From: jprocter <Jim Procter>
Date: Tue, 14 Apr 2009 12:32:14 +0000 (+0000)
Subject: patch to fix occasional arrayoutofbounds exception when working with hidden columns... 
X-Git-Tag: Release_2_5~318
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=eb5197242ba17fcff4ce0e18419ca81a63418f7a;hp=aa25fa143274ada02f7dfe5209864ff1231b8e65;p=jalview.git

patch to fix occasional arrayoutofbounds exception when working with hidden columns and ragged annotation rows
---

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;
       }