X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=76ad093130eb3b2f39cf0f4239f95003e707b754;hb=refs%2Fheads%2Ffeatures%2FJAL-2465_No-mapping_Jmol-structures-loaded-via-url;hp=e37c55eb8688e50312e58c40142954da324049fd;hpb=0585c8478eccc42896dbd1a4d365ecdc913551f2;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index e37c55e..76ad093 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1289,12 +1289,6 @@ public class SequenceGroup implements AnnotatedCollectionI
     return aa;
   }
 
-  /**
-   * Returns a list of annotations that match the specified sequenceRef, calcId
-   * and label, ignoring null values.
-   * 
-   * @return list of AlignmentAnnotation objects
-   */
   @Override
   public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
           String calcId, String label)
@@ -1302,9 +1296,11 @@ public class SequenceGroup implements AnnotatedCollectionI
     ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
     for (AlignmentAnnotation ann : getAlignmentAnnotation())
     {
-      if (ann.getCalcId() != null && ann.getCalcId().equals(calcId)
-              && ann.sequenceRef != null && ann.sequenceRef == seq
-              && ann.label != null && ann.label.equals(label))
+      if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId()
+              .equals(calcId)))
+              && (seq == null || (ann.sequenceRef != null && ann.sequenceRef == seq))
+              && (label == null || (ann.label != null && ann.label
+                      .equals(label))))
       {
         aa.add(ann);
       }
@@ -1358,7 +1354,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     AnnotatedCollectionI ref = ctx;
     while (ref != null)
     {
-      if (ref == this)
+      if (ref == this || ref.getContext() == ctx)
       {
         throw new IllegalArgumentException(
                 "Circular reference in SequenceGroup.context");