std::cout << "Added landmark " << chosen_landmark << std::endl;
-    }
- }
-
-
-int landmark_perturbation(Point_Vector &W, Point_Vector& landmarks, std::vector<int>& landmarks_ind)
-{
-  //******************** Constructing a WL matrix
-  int nbP = W.size();
-  int nbL = landmarks.size();
-  //Point_Vector landmarks_ = landmarks;
-  Euclidean_distance ed;
-  //Equal_d ed;
-  FT lambda = ed.transformed_distance(landmarks[0],landmarks[1]);
-    //FT lambda = 0.1;//Euclidean_distance();
-  std::vector< std::vector <int> > WL(nbP);
-  Tree L(boost::counting_iterator<std::ptrdiff_t>(0),
-         boost::counting_iterator<std::ptrdiff_t>(nbL),
-         typename Tree::Splitter(),
-         STraits(&(landmarks[0])));
-  /*Tree2 L2(boost::counting_iterator<std::ptrdiff_t>(0),
-           boost::counting_iterator<std::ptrdiff_t>(nbL),
-           typename Tree::Splitter(),
-           STraits(&(landmarks[0])));
-  */
-  std::cout << "Enter (D+1) nearest landmarks\n";
-  //std::cout << "Size of the tree is " << L.size() << std::endl;
-  int D = W[0].size();
-  clock_t start, end;
-  start = clock();  
-  for (int i = 0; i < nbP; i++)
-    {
-      //std::cout << "Entered witness number " << i << std::endl;
-      Point_d& w = W[i];
-      //std::cout << "Safely constructed a point\n";
-      ////Search D+1 nearest neighbours from the tree of landmarks L 
-      K_neighbor_search search(L, w, D+1, FT(0), true,
-                               CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,CGAL::Euclidean_distance<Traits_base>>(&(landmarks[0])) );
-      //std::cout << "Safely found nearest landmarks\n";
-      for(K_neighbor_search::iterator it = search.begin(); it != search.end(); ++it)
-        {
-          //std::cout << "Entered KNN_it with point at distance " << it->second << "\n";
-          //Point_etiquette_map::iterator itm = L_i.find(it->first);
-          //assert(itm != L_i.end());
-          //std::cout << "Entered KNN_it with point at distance " << it->second << "\n";
-          WL[i].push_back(it->first);
-          //std::cout << "ITFIRST " << it->first << std::endl;
-          //std::cout << i << " " << it->first << ": " << it->second << std::endl; 
-        }
-      if (i == landmarks_ind[WL[i][0]])
-        {
-          //std::cout << "'";
-          FT dist = ed.transformed_distance(W[i], landmarks[WL[i][1]]);
-          if (dist < lambda)
-            lambda = dist;
-        }
-      //std::cout << "\nBad links total: " << count_badlinks << " Points to perturb: " << perturbL.size() << std::endl;
-      }
-  //std::cout << "\n";
-  end = clock();
-  std::cout << "WL matrix construction on " << nbL << " landmarks took " << (double)(end-start)/CLOCKS_PER_SEC << "s.\n";
-  
-
-  std::string out_file = "wl_result";
-  //write_wl(out_file,WL);
-  
-  //******************** Constructng a witness complex
-  std::cout << "Entered witness complex construction\n";
-  Witness_complex<> witnessComplex;
-  witnessComplex.setNbL(nbL);
-  start = clock();
-  witnessComplex.witness_complex(WL);
-  end = clock();
-  std::cout << "Witness complex construction on " << nbL << " landmarks took " << (double)(end-start)/CLOCKS_PER_SEC << "s.\n";
-  //******************** Making a set of bad link landmarks
-  std::cout << "Entered bad links\n";
-  std::set< int > perturbL;
-  int count_badlinks = 0;
-  std::vector< int > count_bad(D);
-  std::vector< int > count_good(D);
-  //std::cout << "Bad links around ";
-  for (auto u: witnessComplex.complex_vertex_range())
-    if (!witnessComplex.has_good_link(u, count_bad, count_good))
-      {
-        //std::cout << "Landmark " << u << " start!" << std::endl;
-        //perturbL.insert(u);
-        count_badlinks++;
-        //std::cout << u << " ";
-        Point_d& l = landmarks[u];
-        Fuzzy_sphere fs(l, sqrt(lambda)*2, 0, STraits(&(landmarks[0])));
-        L.search(std::insert_iterator<std::set<int>>(perturbL,perturbL.begin()),fs);
-        //L.search(std::inserter(perturbL,perturbL.begin()),fs);
-        //L.search(std::ostream_iterator<int>(std::cout,"\n"),fs);
-        //std::cout << "PerturbL size is " << perturbL.size() << std::endl;
-      }
-  for (unsigned int i = 0; i != count_good.size(); i++)
-    if (count_good[i] != 0)
-      std::cout << "count_good[" << i << "] = " << count_good[i] << std::endl;
-  for (unsigned int i = 0; i != count_bad.size(); i++)
-    if (count_bad[i] != 0)
-      std::cout << "count_bad[" << i << "] = " << count_bad[i] << std::endl;
-  std::cout << "Bad links total: " << count_badlinks << " Points to perturb: " << perturbL.size() << std::endl;
-  //std::cout << "landmark[0][0] before" << landmarks[0][0] << std::endl;
-  //*********************** Perturb bad link landmarks
-  
-  for (auto u: perturbL)
-    {
-      Random_point_iterator rp(D,sqrt(lambda)/4);
-      //std::cout << landmarks[u] << std::endl;
-      
-      std::vector<FT> point;
-      for (int i = 0; i < D; i++)
-        {
-          point.push_back(W[landmarks_ind[u]][i] + (*rp)[i]);
-        }
-      landmarks[u] = Point_d(point);
-      //std::cout << landmarks[u] << std::endl;
-    }
-  
-  //std::cout << "landmark[0][0] after" << landmarks[0][0] << std::endl;
-  std::cout << "lambda=" << lambda << std::endl;
-  // Write the WL matrix in a file
- 
-  /*
-  char buffer[100];
-  int i = sprintf(buffer,"stree_result.txt");
-  
-  if (i >= 0)
-    {
-      std::string out_file = (std::string)buffer;
-      std::ofstream ofs (out_file, std::ofstream::out);
-      witnessComplex.st_to_file(ofs);
-      ofs.close();
-    }
-  */
-  //witnessComplex.write_badlinks("badlinks");
-  //write_edges_gnuplot("landmarks/edges", witnessComplex, landmarks);
-  return count_badlinks;
-}
-
-
-int main (int argc, char * const argv[])
-{
-  if (argc != 3)
-    {
-      std::cerr << "Usage: " << argv[0]
-                << " path_to_point_file nbL \n";
-      return 0;
-    }
-  /*
-  boost::filesystem::path p;
-
-  for (; argc > 2; --argc, ++argv)
-    p /= argv[1];
-  */
-  std::string file_name   = argv[1];
-  int nbL       = atoi(argv[2]);
-  
-  //clock_t start, end;
-  //Construct the Simplex Tree
-  //Witness_complex<> witnessComplex;
- 
-  std::cout << "Let the carnage begin!\n";
-  Point_Vector point_vector;
-  read_points_cust(file_name, point_vector);
-  //std::cout << "Successfully read the points\n";
-  //witnessComplex.setNbL(nbL);
-  //  witnessComplex.witness_complex_from_points(point_vector);
-  int nbP = point_vector.size();
-  //std::vector<std::vector< int > > WL(nbP);
-  //std::set<int> L;
-  Point_Vector L;
-  std::vector<int> chosen_landmarks;
-  //Point_etiquette_map L_i;
-  //start = clock();
-  //witnessComplex.landmark_choice_by_furthest_points(point_vector, point_vector.size(), WL);
-  landmark_choice(point_vector, nbP, nbL, L, chosen_landmarks);
-  int bl = 1;
-
-  mkdir("landmarks", S_IRWXU);
-  const size_t last_slash_idx = file_name.find_last_of("/");
-  if (std::string::npos != last_slash_idx)
-    {
-      file_name.erase(0, last_slash_idx + 1);
-    }
-  write_points("landmarks/initial_pointset",point_vector);
-  //write_points("landmarks/initial_landmarks",L);
-  //for (int i = 0; bl != 0; i++)
-  for (int i = 0; i < 1; i++)
-    {
-      std::cout << "========== Start iteration " << i << " ========\n";
-      bl = landmark_perturbation(point_vector, L, chosen_landmarks);
-      std::ostringstream os(std::ostringstream::ate);;
-      os << "landmarks/landmarks0";
-      write_points(os.str(),L);
-    }
-  //end = clock();
-  
-  /*
-  std::cout << "Landmark choice took "
-            << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
-  start = clock();
-  witnessComplex.witness_complex(WL);
-  //
-  end = clock();
-  std::cout << "Howdy world! The process took "
-       << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
-  */
-  
-  /*
-  out_file = "output/"+file_name+"_"+argv[2]+".stree";
-  std::ofstream ofs (out_file, std::ofstream::out);
-  witnessComplex.st_to_file(ofs);
-  ofs.close();
-
-  out_file = "output/"+file_name+"_"+argv[2]+".badlinks";
-  std::ofstream ofs2(out_file, std::ofstream::out);
-  witnessComplex.write_bad_links(ofs2);
-  ofs2.close();
-  */
-}
diff --git a/src/Witness_complex/example/witness_complex_protected_delaunay.cpp b/src/Witness_complex/example/witness_complex_protected_delaunay.cpp
deleted file mode 100644
index 77a167a5..00000000
--- a/src/Witness_complex/example/witness_complex_protected_delaunay.cpp
+++ /dev/null
@@ -1,604 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Siargey Kachanovich
- *
- *    Copyright (C) 2015  INRIA Sophia Antipolis-Méditerranée (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#include <utility>
-#include <algorithm>
-#include <set>
-#include <iterator>
-#include <chrono>
-
-#include <sys/types.h>
-#include <sys/stat.h>
-//#include <stdlib.h>
-
-//#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Witness_complex.h"
-#include "gudhi/reader_utils.h"
-#include "Torus_distance.h" 
-
-#include <CGAL/Cartesian_d.h>
-#include <CGAL/Search_traits.h>
-#include <CGAL/Search_traits_adapter.h>
-#include <CGAL/property_map.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/Orthogonal_k_neighbor_search.h>
-#include <CGAL/Kd_tree.h>
-#include <CGAL/Euclidean_distance.h>
-#include <CGAL/Kernel_d/Sphere_d.h>
-
-#include <CGAL/Kernel_d/Vector_d.h>
-#include <CGAL/point_generators_d.h>
-#include <CGAL/constructions_d.h>
-#include <CGAL/Fuzzy_sphere.h>
-#include <CGAL/Random.h>
-#include <CGAL/Delaunay_triangulation.h>
-
-
-#include <boost/tuple/tuple.hpp>
-#include <boost/iterator/zip_iterator.hpp>
-#include <boost/iterator/counting_iterator.hpp>
-#include <boost/range/iterator_range.hpp>
-
-using namespace Gudhi;
-//using namespace boost::filesystem;
-
-typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
-typedef K::Point_d Point_d;
-//typedef CGAL::Cartesian_d<double> K;
-//typedef CGAL::Point_d<K> Point_d;
-typedef K::FT FT;
-typedef CGAL::Search_traits<
-  FT, Point_d,
-  typename K::Cartesian_const_iterator_d,
-  typename K::Construct_cartesian_const_iterator_d> Traits_base;
-typedef CGAL::Euclidean_distance<Traits_base> Euclidean_distance;
-
-
-typedef std::vector< Vertex_handle > typeVectorVertex;
-
-//typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
-//typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
-
-typedef CGAL::Search_traits_adapter<
-  std::ptrdiff_t, Point_d*, Traits_base> STraits;
-//typedef K TreeTraits;
-//typedef CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance > Euclidean_adapter;
-//typedef CGAL::Kd_tree<STraits> Kd_tree;
-typedef CGAL::Orthogonal_k_neighbor_search<STraits, CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance>> K_neighbor_search;
-typedef K_neighbor_search::Tree Tree;
-typedef K_neighbor_search::Distance Distance;
-typedef K_neighbor_search::iterator KNS_iterator;
-typedef K_neighbor_search::iterator KNS_range;
-typedef boost::container::flat_map<int, int> Point_etiquette_map;
-typedef CGAL::Kd_tree<STraits> Tree2;
-
-typedef CGAL::Fuzzy_sphere<STraits> Fuzzy_sphere;
-
-typedef std::vector<Point_d> Point_Vector;
-
-//typedef K::Equal_d Equal_d;
-//typedef CGAL::Random_points_in_cube_d<CGAL::Point_d<CGAL::Cartesian_d<FT> > > Random_cube_iterator;
-typedef CGAL::Random_points_in_cube_d<Point_d> Random_cube_iterator;
-typedef CGAL::Random_points_in_ball_d<Point_d> Random_point_iterator;
-
-typedef CGAL::Delaunay_triangulation<K> Delaunay_triangulation;
-typedef Delaunay_triangulation::Facet Facet;
-typedef CGAL::Sphere_d<K> Sphere_d;
-
-bool toric=false;
-
-
-/**
- * \brief Customized version of read_points
- * which takes into account a possible nbP first line
- *
- */
-inline void
-read_points_cust ( std::string file_name , Point_Vector & points)
-{  
-  std::ifstream in_file (file_name.c_str(),std::ios::in);
-  if(!in_file.is_open())
-    {
-      std::cerr << "Unable to open file " << file_name << std::endl;
-      return;
-    }
-  std::string line;
-  double x;
-  while( getline ( in_file , line ) )
-    {
-      std::vector< double > point;
-      std::istringstream iss( line );
-      while(iss >> x) { point.push_back(x); }
-      Point_d p(point.begin(), point.end());
-      if (point.size() != 1)
-        points.push_back(p);
-    }
-  in_file.close();
-}
-
-void generate_points_grid(Point_Vector& W, int width, int D)
-{
-  int nb_points = 1;
-  for (int i = 0; i < D; ++i)
-    nb_points *= width;
-  for (int i = 0; i < nb_points; ++i)
-    {
-      std::vector<double> point;
-      int cell_i = i;
-      for (int l = 0; l < D; ++l)
-        {
-          point.push_back(0.01*(cell_i%width));
-          cell_i /= width;
-        }
-      W.push_back(point);
-    }
-}
-
-void generate_points_random_box(Point_Vector& W, int nbP, int dim)
-{
-  /*
-  Random_cube_iterator rp(dim, 1);
-  for (int i = 0; i < nbP; i++)
-    {
-      std::vector<double> point;
-      for (auto it = rp->cartesian_begin(); it != rp->cartesian_end(); ++it)
-        point.push_back(*it);
-      W.push_back(Point_d(point));
-      rp++;
-    }
-  */
-  Random_cube_iterator rp(dim, 1.0);
-  for (int i = 0; i < nbP; i++)
-    {
-      W.push_back(*rp++);
-    }
-}
-
-
-void write_wl( std::string file_name, std::vector< std::vector <int> > & WL)
-{
-  std::ofstream ofs (file_name, std::ofstream::out);
-  for (auto w : WL)
-    {
-      for (auto l: w)
-        ofs << l << " ";
-      ofs << "\n";
-    }
-  ofs.close();
-}
-
-
-void write_points( std::string file_name, std::vector< Point_d > & points)
-{
-  std::ofstream ofs (file_name, std::ofstream::out);
-  for (auto w : points)
-    {
-      for (auto it = w.cartesian_begin(); it != w.cartesian_end(); ++it)
-        ofs << *it << " ";
-      ofs << "\n";
-    }
-  ofs.close();
-}
-
-void write_edges(std::string file_name, Witness_complex<>& witness_complex, Point_Vector& landmarks)
-{
-  std::ofstream ofs (file_name, std::ofstream::out);
-  for (auto u: witness_complex.complex_vertex_range())
-    for (auto v: witness_complex.complex_vertex_range())
-      {
-        typeVectorVertex edge = {u,v};
-        if (u < v && witness_complex.find(edge) != witness_complex.null_simplex())   
-          {
-            for (auto it = landmarks[u].cartesian_begin(); it != landmarks[u].cartesian_end(); ++it)
-              ofs << *it << " ";
-            ofs << "\n";
-            for (auto it = landmarks[v].cartesian_begin(); it != landmarks[v].cartesian_end(); ++it)
-              ofs << *it << " ";
-            ofs << "\n\n\n";
-          }
-      }
-  ofs.close();
-}
-
-
-/** Function that chooses landmarks from W and place it in the kd-tree L.
- *  Note: nbL hould be removed if the code moves to Witness_complex
- */
-void landmark_choice(Point_Vector &W, int nbP, int nbL, Point_Vector& landmarks, std::vector<int>& landmarks_ind)
-{
-  std::cout << "Enter landmark choice to kd tree\n";
-  int chosen_landmark;
-  Point_d* p;
-  CGAL::Random rand;
-  for (int i = 0; i < nbL; i++)
-    {
-      //      while (!res.second)
-      //  {
-      do chosen_landmark = rand.get_int(0,nbP);
-      while (std::count(landmarks_ind.begin(),landmarks_ind.end(),chosen_landmark)!=0);
-      //rand++;
-      //std::cout << "Chose " << chosen_landmark << std::endl;
-      p = &W[chosen_landmark];
-      //L_i.emplace(chosen_landmark,i);
-      //  }
-      landmarks.push_back(*p);
-      landmarks_ind.push_back(chosen_landmark);
-      //std::cout << "Added landmark " << chosen_landmark << std::endl;
-    }
- }
-
-void insert_delaunay_landmark_with_copies(Point_Vector& W, int chosen_landmark, std::vector<int>& landmarks_ind, Delaunay_triangulation& delaunay, int& landmark_count)
-{
-  int D = W[0].size();
-  int nb_cells = pow(3, D);
-  for (int i = 0; i < nb_cells; ++i)
-    {
-      std::vector<FT> point;
-      int cell_i = i;
-      for (int l = 0; l < D; ++l)
-        {
-                point.push_back(W[chosen_landmark][l] + 2.0*(cell_i%3-1));
-                cell_i /= 3;
-        }
-      delaunay.insert(point);
-    }
-  landmarks_ind.push_back(chosen_landmark);
-  landmark_count++;
-}
-
-
-
-
-////////////////////////////////////////////////////////////////////////
-// OLD CODE VVVVVVVV
-////////////////////////////////////////////////////////////////////////
-
-
-/*
-bool is_violating_protection(Point_d& p, Delaunay_triangulation& t, int D, FT delta)
-{
-  Euclidean_distance ed;
-  Delaunay_triangulation::Vertex_handle v;
-  Delaunay_triangulation::Face f(t.current_dimension()); 
-  Delaunay_triangulation::Facet ft; 
-  Delaunay_triangulation::Full_cell_handle c; 
-  Delaunay_triangulation::Locate_type lt;
-  c = t.locate(p, lt, f, ft, v);
-  for (auto fc_it = t.full_cells_begin(); fc_it != t.full_cells_end(); ++fc_it)
-    if (!t.is_infinite(fc_it))
-      {
-        std::vector<Point_d> vertices;
-        for (auto v_it = fc_it->vertices_begin(); v_it != fc_it->vertices_end(); ++v_it)
-          vertices.push_back((*v_it)->point());
-        Sphere_d cs(D, vertices.begin(), vertices.end());
-        Point_d center_cs = cs.center();
-        FT r = sqrt(ed.transformed_distance(center_cs, fc_it->vertex(1)->point()));
-        FT dist2 = ed.transformed_distance(center_cs, p);
-        //if the new point is inside the protection ball of a non conflicting simplex
-        if (dist2 >= r*r && dist2 <= (r+delta)*(r+delta)) 
-          return true;
-      }
-  return false;
-}
-
-bool triangulation_is_protected(Delaunay_triangulation& t, FT delta)
-{
-  Euclidean_distance ed;
-  int D = t.current_dimension();
-  for (auto fc_it = t.full_cells_begin(); fc_it != t.full_cells_end(); ++fc_it)
-    if (!t.is_infinite(fc_it))
-      for (auto v_it = t.vertices_begin(); v_it != t.vertices_end(); ++v_it)
-        {
-          //check if vertex belongs to the face
-          bool belongs = false;
-          for (auto fc_v_it = fc_it->vertices_begin(); fc_v_it != fc_it->vertices_end(); ++fc_v_it)
-            if (v_it == *fc_v_it)
-              {
-                belongs = true;
-                break;
-              }
-          if (!belongs)
-            {
-              std::vector<Point_d> vertices;
-              for (auto fc_v_it = fc_it->vertices_begin(); fc_v_it != fc_it->vertices_end(); ++fc_v_it)
-                vertices.push_back((*fc_v_it)->point());
-              Sphere_d cs(D, vertices.begin(), vertices.end());
-              Point_d center_cs = cs.center();
-              FT r = sqrt(ed.transformed_distance(center_cs, fc_it->vertex(1)->point()));
-              FT dist2 = ed.transformed_distance(center_cs, v_it->point());
-              //if the new point is inside the protection ball of a non conflicting simplex
-              if (dist2 <= (r+delta)*(r+delta)) 
-                return false;
-            }
-        }
-  return true;
-}
-
-void fill_landmark_copies(Point_Vector& W, Point_Vector& landmarks, std::vector<int>& landmarks_ind)
-{
-  int D = W[0].size();
-  int nb_cells = pow(3, D);
-  int nbL = landmarks_ind.size();
-  // Fill landmarks
-  for (int i = 0; i < nb_cells-1; ++i)
-    for (int j = 0; j < nbL; ++j)
-      {
-        int cell_i = i;
-        Point_d point;
-        for (int l = 0; l < D; ++l)
-          {
-            point.push_back(W[landmarks_ind[j]][l] + 2.0*(cell_i-1));
-            cell_i /= 3;
-          }
-        landmarks.push_back(point);
-      }
-}
-
-void landmark_choice_by_delaunay(Point_Vector& W, int nbP, int nbL, Point_Vector& landmarks, std::vector<int>& landmarks_ind, FT delta)
-{
-  int D = W[0].size();
-  Delaunay_triangulation t(D);
-  CGAL::Random rand;
-  int chosen_landmark;
-  int landmark_count = 0;
-  for (int i = 0; i <= D+1; ++i)
-    {
-      do chosen_landmark = rand.get_int(0,nbP);
-      while (std::count(landmarks_ind.begin(),landmarks_ind.end(),chosen_landmark)!=0);
-      insert_delaunay_landmark_with_copies(W, chosen_landmark, landmarks_ind, t, landmark_count);
-    }
-  while (landmark_count < nbL)
-    {      
-      do chosen_landmark = rand.get_int(0,nbP);
-      while (std::count(landmarks_ind.begin(),landmarks_ind.end(),chosen_landmark)!=0);      
-      // If no conflicts then insert in every copy of T^3
-      if (!is_violating_protection(W[chosen_landmark], t, D, delta))
-        insert_delaunay_landmark_with_copies(W, chosen_landmark, landmarks_ind, t, landmark_count);
-    }
-  fill_landmark_copies(W, landmarks, landmarks_ind);
-}
-
-
-void landmark_choice_protected_delaunay(Point_Vector& W, int nbP, Point_Vector& landmarks, std::vector<int>& landmarks_ind, FT delta)
-{
-  int D = W[0].size();
-  Torus_distance td;
-  Euclidean_distance ed;
-  Delaunay_triangulation t(D);
-  CGAL::Random rand;
-  int landmark_count = 0;
-  std::list<int> index_list;
-  //      shuffle the list of indexes (via a vector)
-  {
-    std::vector<int> temp_vector;
-    for (int i = 0; i < nbP; ++i)
-      temp_vector.push_back(i);
-    unsigned seed = std::chrono::system_clock::now().time_since_epoch().count();
-    std::shuffle(temp_vector.begin(), temp_vector.end(), std::default_random_engine(seed));
-    for (std::vector<int>::iterator it = temp_vector.begin(); it != temp_vector.end(); ++it)
-      index_list.push_front(*it);
-  }
-  //      add the first D+1 vertices to form one non-empty cell 
-  for (int i = 0; i <= D+1; ++i)
-    {
-      insert_delaunay_landmark_with_copies(W, index_list.front(), landmarks_ind, t, landmark_count);
-      index_list.pop_front();
-    }
-  //      add other vertices if they don't violate protection
-  std::list<int>::iterator list_it = index_list.begin();
-  while (list_it != index_list.end())
-    if (!is_violating_protection(W[*list_it], t, D, delta))
-      {
-          // If no conflicts then insert in every copy of T^3      
-          insert_delaunay_landmark_with_copies(W, *list_it, landmarks_ind, t, landmark_count);
-          index_list.erase(list_it);
-          list_it = index_list.begin();
-        }
-    else
-      list_it++;
-  fill_landmark_copies(W, landmarks, landmarks_ind);
-}
-
-
-int landmark_perturbation(Point_Vector &W, int nbL, Point_Vector& landmarks, std::vector<int>& landmarks_ind)
-{
-  //******************** Preface: origin point
-  int D = W[0].size();
-  std::vector<FT> orig_vector;
-  for (int i=0; i<D; i++)
-    orig_vector.push_back(0);
-  Point_d origin(orig_vector);
-
-  //******************** Constructing a WL matrix
-  int nbP = W.size();
-  Euclidean_distance ed;
-  FT lambda = ed.transformed_distance(landmarks[0],landmarks[1]);
-  std::vector<Point_d> landmarks_ext;
-  int nb_cells = 1;
-  for (int i = 0; i < D; ++i)
-    nb_cells *= 3;
-  for (int i = 0; i < nb_cells; ++i)
-      for (int k = 0; k < nbL; ++k)
-        {
-          std::vector<double> point;
-          int cell_i = i;
-          for (int l = 0; l < D; ++l)
-            {
-              point.push_back(landmarks[k][l] + 2.0*((cell_i%3)-1.0));
-              cell_i /= 3;
-            }
-          landmarks_ext.push_back(point);
-        }
-  write_points("landmarks/initial_landmarks",landmarks_ext);
-  STraits traits(&(landmarks_ext[0]));
-  std::vector< std::vector <int> > WL(nbP);
-
-  //********************** Neighbor search in a Kd tree
-  Tree L(boost::counting_iterator<std::ptrdiff_t>(0),
-         boost::counting_iterator<std::ptrdiff_t>(nb_cells*nbL),
-         typename Tree::Splitter(),
-         traits);
-  std::cout << "Enter (D+1) nearest landmarks\n";
-  for (int i = 0; i < nbP; i++)
-    {
-      Point_d& w = W[i];
-      ////Search D+1 nearest neighbours from the tree of landmarks L
-      K_neighbor_search search(L, w, D+1, FT(0), true,
-                               CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance>(&(landmarks_ext[0])) );
-      for(K_neighbor_search::iterator it = search.begin(); it != search.end(); ++it)
-        {
-          if (std::find(WL[i].begin(), WL[i].end(), (it->first)%nbL) == WL[i].end())
-            WL[i].push_back((it->first)%nbL);
-        }
-      if (i == landmarks_ind[WL[i][0]])
-        {
-          FT dist = ed.transformed_distance(W[i], landmarks[WL[i][1]]);
-          if (dist < lambda)
-            lambda = dist;
-        }
-    }
-  std::string out_file = "wl_result";
-  write_wl(out_file,WL);
-  
-  //******************** Constructng a witness complex
-  std::cout << "Entered witness complex construction\n";
-  Witness_complex<> witnessComplex;
-  witnessComplex.setNbL(nbL);
-  witnessComplex.witness_complex(WL);
-
-  //******************** Making a set of bad link landmarks
-  std::cout << "Entered bad links\n";
-  std::set< int > perturbL;
-  int count_badlinks = 0;
-  //std::cout << "Bad links around ";
-  std::vector< int > count_bad(D);
-  std::vector< int > count_good(D);
-  for (auto u: witnessComplex.complex_vertex_range())
-    {
-       if (!witnessComplex.has_good_link(u, count_bad, count_good))
-         {
-           count_badlinks++;
-           Point_d& l = landmarks[u];
-           Fuzzy_sphere fs(l, sqrt(lambda)*3, 0, traits);
-           std::vector<int> curr_perturb;
-           L.search(std::insert_iterator<std::vector<int>>(curr_perturb,curr_perturb.begin()),fs);
-           for (int i: curr_perturb)
-             perturbL.insert(i%nbL);
-       }
-    }
-  for (unsigned int i = 0; i != count_good.size(); i++)
-    if (count_good[i] != 0)
-      std::cout << "count_good[" << i << "] = " << count_good[i] << std::endl;
-  for (unsigned int i = 0; i != count_bad.size(); i++)
-    if (count_bad[i] != 0)
-      std::cout << "count_bad[" << i << "] = " << count_bad[i] << std::endl;
-  std::cout << "\nBad links total: " << count_badlinks << " Points to perturb: " << perturbL.size() << std::endl;
-  
-  //*********************** Perturb bad link landmarks  
-  for (auto u: perturbL)
-    {
-      Random_point_iterator rp(D,sqrt(lambda)/8);
-      std::vector<FT> point;
-      for (int i = 0; i < D; i++)
-        {
-          while (K().squared_distance_d_object()(*rp,origin) < lambda/256)
-            rp++;
-          FT coord = landmarks[u][i] + (*rp)[i];
-          if (coord > 1)
-            point.push_back(coord-1);
-          else if (coord < -1)
-            point.push_back(coord+1);
-          else
-            point.push_back(coord);
-        }
-      landmarks[u] = Point_d(point);
-    }
-  std::cout << "lambda=" << lambda << std::endl;
-  char buffer[100];
-  int i = sprintf(buffer,"stree_result.txt");
-  
-  if (i >= 0)
-    {
-      std::string out_file = (std::string)buffer;
-      std::ofstream ofs (out_file, std::ofstream::out);
-      witnessComplex.st_to_file(ofs);
-      ofs.close();
-    }
-  write_edges("landmarks/edges", witnessComplex, landmarks);
-  return count_badlinks;
-}
-
-
-int main (int argc, char * const argv[])
-{
-  if (argc != 5)
-    {
-      std::cerr << "Usage: " << argv[0]
-                << " nbP nbL dim delta\n";
-      return 0;
-    }
-  int nbP       = atoi(argv[1]);
-  int nbL       = atoi(argv[2]);
-  int dim       = atoi(argv[3]);
-  FT delta      = atof(argv[4]);
-  
-  std::cout << "Let the carnage begin!\n";
-  Point_Vector point_vector;
-  generate_points_random_box(point_vector, nbP, dim);
-  Point_Vector L;
-  std::vector<int> chosen_landmarks;
-  bool ok=false;
-  while (!ok)
-    {
-      ok = true;
-      L = {};
-      chosen_landmarks = {};
-      //landmark_choice_by_delaunay(point_vector, nbP, nbL, L, chosen_landmarks, delta);
-      landmark_choice_protected_delaunay(point_vector, nbP, L, chosen_landmarks, delta);
-      nbL = chosen_landmarks.size();
-      std::cout << "Number of landmarks is " << nbL << std::endl;
-      //int width = (int)pow(nbL, 1.0/dim); landmark_choice_bcc(point_vector, nbP, width, L, chosen_landmarks);
-      for (auto i: chosen_landmarks)
-        {
-          ok = ok && (std::count(chosen_landmarks.begin(),chosen_landmarks.end(),i) == 1);
-          if (!ok) break;
-        }
-      
-    }
-  int bl = nbL, curr_min = bl;
-  write_points("landmarks/initial_pointset",point_vector);
-  //write_points("landmarks/initial_landmarks",L);
-  //for (int i = 0; i < 1; i++)
-  for (int i = 0; bl > 0; i++)
-    {
-      std::cout << "========== Start iteration " << i << "== curr_min(" << curr_min << ")========\n";
-      bl=landmark_perturbation(point_vector, nbL, L, chosen_landmarks);
-      if (bl < curr_min)
-        curr_min=bl;
-      write_points("landmarks/landmarks0",L);
-    }
-  
-}
-*/
diff --git a/src/Witness_complex/example/witness_complex_sphere.cpp b/src/Witness_complex/example/witness_complex_sphere.cpp
deleted file mode 100644
index bf3015fa..00000000
--- a/src/Witness_complex/example/witness_complex_sphere.cpp
+++ /dev/null
@@ -1,457 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Siargey Kachanovich
- *
- *    Copyright (C) 2015  INRIA Sophia Antipolis-Méditerranée (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#include <utility>
-#include <algorithm>
-#include <set>
-#include <iterator>
-
-#include <sys/types.h>
-#include <sys/stat.h>
-//#include <stdlib.h>
-
-//#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Witness_complex.h"
-#include "gudhi/reader_utils.h"
-#include "generators.h"
-#include "output.h"
-//#include <boost/filesystem.hpp> 
-
-//#include <CGAL/Delaunay_triangulation.h>
-#include <CGAL/Cartesian_d.h>
-#include <CGAL/Search_traits.h>
-#include <CGAL/Search_traits_adapter.h>
-#include <CGAL/property_map.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/Orthogonal_k_neighbor_search.h>
-#include <CGAL/Kd_tree.h>
-#include <CGAL/Euclidean_distance.h>
-
-#include <CGAL/Kernel_d/Vector_d.h>
-#include <CGAL/point_generators_d.h>
-#include <CGAL/constructions_d.h>
-#include <CGAL/Fuzzy_sphere.h>
-#include <CGAL/Random.h>
-
-
-#include <boost/tuple/tuple.hpp>
-#include <boost/iterator/zip_iterator.hpp>
-#include <boost/iterator/counting_iterator.hpp>
-#include <boost/range/iterator_range.hpp>
-
-using namespace Gudhi;
-//using namespace boost::filesystem;
-
-typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
-typedef K::FT FT;
-typedef K::Point_d Point_d;
-typedef CGAL::Search_traits<
-  FT, Point_d,
-  typename K::Cartesian_const_iterator_d,
-  typename K::Construct_cartesian_const_iterator_d> Traits_base;
-typedef CGAL::Euclidean_distance<Traits_base> Euclidean_distance;
-
-typedef std::vector< Vertex_handle > typeVectorVertex;
-
-//typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex;
-//typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
-
-typedef CGAL::Search_traits_adapter<
-  std::ptrdiff_t, Point_d*, Traits_base> STraits;
-//typedef K TreeTraits;
-//typedef CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance > Euclidean_adapter;
-//typedef CGAL::Kd_tree<STraits> Kd_tree;
-typedef CGAL::Orthogonal_k_neighbor_search<STraits, CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance>> K_neighbor_search;
-typedef K_neighbor_search::Tree Tree;
-typedef K_neighbor_search::Distance Distance;
-typedef K_neighbor_search::iterator KNS_iterator;
-typedef K_neighbor_search::iterator KNS_range;
-typedef boost::container::flat_map<int, int> Point_etiquette_map;
-typedef CGAL::Kd_tree<STraits> Tree2;
-
-typedef CGAL::Fuzzy_sphere<STraits> Fuzzy_sphere;
-
-typedef std::vector<Point_d> Point_Vector;
-
-//typedef K::Equal_d Equal_d;
-
-bool toric=false;
-
-std::vector<Point_d> convert_to_torus(std::vector< Point_d>& points)
-{
-  std::vector< Point_d > points_torus;
-  for (auto p: points)
-    {
-      FT theta = M_PI*p[0];
-      FT phi = M_PI*p[1];
-      std::vector<FT> p_torus;
-      p_torus.push_back((1+0.2*cos(theta))*cos(phi));
-      p_torus.push_back((1+0.2*cos(theta))*sin(phi));
-      p_torus.push_back(0.2*sin(theta));
-      points_torus.push_back(Point_d(p_torus));
-    }
-  return points_torus;
-}
-
-/** Function that chooses landmarks from W and place it in the kd-tree L.
- *  Note: nbL hould be removed if the code moves to Witness_complex
- */
-void landmark_choice(Point_Vector &W, int nbP, int nbL, Point_Vector& landmarks, std::vector<int>& landmarks_ind)
-{
-  std::cout << "Enter landmark choice to kd tree\n";
-  //std::vector<Point_d> landmarks;
-  int chosen_landmark;
-  //std::pair<Point_etiquette_map::iterator,bool> res = std::make_pair(L_i.begin(),false);
-  Point_d* p;
-  CGAL::Random rand;
-  for (int i = 0; i < nbL; i++)
-    {
-      //      while (!res.second)
-      //  {
-      do chosen_landmark = rand.get_int(0,nbP);
-      while (std::find(landmarks_ind.begin(), landmarks_ind.end(), chosen_landmark) != landmarks_ind.end());
-      //rand++;
-      //std::cout << "Chose " << chosen_landmark << std::endl;
-      p = &W[chosen_landmark];
-      //L_i.emplace(chosen_landmark,i);
-      //  }
-      landmarks.push_back(*p);
-      landmarks_ind.push_back(chosen_landmark);
-      //std::cout << "Added landmark " << chosen_landmark << std::endl;
-    }
- }
-
-/** \brief A test with 600cell, the generalisation of icosaedre in 4d
- */
-void landmark_choice_600cell(Point_Vector&W, int nbP, int nbL, Point_Vector& landmarks, std::vector<int>& landmarks_ind)
-{
-  assert(W[0].size() == 4); //4-dimensionality required
-  FT phi = (1+sqrt(5))/2;
-  FT phi_1 = FT(1)/phi;
-  std::vector<FT> p;
-  // 16 vertices
-  for (FT a = -0.5; a < 1; a += 1)
-    for (FT b = -0.5; b < 1; b += 1)
-      for (FT c = -0.5; c < 1; c += 1)
-        for (FT d = -0.5; d < 1; d += 1)
-          landmarks.push_back(Point_d(std::vector<FT>({a,b,c,d})));
-  // 8 vertices
-  for (FT a = -0.5; a < 1; a += 1)
-    {
-      landmarks.push_back(Point_d(std::vector<FT>({a,0,0,0})));
-      landmarks.push_back(Point_d(std::vector<FT>({0,a,0,0})));
-      landmarks.push_back(Point_d(std::vector<FT>({0,0,a,0})));
-      landmarks.push_back(Point_d(std::vector<FT>({0,0,0,a})));
-    }
-  // 96 vertices
-  for (FT a = -phi/2; a < phi; a += phi)
-    for (FT b = -0.5; b < 1; b += 1)
-      for (FT c = -phi_1/2; c < phi_1; c += phi_1)
-        {
-          landmarks.push_back(Point_d(std::vector<FT>({a,b,c,0})));
-          landmarks.push_back(Point_d(std::vector<FT>({b,a,0,c})));
-          landmarks.push_back(Point_d(std::vector<FT>({c,0,a,b})));
-          landmarks.push_back(Point_d(std::vector<FT>({0,c,b,a})));
-          landmarks.push_back(Point_d(std::vector<FT>({a,c,0,b})));
-          landmarks.push_back(Point_d(std::vector<FT>({a,0,b,c})));
-          landmarks.push_back(Point_d(std::vector<FT>({c,b,0,a})));
-          landmarks.push_back(Point_d(std::vector<FT>({0,b,a,c})));
-          landmarks.push_back(Point_d(std::vector<FT>({b,0,c,a})));
-          landmarks.push_back(Point_d(std::vector<FT>({0,a,c,b})));
-          landmarks.push_back(Point_d(std::vector<FT>({b,c,a,0})));
-          landmarks.push_back(Point_d(std::vector<FT>({c,a,b,0})));
-        }
-  for (int i = 0; i < 120; ++i)
-    landmarks_ind.push_back(i);
-}
-
-int landmark_perturbation(Point_Vector &W, Point_Vector& landmarks, std::vector<int>& landmarks_ind)
-{
-  //********************Preface: origin point
-  clock_t start, end;
-  int D = W[0].size();
-  std::vector<FT> orig_vector;
-  for (int i=0; i<D; i++)
-    orig_vector.push_back(0);
-  Point_d origin(orig_vector);
-  //Distance dist;
-  //dist.transformed_distance(0,1);
-  //******************** Constructing a WL matrix
-  int nbP = W.size();
-  int nbL = landmarks.size();
-  Euclidean_distance ed;
-  FT lambda = ed.transformed_distance(landmarks[0],landmarks[1]);
-  //std::cout << "Lambda=" << lambda << std::endl;
-    //FT lambda = 0.1;//Euclidean_distance();
-  STraits traits(&(landmarks[0]));
-  std::vector< std::vector <int> > WL(nbP);
-  Tree L(boost::counting_iterator<std::ptrdiff_t>(0),
-         boost::counting_iterator<std::ptrdiff_t>(nbL),
-         typename Tree::Splitter(),
-         traits);
-  /*Tree2 L2(boost::counting_iterator<std::ptrdiff_t>(0),
-           boost::counting_iterator<std::ptrdiff_t>(nbL),
-           typename Tree::Splitter(),
-           STraits(&(landmarks[0])));
-  */
-  std::cout << "Enter (D+1) nearest landmarks\n";
-  //std::cout << "Size of the tree is " << L.size() << std::endl;
-  start = clock();
-  for (int i = 0; i < nbP; i++)
-    {
-      //std::cout << "Entered witness number " << i << std::endl;
-      Point_d& w = W[i];
-      //std::cout << "Safely constructed a point\n";
-      ////Search D+1 nearest neighbours from the tree of landmarks L
-      /*
-      if (w[0]>0.95)
-        std::cout << i << std::endl;
-      */
-      K_neighbor_search search(L, w, D, FT(0), true,
-                               //CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance>(&(landmarks[0])) );
-                               CGAL::Distance_adapter<std::ptrdiff_t,Point_d*,Euclidean_distance>(&(landmarks[0])) );
-      //std::cout << "Safely found nearest landmarks\n";
-      for(K_neighbor_search::iterator it = search.begin(); it != search.end(); ++it)
-        {
-          //std::cout << "Entered KNN_it with point at distance " << it->second << "\n";
-          //Point_etiquette_map::iterator itm = L_i.find(it->first);
-          //assert(itm != L_i.end());
-          //std::cout << "Entered KNN_it with point at distance " << it->second << "\n";
-          WL[i].push_back(it->first);
-          //std::cout << "ITFIRST " << it->first << std::endl;
-          //std::cout << i << " " << it->first << ": " << it->second << std::endl; 
-        }
-      if (i == landmarks_ind[WL[i][0]])
-        {
-          //std::cout << "'";
-          FT dist = ed.transformed_distance(W[i], landmarks[WL[i][1]]);
-          if (dist < lambda)
-            lambda = dist;
-        }
-    }
-  //std::cout << "\n";
-  end = clock();
-  std::cout << "Landmark choice for " << nbL << " landmarks took "
-            << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
-  std::string out_file = "wl_result";
-  write_wl(out_file,WL);
-  
-  //******************** Constructng a witness complex
-  std::cout << "Entered witness complex construction\n";
-  Witness_complex<> witnessComplex;
-  witnessComplex.setNbL(nbL);
-  start = clock();
-  witnessComplex.witness_complex(WL);
-  //
-  end = clock();
-  std::cout << "Howdy world! The process took "
-       << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
-  //witnessComplex.witness_complex(WL);
-  /*
-  if (witnessComplex.is_witness_complex(WL))
-    std::cout << "!!YES. IT IS A WITNESS COMPLEX!!\n";
-  else
-    std::cout << "??NO. IT IS NOT A WITNESS COMPLEX??\n";   
-  */ 
-  //******************** Making a set of bad link landmarks
-  std::cout << "Entered bad links\n";
-  std::set< int > perturbL;
-  int count_badlinks = 0;
-  //std::cout << "Bad links around ";
-  std::vector< int > count_bad(D);
-  std::vector< int > count_good(D);
-  for (auto u: witnessComplex.complex_vertex_range())
-    if (!witnessComplex.has_good_link(u, count_bad, count_good))
-      {
-        //std::cout << "Landmark " << u << " start!" << std::endl;
-        //perturbL.insert(u);
-        count_badlinks++;
-        //std::cout << u << " ";
-        Point_d& l = landmarks[u];
-        Fuzzy_sphere fs(l, sqrt(lambda), 0, traits);
-        std::vector<int> curr_perturb;
-        L.search(std::insert_iterator<std::vector<int>>(curr_perturb,curr_perturb.begin()),fs);
-        for (int i: curr_perturb)
-          perturbL.insert(i%nbL);
-        //L.search(std::inserter(perturbL,perturbL.begin()),fs);
-        //L.search(std::ostream_iterator<int>(std::cout,"\n"),fs);
-        //std::cout << "PerturbL size is " << perturbL.size() << std::endl;
-      }
-  for (unsigned int i = 0; i != count_good.size(); i++)
-    if (count_good[i] != 0)
-      std::cout << "count_good[" << i << "] = " << count_good[i] << std::endl;
-  for (unsigned int i = 0; i != count_bad.size(); i++)
-    if (count_bad[i] != 0)
-      std::cout << "count_bad[" << i << "] = " << count_bad[i] << std::endl;
-  std::cout << "\nBad links total: " << count_badlinks << " Points to perturb: " << perturbL.size() << std::endl;
-  //std::cout << "landmark[0][0] before" << landmarks[0][0] << std::endl;
-  //*********************** Perturb bad link landmarks
-  
-  for (auto u: perturbL)
-    {
-      Random_point_iterator rp(D,sqrt(lambda)/8*nbL/count_badlinks);
-      //std::cout << landmarks[u] << std::endl;
-      
-      std::vector<FT> point;
-      for (int i = 0; i < D; i++)
-        {
-          while (K().squared_distance_d_object()(*rp,origin) < lambda/256)
-            rp++;
-          FT coord = W[landmarks_ind[u]][i] + (*rp)[i];
-          //FT coord = landmarks[u][i] + (*rp)[i];
-          if (coord > 1)
-            point.push_back(coord-1);
-          else if (coord < -1)
-            point.push_back(coord+1);
-          else
-            point.push_back(coord);
-        }
-      landmarks[u] = Point_d(point);
-      //std::cout << landmarks[u] << std::endl;
-    }
-  
-  //std::cout << "landmark[0][0] after" << landmarks[0][0] << std::endl;
-  std::cout << "lambda=" << lambda << std::endl;
-
-  //std::cout << "WL size" << WL.size() << std::endl;
-  /*
-  std::cout << "L:" << std::endl;
-  for (int i = 0; i < landmarks.size(); i++)
-      std::cout << landmarks[i] << std::endl;
-  */
-  
-  char buffer[100];
-  int i = sprintf(buffer,"stree_result.txt");
-  
-  if (i >= 0)
-    {
-      std::string out_file = (std::string)buffer;
-      std::ofstream ofs (out_file, std::ofstream::out);
-      witnessComplex.st_to_file(ofs);
-      ofs.close();
-    }
-  write_edges("landmarks/edges", witnessComplex, landmarks);
-  std::cout << Distance().transformed_distance(Point_d(std::vector<double>({0.1,0.1})), Point_d(std::vector<double>({1.9,1.9}))) << std::endl;
-  return count_badlinks;
-}
-
-
-int main (int argc, char * const argv[])
-{
-  
-  if (argc != 4)
-    {
-      std::cerr << "Usage: " << argv[0]
-                << " nbP nbL dim\n";
-      return 0;
-    }
-  /*
-  boost::filesystem::path p;
-  for (; argc > 2; --argc, ++argv)
-    p /= argv[1];
-  */
-  
-  int nbP       = atoi(argv[1]);
-  int nbL       = atoi(argv[2]);
-  int dim       = atoi(argv[3]);
-  //clock_t start, end;
-  //Construct the Simplex Tree
-  //Witness_complex<> witnessComplex;
- 
-  std::cout << "Let the carnage begin!\n";
-  Point_Vector point_vector;
-  //read_points_cust(file_name, point_vector);
-  generate_points_sphere(point_vector, nbP, dim);
-  /*
-  for (auto &p: point_vector)
-    {
-      assert(std::count(point_vector.begin(),point_vector.end(),p) == 1);
-    }
-  */
-  //std::cout << "Successfully read the points\n";
-  //witnessComplex.setNbL(nbL);
-  //  witnessComplex.witness_complex_from_points(point_vector);
-  //int nbP = point_vector.size();
-  //std::vector<std::vector< int > > WL(nbP);
-  //std::set<int> L;
-  Point_Vector L;
-  std::vector<int> chosen_landmarks;
-  //Point_etiquette_map L_i;
-  //start = clock();
-  //witnessComplex.landmark_choice_by_furthest_points(point_vector, point_vector.size(), WL);
-  bool ok=false;
-  while (!ok)
-    {
-      ok = true;
-      L = {};
-      chosen_landmarks = {};
-      landmark_choice(point_vector, nbP, nbL, L, chosen_landmarks);
-      //landmark_choice_600cell(point_vector, nbP, nbL, L, chosen_landmarks);
-      /*
-      for (auto i: chosen_landmarks)
-        {
-          ok = ok && (std::count(chosen_landmarks.begin(),chosen_landmarks.end(),i) == 1);
-          if (!ok) break;
-        }
-      */
-    }
-  int bl = nbL, curr_min = bl;
-  //write_points("landmarks/initial_pointset",point_vector);
-  //write_points("landmarks/initial_landmarks",L);
-  
-  for (int i = 0; bl > 0; i++)
-    //for (int i = 0; i < 1; i++)
-    {
-      std::cout << "========== Start iteration " << i << "== curr_min(" << curr_min << ")========\n";
-      bl=landmark_perturbation(point_vector, L, chosen_landmarks);
-      if (bl < curr_min)
-        curr_min=bl;
-      //write_points("landmarks/landmarks0",L);
-    }
-  //end = clock();
-  
-  /*
-  std::cout << "Landmark choice took "
-            << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
-  start = clock();
-  witnessComplex.witness_complex(WL);
-  //
-  end = clock();
-  std::cout << "Howdy world! The process took "
-       << (double)(end-start)/CLOCKS_PER_SEC << " s. \n";
-  */
-  
-  /*
-  out_file = "output/"+file_name+"_"+argv[2]+".stree";
-  std::ofstream ofs (out_file, std::ofstream::out);
-  witnessComplex.st_to_file(ofs);
-  ofs.close();
-
-  out_file = "output/"+file_name+"_"+argv[2]+".badlinks";
-  std::ofstream ofs2(out_file, std::ofstream::out);
-  witnessComplex.write_bad_links(ofs2);
-  ofs2.close();
-  */
-}
diff --git a/src/cmake/modules/FindEigen3.cmake b/src/cmake/modules/FindEigen3.cmake
new file mode 100644
index 00000000..70c07dfb
--- /dev/null
+++ b/src/cmake/modules/FindEigen3.cmake
@@ -0,0 +1,86 @@
+# - Try to find Eigen3 lib
+#
+# This module supports requiring a minimum version, e.g. you can do
+#   find_package(Eigen3 3.1.2)
+# to require version 3.1.2 or newer of Eigen3.
+#
+# Once done this will define
+#
+#  EIGEN3_FOUND - system has eigen lib with correct version
+#  EIGEN3_INCLUDE_DIR - the eigen include directory
+#  EIGEN3_VERSION - eigen version
+
+# Copyright (c) 2006, 2007 Montel Laurent, <montel@kde.org>
+# Copyright (c) 2008, 2009 Gael Guennebaud, <g.gael@free.fr>
+# Copyright (c) 2009 Benoit Jacob <jacob.benoit.1@gmail.com>
+# Redistribution and use is allowed according to the terms of the 2-clause BSD license.
+
+include(FindPackageHandleStandardArgs)
+
+if(NOT Eigen3_FIND_VERSION)
+  if(NOT Eigen3_FIND_VERSION_MAJOR)
+    set(Eigen3_FIND_VERSION_MAJOR 2)
+  endif(NOT Eigen3_FIND_VERSION_MAJOR)
+  if(NOT Eigen3_FIND_VERSION_MINOR)
+    set(Eigen3_FIND_VERSION_MINOR 91)
+  endif(NOT Eigen3_FIND_VERSION_MINOR)
+  if(NOT Eigen3_FIND_VERSION_PATCH)
+    set(Eigen3_FIND_VERSION_PATCH 0)
+  endif(NOT Eigen3_FIND_VERSION_PATCH)
+
+  set(Eigen3_FIND_VERSION "${Eigen3_FIND_VERSION_MAJOR}.${Eigen3_FIND_VERSION_MINOR}.${Eigen3_FIND_VERSION_PATCH}")
+endif(NOT Eigen3_FIND_VERSION)
+
+macro(_eigen3_get_version)
+  file(READ "${EIGEN3_INCLUDE_DIR}/Eigen/src/Core/util/Macros.h" _eigen3_version_header)
+
+  string(REGEX MATCH "define[ \t]+EIGEN_WORLD_VERSION[ \t]+([0-9]+)" _eigen3_world_version_match "${_eigen3_version_header}")
+  set(EIGEN3_WORLD_VERSION "${CMAKE_MATCH_1}")
+  string(REGEX MATCH "define[ \t]+EIGEN_MAJOR_VERSION[ \t]+([0-9]+)" _eigen3_major_version_match "${_eigen3_version_header}")
+  set(EIGEN3_MAJOR_VERSION "${CMAKE_MATCH_1}")
+  string(REGEX MATCH "define[ \t]+EIGEN_MINOR_VERSION[ \t]+([0-9]+)" _eigen3_minor_version_match "${_eigen3_version_header}")
+  set(EIGEN3_MINOR_VERSION "${CMAKE_MATCH_1}")
+
+  set(EIGEN3_VERSION ${EIGEN3_WORLD_VERSION}.${EIGEN3_MAJOR_VERSION}.${EIGEN3_MINOR_VERSION})
+endmacro(_eigen3_get_version)
+
+set(EIGEN3_USE_FILE "UseEigen3")
+
+if (EIGEN3_INCLUDE_DIR)
+
+  if (EXISTS ${EIGEN3_INCLUDE_DIR}/signature_of_eigen3_matrix_library)
+    # in cache already and valid
+    _eigen3_get_version()
+    set(EIGEN3_FOUND ${EIGEN3_VERSION_OK})
+
+    find_package_handle_standard_args(Eigen3 
+      REQUIRED_VARS EIGEN3_INCLUDE_DIR
+      VERSION_VAR EIGEN3_VERSION)
+
+  else()
+    message(STATUS "Eigen3 path specified in cmake variable EIGEN3_INCLUDE_DIR is "
+                    "set to ${EIGEN3_INCLUDE_DIR}, but that path does not contains the file "
+                    "signature_of_eigen3_matrix_library and is considered as invalid.")
+  endif()
+
+
+
+else (EIGEN3_INCLUDE_DIR)
+
+  find_path(EIGEN3_INCLUDE_DIR NAMES signature_of_eigen3_matrix_library
+      HINTS ENV EIGEN3_INC_DIR
+            ENV EIGEN3_DIR
+      PATHS ${KDE4_INCLUDE_DIR}
+      PATH_SUFFIXES include eigen3 eigen
+      DOC "Directory containing the Eigen3 header files"
+    )
+
+  if(EIGEN3_INCLUDE_DIR)
+    _eigen3_get_version()
+  endif(EIGEN3_INCLUDE_DIR)
+
+  find_package_handle_standard_args(Eigen3 
+    REQUIRED_VARS EIGEN3_INCLUDE_DIR
+    VERSION_VAR EIGEN3_VERSION)
+
+endif(EIGEN3_INCLUDE_DIR)
diff --git a/src/cmake/modules/UseEigen3.cmake b/src/cmake/modules/UseEigen3.cmake
new file mode 100644
index 00000000..e3ed18be
--- /dev/null
+++ b/src/cmake/modules/UseEigen3.cmake
@@ -0,0 +1,9 @@
+# This module setups the compiler for using Eigen v3 library.
+# It assumes that find_package(Eigen3) was already called.
+
+
+include_directories( SYSTEM ${EIGEN3_INCLUDE_DIR} )
+
+add_definitions(-DCGAL_EIGEN3_ENABLED)
+
+set (EIGEN3_SETUP TRUE)
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 315aa0ac..41b8ba1e 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -1,72 +1,115 @@
-/**
-\mainpage 
-
-\image html "Gudhi_banner.jpg" "" width=20cm
-
-The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic C++ library for 
-topological analysis of high-dimensional data whose goal is to provide robust, efficient, flexible and easy to use 
-implementations of 
-state-of-the-art algorithms and data structures for computational topology.
-This library is part of the <a href="https://project.inria.fr/gudhi/">Gudhi project</a>.
-
-The current release of the library allows to use several data-structures for simplicial complexes :
-simplex tree, Hasse diagram or skeleton-blocker. Several  operations can then be done on top of these
-representations such as persistent homology computation or simplification. 
-All data-structures are generic and several of their aspects (such as stored elements, policies) 
-can be parameterized via template classes.
-We refer to 
-\cite gudhilibrary_ICMS14
-for a detailed description of the design of the library.
-
-\section installation Gudhi installation
-
-As Gudhi is a header only library, there is no need to install the library.
-
-Examples of Gudhi headers inclusion can be found in \ref demos.
-
-
-\section compiling Compiling
-
-The library uses c++11 and requires <a href="http://www.boost.org/">Boost</a> with version 1.48.0 or more recent.
-It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2013. 
-
-
-\subsection gmp GMP:
-The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision
-arithmetic, operating on signed integers, rational numbers, and floating point numbers.
-
-The following examples require the <a href="http://gmplib.org/">GNU Multiple Precision Arithmetic Library</a> (GMP) 
-and will not be built if GMP is not installed:
-  - Persistent_cohomology/rips_multifield_persistence
-  - Simplex_tree/simplex_tree_from_alpha_shapes_3
-
-Having GMP version 4.2 or higher installed is recommended.
-
-\subsection cgal CGAL:
-CGAL is a C++ library which provides easy access to efficient and reliable geometric algorithms.
-
-The following example requires the <a href="http://www.cgal.org/">Computational Geometry Algorithms Library</a> (CGAL) 
-and will not be built if CGAL is not installed:
-  - Simplex_tree/simplex_tree_from_alpha_shapes_3
-
-Having CGAL version 4.4 or higher installed is recommended. The procedure to install this library according to
-your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html
-
-\subsection demos Demos and examples
-
-To build the demos and libraries, run the following commands in a terminal:
+/*! \mainpage
+ * \image html "Gudhi_banner.jpg" "" width=20cm
+ * 
+ * \section Introduction Introduction
+ * The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic open source C++ library for
+ * Computational Topology and Topological Data Analysis
+ * (<a class="el" target="_blank" href="https://en.wikipedia.org/wiki/Topological_data_analysis">TDA</a>).
+ * The GUDHI library is developed as part of the
+ * <a class="el" target="_blank" href="https://project.inria.fr/gudhi/">GUDHI project</a> supported by the European
+ * Research Council. The GUDHI library intends  to help the development of new algorithmic solutions in TDA and their
+ * transfer to applications. It provides robust, efficient, flexible and easy to use implementations of
+ * state-of-the-art algorithms and data structures.
+ * 
+ * The current release of the GUDHI library includes:
+ * 
+ * \li Data structures to represent, construct and manipulate simplicial complexes.
+ * \li Algorithms to compute persistent homology and multi-field persistent homology.
+ * \li Simplication of simplicial complexes by edge contraction.
+ * 
+ * All data-structures are generic and several of their aspects can be parameterized via template classes.
+ * We refer to \cite gudhilibrary_ICMS14 for a detailed description of the design of the library.
+ *
+ * The library is available <a class="el" target="_blank" href="https://gforge.inria.fr/frs/?group_id=3865">here</a>
+ * and the documentation is available at this <a class="el" href="http://gudhi.gforge.inria.fr/doc/latest/">
+ * webpage</a>.
+ * 
+ * The library comes with data sets, \ref demos and \ref testsuites.
+ * 
+ * Gudhi is also accessible though the
+ * <a class="el" target="_blank" href="https://cran.r-project.org/web/packages/TDA/index.html">R package TDA</a>
+ * (Statistical Tools for Topological Data Analysis).
+ * 
+ * The development of the GUDHI library is steered by an Editorial Board composed of:
+ * 
+ * \li <a class="el" target="_blank" href="http://www-sop.inria.fr/members/Jean-Daniel.Boissonnat/">
+ * Jean-Daniel Boissonnat</a> | INRIA Sophia Antipolis - Méditerranée
+ * \li <a class="el" target="_blank" href="http://geometrica.saclay.inria.fr/team/Marc.Glisse/">Marc Glisse</a> | INRIA Saclay - Ile de France
+ * \li Clément Jamin | INRIA Sophia Antipolis - Méditerranée
+ * \li Vincent Rouvreau | INRIA Saclay - Ile de France
+ * 
+*/
 
-\verbatim
-cd /path-to-gudhi/
+/*! \page installation Gudhi installation
+ * As Gudhi is a header only library, there is no need to install the library.
+ * 
+ * Examples of Gudhi headers inclusion can be found in \ref demos.
+ * 
+ * \section compiling Compiling
+ * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> with version 1.48.0 or
+ * more recent. It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2013.
+ * 
+ * \subsection gmp GMP:
+ * The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision
+ * arithmetic, operating on signed integers, rational numbers, and floating point numbers.
+ * 
+ * The following example requires the <a target="_blank" href="http://gmplib.org/">GNU Multiple Precision Arithmetic
+ * Library</a> (GMP) and will not be built if GMP is not installed:
+ * \li Persistent_cohomology/rips_multifield_persistence
+ *
+ * Having GMP version 4.2 or higher installed is recommended.
+ * 
+ * \subsection cgal CGAL:
+ * CGAL is a C++ library which provides easy access to efficient and reliable geometric algorithms.
+ * 
+ * The following examples require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms
+ * Library</a> (CGAL) and will not be built if CGAL is not installed:
+ * \li GudhUI
+ * \li Persistent_cohomology/alpha_shapes_persistence
+ * \li Simplex_tree/simplex_tree_from_alpha_shapes_3
+ * 
+ * Having CGAL version 4.4 or higher installed is recommended. The procedure to install this library according to
+ * your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html
+ * 
+ * \subsection demos Demos and examples
+ * To build the demos and libraries, run the following commands in a terminal:
+\verbatim  cd /path-to-gudhi/
 mkdir build
 cd build/
 cmake ..
-make
-\endverbatim
-
-\details 
+make \endverbatim
+ * 
+ * \subsection testsuites Test suites
+ * To test your build, run the following command in a terminal:
+ * \verbatim  make test \endverbatim
+ * 
+ * \section Contributions Bug reports and contributions
+ * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to:
+ * \verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
+ * 
+ * Gudhi is open to external contributions. If you want to join our development team, please contact us.
+ * 
+*/
 
-\copyright GNU General Public License v3.                         
-\verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
+/*! \page Upcoming Upcoming
+ *
+ * The library is under active development. New packages to be released next include:
+ * \li Alpha complex.
+ * \li Bottleneck distance.
+ * \li Zig zag persistence.
+ * \li Witness complex.
+ * \li Tangential complex.
+ * \li Clustering.
+*/
 
+/*! \page Citation Acknowledging the GUDHI library
+ * We kindly ask users to cite the GUDHI library as appropriately as possible in their papers, and to mention the use
+ * of the GUDHI library on the web pages of their projects using GUDHI and provide us with links to these web pages.
+ * Feel free to contact us in case you have any question or remark on this topic.
+ * 
+ * We provide \ref GudhiBibtex entries for the modules of the User and Reference Manual, as well as for publications
+ * directly related to the GUDHI library.
+ * \section GudhiBibtex GUDHI bibtex
+ * \verbinclude  biblio/how_to_cite_gudhi.bib
 */
+
diff --git a/src/common/include/gudhi/Clock.h b/src/common/include/gudhi/Clock.h
index 08096c05..04c6ffb9 100644
--- a/src/common/include/gudhi/Clock.h
+++ b/src/common/include/gudhi/Clock.h
@@ -1,82 +1,79 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-
-#ifndef GUDHI_CLOCK_H_
-#define GUDHI_CLOCK_H_
-
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef CLOCK_H_
+#define CLOCK_H_
 
 #include <boost/date_time/posix_time/posix_time.hpp>
 
-class Clock{
-
-public:
-	Clock():end_called(false){
-		startTime = boost::posix_time::microsec_clock::local_time( );
-	}
-
-	Clock(const std::string& msg_){
-		end_called = false;
-		begin();
-		msg = msg_;
-	}
-
-
-	void begin() const{
-		end_called = false;
-		startTime = boost::posix_time::microsec_clock::local_time( );
-	}
-
-	void end() const{
-		end_called = true;
-		endTime = boost::posix_time::microsec_clock::local_time( );
-	}
-
-	void print() const{
-		std::cout << *this << std::endl;
-	}
-
-	friend std::ostream& operator<< (std::ostream& stream,const Clock& clock){
-		if(!clock.end_called)
-			clock.end();
-
-		if(!clock.end_called) stream << "end not called";
-		else{
-			stream << clock.msg <<":"<<clock.num_seconds() <<"s";
-		}
-		return stream;
-
-	}
-
-	double num_seconds() const{
-		if(!end_called) return -1;
-		return (endTime-startTime).total_milliseconds()/1000.;
-	}
-
-private:
-	mutable boost::posix_time::ptime startTime, endTime;
-	mutable bool end_called;
-	std::string msg;
-
+#include <string>
+
+class Clock {
+ public:
+  Clock() : end_called(false) {
+    startTime = boost::posix_time::microsec_clock::local_time();
+  }
+
+  Clock(const std::string& msg_) {
+    end_called = false;
+    begin();
+    msg = msg_;
+  }
+
+  void begin() const {
+    end_called = false;
+    startTime = boost::posix_time::microsec_clock::local_time();
+  }
+
+  void end() const {
+    end_called = true;
+    endTime = boost::posix_time::microsec_clock::local_time();
+  }
+
+  void print() const {
+    std::cout << *this << std::endl;
+  }
+
+  friend std::ostream& operator<<(std::ostream& stream, const Clock& clock) {
+    if (!clock.end_called)
+      clock.end();
+
+    if (!clock.end_called) {
+      stream << "end not called";
+    } else {
+      stream << clock.msg << ":" << clock.num_seconds() << "s";
+    }
+    return stream;
+  }
+
+  double num_seconds() const {
+    if (!end_called) return -1;
+    return (endTime - startTime).total_milliseconds() / 1000.;
+  }
+
+ private:
+  mutable boost::posix_time::ptime startTime, endTime;
+  mutable bool end_called;
+  std::string msg;
 };
 
-
-#endif /* GUDHI_CLOCK_H_ */
+#endif  // CLOCK_H_
diff --git a/src/common/include/gudhi/Off_reader.h b/src/common/include/gudhi/Off_reader.h
index e29218d8..81b9e634 100644
--- a/src/common/include/gudhi/Off_reader.h
+++ b/src/common/include/gudhi/Off_reader.h
@@ -1,13 +1,10 @@
-/*
- * Off_reader.h
- *  Created on: Nov 28, 2014
- * This file is part of the Gudhi Library. The Gudhi library
+/*    This file is part of the Gudhi Library. The Gudhi library
  *    (Geometric Understanding in Higher Dimensions) is a generic C++
  *    library for computational topology.
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-M�diterran�e (France)
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
@@ -25,14 +22,15 @@
  */
 
 
-#ifndef GUDHI_OFF_READER_H_
-#define GUDHI_OFF_READER_H_
+#ifndef OFF_READER_H_
+#define OFF_READER_H_
 
 
 #include <sstream>
 #include <iostream>
 #include <iterator>
-
+#include <string>
+#include <vector>
 
 namespace Gudhi {
 
@@ -48,151 +46,144 @@ namespace Gudhi {
  *
  * The number of edges num_edges is optional and can be left to zero.
  */
-class Off_reader{
-public:
-	Off_reader(std::ifstream& stream):stream_(stream){
-	}
-//	Off_reader(const std::string& name):stream_(name){
-//		if(!stream_.is_open())
-//			std::cerr <<"could not open file \n";
-//	}
-
-	~Off_reader(){
-		stream_.close();
-	}
-
-	/**
-	 * read an off file and calls the following methods :
-	 * void init(int dim,int num_vertices,int num_faces,int num_edges); //num_edges may not be set
-	 * void point(const std::vector<double>& point);
-	 * void maximal_face(const std::list<int>& face);
-	 * void done();
-	 * of the visitor when reading a point or a maximal face.
-	 */
-	template<typename OffVisitor>
-	bool read(OffVisitor& off_visitor){
-		bool success_read_off_preambule = read_off_preambule(off_visitor);
-		if(!success_read_off_preambule) {
-			std::cerr <<"could not read off preambule\n";
-			return false;
-		}
-
-		bool success_read_off_points = read_off_points(off_visitor);
-		if(!success_read_off_points) {
-			std::cerr <<"could not read off points\n";
-			return false;
-		}
-
-		bool success_read_off_faces = read_off_faces(off_visitor);
-		if(!success_read_off_faces) {
-			std::cerr <<"could not read off faces\n";
-			return false;
-		}
-
-		off_visitor.done();
-		return success_read_off_preambule && success_read_off_points && success_read_off_faces;
-	}
-
-private:
-	std::ifstream& stream_;
-
-	struct Off_info{
-		int dim;
-		int num_vertices;
-		int num_edges;
-		int num_faces;
-	};
-
-	Off_info off_info_;
-
-	template<typename OffVisitor>
-	bool read_off_preambule(OffVisitor& off_visitor){
-		std::string line;
-		if(!goto_next_uncomment_line(line)) return false;
-
-		bool is_off_file = (line.find("OFF") != std::string::npos);
-		bool is_noff_file = (line.find("nOFF") != std::string::npos);
-
-    	if(!is_off_file && !is_noff_file) {
-    		std::cerr << line<<std::endl;
-    		std::cerr << "missing off header\n";
-    		return false;
-    	}
-
-    	if(!goto_next_uncomment_line(line)) return false;
-    	std::istringstream iss(line);
-   		if(is_off_file){
-	  		off_info_.dim = 3;
-	  		if(!(iss >> off_info_.num_vertices >> off_info_.num_faces >> off_info_.num_edges)){
-	  			std::cerr << "incorrect number of vertices/faces/edges\n";
-	  			return false;
-	  		}
-		}
-		else
-			if(!(iss >> off_info_.dim >> off_info_.num_vertices >> off_info_.num_faces >> off_info_.num_edges)){
-				std::cerr << "incorrect number of vertices/faces/edges\n";
-				return false;
-			}
-   		off_visitor.init(off_info_.dim,off_info_.num_vertices,off_info_.num_faces,off_info_.num_edges);
-
-   		return true;
-	}
-
-	bool goto_next_uncomment_line(std::string& uncomment_line){
-		uncomment_line.clear();
-		do
-			std::getline(stream_, uncomment_line);
-    	while(uncomment_line[0] == '%');// || uncomment_line.empty());
-		return (uncomment_line.size()>0 && uncomment_line[0] != '%');
-	}
-
-
-	template<typename OffVisitor>
-	bool read_off_points(OffVisitor& visitor){
-		int num_vertices_to_read = off_info_.num_vertices;
-		while(num_vertices_to_read--){
-			std::string line;
-			if(!goto_next_uncomment_line(line)) return false;
-			std::vector<double> point;
-			std::istringstream iss(line);
-			point.assign(std::istream_iterator<double>(iss),std::istream_iterator<double>());
-//			if(point.size() != off_info_.dim) return false;
-			visitor.point(point);
-		}
-		return true;
-	}
-
-	template<typename OffVisitor>
-	bool read_off_faces(OffVisitor& visitor){
-		std::string line;
-		while(goto_next_uncomment_line(line)){
-			std::istringstream iss(line);
-			int num_face_vertices;
-			iss >> num_face_vertices;
-			std::vector<int> face;
-			face.assign(std::istream_iterator<int>(iss),std::istream_iterator<int>());
-			if(!face.size() == off_info_.num_vertices) return false;
-			visitor.maximal_face(face);
-		}
-		return true;
-	}
+class Off_reader {
+ public:
+  Off_reader(std::ifstream& stream) : stream_(stream) { }
+  // Off_reader(const std::string& name):stream_(name){
+  //   if(!stream_.is_open())
+  //   std::cerr <<"could not open file \n";
+  // }
+
+  ~Off_reader() {
+    stream_.close();
+  }
+
+  /**
+   * read an off file and calls the following methods :
+   * void init(int dim,int num_vertices,int num_faces,int num_edges); //num_edges may not be set
+   * void point(const std::vector<double>& point);
+   * void maximal_face(const std::list<int>& face);
+   * void done();
+   * of the visitor when reading a point or a maximal face.
+   */
+  template<typename OffVisitor>
+  bool read(OffVisitor& off_visitor) {
+    bool success_read_off_preambule = read_off_preambule(off_visitor);
+    if (!success_read_off_preambule) {
+      std::cerr << "could not read off preambule\n";
+      return false;
+    }
+
+    bool success_read_off_points = read_off_points(off_visitor);
+    if (!success_read_off_points) {
+      std::cerr << "could not read off points\n";
+      return false;
+    }
+
+    bool success_read_off_faces = read_off_faces(off_visitor);
+    if (!success_read_off_faces) {
+      std::cerr << "could not read off faces\n";
+      return false;
+    }
+
+    off_visitor.done();
+    return success_read_off_preambule && success_read_off_points && success_read_off_faces;
+  }
+
+ private:
+  std::ifstream& stream_;
+
+  struct Off_info {
+    int dim;
+    int num_vertices;
+    int num_edges;
+    int num_faces;
+  };
+
+  Off_info off_info_;
+
+  template<typename OffVisitor>
+  bool read_off_preambule(OffVisitor& off_visitor) {
+    std::string line;
+    if (!goto_next_uncomment_line(line)) return false;
+
+    bool is_off_file = (line.find("OFF") != std::string::npos);
+    bool is_noff_file = (line.find("nOFF") != std::string::npos);
+
+    if (!is_off_file && !is_noff_file) {
+      std::cerr << line << std::endl;
+      std::cerr << "missing off header\n";
+      return false;
+    }
+
+    if (!goto_next_uncomment_line(line)) return false;
+    std::istringstream iss(line);
+    if (is_off_file) {
+      off_info_.dim = 3;
+      if (!(iss >> off_info_.num_vertices >> off_info_.num_faces >> off_info_.num_edges)) {
+        std::cerr << "incorrect number of vertices/faces/edges\n";
+        return false;
+      }
+    } else {
+      if (!(iss >> off_info_.dim >> off_info_.num_vertices >> off_info_.num_faces >> off_info_.num_edges)) {
+        std::cerr << "incorrect number of vertices/faces/edges\n";
+        return false;
+      }
+    }
+    off_visitor.init(off_info_.dim, off_info_.num_vertices, off_info_.num_faces, off_info_.num_edges);
+
+    return true;
+  }
+
+  bool goto_next_uncomment_line(std::string& uncomment_line) {
+    uncomment_line.clear();
+    do
+      std::getline(stream_, uncomment_line); while (uncomment_line[0] == '%');  // || uncomment_line.empty());
+    return (uncomment_line.size() > 0 && uncomment_line[0] != '%');
+  }
+
+  template<typename OffVisitor>
+  bool read_off_points(OffVisitor& visitor) {
+    int num_vertices_to_read = off_info_.num_vertices;
+    while (num_vertices_to_read--) {
+      std::string line;
+      if (!goto_next_uncomment_line(line)) return false;
+      std::vector<double> point;
+      std::istringstream iss(line);
+      point.assign(std::istream_iterator<double>(iss), std::istream_iterator<double>());
+      // if(point.size() != off_info_.dim) return false;
+      visitor.point(point);
+    }
+    return true;
+  }
+
+  template<typename OffVisitor>
+  bool read_off_faces(OffVisitor& visitor) {
+    std::string line;
+    while (goto_next_uncomment_line(line)) {
+      std::istringstream iss(line);
+      int num_face_vertices;
+      iss >> num_face_vertices;
+      std::vector<int> face;
+      face.assign(std::istream_iterator<int>(iss), std::istream_iterator<int>());
+      if (face.size() != off_info_.dim) return false;
+      visitor.maximal_face(face);
+    }
+    return true;
+  }
 };
 
-
 template<typename OFFVisitor>
-void read_off(const std::string& name_file_off,OFFVisitor& vis){
-	std::ifstream stream(name_file_off);
-	if(!stream.is_open())
-		std::cerr <<"could not open file \n";
-	else{
-		Off_reader off_reader(stream);
-		off_reader.read(vis);
-	}
+void read_off(const std::string& name_file_off, OFFVisitor& vis) {
+  std::ifstream stream(name_file_off);
+  if (!stream.is_open()) {
+    std::cerr << "could not open file \n";
+  } else {
+    Off_reader off_reader(stream);
+    off_reader.read(vis);
+  }
 }
 
-
-
 }  // namespace Gudhi
 
-
-#endif /* GUDHI_OFF_READER_H_ */
+#endif  // OFF_READER_H_
diff --git a/src/common/include/gudhi/Point.h b/src/common/include/gudhi/Point.h
index 4023445b..0479e71e 100644
--- a/src/common/include/gudhi/Point.h
+++ b/src/common/include/gudhi/Point.h
@@ -1,13 +1,10 @@
-/*
- * Basic_geometry.h
- *  Created on: Feb 10, 2015
- * This file is part of the Gudhi Library. The Gudhi library 
+/*    This file is part of the Gudhi Library. The Gudhi library 
  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
  *    library for computational topology.
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-M�diterran�e (France)
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
@@ -24,9 +21,8 @@
  * 
  */
 
-
-#ifndef BASIC_GEOMETRY_H_
-#define BASIC_GEOMETRY_H_
+#ifndef POINT_H_
+#define POINT_H_
 
 #include <cmath>
 #include <vector>
@@ -34,143 +30,141 @@
 #include <cstddef>
 #include <initializer_list>
 
-class Point_d{
-public:
-	Point_d(size_t dim=3):coords_(dim,0){}
-	Point_d(const Point_d& other):coords_(other.coords_){}
-	Point_d(const std::initializer_list<double>& list):coords_(list) {
-	}
-	template<typename CoordsIt>
-	Point_d(CoordsIt begin,CoordsIt end):coords_(begin,end){}
-
-	size_t dimension() const{
-		return coords_.size();
-	}
-
-	double x() const{
-		return coords_[0];
-	}
-
-	double y() const{
-		return coords_[1];
-	}
-
-	double z() const{
-		return coords_[2];
-	}
-
-	double& x(){
-		return coords_[0];
-	}
-
-	double& y(){
-		return coords_[1];
-	}
-
-	double& z(){
-		return coords_[2];
-	}
-
-	std::vector<double>::const_iterator begin() const{
-		return coords_.begin();
-	}
-
-	std::vector<double>::const_iterator end() const{
-		return coords_.end();
-	}
-
-	double& operator[](unsigned i){
-		return coords_[i];
-	}
-	const double& operator[](unsigned i) const{
-		return coords_[i];
-	}
-
-	double squared_norm() const{
-		double res = 0;
-		for(auto x : coords_)
-			res+= x*x;
-		return res;
-	}
-
-	friend double squared_dist(const Point_d& p1,const Point_d& p2){
-		assert(p1.dimension()==p2.dimension());
-		double res = 0;
-		for(unsigned i = 0; i < p1.coords_.size(); ++i)
-			res+= (p1[i]-p2[i])*(p1[i]-p2[i]);
-		return res;
-	}
-
-	/**
-	 * dot product
-	 */
-	double operator*(const Point_d& other) const{
-		assert(dimension()==other.dimension());
-		double res = 0;
-		for(unsigned i = 0; i < coords_.size(); ++i)
-			res+= coords_[i]*other[i];
-		return res;
-	}
-
-	/**
-	 * only if points have dimension 3
-	 */
-	Point_d cross_product(const Point_d& other){
-		assert(dimension()==3 && other.dimension()==3);
-		Point_d res(3);
-		res[0] = (*this)[1] * other[2] - (*this)[2] * other[1];
-		res[1] = (*this)[2] * other[0] - (*this)[0] * other[2];
-		res[2] = (*this)[0] * other[1] - (*this)[1] * other[0];
-		return res;
-	}
-
-	Point_d operator+(const Point_d& other) const{
-		assert(dimension()==other.dimension());
-		Point_d res(dimension());
-		for(unsigned i = 0; i < coords_.size(); ++i)
-			res[i] = (*this)[i] + other[i];
-		return res;
-	}
-
-	Point_d operator*(double lambda) const{
-		Point_d res(dimension());
-		for(unsigned i = 0; i < coords_.size(); ++i)
-			res[i] = (*this)[i] * lambda;
-		return res;
-	}
-
-	Point_d operator/(double lambda) const{
-		Point_d res(dimension());
-		for(unsigned i = 0; i < coords_.size(); ++i)
-			res[i] = (*this)[i] / lambda;
-		return res;
-	}
-
-	Point_d operator-(const Point_d& other) const{
-		assert(dimension()==other.dimension());
-		Point_d res(dimension());
-		for(unsigned i = 0; i < coords_.size(); ++i)
-			res[i] = (*this)[i] - other[i];
-		return res;
-	}
-
-	friend Point_d unit_normal(const Point_d& p1,const Point_d& p2,const Point_d& p3){
-		assert(p1.dimension()==3);
-		assert(p2.dimension()==3);
-		assert(p3.dimension()==3);
-		Point_d p1p2 = p2 - p1;
-		Point_d p1p3 = p3 - p1;
-		Point_d res(p1p2.cross_product(p1p3));
-		return res / std::sqrt(res.squared_norm());
-	}
-
-
-private:
-	std::vector<double> coords_;
+class Point_d {
+ public:
+  Point_d(size_t dim = 3) : coords_(dim, 0) { }
+
+  Point_d(const Point_d& other) : coords_(other.coords_) { }
+
+  Point_d(const std::initializer_list<double>& list) : coords_(list) { }
+
+  template<typename CoordsIt>
+  Point_d(CoordsIt begin, CoordsIt end) : coords_(begin, end) { }
+
+  size_t dimension() const {
+    return coords_.size();
+  }
+
+  double x() const {
+    return coords_[0];
+  }
+
+  double y() const {
+    return coords_[1];
+  }
+
+  double z() const {
+    return coords_[2];
+  }
+
+  double& x() {
+    return coords_[0];
+  }
+
+  double& y() {
+    return coords_[1];
+  }
+
+  double& z() {
+    return coords_[2];
+  }
+
+  std::vector<double>::const_iterator begin() const {
+    return coords_.begin();
+  }
+
+  std::vector<double>::const_iterator end() const {
+    return coords_.end();
+  }
+
+  double& operator[](unsigned i) {
+    return coords_[i];
+  }
+
+  const double& operator[](unsigned i) const {
+    return coords_[i];
+  }
+
+  double squared_norm() const {
+    double res = 0;
+    for (auto x : coords_)
+      res += x * x;
+    return res;
+  }
+
+  friend double squared_dist(const Point_d& p1, const Point_d& p2) {
+    assert(p1.dimension() == p2.dimension());
+    double res = 0;
+    for (unsigned i = 0; i < p1.coords_.size(); ++i)
+      res += (p1[i] - p2[i])*(p1[i] - p2[i]);
+    return res;
+  }
+
+  /**
+   * dot product
+   */
+  double operator*(const Point_d& other) const {
+    assert(dimension() == other.dimension());
+    double res = 0;
+    for (unsigned i = 0; i < coords_.size(); ++i)
+      res += coords_[i] * other[i];
+    return res;
+  }
+
+  /**
+   * only if points have dimension 3
+   */
+  Point_d cross_product(const Point_d& other) {
+    assert(dimension() == 3 && other.dimension() == 3);
+    Point_d res(3);
+    res[0] = (*this)[1] * other[2] - (*this)[2] * other[1];
+    res[1] = (*this)[2] * other[0] - (*this)[0] * other[2];
+    res[2] = (*this)[0] * other[1] - (*this)[1] * other[0];
+    return res;
+  }
+
+  Point_d operator+(const Point_d& other) const {
+    assert(dimension() == other.dimension());
+    Point_d res(dimension());
+    for (unsigned i = 0; i < coords_.size(); ++i)
+      res[i] = (*this)[i] + other[i];
+    return res;
+  }
+
+  Point_d operator*(double lambda) const {
+    Point_d res(dimension());
+    for (unsigned i = 0; i < coords_.size(); ++i)
+      res[i] = (*this)[i] * lambda;
+    return res;
+  }
+
+  Point_d operator/(double lambda) const {
+    Point_d res(dimension());
+    for (unsigned i = 0; i < coords_.size(); ++i)
+      res[i] = (*this)[i] / lambda;
+    return res;
+  }
+
+  Point_d operator-(const Point_d& other) const {
+    assert(dimension() == other.dimension());
+    Point_d res(dimension());
+    for (unsigned i = 0; i < coords_.size(); ++i)
+      res[i] = (*this)[i] - other[i];
+    return res;
+  }
+
+  friend Point_d unit_normal(const Point_d& p1, const Point_d& p2, const Point_d& p3) {
+    assert(p1.dimension() == 3);
+    assert(p2.dimension() == 3);
+    assert(p3.dimension() == 3);
+    Point_d p1p2 = p2 - p1;
+    Point_d p1p3 = p3 - p1;
+    Point_d res(p1p2.cross_product(p1p3));
+    return res / std::sqrt(res.squared_norm());
+  }
+
+ private:
+  std::vector<double> coords_;
 };
 
-
-
-
-
-#endif /* BASIC_GEOMETRY_H_ */
+#endif  // POINT_H_
diff --git a/src/common/include/gudhi/Simple_object_pool.h b/src/common/include/gudhi/Simple_object_pool.h
new file mode 100644
index 00000000..fb9c8e23
--- /dev/null
+++ b/src/common/include/gudhi/Simple_object_pool.h
@@ -0,0 +1,81 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Marc Glisse
+ *
+ *    Copyright (C) 2015  INRIA Saclay - Ile de France
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef SIMPLE_OBJECT_POOL_H_
+#define SIMPLE_OBJECT_POOL_H_
+
+#include <boost/pool/pool.hpp>
+#include <utility>
+
+namespace Gudhi {
+
+/** \private
+ * This is a simpler version of boost::object_pool, that requires
+ * that users explicitly destroy all objects. This lets the
+ * performance scale much better, see
+ * https://svn.boost.org/trac/boost/ticket/3789 .
+ */
+template <class T>
+class Simple_object_pool : protected boost::pool<boost::default_user_allocator_malloc_free> {
+ protected:
+  typedef boost::pool<boost::default_user_allocator_malloc_free> Base;
+  typedef T* pointer;
+
+  Base& base() {
+    return *this;
+  }
+
+  Base const& base()const {
+    return *this;
+  }
+
+ public:
+  typedef T element_type;
+  typedef boost::default_user_allocator_malloc_free user_allocator;
+  typedef typename Base::size_type size_type;
+  typedef typename Base::difference_type difference_type;
+
+  template<class...U>
+  Simple_object_pool(U&&...u) : Base(sizeof (T), std::forward<U>(u)...) { }
+
+  template<class...U>
+  pointer construct(U&&...u) {
+    void* p = base().malloc BOOST_PREVENT_MACRO_SUBSTITUTION();
+    assert(p);
+    try {
+      new(p) T(std::forward<U>(u)...);
+    }    catch (...) {
+      base().free BOOST_PREVENT_MACRO_SUBSTITUTION(p);
+      throw;
+    }
+    return static_cast<pointer> (p);
+  }
+
+  void destroy(pointer p) {
+    p->~T();
+    base().free BOOST_PREVENT_MACRO_SUBSTITUTION(p);
+  }
+};
+
+}  // namespace Gudhi
+
+#endif  // SIMPLE_OBJECT_POOL_H_
diff --git a/src/common/include/gudhi/Test.h b/src/common/include/gudhi/Test.h
index 18b7ca82..6024c822 100644
--- a/src/common/include/gudhi/Test.h
+++ b/src/common/include/gudhi/Test.h
@@ -1,5 +1,28 @@
-#ifndef __TEST_H
-#define __TEST_H
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ * 
+ */
+
+#ifndef TEST_H_
+#define TEST_H_
 
 #include <list>
 #include <string>
@@ -8,78 +31,75 @@
 #include <iostream>
 
 
-#define TEST(a) std::cout << "TEST: " << (a)<<std::endl
-#define TESTMSG(a,b) std::cout << "TEST: " << a<<b<<std::endl
-#define TESTVALUE(a) std::cout << "TEST: " <<  #a << ": " << a<<std::endl
-
+#define TEST(a) std::cout << "TEST: " << (a) << std::endl
+#define TESTMSG(a, b) std::cout << "TEST: " << a << b << std::endl
+#define TESTVALUE(a) std::cout << "TEST: " <<  #a << ": " << a << std::endl
 
 /**
  * Class to perform test
  */
 
-class Test
-{
-private :
-	std::string name;
-	bool (*test)();
-
-	std::string separation() const{
-		return "+++++++++++++++++++++++++++++++++++++++++++++++++\n";
-	}
-
-	std::string print_between_plus(std::string& s) const{
-		std::stringstream res;
-		res << "+++++++++++++++++"<<s<<"+++++++++++++++++\n";
-		return res.str();
-	}
-
-
-public:
-	Test(std::string name_,bool (*test_)()){
-		name=name_;
-		test =test_;
-	}
-
-	bool run(){
-		std::cout << print_between_plus(name);
-		return test();
-	}
-	std::string getName(){
-		return name;
-	}
+class Test {
+ private:
+  std::string name;
+  bool (*test)();
+
+  std::string separation() const {
+    return "+++++++++++++++++++++++++++++++++++++++++++++++++\n";
+  }
+
+  std::string print_between_plus(std::string& s) const {
+    std::stringstream res;
+    res << "+++++++++++++++++" << s << "+++++++++++++++++\n";
+    return res.str();
+  }
+
+ public:
+  Test(std::string name_, bool (*test_)()) {
+    name = name_;
+    test = test_;
+  }
+
+  bool run() {
+    std::cout << print_between_plus(name);
+    return test();
+  }
+
+  std::string getName() {
+    return name;
+  }
 };
 
-
-class Tests
-{
-private:
-	std::list<Test> tests;
-
-public:
-	void add(std::string name_,bool (*test_)()){
-		Test test(name_,test_);
-		tests.push_back(test);
-	}
-	bool run(){
-		bool tests_succesful(true);
-		std::vector<bool> res;
-		for (Test test : tests){
-			res.push_back(test.run());
-		}
-		std::cout << "\n\n results of tests : "<<std::endl;
-		int i=0;
-		for (Test t : tests){
-			std::cout << "Test "<<i<< " \""<<t.getName()<<"\"  -->  ";
-			if (res[i++]) std::cout << "OK"<<std::endl;
-			else {
-				std::cout << "Fail"<<std::endl;
-				tests_succesful = false;
-				break;
-			}
-		}
-		return tests_succesful;
-
-	}
+class Tests {
+ private:
+  std::list<Test> tests;
+
+ public:
+  void add(std::string name_, bool (*test_)()) {
+    Test test(name_, test_);
+    tests.push_back(test);
+  }
+
+  bool run() {
+    bool tests_succesful(true);
+    std::vector<bool> res;
+    for (Test test : tests) {
+      res.push_back(test.run());
+    }
+    std::cout << "\n\n results of tests : " << std::endl;
+    int i = 0;
+    for (Test t : tests) {
+      std::cout << "Test " << i << " \"" << t.getName() << "\"  -->  ";
+      if (res[i++]) {
+        std::cout << "OK" << std::endl;
+      } else {
+        std::cout << "Fail" << std::endl;
+        tests_succesful = false;
+        break;
+      }
+    }
+    return tests_succesful;
+  }
 };
 
-#endif
+#endif  // TEST_H_
diff --git a/src/common/include/gudhi/Utils.h b/src/common/include/gudhi/Utils.h
index 7678685c..43916f11 100644
--- a/src/common/include/gudhi/Utils.h
+++ b/src/common/include/gudhi/Utils.h
@@ -1,48 +1,46 @@
- /*    This file is part of the Gudhi Library. The Gudhi library
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-#ifndef GUDHI_UTILS_H_
-#define GUDHI_UTILS_H_
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+#ifndef UTILS_H_
+#define UTILS_H_
 
 
-#define PRINT(a) std::cerr << #a << ": " << (a) << " (DISP)"<<std::endl
+#define PRINT(a) std::cerr << #a << ": " << (a) << " (DISP)" << std::endl
 
-//#define DBG_VERBOSE
+// #define DBG_VERBOSE
 #ifdef DBG_VERBOSE
-#define DBG(a) std::cerr << "DBG: " << (a)<<std::endl
-#define DBGMSG(a,b) std::cerr << "DBG: " << a<<b<<std::endl
-#define DBGVALUE(a) std::cerr << "DBG: " <<  #a << ": " << a<<std::endl
-#define DBGCONT(a) std::cerr << "DBG: container "<< #a<<" -> "; for(auto x:a) std::cerr<< x << ","; std::cerr<<std::endl
+#define DBG(a) std::cerr << "DBG: " << (a) << std::endl
+#define DBGMSG(a, b) std::cerr << "DBG: " << a << b << std::endl
+#define DBGVALUE(a) std::cerr << "DBG: " <<  #a << ": " << a << std::endl
+#define DBGCONT(a) std::cerr << "DBG: container " << #a << " -> "; for (auto x : a) std::cerr << x << ","; std::cerr <<
+std::endl
 #else
-//#define DBG(a) a
-//#define DBGMSG(a,b) b
-//#define DBGVALUE(a) a
-//#define DBGCONT(a) a
+// #define DBG(a) a
+// #define DBGMSG(a,b) b
+// #define DBGVALUE(a) a
+// #define DBGCONT(a) a
 #define DBG(a)
-#define DBGMSG(a,b)
+#define DBGMSG(a, b)
 #define DBGVALUE(a)
 #define DBGCONT(a)
 #endif
 
-
-
-
-#endif /* UTILS_H_ */
+#endif  // UTILS_H_
diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h
index 7a2ab035..e5c79ded 100644
--- a/src/common/include/gudhi/distance_functions.h
+++ b/src/common/include/gudhi/distance_functions.h
@@ -1,37 +1,41 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       Clément Maria
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       Clément Maria
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef DISTANCE_FUNCTIONS_H_
+#define DISTANCE_FUNCTIONS_H_
 
 /* Compute the Euclidean distance between two Points given
  * by a range of coordinates. The points are assumed to have 
  * the same dimension. */
 template< typename Point >
-double euclidean_distance( Point &p1, Point &p2)
-{
+double euclidean_distance(Point &p1, Point &p2) {
   double dist = 0.;
-  auto it1 = p1.begin(); auto it2 = p2.begin();
-  for(; it1 != p1.end(); ++it1, ++it2) 
-    { 
-      double tmp = *it1 - *it2;
-      dist += tmp*tmp; 
-    }
-    return sqrt(dist);
+  auto it1 = p1.begin();
+  auto it2 = p2.begin();
+  for (; it1 != p1.end(); ++it1, ++it2) {
+    double tmp = *it1 - *it2;
+    dist += tmp*tmp;
+  }
+  return sqrt(dist);
 }
+
+#endif  // DISTANCE_FUNCTIONS_H_
diff --git a/src/common/include/gudhi/graph_simplicial_complex.h b/src/common/include/gudhi/graph_simplicial_complex.h
index 1ad9dabd..042ef516 100644
--- a/src/common/include/gudhi/graph_simplicial_complex.h
+++ b/src/common/include/gudhi/graph_simplicial_complex.h
@@ -1,96 +1,99 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       Clément Maria
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       Clément Maria
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
 
-#ifndef GUDHI_GRAPH_SIMPLICIAL_COMPLEX_FILTRATION_TAG_H
-#define GUDHI_GRAPH_SIMPLICIAL_COMPLEX_FILTRATION_TAG_H
+#ifndef GRAPH_SIMPLICIAL_COMPLEX_H_
+#define GRAPH_SIMPLICIAL_COMPLEX_H_
 
 #include <boost/graph/adjacency_list.hpp>
 
+#include <utility>  // for pair<>
+#include <vector>
+#include <map>
+
 /* Edge tag for Boost PropertyGraph. */
 struct edge_filtration_t {
   typedef boost::edge_property_tag kind;
 };
+
 /* Vertex tag for Boost PropertyGraph. */
 struct vertex_filtration_t {
   typedef boost::vertex_property_tag kind;
 };
 
-typedef int                                       Vertex_handle;
-typedef double                                    Filtration_value;
+typedef int Vertex_handle;
+typedef double Filtration_value;
 typedef boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS
-                              , boost::property < vertex_filtration_t, Filtration_value >
-                              , boost::property < edge_filtration_t, Filtration_value > 
-                              >                   Graph_t;
+, boost::property < vertex_filtration_t, Filtration_value >
+, boost::property < edge_filtration_t, Filtration_value >
+> Graph_t;
 typedef std::pair< Vertex_handle, Vertex_handle > Edge_t;
 
 /** \brief Output the proximity graph of the points.
-  *
-  * If points contains n elements, the proximity graph is the graph 
-  * with n vertices, and an edge [u,v] iff the distance function between 
-  * points u and v is smaller than threshold.
-  *
-  * The type PointCloud furnishes .begin() and .end() methods, that return
-  * iterators with value_type Point.
-  */
+ *
+ * If points contains n elements, the proximity graph is the graph 
+ * with n vertices, and an edge [u,v] iff the distance function between 
+ * points u and v is smaller than threshold.
+ *
+ * The type PointCloud furnishes .begin() and .end() methods, that return
+ * iterators with value_type Point.
+ */
 template< typename PointCloud
-        , typename Point >
-Graph_t compute_proximity_graph( PointCloud &points
-                               , Filtration_value threshold 
-                               , Filtration_value distance(Point p1, Point p2) )
-{
-  std::vector< Edge_t >                       edges;
-  std::vector< Filtration_value >             edges_fil;
+, typename Point >
+Graph_t compute_proximity_graph(PointCloud &points
+                                , Filtration_value threshold
+                                , Filtration_value distance(Point p1, Point p2)) {
+  std::vector< Edge_t > edges;
+  std::vector< Filtration_value > edges_fil;
   std::map< Vertex_handle, Filtration_value > vertices;
 
   Vertex_handle idx_u, idx_v;
   Filtration_value fil;
   idx_u = 0;
-  for(auto it_u = points.begin(); it_u != points.end(); ++it_u) 
-  {
-    idx_v = idx_u+1;
-    for(auto it_v = it_u+1; it_v != points.end(); ++it_v, ++idx_v)
-    {
-      fil = distance(*it_u,*it_v);
-      if(fil <= threshold) {
-        edges.emplace_back(idx_u,idx_v);
+  for (auto it_u = points.begin(); it_u != points.end(); ++it_u) {
+    idx_v = idx_u + 1;
+    for (auto it_v = it_u + 1; it_v != points.end(); ++it_v, ++idx_v) {
+      fil = distance(*it_u, *it_v);
+      if (fil <= threshold) {
+        edges.emplace_back(idx_u, idx_v);
         edges_fil.push_back(fil);
       }
     }
     ++idx_u;
   }
 
-  Graph_t skel_graph( edges.begin()
-                    , edges.end()
-                    , edges_fil.begin()
-                    , idx_u); //number of points labeled from 0 to idx_u-1
+  Graph_t skel_graph(edges.begin()
+                     , edges.end()
+                     , edges_fil.begin()
+                     , idx_u);  // number of points labeled from 0 to idx_u-1
 
-  auto vertex_prop = boost::get(vertex_filtration_t(),skel_graph);
+  auto vertex_prop = boost::get(vertex_filtration_t(), skel_graph);
 
   boost::graph_traits<Graph_t>::vertex_iterator vi, vi_end;
-  for ( std::tie(vi, vi_end) = boost::vertices(skel_graph); 
-        vi != vi_end; ++vi )
-  { boost::put(vertex_prop, *vi, 0.); }
- 
+  for (std::tie(vi, vi_end) = boost::vertices(skel_graph);
+       vi != vi_end; ++vi) {
+    boost::put(vertex_prop, *vi, 0.);
+  }
+
   return skel_graph;
 }
 
-#endif // GUDHI_GRAPH_SIMPLICIAL_COMPLEX_FILTRATION_TAG_H
+#endif  // GRAPH_SIMPLICIAL_COMPLEX_H_
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index ab12c268..e05714c7 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -1,32 +1,38 @@
- /*    This file is part of the Gudhi Library. The Gudhi library 
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
-  *    library for computational topology.
-  *
-  *    Author(s):       Clément Maria
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-
-#ifndef GUDHI_READER_UTILS_H
-#define GUDHI_READER_UTILS_H
+/*    This file is part of the Gudhi Library. The Gudhi library 
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ *    library for computational topology.
+ *
+ *    Author(s):       Clément Maria
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Méditerranée (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef READER_UTILS_H_
+#define READER_UTILS_H_
+
+#include <gudhi/graph_simplicial_complex.h>
+
+#include <boost/graph/adjacency_list.hpp>
 
 #include <iostream>
 #include <fstream>
-#include <boost/graph/adjacency_list.hpp>
-#include "gudhi/graph_simplicial_complex.h"
+#include <map>
+#include <limits>  // for numeric_limits<>
+#include <string>
+#include <vector>
 
 /**
  * \brief Read a set of points to turn it
@@ -37,22 +43,21 @@
  * X21 X22 ... X2d
  * etc
  */
-inline void
-read_points ( std::string file_name
-            , std::vector< std::vector< double > > & points)
-{  
-  std::ifstream in_file (file_name.c_str(),std::ios::in);
-  if(!in_file.is_open()) {
+inline void read_points(std::string file_name, std::vector< std::vector< double > > & points) {
+  std::ifstream in_file(file_name.c_str(), std::ios::in);
+  if (!in_file.is_open()) {
     std::cerr << "Unable to open file " << file_name << std::endl;
-    return;}
+    return;
+  }
 
   std::string line;
   double x;
-  while( getline ( in_file , line ) )
-  {
+  while (getline(in_file, line)) {
     std::vector< double > point;
-    std::istringstream iss( line );
-    while(iss >> x) { point.push_back(x); }
+    std::istringstream iss(line);
+    while (iss >> x) {
+      point.push_back(x);
+    }
     points.push_back(point);
   }
   in_file.close();
@@ -70,53 +75,64 @@ read_points ( std::string file_name
  * Every simplex must appear exactly once.
  * Simplices of dimension more than 1 are ignored.
  */
-inline Graph_t
-read_graph ( std::string file_name )
-{
-  std::ifstream in_ (file_name.c_str(),std::ios::in);
-  if(!in_.is_open()) { std::cerr << "Unable to open file " << file_name << std::endl; }
-
-  std::vector< Edge_t >                       edges;
-  std::vector< Filtration_value >             edges_fil;
+inline Graph_t read_graph(std::string file_name) {
+  std::ifstream in_(file_name.c_str(), std::ios::in);
+  if (!in_.is_open()) {
+    std::cerr << "Unable to open file " << file_name << std::endl;
+  }
+
+  std::vector< Edge_t > edges;
+  std::vector< Filtration_value > edges_fil;
   std::map< Vertex_handle, Filtration_value > vertices;
-  
-  std::string      line;
-  int              dim;
-  Vertex_handle    u,v,max_h = -1;
+
+  std::string line;
+  int dim;
+  Vertex_handle u, v, max_h = -1;
   Filtration_value fil;
-  while( getline ( in_ , line ) )
-  {
-    std::istringstream iss( line );
-    while(iss >> dim) {
-      switch ( dim ) {
-        case 0 : {
-          iss >> u; iss >> fil; 
+  while (getline(in_, line)) {
+    std::istringstream iss(line);
+    while (iss >> dim) {
+      switch (dim) {
+        case 0:
+        {
+          iss >> u;
+          iss >> fil;
           vertices[u] = fil;
-          if(max_h < u) { max_h = u; }
+          if (max_h < u) {
+            max_h = u;
+          }
           break;
         }
-        case 1 : {
-          iss >> u; iss >> v; iss >> fil;
-          edges.push_back(Edge_t(u,v));
+        case 1:
+        {
+          iss >> u;
+          iss >> v;
+          iss >> fil;
+          edges.push_back(Edge_t(u, v));
           edges_fil.push_back(fil);
           break;
         }
-        default: {break;} 
-      } 
+        default:
+        {
+          break;
+        }
+      }
     }
   }
   in_.close();
 
-  if((size_t)(max_h+1) != vertices.size())
-    { std::cerr << "Error: vertices must be labeled from 0 to n-1 \n"; }
+  if ((size_t) (max_h + 1) != vertices.size()) {
+    std::cerr << "Error: vertices must be labeled from 0 to n-1 \n";
+  }
 
-  Graph_t skel_graph(edges.begin(),edges.end(),edges_fil.begin(),vertices.size());
-  auto vertex_prop = boost::get(vertex_filtration_t(),skel_graph);
+  Graph_t skel_graph(edges.begin(), edges.end(), edges_fil.begin(), vertices.size());
+  auto vertex_prop = boost::get(vertex_filtration_t(), skel_graph);
 
   boost::graph_traits<Graph_t>::vertex_iterator vi, vi_end;
   auto v_it = vertices.begin();
-  for (std::tie(vi, vi_end) = boost::vertices(skel_graph); vi != vi_end; ++vi,++v_it)
-  { boost::put(vertex_prop, *vi, v_it->second); }
+  for (std::tie(vi, vi_end) = boost::vertices(skel_graph); vi != vi_end; ++vi, ++v_it) {
+    boost::put(vertex_prop, *vi, v_it->second);
+  }
 
   return skel_graph;
 }
@@ -133,17 +149,15 @@ read_graph ( std::string file_name )
  * Every simplex must appear exactly once.
  * Simplices of dimension more than 1 are ignored.
  */
-template< typename Vertex_handle
-        , typename Filtration_value >
-bool read_simplex ( std::istream                 & in_                     
-                  , std::vector< Vertex_handle > & simplex
-                  , Filtration_value             & fil )
-{
-  int dim=0;
-  if(!(in_ >> dim)) return false;
+template< typename Vertex_handle, typename Filtration_value >
+bool read_simplex(std::istream & in_, std::vector< Vertex_handle > & simplex, Filtration_value & fil) {
+  int dim = 0;
+  if (!(in_ >> dim)) return false;
   Vertex_handle v;
-  for(int i=0; i<dim+1; ++i)
-  { in_ >> v; simplex.push_back(v); }
+  for (int i = 0; i < dim + 1; ++i) {
+    in_ >> v;
+    simplex.push_back(v);
+  }
   in_ >> fil;
   in_.ignore((std::numeric_limits<std::streamsize>::max)(), '\n'); // ignore until the carriage return
   return true;
@@ -162,20 +176,21 @@ bool read_simplex ( std::istream                 & in_
  * Dimi ki1 ki2 ... kiDimi Fili means that the ith simplex in the 
  * filtration has dimension Dimi, filtration value fil1 and simplices with 
  * key ki1 ... kiDimi in its boundary.*/
-template< typename Simplex_key
-        , typename Filtration_value >
-bool read_hasse_simplex ( std::istream                 & in_  
-                        , std::vector< Simplex_key >   & boundary
-                        , Filtration_value             & fil )
-{
+template< typename Simplex_key, typename Filtration_value >
+bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundary, Filtration_value & fil) {
   int dim;
-  if(!(in_ >> dim)) return false;
-  if(dim == 0) {in_ >> fil; return true;}
+  if (!(in_ >> dim)) return false;
+  if (dim == 0) {
+    in_ >> fil;
+    return true;
+  }
   Simplex_key key;
-  for(int i=0; i<dim+1; ++i) 
-  { in_ >> key; boundary.push_back(key); }
+  for (int i = 0; i < dim + 1; ++i) {
+    in_ >> key;
+    boundary.push_back(key);
+  }
   in_ >> fil;
   return true;
 }
 
-#endif // GUDHI_READER_UTILS_H
+#endif  // READER_UTILS_H_
author	skachano <skachano@636b058d-ea47-450e-bf9e-a15bfbe3eedb>	2015-12-07 14:45:43 +0000
committer	skachano <skachano@636b058d-ea47-450e-bf9e-a15bfbe3eedb>	2015-12-07 14:45:43 +0000
commit	c4078affdbf6fac7150c10ade96fcb72270ac013 (patch)
tree	1ad197bb90078a56036a49c6ee3766a032f85e63
parent	f70e386fc98f1dbd8287d1cb7cc715710a8f751b (diff)
parent	061e43a2a48525bc5a69482a1ea80f20ff505e55 (diff)