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//
// opticluster.h
// Mothur
//
// Created by Sarah Westcott on 4/20/16.
// Copyright (c) 2016 Schloss Lab. All rights reserved.
//
#ifndef __Mothur__opticluster__
#define __Mothur__opticluster__
#include "cluster.hpp"
#include "optimatrix.h"
#include "calculator.h"
#include "mcc.hpp"
#include "sensitivity.hpp"
#include "specificity.hpp"
#include "fdr.hpp"
#include "npv.hpp"
#include "ppv.hpp"
#include "f1score.hpp"
#include "tp.hpp"
#include "fp.hpp"
#include "fpfn.hpp"
#include "tptn.hpp"
#include "tn.hpp"
#include "fn.hpp"
#include "accuracy.hpp"
/***********************************************************************/
/*
#ifdef UNIT_TEST
friend class TestOptiCluster;
OptiCluster() : Cluster() { m = MothurOut::getInstance(); truePositives = 0; trueNegatives = 0; falseNegatives = 0; falsePositives = 0; } //for testing class
void setVariables(OptiData* mt, ClusterMetric* met) { matrix = mt; metric = met; }
#endif
*/
class OptiCluster : public Cluster {
public:
OptiCluster(OptiData* mt, ClusterMetric* met, long long ns);
~OptiCluster() = default;
bool updateDistance(PDistCell& colCell, PDistCell& rowCell) { return false; }
string getTag() { string tag = "opti_" + metric->getName(); return tag; }
long long getNumBins();
int initialize(double&, bool, string); //randomize and place in "best" OTUs
bool update(double&); //returns whether list changed and MCC
vector<double> getStats( double&, double&, double&, double&);
ListVector* getList();
protected:
OptiData* matrix;
ClusterMetric* metric;
vector<int> randomizeSeqs;
vector< vector<long long> > bins; //bin[0] -> seqs in bin[0]
map<long long, string> binLabels; //for fitting - maps binNumber to existing reference label
map<long long, long long> seqBin; //sequence# -> bin#
long long numSeqs, insertLocation, numSingletons;
double truePositives, trueNegatives, falsePositives, falseNegatives;
long long findInsert();
vector<double> getCloseFarCounts(long long seq, long long newBin);
vector<double> getFitStats( long long&, long long&, long long&, long long&);
};
#endif /* defined(__Mothur__opticluster__) */
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