Merge branch 'develop' into feature/JAL-4386_calculate_tree_using_secondary_structure...

diff --cc resources/lang/Messages.properties
Simple merge

diff --cc src/jalview/api/AlignViewportI.java
index b7747f5,e7afee0..9624f83
--- 1/src/jalview/api/AlignViewportI.java
--- 2/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@@ -575,9 -565,16 +575,19 @@@ public interface AlignViewportI extend
     * @return
     */
    Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
+   /**
+    * notify all concerned that the alignment data has changed and derived data
+    * needs to be recalculated
+    */
+   public void notifyAlignmentChanged();
  
+   /**
+    * retrieve a matrix associated with the view's alignment's annotation 
+    * @param alignmentAnnotation
+    * @return contact matrix or NULL
+    */
    ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
 +
 +  ProfilesI getSequenceSSConsensusHash();
 +
  }

diff --cc src/jalview/gui/AlignFrame.java
Simple merge

diff --cc src/jalview/gui/PopupMenu.java
Simple merge

diff --cc src/jalview/jbgui/GAlignFrame.java
Simple merge

diff --cc src/jalview/viewmodel/AlignmentViewport.java
Simple merge