8 * Created by westcott on 9/8/09.
9 * Copyright 2009 Schloss Lab. All rights reserved.
17 #include "database.hpp"
19 /***********************************************************/
20 //This class was created using the algorythms described in
21 //CHIMERA_CHECK version 2.7 written by Niels Larsen.
23 /***********************************************************/
25 class ChimeraCheckRDP : public Chimera {
28 ChimeraCheckRDP(string, string);
34 void setCons(string){};
35 void setQuantiles(string q) {};
40 vector<linePair*> lines;
41 vector<Sequence*> querySeqs;
45 vector< vector<sim> > IS; //IS[0] is the vector of IS values for each window for querySeqs[0]
49 //map<string, vector< map<int, int> > >:: iterator it;
50 //map<int, int>::iterator it2;
52 vector<Sequence> closest; //closest[0] is the closest overall seq to querySeqs[0].
54 string fastafile, templateFile;
55 map<string, string> names;
57 vector<sim> findIS(int);
58 int calcKmers(map<int, int>, map<int, int>);
60 void makeSVGpic(vector<sim>, int);
61 void readName(string);
63 void createProcessesIS();
67 /***********************************************************/