Merge last trunk modifications

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/sparserips-glisse@3335 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 41b78dbadb13e3eca889479c1112814b2b58f679

2 files changed, 16 insertions, 3 deletions

diff --git a/src/Persistent_cohomology/concept/FilteredComplex.h b/src/Persistent_cohomology/concept/FilteredComplex.h
index c19698df..d6b662e9 100644
--- a/src/Persistent_cohomology/concept/FilteredComplex.h
+++ b/src/Persistent_cohomology/concept/FilteredComplex.h
@@ -31,7 +31,7 @@ struct FilteredComplex
   typedef unspecified      Simplex_handle;
 /** \brief Key associated to each simplex. 
   *
-  * Must be a signed integer type. */
+  * Must be an integer type. */
   typedef unspecified      Simplex_key;
 /** \brief Type for the value of the filtration function.
   *
@@ -67,8 +67,8 @@ struct FilteredComplex
   Simplex_key              key      ( Simplex_handle sh );
 /** \brief Returns the simplex that has index idx in the filtration.
  *
- * This is never called on null_key(). */
-  Simplex_handle           simplex  ( Simplex_key idx );
+ * This is only called on valid indices. */
+  Simplex_handle           simplex  ( size_t idx );
 /** \brief Assign a key to a simplex. */
   void                     assign_key(Simplex_handle sh, Simplex_key key);
  
diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
index 4dbe82c7..3113a22c 100644
--- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
+++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
@@ -162,6 +162,19 @@ persistence diagram with a family of field coefficients.
 Rips_complex/rips_distance_matrix_persistence.cpp</a> computes the Rips complex of a distance matrix and
 outputs its persistence diagram.
 
+The file should contain square or lower triangular distance matrix with semicolons as separators.
+The code do not check if it is dealing with a distance matrix. It is the user responsibility to provide a valid input.
+Please refer to data/distance_matrix/lower_triangular_distance_matrix.csv for an example of a file.
+
+\li <a href="_rips_complex_2rips_correlation_matrix_persistence_8cpp-example.html">
+Rips_complex/rips_correlation_matrix_persistence.cpp</a>
+computes the Rips complex of a correlation matrix and outputs its persistence diagram.
+
+Note that no check is performed if the matrix given as the input is a correlation matrix.
+It is the user responsibility to ensure that this is the case. The input is to be given either as a square or a lower
+triangular matrix.
+Please refer to data/correlation_matrix/lower_triangular_correlation_matrix.csv for an example of a file.
+
 \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html">
 Alpha_complex/alpha_complex_3d_persistence.cpp</a> computes the persistent homology with
 \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file.