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//
// optiblastmatrix.hpp
// Mothur
//
// Created by Sarah Westcott on 5/10/18.
// Copyright © 2018 Schloss Lab. All rights reserved.
//
#ifndef optiblastmatrix_hpp
#define optiblastmatrix_hpp
#include "optidata.hpp"
class OptiBlastMatrix : public OptiData {
public:
OptiBlastMatrix(string, string, string, bool, double c, int l, float p, bool min);
~OptiBlastMatrix(){ }
vector< set<long long> > getBlastOverlap() { return blastOverlap; }
string getOverlapName(long long); //name from nameMap index
protected:
vector<string> overlapNameMap;
vector< set<long long> > blastOverlap; //empty unless reading a blast file.
string distFile, namefile, countfile, format;
bool sim, minWanted;
float penalty;
int length;
int readBlast();
int readBlastNames(map<string, long long>& nameAssignment);
};
#endif /* optiblastmatrix_hpp */
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