X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedsorclass.cpp;fp=sharedsorclass.cpp;h=c9debf7748662b8ebc2464f3d2e70fd7610a72ce;hb=20a2d0350a737a434c89f303662d64a8eeea7b05;hp=0000000000000000000000000000000000000000;hpb=bbb5879a7e566935c23d63d42bb945072424b939;p=mothur.git diff --git a/sharedsorclass.cpp b/sharedsorclass.cpp new file mode 100644 index 0000000..c9debf7 --- /dev/null +++ b/sharedsorclass.cpp @@ -0,0 +1,52 @@ +/* + * sharedsorclass.cpp + * Dotur + * + * Created by Sarah Westcott on 1/8/09. + * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved. + * + */ + +#include "sharedsorclass.h" + +/***********************************************************************/ + +EstOutput SharedSorClass::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) { + try { + int S1, S2, S12, tempA, tempB; + S1 = 0; S2 = 0; S12 = 0; tempA = 0; tempB = 0; + + /*S1, S2 = number of OTUs observed or estimated in A and B + S12=number of OTUs shared between A and B */ + + data.resize(1,0); + + for (int i = 0; i < shared1->size(); i++) { + //store in temps to avoid multiple repetitive function calls + tempA = shared1->getAbundance(i); + tempB = shared2->getAbundance(i); + + S1 += tempA; + S2 += tempB; + + //they are shared + if ((tempA != 0) && (tempB != 0)) { S12++; } + } + + data[0] = (2 * S12) / (float)(S1 + S2); + + if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; } + + return data; + } + catch(exception& e) { + cout << "Standard Error: " << e.what() << " has occurred in the SharedSorClass class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } + catch(...) { + cout << "An unknown error has occurred in the SharedSorClass class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } +} + +/***********************************************************************/