7 * Created by westcott on 9/23/09.
8 * Copyright 2009 Schloss Lab. All rights reserved.
15 /***********************************************************************/
16 //This class was modeled after the chimeraMaligner written by the Broad Institute
17 /**********************************************************************/
22 Maligner(vector<Sequence*>, int, int, int, float, int, int, string);
25 string getResults(Sequence*, DeCalculator*);
26 float getPercentID() { return percentIdenticalQueryChimera; }
27 vector<results> getOutput() { return outputResults; }
32 vector<Sequence*> refSeqs;
34 int numWanted, matchScore, misMatchPenalty, minCoverage, minSimilarity;
36 float minDivR, percentIdenticalQueryChimera;
37 vector<results> outputResults;
38 map<int, int> spotMap;
40 vector<Sequence*> minCoverageFilter(vector<Sequence*>); //removes top matches that do not have minimum coverage with query.
41 int computeChimeraPenalty();
42 void verticalFilter(vector<Sequence*>);
44 vector< vector<score_struct> > buildScoreMatrix(int, int);
45 void fillScoreMatrix(vector<vector<score_struct> >&, vector<Sequence*>, int);
46 vector<score_struct> extractHighestPath(vector<vector<score_struct> >);
47 vector<trace_struct> mapTraceRegionsToAlignment(vector<score_struct>, vector<Sequence*>);
48 string constructChimericSeq(vector<trace_struct>, vector<Sequence*>);
49 float computePercentID(string, string);
50 string chimeraMaligner(int, DeCalculator*);
51 vector<Sequence*> getBlastSeqs(Sequence*, int);
55 /***********************************************************************/