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//
// optifitcluster.hpp
// Mothur
//
// Created by Sarah Westcott on 5/10/18.
// Copyright © 2018 Schloss Lab. All rights reserved.
//
#ifndef optifitcluster_hpp
#define optifitcluster_hpp
#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"
#include "opticluster.h"
/***********************************************************************/
class OptiFitCluster : public Cluster {
public:
OptiFitCluster(OptiData* mt, ClusterMetric* met, long long ns);
~OptiFitCluster() = default;
int initialize(double& value, bool randomize, vector<vector< string > > existingBins, vector<string>, string, bool);
bool update(double&); //returns whether list changed and MCC
bool updateDistance(PDistCell& colCell, PDistCell& rowCell) { return false; } //inheritance compliant
string getTag() { string tag = "optifit_" + metric->getName(); return tag; }
long long getNumBins();
long long getNumFitBins();
vector<double> getStats( double&, double&, double&, double&); //combo stats
vector<double> getFitStats( double&, double&, double&, double&); //fitted seqs stats
ListVector* getList();
ListVector* getFittedList(string, bool);
set<string> getUnfittedNames() { return unfittedNames; }
protected:
MothurOut* m;
Utils util;
ClusterMetric* metric;
OptiData* matrix;
map<long long, long long> seqBin; //sequence# -> bin#
vector<long long> 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
long long maxRefBinNumber;
bool closed, denovo;
set<string> unfittedNames;
double fittruePositives, fittrueNegatives, fitfalsePositives, fitfalseNegatives, combotruePositives, combotrueNegatives, combofalsePositives, combofalseNegatives;
long long numFitSeqs, insertLocation, numFitSingletons;
long long numComboSeqs, numComboSingletons;
int findInsert();
vector<double> getCloseFarCounts(long long seq, long long newBin);
vector<double> getCloseFarFitCounts(long long seq, long long newBin);
ListVector* clusterUnfitted(OptiData*, string);
};
#endif /* optifitcluster_hpp */
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