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 {
24 vector<string> getRequiredParameters();
25 vector<string> getValidParameters();
26 vector<string> getRequiredFiles();
27 map<string, vector<string> > getOutputFiles() { return outputTypes; }
34 string phylipfile, filename, fbase, outputDir;
35 vector<string> outputNames;
36 map<string, vector<string> > outputTypes;
37 LinearAlgebra linearCalc;
39 void get_comment(istream&, char, char);
40 void recenter(double, vector<vector<double> >, vector<vector<double> >&);
41 void output(string, vector<string>, vector<vector<double> >&, vector<double>);
45 /*****************************************************************/