chimeraccodecommand.h

   1 #ifndef CHIMERACCODECOMMAND_H
   2 #define CHIMERACCODECOMMAND_H
   3
   4 /*
   5  *  chimeraccodecommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 3/30/10.
   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 ChimeraCcodeCommand : public Command {
  21 public:
  22         ChimeraCcodeCommand(string);
  23         ChimeraCcodeCommand();
  24         ~ChimeraCcodeCommand();
  25         vector<string> getRequiredParameters();
  26         vector<string> getValidParameters();
  27         vector<string> getRequiredFiles();
  28         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  29         int execute();
  30         void help();
  31
  32
  33 private:
  34         struct linePair {
  35                 unsigned long int start;
  36                 unsigned long int end;
  37                 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
  38         };
  39         vector<int> processIDS;   //processid
  40         vector<linePair*> lines;
  41
  42         int driver(linePair*, string, string, string);
  43         int createProcesses(string, string, string);
  44
  45         #ifdef USE_MPI
  46         int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
  47         #endif
  48
  49         bool abort, filter;
  50         string fastafile, templatefile, outputDir, maskfile;
  51         int processors, window, numwanted, numSeqs, templateSeqsLength;
  52         Chimera* chimera;
  53         vector<string> fastaFileNames;
  54         vector<string> outputNames;
  55         map<string, vector<string> > outputTypes;
  56
  57
  58 };
  59
  60 /***********************************************************/
  61
  62 #endif
  63