From b2915cf5f0efece6f8b5a5075b0a7327b3b6a3b3 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 18 Jan 2007 16:16:34 +0000
Subject: [PATCH] Is secondary structure label modified

---
 src/jalview/datamodel/AlignmentAnnotation.java |   15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index d6eb3ea..a97ca7f 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -120,11 +120,16 @@ public class AlignmentAnnotation
           hasIcons = true;
         }
 
-        if (annotations[i].secondaryStructure != 'H'
-            && annotations[i].secondaryStructure != 'E'
-            && annotations[i].secondaryStructure != '-')
+        if (annotations[i].displayCharacter.length()==1
+            && !annotations[i].displayCharacter.equals("H")
+            && !annotations[i].displayCharacter.equals("E")
+            && !annotations[i].displayCharacter.equals("-"))
         {
-          nonSSLabel = true;
+          if(jalview.schemes.ResidueProperties.aaIndex
+             [annotations[i].displayCharacter.charAt(0)]>0)
+          {
+            nonSSLabel = true;
+          }
         }
 
         if (annotations[i].displayCharacter.length() > 0)
@@ -143,8 +148,6 @@ public class AlignmentAnnotation
             annotations[j].displayCharacter
                 =String.valueOf(annotations[j].secondaryStructure);
             annotations[j].secondaryStructure = ' ';
-            if(annotations[j].description.length()<1)
-              annotations[j].description = annotations[j].displayCharacter;
           }
 
         }
-- 
1.7.10.2