X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=785dd1416dc594198eb16b84cd878fc78ee573da;hb=2288325efdb30bead1f6a3ad264d5e0c6b9cc752;hp=3cb06c1b7d84aa139d4e4483e80b522b5a3ace5f;hpb=a57976ba40e1abe6d7c1940386e1a25419ef9c9d;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 3cb06c1..785dd14 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -21,6 +21,7 @@
 package jalview.api;
 
 import jalview.analysis.Conservation;
+import jalview.analysis.TreeModel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
@@ -430,9 +431,19 @@ public interface AlignViewportI extends ViewStyleI
    */
   void setFollowHighlight(boolean b);
 
+  /**
+   * configure the feature renderer with predefined feature settings
+   * 
+   * @param featureSettings
+   */
   public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
 
   /**
+   * Apply the given feature settings on top of existing feature settings.
+   */
+  public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings);
+
+  /**
    * check if current selection group is defined on the view, or is simply a
    * temporary group.
    * 
@@ -485,4 +496,36 @@ public interface AlignViewportI extends ViewStyleI
    */
   @Override
   void setProteinFontAsCdna(boolean b);
+
+  public abstract TreeModel getCurrentTree();
+
+  public abstract void setCurrentTree(TreeModel tree);
+
+  /**
+   * @param update
+   *          - set the flag for updating structures on next repaint
+   */
+  void setUpdateStructures(boolean update);
+
+  /**
+   *
+   * @return true if structure views will be updated on next refresh
+   */
+  boolean isUpdateStructures();
+
+  /**
+   * check if structure views need to be updated, and clear the flag afterwards.
+   * 
+   * @return if an update is needed
+   */
+  boolean needToUpdateStructureViews();
+
+  /**
+   * Adds sequencegroup to the alignment in the view. Also adds a group to the
+   * complement view if one is defined.
+   * 
+   * @param sequenceGroup
+   *          - a group defined on sequences in the alignment held by the view
+   */
+  void addSequenceGroup(SequenceGroup sequenceGroup);
 }