From eb5197242ba17fcff4ce0e18419ca81a63418f7a Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 14 Apr 2009 12:32:14 +0000
Subject: [PATCH] patch to fix occasional arrayoutofbounds exception when
 working with hidden columns and ragged annotation rows

---
 src/jalview/datamodel/ColumnSelection.java |    6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index ca54570..9dbaced 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -998,15 +998,17 @@ public class ColumnSelection
       if (end > blockStart)
       {
         annels.addElement(els = new Annotation[end - blockStart + 1]);
-        if (end - blockStart + 1 <= alignmentAnnotation.annotations.length)
+        if ((els.length+blockStart)<= alignmentAnnotation.annotations.length)
         {
+          // copy just the visible segment of the annotation row
           System.arraycopy(alignmentAnnotation.annotations, blockStart,
                   els, 0, els.length);
         }
         else
         {
+          // copy to the end of the annotation row
           System.arraycopy(alignmentAnnotation.annotations, blockStart,
-                  els, 0, (end - blockStart + 1));
+                  els, 0, (alignmentAnnotation.annotations.length - blockStart));
         }
         w += els.length;
       }
-- 
1.7.10.2