X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedsorclass.cpp;h=85609dad69311e08474a2115755d74761052ab13;hb=541bab1dac00688b4c3a8c4a95ab464412663c50;hp=c9debf7748662b8ebc2464f3d2e70fd7610a72ce;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/sharedsorclass.cpp b/sharedsorclass.cpp
index c9debf7..85609da 100644
--- a/sharedsorclass.cpp
+++ b/sharedsorclass.cpp
@@ -11,9 +11,9 @@
 
 /***********************************************************************/
 
-EstOutput SharedSorClass::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput SorClass::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 SharedSorClass::getValues(SharedRAbundVector* shared1, SharedRAbundVec
 
 		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);
 
-			S1 += tempA;
-			S2 += tempB;
+			//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] = (2 * S12) / (float)(S1 + S2);
+		data[0] = 1.0-(2 * S12) / (float)(S1 + S2);
 		
 		if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
 		
 		return data;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedSorClass class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SorClass", "getValues");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedSorClass class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/