X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedbraycurtis.cpp;h=3711ce77cbb312e5dc2ee2aba14e1856bb942d12;hb=70491a12902e89b85cfa6b44a7b7fbe066ee2ac1;hp=0f29b2393f76b80f74cec7b59cb971fc58dd4a68;hpb=c537597ec5ebd47b4898da87ae03b0c2aeced354;p=mothur.git

diff --git a/sharedbraycurtis.cpp b/sharedbraycurtis.cpp
index 0f29b23..3711ce7 100644
--- a/sharedbraycurtis.cpp
+++ b/sharedbraycurtis.cpp
@@ -11,52 +11,42 @@
 
 /***********************************************************************/
 //This is used by SharedJAbund and SharedSorAbund
-EstOutput BrayCurtis::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput BrayCurtis::getValues(vector<SharedRAbundVector*> shared) {
 	try {	
-		EstOutput data;
 		data.resize(1,0);
 		
-		int sumSharedA, sumSharedB, sumSharedAB, tempA, tempB;
+		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 sum of all shared otus in A
+		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 < shared1->size(); i++) {
+		for (int i = 0; i < shared[0]->getNumBins(); i++) {
 			//store in temps to avoid multiple repetitive function calls
-			tempA = shared1->getAbundance(i);
-			tempB = shared2->getAbundance(i);
-
+			tempA = shared[0]->getAbundance(i);
+			tempB = shared[1]->getAbundance(i);
 			
-			if ((tempA != 0) && (tempB != 0)) {//they are shared
-				sumSharedA += tempA;
-				sumSharedB += tempB;
+			sumSharedA += tempA;
+			sumSharedB += tempB;
 				
-				//sum the min of tempA and tempB
-				if (tempA < tempB) { sumSharedAB += tempA; }
-				else  { sumSharedAB += tempB; }				
-			}
+			//sum the min of tempA and tempB
+			if (tempA < tempB) { sumSharedAB += tempA; }
+			else  { sumSharedAB += tempB; }				
 		}
 		
-		data[0] = (2 * sumSharedAB) / (float)( sumSharedA + sumSharedB);
+		data[0] = 1.0 - (2 * sumSharedAB) / (float)( sumSharedA + sumSharedB);
 		
 		if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
 				
 		return data;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the BrayCurtis class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "BrayCurtis", "getValues");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the BrayCurtis class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
-
-
 }
 
 /***********************************************************************/