added modify names parameter to set.dir

[mothur.git] / nmdscommand.h

diff --git a/nmdscommand.h b/nmdscommand.h
index 7979c67a3eb9d043c8e19ef2429a9e5ffdff57b0..92b694864a6d15f5b5dc20f176a271a7506ae6eb 100644 (file)
--- 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&);