Merge branch 'improvement/JAL-3783_upgrade_to_groovy-4' into bug/JAL-4298_java_consol...

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

diff --git a/src/jalview/datamodel/ContactMapHolderI.java b/src/jalview/datamodel/ContactMapHolderI.java
index 624a03e..342abf8 100644 (file)
--- a/src/jalview/datamodel/ContactMapHolderI.java
+++ b/src/jalview/datamodel/ContactMapHolderI.java
@@ -6,10 +6,13 @@ public interface ContactMapHolderI
 {
   /**
    * resolve a contact list instance (if any) associated with the annotation row
-   * and column position
+   * and column position Columns of ContactMap are indexed relative to context
+   * object (columns of alignment, positions on sequence relative to
+   * sequence.getStart())
    * 
    * @param _aa
    * @param column
+   *          - base 0 column index
    * @return
    */
   ContactListI getContactListFor(AlignmentAnnotation _aa, int column);
@@ -18,4 +21,8 @@ public interface ContactMapHolderI
 
   Collection<ContactMatrixI> getContactMaps();
 
+  public ContactMatrixI getContactMatrixFor(AlignmentAnnotation ann);
+
+  void addContactListFor(AlignmentAnnotation annotation, ContactMatrixI cm);
+
 }