JAL-2349 fix off by one when resolving columns for sequence associated contact matrix

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

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