dont set seqref null if index incorrect

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 2053fef..2ce076a 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -367,7 +367,6 @@ public class AnnotationFile
           catch (Exception ex)\r
           {\r
             refSeqIndex = 1;\r
-            refSeq=null;\r
           }\r
 \r
           continue ;\r
@@ -433,6 +432,7 @@ public class AnnotationFile
 \r
         if (refSeq != null)\r
         {\r
+          System.out.println(refSeq.getName()+" "+refSeqIndex);\r
           annotation.createSequenceMapping(refSeq, refSeqIndex, false);\r
           annotation.adjustForAlignment();\r
           refSeq.addAlignmentAnnotation(annotation);\r