Maps are usually added to DbRefs which are added to dataset sequences.

diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index 867b498..a4ee585 100644 (file)
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -53,7 +53,7 @@ public class Sequencemapping extends Rangetype
       {\r
         jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: "+from+" doesn't match the local mapping sequence.");\r
       }\r
-      if (ds!=null && sequenceMapping.getV_parent()!=ds)\r
+      if (ds!=null && sequenceMapping.is__stored_in_document() && sequenceMapping.getV_parent()!=ds)\r
       {\r
         jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: "+ds+" doesn't match the parent of the bound sequence mapping object.");\r
       }\r