checking in chimera files in progress after move to michigan

[mothur.git] / ccode.h

diff --git a/ccode.h b/ccode.h
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+#ifndef CCODE_H
+#define CCODE_H
+
+/*
+ *  ccode.h
+ *  Mothur
+ *
+ *  Created by westcott on 8/24/09.
+ *  Copyright 2009 Schloss LAB. All rights reserved.
+ *
+ */
+
+#include "chimera.h"
+#include "dist.h"
+#include "decalc.h"
+
+//This class was created using the algorythms described in the 
+// "Evaluating putative chimeric sequences from PCR-amplified products" paper 
+//by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.
+
+/***********************************************************/
+
+class Ccode : public Chimera {
+       
+       public:
+               Ccode(string, string);  
+               ~Ccode();
+               
+               void getChimeras();
+               void print(ostream&);
+               
+               void setCons(string c)          {}
+               void setQuantiles(string q) {}
+               
+               
+       private:
+       
+               Dist* distCalc;
+               DeCalculator* decalc;
+               int iters;
+               string fastafile, templateFile;
+               
+               
+               vector<linePair*> lines;
+               vector<linePair*> templateLines;
+               vector<Sequence*> querySeqs;
+               vector<Sequence*> templateSeqs;
+               
+               vector< vector<Sequence*> > closest;  //bestfit[0] is a vector of sequence at are closest to queryseqs[0]...
+               
+               vector< vector<Sequence*> > findClosest(int, int, int); 
+               void removeSeqs(vector<Sequence*>);  //removes sequences from closest that are to different of too similar to eachother. 
+               
+               void createProcessesClosest();
+               
+};
+
+/***********************************************************/
+
+#endif
+
+