X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedjackknife.cpp;h=0998db8fe3106bbb40c26dc8621d37030fb275c3;hp=c1e5ff4ec4c56a1f5eddad239a9b21f6e0deb72c;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=74c78f9abd9e733f0c2f812efec97a76632fcbf8

diff --git a/sharedjackknife.cpp b/sharedjackknife.cpp
index c1e5ff4..0998db8 100644
--- a/sharedjackknife.cpp
+++ b/sharedjackknife.cpp
@@ -88,8 +88,7 @@ EstOutput SharedJackknife::getValues(vector<SharedRAbundVector*> vectorShared){
 		SharedRAbundVector* shared1 = vectorShared[0];
 		SharedRAbundVector* shared2 = vectorShared[1];
 		if(numGroups == -1) {
-			globaldata = GlobalData::getInstance();
-			numGroups = globaldata->Groups.size();
+			numGroups = m->getNumGroups();
 		}
 
 		if(callCount == numGroups*(numGroups-1)/2) {
@@ -116,17 +115,11 @@ EstOutput SharedJackknife::getValues(vector<SharedRAbundVector*> vectorShared){
 			data[0] = rdata[0];
 			data[1] = rdata[1];
 			data[2] = rdata[2];
-			
-			//cout << "sT = " << data[0] << "    lower confLimit = " << data[1] << "     upper confLimit = " << data[2] << "\n";
+		
 			if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
 			if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
 			if (isnan(data[2]) || isinf(data[0])) { data[2] = 0; }
 			
-			/*for(int i = 0; i < groups.size(); i++)
-				cout << groups.at(i)->getGroup() << " ";
-			cout << "\n";
-			cout << groups.size() << "     " << data[0] << "    " << data[1] << "     " << data[2] << "\n\n";*/
-			
 			return data;
 		}
 		
@@ -142,13 +135,9 @@ EstOutput SharedJackknife::getValues(vector<SharedRAbundVector*> vectorShared){
 	}
 		
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SharedJackknife class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SharedJackknife", "getValues");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SharedJackknife class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /***********************************************************************/