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