nmdscommand.h

   1 #ifndef NMDSCOMMAND_H
   2 #define NMDSCOMMAND_H
   3
   4 /*
   5  *  nmdscommand.h
   6  *  mothur
   7  *
   8  *  Created by westcott on 1/11/11.
   9  *  Copyright 2011 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "linearalgebra.h"
  15
  16
  17 /*
  18  Translated from the nmds.R code written by Sarah Goslee using,
  19
  20  # Non-metric multidimensional scaling function
  21  # using the majorization algorithm from
  22  # Borg & Groenen 1997, Modern Multidimensional Scaling.
  23  #
  24
  25  # also referenced (Kruskal 1964)
  26
  27  */
  28
  29 /*****************************************************************/
  30 class NMDSCommand : public Command {
  31
  32 public:
  33         NMDSCommand(string);
  34         NMDSCommand();
  35         ~NMDSCommand(){}
  36
  37         vector<string> setParameters();
  38         string getCommandName()                 { return "nmds";                                        }
  39         string getCommandCategory()             { return "Hypothesis Testing";          }
  40         string getHelpString();
  41
  42         int execute();
  43         void help() { m->mothurOut(getHelpString()); }
  44
  45 private:
  46
  47         bool abort;
  48         string phylipfile, outputDir, axesfile;
  49         int maxdim, mindim, maxIters, iters;
  50         double epsilon;
  51         vector<string> outputNames;
  52         LinearAlgebra linearCalc;
  53
  54         vector< vector<double> > nmdsCalc(vector< vector<double> >&, vector< vector<double> >&, double&);
  55         vector< vector<double> > getConfiguration(vector< vector<double> >&, int);
  56         vector< vector<double> > generateStartingConfiguration(int, int); //pass in numNames, return axes
  57         int normalizeConfiguration(vector< vector<double> >&, int, int);
  58         double calculateStress(vector< vector<double> >&, vector< vector<double> >&);
  59         vector< vector<double> > readAxes(vector<string>);
  60         int output(vector< vector<double> >&, vector<string>&, ofstream&);
  61 };
  62
  63 /*****************************************************************/
  64
  65 #endif
  66
  67