Merge remote-tracking branch 'origin/feature/JAL-4386_calculate_tree_using_secondary_...

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

diff --cc src/jalview/api/AlignViewportI.java
index 404d8ea,9624f83..126c8c1
--- 1/src/jalview/api/AlignViewportI.java
--- 2/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@@ -575,13 -575,19 +575,23 @@@ 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();
 +  Map<String, ProfilesI> getSequenceSSConsensusHash();
 +
 +  List<String> getSecondaryStructureSources();
 +
 +  void setSecondaryStructureSources(List<String> secondaryStructureSources);
  
  }

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