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#ifndef PHYLOTYPECOMMAND_H
#define PHYLOTYPECOMMAND_H
/*
* phylotypecommand.h
* Mothur
*
* Created by westcott on 11/20/09.
* Copyright 2009 Schloss Lab. All rights reserved.
*
*/
#include "taxonomyequalizer.h"
#include "command.hpp"
/*************************************************************************/
class PhylotypeCommand : public Command {
public:
PhylotypeCommand(string);
~PhylotypeCommand(){}
vector<string> setParameters();
string getCommandName() { return "phylotype"; }
string getCommandCategory() { return "Clustering"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Phylotype"; }
string getDescription() { return "cluster your sequences into OTUs based on their classifications"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, allLines;
string taxonomyFileName, label, namefile, countfile;
set<string> labels; //holds labels to be used
int cutoff;
map<string, string> namemap;
vector<string> outputNames;
map<int, int> currentNodes;
map<int, int> parentNodes;
map<int, int>::iterator itCurrent;
};
/*************************************************************************/
#endif
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