added warning about merging with something above cutoff to cluster. working on chimeras

[mothur.git] / bellerophon.h

diff --git a/bellerophon.h b/bellerophon.h
index 3f28e5b9873bc2a8d16cc68d266b42963ccbc461..dd5b3da8035cf1528c07a2964f17b9b1aa051cab 100644 (file)
--- a/bellerophon.h
+++ b/bellerophon.h
@@ -13,48 +13,38 @@
 
 #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&);
+               int getChimeras();
+               void print(ostream&, ostream&);
+               
+               void setCons(string){};
+               void setQuantiles(string) {};
                
                
        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 createSparseMatrix(int, int, SparseMatrix*, vector<Sequence>);
-       
-
-               
-
 };
 
 /***********************************************************/