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[mothur.git] / sharedbraycurtis.cpp

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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 = 0; sumSharedB = 0; 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]->getAbundance(i);
+                       tempB = shared[1]->getAbundance(i);
+                       
+                       sumSharedA += tempA;
+                       sumSharedB += tempB;
+                               
+                       //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);
+       }
+}
+
+/***********************************************************************/