X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=e37c55eb8688e50312e58c40142954da324049fd;hb=863529ed7d15dd5812cf280d82bfd53734b424a1;hp=a1579c5349d3dd0b0a8390ecd9f998e110fd3c6a;hpb=b2b7e99113e1f0962140fc72d989cc826799a2d4;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index a1579c5..e37c55e 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1347,13 +1347,25 @@ public class SequenceGroup implements AnnotatedCollectionI
   private AnnotatedCollectionI context;
 
   /**
-   * set the alignment or group context for this group
+   * Sets the alignment or group context for this group
    * 
-   * @param context
+   * @param ctx
+   * @throws IllegalArgumentException
+   *           if setting the context would result in a circular reference chain
    */
-  public void setContext(AnnotatedCollectionI context)
+  public void setContext(AnnotatedCollectionI ctx)
   {
-    this.context = context;
+    AnnotatedCollectionI ref = ctx;
+    while (ref != null)
+    {
+      if (ref == this)
+      {
+        throw new IllegalArgumentException(
+                "Circular reference in SequenceGroup.context");
+      }
+      ref = ref.getContext();
+    }
+    this.context = ctx;
   }
 
   /*
@@ -1399,4 +1411,24 @@ public class SequenceGroup implements AnnotatedCollectionI
     }
     return false;
   }
+
+  /**
+   * @param seq
+   * @return true if seq is a member of the group
+   */
+
+  public boolean contains(SequenceI seq1)
+  {
+    return sequences.contains(seq1);
+  }
+
+  /**
+   * @param seq
+   * @param apos
+   * @return true if startRes<=apos and endRes>=apos and seq is in the group
+   */
+  public boolean contains(SequenceI seq, int apos)
+  {
+    return (startRes <= apos && endRes >= apos) && sequences.contains(seq);
+  }
 }