8 * Created by westcott on 8/24/09.
9 * Copyright 2009 Schloss LAB. All rights reserved.
17 //This class was created using the algorythms described in the
18 // "Evaluating putative chimeric sequences from PCR-amplified products" paper
19 //by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.
21 /***********************************************************/
23 class Ccode : public Chimera {
26 Ccode(string, string);
32 void setCons(string c) {}
33 void setQuantiles(string q) {}
41 string fastafile, templateFile;
44 vector<linePair*> lines;
45 vector<linePair*> templateLines;
46 vector<Sequence*> querySeqs;
47 vector<Sequence*> templateSeqs;
49 vector< vector<Sequence*> > closest; //bestfit[0] is a vector of sequence at are closest to queryseqs[0]...
51 vector< vector<Sequence*> > findClosest(int, int, int);
52 void removeSeqs(vector<Sequence*>); //removes sequences from closest that are to different of too similar to eachother.
54 void createProcessesClosest();
58 /***********************************************************/