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
  20 //***********************************************************************/
  21 //This class was modeled after the chimeraSlayer written by the Broad Institute
  22 /***********************************************************************/
  23
  24 class ChimeraSlayer : public Chimera {
  25
  26         public:
  27                 ChimeraSlayer(string, string, bool, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool, string, int);
  28                 ChimeraSlayer(string, string, bool, map<string, int>&, string,  int, int, int, int, float, int, int, int, int, int, int, int, int, bool, string, int);
  29                 ChimeraSlayer(string, string, bool, map<string, int>&, string,  int, int, int, int, float, int, int, int, int, int, int, int, int, bool, string, int, bool);
  30
  31                 ~ChimeraSlayer();
  32
  33                 int getChimeras(Sequence*);
  34                 Sequence print(ostream&, ostream&);
  35                 Sequence print(ostream&, ostream&, data_results, data_results);
  36                 void printHeader(ostream&);
  37                 int doPrep();
  38                 int getNumNoParents() { return numNoParents; }
  39                 data_results getResults() { return printResults; }
  40
  41                 #ifdef USE_MPI
  42                 Sequence print(MPI_File&, MPI_File&);
  43                 Sequence print(MPI_File&, MPI_File&, data_results, data_results, bool&);
  44                 #endif
  45
  46         private:
  47                 Sequence querySeq;
  48                 Sequence trimQuery;
  49                 DeCalculator decalc;
  50                 Database* databaseRight;
  51                 Database* databaseLeft;
  52                 map<string, int> priority; //for template=self, seqname, seqAligned, abundance
  53                 set<string> chimericSeqs; //for template=self, so we don't add chimeric sequences to the userTemplate set
  54                 int numNoParents, threadID;
  55
  56                 vector<data_struct>  chimeraResults;
  57                 data_results printResults;
  58                 string chimeraFlags, searchMethod, fastafile, blastlocation;
  59                 bool realign, trimChimera;
  60                 int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
  61                 float divR;
  62
  63                 void printBlock(data_struct, string, ostream&);
  64                 void printBlock(data_results, data_results, bool, bool, string, ostream&);
  65                 string getBlock(data_struct, string);
  66                 string getBlock(data_results, data_results, bool, bool, string);
  67                 //int readNameFile(string);
  68                 vector<Sequence*> getTemplate(Sequence, vector<Sequence*>&);
  69                 vector<Sequence> getRefSeqs(Sequence, vector<Sequence*>&, vector<Sequence*>&);
  70                 vector<Sequence> getBlastSeqs(Sequence, vector<Sequence*>&, int);
  71                 vector<Sequence> getKmerSeqs(Sequence, vector<Sequence*>&, int);
  72
  73 };
  74
  75 /************************************************************************/
  76
  77 #endif
  78
  79