X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=fa0a3b05543a3f636680b5e4286cce9dd11282f8;hb=dd78fb858ae1d6b7704ddb29617029f429f07e9b;hp=931eba62c1cf83b8dda2771187cfe7016a41c665;hpb=bf8275c621048462bd0275e31bf490dca443b477;p=jalview.git

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 931eba6..fa0a3b0 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -20,6 +20,7 @@
  */
 package jalview.api;
 
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
 import jalview.analysis.TreeModel;
 import jalview.datamodel.AlignmentAnnotation;
@@ -490,4 +491,55 @@ public interface AlignViewportI extends ViewStyleI
   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);
+
+  /**
+   * Returns true if autocalculated annotations are shown above other
+   * annotations, false if below
+   * 
+   * @return
+   */
+  boolean isShowAutocalculatedAbove();
+
+  /**
+   * Sets the flag for whether autocalculated annotations are shown above (true)
+   * or below (false) other annotations
+   * 
+   * @param showAutocalculatedAbove
+   */
+  void setShowAutocalculatedAbove(boolean showAutocalculatedAbove);
+
+  /**
+   * Sets the sort order to apply to annotations
+   * 
+   * @param sortAnnotationsBy
+   */
+  void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy);
 }