chimeracheckcommand.h

   1 #ifndef CHIMERACHECKCOMMAND_H
   2 #define CHIMERACHECKCOMMAND_H
   3
   4 /*
   5  *  chimeracheckcommand.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 #include "chimeracheckrdp.h"
  17
  18
  19 /***********************************************************/
  20
  21 class ChimeraCheckCommand : public Command {
  22 public:
  23         ChimeraCheckCommand(string);
  24         ~ChimeraCheckCommand();
  25         int execute();
  26         void help();
  27
  28
  29 private:
  30
  31         struct linePair {
  32                 unsigned long int start;
  33                 unsigned long int end;
  34                 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
  35         };
  36
  37         vector<int> processIDS;   //processid
  38         vector<linePair*> lines;
  39
  40         int driver(linePair*, string, string);
  41         int createProcesses(string, string);
  42
  43         #ifdef USE_MPI
  44         int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long int>&);
  45         #endif
  46
  47         bool abort, svg;
  48         string fastafile, templatefile, namefile, outputDir;
  49         int processors, increment, ksize, numSeqs, templateSeqsLength;
  50         Chimera* chimera;
  51         vector<string> fastaFileNames;
  52         vector<string> nameFileNames;
  53         vector<string> outputNames;
  54
  55 };
  56
  57 /***********************************************************/
  58
  59 #endif
  60
  61