moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / nmdscommand.h

diff --git a/nmdscommand.h b/nmdscommand.h
deleted file mode 100644 (file)
index c05c9fe..0000000
--- a/nmdscommand.h
+++ /dev/null
@@ -1,69 +0,0 @@
-#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();
-       ~NMDSCommand(){}
-       
-       vector<string> setParameters();
-       string getCommandName()                 { return "nmds";                                        }
-       string getCommandCategory()             { return "Hypothesis Testing";          }
-       string getHelpString(); 
-       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, outputDir, 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
-
-