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//
// clusterfitcommand.hpp
// Mothur
//
// Created by Sarah Westcott on 1/22/18.
// Copyright © 2018 Schloss Lab. All rights reserved.
//
#ifndef clusterfitcommand_hpp
#define clusterfitcommand_hpp
#include "command.hpp"
#include "listvector.hpp"
#include "cluster.hpp"
#include "counttable.h"
#include "optifitcluster.hpp"
#include "optirefmatrix.hpp"
#include "calculator.h"
#include "distancecommand.h"
#include "aligncommand.h"
#include "filterseqscommand.h"
#include "uniqueseqscommand.h"
#include "listseqscommand.h"
#include "getdistscommand.h"
#include "getseqscommand.h"
class ClusterFitCommand : public Command {
public:
ClusterFitCommand(string);
~ClusterFitCommand();
vector<string> setParameters();
string getCommandName() { return "cluster.fit"; }
string getCommandCategory() { return "Clustering"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "\nhttp://www.mothur.org/wiki/Cluster.fit"; }
string getDescription() { return "fit your sequences into existing OTUs"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, sim, print_start, selfReference, printref, createAccnos;
string refdistfile, reffastafile, refnamefile, refcountfile, reflistfile, refNameOrCount;
string namefile, refformat, distfile, countfile, fastafile, columnfile, nameOrCount, accnosfile;
string comboDistFile;
string method, fileroot, tag, inputDir, metric, initialize, metricName, refWeight;
double cutoff, stableMetric;
float adjust, fitPercent;
int precision, length, maxIters, processors, denovoIters;
vector<string> outputNames, listFiles;
unsigned long loops;
ListVector* runUserRefOptiCluster(OptiData*&, ClusterMetric*&, map<string, int>&, string, vector<string>, vector<vector<string> > );
string runRefOptiCluster(OptiData*&, ClusterMetric*&, ListVector*&, map<string, int>&, string);
string runDenovoOptiCluster(OptiData*&, ClusterMetric*&, map<string, int>&, string);
ListVector* clusterRefs(OptiData*& refsMatrix, ClusterMetric*&);
void createReferenceNameCount();
string calcDists();
void runSensSpec(OptiData*& matrix, ClusterMetric*& userMetric, ListVector*& list, map<string, int>& counts, ofstream&);
string compareSensSpec(OptiData*& matrix, ClusterMetric*& userMetric, ofstream& sensSpecFile);
//string runSensSpec(string distFileName, string dupsFile, string dupsFormat, ClusterMetric*&, string);
void outputSteps(string outputName, bool& printHeaders, double tp, double tn, double fp, double fn, vector<double> results, long long numBins, double fittp, double fittn, double fitfp, double fitfn, vector<double> fitresults, long long numFitBins, int, bool, int);
};
#endif /* clusterfitcommand_hpp */
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