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#ifndef READBLAST_H
#define READBLAST_H
/*
* readblast.h
* Mothur
*
* Created by westcott on 12/10/09.
* Copyright 2009 Schloss Lab. All rights reserved.
*
*/
#include "mothur.h"
#include "sparsedistancematrix.h"
#include "nameassignment.hpp"
/****************************************************************************************/
//Note: this class creates a sparsematrix and list if the read is executed, but does not delete them on deconstruction.
//the user of this object is responsible for deleting the matrix and list if they call the read or there will be a memory leak
//it is done this way so the read can be deleted and the information still used.
class ReadBlast {
public:
ReadBlast(string, float, float, int, bool); //blastfile, cutoff, penalty, length of overlap, min or max bsr
~ReadBlast() = default;
int read(NameAssignment*);
SparseDistanceMatrix* getDistMatrix() { return matrix; }
vector<seqDist> getOverlapMatrix() { return overlap; }
string getOverlapFile() { return overlapFile; }
string getDistFile() { return distFile; }
private:
string blastfile, overlapFile, distFile;
int length; //number of amino acids overlapped
float penalty, cutoff; //penalty is used to adjust error rate
bool minWanted; //if true choose min bsr, if false choose max bsr
SparseDistanceMatrix* matrix;
vector<seqDist> overlap;
MothurOut* m;
Utils util;
int readNames(NameAssignment*);
};
/*******************************************************************************************/
#endif
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