splitgroupscommand.h

   1 #ifndef SPLITGROUPSCOMMAND_H
   2 #define SPLITGROUPSCOMMAND_H
   3
   4 /*
   5  *  splitgroupscommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 9/20/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 /* split.groups - given a group file, split sequences and names files in to separate files *.group1.fasta and .group1.names. */
  15
  16
  17 #include "command.hpp"
  18 #include "groupmap.h"
  19 #include "sequence.hpp"
  20
  21 /***************************************************************************************/
  22
  23 class SplitGroupCommand : public Command {
  24
  25 public:
  26         SplitGroupCommand(string);
  27         SplitGroupCommand();
  28         ~SplitGroupCommand() {}
  29
  30         vector<string> setParameters();
  31         string getCommandName()                 { return "split.groups";                                }
  32         string getCommandCategory()             { return "Sequence Processing";         }
  33
  34         string getHelpString();
  35     string getOutputPattern(string);
  36         string getCitation() { return "http://www.mothur.org/wiki/Split.group"; }
  37         string getDescription()         { return "split a name or fasta file by group"; }
  38
  39
  40         int execute();
  41         void help() { m->mothurOut(getHelpString()); }
  42
  43 private:
  44         vector<string> outputNames;
  45
  46         string outputDir, namefile, groupfile, countfile, groups, fastafile;
  47         vector<string> Groups;
  48         bool abort;
  49
  50     int runNameGroup();
  51     int runCount();
  52 };
  53
  54 /***************************************************************************************/
  55
  56 #endif
  57
  58
  59