X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=nmdscommand.h;h=7979c67a3eb9d043c8e19ef2429a9e5ffdff57b0;hb=41f654a317afba7f4dba3fcd0a6557773528845a;hp=d7bedcf7f9c37a6f8091d32792c10a160be3e5c5;hpb=c921bbf0623d5200f69b5d83b3c70ea533c69412;p=mothur.git

diff --git a/nmdscommand.h b/nmdscommand.h
index d7bedcf..7979c67 100644
--- 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&);	
 };
 
 /*****************************************************************/