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 GlobalData;
  18
  19 class MergeGroupsCommand : public Command {
  20
  21 public:
  22         MergeGroupsCommand(string);
  23         MergeGroupsCommand();
  24         ~MergeGroupsCommand();
  25         vector<string> getRequiredParameters();
  26         vector<string> getValidParameters();
  27         vector<string> getRequiredFiles();
  28         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  29         int execute();
  30         void help();
  31
  32 private:
  33         GlobalData* globaldata;
  34         GroupMap* designMap;
  35         vector<SharedRAbundVector*> lookup;
  36         map<string, vector<string> > outputTypes;
  37
  38         bool abort, allLines, pickedGroups;
  39         set<string> labels; //holds labels to be used
  40         string groups, label, outputDir, inputDir, designfile, sharedfile;
  41         vector<string> Groups, outputNames;
  42
  43         int process(vector<SharedRAbundVector*>&, ofstream&);
  44 };
  45
  46 #endif
  47