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#ifndef NMDSCOMMAND_H
#define NMDSCOMMAND_H
/*
* nmdscommand.h
* mothur
*
* Created by westcott on 1/11/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "linearalgebra.h"
/*
Translated from the nmds.R code written by Sarah Goslee using,
# Non-metric multidimensional scaling function
# using the majorization algorithm from
# Borg & Groenen 1997, Modern Multidimensional Scaling.
#
# also referenced (Kruskal 1964)
*/
/*****************************************************************/
class NMDSCommand : public Command {
public:
NMDSCommand(string);
~NMDSCommand(){}
vector<string> setParameters();
string getCommandName() { return "nmds"; }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "Borg, Groenen (1997). Non-metric multidimensional scaling function using the majorization algorithm, in Modern Multidimensional Scaling. Ed. T.F. Cox and M.A.A. Cox. Chapman and Hall. \nhttp://www.mothur.org/wiki/Nmds"; }
string getDescription() { return "nmds"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort;
string phylipfile, axesfile;
int maxdim, mindim, maxIters, iters;
double epsilon;
vector<string> outputNames;
LinearAlgebra linearCalc;
vector< vector<double> > nmdsCalc(vector< vector<double> >&, vector< vector<double> >&, double&);
vector< vector<double> > getConfiguration(vector< vector<double> >&, int);
vector< vector<double> > generateStartingConfiguration(int, int); //pass in numNames, return axes
int normalizeConfiguration(vector< vector<double> >&, int, int);
double calculateStress(vector< vector<double> >&, vector< vector<double> >&);
vector< vector<double> > readAxes(vector<string>);
int output(vector< vector<double> >&, vector<string>&, ofstream&);
};
/*****************************************************************/
#endif
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