From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 7 Nov 2017 15:58:36 +0000 (+0000)
Subject: JAL-2684 JAL-2822 avoid out of bounds exception if edit position is beyond sequence... 
X-Git-Tag: Release_2_11_1_0~98^2~17
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a8e189bdbb33587c4c9cd6f9d5560cfce866edf4;p=jalview.git

JAL-2684 JAL-2822 avoid out of bounds exception if edit position is beyond sequence string length
---

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index d02dbc3..334f30d 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -758,9 +758,14 @@ public class EditCommand implements CommandI
               new String(command.string[i]));
       int ipos = command.seqs[i].findPosition(start)
               - command.seqs[i].getStart();
-      tmp.append(oldstring.substring(end));
+      if (end < oldstring.length())
+      {
+        tmp.append(oldstring.substring(end));
+      }
       command.seqs[i].setSequence(tmp.toString());
-      command.string[i] = oldstring.substring(start, end).toCharArray();
+      command.string[i] = oldstring
+              .substring(start, Math.min(end, oldstring.length()))
+              .toCharArray();
       String nogapold = AlignSeq.extractGaps(Comparison.GapChars,
               new String(command.string[i]));