Merged latest trunk changes to my_branch and fix

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/TDA_dev_1.1.0@409 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 2463ee9b0f8b69e3edbda4e8189eb61606e0af93

2 files changed, 40 insertions, 38 deletions

diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index 5255988a..31071061 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -1,36 +1,38 @@
 cmake_minimum_required(VERSION 2.6)
 project(GUDHIExPersCohom)
 
-
-add_executable(rips_persistence rips_persistence.cpp)
-target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
-
-add_test(rips_persistence_2 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 2 -m 100)
-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_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 3 -m 100)
-   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)
-      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(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)
+# problem with Visual Studio link on Boost program_options
+if (!MSVC)
+   add_executable(rips_persistence rips_persistence.cpp)
+   target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+   
+   add_test(rips_persistence_2 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 2 -m 100)
+   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_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 3 -m 100)
+      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)
+         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(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)
+      endif()
+   
    endif()
-
 endif()
diff --git a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp b/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp
index a88a9df0..0591a0ca 100644
--- a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp
@@ -45,7 +45,7 @@ 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_3;
 
 // filtration with alpha values needed type definition
 typedef Alpha_shape_3::FT Alpha_value_type;
@@ -56,7 +56,7 @@ typedef CGAL::Dispatch_output_iterator<
                      > > Dispatch;
 typedef Alpha_shape_3::Cell_handle   Cell_handle;
 typedef Alpha_shape_3::Facet         Facet;
-typedef Alpha_shape_3::Edge          Edge;
+typedef Alpha_shape_3::Edge          Edge_3;
 typedef std::list<Alpha_shape_3::Vertex_handle> Vertex_list;
 
 // gudhi type definition
@@ -94,7 +94,7 @@ Vertex_list from (const Facet& fct)
   }
   return the_list;
 }
-Vertex_list from (const Edge& edg)
+Vertex_list from (const Edge_3& edg)
 {
   Vertex_list the_list;
   for (auto i = 0; i < 4; i++)
@@ -151,14 +151,14 @@ int main (int argc, char * const argv[])
 
   // Read points from file
   std::string filegraph   = argv[1];
-  std::list<Point> lp;
+  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
-  Point p;
+  Point_3 p;
   for( ; n>0 ; n--)    {
     is >> p;
     lp.push_back(p);
@@ -212,12 +212,12 @@ int main (int argc, char * const argv[])
         dim_max=2; // Facet is of dim 2
       }
     }
-    else if (const Edge* edge = CGAL::object_cast<Edge>(&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 is of dim 1
+        dim_max=1; // Edge_3 is of dim 1
       }
     }
     else if (const Alpha_shape_3::Vertex_handle* vertex = CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator))