include what you use

8 files changed, 97 insertions, 99 deletions

diff --git a/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Combination_iterator.h b/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Combination_iterator.h
index 36bf4b55..ce6a34ec 100644
--- a/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Combination_iterator.h
+++ b/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Combination_iterator.h
@@ -83,7 +83,7 @@ public:
     }
   }
   
-protected:
+ private:
   value_t value_; // the dereference value
   bool is_end_;   // is true when the current permutation is the final one 
 
diff --git a/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Integer_combination_iterator.h b/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Integer_combination_iterator.h
index 8bf75711..c4e86a36 100644
--- a/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Integer_combination_iterator.h
+++ b/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Integer_combination_iterator.h
@@ -25,11 +25,11 @@ typedef unsigned uint;
  *  Based on the algorithm by Mifsud.
 */
 class Integer_combination_iterator : public boost::iterator_facade< Integer_combination_iterator,
-								    std::vector<uint> const,
-								    boost::forward_traversal_tag> {
-  typedef std::vector<uint> value_t;
+                                                                    std::vector<uint> const,
+                                                                    boost::forward_traversal_tag> {
+  using value_t = std::vector<uint>;
   
-protected:
+ private:
   friend class boost::iterator_core_access;
   
   bool equal(Integer_combination_iterator const& other) const {
@@ -71,7 +71,6 @@ protected:
   }
 
 public:
-
   template <class Bound_range>
   Integer_combination_iterator(const uint& n, const uint& k, const Bound_range& bounds)
     :
@@ -109,8 +108,8 @@ public:
 
   // Used for the creating an end iterator
   Integer_combination_iterator() : is_end_(true), n_(0), k_(0) {}
-  
-protected:
+
+ private:
   value_t value_; // the dereference value
   bool is_end_;   // is true when the current integer combination is the final one 
 
diff --git a/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Ordered_set_partition_iterator.h b/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Ordered_set_partition_iterator.h
index 73b98337..d6f9f121 100644
--- a/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Ordered_set_partition_iterator.h
+++ b/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Ordered_set_partition_iterator.h
@@ -13,8 +13,10 @@
 
 #include <vector>
 #include <limits>
+
 #include <gudhi/Permutahedral_representation/Permutation_iterator.h>
 #include <gudhi/Permutahedral_representation/Set_partition_iterator.h>
+
 #include <boost/range/iterator_range.hpp>
 
 namespace Gudhi {
@@ -48,11 +50,11 @@ struct Ordered_set_partition {
  *   
 */
 class Ordered_set_partition_iterator : public boost::iterator_facade< Ordered_set_partition_iterator,
-								      Ordered_set_partition const,
-								      boost::forward_traversal_tag> {
-  typedef Ordered_set_partition value_t;
+                                                                      Ordered_set_partition const,
+                                                                      boost::forward_traversal_tag> {
+  using value_t = Ordered_set_partition;
   
-protected:
+ private:
   friend class boost::iterator_core_access;
 
   bool equal(Ordered_set_partition_iterator const& other) const {
@@ -66,22 +68,19 @@ protected:
   void increment() {
     if (++value_.p_it_ == p_end_) {
       if (++value_.s_it_ == s_end_) {
-	is_end_ = true;
-	return;
+        is_end_ = true;
+        return;
       }
       else
-	value_.p_it_.reinitialize();
+        value_.p_it_.reinitialize();
     }
   }
   
-public:
-  
+ public:
   Ordered_set_partition_iterator(const uint& n, const uint& k)
     :
     value_({Set_partition_iterator(n,k), Permutation_iterator(k)}),
-    is_end_(n == 0)
-  {
-  }
+    is_end_(n == 0) {}
 
   // Used for the creating an end iterator
   Ordered_set_partition_iterator() : is_end_(true) {}
@@ -92,7 +91,7 @@ public:
     value_.s_it_.reinitialize();
   }
   
-protected:
+ private:
   Set_partition_iterator s_end_; // Set partition iterator and the corresponding end iterator
   Permutation_iterator p_end_; // Permutation iterator and the corresponding end iterator
   value_t value_;         // the dereference value
diff --git a/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Permutahedral_representation_iterators.h b/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Permutahedral_representation_iterators.h
index e892b73b..d42e892a 100644
--- a/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Permutahedral_representation_iterators.h
+++ b/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Permutahedral_representation_iterators.h
@@ -20,7 +20,7 @@
 
 #include <vector>
 #include <iostream>
-#include <algorithm>
+#include <algorithm>  // for std::find
 
 namespace Gudhi {
 
@@ -37,15 +37,15 @@ namespace coxeter_triangulation {
  * Forward iterator, 'value_type' is Permutahedral_representation::Vertex.*/
 template <class Permutahedral_representation>
 class Vertex_iterator : public boost::iterator_facade< Vertex_iterator<Permutahedral_representation>,
-						       typename Permutahedral_representation::Vertex const,
-						       boost::forward_traversal_tag> {
-protected:
+                                                       typename Permutahedral_representation::Vertex const,
+                                                       boost::forward_traversal_tag> {
+ private:
   friend class boost::iterator_core_access;
 
   using Vertex = typename Permutahedral_representation::Vertex;
   using Ordered_partition = typename Permutahedral_representation::OrderedSetPartition;
 
-  typedef Vertex value_t;
+  using value_t = Vertex;
 
   
   bool equal(Vertex_iterator const& other) const {
@@ -60,12 +60,12 @@ protected:
     std::size_t d = value_.size();
     for (auto i: *o_it_)
       if (i != d)
-	value_[i]++;
+        value_[i]++;
       else
-	for (std::size_t j = 0; j < d; j++)
-	  value_[j]--;
+        for (std::size_t j = 0; j < d; j++)
+          value_[j]--;
   }
-		       
+                       
   void increment() {
     if (is_end_)
       return;
@@ -84,9 +84,8 @@ public:
   {}
 
   Vertex_iterator() : is_end_(true) {}
-  
-  
-protected:
+
+ private:
   typename Ordered_partition::const_iterator o_it_, o_end_; 
   value_t value_;
   bool is_end_;
@@ -100,11 +99,11 @@ protected:
  * Forward iterator, value_type is Permutahedral_representation. */
 template <class Permutahedral_representation>
 class Face_iterator : public boost::iterator_facade< Face_iterator<Permutahedral_representation>,
-						     Permutahedral_representation const,
-						     boost::forward_traversal_tag> {
-  typedef Permutahedral_representation value_t;
+                                                     Permutahedral_representation const,
+                                                     boost::forward_traversal_tag> {
+  using value_t = Permutahedral_representation;
   
-protected:
+ private:
   friend class boost::iterator_core_access;
 
   using Vertex = typename Permutahedral_representation::Vertex;
@@ -130,9 +129,8 @@ protected:
     // Combination *c_it_ is supposed to be sorted in increasing order
     value_ = face_from_indices<Permutahedral_representation>(simplex_, *c_it_);
   }
-  
+
 public:
-  
   Face_iterator(const Permutahedral_representation& simplex, const uint& k)
     : simplex_(simplex),
       k_(k),
@@ -147,7 +145,7 @@ public:
   // Used for the creating an end iterator
   Face_iterator() : is_end_(true) {}
   
-protected:
+ private:
   Permutahedral_representation simplex_; // Input simplex
   uint k_;
   uint l_; // Dimension of the input simplex
@@ -165,11 +163,11 @@ protected:
  * Forward iterator, value_type is Permutahedral_representation. */
 template <class Permutahedral_representation>
 class Coface_iterator : public boost::iterator_facade< Coface_iterator<Permutahedral_representation>,
-						       Permutahedral_representation const,
-						       boost::forward_traversal_tag> {
-  typedef Permutahedral_representation value_t;
-  
-protected:
+                                                       Permutahedral_representation const,
+                                                       boost::forward_traversal_tag> {
+  using value_t = Permutahedral_representation;
+
+ private:
   friend class boost::iterator_core_access;
 
   using Vertex = typename Permutahedral_representation::Vertex;
@@ -187,20 +185,20 @@ protected:
     uint i = 0;
     for (; i < k_+1; i++) {
       if (++(o_its_[i]) != o_end_)
-	break;
+        break;
     }
     if (i == k_+1) {
       if (++i_it_ == i_end_) {
-	is_end_ = true;
-	return;
+        is_end_ = true;
+        return;
       }
       o_its_.clear();
       for (uint j = 0; j < k_ + 1; j++)
-	o_its_.emplace_back(Ordered_set_partition_iterator(simplex_.partition()[j].size(), (*i_it_)[j]+1));
+        o_its_.emplace_back(Ordered_set_partition_iterator(simplex_.partition()[j].size(), (*i_it_)[j]+1));
     }
     else
       for (uint j = 0; j < i; j++)
-	o_its_[j].reinitialize();
+        o_its_[j].reinitialize();
     update_value();
   }
 
@@ -212,30 +210,29 @@ protected:
     for (; u_ <= (*i_it_)[k_]; u_++) {
       auto range = (*o_its_[k_])[u_];
       if (std::find(range.begin(), range.end(), t_) != range.end())
-	break;
+        break;
     }
     uint i = 0;
     for (uint j = u_+1; j <= (*i_it_)[k_]; j++, i++)
       for (uint b: (*o_its_[k_])[j]) {
-	uint c = simplex_.partition()[k_][b];
+        uint c = simplex_.partition()[k_][b];
         value_.partition()[i].push_back(c);
-	value_.vertex()[c]--;
+        value_.vertex()[c]--;
       }
     for (uint h = 0; h < k_; h++)
       for (uint j = 0; j <= (*i_it_)[h]; j++, i++) {
-	for (uint b: (*o_its_[h])[j])
-	  value_.partition()[i].push_back(simplex_.partition()[h][b]);
+        for (uint b: (*o_its_[h])[j])
+          value_.partition()[i].push_back(simplex_.partition()[h][b]);
       }
     for (uint j = 0; j <= u_; j++, i++)
       for (uint b: (*o_its_[k_])[j])
-	value_.partition()[i].push_back(simplex_.partition()[k_][b]);
+        value_.partition()[i].push_back(simplex_.partition()[k_][b]);
     // sort the values in each part (probably not needed)
     for (auto& part: value_.partition())
       std::sort(part.begin(), part.end());
   }
-  
-public:
-  
+
+ public:
   Coface_iterator(const Permutahedral_representation& simplex, const uint& l)
     : simplex_(simplex),
       d_(simplex.vertex().size()),
@@ -248,8 +245,8 @@ public:
     uint j = 0;
     for (; j < simplex_.partition()[k_].size(); j++)
       if (simplex_.partition()[k_][j] == d_) {
-	t_ = j;
-	break;
+        t_ = j;
+        break;
       }
     if (j == simplex_.partition()[k_].size()) {
       std::cerr << "Coface iterator: the argument simplex is not a permutahedral representation\n";
@@ -263,8 +260,8 @@ public:
 
   // Used for the creating an end iterator
   Coface_iterator() : is_end_(true) {}
-  
-protected:
+
+ private:
   Permutahedral_representation simplex_; // Input simplex
   uint d_; // Ambient dimension
   uint l_; // Dimension of the coface
diff --git a/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Permutation_iterator.h b/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Permutation_iterator.h
index ed1fb337..e0142bf4 100644
--- a/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Permutation_iterator.h
+++ b/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Permutation_iterator.h
@@ -11,7 +11,9 @@
 #ifndef PERMUTAHEDRAL_REPRESENTATION_PERMUTATION_ITERATOR_H_
 #define PERMUTAHEDRAL_REPRESENTATION_PERMUTATION_ITERATOR_H_
 
+#include <cstdlib>  // for std::size_t
 #include <vector>
+
 #include <boost/range/iterator_range.hpp>
 
 namespace Gudhi {
@@ -24,11 +26,11 @@ typedef unsigned uint;
  *   Based on the optimization of the Heap's algorithm by Sedgewick.
 */
 class Permutation_iterator : public boost::iterator_facade< Permutation_iterator,
-							    std::vector<uint> const,
-							    boost::forward_traversal_tag> {
-  typedef std::vector<uint> value_t;
+                                                            std::vector<uint> const,
+                                                            boost::forward_traversal_tag> {
+  using value_t = std::vector<uint>;
   
-protected:
+ private:
   friend class boost::iterator_core_access;
 
   bool equal(Permutation_iterator const& other) const {
@@ -70,12 +72,12 @@ protected:
       ct_ = 5;
       uint j = 2;
       while (d_[j] == j+1) {
-	d_[j] = 0;
-	++j;
+        d_[j] = 0;
+        ++j;
       }
       if (j == n_ - 1) {
-	is_end_ = true;
-	return;
+        is_end_ = true;
+        return;
       }
       uint k = j+1;
       uint x = (k%2 ? d_[j] : 0);
@@ -117,8 +119,8 @@ public:
     if (n_ > 0)
       is_end_ = false;
   }
-  
-protected:
+
+ private:
   value_t value_; // the dereference value
   bool is_end_;   // is true when the current permutation is the final one 
   bool optim_3_;  // true if n>=3. for n >= 3, the algorithm is optimized
diff --git a/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Set_partition_iterator.h b/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Set_partition_iterator.h
index 26bbc1ef..bd1770bc 100644
--- a/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Set_partition_iterator.h
+++ b/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Set_partition_iterator.h
@@ -25,11 +25,11 @@ typedef unsigned uint;
  *   
 */
 class Set_partition_iterator : public boost::iterator_facade< Set_partition_iterator,
-							      std::vector<std::vector<uint> > const,
-							      boost::forward_traversal_tag> {
-  typedef std::vector<std::vector<uint> > value_t;
-  
-protected:
+                                                              std::vector<std::vector<uint> > const,
+                                                              boost::forward_traversal_tag> {
+  using value_t = std::vector<std::vector<uint>>;
+
+ private:
   friend class boost::iterator_core_access;
 
   bool equal(Set_partition_iterator const& other) const {
@@ -54,7 +54,7 @@ protected:
     }
     uint i = n_ - 1;
     while (rgs_[i] + 1 > max_[i] ||
-	   rgs_[i] + 1 >= k_)
+           rgs_[i] + 1 >= k_)
       i--;
     if (i == 0) {
       is_end_ = true;
@@ -71,16 +71,15 @@ protected:
     uint p = k_;
     if (mm < p)
       do {
-	max_[i] = p;
-	--i;
-	--p;
-	rgs_[i] = p;
+        max_[i] = p;
+        --i;
+        --p;
+        rgs_[i] = p;
       } while (max_[i] < p);
     update_value();
   }
   
-public:
-  
+ public:
   Set_partition_iterator(const uint& n, const uint& k)
     :
     value_(k),
@@ -116,12 +115,12 @@ public:
       max_[i] = rgs_[i-1] + 1;
     update_value();
   }
-  
-protected:
+
+ private:
   value_t value_;         // the dereference value
   std::vector<uint> rgs_; // restricted growth string
   std::vector<uint> max_; // max_[i] = max(rgs_[0],...,rgs[i-1]) + 1
-  bool is_end_;   // is true when the current permutation is the final one 
+  bool is_end_;           // is true when the current permutation is the final one 
 
   uint n_;
   uint k_;
diff --git a/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Size_range.h b/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Size_range.h
index 262915fb..f41335e9 100644
--- a/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Size_range.h
+++ b/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Size_range.h
@@ -11,8 +11,9 @@
 #ifndef PERMUTAHEDRAL_REPRESENTATION_SIZE_RANGE_H_
 #define PERMUTAHEDRAL_REPRESENTATION_SIZE_RANGE_H_
 
+#include <cstdlib>  // for std::size_t
+
 #include <boost/range/iterator_range.hpp>
-#include <cstdlib>         // std::size_t
 
 namespace Gudhi {
 
@@ -22,11 +23,11 @@ namespace coxeter_triangulation {
  */
 template <class T_it>
 class Size_iterator : public boost::iterator_facade< Size_iterator<T_it>,
-						     std::size_t const,
-						     boost::forward_traversal_tag> {
+                                                     std::size_t const,
+                                                     boost::forward_traversal_tag> {
   friend class boost::iterator_core_access;
 
-protected:
+ private:
   bool equal(Size_iterator const& other) const {
     return (is_end_ && other.is_end_);
   }
@@ -43,15 +44,14 @@ protected:
     value_ = t_it_->size()-1;
   }
 
-public:
-
+ public:
   Size_iterator(const T_it& t_begin, const T_it& t_end)
     : t_it_(t_begin), t_end_(t_end), is_end_(t_begin == t_end) {
     if (!is_end_)
       value_ = t_it_->size()-1;
   }
 
-protected:
+ private:
   T_it t_it_, t_end_;
   bool is_end_;
   std::size_t value_;
@@ -61,7 +61,7 @@ template <class T>
 class Size_range {
   const T& t_;
 
-public:
+ public:
   typedef Size_iterator<typename T::const_iterator> iterator;
   
   Size_range(const T& t) : t_(t) {}
diff --git a/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/face_from_indices.h b/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/face_from_indices.h
index c658a06d..21ee3c8b 100644
--- a/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/face_from_indices.h
+++ b/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/face_from_indices.h
@@ -15,6 +15,9 @@ namespace Gudhi {
 
 namespace coxeter_triangulation {
 
+#include <cstdlib>  // for std::size_t
+#include <algorithm>
+
  /** \brief Computes the permutahedral representation of a face of a given simplex
   *  and a range of the vertex indices that compose the face.
   *
@@ -25,10 +28,9 @@ namespace coxeter_triangulation {
   * @param[in] simplex Input simplex.
   * @param[in] indices Input range of indices.
   */
-template <class Permutahedral_representation,
-	  class Index_range>
+template <class Permutahedral_representation, class Index_range>
 Permutahedral_representation face_from_indices(const Permutahedral_representation& simplex,
-					       const Index_range& indices) {
+                                               const Index_range& indices) {
   using range_index = typename Index_range::value_type;
   using Ordered_set_partition = typename Permutahedral_representation::OrderedSetPartition;
   using Part = typename Ordered_set_partition::value_type;