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[mothur.git] / mantelcommand.h

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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();
+       ~MantelCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "mantel";                                      }
+       string getCommandCategory()             { return "Hypothesis Testing";          }
+       string getHelpString(); 
+       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, outputDir, method;
+       bool abort;
+       int iters;
+       
+       vector<string> outputNames;
+};
+
+
+#endif
+
+
+