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

[mussa.git] / alg / nway_entropy.cpp

diff --git a/alg/nway_entropy.cpp b/alg/nway_entropy.cpp
index 13a42c5b6ccd4b1e6357b952e9673d2f17e95fb6..94f47f5e24891db3d975759b5eb9377cf20f3e9e 100644 (file)
--- a/alg/nway_entropy.cpp
+++ b/alg/nway_entropy.cpp
@@ -20,13 +20,13 @@ using namespace std;
 
 
 void
-NwayPaths::setup_ent(double new_entropy_thres, vector<string> some_seqs)
+NwayPaths::setup_ent(double new_entropy_thres, vector<Sequence> some_seqs)
 {
   ent_thres = new_entropy_thres;
 
   c_sequences.clear();
   for (vector<string>::size_type i = 0; i < some_seqs.size(); i++)
-    c_sequences.push_back((char *)some_seqs[i].c_str());
+    c_sequences.push_back((char *)some_seqs[i].get_sequence().c_str());
 }
 
 
@@ -196,7 +196,7 @@ NwayPaths::entropy_path_search(vector<vector<FLPs> > all_comparisons)
         // check entropy <---------------------------------------------------
         avg_entropy = path_entropy(path);
         if (avg_entropy <= ent_thres)
-          pathz.push_back(ConservedPath(avg_entropy, path));
+          pathz.push_back(ConservedPath(win_size, avg_entropy, path));
         
         // now advance the right iterator
         not_advanced = true;