1 #ifndef MERGEGROUPSCOMMAND_H
2 #define MERGEGROUPSCOMMAND_H
8 * Created by westcott on 1/24/11.
9 * Copyright 2011 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "inputdata.h"
15 #include "sharedrabundvector.h"
19 class MergeGroupsCommand : public Command {
22 MergeGroupsCommand(string);
24 ~MergeGroupsCommand();
25 vector<string> getRequiredParameters();
26 vector<string> getValidParameters();
27 vector<string> getRequiredFiles();
28 map<string, vector<string> > getOutputFiles() { return outputTypes; }
33 GlobalData* globaldata;
35 vector<SharedRAbundVector*> lookup;
36 map<string, vector<string> > outputTypes;
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;
43 int process(vector<SharedRAbundVector*>&, ofstream&);