chimerapintailcommand.h

   1 #ifndef CHIMERAPINTAILCOMMAND_H
   2 #define CHIMERAPINTAILCOMMAND_H
   3
   4 /*
   5  *  chimerapintailcommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 4/1/10.
   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 ChimeraPintailCommand : public Command {
  21
  22 public:
  23
  24         ChimeraPintailCommand(string);
  25         ~ChimeraPintailCommand();
  26         int execute();
  27         void help();
  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, string);
  41         int createProcesses(string, string, string);
  42
  43         #ifdef USE_MPI
  44         int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
  45         #endif
  46
  47         bool abort, filter;
  48         string fastafile, templatefile, consfile, quanfile, maskfile, outputDir, inputDir;
  49         int processors, window, increment, numSeqs, templateSeqsLength;
  50         Chimera* chimera;
  51         vector<string> outputNames;
  52         vector<string> fastaFileNames;
  53
  54
  55 };
  56
  57 /***********************************************************/
  58
  59 #endif
  60
  61