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#ifndef MALIGNER_H
#define MALIGNER_H
/*
* maligner.h
* Mothur
*
* Created by westcott on 9/23/09.
* Copyright 2009 Schloss Lab. All rights reserved.
*
*/
#include "decalc.h"
#include "chimera.h"
#include "database.hpp"
/***********************************************************************/
//This class was modeled after the chimeraMaligner written by the Broad Institute
/**********************************************************************/
class Maligner {
public:
Maligner(vector<Sequence>, int, int, float, int, int); //int, int, int, , string, Database*, Database*
~Maligner() {};
string getResults(Sequence, DeCalculator);
float getPercentID() { return percentIdenticalQueryChimera; }
vector<results> getOutput() { return outputResults; }
private:
Sequence query;
vector<Sequence> refSeqs;
vector<Sequence> db;
int minCoverage, minSimilarity, matchScore, misMatchPenalty;
float minDivR, percentIdenticalQueryChimera;
vector<results> outputResults;
map<int, int> spotMap;
vector<int> unalignedMap;
vector<Sequence> minCoverageFilter(vector<Sequence>); //removes top matches that do not have minimum coverage with query.
int computeChimeraPenalty();
vector<Sequence> verticalFilter(vector<Sequence>);
vector< vector<score_struct> > buildScoreMatrix(int, int);
void fillScoreMatrix(vector<vector<score_struct> >&, vector<Sequence>, int);
vector<score_struct> extractHighestPath(vector<vector<score_struct> >);
vector<trace_struct> mapTraceRegionsToAlignment(vector<score_struct>);
string constructChimericSeq(vector<trace_struct>, vector<Sequence>);
string constructAntiChimericSeq(vector<trace_struct>, vector<Sequence>);
float computePercentID(string, string);
string chimeraMaligner(int, DeCalculator);
MothurOut* m;
};
/***********************************************************************/
#endif
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