Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-4134_treeviewerfo...

diff --cc src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
Simple merge

diff --cc src/jalview/ws/dbsources/EBIAlfaFold.java
index dd71ec3,8592bd3..d9cbbd9
--- 1/src/jalview/ws/dbsources/EBIAlfaFold.java
--- 2/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@@ -469,15 -495,9 +496,9 @@@ public class EBIAlfaFold extends EbiFil
  
      ContactMatrixI matrix = new PAEContactMatrix(sm.getSequence(),
              (Map<String, Object>) pae_obj);
 -
 +    ((PAEContactMatrix) matrix).makeGroups(5f, true);
      AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
-     // sm.getSequence().addAlignmentAnnotation(cmannot);
-     sm.transfer(cmannot);
-     // return true;
- 
-     StructureSelectionManager ssm = StructureSelectionManager
-             .getStructureSelectionManager(Desktop.instance);
-     List<AlignedCodonFrame> acfList = ssm.getSequenceMappings();
+     sm.getSequence().addAlignmentAnnotation(cmannot);
  
      return true;
    }