8 * Created by westcott on 9/8/09.
9 * Copyright 2009 Schloss Lab. All rights reserved.
17 #include "database.hpp"
19 //This class was created using the algorythms described in
20 //CHIMERA_CHECK version 2.7 written by Niels Larsen.
22 /***********************************************************/
24 class ChimeraCheckRDP : public Chimera {
27 ChimeraCheckRDP(string, string);
33 void setCons(string){};
34 void setQuantiles(string q) {};
39 vector<linePair*> lines;
40 vector<Sequence*> querySeqs;
44 vector< vector<sim> > IS; //IS[0] is the vector of IS values for each window for querySeqs[0]
48 //map<string, vector< map<int, int> > >:: iterator it;
49 //map<int, int>::iterator it2;
51 vector<Sequence> closest; //closest[0] is the closest overall seq to querySeqs[0].
53 string fastafile, templateFile;
54 map<string, string> names;
56 vector<sim> findIS(int);
57 int calcKmers(map<int, int>, map<int, int>);
59 void makeSVGpic(vector<sim>, int);
60 void readName(string);
62 void createProcessesIS();
66 /***********************************************************/