chimeraslayercommand.h

   1 #ifndef CHIMERASLAYERCOMMAND_H
   2 #define CHIMERASLAYERCOMMAND_H
   3
   4 /*
   5  *  chimeraslayercommand.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
  17 /***********************************************************/
  18
  19 class ChimeraSlayerCommand : public Command {
  20 public:
  21         ChimeraSlayerCommand(string);
  22         ChimeraSlayerCommand();
  23         ~ChimeraSlayerCommand() {}
  24
  25         vector<string> setParameters();
  26         string getCommandName()                 { return "chimera.slayer";              }
  27         string getCommandCategory()             { return "Sequence Processing"; }
  28         string getHelpString();
  29         string getCitation() { return "http://www.mothur.org/wiki/Chimera.slayer"; }
  30
  31
  32         int execute();
  33         void help() { m->mothurOut(getHelpString()); }
  34
  35 private:
  36
  37         struct linePair {
  38                 unsigned long int start;
  39                 unsigned long int end;
  40                 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
  41         };
  42
  43         vector<int> processIDS;   //processid
  44         vector<linePair*> lines;
  45
  46         int driver(linePair*, string, string, string, string);
  47         int createProcesses(string, string, string, string);
  48         int divideInHalf(Sequence, string&, string&);
  49         map<string, int> sortFastaFile(string, string);
  50
  51         #ifdef USE_MPI
  52         int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
  53         #endif
  54
  55         bool abort, realign, trim, trimera;
  56         string fastafile, templatefile, outputDir, search, namefile;
  57         int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
  58         float divR;
  59         Chimera* chimera;
  60
  61         vector<string> outputNames;
  62         vector<string> fastaFileNames;
  63         vector<string> nameFileNames;
  64
  65 };
  66
  67 /***********************************************************/
  68
  69 #endif
  70
  71