JAL-2772 check array bounds for sequence access

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 796937d..2ee412b 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1827,7 +1827,9 @@ public class Sequence extends ASequence implements SequenceI
      * and we may have included adjacent or enclosing features;
      * remove any that are not enclosing, non-contact features
      */
-    if (endPos > this.end || Comparison.isGap(sequence[toColumn - 1]))
+    boolean endColumnIsGapped = toColumn > 0 && toColumn <= sequence.length
+            && Comparison.isGap(sequence[toColumn - 1]);
+    if (endPos > this.end || endColumnIsGapped)
     {
       ListIterator<SequenceFeature> it = result.listIterator();
       while (it.hasNext())