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         ~PCACommand();
  23         vector<string> getRequiredParameters();
  24         vector<string> getValidParameters();
  25         vector<string> getRequiredFiles();
  26         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  27         int execute();
  28         void help();
  29
  30 private:
  31
  32         bool abort;
  33         string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
  34         float cutoff, precision;
  35         vector<string> outputNames;
  36         map<string, vector<string> > outputTypes;
  37
  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>);
  47
  48 };
  49
  50 /*****************************************************************/
  51
  52 #endif
  53