chimeraslayercommand.h

   1 #ifndef CHIMERASLAYERCOMMAND_H
   2 #define CHIMERASLAYERCOMMAND_H
   3
   4 /*
   5  *  chimeraslayercommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 3/31/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "mothur.h"
  14 #include "command.hpp"
  15 #include "chimera.h"
  16
  17 /***********************************************************/
  18
  19 class ChimeraSlayerCommand : public Command {
  20 public:
  21         ChimeraSlayerCommand(string);
  22         ChimeraSlayerCommand();
  23         ~ChimeraSlayerCommand() {}
  24
  25         vector<string> setParameters();
  26         string getCommandName()                 { return "chimera.slayer";              }
  27         string getCommandCategory()             { return "Sequence Processing"; }
  28         string getHelpString();
  29
  30         int execute();
  31         void help() { m->mothurOut(getHelpString()); }
  32
  33 private:
  34
  35         struct linePair {
  36                 unsigned long int start;
  37                 unsigned long int end;
  38                 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
  39         };
  40
  41         vector<int> processIDS;   //processid
  42         vector<linePair*> lines;
  43
  44         int driver(linePair*, string, string, string, string);
  45         int createProcesses(string, string, string, string);
  46         int divideInHalf(Sequence, string&, string&);
  47         map<string, int> sortFastaFile(string, string);
  48
  49         #ifdef USE_MPI
  50         int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
  51         #endif
  52
  53         bool abort, realign, trim, trimera;
  54         string fastafile, templatefile, outputDir, search, namefile;
  55         int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
  56         float divR;
  57         Chimera* chimera;
  58
  59         vector<string> outputNames;
  60         vector<string> fastaFileNames;
  61         vector<string> nameFileNames;
  62
  63 };
  64
  65 /***********************************************************/
  66
  67 #endif
  68
  69