X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=nmdscommand.h;h=92b694864a6d15f5b5dc20f176a271a7506ae6eb;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=d7bedcf7f9c37a6f8091d32792c10a160be3e5c5;hpb=c921bbf0623d5200f69b5d83b3c70ea533c69412;p=mothur.git

diff --git a/nmdscommand.h b/nmdscommand.h
index d7bedcf..92b6948 100644
--- a/nmdscommand.h
+++ b/nmdscommand.h
@@ -32,22 +32,27 @@ 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, trace;
+	bool abort;
 	string phylipfile, outputDir, axesfile;
 	int maxdim, mindim, maxIters, iters;
 	double epsilon;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 	LinearAlgebra linearCalc;
 	
 	vector< vector<double> > nmdsCalc(vector< vector<double> >&, vector< vector<double> >&, double&);
@@ -56,14 +61,7 @@ private:
 	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&);
-
-	//vector<seqDist> satisfyMonotonicity(vector<seqDist>, vector<int>);
-	//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> >&);
-	
+	int output(vector< vector<double> >&, vector<string>&, ofstream&);	
 };
 
 /*****************************************************************/