X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedbraycurtis.cpp;fp=sharedbraycurtis.cpp;h=3711ce77cbb312e5dc2ee2aba14e1856bb942d12;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/sharedbraycurtis.cpp b/sharedbraycurtis.cpp
new file mode 100644
index 0000000..3711ce7
--- /dev/null
+++ b/sharedbraycurtis.cpp
@@ -0,0 +1,52 @@
+/*
+ *  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);
+	}
+}
+
+/***********************************************************************/