7 * Created by westcott on 9/23/09.
8 * Copyright 2009 Schloss Lab. All rights reserved.
14 /***********************************************************************/
15 //This class was modeled after the chimeraMaligner written by the Broad Institute
16 /***********************************************************************/
23 /***********************************************************************/
29 /***********************************************************************/
35 float queryToParentLocal;
39 /**********************************************************************/
44 Maligner(vector<Sequence*>, int, int, int, float, int);
47 string getResults(Sequence*);
48 float getPercentID() { return percentIdenticalQueryChimera; }
49 vector<results> getOutput() { return outputResults; }
55 vector<Sequence*> refSeqs;
57 int numWanted, matchScore, misMatchPenalty, minCoverage;
58 float minDivR, percentIdenticalQueryChimera;
59 vector<results> outputResults;
61 vector<Sequence*> minCoverageFilter(vector<Sequence*>); //removes top matches that do not have minimum coverage with query.
62 int computeChimeraPenalty();
63 void verticalFilter(vector<Sequence*>);
65 vector< vector<score_struct> > buildScoreMatrix(int, int);
66 void fillScoreMatrix(vector<vector<score_struct> >&, vector<Sequence*>, int);
67 vector<score_struct> extractHighestPath(vector<vector<score_struct> >);
68 vector<trace_struct> mapTraceRegionsToAlignment(vector<score_struct>, vector<Sequence*>);
69 string constructChimericSeq(vector<trace_struct>, vector<Sequence*>);
70 float computePercentID(string, string);
74 /***********************************************************************/