ticket:62 fix local alignment

[mussa.git] / alg / mussa.hpp

diff --git a/alg/mussa.hpp b/alg/mussa.hpp
index 0a724e7904450899175eeec336dfe9e154e4bec2..4fae7de68b8f90be4f34f98a420ffe97319c389b 100644 (file)
--- a/alg/mussa.hpp
+++ b/alg/mussa.hpp
@@ -81,6 +81,13 @@ class Mussa
     //! return the refined paths found by the nway analysis.
     const NwayPaths& paths() const;
 
+    //! given selected_paths, and view_paths, compute per base pair matches
+    //template <class IteratorT>
+    void createLocalAlignment(std::list<ConservedPath>::iterator begin, 
+                              std::list<ConservedPath>::iterator end,
+                              std::list<ConservedPath::path_type>& result,
+                              std::list<std::vector<bool> >& reversed);
+
     //! run seqcomp and the nway filtering algorithm.
     /*!analyze will run seqcomp and then the nway algorithm
      * on whatever sequences have been loaded into this mussa instance.