X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=82aff3329e5190320ad2de32b8726bf69f9bc478;hb=a96d51f58325f8429c5792ae554243de5628d62a;hp=96b197250107b2f9853aa39d7a209b0e9e27750f;hpb=9ca6b95ab67df6eaeea56765cc293133da436e76;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 96b1972..82aff33 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -178,11 +178,15 @@ public interface AlignmentI
   public void setAnnotationIndex(AlignmentAnnotation aa, int index);
 
   /**
-   * Deletes a specific AlignmentAnnotation from the alignment.
-   *
+   * 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.
+   * 
    * @param aa the annotation to delete
+   * @return true if annotation was deleted from this alignment.
    */
-  public void deleteAnnotation(AlignmentAnnotation aa);
+  public boolean deleteAnnotation(AlignmentAnnotation aa);
 
   /**
    * Get the annotation associated with this alignment
@@ -244,7 +248,51 @@ public interface AlignmentI
    */
   public CigarArray getCompactAlignment();
 
+  /**
+   * Set an arbitrary key value pair for an alignment.
+   * Note: both key and value objects should return a 
+   * meaningful, human readable response to .toString()
+   * @param key
+   * @param value
+   */
   public void setProperty(Object key, Object value);
-
+  /**
+   * Get a named property from the alignment. 
+   * @param key
+   * @return value of property
+   */
   public Object getProperty(Object key);
+  /**
+   * Get the property hashtable.
+   * @return hashtable of alignment properties (or null if none are defined)
+   */
+  public Hashtable getProperties();
+
+  /**
+   * add a reference to a frame of aligned codons for this alignment
+   * @param codons
+   */
+  public void addCodonFrame(AlignedCodonFrame codons);
+  /**
+   * remove a particular codon frame reference from this alignment
+   * @param codons
+   * @return true if codon frame was removed.
+   */
+  public boolean removeCodonFrame(AlignedCodonFrame codons);
+  /**
+   * get all codon frames associated with this alignment
+   * @return
+   */
+  public AlignedCodonFrame[] getCodonFrames();
+  /**
+   * get a particular codon frame
+   * @param index
+   * @return
+   */
+  public AlignedCodonFrame getCodonFrame(int index);
+  /**
+   * get codon frames involving sequenceI
+   */
+  public AlignedCodonFrame[] getCodonFrame(SequenceI seq);
+  
 }