private:
- bool abort, trace;
+ bool abort;
string phylipfile, outputDir, axesfile;
int maxdim, mindim, maxIters, iters;
double epsilon;
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&);
};
/*****************************************************************/