X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=2e0903df8381b33829cc85e886ce21277ed8bf5f;hb=fa7f47950cccf7241aad97c1f6c99700e5a476f7;hp=8b947eb415097a95f9a944596d96eac285e4a966;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 8b947eb..2e0903d 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -204,7 +204,7 @@ public interface AlignmentI
 
   /**
    * Deletes a specific AlignmentAnnotation from the alignment, and removes its
-   * reference from any SequenceI object's annotation if and only if aa is
+   * reference from any SequenceI or SequenceGroup object's annotation if and only if aa is
    * contained within the alignment's annotation vector. Otherwise, it will do
    * nothing.
    * 
@@ -215,6 +215,20 @@ public interface AlignmentI
   public boolean deleteAnnotation(AlignmentAnnotation aa);
 
   /**
+   * Deletes a specific AlignmentAnnotation from the alignment, and optionally removes any
+   * reference from any SequenceI or SequenceGroup object's annotation if and only if aa is
+   * contained within the alignment's annotation vector. Otherwise, it will do
+   * nothing.
+   * 
+   * @param aa
+   *          the annotation to delete
+   * @param unhook
+   *          flag indicating if any references should be removed from annotation - use this if you intend to add the annotation back into the alignment
+   * @return true if annotation was deleted from this alignment.
+   */
+  public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook);
+
+  /**
    * Get the annotation associated with this alignment (this can be null if no
    * annotation has ever been created on the alignment)
    *