Mussa aligned sequence view seems to work

[mussa.git] / alg / conserved_path.hpp

diff --git a/alg/conserved_path.hpp b/alg/conserved_path.hpp
index cc2dda1736a9a6b326dfd14ac1153c907de010db..6217474c9bd4a9dade4988ae6fedee6eef741bb4 100644 (file)
--- a/alg/conserved_path.hpp
+++ b/alg/conserved_path.hpp
@@ -38,6 +38,8 @@ struct ConservedPath
   bool nextTo(const ConservedPath& next) const;
   //! indicate which elements of the path are reversed
   std::vector<bool> reverseComplimented() const;
+  //! return the list of indexes normalized (to the left)
+  std::vector<path_element> normalizedIndexes() const;
 
   //! either number of conserved bases or average entropy
   double score;
@@ -52,6 +54,7 @@ struct ExtendedConservedPath : public ConservedPath
   ExtendedConservedPath(int win_size, ConservedPath conserved_path);
   ExtendedConservedPath(int win_size, double score, std::vector<int> path);
 
+  std::vector<ConservedPath::path_element> ExtendedConservedPath::normalizedIndexes() const;
   //! extend our current path
   /*! (aka increment our window size  by growth)
    */