X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=nmdscommand.h;h=92b694864a6d15f5b5dc20f176a271a7506ae6eb;hb=372fb21ea66ced432b109225851a1b80ef0491a3;hp=7979c67a3eb9d043c8e19ef2429a9e5ffdff57b0;hpb=41f654a317afba7f4dba3fcd0a6557773528845a;p=mothur.git

diff --git a/nmdscommand.h b/nmdscommand.h
index 7979c67..92b6948 100644
--- a/nmdscommand.h
+++ b/nmdscommand.h
@@ -32,13 +32,19 @@ 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:
 	
@@ -47,7 +53,6 @@ private:
 	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&);