Fix cppcheck

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/relaxed-witness@2122 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 92d11c064056138ce4aa8cbe3a42df29a8a5ca7d

7 files changed, 45 insertions, 49 deletions

diff --git a/src/Witness_complex/example/example_strong_witness_persistence.cpp b/src/Witness_complex/example/example_strong_witness_persistence.cpp
index 5efe69fd..f786fe7b 100644
--- a/src/Witness_complex/example/example_strong_witness_persistence.cpp
+++ b/src/Witness_complex/example/example_strong_witness_persistence.cpp
@@ -126,13 +126,14 @@ void program_options(int argc, char * argv[]
       "Name of file containing a point set in off format.");
 
   po::options_description visible("Allowed options", 100);
+  Filtration_value default_alpha = std::numeric_limits<Filtration_value>::infinity();
   visible.add_options()
       ("help,h", "produce help message")
       ("landmarks,l", po::value<int>(&nbL),
        "Number of landmarks to choose from the point cloud.")
       ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
        "Name of file in which the persistence diagram is written. Default print in std::cout")
-      ("max-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(std::numeric_limits<Filtration_value>::infinity()),
+      ("max-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(default_alpha),
        "Maximal squared relaxation parameter.")
       ("field-charac,p", po::value<int>(&p)->default_value(11),
        "Characteristic p of the coefficient field Z/pZ for computing homology.")
diff --git a/src/Witness_complex/example/example_witness_complex_persistence.cpp b/src/Witness_complex/example/example_witness_complex_persistence.cpp
index 364a114a..a1146922 100644
--- a/src/Witness_complex/example/example_witness_complex_persistence.cpp
+++ b/src/Witness_complex/example/example_witness_complex_persistence.cpp
@@ -34,18 +34,17 @@
 #include <vector>
 #include <limits>  // infinity
 
-using namespace Gudhi;
-using namespace Gudhi::persistent_cohomology;
+using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
+using Point_d = K::Point_d;
 
-typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
-typedef typename K::Point_d Point_d;
+using Point_vector = std::vector<Point_d>;
+using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex<K>;
+using SimplexTree = Gudhi::Simplex_tree<>;
 
-typedef typename std::vector<Point_d> Point_vector;
-typedef typename Gudhi::witness_complex::Euclidean_witness_complex<K> Witness_complex;
-typedef Gudhi::Simplex_tree<> SimplexTree;
+using Filtration_value = SimplexTree::Filtration_value;
 
-typedef int Vertex_handle;
-typedef double Filtration_value;
+using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<SimplexTree, Field_Zp>;
 
 void program_options(int argc, char * argv[]
                      , int & nbL
@@ -83,9 +82,9 @@ int main(int argc, char * argv[]) {
   // Compute witness complex
   Witness_complex witness_complex(landmarks,
                                   witnesses);
-  
+
   witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d);
-  
+
   std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
   std::cout << "   and has dimension " << simplex_tree.dimension() << " \n";
 
@@ -93,7 +92,7 @@ int main(int argc, char * argv[]) {
   simplex_tree.initialize_filtration();
 
   // Compute the persistence diagram of the complex
-  persistent_cohomology::Persistent_cohomology<SimplexTree, Field_Zp > pcoh(simplex_tree);
+  Persistent_cohomology pcoh(simplex_tree);
   // initializes the coefficient field for homology
   pcoh.init_coefficients(p);
 
@@ -120,15 +119,14 @@ void program_options(int argc, char * argv[]
                      , int & p
                      , int & dim_max
                      , Filtration_value & min_persistence) {
-  
   namespace po = boost::program_options;
-  
+
   po::options_description hidden("Hidden options");
   hidden.add_options()
       ("input-file", po::value<std::string>(&file_name),
       "Name of file containing a point set in off format.");
-  
 
+  Filtration_value default_alpha = std::numeric_limits<Filtration_value>::infinity();
   po::options_description visible("Allowed options", 100);
   visible.add_options()
       ("help,h", "produce help message")
@@ -136,7 +134,7 @@ void program_options(int argc, char * argv[]
        "Number of landmarks to choose from the point cloud.")
       ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
        "Name of file in which the persistence diagram is written. Default print in std::cout")
-      ("max-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(std::numeric_limits<Filtration_value>::infinity()),
+      ("max-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(default_alpha),
        "Maximal squared relaxation parameter.")
       ("field-charac,p", po::value<int>(&p)->default_value(11),
        "Characteristic p of the coefficient field Z/pZ for computing homology.")
@@ -144,7 +142,7 @@ void program_options(int argc, char * argv[]
        "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals")
       ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(std::numeric_limits<int>::max()),
        "Maximal dimension of the weak witness complex we want to compute.");
-  
+
   po::positional_options_description pos;
   pos.add("input-file", 1);
 
@@ -155,7 +153,7 @@ void program_options(int argc, char * argv[]
   po::store(po::command_line_parser(argc, argv).
             options(all).positional(pos).run(), vm);
   po::notify(vm);
-  
+
   if (vm.count("help") || !vm.count("input-file")) {
     std::cout << std::endl;
     std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
@@ -171,4 +169,3 @@ void program_options(int argc, char * argv[]
     std::abort();
   }
 }
-
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 4e29a40d..0a05173a 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
@@ -36,7 +36,6 @@ namespace witness_complex {
  *          If all the landmarks are present in the list, iterator returns the specific end value
  *          of the corresponding 'Active_witness' object.
  */
-  
 template< typename Active_witness,
           typename Id_distance_pair,
           typename INS_iterator >
@@ -47,15 +46,14 @@ class Active_witness_iterator
                                    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;
 
   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
+  Pair_iterator lh_;  // landmark handle
+  bool is_end_;  // true only if the pointer is end and there are no more neighbors to add
 
  public:
   Active_witness_iterator(Active_witness* aw)
@@ -87,7 +85,8 @@ class Active_witness_iterator
 
   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."));
+    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
 
     lh_++;
@@ -105,5 +104,5 @@ class Active_witness_iterator
 
 }  // namespace witness_complex
 }  // namespace Gudhi
-  
+
 #endif  // ACTIVE_WITNESS_ACTIVE_WITNESS_ITERATOR_H_
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 6870c183..fb669ef8 100644
--- a/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h
@@ -83,13 +83,13 @@ class Euclidean_strong_witness_complex
                                    const WitnessRange &  witnesses)
     : landmarks_(std::begin(landmarks), std::end(landmarks)), landmark_tree_(landmarks_) {
     nearest_landmark_table_.reserve(boost::size(witnesses));
-    for (auto w: 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> 
+  template <typename Vertex_handle>
   Point_d get_point(Vertex_handle vertex) const {
     return landmarks_[vertex];
   }
@@ -101,4 +101,4 @@ class Euclidean_strong_witness_complex
 
 }  // namespace Gudhi
 
-#endif // EUCLIDEAN_STRONG_WITNESS_COMPLEX_H_
+#endif  // EUCLIDEAN_STRONG_WITNESS_COMPLEX_H_
diff --git a/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h b/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h
index 146271f7..6afe9a5d 100644
--- a/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h
@@ -33,7 +33,7 @@
 #include <limits>
 
 namespace Gudhi {
-  
+
 namespace witness_complex {
 
 /**
@@ -46,8 +46,10 @@ 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_witness_complex : public Witness_complex<std::vector<typename Gudhi::spatial_searching::Kd_tree_search<Kernel_, std::vector<typename Kernel_::Point_d>>::INS_range>> {
-private:
+class Euclidean_witness_complex
+    : public 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;
@@ -64,7 +66,7 @@ private:
   Kd_tree                             landmark_tree_;
   using Witness_complex<Nearest_landmark_table>::nearest_landmark_table_;
 
-public:
+ public:
   /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
   /* @name Constructor
    */
@@ -81,24 +83,22 @@ public:
             typename WitnessRange >
   Euclidean_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)
+    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.
    *  @param[in] vertex Vertex handle of the point to retrieve.
    */
-  Point_d get_point( Vertex_handle vertex ) const
-  {
+  Point_d get_point(Vertex_handle vertex) const {
     return landmarks_[vertex];
   }
 
   //@}
 };
-  
+
 }  // namespace witness_complex
 
 }  // namespace Gudhi
diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h
index 3fbbb366..6708ac29 100644
--- a/src/Witness_complex/include/gudhi/Strong_witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.h
@@ -79,8 +79,8 @@ class Strong_witness_complex {
    *         The range of pairs must admit a member type 'iterator'. The dereference type 
    *         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)) {
+  Strong_witness_complex(Nearest_landmark_table_ const & 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' 
@@ -110,7 +110,7 @@ class Strong_witness_complex {
       std::cerr << "Strong witness complex cannot create complex - limit dimension must be non-negative.\n";
       return false;
     }
-    for (auto w: nearest_landmark_table_) {
+    for (auto w : nearest_landmark_table_) {
       ActiveWitness aw(w);
       typeVectorVertex simplex;
       typename ActiveWitness::iterator aw_it = aw.begin();
@@ -121,7 +121,7 @@ class Strong_witness_complex {
         aw_it++;
       }
       // continue inserting limD-faces of the following simplices
-      typeVectorVertex& vertices = simplex; //'simplex' now will be called vertices
+      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,
@@ -153,7 +153,7 @@ class Strong_witness_complex {
     if (dim > 0) {
       while (curr_it != vertices.end()) {
         simplex.push_back(*curr_it);
-        ++curr_it;        
+        ++curr_it;
         add_all_faces_of_dimension(dim-1,
                                    vertices,
                                    curr_it,
@@ -169,14 +169,13 @@ class Strong_witness_complex {
                                    filtration_value,
                                    simplex,
                                    sc);
-      } 
+      }
     } 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 c0506367..a79bf294 100644
--- a/src/Witness_complex/include/gudhi/Witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Witness_complex.h
@@ -183,7 +183,7 @@ class Witness_complex {
         simplex.push_back(l_it->first);
         double filtration_value = 0;
         // if norelax_dist is infinite, relaxation is 0.
-        if (l_it->second > norelax_dist2) 
+        if (l_it->second > norelax_dist2)
           filtration_value = l_it->second - norelax_dist2;
         if (all_faces_in(simplex, &filtration_value, sc)) {
           will_be_active = true;