X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=df8fe874d9a3bf98bc03b515a1ac29d70bd60e4c;hb=04e88679fd837e9fe36d186e5eacdd5f13a89927;hp=906acc1121a878d5626cf91b3f13a12742d26e21;hpb=a57976ba40e1abe6d7c1940386e1a25419ef9c9d;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 906acc1..df8fe87 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -43,9 +43,11 @@ import java.awt.event.AdjustmentEvent;
 import java.awt.event.AdjustmentListener;
 import java.awt.event.ComponentAdapter;
 import java.awt.event.ComponentEvent;
+import java.awt.image.BufferedImage;
 import java.beans.PropertyChangeEvent;
 import java.util.List;
 
+@SuppressWarnings("serial")
 public class AlignmentPanel extends Panel
         implements AdjustmentListener, AlignmentViewPanel, ViewportListenerI
 {
@@ -73,23 +75,6 @@ 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
@@ -194,6 +179,7 @@ public class AlignmentPanel extends Panel
     return av;
   }
 
+  @Override
   public SequenceRenderer getSequenceRenderer()
   {
     return seqPanel.seqCanvas.sr;
@@ -432,14 +418,14 @@ public class AlignmentPanel extends Panel
   public boolean scrollTo(int ostart, int end, int seqIndex,
           boolean scrollToNearest, boolean redrawOverview)
   {
-    int startv, endv, starts, ends, width;
+    int startv, endv, starts, ends;//, width;
 
     int start = -1;
     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))
@@ -686,14 +672,9 @@ 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;
@@ -1179,4 +1160,10 @@ public class AlignmentPanel extends Panel
 
   }
 
+  @Override
+  public void overviewDone(BufferedImage miniMe)
+  {
+    overviewPanel.canvas.finalizeDraw(miniMe);
+  }
+
 }