ticket:62 fix local alignment

[mussa.git] / alg / nway_paths.hpp

diff --git a/alg/nway_paths.hpp b/alg/nway_paths.hpp
index acbef47475a70a62b36e3879946b3bf284fef690..a25cfcebeaf751e3b6669a8d14228dfa440807f3 100644 (file)
--- a/alg/nway_paths.hpp
+++ b/alg/nway_paths.hpp
@@ -28,7 +28,7 @@ class NwayPaths
   friend class SeqView;
   protected:
     int threshold;
-    int win_size;
+    size_t win_size;
     int soft_thres;
 
     double ent_thres;
@@ -75,13 +75,13 @@ class NwayPaths
     std::list<ConservedPath>::iterator pbegin() { return pathz.begin() ; }
     std::list<ConservedPath>::iterator pend() { return pathz.end() ; }
     size_t path_size() const { return refined_pathz.size(); }
-    std::list<ExtendedConservedPath>::iterator rpbegin() { return refined_pathz.begin() ; }
-    std::list<ExtendedConservedPath>::iterator rpend() { return refined_pathz.end() ; }
+    std::list<ConservedPath>::iterator rpbegin() { return refined_pathz.begin() ; }
+    std::list<ConservedPath>::iterator rpend() { return refined_pathz.end() ; }
     size_t refined_path_size() const { return refined_pathz.size(); }
 
     // these probably shouldn't be public, but lets start 
     // simple
     std::list<ConservedPath> pathz;
-    std::list<ExtendedConservedPath > refined_pathz;
+    std::list<ConservedPath > refined_pathz;
 };
 #endif