JAL-2349 interfaces and logic for adding contact matrices as an alignment’s annotatio...

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 7274e5f..8ddba6c 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -556,4 +556,16 @@ public interface AlignmentI extends AnnotatedCollectionI
    * @return
    */
   public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
+
+  /**
+   * 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);
 }