Update mussa to build on ubuntu 10.04 with qt 4.6.2 +boost 1.40.0.1

[mussa.git] / alg / nway_paths.hpp

diff --git a/alg/nway_paths.hpp b/alg/nway_paths.hpp
index 8725432a7880f78f95d0777651183fc59b4b4e34..686e27f524602521efc24af61d1fe08a22795299 100644 (file)
--- a/alg/nway_paths.hpp
+++ b/alg/nway_paths.hpp
@@ -35,6 +35,7 @@ signals:
   void progress(const QString& description, int cur, int max);
 
 public:
+    typedef size_t size_type;
     typedef std::list<ConservedPath> ConservedPaths;
     
     NwayPaths();
@@ -62,7 +63,7 @@ public:
 
   // old recursive transitive nway ... has issues checking all links?
     void find_paths_r(std::vector<std::vector<FLPs> > all_comparisons);
-    void path_search(std::vector<std::vector<FLPs> > all_comparisons, ConservedPath path, size_t depth);
+    void path_search(std::vector<std::vector<FLPs> > all_comparisons, ConservedPath path, size_type depth);
 
     void simple_refine();
     void save(boost::filesystem::path save_file_path);
@@ -71,7 +72,7 @@ public:
     void add_path(int threshold, std::vector<int>& loaded_path);
     void add_path(ConservedPath loaded_path);
     //! how many sequences are in our comparison
-    size_t sequence_count();
+    size_type sequence_count() const;
 
     void find_paths(std::vector<std::vector<FLPs> > all_comparisons);
     void refine();
@@ -83,11 +84,12 @@ public:
     // they'll have problems when being called from within a const object
     ConservedPaths::iterator pbegin() { return pathz.begin() ; }
     ConservedPaths::iterator pend() { return pathz.end() ; }
-    size_t path_size() const { return refined_pathz.size(); }
+    size_type path_size() const { return pathz.size(); }
     ConservedPaths::iterator rpbegin() { return refined_pathz.begin() ; }
     ConservedPaths::iterator rpend() { return refined_pathz.end() ; }
-    size_t refined_path_size() const { return refined_pathz.size(); }
+    size_type refined_path_size() const { return refined_pathz.size(); }
 
+    size_type size() const;
     // these probably shouldn't be public, but lets start 
     // simple
     ConservedPaths pathz;
@@ -95,11 +97,10 @@ public:
 
 protected:
     int threshold;
-    size_t win_size;
+    size_type win_size;
     int soft_thres;
 
     double ent_thres;
     std::vector<char *> c_sequences; //used by entropy_path_search
-
 };
 #endif