X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;fp=src%2Fjalview%2Fdatamodel%2FSequence.java;h=0652fb5fa0951b268c3a6a5720c2dc6afdf8bc97;hb=0b2e0f52baa343973a6c9b1e652ff584ce418fa0;hp=69d6da255c4facc7965454f74e5eaf5d7a3885b0;hpb=e34a708f67ff7496cb76c66a3d7b6f8e47518c02;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 69d6da2..0652fb5 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -879,22 +879,30 @@ public class Sequence implements SequenceI
     return datasetSequence;
   }
 
+  /**
+   * Returns a new array containing this sequence's annotations, or null.
+   */
   public AlignmentAnnotation[] getAnnotation()
   {
-    if (annotation == null)
-    {
-      return null;
-    }
-
-    AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()];
-    for (int r = 0; r < ret.length; r++)
-    {
-      ret[r] = annotation.elementAt(r);
-    }
+    return annotation == null ? null : annotation
+            .toArray(new AlignmentAnnotation[annotation.size()]);
+  }
 
-    return ret;
+  /**
+   * Returns true if this sequence has the given annotation (by object
+   * identity).
+   */
+  @Override
+  public boolean hasAnnotation(AlignmentAnnotation ann)
+  {
+    return annotation == null ? false : annotation.contains(ann);
   }
 
+  /**
+   * Add the given annotation, if not already added, and set its sequence ref to
+   * be this sequence. Does nothing if this sequence's annotations already
+   * include this annotation (by identical object reference).
+   */
   public void addAlignmentAnnotation(AlignmentAnnotation annotation)
   {
     if (this.annotation == null)