8 * Created by westcott on 1/4/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
16 /*****************************************************************/
17 class PCACommand : public Command {
23 vector<string> getRequiredParameters();
24 vector<string> getValidParameters();
25 vector<string> getRequiredFiles();
26 map<string, vector<string> > getOutputFiles() { return outputTypes; }
33 string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
34 float cutoff, precision;
35 vector<string> outputNames;
36 map<string, vector<string> > outputTypes;
38 void get_comment(istream&, char, char);
39 int read_phylip(istream&, int, vector<string>&, vector<vector<double> >&);
40 void read(string, vector<string>&, vector<vector<double> >&);
41 double pythag(double, double);
42 void matrix_mult(vector<vector<double> >, vector<vector<double> >, vector<vector<double> >&);
43 void recenter(double, vector<vector<double> >, vector<vector<double> >&);
44 void tred2(vector<vector<double> >&, vector<double>&, vector<double>&);
45 void qtli(vector<double>&, vector<double>&, vector<vector<double> >&);
46 void output(string, vector<string>, vector<vector<double> >, vector<double>);
50 /*****************************************************************/