chimeracheckcommand.h

   1 #ifndef CHIMERACHECKCOMMAND_H
   2 #define CHIMERACHECKCOMMAND_H
   3
   4 /*
   5  *  chimeracheckcommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 3/31/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "mothur.h"
  14 #include "command.hpp"
  15 #include "chimera.h"
  16 #include "chimeracheckrdp.h"
  17
  18
  19 /***********************************************************/
  20
  21 class ChimeraCheckCommand : public Command {
  22 public:
  23         ChimeraCheckCommand(string);
  24         ChimeraCheckCommand();
  25         ~ChimeraCheckCommand(){}
  26
  27         vector<string> setParameters();
  28         string getCommandName()                 { return "chimera.check";               }
  29         string getCommandCategory()             { return "Sequence Processing"; }
  30         string getHelpString();
  31         string getCitation() { return "CHIMERA_CHECK version 2.7 written by Niels Larsen (http://wdcm.nig.ac.jp/RDP/docs/chimera_doc.html) \nhttp://www.mothur.org/wiki/Chimera.check"; }
  32         string getDescription()         { return "detect chimeric sequences"; }
  33
  34         int execute();
  35         void help() { m->mothurOut(getHelpString()); }
  36
  37
  38 private:
  39
  40         struct linePair {
  41                 unsigned long int start;
  42                 unsigned long int end;
  43                 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
  44         };
  45
  46         vector<int> processIDS;   //processid
  47         vector<linePair*> lines;
  48
  49         int driver(linePair*, string, string);
  50         int createProcesses(string, string);
  51
  52         #ifdef USE_MPI
  53         int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long int>&);
  54         #endif
  55
  56         bool abort, svg;
  57         string fastafile, templatefile, namefile, outputDir;
  58         int processors, increment, ksize, numSeqs, templateSeqsLength;
  59         Chimera* chimera;
  60         vector<string> fastaFileNames;
  61         vector<string> nameFileNames;
  62         vector<string> outputNames;
  63 };
  64
  65 /***********************************************************/
  66
  67 #endif
  68
  69