Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629

[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 19eaf78..d0538c1 100644 (file)
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -445,6 +445,7 @@ 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)
@@ -500,14 +501,11 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
 
     SequenceI seq = sm.getSequence();
     Console.debug("##### SEQUENCE FOUND=" + seq.getName());
-    Map<String, Object> paeObject = (Map<String, Object>) pae_obj;
-
-    ContactMatrixI matrix = new PAEContactMatrix(seq, paeObject);
+    ContactMatrixI matrix = new PAEContactMatrix(seq,
+            (Map<String, Object>) pae_obj);
+    ((PAEContactMatrix) matrix).makeGroups(5f, true);
     AlignmentAnnotation cmannot = seq.addContactList(matrix);
-    if (label != null)
-    {
-      cmannot.label = label;
-    }
+    seq.addAlignmentAnnotation(cmannot);
     // seq.addAlignmentAnnotation(cmannot);
 
     return true;