From: Renia Correya <rcorreya001@dundee.ac.uk>
Date: Tue, 28 May 2024 10:18:34 +0000 (+0100)
Subject: Merge remote-tracking branch 'origin/feature/JAL-4386_calculate_tree_using_secondary_... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2727492d498ee6d7155fff30379c338cdf4ecf24;p=jalview.git

Merge remote-tracking branch 'origin/feature/JAL-4386_calculate_tree_using_secondary_structure_annotation' into feature/JAL-4386_calculate_tree_using_secondary_structure_annotation
---

2727492d498ee6d7155fff30379c338cdf4ecf24
diff --cc src/jalview/api/AlignViewportI.java
index 404d8ea,9624f83..126c8c1
--- a/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);
  
  }