X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColumnChooser.java;h=3a7188ea47d3aa8966a830ed9032bec812a17ad1;hb=1810df9d010000e434975a8a4e68dcbda238f7f1;hp=22978c33ca09c32df9c0e11dc0c83598f9021eb8;hpb=12d4dfa00a5e93ae1de1d8409c6d5ca2bc8af13f;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationColumnChooser.java b/src/jalview/appletgui/AnnotationColumnChooser.java
index 22978c3..3a7188e 100644
--- a/src/jalview/appletgui/AnnotationColumnChooser.java
+++ b/src/jalview/appletgui/AnnotationColumnChooser.java
@@ -46,7 +46,7 @@ import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.TextEvent;
 import java.awt.event.TextListener;
-import java.util.Iterator;
+import java.util.ArrayList;
 import java.util.Vector;
 
 //import javax.swing.JPanel;
@@ -142,7 +142,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     }
     setOldHiddenColumns(av.getAlignment().getHiddenColumns());
     adjusting = true;
-    Vector<String> list = new Vector<String>();
+    Vector<String> list = new Vector<>();
     int index = 1;
     for (int i = 0; i < anns.length; i++)
     {
@@ -298,16 +298,16 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         HiddenColumns oldHidden = av
                 .getAnnotationColumnSelectionState()
                 .getOldHiddenColumns();
-        if (oldHidden != null && oldHidden.getHiddenRegions() != null
-                && !oldHidden.getHiddenRegions().isEmpty())
+        if (oldHidden != null)
         {
-          for (Iterator<int[]> itr = oldHidden.getHiddenRegions()
-                  .iterator(); itr.hasNext();)
+          ArrayList<int[]> regions = oldHidden.getHiddenColumnsCopy();
+          for (int[] positions : regions)
           {
-            int positions[] = itr.next();
             av.hideColumns(positions[0], positions[1]);
           }
         }
+        // TODO not clear why we need to hide all the columns (above) if we are
+        // going to copy the hidden columns over wholesale anyway
         av.getAlignment().setHiddenColumns(oldHidden);
       }
       av.sendSelection();