clang format files

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@3216 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 09a40b92cc8e0cc1a08f962de14daed975338d1c

3 files changed, 45 insertions, 52 deletions

diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h
index 0c1acba7..3f02206b 100644
--- a/src/Rips_complex/doc/Intro_rips_complex.h
+++ b/src/Rips_complex/doc/Intro_rips_complex.h
@@ -167,7 +167,8 @@ namespace rips_complex {
  * 
  * \include Rips_complex/one_skeleton_rips_from_correlation_matrix_for_doc.txt
  * 
- * All the other constructions discussed for Rips complex for distance matrix can be also performed for Rips complexes construction from correlation matrices.
+ * All the other constructions discussed for Rips complex for distance matrix can be also performed for Rips complexes
+ * construction from correlation matrices.
  * 
  */
 /** @} */  // end defgroup rips_complex
diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp
index d1ccbf31..0da1dc20 100644
--- a/src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp
+++ b/src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp
@@ -42,17 +42,16 @@ int main() {
   }
 
   //-----------------------------------------------------------------------------
-  // Now the correlation matrix is a distance matrix and can be processed further. 
+  // Now the correlation matrix is a distance matrix and can be processed further.
   //-----------------------------------------------------------------------------
   Distance_matrix distances = correlations;
 
   //------------------------------------------------------------------------------
-  //Note that this treshold mean that the points in the distance 1, i.e. corelation
-  //0 will be connected. 
+  // Note that this treshold mean that the points in the distance 1, i.e. corelation
+  // 0 will be connected.
   //------------------------------------------------------------------------------
   double threshold = 1.0;
-  
-  
+
   Rips_complex rips_complex_from_points(distances, threshold);
 
   Simplex_tree stree;
@@ -63,7 +62,7 @@ int main() {
   // above, which is 1 - initial correlation matrix. Only this way, we obtain
   // a complex with filtration. If a correlation matrix is used instead, we would
   // have a reverse filtration (i.e. filtration of boundary of each simplex S
-  // is greater or equal to the filtration of S). 
+  // is greater or equal to the filtration of S).
   // ----------------------------------------------------------------------------
   std::cout << "Rips complex is of dimension " << stree.dimension() << " - " << stree.num_simplices() << " simplices - "
             << stree.num_vertices() << " vertices." << std::endl;
diff --git a/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp b/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp
index 676ef793..3fe0edb0 100644
--- a/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp
+++ b/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp
@@ -39,7 +39,7 @@ 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>;
 using Correlation_matrix = std::vector<std::vector<Filtration_value>>;
-using intervals_common = Gudhi::Persistence_interval_common< double , int >;
+using intervals_common = Gudhi::Persistence_interval_common<double, int>;
 
 void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::string& filediag,
                      Filtration_value& correlation_min, int& dim_max, int& p, Filtration_value& min_persistence);
@@ -69,16 +69,14 @@ int main(int argc, char* argv[]) {
   }
 
   Filtration_value threshold;
-  //If the correlation_min, being minimal corelation is in the range [0,1],
-  //change it to 1-correlation_min
-  if ( ( correlation_min>=0 ) && ( correlation_min<=1 ) )
-  {
-	  threshold = 1-correlation_min;
-  }
-  else
-  {
-	  std::cout << "Wrong value of the treshold corelation (should be between 0 and 1). The program will now terminate.\n";
-	  return 1;
+  // If the correlation_min, being minimal corelation is in the range [0,1],
+  // change it to 1-correlation_min
+  if ((correlation_min >= 0) && (correlation_min <= 1)) {
+    threshold = 1 - correlation_min;
+  } else {
+    std::cout
+        << "Wrong value of the treshold corelation (should be between 0 and 1). The program will now terminate.\n";
+    return 1;
   }
 
   Rips_complex rips_complex_from_file(correlations, threshold);
@@ -97,34 +95,30 @@ int main(int argc, char* argv[]) {
   Persistent_cohomology pcoh(simplex_tree);
   // initializes the coefficient field for homology
   pcoh.init_coefficients(p);
-  //compute persistence
+  // compute persistence
   pcoh.compute_persistent_cohomology(min_persistence);
 
-
-  //invert the persistence diagram
+  // invert the persistence diagram
   auto pairs = pcoh.get_persistent_pairs();
-  std::vector< intervals_common > processed_persistence_intervals;
-  processed_persistence_intervals.reserve( pairs.size() );
-  for (auto pair :pairs )
-  {
-	  double birth = 1-simplex_tree.filtration( get<0>(pair) );
-	  double death = 1-simplex_tree.filtration( get<1>(pair) );
-	  unsigned dimension = (unsigned)simplex_tree.dimension( get<0>(pair) );
-	  int field = get<2>(pair);
-	  processed_persistence_intervals.push_back(
-	  intervals_common(birth, death,dimension,field)
-	  );
+  std::vector<intervals_common> processed_persistence_intervals;
+  processed_persistence_intervals.reserve(pairs.size());
+  for (auto pair : pairs) {
+    double birth = 1 - simplex_tree.filtration(get<0>(pair));
+    double death = 1 - simplex_tree.filtration(get<1>(pair));
+    unsigned dimension = (unsigned)simplex_tree.dimension(get<0>(pair));
+    int field = get<2>(pair);
+    processed_persistence_intervals.push_back(intervals_common(birth, death, dimension, field));
   }
 
-  //sort the processed intervals:
-  std::sort( processed_persistence_intervals.begin() , processed_persistence_intervals.end() );
+  // sort the processed intervals:
+  std::sort(processed_persistence_intervals.begin(), processed_persistence_intervals.end());
 
-  //and write them to a file
+  // and write them to a file
   if (filediag.empty()) {
     write_persistence_intervals_to_stream(processed_persistence_intervals);
   } else {
     std::ofstream out(filediag);
-    write_persistence_intervals_to_stream(processed_persistence_intervals,out);
+    write_persistence_intervals_to_stream(processed_persistence_intervals, out);
     out.close();
   }
   return 0;
@@ -134,23 +128,22 @@ void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::
                      Filtration_value& correlation_min, int& dim_max, int& p, Filtration_value& min_persistence) {
   namespace po = boost::program_options;
   po::options_description hidden("Hidden options");
-  hidden.add_options()
-      ("input-file", po::value<std::string>(&csv_matrix_file),
-       "Name of file containing a corelation matrix. Can be square or lower triangular matrix. Separator is ';'.");
+  hidden.add_options()(
+      "input-file", po::value<std::string>(&csv_matrix_file),
+      "Name of file containing a corelation matrix. Can be square or lower triangular matrix. Separator is ';'.");
   po::options_description visible("Allowed options", 100);
-  visible.add_options()
-      ("help,h", "produce help message")
-      ("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")
-      ("min-edge-corelation,c",
-       po::value<Filtration_value>(&correlation_min)->default_value(0),
-       "Minimal corelation of an edge for the Rips complex construction.")
-      ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
-       "Maximal dimension of the Rips complex we want to compute.")
-      ("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),
-       "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals");
+  visible.add_options()("help,h", "produce help message")(
+      "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")(
+      "min-edge-corelation,c", po::value<Filtration_value>(&correlation_min)->default_value(0),
+      "Minimal corelation of an edge for the Rips complex construction.")(
+      "cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
+      "Maximal dimension of the Rips complex we want to compute.")(
+      "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),
+      "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length "
+      "intervals");
 
   po::positional_options_description pos;
   pos.add("input-file", 1);