X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcoacommand.h;fp=pcoacommand.h;h=3d24f6a97f799f1c8627ef40d5dbec888da51dc6;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/pcoacommand.h b/pcoacommand.h
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+++ b/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
+