added sorted option to get.rabund command

[mothur.git] / bellerophon.h

diff --git a/bellerophon.h b/bellerophon.h
new file mode 100644 (file)
index 0000000..3f28e5b
--- /dev/null
+++ b/bellerophon.h
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+#ifndef BELLEROPHON_H
+#define BELLEROPHON_H
+
+/*
+ *  bellerophon.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 7/9/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+
+#include "chimera.h"
+#include "filterseqscommand.h"
+#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;
+
+};
+
+
+/***********************************************************/
+
+class Bellerophon : public Chimera {
+       
+       public:
+               Bellerophon(string);    
+               ~Bellerophon() {};
+               
+               void getChimeras();
+               void print(ostream&);
+               
+               
+       private:
+               Dist* distCalculator;
+               FilterSeqsCommand* filterSeqs;
+               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>);
+       
+
+               
+
+};
+
+/***********************************************************/
+
+#endif
+