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                 unsigned long int end;
  33                 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
  34         };
  35
  36         vector<int> processIDS;   //processid
  37         vector<linePair*> lines;
  38
  39         int driver(linePair*, string, string, string);
  40         int createProcesses(string, string, string);
  41
  42         #ifdef USE_MPI
  43         int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
  44         #endif
  45
  46         bool abort, realign;
  47         string fastafile, templatefile, outputDir, search;
  48         int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
  49         float divR;
  50         Chimera* chimera;
  51
  52         vector<string> outputNames;
  53         vector<string> fastaFileNames;
  54
  55 };
  56
  57 /***********************************************************/
  58
  59 #endif
  60
  61