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 class ChimeraSlayer : public Chimera {
  23
  24         public:
  25                 ChimeraSlayer(string, string, bool, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
  26                 ChimeraSlayer(string, string, bool, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
  27
  28                 ~ChimeraSlayer();
  29
  30                 int getChimeras(Sequence*);
  31                 Sequence* print(ostream&, ostream&);
  32                 Sequence* print(ostream&, ostream&, data_results, data_results);
  33                 void printHeader(ostream&);
  34                 int doPrep();
  35                 data_results getResults() { return printResults; }
  36
  37                 #ifdef USE_MPI
  38                 Sequence* print(MPI_File&, MPI_File&);
  39                 Sequence* print(MPI_File&, MPI_File&, data_results, data_results);
  40                 #endif
  41
  42         private:
  43                 Sequence* querySeq;
  44                 Sequence trimQuery;
  45                 DeCalculator* decalc;
  46                 map<int, int>  spotMap;
  47                 Database* databaseRight;
  48                 Database* databaseLeft;
  49                 vector<Sequence*> userTemplate;  //when template=self, the query file is sorted from most abundance to least abundant
  50                                                                                  //userTemplate grows as the query file is processed by adding sequences that are not chimeric
  51                 set<string> namesOfChimericSeqs; //only used when template=self
  52
  53                 vector<data_struct>  chimeraResults;
  54                 data_results printResults;
  55                 string chimeraFlags, searchMethod, fastafile;
  56                 bool realign, trimChimera;
  57                 int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
  58                 float divR;
  59
  60                 void printBlock(data_struct, string, ostream&);
  61                 void printBlock(data_results, data_results, bool, bool, string, ostream&);
  62                 string getBlock(data_struct, string);
  63                 string getBlock(data_results, data_results, bool, bool, string);
  64                 //int readNameFile(string);
  65                 int getTemplate(Sequence*);
  66
  67 };
  68
  69 /************************************************************************/
  70
  71 #endif
  72
  73