X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=19ab59aa10c076aa3970840f1ad0da3799a58270;hb=refs%2Fheads%2Fmerge%2FJAL-3285_mchmmer_with_211_develop;hp=906acc1121a878d5626cf91b3f13a12742d26e21;hpb=106a3890f956e2aa7780b2985f4326655912a558;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 906acc1..19ab59a 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -73,23 +73,6 @@ public class AlignmentPanel extends Panel
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
 
-  @Override
-  public void finalize() throws Throwable
-  {
-    alignFrame = null;
-    av = null;
-    vpRanges = null;
-    seqPanel = null;
-    seqPanelHolder = null;
-    sequenceHolderPanel = null;
-    scalePanel = null;
-    scalePanelHolder = null;
-    annotationPanel = null;
-    annotationPanelHolder = null;
-    annotationSpaceFillerHolder = null;
-    super.finalize();
-  }
-
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
     try
@@ -438,8 +421,8 @@ public class AlignmentPanel extends Panel
     if (av.hasHiddenColumns())
     {
       AlignmentI al = av.getAlignment();
-      start = al.getHiddenColumns().findColumnPosition(ostart);
-      end = al.getHiddenColumns().findColumnPosition(end);
+      start = al.getHiddenColumns().absoluteToVisibleColumn(ostart);
+      end = al.getHiddenColumns().absoluteToVisibleColumn(end);
       if (start == end)
       {
         if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart))
@@ -571,8 +554,8 @@ public class AlignmentPanel extends Panel
     // this is called after loading new annotation onto alignment
     if (alignFrame.getSize().height == 0)
     {
-      System.out.println(
-              "adjustAnnotationHeight frame size zero NEEDS FIXING");
+      // panel not laid out yet?
+      return;
     }
     fontChanged();
     validateAnnotationDimensions(true);
@@ -686,14 +669,9 @@ public class AlignmentPanel extends Panel
     }
     else
     {
-      int width = av.getAlignment().getWidth();
+      int width = av.getAlignment().getVisibleWidth();
       int height = av.getAlignment().getHeight();
 
-      if (av.hasHiddenColumns())
-      {
-        width = av.getAlignment().getHiddenColumns()
-                .findColumnPosition(width);
-      }
       if (x < 0)
       {
         x = 0;