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"
15 #include "sharedrabundvector.h"
18 class GetRelAbundCommand : public Command {
21 GetRelAbundCommand(string);
23 ~GetRelAbundCommand(){}
25 vector<string> setParameters();
26 string getCommandName() { return "get.relabund"; }
27 string getCommandCategory() { return "OTU-Based Approaches"; }
29 string getHelpString();
30 string getOutputPattern(string);
31 string getCitation() { return "http://www.mothur.org/wiki/Get.relabund"; }
32 string getDescription() { return "calculates the relative abundance of each OTU in a sample"; }
36 void help() { m->mothurOut(getHelpString()); }
40 vector<SharedRAbundVector*> lookup;
42 bool abort, allLines, pickedGroups;
43 set<string> labels; //holds labels to be used
44 string groups, label, outputDir, scale, sharedfile;
45 vector<string> Groups, outputNames;
47 int getRelAbundance(vector<SharedRAbundVector*>&, ofstream&);