Merge last trunk modification

Fix doc issue
Still doc issue


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1739 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0a99345f06e93a3525691699a6fe1505979e8e8e

3 files changed, 49 insertions, 46 deletions

diff --git a/src/Alpha_complex/example/Alpha_complex_from_off.cpp b/src/Alpha_complex/example/Alpha_complex_from_off.cpp
index 4f381d9f..d411e90a 100644
--- a/src/Alpha_complex/example/Alpha_complex_from_off.cpp
+++ b/src/Alpha_complex/example/Alpha_complex_from_off.cpp
@@ -1,4 +1,7 @@
 #include <gudhi/Alpha_complex.h>
+// to construct a simplex_tree from alpha complex
+#include <gudhi/Simplex_tree.h>
+
 #include <CGAL/Epick_d.h>
 
 #include <iostream>
@@ -21,7 +24,7 @@ int main(int argc, char **argv) {
   // Init of an alpha complex from an OFF file
   // ----------------------------------------------------------------------------
   using Kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
-  Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_name, alpha_square_max_value);
+  Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_name);
 
   std::streambuf* streambufffer;
   std::ofstream ouput_file_stream;
@@ -33,23 +36,27 @@ int main(int argc, char **argv) {
     streambufffer = std::cout.rdbuf();
   }
 
-  std::ostream output_stream(streambufffer);
-
-  // ----------------------------------------------------------------------------
-  // Display information about the alpha complex
-  // ----------------------------------------------------------------------------
-  output_stream << "Alpha complex is of dimension " << alpha_complex_from_file.dimension() <<
-      " - " << alpha_complex_from_file.num_simplices() << " simplices - " <<
-      alpha_complex_from_file.num_vertices() << " vertices." << std::endl;
-
-  output_stream << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl;
-  for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) {
-    output_stream << "   ( ";
-    for (auto vertex : alpha_complex_from_file.simplex_vertex_range(f_simplex)) {
-      output_stream << vertex << " ";
+  Gudhi::Simplex_tree<> simplex;
+  if (alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) {
+    std::ostream output_stream(streambufffer);
+
+    // ----------------------------------------------------------------------------
+    // Display information about the alpha complex
+    // ----------------------------------------------------------------------------
+    output_stream << "Alpha complex is of dimension " << simplex.dimension() <<
+        " - " << simplex.num_simplices() << " simplices - " <<
+        simplex.num_vertices() << " vertices." << std::endl;
+
+    output_stream << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" <<
+        std::endl;
+    for (auto f_simplex : simplex.filtration_simplex_range()) {
+      output_stream << "   ( ";
+      for (auto vertex : simplex.simplex_vertex_range(f_simplex)) {
+        output_stream << vertex << " ";
+      }
+      output_stream << ") -> " << "[" << simplex.filtration(f_simplex) << "] ";
+      output_stream << std::endl;
     }
-    output_stream << ") -> " << "[" << alpha_complex_from_file.filtration(f_simplex) << "] ";
-    output_stream << std::endl;
   }
   ouput_file_stream.close();
   return 0;
diff --git a/src/Alpha_complex/example/Alpha_complex_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_from_points.cpp
index a17f1d6d..c19f7cc8 100644
--- a/src/Alpha_complex/example/Alpha_complex_from_points.cpp
+++ b/src/Alpha_complex/example/Alpha_complex_from_points.cpp
@@ -1,5 +1,8 @@
-#include <CGAL/Epick_d.h>
 #include <gudhi/Alpha_complex.h>
+// to construct a simplex_tree from alpha complex
+#include <gudhi/Simplex_tree.h>
+
+#include <CGAL/Epick_d.h>
 
 #include <iostream>
 #include <string>
@@ -40,23 +43,26 @@ int main(int argc, char **argv) {
   // ----------------------------------------------------------------------------
   // Init of an alpha complex from the list of points
   // ----------------------------------------------------------------------------
-  Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_points(points, alpha_square_max_value);
+  Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_points(points);
 
-  // ----------------------------------------------------------------------------
-  // Display information about the alpha complex
-  // ----------------------------------------------------------------------------
-  std::cout << "Alpha complex is of dimension " << alpha_complex_from_points.dimension() <<
-      " - " << alpha_complex_from_points.num_simplices() << " simplices - " <<
-      alpha_complex_from_points.num_vertices() << " vertices." << std::endl;
-
-  std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl;
-  for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
-    std::cout << "   ( ";
-    for (auto vertex : alpha_complex_from_points.simplex_vertex_range(f_simplex)) {
-      std::cout << vertex << " ";
+  Gudhi::Simplex_tree<> simplex;
+  if (alpha_complex_from_points.create_complex(simplex, alpha_square_max_value)) {
+    // ----------------------------------------------------------------------------
+    // Display information about the alpha complex
+    // ----------------------------------------------------------------------------
+    std::cout << "Alpha complex is of dimension " << simplex.dimension() <<
+        " - " << simplex.num_simplices() << " simplices - " <<
+        simplex.num_vertices() << " vertices." << std::endl;
+
+    std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl;
+    for (auto f_simplex : simplex.filtration_simplex_range()) {
+      std::cout << "   ( ";
+      for (auto vertex : simplex.simplex_vertex_range(f_simplex)) {
+        std::cout << vertex << " ";
+      }
+      std::cout << ") -> " << "[" << simplex.filtration(f_simplex) << "] ";
+      std::cout << std::endl;
     }
-    std::cout << ") -> " << "[" << alpha_complex_from_points.filtration(f_simplex) << "] ";
-    std::cout << std::endl;
   }
   return 0;
 }
diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt
index c0ecf0d1..71a95d61 100644
--- a/src/Alpha_complex/example/CMakeLists.txt
+++ b/src/Alpha_complex/example/CMakeLists.txt
@@ -5,13 +5,7 @@ project(Alpha_complex_examples)
 # cmake -DCGAL_DIR=~/workspace/CGAL-4.7-Ic-41 ../../..
 if(CGAL_FOUND)
   if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-    message(STATUS "CGAL version: ${CGAL_VERSION}.")
-
-    find_package(Eigen3 3.1.0)
     if (EIGEN3_FOUND)
-      message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
-      include( ${EIGEN3_USE_FILE} )
-
       add_executable ( alphapoints Alpha_complex_from_points.cpp )
       target_link_libraries(alphapoints  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY})
       add_executable ( alphaoffreader Alpha_complex_from_off.cpp )
@@ -34,10 +28,6 @@ if(CGAL_FOUND)
         add_test(alphaoffreader_doc_60_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt)
         add_test(alphaoffreader_doc_32_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt)
       endif()
-    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()
+    endif(EIGEN3_FOUND)
+  endif(NOT CGAL_VERSION VERSION_LESS 4.7.0)
+endif(CGAL_FOUND)