+/*
+ * sharedsorclass.cpp
+ * Dotur
+ *
+ * Created by Sarah Westcott on 1/8/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "sharedsorclass.h"
+
+/***********************************************************************/
+
+EstOutput SorClass::getValues(vector<SharedRAbundVector*> shared) {
+ try {
+ double 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 < shared[0]->getNumBins(); i++) {
+ //store in temps to avoid multiple repetitive function calls
+ tempA = shared[0]->getAbundance(i);
+ tempB = shared[1]->getAbundance(i);
+
+ //find number of bins in shared1 and shared2
+ if (tempA != 0) { S1++; }
+ if (tempB != 0) { S2++; }
+
+ //they are shared
+ if ((tempA != 0) && (tempB != 0)) { S12++; }
+ }
+
+ data[0] = 1.0-(2 * S12) / (float)(S1 + S2);
+
+ if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SorClass", "getValues");
+ exit(1);
+ }
+}
+
+/***********************************************************************/