Check displayChar is not null

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 2ce076a..12c128a 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -140,7 +140,8 @@ public class AnnotationFile
               text.append(comma + row.annotations[j].secondaryStructure);\r
               comma = ",";\r
             }\r
-            if (row.annotations[j].displayCharacter.length() > 0\r
+            if (row.annotations[j].displayCharacter!=null\r
+                && row.annotations[j].displayCharacter.length() > 0\r
                 && !row.annotations[j].displayCharacter.equals(" "))\r
             {\r
               text.append(comma + row.annotations[j].displayCharacter);\r
@@ -432,7 +433,6 @@ 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