Merge branch 'develop' into features/mchmmer

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

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index ea921c7..6b3cbe8 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 getSequenceConsensusHash();
+  ProfilesI getConsensusProfiles();
 
   /**
    * Get consensus data table for the cDNA complement of this alignment (if any)
@@ -139,7 +139,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
-  AlignmentAnnotation getAlignmentGapAnnotation();
+  AlignmentAnnotation getOccupancyAnnotation();
 
   /**
    * get the container for cDNA complement consensus annotation
@@ -178,7 +178,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @param hconsensus
    */
-  void setSequenceConsensusHash(ProfilesI hconsensus);
+  void setConsensusProfiles(ProfilesI hconsensus);
 
   /**
    * Set the cDNA complement consensus for the viewport
@@ -495,27 +495,17 @@ public interface AlignViewportI extends ViewStyleI
   @Override
   void setProteinFontAsCdna(boolean b);
 
-  void setSequenceInformationHashes(List<ProfilesI> info);
+  void setHmmProfiles(ProfilesI info);
 
-  List<ProfilesI> getSequenceInformationHashes();
-
-  ProfilesI getSequenceInformationHash(int index);
-
-  List<AlignmentAnnotation> getInformationAnnotations();
-
-  void setSequenceInformationHash(ProfilesI info, int index);
-
-  /**
-   * Initiates the information annotation for all uninitiated sequences.
-   */
-  void initInformation();
+  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();