X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedjclass.cpp;h=ed21335eddc1ab2360d74b761ea9eff842c6791a;hp=6557a0f16b8d4eab412d82616e8d74cb99374b86;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed

diff --git a/sharedjclass.cpp b/sharedjclass.cpp
index 6557a0f..ed21335 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 
@@ -21,32 +21,29 @@ 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]->getNumBins(); 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++; }
 		}
 		
-		data[0] = S12 / (float)(S1 + S2 - S12);
+		data[0] = 1.0 - S12 / (float)(S1 + S2 - S12);
 		
 		if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
 		
 		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);
-	}	
 }
 
 /***********************************************************************/