Merge branch 'develop' into features/JAL-4134_use_annotation_row_for_colours_and_groups

[jalview.git] / src / jalview / ws / dbsources / EBIAlfaFold.java

diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java
index a734f52..fd10c79 100644 (file)
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -44,6 +44,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GroupSet;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -447,7 +448,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     }
     ContactMatrixI matrix = new PAEContactMatrix(sequence,
             (Map<String, Object>) paeDict);
-    ((PAEContactMatrix) matrix).makeGroups(5f, true);
+    matrix.setGroupSet(GroupSet.makeGroups(matrix, 5f, true));
 
     AlignmentAnnotation cmannot = sequence.addContactList(matrix);
     if (label != null)
@@ -505,8 +506,8 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     SequenceI seq = sm.getSequence();
     ContactMatrixI matrix = new PAEContactMatrix(seq,
             (Map<String, Object>) pae_obj);
-    ((PAEContactMatrix) matrix).makeGroups(5f, true);
-    AlignmentAnnotation cmannot = seq.addContactList(matrix);
+    matrix.setGroupSet(GroupSet.makeGroups(matrix, 5f, true));
+    AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
     /* this already happens in Sequence.addContactList()
      seq.addAlignmentAnnotation(cmannot);
      */