added modify names parameter to set.dir

[mothur.git] / nmdscommand.h

diff --git a/nmdscommand.h b/nmdscommand.h
index d7bedcf7f9c37a6f8091d32792c10a160be3e5c5..92b694864a6d15f5b5dc20f176a271a7506ae6eb 100644 (file)
--- 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&);      
 };
 
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