8 * Created by westcott on 1/4/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "linearalgebra.h"
17 /*****************************************************************/
18 class PCOACommand : public Command {
25 vector<string> setParameters();
26 string getCommandName() { return "pcoa"; }
27 string getCommandCategory() { return "Hypothesis Testing"; }
28 string getOutputFileNameTag(string, string);
29 string getHelpString();
30 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"; }
31 string getDescription() { return "pcoa"; }
34 void help() { m->mothurOut(getHelpString()); }
39 string phylipfile, filename, fbase, outputDir;
40 vector<string> outputNames;
41 LinearAlgebra linearCalc;
43 void get_comment(istream&, char, char);
44 void output(string, vector<string>, vector<vector<double> >&, vector<double>);
48 /*****************************************************************/