JAL-629 allow comments in argfiles '#'

[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 5165d04..19eaf78 100644 (file)
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -498,16 +498,17 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
       return false;
     }
 
-    ContactMatrixI matrix = new PAEContactMatrix(sm.getSequence(),
-            (Map<String, Object>) pae_obj);
+    SequenceI seq = sm.getSequence();
+    Console.debug("##### SEQUENCE FOUND=" + seq.getName());
+    Map<String, Object> paeObject = (Map<String, Object>) pae_obj;
 
-    AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
+    ContactMatrixI matrix = new PAEContactMatrix(seq, paeObject);
+    AlignmentAnnotation cmannot = seq.addContactList(matrix);
     if (label != null)
     {
-      Console.debug("Setting annotation label to '" + label + "'");
       cmannot.label = label;
     }
-    sm.getSequence().addAlignmentAnnotation(cmannot);
+    // seq.addAlignmentAnnotation(cmannot);
 
     return true;
   }