Merge + fix

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/coface@688 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0c732aea08e3999fb4cd54eedd1be9caf5b4b455

6 files changed, 26 insertions, 23 deletions

diff --git a/src/GudhUI/model/Model.h b/src/GudhUI/model/Model.h
index 87545989..17a7d278 100644
--- a/src/GudhUI/model/Model.h
+++ b/src/GudhUI/model/Model.h
@@ -315,7 +315,8 @@ private:
 	void run_chomp(){
 		save_complex_in_file_for_chomp();
 		std::cout << "Call CHOMP library\n";
-		system("utils/homsimpl chomp.sim");
+		int returnValue = system("utils/homsimpl chomp.sim");
+		std::cout << "CHOMP returns" << returnValue << std::endl;
 	}
 
 	void save_complex_in_file_for_chomp(){
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 2349cdac..2a4c8692 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h
@@ -85,7 +85,7 @@ class Field_Zp {
     return add_id_all;
   }
   /** \brief Returns the multiplicative identity \f$1_{\Bbbk}\f$ of the field.*/
-  const Element& multiplicative_identity(Element P = 0) const {
+  const Element& multiplicative_identity(Element = 0) const {
     return mult_id_all;
   }
   /** Returns the inverse in the field. Modifies P.*/
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index f5add449..0c2c851a 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -329,7 +329,7 @@ class Simplex_tree {
   /** \brief Returns the filtration value of a simplex.
    *
    * Called on the null_simplex, returns INFINITY. */
-  Filtration_value filtration(Simplex_handle sh) {
+  Filtration_value filtration(Simplex_handle sh) const {
     if (sh != null_simplex()) {
       return sh->second.filtration();
     } else {
@@ -337,34 +337,34 @@ class Simplex_tree {
     }  // filtration(); }
   }
   /** \brief Returns an upper bound of the filtration values of the simplices. */
-  Filtration_value filtration() {
+  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() {
+  Simplex_handle null_simplex() const {
     return Dictionary_it(NULL);
   }
   /** \brief Returns a key different for all keys associated to the
    * simplices of the simplicial complex. */
-  Simplex_key null_key() {
+  Simplex_key null_key() const {
     return -1;
   }
   /** \brief Returns a Vertex_handle different from all Vertex_handles associated
    * to the vertices of the simplicial complex. */
-  Vertex_handle null_vertex() {
+  Vertex_handle null_vertex() const {
     return null_vertex_;
   }
   /** \brief Returns the number of vertices in the complex. */
-  size_t num_vertices() {
+  size_t num_vertices() const {
     return root_.members_.size();
   }
   /** \brief Returns the number of simplices in the complex.
    *
    * Does not count the empty simplex. */
-  const unsigned int& num_simplices() const {
+  unsigned int num_simplices() const {
     return num_simplices_;
   }
 
@@ -381,13 +381,13 @@ class Simplex_tree {
     return dim - 1;
   }
   /** \brief Returns an upper bound on the dimension of the simplicial complex. */
-  int dimension() {
+  int dimension() const {
     return dimension_;
   }
 
   /** \brief Returns true iff the node in the simplex tree pointed by
    * sh has children.*/
-  bool has_children(Simplex_handle sh) {
+  bool has_children(Simplex_handle sh) const {
     return (sh->second.children()->parent() == sh->first);
   }
   
@@ -569,7 +569,7 @@ class Simplex_tree {
     threshold_ = fil;
   }
   /** Set a number of simplices for the simplicial complex. */
-  void set_num_simplices(const unsigned int& num_simplices) {
+  void set_num_simplices(unsigned int num_simplices) {
     num_simplices_ = num_simplices;
   }
   /** Set a dimension for the simplicial complex. */
@@ -611,7 +611,7 @@ 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 found.
+	 *\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
@@ -865,10 +865,10 @@ public:
   }
   /** \brief Intersects Dictionary 1 [begin1;end1) with Dictionary 2 [begin2,end2)
    * and assigns the maximal possible Filtration_value to the Nodes. */
-  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) {
+  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) {
     if (begin1 == end1 || begin2 == end2)
       return;  // ----->>
     while (true) {
@@ -895,8 +895,8 @@ public:
     }
   }
   /** Maximum over 3 values.*/
-  Filtration_value maximum(Filtration_value a, Filtration_value b,
-                           Filtration_value c) {
+  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);
   }
diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp
index 92fa17f3..126e32ec 100644
--- a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp
+++ b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp
@@ -64,8 +64,10 @@ int main (int argc, char *argv[]){
 	// or edges, complex.num_vertices() and complex.num_edges() are
 	// more appropriated!
 	unsigned num_vertices = 0;
-	for(auto v : complex.vertex_range())
-		++num_vertices;
+	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();
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
index 049db6d5..289819b5 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
@@ -109,7 +109,7 @@ and point access in addition.
 \subsection Visitor
 
 The class Skeleton_blocker_complex has a visitor that is called when usual operations such as adding an edge or remove a vertex are called.
-You may want to use this visitor to compute statistics or to update another data-structure (for instance this visitor is heavily used in the \ref contr package. 
+You may want to use this visitor to compute statistics or to update another data-structure (for instance this visitor is heavily used in the \ref contr package).
 
 
 
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 86a12d90..dd8d898e 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h
@@ -223,7 +223,7 @@ void Skeleton_blocker_complex<SkeletonBlockerDS>::add_simplex(const Simplex_hand
 
   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;
+      // std::cout << "add edge" << *u_it << " " << *v_it << std::endl;
       add_edge(*u_it, *v_it);
     }
   remove_blocker_include_in_simplex(sigma);