X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=7966f5e91d42d68ae434551ca01aa515db7d20ec;hb=8d20883646e6a422e617b489f00671edb3419471;hp=4499038258ddaf1ee4c2246e01e11e69b8237f42;hpb=1fd1cc0f68292041908b4a10e62d68d98cb756a7;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 4499038..7966f5e 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -502,9 +502,13 @@ public class AlignmentAnnotation
     public char charAt(int index)
     {
       return ((index + offset < 0) || (index + offset) >= max
-              || annotations[index + offset] == null || (annotations[index
- + offset].secondaryStructure <= ' ') ? ' '
-              : annotations[index + offset].displayCharacter.charAt(0));
+              || annotations[index + offset] == null
+              || (annotations[index + offset].secondaryStructure <= ' ') ? ' '
+              : annotations[index + offset].displayCharacter == null
+                      || annotations[index + offset].displayCharacter
+                              .length() == 0 ? annotations[index + offset].secondaryStructure
+                      : annotations[index + offset].displayCharacter
+                              .charAt(0));
     }
 
     @Override
@@ -516,7 +520,9 @@ public class AlignmentAnnotation
       for (int i = offset; i < mx; i++)
       {
         string[i] = (annotations[i] == null || (annotations[i].secondaryStructure <= 32)) ? ' '
-                : annotations[i].displayCharacter.charAt(0);
+                : (annotations[i].displayCharacter == null
+                        || annotations[i].displayCharacter.length() == 0 ? annotations[i].secondaryStructure
+                        : annotations[i].displayCharacter.charAt(0));
       }
       return new String(string);
     }