JAL-2541 length check in deleteChars (redoing lost commit 4a4bc78)

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 80de543..6aaa68b 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1159,9 +1159,9 @@ public class Sequence extends ASequence implements SequenceI
     // the very large sequence case
     int eindex = -1, sindex = -1;
     boolean ecalc = false, scalc = false;
-    for (int s = i; s < j; s++)
+    for (int s = i; s < j && s < sequence.length; s++)
     {
-      if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+      if (!Comparison.isGap(sequence[s]))
       {
         if (createNewDs)
         {