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 getOutputFileNameTag(string, string);
+ string getHelpString();
+ 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&);
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&);
};
/*****************************************************************/