X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=e77ae544fa315f1f6a91eedd47228113d5852ad2;hb=fd8dc2879b13709703b57dd7ed4b3754b253e12f;hp=a75adbbb13f1f9b8fc051d4053070e8733d58864;hpb=ab67e99fb7336d0f4411488d9f843c720ab6b418;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index a75adbb..e77ae54 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1900,7 +1900,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   static StringBuffer copiedSequences;
 
-  static Vector copiedHiddenColumns;
+  static Vector<int[]> copiedHiddenColumns;
 
   protected void copy_actionPerformed()
   {
@@ -1924,12 +1924,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
     {
-      copiedHiddenColumns = new Vector();
+      copiedHiddenColumns = viewport.getAlignment().getHiddenColumns()
+              .getHiddenColumnsCopy();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
-      for (int[] region : viewport.getAlignment().getHiddenColumns())
+      for (int[] region : copiedHiddenColumns)
       {
-        copiedHiddenColumns.addElement(new int[] {
-            region[0] - hiddenOffset, region[1] - hiddenOffset });
+        region[0] = region[0] - hiddenOffset;
+        region[1] = region[1] - hiddenOffset;
       }
     }
     else
@@ -2044,7 +2045,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         {
           for (int i = 0; i < copiedHiddenColumns.size(); i++)
           {
-            int[] region = (int[]) copiedHiddenColumns.elementAt(i);
+            int[] region = copiedHiddenColumns.elementAt(i);
             af.viewport.hideColumns(region[0], region[1]);
           }
         }