JAL-1705 include stop codons in derived CDS; support ensemblgenomes

[jalview.git] / src / jalview / analysis / AlignmentUtils.java

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index e624ce7..2f9fcb2 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -55,6 +55,7 @@ import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
+import java.util.NoSuchElementException;
 import java.util.Set;
 import java.util.TreeMap;
 
@@ -1159,6 +1160,9 @@ public class AlignmentUtils
       } catch (IncompleteCodonException e)
       {
         // possible incomplete trailing codon - ignore
+      } catch (NoSuchElementException e)
+      {
+        // possibly peptide lacking STOP
       }
     }
   }