CppCheck and CppLint fixes for alpha complexes

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@1047 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: a9b42ad2f8751384b5227fa3da8f380cda9b3696

11 files changed, 37 insertions, 46 deletions

diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h
index deecf93f..f55d7029 100644
--- a/src/Alpha_complex/doc/Intro_alpha_complex.h
+++ b/src/Alpha_complex/doc/Intro_alpha_complex.h
@@ -161,8 +161,8 @@ namespace alphacomplex {
  */
 /** @} */  // end defgroup alpha_complex
 
-} // namespace alphacomplex
+}  // namespace alphacomplex
 
-} // namespace Gudhi
+}  // namespace Gudhi
 
 #endif  // INTRO_ALPHA_COMPLEX_H_
diff --git a/src/Alpha_complex/example/Alpha_complex_from_off.cpp b/src/Alpha_complex/example/Alpha_complex_from_off.cpp
index 80445a22..18a1a20d 100644
--- a/src/Alpha_complex/example/Alpha_complex_from_off.cpp
+++ b/src/Alpha_complex/example/Alpha_complex_from_off.cpp
@@ -27,7 +27,7 @@ int main(int argc, char **argv) {
 
   std::streambuf* streambufffer;
   std::ofstream ouput_file_stream;
-  
+
   if (argc == 4) {
     ouput_file_stream.open(std::string(argv[3]));
     streambufffer = ouput_file_stream.rdbuf();
diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h
index a69afb51..eab66384 100644
--- a/src/Alpha_complex/include/gudhi/Alpha_complex.h
+++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h
@@ -20,8 +20,8 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef ALPHA_COMPLEX_H_
-#define ALPHA_COMPLEX_H_
+#ifndef DOC_ALPHA_COMPLEX_INTRO_ALPHA_COMPLEX_H_
+#define DOC_ALPHA_COMPLEX_INTRO_ALPHA_COMPLEX_H_
 
 // to construct a simplex_tree from Delaunay_triangulation
 #include <gudhi/graph_simplicial_complex.h>
@@ -97,7 +97,6 @@ class Alpha_complex : public Simplex_tree<> {
 
   // Double map type to switch from CGAL vertex iterator to simplex tree vertex handle and vice versa.
   typedef typename std::map< CGAL_vertex_iterator, Vertex_handle > Map_vertex_iterator_to_handle;
-  //typedef typename std::map< Vertex_handle, CGAL_vertex_iterator > Map_vertex_handle_to_iterator;
   typedef typename std::vector< CGAL_vertex_iterator > Vector_vertex_iterator;
 
  private:
@@ -141,7 +140,7 @@ class Alpha_complex : public Simplex_tree<> {
   Alpha_complex(Delaunay_triangulation* triangulation_ptr,
                 Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity())
       : triangulation_(triangulation_ptr) {
-   init(max_alpha_square);
+    init(max_alpha_square);
   }
 
   /** \brief Alpha_complex constructor from a list of points.
@@ -160,17 +159,17 @@ class Alpha_complex : public Simplex_tree<> {
       : triangulation_(nullptr) {
     auto first = std::begin(points);
     auto last = std::end(points);
-    
+
     GUDHI_CHECK((first == last),
-                std::invalid_argument ("Alpha_complex::Alpha_complex(InputPointRange) - Empty input point range"));
-    
+                std::invalid_argument("Alpha_complex::Alpha_complex(InputPointRange) - Empty input point range"));
+
     if (first != last) {
       // point_dimension function initialization
       Point_Dimension point_dimension = kernel_.point_dimension_d_object();
 
       // Delaunay triangulation is point dimension minus one.
       triangulation_ = new Delaunay_triangulation(point_dimension(*first) - 1);
-    
+
       size_type inserted = triangulation_->insert(first, last);
       if (inserted != (last -first)) {
         std::cerr << "Alpha_complex - insertion failed " << inserted << " != " << (last -first) << "\n";
@@ -227,7 +226,7 @@ class Alpha_complex : public Simplex_tree<> {
     }
 
     set_dimension(triangulation_->maximal_dimension());
-    // set_filtration to +inf for prune_above_filtration to be done (if necessary) 
+    // set_filtration to +inf for prune_above_filtration to be done (if necessary)
     set_filtration(std::numeric_limits<Filtration_value>::infinity());
 
     // --------------------------------------------------------------------------------------------
@@ -247,7 +246,7 @@ class Alpha_complex : public Simplex_tree<> {
       }
     }
     // --------------------------------------------------------------------------------------------
-    
+
     // --------------------------------------------------------------------------------------------
     // Simplex_tree construction from loop on triangulation finite full cells list
     for (auto cit = triangulation_->finite_full_cells_begin(); cit != triangulation_->finite_full_cells_end(); ++cit) {
@@ -393,4 +392,4 @@ class Alpha_complex : public Simplex_tree<> {
 
 }  // namespace Gudhi
 
-#endif  // ALPHA_COMPLEX_H_
+#endif  // DOC_ALPHA_COMPLEX_INTRO_ALPHA_COMPLEX_H_
diff --git a/src/GudhUI/model/Model.h b/src/GudhUI/model/Model.h
index 99a82eba..1c39c0d7 100644
--- a/src/GudhUI/model/Model.h
+++ b/src/GudhUI/model/Model.h
@@ -71,7 +71,7 @@ class CGAL_geometric_flag_complex_wrapper {
 
   void maximal_face(std::vector<int> vertices) {
     if (!load_only_points_) {
-      //std::cout << "size:" << vertices.size() << std::endl;
+      // std::cout << "size:" << vertices.size() << std::endl;
       for (int i = 0; i < vertices.size(); ++i)
         for (int j = i + 1; j < vertices.size(); ++j)
           complex_.add_edge(Vertex_handle(vertices[i]), Vertex_handle(vertices[j]));
diff --git a/src/GudhUI/utils/Bar_code_persistence.h b/src/GudhUI/utils/Bar_code_persistence.h
index a4cd8156..b527d684 100644
--- a/src/GudhUI/utils/Bar_code_persistence.h
+++ b/src/GudhUI/utils/Bar_code_persistence.h
@@ -12,6 +12,10 @@
 #include <vector>
 #include <limits>  // NaN, infinity
 #include <utility>  // for pair
+#include <string>
+
+#ifndef UTILS_BAR_CODE_PERSISTENCE_H_
+#define UTILS_BAR_CODE_PERSISTENCE_H_
 
 class Bar_code_persistence {
  private:
@@ -21,7 +25,6 @@ class Bar_code_persistence {
   double max_death;
 
  public:
-
   Bar_code_persistence()
       : min_birth(std::numeric_limits<double>::quiet_NaN()),
       max_death(std::numeric_limits<double>::quiet_NaN()) { }
@@ -45,13 +48,13 @@ class Bar_code_persistence {
     QGraphicsScene * scene = new QGraphicsScene();
     view->setScene(scene);
     double ratio = 600.0 / (max_death - min_birth);
-    //std::cout << "min_birth=" << min_birth << " - max_death=" << max_death << " - ratio=" << ratio << std::endl;
+    // std::cout << "min_birth=" << min_birth << " - max_death=" << max_death << " - ratio=" << ratio << std::endl;
 
     double height = 0.0, birth = 0.0, death = 0.0;
     int pers_num = 1;
     for (auto& persistence : persistence_vector) {
       height = 5.0 * pers_num;
-      //std::cout << "[" << pers_num << "] birth=" << persistence.first << " - death=" << persistence.second << std::endl;
+      // std::cout << "[" << pers_num << "] birth=" << persistence.first << " - death=" << persistence.second << std::endl;
       if (std::isfinite(persistence.first))
         birth = ((persistence.first - min_birth) * ratio) + 50.0;
       else
@@ -83,3 +86,5 @@ class Bar_code_persistence {
     view->show();
   }
 };
+
+#endif  // UTILS_BAR_CODE_PERSISTENCE_H_
diff --git a/src/GudhUI/utils/Persistence_compute.h b/src/GudhUI/utils/Persistence_compute.h
index 1f04cc6b..97165490 100644
--- a/src/GudhUI/utils/Persistence_compute.h
+++ b/src/GudhUI/utils/Persistence_compute.h
@@ -85,7 +85,6 @@ template<typename SkBlComplex> class Persistence_compute {
     stream << "p dimension birth death: \n";
 
     pcoh.output_diagram(stream);
-    
   }
 };
 
diff --git a/src/GudhUI/view/FirstCoordProjector.h b/src/GudhUI/view/FirstCoordProjector.h
index 3ceda3f5..a4027b7f 100644
--- a/src/GudhUI/view/FirstCoordProjector.h
+++ b/src/GudhUI/view/FirstCoordProjector.h
@@ -36,7 +36,6 @@ class FirstCoordProjector3D : public Projector3D {
     return Point_3(p.x(), p.y(), p.z());
     else if  (p.dimension() >= 2)
     return Point_3(p.x(), p.y(), 0.0);
-
   }
 };
 
diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
index ac208957..f81951ce 100644
--- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
@@ -39,9 +39,6 @@
 #include <list>
 #include <vector>
 
-using namespace Gudhi;
-using namespace Gudhi::persistent_cohomology;
-
 // Alpha_shape_3 templates type definitions
 typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel;
 typedef CGAL::Alpha_shape_vertex_base_3<Kernel> Vb;
@@ -66,11 +63,12 @@ typedef Alpha_shape_3::Edge Edge_3;
 typedef std::list<Alpha_shape_3::Vertex_handle> Vertex_list;
 
 // gudhi type definition
-typedef Simplex_tree<Simplex_tree_options_fast_persistence> ST;
+typedef Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence> ST;
 typedef ST::Vertex_handle Simplex_tree_vertex;
 typedef std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex > Alpha_shape_simplex_tree_map;
 typedef std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex> Alpha_shape_simplex_tree_pair;
 typedef std::vector< Simplex_tree_vertex > Simplex_tree_vector_vertex;
+typedef Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp > PCOH;
 
 Vertex_list from(const Cell_handle& ch) {
   Vertex_list the_list;
@@ -131,12 +129,7 @@ int main(int argc, char * const argv[]) {
     usage(argv[0]);
   }
 
-  int coeff_field_characteristic = 0;
-  int returnedScanValue = sscanf(argv[2], "%d", &coeff_field_characteristic);
-  if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) {
-    std::cerr << "Error: " << argv[2] << " is not correct\n";
-    usage(argv[0]);
-  }
+  int coeff_field_characteristic = atoi(argv[2]);
 
   Filtration_value min_persistence = 0.0;
   returnedScanValue = sscanf(argv[3], "%lf", &min_persistence);
@@ -282,7 +275,7 @@ int main(int argc, char * const argv[]) {
 
   std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
   // Compute the persistence diagram of the complex
-  Persistent_cohomology< ST, Field_Zp > pcoh(simplex_tree);
+  PCOH pcoh(simplex_tree);
   // initializes the coefficient field for homology
   pcoh.init_coefficients(coeff_field_characteristic);
 
diff --git a/src/common/example/Delaunay_triangulation_off_rw.cpp b/src/common/example/Delaunay_triangulation_off_rw.cpp
index 75e4fafb..4c7a9aaf 100644
--- a/src/common/example/Delaunay_triangulation_off_rw.cpp
+++ b/src/common/example/Delaunay_triangulation_off_rw.cpp
@@ -10,12 +10,12 @@
 // Use dynamic_dimension_tag for the user to be able to set dimension
 typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > K;
 typedef CGAL::Delaunay_triangulation<K> T;
-// The triangulation uses the default instantiation of the 
+// The triangulation uses the default instantiation of the
 // TriangulationDataStructure template parameter
 
 void usage(char * const progName) {
   std::cerr << "Usage: " << progName << " inputFile.off outputFile.off" << std::endl;
-  exit(-1); // ----- >>
+  exit(-1);
 }
 
 int main(int argc, char **argv) {
@@ -30,9 +30,9 @@ int main(int argc, char **argv) {
   // Check the read operation was correct
   if (!off_reader.is_valid()) {
     std::cerr << "Unable to read file " << offInputFile << std::endl;
-    exit(-1); // ----- >>
+    exit(-1);
   }
-  
+
   // Retrieve the triangulation
   T* triangulation = off_reader.get_complex();
   // Operations on triangulation
@@ -47,8 +47,8 @@ int main(int argc, char **argv) {
   // Check the write operation was correct
   if (!off_writer.is_valid()) {
     std::cerr << "Unable to write file " << offOutputFile << std::endl;
-    exit(-1); // ----- >>
+    exit(-1);
   }
-  
+
   return 0;
-}
\ No newline at end of file
+}
diff --git a/src/common/include/gudhi/Delaunay_triangulation_off_io.h b/src/common/include/gudhi/Delaunay_triangulation_off_io.h
index 529774f0..e623cf7b 100644
--- a/src/common/include/gudhi/Delaunay_triangulation_off_io.h
+++ b/src/common/include/gudhi/Delaunay_triangulation_off_io.h
@@ -44,8 +44,8 @@ class Delaunay_triangulation_off_visitor_reader {
   Complex* complex_;
   typedef typename Complex::Point Point;
   std::vector<Point> point_cloud;
- public:
 
+ public:
   // TODO(VR) : Pass a Complex as a parameter is required, even if not used. Otherwise, compilation is KO.
 
   /** \brief Delaunay_triangulation_off_visitor_reader constructor
@@ -153,7 +153,6 @@ class Delaunay_triangulation_off_visitor_reader {
 template<typename Complex>
 class Delaunay_triangulation_off_reader {
  public:
-
   /** \brief Reads the OFF file and constructs the Delaunay triangulation from the points
    * that are in the OFF file.
    *
@@ -180,7 +179,6 @@ class Delaunay_triangulation_off_reader {
       std::cerr << "Delaunay_triangulation_off_reader::Delaunay_triangulation_off_reader could not open file " <<
           name_file << "\n";
     }
-
   }
 
   /** \brief Returns if the OFF file read operation was successful or not.
@@ -201,7 +199,6 @@ class Delaunay_triangulation_off_reader {
     if (valid_)
       return complex_;
     return nullptr;
-
   }
 
  private:
@@ -285,7 +282,6 @@ class Delaunay_triangulation_off_writer {
       }
 
       for (auto cit = complex_ptr->finite_full_cells_begin(); cit != complex_ptr->finite_full_cells_end(); ++cit) {
-        std::vector<int> vertexVector;
         stream << std::distance(cit->vertices_begin(), cit->vertices_end()) << " ";
         for (auto vit = cit->vertices_begin(); vit != cit->vertices_end(); ++vit) {
           stream << points_to_vh[(*vit)->point()] - 1 << " ";
@@ -299,7 +295,7 @@ class Delaunay_triangulation_off_writer {
           name_file << "\n";
     }
   }
-  
+
   /** \brief Returns if the OFF write operation was successful or not.
    *
    * @return OFF file write status.
@@ -313,6 +309,6 @@ class Delaunay_triangulation_off_writer {
   bool valid_;
 };
 
-} // namespace Gudhi
+}  // namespace Gudhi
 
 #endif  // DELAUNAY_TRIANGULATION_OFF_IO_H_
diff --git a/src/common/include/gudhi/Off_reader.h b/src/common/include/gudhi/Off_reader.h
index e45a7600..2420ae72 100644
--- a/src/common/include/gudhi/Off_reader.h
+++ b/src/common/include/gudhi/Off_reader.h
@@ -160,7 +160,7 @@ class Off_reader {
       iss >> num_face_vertices;
       std::vector<int> face;
       face.assign(std::istream_iterator<int>(iss), std::istream_iterator<int>());
-      //if (face.size() != (off_info_.dim + 1)) return false;
+      // if (face.size() != (off_info_.dim + 1)) return false;
       visitor.maximal_face(face);
     }
     return true;