added Jensen-Shannon calc. working on get.communitytype command. fixed bug in get...

[mothur.git] / communitytype.h

diff --git a/communitytype.h b/communitytype.h
new file mode 100644 (file)
index 0000000..59291f5
--- /dev/null
+++ b/communitytype.h
@@ -0,0 +1,75 @@
+//
+//  communitytype.h
+//  Mothur
+//
+//  Created by SarahsWork on 12/3/13.
+//  Copyright (c) 2013 Schloss Lab. All rights reserved.
+//
+
+#ifndef Mothur_communitytype_h
+#define Mothur_communitytype_h
+
+#define EPSILON numeric_limits<double>::epsilon()
+
+
+#include "mothurout.h"
+#include "linearalgebra.h"
+/**************************************************************************************************/
+
+class CommunityTypeFinder {
+    
+public:
+       CommunityTypeFinder(){  m = MothurOut::getInstance();  }
+       virtual ~CommunityTypeFinder(){};
+    
+    virtual void printZMatrix(string, vector<string>);
+    virtual void printRelAbund(string, vector<string>);
+    virtual void printFitData(ofstream&) {}
+    virtual void printFitData(ostream&, double) {}
+    virtual void printSilData(ofstream&, double, vector<double>);
+    virtual void printSilData(ostream&, double, vector<double>);
+    
+    virtual double getNLL()     {    return currNLL;        }
+    virtual double getAIC()     {    return aic;            }
+    virtual double getBIC()     {    return bic;            }
+    virtual double getLogDet()  {    return logDeterminant; }
+    virtual double getLaplace() {    return laplace;        }
+    
+    virtual double calcCHIndex(vector< vector< double> >) {return 0;}  //Calinski-Harabasz
+    virtual vector<double> calcSilhouettes(vector< vector< double> >) {  vector<double> s; return s; } //if none provided by child class
+
+
+protected:
+    
+    int findkMeans();
+    vector<vector<double> > getHessian();
+    double psi1(double);
+    double psi(double);
+    double cheb_eval(const double[], int, double);
+
+    
+       MothurOut* m;
+    vector<vector<double> > zMatrix;
+    vector<vector<double> > lambdaMatrix;
+    vector<vector<double> > error;
+    vector<vector<int> > countMatrix;
+    vector<double> weights;
+
+
+
+    int numPartitions;
+    int numSamples;
+    int numOTUs;
+    int currentPartition;
+    
+    double currNLL, aic, bic, logDeterminant, laplace;
+     
+       
+};
+
+/**************************************************************************************************/
+
+
+
+
+#endif