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
  20 class ChimeraSlayerCommand : public Command {
  21 public:
  22         ChimeraSlayerCommand(string);
  23         ~ChimeraSlayerCommand();
  24         int execute();
  25         void help();
  26
  27
  28 private:
  29
  30         struct linePair {
  31                 unsigned long int start;
  32                 int numSeqs;
  33                 linePair(unsigned long int i, int j) : start(i), numSeqs(j) {}
  34         };
  35         vector<int> processIDS;   //processid
  36         vector<linePair*> lines;
  37
  38         int driver(linePair*, string, string, string);
  39         int createProcesses(string, string, string);
  40
  41         #ifdef USE_MPI
  42         int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<long>&);
  43         #endif
  44
  45         bool abort, realign;
  46         string fastafile, templatefile, outputDir, search;
  47         int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
  48         float divR;
  49         Chimera* chimera;
  50
  51         vector<string> outputNames;
  52         vector<string> fastaFileNames;
  53
  54 };
  55
  56 /***********************************************************/
  57
  58 #endif
  59
  60