X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ccode.h;fp=ccode.h;h=a4860dcb83ee16ddaca43afd6cc4adb4a1973adc;hb=f7fbd74ffedcf62217109c22e828453eaefa1458;hp=0000000000000000000000000000000000000000;hpb=9870d254dfde04d59f795cc6aa395171ce787213;p=mothur.git

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
+
+