X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEBIAlfaFold.java;h=6b27488b24a67750f23a9e24735292502412817b;hb=6ca8a32d88328b8f2162512f41c657c87e131045;hp=d0538c1c1e4f0b57d9e1e3e7d9c4842501c57451;hpb=b7e9e2edf0c1557089eff0e4b5c17c0b31e698c2;p=jalview.git

diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java
index d0538c1..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;
@@ -314,6 +315,8 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
 
     if (isStruct)
     {
+      // ###### WRITE A TEST for this bit of the logic addAlphaFoldPAE with
+      // different params.
       StructureSelectionManager ssm = StructureSelectionManager
               .getStructureSelectionManager(Desktop.instance);
       if (ssm != null)
@@ -445,7 +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)
@@ -474,6 +476,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     return paeDict;
   }
 
+  // ###### TEST THIS
   public static boolean importPaeJSONAsContactMatrixToStructure(
           StructureMapping[] smArray, InputStream paeInput, String label)
           throws IOException, ParseException
@@ -500,14 +503,12 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     }
 
     SequenceI seq = sm.getSequence();
-    Console.debug("##### SEQUENCE FOUND=" + seq.getName());
     ContactMatrixI matrix = new PAEContactMatrix(seq,
             (Map<String, Object>) pae_obj);
-    ((PAEContactMatrix) matrix).makeGroups(5f, true);
-    AlignmentAnnotation cmannot = seq.addContactList(matrix);
-    seq.addAlignmentAnnotation(cmannot);
-    // seq.addAlignmentAnnotation(cmannot);
-
+    AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
+    /* this already happens in Sequence.addContactList()
+     seq.addAlignmentAnnotation(cmannot);
+     */
     return true;
   }