From: tva <tva@10.205.251.175>
Date: Wed, 5 Jun 2019 12:27:32 +0000 (+0100)
Subject: JAL-3285 add unmerged features to AlignViewportI
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c8d7bf9cc0c152249d53fd538cf73a7891b22ac9;p=jalview.git

JAL-3285 add unmerged features to AlignViewportI
---

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index ab0aeed..e2a13d4 100644
--- 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