7 * Created by westcott on 12/10/09.
8 * Copyright 2009 Schloss Lab. All rights reserved.
13 #include "sparsedistancematrix.h"
14 #include "nameassignment.hpp"
16 /****************************************************************************************/
18 //Note: this class creates a sparsematrix and list if the read is executed, but does not delete them on deconstruction.
19 //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
20 //it is done this way so the read can be deleted and the information still used.
25 ReadBlast(string, float, float, int, bool, bool); //blastfile, cutoff, penalty, length of overlap, min or max bsr, hclusterWanted
28 int read(NameAssignment*);
29 SparseDistanceMatrix* getDistMatrix() { return matrix; }
30 vector<seqDist> getOverlapMatrix() { return overlap; }
31 string getOverlapFile() { return overlapFile; }
32 string getDistFile() { return distFile; }
35 string blastfile, overlapFile, distFile;
36 int length; //number of amino acids overlapped
37 float penalty, cutoff; //penalty is used to adjust error rate
38 bool minWanted; //if true choose min bsr, if false choose max bsr
41 SparseDistanceMatrix* matrix;
42 vector<seqDist> overlap;
45 int readNames(NameAssignment*);
48 /*******************************************************************************************/