X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=5a2c46e0b3e2be52032af8a67f02cfbefdde6cfc;hb=d6e1bbede5adc04f34c969213ac6a4c6d9e5d34a;hp=7f6b08acbf38406195da64fb85a973a76b089a28;hpb=aae9a99e127a20cfd7def2ced9265dcf669bf737;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 7f6b08a..5a2c46e 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -168,33 +168,35 @@ public class AlignmentAnnotation
             }
         }
 
-        if(!drawValues)
-        {
-          for (int i = 0; i < annotations.length; i++)
-          {
-            if (annotations[i] != null)
-              annotations[i].displayCharacter = "";
-          }
-        }
-
         graphMin = min;
         graphMax = max;
 
         for (int i = 0; i < annotations.length; i++)
         {
-            if ((annotations[i] != null) &&
-                    ((annotations[i].secondaryStructure == 'H') ||
+            if (!hasIcons
+                && annotations[i] != null
+                && ((annotations[i].secondaryStructure == 'H') ||
                     (annotations[i].secondaryStructure == 'E')))
             {
                 hasIcons = true;
             }
 
-            if ((annotations[i] != null) &&
-                    (annotations[i].displayCharacter.length() > 0))
+            if (!hasText
+                && annotations[i]!=null
+                && annotations[i].displayCharacter.length() > 0)
             {
                 hasText = true;
             }
         }
+
+        if(!drawValues && graphType!=NO_GRAPH)
+        {
+          for (int i = 0; i < annotations.length; i++)
+          {
+            if (annotations[i] != null)
+              annotations[i].displayCharacter = "";
+          }
+        }
     }
 
     /**
@@ -299,9 +301,16 @@ public class AlignmentAnnotation
       {
           int a=0, aSize = sequenceRef.getLength();
 
+          if(aSize == 0)
+          {
+            //Its been deleted
+            return;
+          }
+
           int position;
           Annotation[] temp = new Annotation[aSize];
           Integer index;
+
           for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
           {
               index = new Integer(a);