removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / nmdscommand.h

diff --git a/nmdscommand.h b/nmdscommand.h
index 7979c67a3eb9d043c8e19ef2429a9e5ffdff57b0..861e8eaf95eb79a02c4e918a732f13c19f3ce845 100644 (file)
--- a/nmdscommand.h
+++ b/nmdscommand.h
@@ -32,13 +32,15 @@ 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(); 
+       
+       int execute();
+       void help() { m->mothurOut(getHelpString()); }
        
 private:
        
@@ -47,7 +49,6 @@ 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&);