X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=c3396b6553f753c2bef3c96be9ad957ade806012;hb=aad4f693fc478138fd225741acf1f8d44defd162;hp=470497e12ceff0a258443205d43fa153667df87b;hpb=c11a4dfd307ba4a13d1b4cd7d5a21f8a56a06da9;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 470497e..c3396b6 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -258,9 +258,10 @@ public class AlignmentAnnotation
       }
 
       /**
-       * Attach the annotation to seqRef, starting from startRes position.
+       * Attach the annotation to seqRef, starting from startRes position. If alreadyMapped is true then the indices of the annotation[] array are sequence positions rather than alignment column positions.
        * @param seqRef
        * @param startRes
+       * @param alreadyMapped
        */
       public void createSequenceMapping(SequenceI seqRef,
                                         int startRes,