pcoacommand.h

   1 #ifndef PCOACOMMAND_H
   2 #define PCOACOMMAND_H
   3
   4 /*
   5  *  pcoacommand.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 #include "linearalgebra.h"
  15
  16
  17 /*****************************************************************/
  18 class PCOACommand : public Command {
  19
  20 public:
  21         PCOACommand(string);
  22         PCOACommand();
  23         ~PCOACommand();
  24         vector<string> getRequiredParameters();
  25         vector<string> getValidParameters();
  26         vector<string> getRequiredFiles();
  27         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  28         int execute();
  29         void help();
  30
  31 private:
  32
  33         bool abort, metric;
  34         string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
  35         float cutoff, precision;
  36         vector<string> outputNames;
  37         map<string, vector<string> > outputTypes;
  38         LinearAlgebra linearCalc;
  39
  40         void get_comment(istream&, char, char);
  41         int read_phylip(istream&, int, vector<string>&, vector<vector<double> >&);
  42         void read(string, vector<string>&, vector<vector<double> >&);
  43         void recenter(double, vector<vector<double> >, vector<vector<double> >&);
  44         void output(string, vector<string>, vector<vector<double> >&, vector<double>);
  45
  46 };
  47
  48 /*****************************************************************/
  49
  50 #endif
  51