JAL-885; hasRNAStructure method was introduced to AlignmentI and

[jalview.git] / src / jalview / datamodel / AlignmentI.java

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 8b947eb..05d3a10 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -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
@@ -215,6 +215,22 @@ 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)
    * 
@@ -245,6 +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
    * 
    */