X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedsorclass.cpp;h=85609dad69311e08474a2115755d74761052ab13;hb=541bab1dac00688b4c3a8c4a95ab464412663c50;hp=3bb22198303465ed5038464e32e8f3e168f16cc9;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;p=mothur.git

diff --git a/sharedsorclass.cpp b/sharedsorclass.cpp
index 3bb2219..85609da 100644
--- a/sharedsorclass.cpp
+++ b/sharedsorclass.cpp
@@ -13,7 +13,7 @@
 
 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 
@@ -21,7 +21,7 @@ EstOutput SorClass::getValues(vector<SharedRAbundVector*> shared) {
 
 		data.resize(1,0);
 		
-		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);
@@ -34,14 +34,14 @@ EstOutput SorClass::getValues(vector<SharedRAbundVector*> 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) {
-		errorOut(e, "SorClass", "getValues");
+		m->errorOut(e, "SorClass", "getValues");
 		exit(1);
 	}
 }