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#ifndef GETLISTCOUNTCOMMAND_H
#define GETLISTCOUNTCOMMAND_H
/*
* getlistcountcommand.h
* Mothur
*
* Created by westcott on 10/12/09.
* Copyright 2009 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "inputdata.h"
#include "listvector.hpp"
/**********************************************************/
class GetListCountCommand : public Command {
public:
GetListCountCommand(string);
GetListCountCommand();
~GetListCountCommand(){}
vector<string> setParameters();
string getCommandName() { return "get.otulist"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getCitation() { return "http://www.mothur.org/wiki/Get.otulist"; }
string getDescription() { return "lists each OTU number and the sequence contained in that OTU"; }
string getHelpString();
string getOutputPattern(string);
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
ListVector* list;
InputData* input;
bool abort, allLines;
set<string> labels; //holds labels to be used
string label, listfile, outputDir, sort;
ofstream out;
vector<string> outputNames;
void process(ListVector*);
};
/**********************************************************/
#endif
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