X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedbraycurtis.cpp;h=3711ce77cbb312e5dc2ee2aba14e1856bb942d12;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=9a63cdf9c0a3cbf37fd2ef179ef5bd8ff3229bc7;hpb=50ed3b6104d5821d6184f882e1e1423d47dcbf10;p=mothur.git

diff --git a/sharedbraycurtis.cpp b/sharedbraycurtis.cpp
index 9a63cdf..3711ce7 100644
--- a/sharedbraycurtis.cpp
+++ b/sharedbraycurtis.cpp
@@ -15,7 +15,7 @@ EstOutput BrayCurtis::getValues(vector<SharedRAbundVector*> shared) {
 	try {	
 		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 
@@ -24,7 +24,7 @@ EstOutput BrayCurtis::getValues(vector<SharedRAbundVector*> shared) {
 		sumSharedAB = the sum of the minimum otus int all shared otus in AB.
 		*/
 		
-		for (int i = 0; i < shared[0]->size(); i++) {
+		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);
@@ -37,22 +37,16 @@ EstOutput BrayCurtis::getValues(vector<SharedRAbundVector*> shared) {
 			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);
-	}	
-
-
 }
 
 /***********************************************************************/