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 getOutputFileNameTag(string, string);
  29         string getHelpString();
  30         string getCitation() { return "McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Pcoa"; }
  31         string getDescription()         { return "pcoa"; }
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35
  36 private:
  37
  38         bool abort, metric;
  39         string phylipfile, filename, fbase, outputDir;
  40         vector<string> outputNames;
  41         LinearAlgebra linearCalc;
  42
  43         void get_comment(istream&, char, char);
  44         void output(string, vector<string>, vector<vector<double> >&, vector<double>);
  45
  46 };
  47
  48 /*****************************************************************/
  49
  50 #endif
  51