Merge branch 'features/JAL-2349_matrixvis' into merge/develop_JAL-2340_matrixvis

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 93a2456..862a2bf 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -624,4 +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);
 }