7 * Created by westcott on 9/23/09.
8 * Copyright 2009 Schloss Lab. All rights reserved.
14 #include "database.hpp"
16 /***********************************************************************/
17 //This class was modeled after the chimeraMaligner written by the Broad Institute
18 /**********************************************************************/
23 Maligner(vector<Sequence*>, int, int, float, int, int); //int, int, int, , string, Database*, Database*
26 string getResults(Sequence*, DeCalculator*);
27 float getPercentID() { return percentIdenticalQueryChimera; }
28 vector<results> getOutput() { return outputResults; }
33 vector<Sequence*> refSeqs;
35 int minCoverage, minSimilarity, matchScore, misMatchPenalty;
36 float minDivR, percentIdenticalQueryChimera;
37 vector<results> outputResults;
38 map<int, int> spotMap;
39 vector<int> unalignedMap;
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 string constructAntiChimericSeq(vector<trace_struct>, vector<Sequence*>);
50 float computePercentID(string, string);
51 string chimeraMaligner(int, DeCalculator*);
56 /***********************************************************************/