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[mothur.git] / pcoacommand.h

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+#ifndef PCOACOMMAND_H
+#define PCOACOMMAND_H
+
+/*
+ *  pcoacommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 1/4/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+ 
+#include "command.hpp"
+#include "linearalgebra.h"
+
+
+/*****************************************************************/
+class PCOACommand : public Command {
+       
+public:
+       PCOACommand(string);    
+       PCOACommand();
+       ~PCOACommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "pcoa";                                        }
+       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/Pcoa"; }
+       string getDescription()         { return "pcoa"; }
+
+       int execute();
+       void help() { m->mothurOut(getHelpString()); }
+       
+private:
+
+       bool abort, metric;
+       string phylipfile, filename, fbase, outputDir;
+       vector<string> outputNames;
+       LinearAlgebra linearCalc;
+       
+       void get_comment(istream&, char, char);
+       void output(string, vector<string>, vector<vector<double> >&, vector<double>);
+       
+};
+       
+/*****************************************************************/
+       
+#endif
+