working on nmds command

[mothur.git] / nmdscommand.h

diff --git a/nmdscommand.h b/nmdscommand.h
index d7bedcf7f9c37a6f8091d32792c10a160be3e5c5..7979c67a3eb9d043c8e19ef2429a9e5ffdff57b0 100644 (file)
--- a/nmdscommand.h
+++ b/nmdscommand.h
@@ -42,7 +42,7 @@ public:
        
 private:
        
-       bool abort, trace;
+       bool abort;
        string phylipfile, outputDir, axesfile;
        int maxdim, mindim, maxIters, iters;
        double epsilon;
@@ -56,14 +56,7 @@ 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&);      
 };
 
 /*****************************************************************/