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[mothur.git] / hellinger.cpp

diff --git a/hellinger.cpp b/hellinger.cpp
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+/*
+ *  hellinger.cpp
+ *  Mothur
+ *
+ *  Created by westcott on 12/15/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "hellinger.h"
+
+/***********************************************************************/
+EstOutput Hellinger::getValues(vector<SharedRAbundVector*> shared) {
+       try {
+               data.resize(1,0);
+               
+               double sumA = 0.0;
+               double sumB = 0.0;
+               
+               //calc the 2 denominators
+               for (int i = 0; i < shared[0]->getNumBins(); i++) { 
+                       sumA += shared[0]->getAbundance(i);
+                       sumB += shared[1]->getAbundance(i);
+               }
+               
+               
+               //calc sum
+               double sum = 0.0;
+               for (int i = 0; i < shared[0]->getNumBins(); i++) { 
+                       
+                       int Aij = shared[0]->getAbundance(i);
+                       int Bij = shared[1]->getAbundance(i);
+                       
+                       double term1 = sqrt((Aij / sumA));
+                       double term2 = sqrt((Bij / sumB));
+                       
+                       sum += ((term1 - term2) * (term1 - term2));
+               }
+               
+               data[0] = sqrt(sum);
+               
+               if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+               
+               return data;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "Hellinger", "getValues");
+               exit(1);
+       }
+}
+/***********************************************************************/
+
+