X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedkulczynski.cpp;h=5c91ddb65c654c5788c748596e87ddda94ae25f1;hp=30c8c7a34a9b1d79f99637fa6c1874df2dd0f3d9;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=25cde7ff05bbe741da1712f2c740e0bc8706e523

diff --git a/sharedkulczynski.cpp b/sharedkulczynski.cpp
index 30c8c7a..5c91ddb 100644
--- a/sharedkulczynski.cpp
+++ b/sharedkulczynski.cpp
@@ -2,7 +2,7 @@
  *  sharedkulczynski.cpp
  *  Mothur
  *
- *  Created by John Westcott on 3/24/09.
+ *  Created by Sarah Westcott on 3/24/09.
  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
@@ -11,9 +11,9 @@
 
 /***********************************************************************/
 
-EstOutput SharedKulczynski::getValues(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
+EstOutput Kulczynski::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 
@@ -21,10 +21,10 @@ EstOutput SharedKulczynski::getValues(SharedRAbundVector* shared1, SharedRAbundV
 
 		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++; } 
@@ -33,20 +33,16 @@ EstOutput SharedKulczynski::getValues(SharedRAbundVector* shared1, SharedRAbundV
 			if ((tempA != 0) && (tempB != 0)) {	S12++; }
 		}
 		
-		data[0] = S12 / (float)(S1 + S2 - (2 * S12));
+		data[0] = 1.0 - S12 / (float)(S1 + S2 - (2 * 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 SharedKulczynski class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Kulczynski", "getValues");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedKulczynski class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/