X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FContactMapHolderI.java;h=342abf835fb4f9294a9778419c54cc63ab038fa8;hb=07711595213cb89a9c42e2659c7b208b4a8b8d39;hp=ba23e6773d2e2b026133ebab11f076cbe27cc75a;hpb=51ff7ec3b6914f3c69b35e91e69d10c88aaf5270;p=jalview.git

diff --git a/src/jalview/datamodel/ContactMapHolderI.java b/src/jalview/datamodel/ContactMapHolderI.java
index ba23e67..342abf8 100644
--- 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);