JAL-4134 column grouping model and methods moved to their own object held by by Conta...

[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 d9cbbd9..5d88e89 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;
@@ -442,7 +443,7 @@ 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);
     pdbAlignment.addAnnotation(cmannot);
@@ -496,7 +497,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
 
     ContactMatrixI matrix = new PAEContactMatrix(sm.getSequence(),
             (Map<String, Object>) pae_obj);
-    ((PAEContactMatrix) matrix).makeGroups(5f, true);
+    matrix.setGroupSet(GroupSet.makeGroups(matrix,5f, true));
     AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
     sm.getSequence().addAlignmentAnnotation(cmannot);