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, int, float, 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 numWanted, matchScore, misMatchPenalty, minCoverage, minSimilarity;
37 float minDivR, percentIdenticalQueryChimera;
38 vector<results> outputResults;
39 vector<int> indexes; //stores index into template seqs of the refSeqs, so we can return the whole sequence rather than the trimmed and filtered one
40 map<int, int> spotMap;
41 Database* databaseLeft;
42 Database* databaseRight;
44 vector<Sequence*> minCoverageFilter(vector<Sequence*>); //removes top matches that do not have minimum coverage with query.
45 int computeChimeraPenalty();
46 void verticalFilter(vector<Sequence*>);
48 vector< vector<score_struct> > buildScoreMatrix(int, int);
49 void fillScoreMatrix(vector<vector<score_struct> >&, vector<Sequence*>, int);
50 vector<score_struct> extractHighestPath(vector<vector<score_struct> >);
51 vector<trace_struct> mapTraceRegionsToAlignment(vector<score_struct>, vector<Sequence*>);
52 string constructChimericSeq(vector<trace_struct>, vector<Sequence*>);
53 float computePercentID(string, string);
54 string chimeraMaligner(int, DeCalculator*);
55 vector<Sequence*> getBlastSeqs(Sequence*, int);
56 vector<Sequence*> getKmerSeqs(Sequence*, int);
61 /***********************************************************************/