X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignmentViewPanel.java;h=0b1ca219421cbae59acba8e959675d0cb49355e6;hb=bf8275c621048462bd0275e31bf490dca443b477;hp=a5453638060f4811f0783a0d6c6f3620aff741f2;hpb=25aaaa87042b3f507ad4348120df7dd073182759;p=jalview.git

diff --git a/src/jalview/api/AlignmentViewPanel.java b/src/jalview/api/AlignmentViewPanel.java
index a545363..0b1ca21 100644
--- a/src/jalview/api/AlignmentViewPanel.java
+++ b/src/jalview/api/AlignmentViewPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -32,6 +32,8 @@ import jalview.structure.StructureSelectionManager;
 public interface AlignmentViewPanel extends OOMHandlerI
 {
 
+  AlignViewportI getAlignViewport();
+
   AlignmentI getAlignment();
 
   StructureSelectionManager getStructureSelectionManager();
@@ -41,9 +43,10 @@ public interface AlignmentViewPanel extends OOMHandlerI
    * 
    * @param updateOverview
    *          - if true, the overview panel will also be updated and repainted
+   * @param updateStructures
+   *          - if true then any linked structure views will also be updated
    */
-
-  void paintAlignment(boolean updateOverview);
+  void paintAlignment(boolean updateOverview, boolean updateStructures);
 
   /**
    * automatically adjust annotation panel height for new annotation whilst
@@ -54,7 +57,7 @@ public interface AlignmentViewPanel extends OOMHandlerI
   FeatureRenderer getFeatureRenderer();
 
   FeatureRenderer cloneFeatureRenderer();
-  
+
   /**
    * 
    * @return displayed name for the view