Merge branch 'develop' into bug/JAL-4235_gradle_task_jalviewjsTranspile_does_not_fail...

[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 fd10c79..6b27488 100644 (file)
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -176,7 +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;
@@ -448,7 +448,6 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     }
     ContactMatrixI matrix = new PAEContactMatrix(sequence,
             (Map<String, Object>) paeDict);
-    matrix.setGroupSet(GroupSet.makeGroups(matrix, 5f, true));
 
     AlignmentAnnotation cmannot = sequence.addContactList(matrix);
     if (label != null)
@@ -506,7 +505,6 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     SequenceI seq = sm.getSequence();
     ContactMatrixI matrix = new PAEContactMatrix(seq,
             (Map<String, Object>) pae_obj);
-    matrix.setGroupSet(GroupSet.makeGroups(matrix, 5f, true));
     AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
     /* this already happens in Sequence.addContactList()
      seq.addAlignmentAnnotation(cmannot);