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.group";                         }
  32         string getCommandCategory()             { return "Sequence Processing";         }
  33         string getHelpString();
  34         string getCitation() { return "http://www.mothur.org/wiki/Split.group"; }
  35         string getDescription()         { return "split a name or fasta file by group"; }
  36
  37
  38         int execute();
  39         void help() { m->mothurOut(getHelpString()); }
  40
  41 private:
  42         int readNames();
  43         int splitFasta();
  44
  45         vector<string> outputNames;
  46         map<string, vector<string> > nameMap;
  47         map<string, vector<string> >::iterator itNames;
  48         GroupMap* groupMap;
  49
  50         string outputDir, namefile, groupfile, groups, fastafile;
  51         vector<string> Groups;
  52         bool abort;
  53 };
  54
  55 /***************************************************************************************/
  56
  57 #endif
  58
  59
  60