1 #ifndef CHIMERASLAYER_H
2 #define CHIMERASLAYER_H
8 * Created by westcott on 9/25/09.
9 * Copyright 2009 Schloss Lab. All rights reserved.
18 /***********************************************************************/
19 //This class was modeled after the chimeraSlayer written by the Broad Institute
20 /***********************************************************************/
23 class ChimeraSlayer : public Chimera {
26 ChimeraSlayer(string, string);
32 void setCons(string){};
33 void setQuantiles(string q) {};
40 vector<linePair*> lines;
41 vector<Sequence*> querySeqs;
42 vector<Sequence*> templateSeqs;
43 vector< map<int, int> > spotMap;
45 vector< vector<data_struct> > chimeraResults;
46 vector<string> chimeraFlags;
48 string fastafile, templateFile;
50 Sequence* getSequence(string); //find sequence from name
51 void printBlock(data_struct, ostream&, int i);
54 /************************************************************************/