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#ifndef COLLECTSHAREDCOMMAND_H
#define COLLECTSHAREDCOMMAND_H
/*
* collectsharedcommand.h
* Dotur
*
* Created by Sarah Westcott on 1/2/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "command.hpp"
#include "sharedordervector.h"
#include "inputdata.h"
#include "collect.h"
#include "display.h"
#include "validcalculator.h"
class CollectSharedCommand : public Command {
public:
CollectSharedCommand(string);
~CollectSharedCommand();
vector<string> setParameters();
string getCommandName() { return "collect.shared"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "Schloss PD, Handelsman J (2006). Introducing SONS, A tool that compares the membership of microbial communities. Appl Environ Microbiol 72: 6773-9. \nhttp://www.mothur.org/wiki/Collect.shared"; }
string getDescription() { return "generates collector's curves for calculators, which describe the similarity between communities or their shared richness"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
vector<Display*> cDisplays;
float freq;
bool abort, allLines, all;
set<string> labels; //holds labels to be used
string label, calc, groups, sharedfile;
vector<string> Estimators, Groups, outputNames;
};
#endif
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