X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=canberra.cpp;fp=canberra.cpp;h=9ab6234ae3119c4f3b103f314e97e9c69d793780;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/canberra.cpp b/canberra.cpp
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+++ b/canberra.cpp
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+/*
+ *  canberra.cpp
+ *  Mothur
+ *
+ *  Created by westcott on 12/14/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "canberra.h"
+
+/***********************************************************************/
+
+EstOutput Canberra::getValues(vector<SharedRAbundVector*> shared) {
+	try {
+		data.resize(1,0);
+		
+		int numSharedOTUS = 0;
+		
+		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);
+			
+			//is this otu shared
+			if ((Aij != 0) && (Bij != 0)) { numSharedOTUS++; }
+			
+			if ((Aij + Bij) != 0) { 
+				sum += ((abs(Aij - Bij)) / (float) (Aij + Bij));
+			}
+		}
+		
+		data[0] = (1 / (float) shared[0]->getNumBins()) * sum;
+		
+		if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+		
+		return data;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Canberra", "getValues");
+		exit(1);
+	}
+}
+
+/***********************************************************************/