Fix TBB issue in CMake

Add TBB in Doxygen



git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Doxygen_for_GUDHI_1.3.0@1086 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: e3d3251431193d21ebf9344c230d12df624cd905

13 files changed, 163 insertions, 19 deletions

diff --git a/CMakeLists.txt b/CMakeLists.txt
index abb66ec2..9cb8b86b 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -58,6 +58,10 @@ else()
   # Find TBB package for parallel sort - not mandatory, just optional.
   set(TBB_FIND_QUIETLY ON)
   find_package(TBB)
+  if (TBB_FOUND)
+    message("TBB found in ${TBB_LIBRARY_DIRS}")
+    add_definitions(-DGUDHI_USE_TBB)
+  endif()
 
   # Required programs for unitary tests purpose
   FIND_PROGRAM( GCOVR_PATH gcovr )
diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt
index 8f9cfa80..ad86b763 100644
--- a/src/Bitmap_cubical_complex/example/CMakeLists.txt
+++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt
@@ -2,16 +2,25 @@ cmake_minimum_required(VERSION 2.6)
 project(GUDHIBitmap)
 
 add_executable ( Bitmap_cubical_complex Bitmap_cubical_complex.cpp )
-target_link_libraries(Bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})	
+target_link_libraries(Bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(Bitmap_cubical_complex ${TBB_RELEASE_LIBRARY})
+endif()
 add_test(Bitmap_cubical_complex_one_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt)
 add_test(Bitmap_cubical_complex_two_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
 
 add_executable ( Random_bitmap_cubical_complex Random_bitmap_cubical_complex.cpp )
-target_link_libraries(Random_bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})	
+target_link_libraries(Random_bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(Random_bitmap_cubical_complex ${TBB_RELEASE_LIBRARY})
+endif()
 add_test(Random_bitmap_cubical_complex ${CMAKE_CURRENT_BINARY_DIR}/Random_bitmap_cubical_complex 2 100 100)
 
 add_executable ( Bitmap_cubical_complex_periodic_boundary_conditions Bitmap_cubical_complex_periodic_boundary_conditions.cpp )
-target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${Boost_SYSTEM_LIBRARY})	
+target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${Boost_SYSTEM_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${TBB_RELEASE_LIBRARY})
+endif()
 add_test(Bitmap_cubical_complex_periodic_2d_torus ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex_periodic_boundary_conditions ${CMAKE_SOURCE_DIR}/data/bitmap/2d_torus.txt)
 add_test(Bitmap_cubical_complex_periodic_3d_torus ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex_periodic_boundary_conditions ${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt)
 
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
index 54ae47d0..a6ba60d3 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
@@ -546,7 +546,8 @@ void Bitmap_cubical_complex<T>::initialize_simplex_associated_to_key() {
   this->simplex_associated_to_key = std::vector<size_t>(this->data.size());
   std::iota(std::begin(simplex_associated_to_key), std::end(simplex_associated_to_key), 0);
 #ifdef GUDHI_USE_TBB
-  tbb::parallel_sort(simplex_associated_to_key, is_before_in_filtration<T>(this));
+  tbb::parallel_sort(simplex_associated_to_key.begin(), simplex_associated_to_key.end(),
+                     is_before_in_filtration<T>(this));
 #else
   std::sort(simplex_associated_to_key.begin(), simplex_associated_to_key.end(), is_before_in_filtration<T>(this));
 #endif
diff --git a/src/Bitmap_cubical_complex/test/CMakeLists.txt b/src/Bitmap_cubical_complex/test/CMakeLists.txt
index 97c374e6..96a41c62 100644
--- a/src/Bitmap_cubical_complex/test/CMakeLists.txt
+++ b/src/Bitmap_cubical_complex/test/CMakeLists.txt
@@ -16,6 +16,9 @@ endif()
 
 add_executable ( BitmapCCUT Bitmap_test.cpp )
 target_link_libraries(BitmapCCUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(BitmapCCUT ${TBB_RELEASE_LIBRARY})
+endif()
 
 # Unitary tests
 add_test(NAME BitmapCCUT
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 40b7dd58..d4abe96d 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -53,6 +53,10 @@ else()
   # Find TBB package for parallel sort - not mandatory, just optional.
   set(TBB_FIND_QUIETLY ON)
   find_package(TBB)
+  if (TBB_FOUND)
+    message("TBB found in ${TBB_LIBRARY_DIRS}")
+    add_definitions(-DGUDHI_USE_TBB)
+  endif()
 
   # BOOST ISSUE result_of vs C++11
   add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE)
diff --git a/src/Doxyfile b/src/Doxyfile
index f7fba3e6..63e7145c 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile
@@ -780,7 +780,8 @@ RECURSIVE              = YES
 # run.
 
 EXCLUDE                = data/ \
-	GudhUI/
+	                     example/ \
+	                     GudhUI/
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
@@ -813,14 +814,15 @@ EXCLUDE_SYMBOLS        =
 # that contain example code fragments that are included (see the \include
 # command).
 
-EXAMPLE_PATH           = biblio/
+EXAMPLE_PATH           = biblio/ \
+	example/
 
 # 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
 # *.h) to filter out the source-files in the directories. If left blank all
 # files are included.
 
-EXAMPLE_PATTERNS       =
+EXAMPLE_PATTERNS       = 
 
 # If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
 # searched for input files to be used with the \include or \dontinclude commands
diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt
index 1ee43d91..fd7397ea 100644
--- a/src/GudhUI/CMakeLists.txt
+++ b/src/GudhUI/CMakeLists.txt
@@ -57,6 +57,9 @@ if ( CGAL_FOUND AND QT4_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND )
 	
   target_link_libraries( GudhUI ${QT_LIBRARIES} ${QGLVIEWER_LIBRARIES} )
   target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} )	
+if (TBB_FOUND)
+  target_link_libraries( GudhUI ${TBB_RELEASE_LIBRARY})
+endif()
 
 else()
   message(STATUS "NOTICE: GudhUI requires CGAL, the QGLViewer, OpenGL and Qt4, and will not be compiled.")
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index 95506631..9702a5f9 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -7,24 +7,37 @@ add_definitions( -DBOOST_ALL_DYN_LINK )
 
 add_executable(plain_homology plain_homology.cpp)
 target_link_libraries(plain_homology ${Boost_SYSTEM_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(plain_homology ${TBB_RELEASE_LIBRARY})
+endif()
 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})
+if (TBB_FOUND)
+  target_link_libraries(persistence_from_simple_simplex_tree ${TBB_RELEASE_LIBRARY})
+endif()
 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})
-   
+if (TBB_FOUND)
+  target_link_libraries(rips_persistence ${TBB_RELEASE_LIBRARY})
+endif()
 add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 3 -m 100)
    
 add_executable(parallel_rips_persistence parallel_rips_persistence.cpp)
 target_link_libraries(parallel_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
-   
+if (TBB_FOUND)
+  target_link_libraries(parallel_rips_persistence ${TBB_RELEASE_LIBRARY})
+endif()
 add_test(parallel_rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/parallel_rips_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.txt -r 0.3 -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})
+if (TBB_FOUND)
+  target_link_libraries(persistence_from_file ${TBB_RELEASE_LIBRARY})
+endif()
 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)
    
@@ -34,10 +47,16 @@ if(GMPXX_FOUND AND GMP_FOUND)
 
    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})
+   if (TBB_FOUND)
+     target_link_libraries(rips_multifield_persistence ${TBB_RELEASE_LIBRARY})
+   endif()
    add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -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 (TBB_FOUND)
+     target_link_libraries(performance_rips_persistence ${TBB_RELEASE_LIBRARY})
+   endif()
 
    if(CGAL_FOUND)
      if (CMAKE_BUILD_TYPE MATCHES Debug)
@@ -46,6 +65,9 @@ if(GMPXX_FOUND AND GMP_FOUND)
      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})
+     if (TBB_FOUND)
+       target_link_libraries(alpha_shapes_persistence ${TBB_RELEASE_LIBRARY})
+     endif()
      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()
diff --git a/src/Persistent_cohomology/test/CMakeLists.txt b/src/Persistent_cohomology/test/CMakeLists.txt
index d16be5be..459cc000 100644
--- a/src/Persistent_cohomology/test/CMakeLists.txt
+++ b/src/Persistent_cohomology/test/CMakeLists.txt
@@ -12,6 +12,9 @@ endif()
 
 add_executable ( PersistentCohomologyUT persistent_cohomology_unit_test.cpp )
 target_link_libraries(PersistentCohomologyUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(PersistentCohomologyUT ${TBB_RELEASE_LIBRARY})
+endif()
 
 # Unitary tests
 add_test(NAME PersistentCohomologyUT 
@@ -22,7 +25,10 @@ add_test(NAME PersistentCohomologyUT
 
 if(GMPXX_FOUND AND GMP_FOUND)
   add_executable ( PersistentCohomologyMultiFieldUT persistent_cohomology_unit_test_multi_field.cpp )
-  target_link_libraries(PersistentCohomologyMultiFieldUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+target_link_libraries(PersistentCohomologyMultiFieldUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+if (TBB_FOUND)
+  target_link_libraries(PersistentCohomologyMultiFieldUT ${TBB_RELEASE_LIBRARY})
+endif()
 
   # Unitary tests
   add_test(NAME PersistentCohomologyMultiFieldUT
diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt
index 200161a6..89a4e053 100644
--- a/src/Simplex_tree/example/CMakeLists.txt
+++ b/src/Simplex_tree/example/CMakeLists.txt
@@ -2,10 +2,16 @@ cmake_minimum_required(VERSION 2.6)
 project(GUDHISimplexTreeFromFile)
 
 add_executable ( simplex_tree_from_cliques_of_graph simplex_tree_from_cliques_of_graph.cpp )
+if (TBB_FOUND)
+  target_link_libraries(simplex_tree_from_cliques_of_graph ${TBB_RELEASE_LIBRARY})
+endif()
 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 )
+if (TBB_FOUND)
+  target_link_libraries(simple_simplex_tree ${TBB_RELEASE_LIBRARY})
+endif()
 add_test(simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/simple_simplex_tree)
 
 add_executable ( mini_simplex_tree mini_simplex_tree.cpp )
@@ -16,5 +22,8 @@ add_test(mini_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/mini_simplex_tree)
 if(GMP_FOUND AND CGAL_FOUND)
   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} ${Boost_SYSTEM_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(simplex_tree_from_alpha_shapes_3 ${TBB_RELEASE_LIBRARY})
+  endif()
   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()
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index ba09db63..dea475ac 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -797,10 +797,11 @@ class Simplex_tree {
      * possible.
      */
 #ifdef GUDHI_USE_TBB
-    tbb::parallel_sort(filtration_vect_, is_before_in_filtration(this));
+    std::cout << "TBB is ON !!!" << std::endl;
+    tbb::parallel_sort(filtration_vect_.begin(), filtration_vect_.end(), is_before_in_filtration(this));
 #else
-    std::stable_sort(filtration_vect_.begin(), filtration_vect_.end(),
-                     is_before_in_filtration(this));
+    std::cout << "TBB is OFF..." << std::endl;
+    std::stable_sort(filtration_vect_.begin(), filtration_vect_.end(), is_before_in_filtration(this));
 #endif
   }
 
diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt
index 1f2f7d33..609d8669 100644
--- a/src/Simplex_tree/test/CMakeLists.txt
+++ b/src/Simplex_tree/test/CMakeLists.txt
@@ -12,6 +12,9 @@ endif()
 
 add_executable ( SimplexTreeUT simplex_tree_unit_test.cpp )
 target_link_libraries(SimplexTreeUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(SimplexTreeUT ${TBB_RELEASE_LIBRARY})
+endif()
 
 # Do not forget to copy test files in current binary dir
 file(COPY "simplex_tree_for_unit_test.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 6f3d8603..1e088552 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -148,21 +148,72 @@
  * 
  * 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
+ * \li <a href="_persistent_cohomology_2alpha_shapes_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_shapes_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2performance_rips_persistence_8cpp-example.html">
+ * Persistent_cohomology/performance_rips_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html">
+ * Persistent_cohomology/rips_multifield_persistence.cpp</a>
+ * \li <a href="_simplex_tree_2simplex_tree_from_alpha_shapes_3_8cpp-example.html">
+ * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp</a>
  *
  * 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.
  * 
+ * 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
+ * 
  * 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
+ * \li <a href="_persistent_cohomology_2alpha_shapes_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_shapes_persistence.cpp</a>
+ * \li <a href="_simplex_tree_2simplex_tree_from_alpha_shapes_3_8cpp-example.html">
+ * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp</a>
  * 
- * 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
+ * The following example requires CGAL version &ge; 4.6:
+ * \li <a href="_witness_complex_2witness_complex_sphere_8cpp-example.html">
+ * Witness_complex/witness_complex_sphere.cpp</a>
+ * 
+ * \subsection tbb Threading Building Blocks:
+ * <a target="_blank" href="https://www.threadingbuildingblocks.org/">Intel&reg; TBB</a> lets you easily write parallel
+ * C++ programs that take full advantage of multicore performance, that are portable and composable, and that have
+ * future-proof scalability.
+ * 
+ * Having Intel&reg; TBB installed is recommended to parallelize and accelerate some GUDHI computations.
+ * 
+ * The following examples are using Intel&reg; TBB if installed:
+ * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_8cpp-example.html">
+ * Bitmap_cubical_complex/Bitmap_cubical_complex.cpp</a>
+ * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_periodic_boundary_conditions_8cpp-example.html">
+ * Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp</a>
+ * \li <a href="_bitmap_cubical_complex_2_random_bitmap_cubical_complex_8cpp-example.html">
+ * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp</a>
+ * \li <a href="_persistent_cohomology_2alpha_shapes_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_shapes_persistence.cpp</a>
+ * \li <a href="_simplex_tree_2simple_simplex_tree_8cpp-example.html">
+ * Simplex_tree/simple_simplex_tree.cpp</a>
+ * \li <a href="_simplex_tree_2simplex_tree_from_alpha_shapes_3_8cpp-example.html">
+ * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp</a>
+ * \li <a href="_simplex_tree_2simplex_tree_from_cliques_of_graph_8cpp-example.html">
+ * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp</a>
+ * \li <a href="_persistent_cohomology_2alpha_shapes_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_shapes_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2parallel_rips_persistence_8cpp-example.html">
+ * Persistent_cohomology/parallel_rips_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2performance_rips_persistence_8cpp-example.html">
+ * Persistent_cohomology/performance_rips_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2persistence_from_file_8cpp-example.html">
+ * Persistent_cohomology/persistence_from_file.cpp</a>
+ * \li <a href="_persistent_cohomology_2persistence_from_simple_simplex_tree_8cpp-example.html">
+ * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp</a>
+ * \li <a href="_persistent_cohomology_2plain_homology_8cpp-example.html">
+ * Persistent_cohomology/plain_homology.cpp</a>
+ * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html">
+ * Persistent_cohomology/rips_multifield_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2rips_persistence_8cpp-example.html">
+ * Persistent_cohomology/rips_persistence.cpp</a>
  * 
  * \subsection demos Demos and examples
  * To build the demos and libraries, run the following commands in a terminal:
@@ -206,3 +257,29 @@ make \endverbatim
  * \verbinclude  biblio/how_to_cite_gudhi.bib
 */
 
+// List of Gudhi examples - Doxygen needs at least a file tag to analyse comments
+/*! @file Examples
+ * @example Bitmap_cubical_complex/Bitmap_cubical_complex.cpp
+ * @example Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
+ * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp
+ * @example Contraction/Garland_heckbert.cpp
+ * @example Contraction/Rips_contraction.cpp
+ * @example Persistent_cohomology/alpha_shapes_persistence.cpp
+ * @example Persistent_cohomology/parallel_rips_persistence.cpp
+ * @example Persistent_cohomology/performance_rips_persistence.cpp
+ * @example Persistent_cohomology/persistence_from_file.cpp
+ * @example Persistent_cohomology/persistence_from_simple_simplex_tree.cpp
+ * @example Persistent_cohomology/plain_homology.cpp
+ * @example Persistent_cohomology/rips_multifield_persistence.cpp
+ * @example Persistent_cohomology/rips_persistence.cpp
+ * @example Simplex_tree/mini_simplex_tree.cpp
+ * @example Simplex_tree/simple_simplex_tree.cpp
+ * @example Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp
+ * @example Simplex_tree/simplex_tree_from_cliques_of_graph.cpp
+ * @example Skeleton_blocker/Skeleton_blocker_from_simplices.cpp
+ * @example Skeleton_blocker/Skeleton_blocker_iteration.cpp
+ * @example Skeleton_blocker/Skeleton_blocker_link.cpp
+ * @example Witness_complex/witness_complex_from_file.cpp
+ * @example Witness_complex/witness_complex_sphere.cpp
+ */
+