From 555361f1a668c138550f0cc95cbf089377e84561 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 20 Apr 2007 15:34:06 +0000
Subject: [PATCH] fix null annotation values

---
 src/jalview/datamodel/AlignmentAnnotation.java |   30 +++++++++++++-----------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 27ccd4c..81ea36f 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -132,32 +132,34 @@ public class AlignmentAnnotation
         padGaps = false;
         continue;
       }
-
       if (annotations[i].secondaryStructure == 'H' ||
           annotations[i].secondaryStructure == 'E')
       {
-        hasIcons = true;
+          hasIcons = true;
       }
 
-      if (annotations[i].displayCharacter.length() == 1
+      if (annotations[i].displayCharacter!=null)
+      {
+        if (annotations[i].displayCharacter.length() == 1
           && !annotations[i].displayCharacter.equals("H")
           && !annotations[i].displayCharacter.equals("E")
           && !annotations[i].displayCharacter.equals("-")
           && !annotations[i].displayCharacter.equals("."))
-      {
-        if (jalview.schemes.ResidueProperties.aaIndex
-            [annotations[i].displayCharacter.charAt(0)] < 23)
         {
-          nonSSLabel = true;
+          if (jalview.schemes.ResidueProperties.aaIndex
+                  [annotations[i].displayCharacter.charAt(0)] < 23)
+          {
+            nonSSLabel = true;
+          }
         }
-      }
 
-      if (annotations[i].displayCharacter.length() > 0)
-      {
-        hasText = true;
+        if (annotations[i].displayCharacter.length() > 0)
+        {
+          hasText = true;
+        }
+        else
+          padGaps = false;
       }
-      else
-        padGaps = false;
     }
 
 
@@ -226,7 +228,7 @@ public class AlignmentAnnotation
           continue;
         }
 
-        if (drawValues && annotations[i].displayCharacter.length() > 1)
+        if (drawValues && annotations[i].displayCharacter!=null && annotations[i].displayCharacter.length() > 1)
         {
           drawValues = false;
         }
-- 
1.7.10.2