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#ifndef GETSABUNDCOMMAND_H
#define GETSABUNDCOMMAND_H
/*
* getsabundcommand.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 "sabundvector.hpp"
class GetSAbundCommand : public Command {
public:
GetSAbundCommand(string);
~GetSAbundCommand() = default;
vector<string> setParameters();
string getCommandName() { return "get.sabund"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.sabund"; }
string getDescription() { return "creates a sabund file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string filename, format, inputfile, listfile, rabundfile, countfile;
ofstream out;
vector<string> outputNames;
bool abort, allLines;
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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