X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedjclass.cpp;h=ede4e31264d49b1cc26ccb4e684262ec6f1c1d3e;hb=1e39c7af79c75317b61e457bf72a14e2138902fc;hp=52591f5b8cf05f707857e771a299e6cb9ecd41aa;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/sharedjclass.cpp b/sharedjclass.cpp
index 52591f5..ede4e31 100644
--- a/sharedjclass.cpp
+++ b/sharedjclass.cpp
@@ -11,9 +11,9 @@
 
 /***********************************************************************/
 
-EstOutput SharedJclass::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput Jclass::getValues(vector<SharedRAbundVector*> shared) {
 	try {
-		int S1, S2, S12, tempA, tempB;
+		double S1, S2, S12, tempA, tempB;
 		S1 = 0; S2 = 0; S12 = 0; tempA = 0; tempB = 0; 
 		
 		/*S1, S2 = number of OTUs observed or estimated in A and B 
@@ -21,13 +21,14 @@ EstOutput SharedJclass::getValues(SharedRAbundVector* shared1, SharedRAbundVecto
 
 		data.resize(1,0);
 		
-		for (int i = 0; i < shared1->size(); i++) {
+		for (int i = 0; i < shared[0]->size(); i++) {
 			//store in temps to avoid multiple repetitive function calls
-			tempA = shared1->getAbundance(i);
-			tempB = shared2->getAbundance(i);
-
-			S1 += tempA;
-			S2 += tempB;
+			tempA = shared[0]->getAbundance(i);
+			tempB = shared[1]->getAbundance(i);
+			
+			//find number of bins in shared1 and shared2
+			if (tempA != 0) { S1++; }
+			if (tempB != 0) { S2++; } 
 			
 			//they are shared
 			if ((tempA != 0) && (tempB != 0)) {	S12++; }
@@ -40,12 +41,9 @@ EstOutput SharedJclass::getValues(SharedRAbundVector* shared1, SharedRAbundVecto
 		return data;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedJclass class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Jclass", "getValues");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedJclass class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
+
 /***********************************************************************/