readblast.h

   1 #ifndef READBLAST_H
   2 #define READBLAST_H
   3 /*
   4  *  readblast.h
   5  *  Mothur
   6  *
   7  *  Created by westcott on 12/10/09.
   8  *  Copyright 2009 Schloss Lab. All rights reserved.
   9  *
  10  */
  11
  12 #include "mothur.h"
  13 #include "sparsedistancematrix.h"
  14 #include "nameassignment.hpp"
  15
  16 /****************************************************************************************/
  17
  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.
  21
  22 class ReadBlast {
  23
  24 public:
  25         ReadBlast(string, float, float, int, bool, bool); //blastfile, cutoff, penalty, length of overlap, min or max bsr, hclusterWanted
  26         ~ReadBlast() {}
  27
  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;        }
  33
  34 private:
  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
  39         bool hclusterWanted;
  40
  41         SparseDistanceMatrix* matrix;
  42         vector<seqDist> overlap;
  43         MothurOut* m;
  44
  45         int readNames(NameAssignment*);
  46 };
  47
  48 /*******************************************************************************************/
  49
  50 #endif
  51