Fix issues

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1795 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c4763818a5845eb884b245eca8c78ed60c1a28ca

3 files changed, 9 insertions, 128 deletions

diff --git a/src/cython/include/Alpha_complex_interface.h b/src/cython/include/Alpha_complex_interface.h
index 07f5b5b4..15384206 100644
--- a/src/cython/include/Alpha_complex_interface.h
+++ b/src/cython/include/Alpha_complex_interface.h
@@ -27,7 +27,6 @@
 #include <gudhi/Alpha_complex.h>
 #include <CGAL/Epick_d.h>
 
-#include "Persistent_cohomology_interface.h"
 #include "Simplex_tree_interface.h"
 
 #include <vector>
@@ -50,111 +49,14 @@ class Alpha_complex_interface {
   typedef typename Simplex_tree<>::Simplex_key Simplex_key;
 
  public:
-  Alpha_complex_interface(std::vector<std::vector<double>>&points)
-  : pcoh_(nullptr) {
+  Alpha_complex_interface(std::vector<std::vector<double>>&points) {
     alpha_complex_ = new Alpha_complex<Dynamic_kernel>(points);
   }
 
-  Alpha_complex_interface(std::string off_file_name, bool from_file = true)
-  : pcoh_(nullptr) {
+  Alpha_complex_interface(std::string off_file_name, bool from_file = true) {
     alpha_complex_ = new Alpha_complex<Dynamic_kernel>(off_file_name);
   }
 
-  bool find_simplex(const Simplex& vh) {
-    return (simplex_tree_.find(vh) != simplex_tree_.null_simplex());
-  }
-
-  bool insert_simplex_and_subfaces(const Simplex& complex, Filtration_value filtration = 0) {
-    Insertion_result result = simplex_tree_.insert_simplex_and_subfaces(complex, filtration);
-    return (result.second);
-  }
-
-  Filtration_value simplex_filtration(const Simplex& complex) {
-    return simplex_tree_.filtration(simplex_tree_.find(complex));
-  }
-
-  void remove_maximal_simplex(const Simplex& complex) {
-    return simplex_tree_.remove_maximal_simplex(simplex_tree_.find(complex));
-  }
-
-  Complex_tree get_filtered_tree() {
-    Complex_tree filtered_tree;
-    for (auto f_simplex : simplex_tree_.filtration_simplex_range()) {
-      Simplex simplex;
-      for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) {
-        simplex.insert(simplex.begin(), vertex);
-      }
-      filtered_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex)));
-    }
-    return filtered_tree;
-
-  }
-
-  Complex_tree get_skeleton_tree(int dimension) {
-    Complex_tree skeleton_tree;
-    for (auto f_simplex : simplex_tree_.skeleton_simplex_range(dimension)) {
-      Simplex simplex;
-      for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) {
-        simplex.insert(simplex.begin(), vertex);
-      }
-      skeleton_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex)));
-    }
-    return skeleton_tree;
-  }
-
-  Complex_tree get_star_tree(const Simplex& complex) {
-    Complex_tree star_tree;
-    for (auto f_simplex : simplex_tree_.star_simplex_range(simplex_tree_.find(complex))) {
-      Simplex simplex;
-      for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) {
-        simplex.insert(simplex.begin(), vertex);
-      }
-      star_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex)));
-    }
-    return star_tree;
-  }
-
-  Complex_tree get_coface_tree(const Simplex& complex, int dimension) {
-    Complex_tree coface_tree;
-    for (auto f_simplex : simplex_tree_.cofaces_simplex_range(simplex_tree_.find(complex), dimension)) {
-      Simplex simplex;
-      for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) {
-        simplex.insert(simplex.begin(), vertex);
-      }
-      coface_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex)));
-    }
-    return coface_tree;
-  }
-
-  // Specific to Witness complex because no inheritance
-  Filtration_value filtration() const {
-    return simplex_tree_.filtration();
-  }
-
-  void set_filtration(Filtration_value fil) {
-    simplex_tree_.set_filtration(fil);
-  }
-
-  void initialize_filtration() {
-    simplex_tree_.initialize_filtration();
-  }
-
-  size_t num_vertices() const {
-    return simplex_tree_.num_vertices();
-  }
-
-  size_t num_simplices() {
-    return simplex_tree_.num_simplices();
-  }
-
-  int dimension() const {
-    return simplex_tree_.dimension();
-  }
-
-  void set_dimension(int dimension) {
-    simplex_tree_.set_dimension(dimension);
-  }
-
   std::vector<double> get_point(int vh) {
     std::vector<double> vd;
     try {
@@ -167,38 +69,12 @@ class Alpha_complex_interface {
     return vd;
   }
 
-  std::vector<std::pair<int, std::pair<double, double>>> get_persistence(int homology_coeff_field, double min_persistence) {
-    if (pcoh_ != nullptr) {
-      delete pcoh_;
-    }
-    pcoh_ = new Persistent_cohomology_interface<Simplex_tree<>>(&simplex_tree_);
-    return pcoh_->get_persistence(homology_coeff_field, min_persistence);
-  }
-  
-  std::vector<int> get_betti_numbers() const {
-    if (pcoh_ != nullptr) {
-      return pcoh_->betti_numbers();
-    }
-    std::vector<int> betti_numbers;
-    return betti_numbers;
-  }
-
-  std::vector<int> get_persistent_betti_numbers(Filtration_value from, Filtration_value to) const {
-    if (pcoh_ != nullptr) {
-      return pcoh_->persistent_betti_numbers(from, to);
-    }
-    std::vector<int> persistent_betti_numbers;
-    return persistent_betti_numbers;
-  }
-  
   void create_simplex_tree(Simplex_tree_interface<>& simplex_tree, double max_alpha_square) {
     alpha_complex_->create_complex(simplex_tree, max_alpha_square);
     simplex_tree.initialize_filtration();
   }
 
  private:
-  Simplex_tree<> simplex_tree_;
-  Persistent_cohomology_interface<Simplex_tree<>>* pcoh_;
   Alpha_complex<Dynamic_kernel>* alpha_complex_;
 };
 
diff --git a/src/cython/include/Simplex_tree_interface.h b/src/cython/include/Simplex_tree_interface.h
index 06ec6d40..8e9dd966 100644
--- a/src/cython/include/Simplex_tree_interface.h
+++ b/src/cython/include/Simplex_tree_interface.h
@@ -28,6 +28,8 @@
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Points_off_io.h>
 
+#include "Persistent_cohomology_interface.h"
+
 #include <vector>
 #include <utility>  // std::pair
 #include <iostream>
@@ -69,10 +71,8 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
     for (auto f_simplex : Simplex_tree<SimplexTreeOptions>::filtration_simplex_range()) {
       Simplex simplex;
       for (auto vertex : Simplex_tree<SimplexTreeOptions>::simplex_vertex_range(f_simplex)) {
-        std::cout << " " << vertex;
         simplex.insert(simplex.begin(), vertex);
       }
-      std::cout << std::endl;
       filtered_tree.push_back(std::make_pair(simplex, Simplex_tree<SimplexTreeOptions>::filtration(f_simplex)));
     }
     return filtered_tree;
@@ -137,6 +137,10 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
     }
   }
 
+  void create_persistence(Gudhi::Persistent_cohomology_interface<Simplex_tree<SimplexTreeOptions>>* pcoh) {
+    pcoh = new Gudhi::Persistent_cohomology_interface<Simplex_tree<SimplexTreeOptions>>(*this);
+  }
+
 };
 
 struct Simplex_tree_options_mini : Simplex_tree_options_full_featured {
diff --git a/src/cython/include/Tangential_complex_interface.h b/src/cython/include/Tangential_complex_interface.h
index 645aad72..e9750e85 100644
--- a/src/cython/include/Tangential_complex_interface.h
+++ b/src/cython/include/Tangential_complex_interface.h
@@ -29,6 +29,7 @@
 #include <CGAL/Epick_d.h>
 
 #include "Persistent_cohomology_interface.h"
+#include "Simplex_tree_interface.h"
 
 #include <vector>
 #include <utility>  // std::pair