JAL-2738 update spike branch with latest

[jalview.git] / src / jalview / api / AlignmentViewPanel.java

diff --git a/src/jalview/api/AlignmentViewPanel.java b/src/jalview/api/AlignmentViewPanel.java
index 09ccbb4..0b1ca21 100644 (file)
--- a/src/jalview/api/AlignmentViewPanel.java
+++ b/src/jalview/api/AlignmentViewPanel.java
@@ -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