fixed trim.seqs bug with qtrim parameter and added num=1 special case to database...

[mothur.git] / nmdscommand.h

diff --git a/nmdscommand.h b/nmdscommand.h
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+#ifndef NMDSCOMMAND_H
+#define NMDSCOMMAND_H
+
+/*
+ *  nmdscommand.h
+ *  mothur
+ *
+ *  Created by westcott on 1/11/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "linearalgebra.h"
+
+
+/*  references used to make this command: "Nonmetric Multidimensional Scalling: A Numerical Method"
+ by J. B. Kruskal  Psychometrika - Vol 29, No. 2 June 1964 */
+
+/*****************************************************************/
+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();
+       
+private:
+       
+       bool abort;
+       string phylipfile, outputDir, axesfile;
+       int dimension, maxIters;
+       double step, cutoff;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
+       LinearAlgebra linearCalc;
+       
+       vector< vector<double> > generateStartingConfiguration(int); //pass in numNames, return axes
+       int normalizeConfiguration(vector< vector<double> >&, int);
+       vector<seqDist> satisfyMonotonicity(vector<seqDist>);
+       double calculateStress(vector<seqDist>&, vector<seqDist>&, double&);
+       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> >&);
+       vector< vector<double> > readAxes(vector<string>);
+       int output(string, string, vector< vector<double> >&, vector<double>&, vector<string>&);
+};
+
+/*****************************************************************/
+
+#endif
+
+