X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bellerophon.h;h=3d05617d50ad0a9dccb05da2d21bc872e8ca842f;hb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;hp=32b38e40328ecccec31359cc112e38f3eeed2924;hpb=2ad3477dcd6a01628712b32e767353f917f2a95a;p=mothur.git

diff --git a/bellerophon.h b/bellerophon.h
index 32b38e4..3d05617 100644
--- a/bellerophon.h
+++ b/bellerophon.h
@@ -13,51 +13,34 @@
 
 #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
 
 /***********************************************************/
 
 class Bellerophon : public Chimera {
 	
 	public:
-		Bellerophon(string);	
+		Bellerophon(string, string);	
 		~Bellerophon() {};
 		
-		void getChimeras();
-		void print(ostream&);
-		
-		void setCons(string){};
-		void setQuantiles(string) {};
-		
+		int getChimeras();
+		int print(ostream&, ostream&);
 		
 	private:
 		Dist* distCalculator;
 		FilterSeqsCommand* filterSeqs;
-		vector<Sequence> seqs;
+		vector<Sequence*> seqs;
 		vector<Preference> pref;
 		string fastafile;
 		int iters;
 		
-		void readSeqs();
-		void generatePreferences(vector<SeqMap>, vector<SeqMap>, int);
+		int generatePreferences(vector<SeqMap>, vector<SeqMap>, int);
 		int createSparseMatrix(int, int, SparseMatrix*, vector<Sequence>);
-	
-
-		
-
 };
 
 /***********************************************************/