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 {
28 string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
29 float cutoff, precision;
30 vector<string> outputNames;
32 void get_comment(istream&, char, char);
33 int read_phylip(istream&, int, vector<string>&, vector<vector<double> >&);
34 void read(string, vector<string>&, vector<vector<double> >&);
35 double pythag(double, double);
36 void matrix_mult(vector<vector<double> >, vector<vector<double> >, vector<vector<double> >&);
37 void recenter(double, vector<vector<double> >, vector<vector<double> >&);
38 void tred2(vector<vector<double> >&, vector<double>&, vector<double>&);
39 void qtli(vector<double>&, vector<double>&, vector<vector<double> >&);
40 void output(string, vector<string>, vector<vector<double> >, vector<double>);
44 /*****************************************************************/