+#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
+
+