X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=communitytype.h;fp=communitytype.h;h=59291f5444f8e00abd4f55a9986f853b285fe8b5;hb=a2cde58c1e72199498a2142983ef040dce36da10;hp=0000000000000000000000000000000000000000;hpb=3e8b80da722e11c72bce957e2f42a6e884dd02b6;p=mothur.git

diff --git a/communitytype.h b/communitytype.h
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+//
+//  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