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

[mothur.git] / qFinderDMM.h

diff --git a/qFinderDMM.h b/qFinderDMM.h
index d94e6cce9f11b89de87d9f756ae490c69aabda72..df7b44305ef38fc417360bebd729357fb6724e2d 100644 (file)
--- a/qFinderDMM.h
+++ b/qFinderDMM.h
@@ -9,27 +9,19 @@
 #ifndef pds_dmm_qFinderDMM_h
 #define pds_dmm_qFinderDMM_h
 
-/**************************************************************************************************/
-
-#include "mothurout.h"
+#include "communitytype.h"
 
 /**************************************************************************************************/
 
-class qFinderDMM {
+class qFinderDMM : public CommunityTypeFinder {
   
 public:
     qFinderDMM(vector<vector<int> >, int);
-    double getNLL()     {    return currNLL;        }  
-    double getAIC()     {    return aic;            }
-    double getBIC()     {    return bic;            }
-    double getLogDet()  {    return logDeterminant; }
-    double getLaplace() {    return laplace;        }
-    void printZMatrix(string, vector<string>);
-    void printRelAbund(string, vector<string>);
-
+    void printFitData(ofstream&);
+    void printFitData(ostream&, double);
+    
 private:
-    MothurOut* m;
-    void kMeans();
+   
     void optimizeLambda();
     void calculatePiK();
 
@@ -37,31 +29,14 @@ private:
     void negativeLogDerivEvidenceLambdaPi(vector<double>&, vector<double>&);
     double getNegativeLogEvidence(vector<double>&, int);
     double getNegativeLogLikelihood();
-    vector<vector<double> > getHessian();
+    
     
     int lineMinimizeFletcher(vector<double>&, vector<double>&, double, double, double, double&, double&, vector<double>&, vector<double>&);
     int bfgs2_Solver(vector<double>&);//, double, double);
-    double cheb_eval(const double[], int, double);
-    double psi(double);
-    double psi1(double);
-
-    vector<vector<int> > countMatrix;
-    vector<vector<double> > zMatrix;
-    vector<vector<double> > lambdaMatrix;
-    vector<double> weights;
-    vector<vector<double> > error;
-    
-    int numPartitions;
-    int numSamples;
-    int numOTUs;
-    int currentPartition;
-    
-    double currNLL;
-    double aic;
-    double bic;
-    double logDeterminant;
-    double laplace;
     
+   
+
+        
 };
 
 /**************************************************************************************************/