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, map<string, int>&, 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                 Database* databaseRight;
  47                 Database* databaseLeft;
  48                 map<string, int> priority; //for template=self, seqname, seqAligned, abundance
  49                 set<string> chimericSeqs; //for template=self, so we don't add chimeric sequences to the userTemplate set
  50
  51                 vector<data_struct>  chimeraResults;
  52                 data_results printResults;
  53                 string chimeraFlags, searchMethod, fastafile;
  54                 bool realign, trimChimera;
  55                 int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
  56                 float divR;
  57
  58                 void printBlock(data_struct, string, ostream&);
  59                 void printBlock(data_results, data_results, bool, bool, string, ostream&);
  60                 string getBlock(data_struct, string);
  61                 string getBlock(data_results, data_results, bool, bool, string);
  62                 //int readNameFile(string);
  63                 vector<Sequence*> getTemplate(Sequence*, vector<Sequence*>&);
  64                 vector<Sequence*> getRefSeqs(Sequence*, vector<Sequence*>&, vector<Sequence*>&);
  65                 vector<Sequence*> getBlastSeqs(Sequence*, vector<Sequence*>&, int);
  66                 vector<Sequence*> getKmerSeqs(Sequence*, vector<Sequence*>&, int);
  67
  68 };
  69
  70 /************************************************************************/
  71
  72 #endif
  73
  74