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

[jalview.git] / src / jalview / io / vamsas / Sequencemapping.java

diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index 48b2982..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
@@ -221,7 +221,7 @@ public class Sequencemapping extends Rangetype
 \r
     if (dsLoc!=null && dsLoc!=dsMap)\r
     {\r
-      dsMap.addCodonFrame(afc);\r
+      dsLoc.addCodonFrame(afc);\r
     }\r
     if (dsMap!=null)\r
     {\r