chimeraslayer.h

   1 #ifndef CHIMERASLAYER_H
   2 #define CHIMERASLAYER_H
   3
   4 /*
   5  *  chimeraslayer.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 9/25/09.
   9  *  Copyright 2009 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "chimera.h"
  15 #include "maligner.h"
  16 #include "slayer.h"
  17
  18 /***********************************************************************/
  19 //This class was modeled after the chimeraSlayer written by the Broad Institute
  20 /***********************************************************************/
  21
  22
  23 class ChimeraSlayer : public Chimera {
  24
  25         public:
  26                 ChimeraSlayer(string, string);
  27                 ~ChimeraSlayer();
  28
  29                 int getChimeras();
  30                 void print(ostream&);
  31
  32                 void setCons(string){};
  33                 void setQuantiles(string q) {};
  34
  35
  36         private:
  37                 DeCalculator* decalc;
  38                 Maligner* maligner;
  39                 Slayer* slayer;
  40                 vector<linePair*> lines;
  41                 vector<Sequence*> querySeqs;
  42                 vector<Sequence*> templateSeqs;
  43                 vector< map<int, int> > spotMap;
  44
  45                 vector< vector<data_struct> > chimeraResults;
  46                 vector<string> chimeraFlags;
  47
  48                 string fastafile, templateFile;
  49
  50                 Sequence* getSequence(string);  //find sequence from name
  51                 void printBlock(data_struct, ostream&, int i);
  52 };
  53
  54 /************************************************************************/
  55
  56 #endif
  57
  58