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
  25         vector<string> setParameters();
  26         string getCommandName()                 { return "pcoa";                                        }
  27         string getCommandCategory()             { return "Hypothesis Testing";          }
  28         string getHelpString();
  29
  30         int execute();
  31         void help() { m->mothurOut(getHelpString()); }
  32
  33 private:
  34
  35         bool abort, metric;
  36         string phylipfile, filename, fbase, outputDir;
  37         vector<string> outputNames;
  38         LinearAlgebra linearCalc;
  39
  40         void get_comment(istream&, char, char);
  41         void output(string, vector<string>, vector<vector<double> >&, vector<double>);
  42
  43 };
  44
  45 /*****************************************************************/
  46
  47 #endif
  48