Fix cpplint

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/distance_matrix_in_rips_module@1771 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 994e3bf769d236d230ac2f7e751aa310dabb74bb

12 files changed, 31 insertions, 33 deletions

diff --git a/src/GudhUI/utils/Persistence_compute.h b/src/GudhUI/utils/Persistence_compute.h
index f7048c28..d2973d84 100644
--- a/src/GudhUI/utils/Persistence_compute.h
+++ b/src/GudhUI/utils/Persistence_compute.h
@@ -75,7 +75,7 @@ template<typename SkBlComplex> class Persistence_compute {
     using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
     using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
     using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>;
-    
+
     Rips_complex rips_complex(points, params.threshold, euclidean_distance<Filtration_value, Point_t>);
 
     Simplex_tree st;
@@ -87,7 +87,6 @@ template<typename SkBlComplex> class Persistence_compute {
       pcoh.compute_persistent_cohomology(params.min_pers);
       stream << "persistence: \n";
       stream << "p dimension birth death: \n";
-  
       pcoh.output_diagram(stream);
     }
   }
diff --git a/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp b/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp
index 7a9e9c8b..ee236d61 100644
--- a/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_distance_matrix_persistence.cpp
@@ -66,17 +66,17 @@ int main(int argc, char * argv[]) {
   if (rips_complex_from_file.create_complex(simplex_tree, dim_max)) {
     std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
     std::cout << "   and has dimension " << simplex_tree.dimension() << " \n";
-  
+
     // Sort the simplices in the order of the filtration
     simplex_tree.initialize_filtration();
-  
+
     // Compute the persistence diagram of the complex
     Persistent_cohomology pcoh(simplex_tree);
     // initializes the coefficient field for homology
     pcoh.init_coefficients(p);
-  
+
     pcoh.compute_persistent_cohomology(min_persistence);
-  
+
     // Output the diagram in filediag
     if (filediag.empty()) {
       pcoh.output_diagram();
diff --git a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
index 6db85d16..aaa71db9 100644
--- a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp
@@ -71,17 +71,17 @@ int main(int argc, char * argv[]) {
   if (rips_complex_from_file.create_complex(simplex_tree, dim_max)) {
     std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
     std::cout << "   and has dimension " << simplex_tree.dimension() << " \n";
-  
+
     // Sort the simplices in the order of the filtration
     simplex_tree.initialize_filtration();
-  
+
     // Compute the persistence diagram of the complex
     Persistent_cohomology pcoh(simplex_tree);
     // initializes the coefficient field for homology
     pcoh.init_coefficients(min_p, max_p);
-  
+
     pcoh.compute_persistent_cohomology(min_persistence);
-  
+
     // Output the diagram in filediag
     if (filediag.empty()) {
       pcoh.output_diagram();
diff --git a/src/Persistent_cohomology/example/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp
index 3fa8aa30..0b1873d4 100644
--- a/src/Persistent_cohomology/example/rips_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence.cpp
@@ -70,17 +70,17 @@ int main(int argc, char * argv[]) {
   if (rips_complex_from_file.create_complex(simplex_tree, dim_max)) {
     std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
     std::cout << "   and has dimension " << simplex_tree.dimension() << " \n";
-  
+
     // Sort the simplices in the order of the filtration
     simplex_tree.initialize_filtration();
-  
+
     // Compute the persistence diagram of the complex
     Persistent_cohomology pcoh(simplex_tree);
     // initializes the coefficient field for homology
     pcoh.init_coefficients(p);
-  
+
     pcoh.compute_persistent_cohomology(min_persistence);
-  
+
     // Output the diagram in filediag
     if (filediag.empty()) {
       pcoh.output_diagram();
diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp
index 54fa3aa1..b1ba494e 100644
--- a/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp
+++ b/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp
@@ -5,6 +5,7 @@
 
 #include <iostream>
 #include <string>
+#include <vector>
 #include <limits>  // for std::numeric_limits
 
 void usage(int nbArgs, char * const progName) {
@@ -38,7 +39,7 @@ int main(int argc, char **argv) {
   distances.push_back({0.77, 0.26});
   distances.push_back({0.99, 0.99, 0.28});
   distances.push_back({0.11, 0.39, 0.97, 0.30});
-  
+
   // ----------------------------------------------------------------------------
   // Init of a rips complex from points
   // ----------------------------------------------------------------------------
diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp
index 26517876..68fc3629 100644
--- a/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp
+++ b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp
@@ -5,6 +5,7 @@
 
 #include <iostream>
 #include <string>
+#include <vector>
 #include <limits>  // for std::numeric_limits
 
 void usage(int nbArgs, char * const progName) {
@@ -33,7 +34,7 @@ int main(int argc, char **argv) {
   points.push_back({0.0, 14.0});
   points.push_back({2.0, 19.0});
   points.push_back({9.0, 17.0});
-  
+
   // ----------------------------------------------------------------------------
   // Init of a rips complex from points
   // ----------------------------------------------------------------------------
diff --git a/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp
index cfada84a..730bfc7c 100644
--- a/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp
+++ b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp
@@ -7,6 +7,7 @@
 
 #include <iostream>
 #include <string>
+#include <vector>
 
 void usage(int nbArgs, char * const progName) {
   std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
diff --git a/src/Rips_complex/example/example_rips_complex_from_off_file.cpp b/src/Rips_complex/example/example_rips_complex_from_off_file.cpp
index 60050cea..469de403 100644
--- a/src/Rips_complex/example/example_rips_complex_from_off_file.cpp
+++ b/src/Rips_complex/example/example_rips_complex_from_off_file.cpp
@@ -7,6 +7,7 @@
 
 #include <iostream>
 #include <string>
+#include <vector>
 
 void usage(int nbArgs, char * const progName) {
   std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
diff --git a/src/Rips_complex/include/gudhi/Rips_complex.h b/src/Rips_complex/include/gudhi/Rips_complex.h
index 63207892..f98a6993 100644
--- a/src/Rips_complex/include/gudhi/Rips_complex.h
+++ b/src/Rips_complex/include/gudhi/Rips_complex.h
@@ -64,7 +64,6 @@ class Rips_complex {
   typedef int Vertex_handle;
 
  public:
-
   /** \brief Rips_complex constructor from a list of points.
    *
    * @param[in] points Range of points.
@@ -87,7 +86,7 @@ class Rips_complex {
    */
   template<typename InputDistanceRange>
   Rips_complex(const InputDistanceRange& distance_matrix, Filtration_value threshold) {
-    compute_proximity_graph(boost::irange((size_t)0,distance_matrix.size()), threshold,
+    compute_proximity_graph(boost::irange((size_t)0, distance_matrix.size()), threshold,
                             [&](size_t i, size_t j){return distance_matrix[j][i];});
   }
 
@@ -106,7 +105,7 @@ class Rips_complex {
   bool create_complex(SimplicialComplexForRips& complex, int dim_max) {
     if (complex.num_vertices() > 0) {
       std::cerr << "Rips_complex create_complex - complex is not empty\n";
-      return false; // ----- >>
+      return false;  // ----- >>
     }
 
     // insert the proximity graph in the simplicial complex
@@ -118,7 +117,7 @@ class Rips_complex {
     return true;
   }
 
- public:
+ private:
   /** \brief Output the proximity graph of the points.
    *
    * If points contains n elements, the proximity graph is the graph 
@@ -133,20 +132,17 @@ class Rips_complex {
                Distance distance) {
     std::vector< std::pair< Vertex_handle, Vertex_handle > > edges;
     std::vector< Filtration_value > edges_fil;
-    std::map< Vertex_handle, Filtration_value > vertices;
 
     // Compute the proximity graph of the points.
     // If points contains n elements, the proximity graph is the graph with n vertices, and an edge [u,v] iff the
     // distance function between points u and v is smaller than threshold.
     // --------------------------------------------------------------------------------------------
     // Creates the vector of edges and its filtration values (returned by distance function)
-    Vertex_handle idx_u, idx_v;
-    Filtration_value fil;
-    idx_u = 0;
+    Vertex_handle idx_u = 0;
     for (auto it_u = std::begin(points); it_u != std::end(points); ++it_u) {
-      idx_v = idx_u + 1;
+      Vertex_handle idx_v = idx_u + 1;
       for (auto it_v = it_u + 1; it_v != std::end(points); ++it_v, ++idx_v) {
-        fil = distance(*it_u, *it_v);
+        Filtration_value fil = distance(*it_u, *it_v);
         if (fil <= threshold) {
           edges.emplace_back(idx_u, idx_v);
           edges_fil.push_back(fil);
@@ -172,11 +168,10 @@ class Rips_complex {
 
  private:
   Graph_t rips_skeleton_graph_;
-
 };
 
-} // namespace rips_complex
+}  // namespace rips_complex
 
-} // namespace Gudhi
+}  // namespace Gudhi
 
 #endif  // RIPS_COMPLEX_H_
diff --git a/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp b/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp
index 13c700c6..1dff4529 100644
--- a/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp
+++ b/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp
@@ -26,6 +26,7 @@
 #include <iostream>
 #include <ctime>
 #include <string>
+#include <utility>  // for std::pair
 
 using namespace Gudhi;
 
diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h
index ed2c1f5d..58a513e7 100644
--- a/src/common/include/gudhi/distance_functions.h
+++ b/src/common/include/gudhi/distance_functions.h
@@ -32,12 +32,12 @@
 /** @brief Compute the Euclidean distance between two Points given by a range of coordinates. The points are assumed to
  * have the same dimension. */
 template< typename Filtration_value, typename Point >
-Filtration_value euclidean_distance(const Point &p1,const Point &p2) {
+Filtration_value euclidean_distance(const Point &p1, const Point &p2) {
   Filtration_value dist = 0.;
   auto it1 = p1.begin();
   auto it2 = p2.begin();
   for (; it1 != p1.end(); ++it1, ++it2) {
-    Filtration_value tmp = (double)(*it1) - (double)(*it2);
+    Filtration_value tmp = static_cast<double>(*it1) - static_cast<double>(*it2);
     dist += tmp*tmp;
   }
   return std::sqrt(dist);
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index ddec5ba7..2d774d4d 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -222,7 +222,7 @@ bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundar
  **/
 template< typename Filtration_value >
 std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from_csv_file(const std::string& filename,
-                                                                                          const char separator=';') {
+                                                                                          const char separator = ';') {
 #ifdef DEBUG_TRACES
   std::cout << "Using procedure read_lower_triangular_matrix_from_csv_file \n";
 #endif  // DEBUG_TRACES
@@ -273,7 +273,6 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from
     }
     if (!values_in_this_line.empty())result.push_back(values_in_this_line);
     ++number_of_line;
-
   }
   in.close();