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
  35         int execute();
  36         void help() { m->mothurOut(getHelpString()); }
  37
  38 private:
  39         int readNames();
  40         int splitFasta();
  41
  42         vector<string> outputNames;
  43         map<string, vector<string> > nameMap;
  44         map<string, vector<string> >::iterator itNames;
  45         GroupMap* groupMap;
  46
  47         string outputDir, namefile, groupfile, groups, fastafile;
  48         vector<string> Groups;
  49         bool abort;
  50 };
  51
  52 /***************************************************************************************/
  53
  54 #endif
  55
  56
  57