X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=nmdscommand.h;h=92b694864a6d15f5b5dc20f176a271a7506ae6eb;hb=3914b0d6480f67df53b1e838f51c4e6155710434;hp=5e4e65596a05a91cfdc6824db1b4086303a0f8e3;hpb=d04f948b1a2a1a2984fc4a45d04403b8c121c5bc;p=mothur.git

diff --git a/nmdscommand.h b/nmdscommand.h
index 5e4e655..92b6948 100644
--- a/nmdscommand.h
+++ b/nmdscommand.h
@@ -14,8 +14,17 @@
 #include "linearalgebra.h"
 
 
-/*  references used to make this command: "Nonmetric Multidimensional Scalling: A Numerical Method"
- by J. B. Kruskal  Psychometrika - Vol 29, No. 2 June 1964 */
+/*  
+ 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 {
@@ -23,34 +32,36 @@ class NMDSCommand : public Command {
 public:
 	NMDSCommand(string);	
 	NMDSCommand();
-	~NMDSCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();	
-	void help();
+	~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, outputDir, axesfile;
-	int dimension, maxIters;
-	double step, cutoff;
+	int maxdim, mindim, maxIters, iters;
+	double epsilon;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 	LinearAlgebra linearCalc;
 	
-	vector< vector<double> > generateStartingConfiguration(int); //pass in numNames, return axes
-	int normalizeConfiguration(vector< vector<double> >&, int);
-	vector<seqDist> satisfyMonotonicity(vector<seqDist>);
-	double calculateStress(vector<seqDist>&, vector<seqDist>&, double&);
-	vector< vector<double> > calculateStressGradientVector(vector<seqDist>&, vector<seqDist>&, double, double, vector< vector<double> >&);
-	double calculateMagnitude(vector< vector<double> >&);
-	double calculateStep(vector< vector<double> >&, vector< vector<double> >&, vector<double>&);
-	vector< vector<double> > calculateNewConfiguration(double, vector< vector<double> >&, vector< vector<double> >&);
+	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(string, string, vector< vector<double> >&, vector<double>&, vector<string>&);
+	int output(vector< vector<double> >&, vector<string>&, ofstream&);	
 };
 
 /*****************************************************************/