From: Jim Procter <jprocter@dundee.ac.uk>
Date: Thu, 16 May 2024 06:53:50 +0000 (+0100)
Subject: Merge branch 'develop' into feature/JAL-4386_calculate_tree_using_secondary_structure... 
X-Git-Tag: Release_2_11_4_0~37^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b4b8a22386a34a447ef6d6d8e33b67544d74bb2a;p=jalview.git

Merge branch 'develop' into feature/JAL-4386_calculate_tree_using_secondary_structure_annotation
---

b4b8a22386a34a447ef6d6d8e33b67544d74bb2a
diff --cc src/jalview/api/AlignViewportI.java
index b7747f5,e7afee0..9624f83
--- a/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();
 +
  }