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 getOutputFileNameTag(string, string);
  28         string getHelpString();
  29         string getCitation() { return "http://www.mothur.org/wiki/Merge.groups"; }
  30         string getDescription()         { return "reads shared file and a design file and merges the groups in the shared file that are in the same grouping in the design file"; }
  31
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35
  36 private:
  37         GroupMap* designMap;
  38         vector<SharedRAbundVector*> lookup;
  39
  40         bool abort, allLines, pickedGroups;
  41         set<string> labels; //holds labels to be used
  42         string groups, label, outputDir, inputDir, designfile, sharedfile, groupfile;
  43         vector<string> Groups, outputNames;
  44
  45         int process(vector<SharedRAbundVector*>&, ofstream&);
  46         int processSharedFile(GroupMap*&);
  47         int processGroupFile(GroupMap*&);
  48 };
  49
  50 #endif
  51