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, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
  27                 ~ChimeraSlayer();
  28
  29                 int getChimeras(Sequence*);
  30                 int print(ostream&, ostream&);
  31                 void printHeader(ostream&);
  32                 int doPrep();
  33
  34                 #ifdef USE_MPI
  35                 int print(MPI_File&, MPI_File&);
  36                 #endif
  37
  38         private:
  39                 Sequence* querySeq;
  40                 DeCalculator* decalc;
  41                 Maligner* maligner;
  42                 Slayer* slayer;
  43                 map<int, int>  spotMap;
  44                 Database* databaseRight;
  45                 Database* databaseLeft;
  46
  47                 vector<data_struct>  chimeraResults;
  48                 string chimeraFlags, searchMethod, fastafile;
  49                 bool realign;
  50                 int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
  51                 float divR;
  52
  53                 void printBlock(data_struct, ostream&);
  54                 string getBlock(data_struct);
  55
  56 };
  57
  58 /************************************************************************/
  59
  60 #endif
  61
  62