JAL-3285 add unmerged features to AlignViewportI

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

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index bcee815..e2a13d4 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -106,7 +106,7 @@ public interface AlignViewportI extends ViewStyleI
 
   ColumnSelection getColumnSelection();
 
-  ProfilesI getConsensusProfiles();
+  ProfilesI getSequenceConsensusHash();
 
   /**
    * Get consensus data table for the cDNA complement of this alignment (if any)
@@ -139,7 +139,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
-  AlignmentAnnotation getOccupancyAnnotation();
+  AlignmentAnnotation getAlignmentGapAnnotation();
 
   /**
    * get the container for cDNA complement consensus annotation
@@ -178,7 +178,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @param hconsensus
    */
-  void setConsensusProfiles(ProfilesI hconsensus);
+  void setSequenceConsensusHash(ProfilesI hconsensus);
 
   /**
    * Set the cDNA complement consensus for the viewport
@@ -388,14 +388,14 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return a copy of this view's current display settings
    */
-  ViewStyleI getViewStyle();
+  public ViewStyleI getViewStyle();
 
   /**
    * update the view's display settings with the given style set
    * 
    * @param settingsForView
    */
-  void setViewStyle(ViewStyleI settingsForView);
+  public void setViewStyle(ViewStyleI settingsForView);
 
   /**
    * Returns a viewport which holds the cDna for this (protein), or vice versa,
@@ -439,7 +439,7 @@ public interface AlignViewportI extends ViewStyleI
    */
   void setFollowHighlight(boolean b);
 
-  void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
+  public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
 
   /**
    * check if current selection group is defined on the view, or is simply a
@@ -500,15 +500,44 @@ public interface AlignViewportI extends ViewStyleI
   ProfilesI getHmmProfiles();
 
   /**
-   * Updates all information annotations.
+   * Registers and starts a worker thread to calculate Information Content
+   * annotation, if it is not already registered
    * 
    * @param ap
    */
-  void updateInformation(AlignmentViewPanel ap);
+  void initInformationWorker(AlignmentViewPanel ap);
 
   boolean isInfoLetterHeight();
 
   abstract TreeModel getCurrentTree();
 
   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);
 }