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         vector<string> getRequiredParameters();
  28         vector<string> getValidParameters();
  29         vector<string> getRequiredFiles();
  30         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  31         int execute();
  32         void help();
  33
  34 private:
  35
  36         struct linePair {
  37                 unsigned long int start;
  38                 unsigned long int end;
  39                 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
  40         };
  41
  42         vector<int> processIDS;   //processid
  43         vector<linePair*> lines;
  44
  45         int driver(linePair*, string, string, string);
  46         int createProcesses(string, string, string);
  47
  48         #ifdef USE_MPI
  49         int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
  50         #endif
  51
  52         bool abort, filter;
  53         string fastafile, templatefile, consfile, quanfile, maskfile, outputDir, inputDir;
  54         int processors, window, increment, numSeqs, templateSeqsLength;
  55         Chimera* chimera;
  56         vector<string> outputNames;
  57         map<string, vector<string> > outputTypes;
  58         vector<string> fastaFileNames;
  59
  60
  61 };
  62
  63 /***********************************************************/
  64
  65 #endif
  66
  67