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 /*  references used to make this command: "Nonmetric Multidimensional Scalling: A Numerical Method"
  18  by J. B. Kruskal  Psychometrika - Vol 29, No. 2 June 1964 */
  19
  20 /*****************************************************************/
  21 class NMDSCommand : public Command {
  22
  23 public:
  24         NMDSCommand(string);
  25         NMDSCommand();
  26         ~NMDSCommand();
  27         vector<string> getRequiredParameters();
  28         vector<string> getValidParameters();
  29         vector<string> getRequiredFiles();
  30         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  31         int execute();
  32         void help();
  33
  34 private:
  35
  36         bool abort;
  37         string phylipfile, outputDir, axesfile;
  38         int dimension, maxIters;
  39         double step, cutoff;
  40         vector<string> outputNames;
  41         map<string, vector<string> > outputTypes;
  42         LinearAlgebra linearCalc;
  43
  44         vector< vector<double> > generateStartingConfiguration(int); //pass in numNames, return axes
  45         int normalizeConfiguration(vector< vector<double> >&, int);
  46         vector<seqDist> satisfyMonotonicity(vector<seqDist>);
  47         double calculateStress(vector<seqDist>&, vector<seqDist>&, double&);
  48         vector< vector<double> > calculateStressGradientVector(vector<seqDist>&, vector<seqDist>&, double, double, vector< vector<double> >&);
  49         double calculateMagnitude(vector< vector<double> >&);
  50         double calculateStep(vector< vector<double> >&, vector< vector<double> >&, vector<double>&);
  51         vector< vector<double> > calculateNewConfiguration(double, vector< vector<double> >&, vector< vector<double> >&);
  52         vector< vector<double> > readAxes(vector<string>);
  53         int output(string, string, vector< vector<double> >&, vector<double>&, vector<string>&);
  54 };
  55
  56 /*****************************************************************/
  57
  58 #endif
  59
  60