Fix cppcheck

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/relaxed-witness@2120 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 49a5c2c6e94d9fbf235eecc92fa30e62980c7c70

6 files changed, 107 insertions, 111 deletions

diff --git a/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h b/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h
index ffc1750f..d41a6811 100644
--- a/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h
+++ b/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h
@@ -24,8 +24,7 @@
 #define ACTIVE_WITNESS_ACTIVE_WITNESS_H_
 
 #include <gudhi/Active_witness/Active_witness_iterator.h>
-#include <vector>
-#include <utility>
+#include <list>
 
 namespace Gudhi {
 
@@ -38,7 +37,7 @@ namespace witness_complex {
 template< typename Id_distance_pair,
           typename INS_range >
 class Active_witness {
-public:  
+ public:
   typedef Active_witness<Id_distance_pair, INS_range> ActiveWitness;
   typedef typename INS_range::iterator INS_iterator;
   typedef Active_witness_iterator< ActiveWitness, Id_distance_pair, INS_iterator > iterator;
@@ -50,22 +49,19 @@ public:
   INS_iterator iterator_end_;
 
   Active_witness(const INS_range& search_range)
-    : search_range_(search_range), iterator_next_(search_range_.begin()), iterator_end_(search_range_.end())
-  {
+    : search_range_(search_range), iterator_next_(search_range_.begin()), iterator_end_(search_range_.end()) {
   }
- 
-  iterator begin()
-  {
+
+  iterator begin() {
     return iterator(this, nearest_landmark_table_.begin());
   }
 
-  iterator end()
-  {
+  iterator end() {
     return iterator(this);
   }
 };
 
-}
-}
-  
+}  // namespace witness_complex
+}  // namespace Gudhi
+
 #endif  // ACTIVE_WITNESS_ACTIVE_WITNESS_H_
diff --git a/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h b/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h
index 69a335fa..4e29a40d 100644
--- a/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h
+++ b/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h
@@ -24,7 +24,7 @@
 #define ACTIVE_WITNESS_ACTIVE_WITNESS_ITERATOR_H_
 
 #include <boost/iterator/iterator_facade.hpp>
-#include <vector>
+#include <list>
 
 namespace Gudhi {
 
@@ -41,30 +41,29 @@ template< typename Active_witness,
           typename Id_distance_pair,
           typename INS_iterator >
 class Active_witness_iterator
-  : public boost::iterator_facade< Active_witness_iterator <Active_witness, Id_distance_pair, INS_iterator>
-, Id_distance_pair const
-, boost::forward_traversal_tag
-, Id_distance_pair const> {
+  : public boost::iterator_facade< Active_witness_iterator <Active_witness, Id_distance_pair, INS_iterator>,
+                                   Id_distance_pair const,
+                                   boost::forward_traversal_tag,
+                                   Id_distance_pair const> {
   friend class boost::iterator_core_access;
-  
+
   //typedef Active_witness<Id_distance_pair, INS_iterator> Active_witness;
   typedef typename std::list<Id_distance_pair>::iterator Pair_iterator;
-  typedef typename Gudhi::witness_complex::Active_witness_iterator<Active_witness, Id_distance_pair, INS_iterator> Iterator;
-  
-  
+  typedef typename Gudhi::witness_complex::Active_witness_iterator<Active_witness,
+                                                                   Id_distance_pair,
+                                                                   INS_iterator> Iterator;
+
   Active_witness *aw_;
   Pair_iterator lh_; // landmark handle
   bool is_end_; // true only if the pointer is end and there are no more neighbors to add
 
-public:
+ public:
   Active_witness_iterator(Active_witness* aw)
-    : aw_(aw), lh_(aw_->nearest_landmark_table_.end()), is_end_(true)
-  {
+    : aw_(aw), lh_(aw_->nearest_landmark_table_.end()), is_end_(true) {
   }
 
   Active_witness_iterator(Active_witness* aw, const Pair_iterator& lh)
-    : aw_(aw), lh_(lh)
-  {
+    : aw_(aw), lh_(lh) {
     is_end_ = false;
     if (lh_ == aw_->nearest_landmark_table_.end()) {
       if (aw_->iterator_next_ == aw_->iterator_end_) {
@@ -76,21 +75,17 @@ public:
       }
     }
   }
-  
-private :
 
-  Id_distance_pair& dereference() const
-  {
+ private :
+  Id_distance_pair& dereference() const {
     return *lh_;
   }
 
-  bool equal(const Iterator& other) const
-  {
+  bool equal(const Iterator& other) const {
     return (is_end_ == other.is_end_) || (lh_ == other.lh_);
   }
-  
-  void increment()
-  {
+
+  void increment() {
     // the neighbor search can't be at the end iterator of a list
     GUDHI_CHECK(!is_end_ && lh_ != aw_->nearest_landmark_table_.end(), std::logic_error("Wrong active witness increment."));
     // if the id of the current landmark is the same as the last one
diff --git a/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h b/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h
index aad05547..6870c183 100644
--- a/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h
@@ -23,17 +23,15 @@
 #ifndef EUCLIDEAN_STRONG_WITNESS_COMPLEX_H_
 #define EUCLIDEAN_STRONG_WITNESS_COMPLEX_H_
 
-#include <utility>
-#include <vector>
-#include <list>
-#include <limits>
-
 #include <gudhi/Strong_witness_complex.h>
 #include <gudhi/Active_witness/Active_witness.h>
 #include <gudhi/Kd_tree_search.h>
 
+#include <utility>
+#include <vector>
+
 namespace Gudhi {
-  
+
 namespace witness_complex {
 
 /**
@@ -46,8 +44,10 @@ namespace witness_complex {
  * href="http://doc.cgal.org/latest/Kernel_d/classCGAL_1_1Epick__d.html">CGAL::Epick_d</a> class.
  */
 template< class Kernel_ >
-class Euclidean_strong_witness_complex : public Strong_witness_complex<std::vector<typename Gudhi::spatial_searching::Kd_tree_search<Kernel_, std::vector<typename Kernel_::Point_d>>::INS_range>> {
-private:
+class Euclidean_strong_witness_complex
+    : public Strong_witness_complex<std::vector<typename Gudhi::spatial_searching::Kd_tree_search<Kernel_,
+                                                                                                  std::vector<typename Kernel_::Point_d>>::INS_range>> {
+ private:
   typedef Kernel_                                                                      K;
   typedef typename K::Point_d                                                          Point_d;
   typedef std::vector<Point_d>                                                         Point_range;
@@ -58,12 +58,12 @@ private:
   typedef typename Nearest_landmark_range::Point_with_transformed_distance Id_distance_pair;
   typedef typename Id_distance_pair::first_type Landmark_id;
   typedef Landmark_id Vertex_handle;
-  
+
  private:
   Point_range                         landmarks_;
   Kd_tree                             landmark_tree_;
   using Strong_witness_complex<Nearest_landmark_table>::nearest_landmark_table_;
-  
+
  public:
   /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
   /* @name Constructor
@@ -81,22 +81,19 @@ private:
             typename WitnessRange >
   Euclidean_strong_witness_complex(const LandmarkRange & landmarks,
                                    const WitnessRange &  witnesses)
-    : landmarks_(std::begin(landmarks), std::end(landmarks)), landmark_tree_(landmarks_)
-  {
+    : landmarks_(std::begin(landmarks), std::end(landmarks)), landmark_tree_(landmarks_) {
     nearest_landmark_table_.reserve(boost::size(witnesses));
     for (auto w: witnesses)
       nearest_landmark_table_.push_back(landmark_tree_.query_incremental_nearest_neighbors(w));
   }
 
-  
   /** \brief Returns the point corresponding to the given vertex.
    */
   template <typename Vertex_handle> 
-  Point_d get_point( Vertex_handle vertex ) const
-  {
+  Point_d get_point(Vertex_handle vertex) const {
     return landmarks_[vertex];
   }
-  
+
   //@}
 };
 
diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h
index ad741794..3fbbb366 100644
--- a/src/Witness_complex/include/gudhi/Strong_witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.h
@@ -23,20 +23,19 @@
 #ifndef STRONG_WITNESS_COMPLEX_H_
 #define STRONG_WITNESS_COMPLEX_H_
 
+#include <gudhi/Active_witness/Active_witness.h>
+#include <gudhi/Kd_tree_search.h>
+
 #include <utility>
 #include <vector>
 #include <list>
 #include <limits>
 
-#include <gudhi/Active_witness/Active_witness.h>
-#include <gudhi/Kd_tree_search.h>
-
 namespace Gudhi {
-  
+
 namespace witness_complex {
 
-/**
- *  \private
+/* \private
  * \class Strong_witness_complex
  * \brief Constructs strong witness complex for a given table of nearest landmarks with respect to witnesses.
  * \ingroup witness_complex
@@ -48,7 +47,7 @@ namespace witness_complex {
  */
 template< class Nearest_landmark_table_ >
 class Strong_witness_complex {
-private:
+ private:
   typedef typename Nearest_landmark_table_::value_type               Nearest_landmark_range;
   typedef std::size_t                                                Witness_id;
   typedef std::size_t                                                Landmark_id;
@@ -57,12 +56,11 @@ private:
   typedef std::list< ActiveWitness >                                 ActiveWitnessList;
   typedef std::vector< Landmark_id >                                 typeVectorVertex;
   typedef std::vector<Nearest_landmark_range>                        Nearest_landmark_table_internal;
-  
   typedef Landmark_id Vertex_handle;
-  
+
  protected:
   Nearest_landmark_table_internal              nearest_landmark_table_;
-  
+
  public:
   /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
   /* @name Constructor
@@ -70,11 +68,9 @@ private:
 
   //@{
 
-  Strong_witness_complex()
-  {
+  Strong_witness_complex() {
   }
 
-  
   /**
    *  \brief Initializes member variables before constructing simplicial complex.
    *  \details Records nearest landmark table.
@@ -84,10 +80,9 @@ private:
    *         of the pair range iterator needs to be 'std::pair<std::size_t, double>'.
    */
    Strong_witness_complex(Nearest_landmark_table_ const & nearest_landmark_table)
-     : nearest_landmark_table_(std::begin(nearest_landmark_table), std::end(nearest_landmark_table))
-  {    
+     : nearest_landmark_table_(std::begin(nearest_landmark_table), std::end(nearest_landmark_table)) {
   }
-  
+
   /** \brief Outputs the strong witness complex of relaxation 'max_alpha_square' 
    *         in a simplicial complex data structure.
    *  \details The function returns true if the construction is successful and false otherwise.
@@ -100,15 +95,15 @@ private:
   template < typename SimplicialComplexForWitness >
   bool create_complex(SimplicialComplexForWitness& complex,
                       double  max_alpha_square,
-                      Landmark_id limit_dimension = std::numeric_limits<Landmark_id>::max()) const      
-  {
+                      Landmark_id limit_dimension = std::numeric_limits<Landmark_id>::max()) const {
     Landmark_id complex_dim = 0;
     if (complex.num_vertices() > 0) {
       std::cerr << "Strong witness complex cannot create complex - complex is not empty.\n";
       return false;
     }
     if (max_alpha_square < 0) {
-      std::cerr << "Strong witness complex cannot create complex - squared relaxation parameter must be non-negative.\n";
+      std::cerr << "Strong witness complex cannot create complex - squared relaxation parameter must be "
+                << "non-negative.\n";
       return false;
     }
     if (limit_dimension < 0) {
@@ -129,7 +124,8 @@ private:
       typeVectorVertex& vertices = simplex; //'simplex' now will be called vertices
       while (aw_it != aw.end() && aw_it->second < lim_dist2) {
         typeVectorVertex facet = {};
-        add_all_faces_of_dimension(limit_dimension, vertices, vertices.begin(), aw_it, aw_it->second - aw.begin()->second, facet, complex);
+        add_all_faces_of_dimension(limit_dimension, vertices, vertices.begin(), aw_it,
+                                   aw_it->second - aw.begin()->second, facet, complex);
         vertices.push_back(aw_it->first);
         aw_it++;
       }
@@ -140,13 +136,12 @@ private:
     return true;
   }
 
-private:
-
+ private:
     /* \brief Adds recursively all the faces of a certain dimension dim-1 witnessed by the same witness.
-   * Iterator is needed to know until how far we can take landmarks to form simplexes.
-   * simplex is the prefix of the simplexes to insert.
-   * The landmark pointed by aw_it is added to all formed simplices.
-   */
+     * Iterator is needed to know until how far we can take landmarks to form simplexes.
+     * simplex is the prefix of the simplexes to insert.
+     * The landmark pointed by aw_it is added to all formed simplices.
+     */
   template < typename SimplicialComplexForWitness >
   void add_all_faces_of_dimension(Landmark_id dim,
                                   typeVectorVertex& vertices,
@@ -154,9 +149,8 @@ private:
                                   typename ActiveWitness::iterator aw_it,
                                   double filtration_value,
                                   typeVectorVertex& simplex,
-                                  SimplicialComplexForWitness& sc) const
-  {
-    if (dim > 0)
+                                  SimplicialComplexForWitness& sc) const {
+    if (dim > 0) {
       while (curr_it != vertices.end()) {
         simplex.push_back(*curr_it);
         ++curr_it;        
@@ -176,7 +170,7 @@ private:
                                    simplex,
                                    sc);
       } 
-    else if (dim == 0) {
+    } else if (dim == 0) {
       simplex.push_back(aw_it->first);
       sc.insert_simplex_and_subfaces(simplex, filtration_value);
       simplex.pop_back();
diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h
index c09e6af9..c0506367 100644
--- a/src/Witness_complex/include/gudhi/Witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Witness_complex.h
@@ -33,7 +33,7 @@
 #include <limits>
 
 namespace Gudhi {
-  
+
 namespace witness_complex {
 
 /**
@@ -49,7 +49,7 @@ namespace witness_complex {
 */
 template< class Nearest_landmark_table_ >
 class Witness_complex {
-private:
+ private:
   typedef typename Nearest_landmark_table_::value_type               Nearest_landmark_range;
   typedef std::size_t                                                Witness_id;
   typedef std::size_t                                                Landmark_id;
@@ -58,12 +58,11 @@ private:
   typedef std::list< ActiveWitness >                                 ActiveWitnessList;
   typedef std::vector< Landmark_id >                                 typeVectorVertex;
   typedef std::vector<Nearest_landmark_range>                        Nearest_landmark_table_internal;
-
   typedef Landmark_id Vertex_handle;
 
  protected:
   Nearest_landmark_table_internal              nearest_landmark_table_;
-  
+
  public:
   /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
   /* @name Constructor
@@ -71,10 +70,9 @@ private:
 
   //@{
 
-  Witness_complex()
-  {
+  Witness_complex() {
   }
-  
+
   /**
    *  \brief Initializes member variables before constructing simplicial complex.
    *  \details Records nearest landmark table.
@@ -85,11 +83,9 @@ private:
    */
 
   Witness_complex(Nearest_landmark_table_ const & nearest_landmark_table)
-    : nearest_landmark_table_(std::begin(nearest_landmark_table), std::end(nearest_landmark_table))
-  {    
+    : nearest_landmark_table_(std::begin(nearest_landmark_table), std::end(nearest_landmark_table)) {
   }
 
-    
   /** \brief Outputs the (weak) witness complex of relaxation 'max_alpha_square'
    *         in a simplicial complex data structure.
    *  \details The function returns true if the construction is successful and false otherwise.
@@ -102,8 +98,7 @@ private:
   template < typename SimplicialComplexForWitness >
   bool create_complex(SimplicialComplexForWitness& complex,
                       double  max_alpha_square,
-                      std::size_t limit_dimension = std::numeric_limits<std::size_t>::max()) const      
-  {
+                      std::size_t limit_dimension = std::numeric_limits<std::size_t>::max()) const {
     if (complex.num_vertices() > 0) {
       std::cerr << "Witness complex cannot create complex - complex is not empty.\n";
       return false;
@@ -118,9 +113,9 @@ private:
     }
     ActiveWitnessList active_witnesses;
     Landmark_id k = 0; /* current dimension in iterative construction */
-    for (auto w: nearest_landmark_table_)
+    for (auto w : nearest_landmark_table_)
       active_witnesses.push_back(ActiveWitness(w));
-    while (!active_witnesses.empty() && k <= limit_dimension ) {
+    while (!active_witnesses.empty() && k <= limit_dimension) {
       typename ActiveWitnessList::iterator aw_it = active_witnesses.begin();
       std::vector<Landmark_id> simplex;
       simplex.reserve(k+1);
@@ -134,10 +129,10 @@ private:
                                              aw_it->end());
         assert(simplex.empty());
         if (!ok)
-          active_witnesses.erase(aw_it++); //First increase the iterator and then erase the previous element
+          active_witnesses.erase(aw_it++);  // First increase the iterator and then erase the previous element
         else
           aw_it++;
-      } 
+      }
       k++;
     }
     complex.set_dimension(k-1);
@@ -159,13 +154,12 @@ private:
                                   typename ActiveWitness::iterator curr_l,
                                   std::vector<Landmark_id>& simplex,
                                   SimplicialComplexForWitness& sc,
-                                  typename ActiveWitness::iterator end) const
-  {
+                                  typename ActiveWitness::iterator end) const {
     if (curr_l == end)
       return false;
     bool will_be_active = false;
     typename ActiveWitness::iterator l_it = curr_l;
-    if (dim > 0)
+    if (dim > 0) {
       for (; l_it->second - alpha2 <= norelax_dist2 && l_it != end; ++l_it) {
         simplex.push_back(l_it->first);
         if (sc.find(simplex) != sc.null_simplex()) {
@@ -183,8 +177,8 @@ private:
         // If norelax_dist is infinity, change to first omitted distance
         if (l_it->second <= norelax_dist2)
           norelax_dist2 = l_it->second;
-      } 
-    else if (dim == 0)
+      }
+    } else if (dim == 0) {
       for (; l_it->second - alpha2 <= norelax_dist2 && l_it != end; ++l_it) {
         simplex.push_back(l_it->first);
         double filtration_value = 0;
@@ -200,12 +194,12 @@ private:
         // If norelax_dist is infinity, change to first omitted distance
         if (l_it->second < norelax_dist2)
           norelax_dist2 = l_it->second;
-      } 
+      }
+    }
     return will_be_active;
   }
-
 };
-  
+
 }  // namespace witness_complex
 
 }  // namespace Gudhi
diff --git a/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h b/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h
index d009caca..b68d75a1 100644
--- a/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h
+++ b/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h
@@ -1,3 +1,25 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Siargey Kachanovich
+ *
+ *    Copyright (C) 2015  INRIA (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
 #ifndef WITNESS_COMPLEX_ALL_FACES_IN_H_
 #define WITNESS_COMPLEX_ALL_FACES_IN_H_
 
@@ -9,16 +31,14 @@ template < typename SimplicialComplexForWitness,
            typename Simplex >
   bool all_faces_in(Simplex& simplex,
                     double* filtration_value,
-                    SimplicialComplexForWitness& sc)
-  {
+                    SimplicialComplexForWitness& sc) {
     typedef typename SimplicialComplexForWitness::Simplex_handle Simplex_handle;
 
     if (simplex.size() == 1)
       return true;                  /* Add vertices unconditionally */
-    
+
     Simplex facet;
-    for (typename Simplex::iterator not_it = simplex.begin(); not_it != simplex.end(); ++not_it)
-      {
+    for (typename Simplex::iterator not_it = simplex.begin(); not_it != simplex.end(); ++not_it) {
         facet.clear();
         for (typename Simplex::iterator it = simplex.begin(); it != simplex.end(); ++it)
           if (it != not_it)