1 #ifndef GETRELABUNDCOMMAND_H
2 #define GETRELABUNDCOMMAND_H
8 * Created by westcott on 6/21/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "inputdata.h"
16 #include "sharedrabundvector.h"
20 class GetRelAbundCommand : public Command {
23 GetRelAbundCommand(string);
25 ~GetRelAbundCommand();
26 vector<string> getRequiredParameters();
27 vector<string> getValidParameters();
28 vector<string> getRequiredFiles();
29 map<string, vector<string> > getOutputFiles() { return outputTypes; }
34 GlobalData* globaldata;
37 vector<SharedRAbundVector*> lookup;
39 bool abort, allLines, pickedGroups;
40 set<string> labels; //holds labels to be used
41 string groups, label, outputDir, scale;
42 vector<string> Groups, outputNames;
43 map<string, vector<string> > outputTypes;
45 int getRelAbundance(vector<SharedRAbundVector*>&, ofstream&);