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#ifndef MANTELCOMMAND_H
#define MANTELCOMMAND_H
/*
* mantelcommand.h
* mothur
*
* Created by westcott on 2/9/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "linearalgebra.h"
class MantelCommand : public Command {
public:
MantelCommand(string);
~MantelCommand(){}
vector<string> setParameters();
string getCommandName() { return "mantel"; }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Mantel"; }
string getDescription() { return "Mantel’s test for correlation between matrices"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string phylipfile1, phylipfile2, method;
bool abort;
int iters;
vector<string> outputNames;
};
#endif
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