define window for showing a mussa alignment

[mussa.git] / alg / conserved_path.cpp

diff --git a/alg/conserved_path.cpp b/alg/conserved_path.cpp
index af2a4a01e1b7392cab10e9bc90eae0ae9b2d725d..56253c9bc6fa5948d5128ca06441c124ff4cf6a6 100644 (file)
--- a/alg/conserved_path.cpp
+++ b/alg/conserved_path.cpp
@@ -22,7 +22,7 @@ ConservedPath::ConservedPath(double s, ConservedPath::path_type path)
     track_indexes(path)
 {
 }
- 
+
 void ConservedPath::clear()
 {
   score = 0.0;
@@ -126,6 +126,22 @@ bool ConservedPath::nextTo(const ConservedPath& next) const
   return true;
 }
 
+vector<bool> ConservedPath::reverseComplimented() const
+{
+  vector<bool> reversed;
+  for (ConservedPath::const_iterator this_itor = begin(); 
+       this_itor != end(); 
+       ++this_itor)
+  {
+    if (*this_itor < 0) 
+      reversed.push_back(true);
+    else
+      reversed.push_back(false);
+  }
+  return reversed;
+
+}
+
 /////////////////////
 ExtendedConservedPath::ExtendedConservedPath()
   : ConservedPath(),