clang format all sources

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_representation_integration@2477 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 326d664483d6700f82be824f79a0bf5c082b4945

1 files changed, 137 insertions, 174 deletions

diff --git a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h
index a4884314..39d485a9 100644
--- a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h
+++ b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h
@@ -20,7 +20,6 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-
 #ifndef READ_PERSISTENCE_FROM_FILE_H_
 #define READ_PERSISTENCE_FROM_FILE_H_
 
@@ -30,184 +29,148 @@
 #include <vector>
 #include <algorithm>
 
+namespace Gudhi {
+namespace Persistence_representations {
 
+/**
+ * Universal procedure to read files with persistence. It ignores the lines starting from # (treat them as comments).
+ * It reads the fist line which is not a comment and assume that there are some numerical entries over there. The
+ *program assume
+ * that each other line in the file, which is not a comment, have the same number of numerical entries (2, 3 or 4).
+ * If there are two numerical entries per line, then the function assume that they are birth/death coordinates.
+ * If there are three numerical entries per line, then the function assume that they are: dimension and birth/death
+ *coordinates.
+ * If there are four numerical entries per line, then the function assume that they are: the characteristic of a filed
+ *over which
+ * persistence was computed, dimension and birth/death coordinates.
+ * The 'inf' string can appear only as a last element of a line.
+ * The procedure returns vector of persistence pairs.
+**/
+std::vector<std::pair<double, double> > read_persistence_intervals_in_one_dimension_from_file(
+    std::string const& filename, int dimension = -1, double what_to_substitute_for_infinite_bar = -1) {
+  bool dbg = false;
+  std::ifstream in;
+  in.open(filename);
+  // checking if the file exist:
+  if (!in.good()) {
+    std::cerr << "The file : " << filename << " do not exist. The program will now terminate \n";
+    throw "The file from which you are trying to read the persistence landscape do not exist. The program will now terminate \n";
+  }
 
-namespace Gudhi
-{
-namespace Persistence_representations
-{
+  std::string line;
+  std::vector<std::pair<double, double> > barcode;
 
-/**
- * Universal procedure to read files with persistence. It ignores the lines starting from # (treat them as comments). 
- * It reads the fist line which is not a comment and assume that there are some numerical entries over there. The program assume
- * that each other line in the file, which is not a comment, have the same number of numerical entries (2, 3 or 4). 
- * If there are two numerical entries per line, then the function assume that they are birth/death coordinates. 
- * If there are three numerical entries per line, then the function assume that they are: dimension and birth/death coordinates. 
- * If there are four numerical entries per line, then the function assume that they are: the characteristic of a filed over which 
- * persistence was computed, dimension and birth/death coordinates. 
- * The 'inf' string can appear only as a last element of a line. 
- * The procedure returns vector of persistence pairs. 
-**/ 
-std::vector<std::pair<double,double> > read_persistence_intervals_in_one_dimension_from_file(std::string const& filename, int dimension=-1 , double what_to_substitute_for_infinite_bar = -1 )
-{
-	bool dbg = false;
-	std::ifstream in;
-	in.open( filename );
-	//checking if the file exist:
-	if ( !in.good() )
-	{
-		std::cerr << "The file : " << filename << " do not exist. The program will now terminate \n";
-		throw "The file from which you are trying to read the persistence landscape do not exist. The program will now terminate \n";
-	}
-	
-	
-	
+  int number_of_entries_per_line = -1;
 
-	std::string line;
-	std::vector< std::pair<double,double> > barcode;
-	
-	int number_of_entries_per_line = -1;
+  while (!in.eof()) {
+    getline(in, line);
+    if (dbg) std::cerr << "Reading line : " << line << std::endl;
+    if (!(line.length() == 0 || line[0] == '#')) {
+      // If we do not know how many entries per line we have, we check it in below.
+      if (number_of_entries_per_line == -1) {
+        number_of_entries_per_line = 0;
+        std::string line_copy(line);
+        if (line_copy.find("inf") != std::string::npos) {
+          size_t np = line_copy.find("inf");
+          // replace symbols 'inf' in line_copy with white spaces:
+          line_copy[np] = ' ';
+          line_copy[np + 1] = ' ';
+          line_copy[np + 2] = ' ';
+          number_of_entries_per_line = 1;
+        }
+        // check how many entries we have in the line.
+        std::stringstream ss(line_copy);
+        double number;
+        std::vector<double> this_line;
+        while (ss >> number) {
+          this_line.push_back(number);
+        }
+        number_of_entries_per_line += (int)this_line.size();
+        if (dbg) {
+          std::cerr << "number_of_entries_per_line : " << number_of_entries_per_line
+                    << ". This number was obtained by analyzing this line : " << line << std::endl;
+        }
+        if ((number_of_entries_per_line < 2) || (number_of_entries_per_line > 4)) {
+          std::cerr << "The input file you have provided have wrong number of numerical entries per line. The program "
+                       "will now terminate. \n";
+          throw "The input file you have provided have wrong number of numerical entries per line. The program will now terminate. \n";
+        }
+      }
+      // In case there is an 'inf' string in this line, we are dealing with this situation in below.
+      if (line.find("inf") != std::string::npos) {
+        if (dbg) {
+          std::cerr << "This line: " << line << " contains infinite interval. \n";
+        }
+        // first we substitute inf by white spaces:
+        size_t np = line.find("inf");
+        line[np] = ' ';
+        line[np + 1] = ' ';
+        line[np + 2] = ' ';
+        if (what_to_substitute_for_infinite_bar != -1) {
+          double beginn, field, dim;
+          std::stringstream lineSS(line);
+          if (number_of_entries_per_line == 4) lineSS >> field;
+          if (number_of_entries_per_line >= 3) {
+            lineSS >> dim;
+          } else {
+            dim = dimension;
+          }
+          lineSS >> beginn;
+          if (dim == dimension) {
+            if (beginn > what_to_substitute_for_infinite_bar) {
+              barcode.push_back(std::make_pair(what_to_substitute_for_infinite_bar, beginn));
+            } else {
+              barcode.push_back(std::make_pair(beginn, what_to_substitute_for_infinite_bar));
+            }
+            if (dbg) {
+              std::cerr << "this is the line that is going to the output : " << beginn << " , "
+                        << what_to_substitute_for_infinite_bar << std::endl;
+            }
+          }
+        } else {
+          // this is a line with infinity. Since the variable what_to_substitute_for_infinite_bar have not been set up,
+          // it means that this line will be skipped.
+          if (dbg) {
+            std::cerr << "We will skip it \n";
+          }
+        }
+        continue;
+      } else {
+        // Then, we read the content of the line. We know that it do not contain 'inf' substring.
+        std::stringstream lineSS(line);
+        double beginn, endd, field, dim;
+        if (number_of_entries_per_line == 4) lineSS >> field;
+        if (number_of_entries_per_line >= 3) {
+          lineSS >> dim;
+        } else {
+          dim = dimension;
+        }
+        lineSS >> beginn;
+        lineSS >> endd;
+        if (beginn > endd) {
+          std::swap(beginn, endd);
+        }
+        if (dim == dimension) {
+          barcode.push_back(std::make_pair(beginn, endd));
+          if (dbg) {
+            std::cerr << "This is a line that is going to the output : " << beginn << " , " << endd << std::endl;
+          }
+        } else {
+          if ((number_of_entries_per_line == 3) && (dimension == -1)) {
+            barcode.push_back(std::make_pair(beginn, endd));
+          }
+        }
+      }
+    } else {
+      if (dbg) {
+        std::cerr << "This is a comment line \n";
+      }
+    }
+  }
+  in.close();
+  if (dbg) std::cerr << "End of reading \n";
 
-	while (!in.eof())
-	{
-		getline(in,line);
-		if ( dbg )std::cerr << "Reading line : " << line << std::endl;
-		if ( !(line.length() == 0 || line[0] == '#') )
-		{
-			//If we do not know how many entries per line we have, we check it in below.
-			if ( number_of_entries_per_line == -1 )
-			{	
-				number_of_entries_per_line = 0;
-				std::string line_copy(line);			
-				if ( line_copy.find("inf") != std::string::npos )
-				{					
-					size_t np = line_copy.find("inf");
-					//replace symbols 'inf' in line_copy with white spaces:					
-					line_copy[np] = ' ';
-					line_copy[np+1] = ' ';
-					line_copy[np+2] = ' ';		
-					number_of_entries_per_line = 1;			
-				}				
-				//check how many entries we have in the line.				
-				std::stringstream ss( line_copy );
-				double number;
-				std::vector<double> this_line;
-				while ( ss >> number )
-				{
-					this_line.push_back( number );
-				}
-				number_of_entries_per_line += (int)this_line.size();						
-				if ( dbg )
-				{
-					std::cerr << "number_of_entries_per_line : " << number_of_entries_per_line << ". This number was obtained by analyzing this line : " << line << std::endl;
-				}
-				if ( (number_of_entries_per_line < 2) || ( number_of_entries_per_line > 4 ) )
-				{
-					std::cerr << "The input file you have provided have wrong number of numerical entries per line. The program will now terminate. \n";
-					throw "The input file you have provided have wrong number of numerical entries per line. The program will now terminate. \n";
-				}
-			}
-			//In case there is an 'inf' string in this line, we are dealing with this situation in below.
-			if ( line.find("inf") != std::string::npos )
-			{
-				if ( dbg )
-				{
-					std::cerr << "This line: " << line << " contains infinite interval. \n";
-				}
-				//first we substitute inf by white spaces:
-				size_t np = line.find("inf");									
-				line[np] = ' ';
-				line[np+1] = ' ';
-				line[np+2] = ' ';	
-				if ( what_to_substitute_for_infinite_bar != -1 )
-				{
-					double beginn, field, dim;
-					std::stringstream lineSS(line);			
-					if ( number_of_entries_per_line == 4 )lineSS >> field;
-					if ( number_of_entries_per_line >= 3 )
-					{
-						 lineSS >> dim;
-					}
-					else
-					{
-						dim = dimension;
-					}
-					lineSS >> beginn;
-					if ( dim == dimension )
-					{
-						if ( beginn > what_to_substitute_for_infinite_bar )
-						{
-							barcode.push_back( std::make_pair( what_to_substitute_for_infinite_bar , beginn ) );
-						}
-						else
-						{
-							barcode.push_back( std::make_pair( beginn , what_to_substitute_for_infinite_bar ) );
-						}
-						if (dbg)
-						{
-							std::cerr << "this is the line that is going to the output : " << beginn << " , " << what_to_substitute_for_infinite_bar << std::endl;
-						}
-					} 
-				}
-				else
-				{
-					//this is a line with infinity. Since the variable what_to_substitute_for_infinite_bar have not been set up, it means that this line will be skipped. 
-					if ( dbg )
-					{
-						std::cerr << "We will skip it \n";
-					}
-				}
-				continue;
-			}
-			else
-			{
-				//Then, we read the content of the line. We know that it do not contain 'inf' substring.
-				std::stringstream lineSS(line);			
-				double beginn, endd, field, dim;
-				if ( number_of_entries_per_line == 4 )lineSS >> field;
-				if ( number_of_entries_per_line >= 3 )
-				{
-					 lineSS >> dim;
-				}
-				else
-				{
-					dim = dimension;
-				}
-				lineSS >> beginn;
-				lineSS >> endd;
-				if ( beginn > endd )
-				{
-					std::swap(beginn,endd);				
-				}
-				if ( dim == dimension )
-				{ 
-					barcode.push_back( std::make_pair( beginn , endd ) );
-					if (dbg)
-					{
-						std::cerr << "This is a line that is going to the output : " <<  beginn << " , " << endd << std::endl;
-					}
-				}
-				else
-				{
-					if ( (number_of_entries_per_line==3) && (dimension == -1) )
-					{
-						barcode.push_back( std::make_pair( beginn , endd ) );
-					}
-				}
-			}
-		}
-		else
-		{
-			if ( dbg )
-			{
-				std::cerr << "This is a comment line \n";
-			}
-		}
-	}
-	in.close();
-	if ( dbg )std::cerr << "End of reading \n";  
-	
-	return barcode;
+  return barcode;
 }  // read_persistence_intervals_in_one_dimension_from_file
 
 }  // namespace Persistence_representations