X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chao1.cpp;h=ad1faa242b81c1520d29fb6395fa5f5825d179ec;hp=c05bdef2b7179a01f722cf497ab67f5b72ed7e3c;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=e4827e0945cbda536064e5a345996b2a7dfcbb81

diff --git a/chao1.cpp b/chao1.cpp
index c05bdef..ad1faa2 100644
--- a/chao1.cpp
+++ b/chao1.cpp
@@ -15,11 +15,21 @@ EstOutput Chao1::getValues(SAbundVector* rank){
 		data.resize(3,0);
 	
 		double sobs = (double)rank->getNumBins();
-	
-		double singles = (double)rank->get(1);
-		double doubles = (double)rank->get(2);
+		
+		//this is a modification do to a vector fill error that occurs when an empty sharedRabund creates a sabund
+		//in that case there is no 1 0r 2.
+		double singles;
+		if (rank->size() > 1) {
+			singles = (double)rank->get(1);
+		}else{ singles = 0.0;  }
+
+		double doubles;
+		if (rank->size() > 2) {
+			 doubles = (double)rank->get(2);
+		}else{ doubles = 0.0;  }
+
 		double chaovar = 0.0000;
-	
+//cout << "singles = " << singles << " doubles = " << doubles << " sobs = " << sobs << endl;	
 		double chao = sobs + singles*(singles-1)/(2*(doubles+1));
 	
 		if(singles > 0 && doubles > 0){
@@ -60,13 +70,9 @@ EstOutput Chao1::getValues(SAbundVector* rank){
 		return data;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Chao1 class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Chao1", "getValues");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Chao1 class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
-};
+}
 
 /***********************************************************************/