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//
// lsrarefaction.cpp
// Mothur
//
// Created by Sarah Westcott on 5/20/19.
// Copyright © 2019 Schloss Lab. All rights reserved.
//
#include "lsrarefaction.hpp"
/***********************************************************************/
LSRarefaction::LSRarefaction(double c) : coverage(c), DiversityCalculator(true) {}
/***********************************************************************/
int compare_doubles2(const void* a, const void* b)
{
double* arg1 = (double *) a;
double* arg2 = (double *) b;
if( *arg1 < *arg2 ) return -1;
else if( *arg1 == *arg2 ) return 0;
else return 1;
}
/***********************************************************************/
vector<double> LSRarefaction::getValues(int numSeqs, vector<mcmcSample>& sampling){ //rank->getNumSeqs(); //nj
try {
#ifdef USE_GSL
DiversityUtils dutils("lsrarefaction");
int nSamples = sampling.size();
double* adMu = nullptr;
double dLower = 0.0, dMedian = 0.0, dUpper = 0.0;
gsl_set_error_handler_off();
t_LSParams* atLSParams;
atLSParams = (t_LSParams *) malloc(nSamples*sizeof(t_LSParams)); //MAX_SAMPLES
//load sampling data
for (int i = 0; i < nSamples; i++) {
if (m->getControl_pressed()) { free(atLSParams); return results; }
atLSParams[i].dMDash = sampling[i].alpha;
atLSParams[i].dV = sampling[i].beta;
atLSParams[i].dNu = sampling[i].dNu;
atLSParams[i].dC = coverage;
atLSParams[i].n = 0;
}
adMu = (double *) malloc(sizeof(double)*nSamples);
for(int i = 0; i < nSamples; i++){ adMu[i] = ((double) numSeqs)*dutils.calcMu(&atLSParams[i]); }
qsort(adMu, nSamples, sizeof(double), compare_doubles2);
dLower = gsl_stats_quantile_from_sorted_data(adMu, 1, nSamples, 0.025);
dMedian = gsl_stats_quantile_from_sorted_data(adMu, 1, nSamples, 0.5);
dUpper = gsl_stats_quantile_from_sorted_data(adMu, 1, nSamples, 0.975);
if (isnan(dLower) || isinf(dLower)) { dLower = 0; }
if (isnan(dMedian) || isinf(dMedian)) { dMedian = 0; }
if (isnan(dUpper) || isinf(dUpper)) { dUpper = 0; }
m->mothurOut("\nLSRarefaction - d_Lower = " + toString(dLower) + " d_Median = " + toString(dMedian) + " d_Upper = " + toString(dUpper) + "\n\n");
results.push_back(dLower); results.push_back(dMedian); results.push_back(dUpper);
//printf("%.2e:%.2e:%.2e ", dLower, dMedian, dUpper);
free(adMu);
free(atLSParams);
#endif
return results;
}
catch(exception& e) {
m->errorOut(e, "LSRarefaction", "getValues");
exit(1);
}
}
/***********************************************************************/
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