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//
// diversityestimatorcommand.hpp
// Mothur
//
// Created by Sarah Westcott on 4/4/19.
// Copyright © 2019 Schloss Lab. All rights reserved.
//
#ifndef diversityestimatorcommand_hpp
#define diversityestimatorcommand_hpp
#include "command.hpp"
#include "inputdata.h"
#include "validcalculator.h"
//******************************************************
class EstimatorSingleCommand : public Command {
public:
EstimatorSingleCommand(string);
~EstimatorSingleCommand(){}
vector<string> setParameters();
string getCommandName() { return "estimator.single"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCommonQuestions();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Estimator.single"; }
string getDescription() { return "This command implements the diversity estimators from https://github.com/chrisquince/DiversityEstimates. https://www.ncbi.nlm.nih.gov/pubmed/18650928"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, allLines, burnSampleSet, burnSet, createSampling, itersSet;
string label, calc, sharedfile, listfile, rabundfile, sabundfile, format, inputfile, samplefile;
double freq, sigmaAlpha, sigmaBeta, sigmaS, sigmaN, coverage;
int iters, burn, burnSample, fitIters;
vector<string> outputNames;
set<string> labels; //holds labels to be used
vector<string> groups, rarefactCalcs, abundCalcs, smallBurn;
map<string, vector<mcmcSample> > sampling;
map<string, vector<mcmcSample> > ::iterator it;
set<string> samplingCalcs;
map<string, string> calcToSamplingCalc;
map<string, string> ::iterator itCalcSample;
int fillSampling(int, int, bool filldNu=false);
int processSingleSample();
int processSharedFile();
int processShared(SharedRAbundVectors*& shared, vector<ofstream*>& out, string fileRoot);
int processSingle(SAbundVector*&, string, vector<ofstream*>&, string);
int runRarefactCalcs(int numSeqs, string groupName, ofstream& out);
vector<string> runSamplingCalcs(SAbundVector*&, string);
vector<double> runAbundCalcs(SAbundVector*&, string groupName);
};
//*******************************************************
#endif /* diversityestimatorcommand_hpp */
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