chimerauchimecommand.h

   1 #ifndef CHIMERAUCHIMECOMMAND_H
   2 #define CHIMERAUCHIMECOMMAND_H
   3
   4
   5 /*
   6  *  chimerauchimecommand.h
   7  *  Mothur
   8  *
   9  *  Created by westcott on 5/13/11.
  10  *  Copyright 2011 Schloss Lab. All rights reserved.
  11  *
  12  */
  13
  14 #include "mothur.h"
  15 #include "command.hpp"
  16
  17 /***********************************************************/
  18
  19 class ChimeraUchimeCommand : public Command {
  20 public:
  21         ChimeraUchimeCommand(string);
  22         ChimeraUchimeCommand();
  23         ~ChimeraUchimeCommand() {}
  24
  25         vector<string> setParameters();
  26         string getCommandName()                 { return "chimera.uchime";              }
  27         string getCommandCategory()             { return "Sequence Processing"; }
  28         string getHelpString();
  29         string getCitation() { return "http://drive5.com/uchime/ \nhttp://www.mothur.org/wiki/Chimera.uchime"; }
  30
  31
  32         int execute();
  33         void help() { m->mothurOut(getHelpString()); }
  34
  35 private:
  36         vector<int> processIDS;   //processid
  37         int driver(string, string, string);
  38         int createProcesses(string, string, string);
  39
  40 #ifdef USE_MPI
  41         int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
  42 #endif
  43
  44         bool abort;
  45         string fastafile, templatefile, outputDir, namefile;
  46         int processors;
  47
  48         vector<string> outputNames;
  49         vector<string> fastaFileNames;
  50         vector<string> nameFileNames;
  51
  52 };
  53
  54 /***********************************************************/
  55
  56 #endif
  57
  58