adjustForAlignment on new seq ref

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 1b7b72a..2053fef 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -367,6 +367,7 @@ public class AnnotationFile
           catch (Exception ex)\r
           {\r
             refSeqIndex = 1;\r
+            refSeq=null;\r
           }\r
 \r
           continue ;\r
@@ -433,6 +434,7 @@ public class AnnotationFile
         if (refSeq != null)\r
         {\r
           annotation.createSequenceMapping(refSeq, refSeqIndex, false);\r
+          annotation.adjustForAlignment();\r
           refSeq.addAlignmentAnnotation(annotation);\r
         }\r
 \r