X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEBIAlfaFold.java;h=6b27488b24a67750f23a9e24735292502412817b;hb=6ca8a32d88328b8f2162512f41c657c87e131045;hp=a734f52fca94e86a3a7e62ffa17d26cb5aee82c1;hpb=c71453f1c7de4cc250700c1b6dd39d061982e794;p=jalview.git

diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java
index a734f52..6b27488 100644
--- 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;
@@ -175,7 +176,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
 
     if (!isValidReference(id))
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "(AFClient) Ignoring invalid alphafold query: '" + id + "'");
       stopQuery();
       return null;
@@ -447,7 +448,6 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     }
     ContactMatrixI matrix = new PAEContactMatrix(sequence,
             (Map<String, Object>) paeDict);
-    ((PAEContactMatrix) matrix).makeGroups(5f, true);
 
     AlignmentAnnotation cmannot = sequence.addContactList(matrix);
     if (label != null)
@@ -505,8 +505,7 @@ 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);
+    AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
     /* this already happens in Sequence.addContactList()
      seq.addAlignmentAnnotation(cmannot);
      */