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
  26         vector<string> setParameters();
  27         string getCommandName()                 { return "chimera.ccode";               }
  28         string getCommandCategory()             { return "Sequence Processing"; }
  29         string getHelpString();
  30
  31         int execute();
  32         void help() { m->mothurOut(getHelpString()); }
  33
  34
  35 private:
  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         vector<int> processIDS;   //processid
  42         vector<linePair*> lines;
  43
  44         int driver(linePair*, string, string, string);
  45         int createProcesses(string, string, string);
  46
  47         #ifdef USE_MPI
  48         int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
  49         #endif
  50
  51         bool abort, filter;
  52         string fastafile, templatefile, outputDir, maskfile;
  53         int processors, window, numwanted, numSeqs, templateSeqsLength;
  54         Chimera* chimera;
  55         vector<string> fastaFileNames;
  56         vector<string> outputNames;
  57 };
  58
  59 /***********************************************************/
  60
  61 #endif
  62