8 * Created by westcott on 8/18/09.
9 * Copyright 2009 Schloss Lab. All rights reserved.
17 //This class was created using the algorythms described in the
18 //"Evaluation of Nearest Neighbor Methods for Detection of Chimeric Small-Subunit rRna Sequences" paper
19 //by J.F. Robison-Cox 1, M.M. Bateson 2 and D.M. Ward 2
22 /***********************************************************/
24 class AlignSim : public Chimera {
27 AlignSim(string, string);
33 void setCons(string){};
34 void setQuantiles(string q) { quanfile = q; };
40 vector<linePair*> lines;
41 vector<linePair*> templateLines;
43 vector<Sequence*> querySeqs;
44 vector<Sequence*> templateSeqs;
46 vector< vector<sim> > IS; //IS[0] is the vector os sim values for each window for querySeqs[0]
47 vector< vector<sim> > templateIS; //templateIS[0] is the vector os sim values for each window for templateSeqs[0]
48 vector<int> windowBreak;
50 string fastafile, templateFile;
53 vector< vector<sim> > findIS(int, int, vector<Sequence*>);
54 vector<Sequence*> findClosestSides(Sequence*, int, vector<int>&, int);
55 int findNumMatchedBases(Sequence, Sequence);
56 vector<int> findWindows();
58 vector< vector<float> > quantile;
60 vector< vector<sim> > createProcessesIS(vector<Sequence*>, vector<linePair*>);
64 /***********************************************************/