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#ifndef GETRELABUNDCOMMAND_H
#define GETRELABUNDCOMMAND_H
/*
* getrelabundcommand.h
* Mothur
*
* Created by westcott on 6/21/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "inputdata.h"
class GetRelAbundCommand : public Command {
public:
GetRelAbundCommand(string);
~GetRelAbundCommand(){}
vector<string> setParameters();
string getCommandName() { return "get.relabund"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.relabund"; }
string getDescription() { return "calculates the relative abundance of each OTU in a sample"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
SharedRAbundVectors* lookup;
bool abort, allLines, pickedGroups;
set<string> labels; //holds labels to be used
string groups, label, scale, sharedfile;
vector<string> Groups, outputNames;
int getRelAbundance(SharedRAbundVectors*&, ofstream&);
};
#endif
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