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 getHelpString();
31 void help() { m->mothurOut(getHelpString()); }
36 string phylipfile, filename, fbase, outputDir;
37 vector<string> outputNames;
38 LinearAlgebra linearCalc;
40 void get_comment(istream&, char, char);
41 void output(string, vector<string>, vector<vector<double> >&, vector<double>);
45 /*****************************************************************/