X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=862a2bf693e2c69a1834b07b57743bc712e91057;hb=8286731258d314669ee6facb627947fe159ac1eb;hp=f129a4cef527d88a4dc29ba82cfe24dd60659024;hpb=552a05df8deb46017d3e1931cfc9a196553f2a45;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index f129a4c..862a2bf 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -595,11 +595,13 @@ public interface AlignmentI extends AnnotatedCollectionI
   AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
 
   /**
-   * Set the hidden columns collection on the alignment
+   * Set the hidden columns collection on the alignment. Answers true if the
+   * hidden column selection changed, else false.
    * 
    * @param cols
+   * @return
    */
-  public void setHiddenColumns(HiddenColumns cols);
+  public boolean setHiddenColumns(HiddenColumns cols);
 
   /**
    * Set the first sequence as representative and hide its insertions. Typically
@@ -622,4 +624,15 @@ public interface AlignmentI extends AnnotatedCollectionI
   public HiddenColumns propagateInsertions(SequenceI profileseq,
           AlignmentView input);
 
+  /**
+   * resolve a contact list instance (if any) associated with the annotation row
+   * and column position
+   * 
+   * @param _aa
+   * @param column
+   * @return
+   */
+  ContactListI getContactListFor(AlignmentAnnotation _aa, int column);
+
+  AlignmentAnnotation addContactList(ContactMatrixI cm);
 }