Fix cpplint

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3149 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: e1cc797f8c24015168a1f84430666e8a156ababa

4 files changed, 73 insertions, 111 deletions

diff --git a/src/Witness_complex/example/example_strong_witness_complex_off.cpp b/src/Witness_complex/example/example_strong_witness_complex_off.cpp
index bc069654..346bef6d 100644
--- a/src/Witness_complex/example/example_strong_witness_complex_off.cpp
+++ b/src/Witness_complex/example/example_strong_witness_complex_off.cpp
@@ -39,10 +39,9 @@ using Point_d = typename K::Point_d;
 using Witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex<K>;
 using Point_vector = std::vector<Point_d>;
 
-int main(int argc, char * const argv[]) {
+int main(int argc, char* const argv[]) {
   if (argc != 5) {
-    std::cerr << "Usage: " << argv[0]
-        << " path_to_point_file number_of_landmarks max_squared_alpha limit_dimension\n";
+    std::cerr << "Usage: " << argv[0] << " path_to_point_file number_of_landmarks max_squared_alpha limit_dimension\n";
     return 0;
   }
 
@@ -56,9 +55,9 @@ int main(int argc, char * const argv[]) {
   Point_vector point_vector, landmarks;
   Gudhi::Points_off_reader<Point_d> off_reader(file_name);
   if (!off_reader.is_valid()) {
-      std::cerr << "Strong witness complex - Unable to read file " << file_name << "\n";
-      exit(-1);  // ----- >>
-    }
+    std::cerr << "Strong witness complex - Unable to read file " << file_name << "\n";
+    exit(-1);  // ----- >>
+  }
   point_vector = Point_vector(off_reader.get_point_cloud());
 
   std::cout << "Successfully read " << point_vector.size() << " points.\n";
@@ -66,16 +65,15 @@ int main(int argc, char * const argv[]) {
 
   // Choose landmarks (decomment one of the following two lines)
   // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
-  Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, nbL, Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks));
-  
+  Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, nbL, Gudhi::subsampling::random_starting_point,
+                                               std::back_inserter(landmarks));
+
   // Compute witness complex
   start = clock();
-  Witness_complex witness_complex(landmarks,
-                                  point_vector);
+  Witness_complex witness_complex(landmarks, point_vector);
 
   witness_complex.create_complex(simplex_tree, alpha2, lim_dim);
   end = clock();
-  std::cout << "Strong witness complex took "
-      << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
+  std::cout << "Strong witness complex took " << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
   std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n";
 }
diff --git a/src/Witness_complex/example/example_witness_complex_sphere.cpp b/src/Witness_complex/example/example_witness_complex_sphere.cpp
index a66da3f9..a6e9b11a 100644
--- a/src/Witness_complex/example/example_witness_complex_sphere.cpp
+++ b/src/Witness_complex/example/example_witness_complex_sphere.cpp
@@ -42,27 +42,25 @@
 /** Write a gnuplot readable file.
  *  Data range is a random access range of pairs (arg, value)
  */
-template < typename Data_range >
-void write_data(Data_range & data, std::string filename) {
+template <typename Data_range>
+void write_data(Data_range& data, std::string filename) {
   std::ofstream ofs(filename, std::ofstream::out);
-  for (auto entry : data)
-    ofs << entry.first << ", " << entry.second << "\n";
+  for (auto entry : data) ofs << entry.first << ", " << entry.second << "\n";
   ofs.close();
 }
 
-int main(int argc, char * const argv[]) {
+int main(int argc, char* const argv[]) {
   using Kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
   using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex<Kernel>;
 
   if (argc != 2) {
-    std::cerr << "Usage: " << argv[0]
-        << " number_of_landmarks \n";
+    std::cerr << "Usage: " << argv[0] << " number_of_landmarks \n";
     return 0;
   }
 
   int number_of_landmarks = atoi(argv[1]);
 
-  std::vector< std::pair<int, double> > l_time;
+  std::vector<std::pair<int, double> > l_time;
 
   // Generate points
   for (int nbP = 500; nbP < 10000; nbP += 500) {
@@ -77,16 +75,16 @@ int main(int argc, char * const argv[]) {
     // Choose landmarks
     start = clock();
     // Gudhi::subsampling::pick_n_random_points(point_vector, number_of_landmarks, std::back_inserter(landmarks));
-    Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, number_of_landmarks, Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks));
+    Gudhi::subsampling::choose_n_farthest_points(K(), point_vector, number_of_landmarks,
+                                                 Gudhi::subsampling::random_starting_point,
+                                                 std::back_inserter(landmarks));
 
     // Compute witness complex
-    Witness_complex witness_complex(landmarks,
-                                    point_vector);
+    Witness_complex witness_complex(landmarks, point_vector);
     witness_complex.create_complex(simplex_tree, 0);
     end = clock();
     double time = static_cast<double>(end - start) / CLOCKS_PER_SEC;
-    std::cout << "Witness complex for " << number_of_landmarks << " landmarks took "
-        << time << " s. \n";
+    std::cout << "Witness complex for " << number_of_landmarks << " landmarks took " << time << " s. \n";
     std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n";
     l_time.push_back(std::make_pair(nbP, time));
   }
diff --git a/src/Witness_complex/utilities/strong_witness_persistence.cpp b/src/Witness_complex/utilities/strong_witness_persistence.cpp
index e3e0c1ee..2fba631b 100644
--- a/src/Witness_complex/utilities/strong_witness_persistence.cpp
+++ b/src/Witness_complex/utilities/strong_witness_persistence.cpp
@@ -47,16 +47,10 @@ using Filtration_value = SimplexTree::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
-                     , std::string & file_name
-                     , std::string & filediag
-                     , Filtration_value & max_squared_alpha
-                     , int & p
-                     , int & dim_max
-                     , Filtration_value & min_persistence);
-
-int main(int argc, char * argv[]) {
+void program_options(int argc, char* argv[], int& nbL, std::string& file_name, std::string& filediag,
+                     Filtration_value& max_squared_alpha, int& p, int& dim_max, Filtration_value& min_persistence);
+
+int main(int argc, char* argv[]) {
   std::string file_name;
   std::string filediag;
   Filtration_value max_squared_alpha;
@@ -70,8 +64,8 @@ int main(int argc, char * argv[]) {
   Point_vector witnesses, landmarks;
   Gudhi::Points_off_reader<Point_d> off_reader(file_name);
   if (!off_reader.is_valid()) {
-      std::cerr << "Witness complex - Unable to read file " << file_name << "\n";
-      exit(-1);  // ----- >>
+    std::cerr << "Witness complex - Unable to read file " << file_name << "\n";
+    exit(-1);  // ----- >>
   }
   witnesses = Point_vector(off_reader.get_point_cloud());
   std::cout << "Successfully read " << witnesses.size() << " points.\n";
@@ -79,11 +73,11 @@ int main(int argc, char * argv[]) {
 
   // Choose landmarks (decomment one of the following two lines)
   // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
-  Gudhi::subsampling::choose_n_farthest_points(K(), witnesses, nbL, Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks));
+  Gudhi::subsampling::choose_n_farthest_points(K(), witnesses, nbL, Gudhi::subsampling::random_starting_point,
+                                               std::back_inserter(landmarks));
 
   // Compute witness complex
-  Strong_witness_complex strong_witness_complex(landmarks,
-                                                witnesses);
+  Strong_witness_complex strong_witness_complex(landmarks, witnesses);
 
   strong_witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d);
 
@@ -112,37 +106,28 @@ int main(int argc, char * argv[]) {
   return 0;
 }
 
-void program_options(int argc, char * argv[]
-                     , int & nbL
-                     , std::string & file_name
-                     , std::string & filediag
-                     , Filtration_value & max_squared_alpha
-                     , int & p
-                     , int & dim_max
-                     , Filtration_value & min_persistence) {
+void program_options(int argc, char* argv[], int& nbL, std::string& file_name, std::string& filediag,
+                     Filtration_value& max_squared_alpha, 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.");
+  hidden.add_options()("input-file", po::value<std::string>(&file_name),
+                       "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(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.")
-      ("min-persistence,m", po::value<Filtration_value>(&min_persistence)->default_value(0),
-       "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 strong witness complex we want to compute.");
+  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(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.")(
+      "min-persistence,m", po::value<Filtration_value>(&min_persistence)->default_value(0),
+      "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 strong witness complex we want to compute.");
 
   po::positional_options_description pos;
   pos.add("input-file", 1);
@@ -151,8 +136,7 @@ void program_options(int argc, char * argv[]
   all.add(visible).add(hidden);
   po::variables_map vm;
 
-  po::store(po::command_line_parser(argc, argv).
-            options(all).positional(pos).run(), vm);
+  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")) {
@@ -170,4 +154,3 @@ void program_options(int argc, char * argv[]
     std::abort();
   }
 }
-
diff --git a/src/Witness_complex/utilities/weak_witness_persistence.cpp b/src/Witness_complex/utilities/weak_witness_persistence.cpp
index a63b0837..23fa93aa 100644
--- a/src/Witness_complex/utilities/weak_witness_persistence.cpp
+++ b/src/Witness_complex/utilities/weak_witness_persistence.cpp
@@ -47,16 +47,10 @@ using Filtration_value = SimplexTree::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
-                     , std::string & file_name
-                     , std::string & filediag
-                     , Filtration_value & max_squared_alpha
-                     , int & p
-                     , int & dim_max
-                     , Filtration_value & min_persistence);
-
-int main(int argc, char * argv[]) {
+void program_options(int argc, char* argv[], int& nbL, std::string& file_name, std::string& filediag,
+                     Filtration_value& max_squared_alpha, int& p, int& dim_max, Filtration_value& min_persistence);
+
+int main(int argc, char* argv[]) {
   std::string file_name;
   std::string filediag;
   Filtration_value max_squared_alpha;
@@ -70,8 +64,8 @@ int main(int argc, char * argv[]) {
   Point_vector witnesses, landmarks;
   Gudhi::Points_off_reader<Point_d> off_reader(file_name);
   if (!off_reader.is_valid()) {
-      std::cerr << "Witness complex - Unable to read file " << file_name << "\n";
-      exit(-1);  // ----- >>
+    std::cerr << "Witness complex - Unable to read file " << file_name << "\n";
+    exit(-1);  // ----- >>
   }
   witnesses = Point_vector(off_reader.get_point_cloud());
   std::cout << "Successfully read " << witnesses.size() << " points.\n";
@@ -79,11 +73,11 @@ int main(int argc, char * argv[]) {
 
   // Choose landmarks (decomment one of the following two lines)
   // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
-  Gudhi::subsampling::choose_n_farthest_points(K(), witnesses, nbL, Gudhi::subsampling::random_starting_point, std::back_inserter(landmarks));
+  Gudhi::subsampling::choose_n_farthest_points(K(), witnesses, nbL, Gudhi::subsampling::random_starting_point,
+                                               std::back_inserter(landmarks));
 
   // Compute witness complex
-  Witness_complex witness_complex(landmarks,
-                                  witnesses);
+  Witness_complex witness_complex(landmarks, witnesses);
 
   witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d);
 
@@ -112,38 +106,28 @@ int main(int argc, char * argv[]) {
   return 0;
 }
 
-
-void program_options(int argc, char * argv[]
-                     , int & nbL
-                     , std::string & file_name
-                     , std::string & filediag
-                     , Filtration_value & max_squared_alpha
-                     , int & p
-                     , int & dim_max
-                     , Filtration_value & min_persistence) {
+void program_options(int argc, char* argv[], int& nbL, std::string& file_name, std::string& filediag,
+                     Filtration_value& max_squared_alpha, 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.");
+  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")
-      ("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(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.")
-      ("min-persistence,m", po::value<Filtration_value>(&min_persistence)->default_value(0),
-       "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.");
+  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(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.")(
+      "min-persistence,m", po::value<Filtration_value>(&min_persistence)->default_value(0),
+      "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);
@@ -152,8 +136,7 @@ void program_options(int argc, char * argv[]
   all.add(visible).add(hidden);
   po::variables_map vm;
 
-  po::store(po::command_line_parser(argc, argv).
-            options(all).positional(pos).run(), vm);
+  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")) {