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#ifndef GETRABUNDCOMMAND_H
#define GETRABUNDCOMMAND_H
/*
* getrabundcommand.h
* Mothur
*
* Created by Sarah Westcott on 6/2/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "command.hpp"
#include "inputdata.h"
#include "listvector.hpp"
class GetRAbundCommand : public Command {
public:
GetRAbundCommand(string);
~GetRAbundCommand(){}
vector<string> setParameters();
string getCommandName() { return "get.rabund"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.rabund"; }
string getDescription() { return "creates a rabund file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string filename, listfile, sabundfile, inputfile, format, countfile, sharedfile;
ofstream out;
vector<string> outputNames, Groups;
bool abort, allLines, sorted;
set<string> labels; //holds labels to be used
string label;
int processList(ofstream& out);
int createRabund(CountTable& ct, ListVector*& list, RAbundVector*& rabund);
};
#endif
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