moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / pcoacommand.h

diff --git a/pcoacommand.h b/pcoacommand.h
deleted file mode 100644 (file)
index 3d24f6a..0000000
--- a/pcoacommand.h
+++ /dev/null
@@ -1,50 +0,0 @@
-#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
-