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[mothur.git] / linearalgebra.h

diff --git a/linearalgebra.h b/linearalgebra.h
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+#ifndef LINEARALGEBRA
+#define LINEARALGEBRA
+
+/*
+ *  linearalgebra.h
+ *  mothur
+ *
+ *  Created by westcott on 1/7/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mothurout.h"
+
+
+class LinearAlgebra {
+       
+public:
+       LinearAlgebra() { m = MothurOut::getInstance(); }
+       ~LinearAlgebra() {}
+       
+       vector<vector<double> > matrix_mult(vector<vector<double> >, vector<vector<double> >);
+       void recenter(double, vector<vector<double> >, vector<vector<double> >&);
+       int tred2(vector<vector<double> >&, vector<double>&, vector<double>&);
+       int qtli(vector<double>&, vector<double>&, vector<vector<double> >&);
+       vector< vector<double> > calculateEuclidianDistance(vector<vector<double> >&, int); //pass in axes and number of dimensions
+       vector< vector<double> > calculateEuclidianDistance(vector<vector<double> >&); //pass in axes
+       vector<vector<double> > getObservedEuclideanDistance(vector<vector<double> >&);
+       double calcPearson(vector<vector<double> >&, vector<vector<double> >&);
+       double calcSpearman(vector<vector<double> >&, vector<vector<double> >&);
+       double calcKendall(vector<vector<double> >&, vector<vector<double> >&);
+       
+       double calcPearson(vector<double>&, vector<double>&, double&);
+       double calcSpearman(vector<double>&, vector<double>&, double&);
+       double calcKendall(vector<double>&, vector<double>&, double&);
+    
+       double calcSpearmanSig(double, double, double, double); //length, f^3 - f where f is the number of ties in x, f^3 - f where f is the number of ties in y, sum of squared diffs in ranks. - designed to find the sif of one score.
+    double calcPearsonSig(double, double); //length, coeff.
+    double calcKendallSig(double, double); //length, coeff.
+    
+    
+private:
+       MothurOut* m;
+       
+       double pythag(double, double);
+    double betacf(const double, const double, const double);
+    double betai(const double, const double, const double);
+    double gammln(const double);
+    double gammp(const double, const double);
+    double gammq(const double, const double);
+    double gser(double&, const double, const double, double&);
+    double gcf(double&, const double, const double, double&);
+    double erfcc(double);
+    
+    double ran0(int&); //for testing 
+    double ran1(int&); //for testing
+    double ran2(int&); //for testing
+    double ran3(int&); //for testing
+    double ran4(int&); //for testing
+    void psdes(unsigned long &, unsigned long &); //for testing
+    
+};
+
+#endif
+