ticket:62 fix local alignment

[mussa.git] / alg / conserved_path.hpp

diff --git a/alg/conserved_path.hpp b/alg/conserved_path.hpp
index 6217474c9bd4a9dade4988ae6fedee6eef741bb4..05d23c91f5205c171156ed27b2328509f1092aeb 100644 (file)
--- a/alg/conserved_path.hpp
+++ b/alg/conserved_path.hpp
@@ -13,7 +13,7 @@ struct ConservedPath
 
   ConservedPath();
   ConservedPath(const ConservedPath& );
-  ConservedPath(double score, path_type path);
+  ConservedPath(size_t window_size, double score, path_type path);
 
   //! reset our path to be empty (including setting threshold to 0)
   void clear();
@@ -40,30 +40,15 @@ struct ConservedPath
   std::vector<bool> reverseComplimented() const;
   //! return the list of indexes normalized (to the left)
   std::vector<path_element> normalizedIndexes() const;
+  //! extend our current path
+  //! (aka increment our window size  by growth)
+  ConservedPath& extend(int growth=1);
 
+  //! window size (really should always be positive
+  size_t window_size;
   //! either number of conserved bases or average entropy
   double score;
   //! offsets into each of our sequences representing the start of our window
   std::vector<path_element> track_indexes;
 };
-
-struct ExtendedConservedPath : public ConservedPath
-{
-  ExtendedConservedPath();
-  ExtendedConservedPath(const ExtendedConservedPath& other);
-  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)
-   */
-  ExtendedConservedPath& extend(int growth=1);
-
-  // output some useful information
-  friend std::ostream& operator<<(std::ostream&, const ExtendedConservedPath&);
-
-  //! size of extended window
-  int window_size;
-};
 #endif