JAL-819 menu options to reinstate missing auto-calculated annotation

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

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 389d9cf..707d03d 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -431,9 +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.
    * 
@@ -518,4 +528,29 @@ public interface AlignViewportI extends ViewStyleI
    *          - a group defined on sequences in the alignment held by the view
    */
   void addSequenceGroup(SequenceGroup sequenceGroup);
+
+  /**
+   * Creates an empty Conservation annotation and adds it to the alignment
+   */
+  void initConservation();
+
+  /**
+   * Creates an empty Quality annotation and adds it to the alignment
+   */
+  void initQuality();
+
+  /**
+   * Creates an empty Consensus annotation and adds it to the alignment
+   */
+  void initConsensus();
+
+  /**
+   * Creates an empty Occupancy annotation and adds it to the alignment
+   */
+  void initOccupancy();
+
+  /**
+   * Creates an empty RNA Structure annotation and adds it to the alignment
+   */
+  void initRNAStructure();
 }