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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"
#include "utils.hpp"
/**************************************************************************************************/
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> >); //Calinski-Harabasz
virtual vector<double> calcSilhouettes(vector< vector< double> >);
protected:
int findkMeans();
vector<vector<double> > getHessian();
double psi1(double);
double psi(double);
double cheb_eval(const double[], int, double);
double rMedoid(vector< vector<double> > x, vector< vector<double> > d);
vector<vector<double> > calcCenters(vector<vector<double> >&, map<int, int>, vector<vector<double> >&);
MothurOut* m;
vector<vector<double> > zMatrix;
vector<vector<double> > lambdaMatrix;
vector<vector<double> > error;
vector<vector<int> > countMatrix;
vector<double> weights;
Utils util;
int numPartitions;
int numSamples;
int numOTUs;
int currentPartition;
double currNLL, aic, bic, logDeterminant, laplace;
};
/**************************************************************************************************/
#endif
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