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         ~ChimeraPintailCommand(){}
  27
  28         vector<string> setParameters();
  29         string getCommandName()                 { return "chimera.pintail";             }
  30         string getCommandCategory()             { return "Sequence Processing"; }
  31         string getHelpString();
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35 private:
  36
  37         struct linePair {
  38                 unsigned long int start;
  39                 unsigned long int end;
  40                 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
  41         };
  42
  43         vector<int> processIDS;   //processid
  44         vector<linePair*> lines;
  45
  46         int driver(linePair*, string, string, string);
  47         int createProcesses(string, string, string);
  48
  49         #ifdef USE_MPI
  50         int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
  51         #endif
  52
  53         bool abort, filter;
  54         string fastafile, templatefile, consfile, quanfile, maskfile, outputDir, inputDir;
  55         int processors, window, increment, numSeqs, templateSeqsLength;
  56         Chimera* chimera;
  57         vector<string> outputNames;
  58         vector<string> fastaFileNames;
  59 };
  60
  61 /***********************************************************/
  62
  63 #endif
  64
  65