mergegroupscommand.h

   1 #ifndef MERGEGROUPSCOMMAND_H
   2 #define MERGEGROUPSCOMMAND_H
   3
   4 /*
   5  *  mergegroupscommand.h
   6  *  mothur
   7  *
   8  *  Created by westcott on 1/24/11.
   9  *  Copyright 2011 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "inputdata.h"
  15 #include "sharedrabundvector.h"
  16
  17 class MergeGroupsCommand : public Command {
  18
  19 public:
  20         MergeGroupsCommand(string);
  21         MergeGroupsCommand();
  22         ~MergeGroupsCommand() {}
  23
  24         vector<string> setParameters();
  25         string getCommandName()                 { return "merge.groups";        }
  26         string getCommandCategory()             { return "General";                     }
  27         string getHelpString();
  28
  29         int execute();
  30         void help() { m->mothurOut(getHelpString()); }
  31
  32 private:
  33         GroupMap* designMap;
  34         vector<SharedRAbundVector*> lookup;
  35
  36         bool abort, allLines, pickedGroups;
  37         set<string> labels; //holds labels to be used
  38         string groups, label, outputDir, inputDir, designfile, sharedfile;
  39         vector<string> Groups, outputNames;
  40
  41         int process(vector<SharedRAbundVector*>&, ofstream&);
  42 };
  43
  44 #endif
  45