X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=2b9e4e625dcd2ad48883d026c16c8005dd149ff0;hb=39f6b55f5b993cd8afaff049861ddeca02e1925d;hp=db3cb8c2837c28018dce334d8fddacec76b7e958;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index db3cb8c..2b9e4e6 100755
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -28,7 +28,7 @@ public class AlignmentPanel
     extends Panel implements AdjustmentListener
 {
 
-  AlignViewport av;
+  public AlignViewport av;
   OverviewPanel overviewPanel;
   SeqPanel seqPanel;
   IdPanel idPanel;
@@ -115,6 +115,16 @@ public class AlignmentPanel
 
   }
 
+  public SequenceRenderer getSequenceRenderer()
+  {
+    return seqPanel.seqCanvas.sr;
+  }
+
+  public FeatureRenderer getFeatureRenderer()
+  {
+    return seqPanel.seqCanvas.fr;
+  }
+
   public void alignmentChanged()
   {
     av.alignmentChanged(this);
@@ -502,6 +512,22 @@ public class AlignmentPanel
 
   }
 
+  public void paintAlignment(boolean updateOverview)
+  {
+    repaint();
+
+    if(updateOverview)
+    {
+      jalview.structure.StructureSelectionManager.getStructureSelectionManager()
+          .sequenceColoursChanged(this);
+
+      if (overviewPanel != null)
+      {
+        overviewPanel.updateOverviewImage();
+      }
+    }
+  }
+
   public void update(Graphics g)
   {
     paint(g);
@@ -548,15 +574,6 @@ public class AlignmentPanel
     scalePanel.repaint();
     annotationPanel.repaint();
     idPanel.idCanvas.repaint();
-
-    if (getBounds() == g.getClipBounds())
-    {
-      if (overviewPanel != null)
-      {
-        overviewPanel.updateOverviewImage();
-      }
-    }
-
   }
 
   protected Panel sequenceHolderPanel = new Panel();