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/*
* sharedbraycurtis.cpp
* Mothur
*
* Created by Sarah Westcott on 3/24/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "sharedbraycurtis.h"
/***********************************************************************/
//This is used by SharedJAbund and SharedSorAbund
EstOutput BrayCurtis::getValues(vector<SharedRAbundVector*> shared) {
try {
data.resize(1,0);
double sumSharedA, sumSharedB, sumSharedAB, tempA, tempB;
sumSharedA = shared[0]->getNumSeqs(); sumSharedB = shared[1]->getNumSeqs(); sumSharedAB = 0;
/*Xi, Yi = abundance of the ith shared OTU in A and B
sumSharedA = the number of otus in A
sumSharedB = the sum of all shared otus in B
sumSharedAB = the sum of the minimum otus int all shared otus in AB.
*/
for (int i = 0; i < shared[0]->getNumBins(); i++) {
//store in temps to avoid multiple repetitive function calls
tempA = shared[0]->get(i);
tempB = shared[1]->get(i);
//sum the min of tempA and tempB
if (tempA < tempB) { sumSharedAB += tempA; }
else { sumSharedAB += tempB; }
}
data[0] = 1.0 - (2 * sumSharedAB) / (float)( sumSharedA + sumSharedB);
if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
return data;
}
catch(exception& e) {
m->errorOut(e, "BrayCurtis", "getValues");
exit(1);
}
}
/***********************************************************************/
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