pcacommand.h

   1 #ifndef PCACOMMAND_H
   2 #define PCACOMMAND_H
   3
   4 /*
   5  *  pcacommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 1/4/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14
  15
  16 /*****************************************************************/
  17 class PCACommand : public Command {
  18
  19 public:
  20         PCACommand(string);
  21         ~PCACommand();
  22         int execute();
  23         void help();
  24
  25 private:
  26
  27         bool abort;
  28         string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
  29         float cutoff, precision;
  30         vector<string> outputNames;
  31
  32         void get_comment(istream&, char, char);
  33         void 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>);
  41
  42 };
  43
  44 /*****************************************************************/
  45
  46 #endif
  47