Merge branch 'develop' into bug/JAL-2225mapMultipleChains

[jalview.git] / src / jalview / appletgui / AlignmentPanel.java

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 8e333ba..270b2f7 100644 (file)
--- 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
@@ -530,7 +513,7 @@ public class AlignmentPanel extends Panel
       vpRanges.scrollToWrappedVisible(start);
     }
 
-    paintAlignment(redrawOverview);
+    paintAlignment(redrawOverview, false);
     return true;
   }
 
@@ -579,7 +562,7 @@ public class AlignmentPanel extends Panel
     apvscroll.addNotify();
     hscroll.addNotify();
     validate();
-    paintAlignment(true);
+    paintAlignment(true, false);
   }
 
   /**
@@ -930,7 +913,8 @@ public class AlignmentPanel extends Panel
    * Repaint the alignment and annotations, and, optionally, any overview window
    */
   @Override
-  public void paintAlignment(boolean updateOverview)
+  public void paintAlignment(boolean updateOverview,
+          boolean updateStructures)
   {
     final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
             av.isShowAutocalculatedAbove());
@@ -938,13 +922,14 @@ public class AlignmentPanel extends Panel
             av.getSortAnnotationsBy());
     repaint();
 
-    if (updateOverview)
+    if (updateStructures)
     {
-      // TODO: determine if this paintAlignment changed structure colours
       jalview.structure.StructureSelectionManager
               .getStructureSelectionManager(av.applet)
               .sequenceColoursChanged(this);
-
+    }
+    if (updateOverview)
+    {
       if (overviewPanel != null)
       {
         overviewPanel.updateOverviewImage();