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
  31         string getHelpString();
  32     string getOutputPattern(string);
  33         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"; }
  34         string getDescription()         { return "detect chimeric sequences"; }
  35
  36         int execute();
  37         void help() { m->mothurOut(getHelpString()); }
  38
  39
  40 private:
  41
  42         struct linePair {
  43                 unsigned long long start;
  44                 unsigned long long end;
  45                 linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
  46         };
  47
  48         vector<int> processIDS;   //processid
  49         vector<linePair*> lines;
  50
  51         int driver(linePair*, string, string);
  52         int createProcesses(string, string);
  53
  54         #ifdef USE_MPI
  55         int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long long>&);
  56         #endif
  57
  58         bool abort, svg, save;
  59         string fastafile, templatefile, namefile, outputDir;
  60         int processors, increment, ksize, numSeqs, templateSeqsLength;
  61         Chimera* chimera;
  62         vector<string> fastaFileNames;
  63         vector<string> nameFileNames;
  64         vector<string> outputNames;
  65 };
  66
  67 /***********************************************************/
  68
  69 #endif
  70
  71