X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=a193997a288937ad7976a1eee9137ffc7d79a00a;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=293ace02f145ca05d948711f8814a4a53594397c;hpb=003129f6b884031ff4a9e738e15d2fee8702f644;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 293ace0..a193997 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -204,9 +204,9 @@ 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
-   * contained within the alignment's annotation vector. Otherwise, it will do
-   * nothing.
+   * 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
@@ -215,8 +215,25 @@ public interface AlignmentI
   public boolean deleteAnnotation(AlignmentAnnotation aa);
 
   /**
-   * Get the annotation associated with this alignment
-   * (this can be null if no annotation has ever been created on the alignment)
+   * 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)
+   * 
    * @return array of AlignmentAnnotation objects
    */
   public AlignmentAnnotation[] getAlignmentAnnotation();
@@ -244,6 +261,13 @@ public interface AlignmentI
   public boolean isNucleotide();
 
   /**
+   * Test if alignment contains RNA structure
+   * 
+   * @return true if RNA structure AligmnentAnnotation was added to alignment
+   */
+  public boolean hasRNAStructure();
+
+  /**
    * Set alignment to be a nucleotide sequence
    * 
    */