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#ifndef OTUHIERARCHYCOMMAND_H
#define OTUHIERARCHYCOMMAND_H
/*
* otuhierarchycommand.h
* Mothur
*
* Created by westcott on 1/19/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "listvector.hpp"
//**********************************************************************************************************************
class OtuHierarchyCommand : public Command {
public:
OtuHierarchyCommand(string);
~OtuHierarchyCommand(){}
vector<string> setParameters();
string getCommandName() { return "otu.hierarchy"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCommonQuestions();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Otu.hierarchy"; }
string getDescription() { return "relates OTUs at different distances"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, asv;
set<string> mylabels; //holds labels to be used
string label, listFile, asvlistFile, taxfile, countfile, output, list1Label, list2Label;
vector<string> outputNames;
void processHierarchy();
void processASV();
vector< vector<string> > getListVectors();
vector< vector<string> > getListVector(string, string&);
};
//**********************************************************************************************************************
#endif
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