checking in chimera files in progress after move to michigan

[mothur.git] / bellerophon.h

diff --git a/bellerophon.h b/bellerophon.h
index bc86c183bb2da0594568dc5949a244115273bea6..b309545e29c18d3ed3669e6e70df3243754551ca 100644 (file)
--- a/bellerophon.h
+++ b/bellerophon.h
@@ -13,20 +13,12 @@
 
 #include "chimera.h"
 #include "filterseqscommand.h"
+#include "sparsematrix.hpp"
 #include "sequence.hpp"
 #include "dist.h"
 
-struct Preference {
-               string name;
-               vector<string> leftParent; //keep the name of closest left associated with the two scores
-               vector<string> rightParent; //keep the name of closest right associated with the two scores
-               vector<float> score;  //so you can keep last score and calc this score and keep whichever is bigger.
-               vector<float> closestLeft;  //keep the closest left associated with the two scores
-               vector<float> closestRight; //keep the closest right associated with the two scores
-               int midpoint;
-
-};
-
+typedef list<PCell>::iterator MatData;
+typedef map<int, float> SeqMap;  //maps sequence to all distance for that seqeunce
 
 /***********************************************************/