X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedlennon.cpp;h=52192756e00cbb5487e1baa9988c1ba0c709ed5a;hp=45dfc6aa8a6762b8125718b3b211a2ef3dc8ba8c;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=25cde7ff05bbe741da1712f2c740e0bc8706e523

diff --git a/sharedlennon.cpp b/sharedlennon.cpp
index 45dfc6a..5219275 100644
--- a/sharedlennon.cpp
+++ b/sharedlennon.cpp
@@ -11,9 +11,9 @@
 
 /***********************************************************************/
 
-EstOutput SharedLennon::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput Lennon::getValues(vector<SharedRAbundVector*> shared) {
 	try {
-		int S1, S2, S12, tempA, tempB, min;
+		double S1, S2, S12, tempA, tempB, min;
 		S1 = 0; S2 = 0; S12 = 0; tempA = 0; tempB = 0; min = 0;
 		
 		/*S1, S2 = number of OTUs observed or estimated in A and B 
@@ -21,10 +21,10 @@ EstOutput SharedLennon::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);
+			tempA = shared[0]->getAbundance(i);
+			tempB = shared[1]->getAbundance(i);
 			
 			if (tempA != 0) { S1++; }
 			if (tempB != 0) { S2++; } 
@@ -39,20 +39,16 @@ EstOutput SharedLennon::getValues(SharedRAbundVector* shared1, SharedRAbundVecto
 		if (tempA < tempB) { min = tempA; }
 		else { min = tempB; }
 		
-		data[0] = S12 / (float)(S12 + min);
+		data[0] = 1.0 - S12 / (float)(S12 + min);
 		
 		if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
 		
 		return data;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedLennon class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Lennon", "getValues");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedLennon class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/