X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=0fcf43dc0ca1ff782c1482d516ac8c055c67bd08;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=8115af4677f66f179eb8ce8879085c45cb902686;hpb=a923c0fa51ce22d052ac06f54b006c57385cc8e0;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 8115af4..0fcf43d 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,6 +14,7 @@
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
@@ -263,10 +264,10 @@ public class AlignmentAnnotation
         		|| annotations[i].secondaryStructure == 'B'
         		|| annotations[i].secondaryStructure == 'C'
         		|| annotations[i].secondaryStructure == 'D'
-        		|| annotations[i].secondaryStructure == '1'
+        		|| annotations[i].secondaryStructure == 'E'
         		|| annotations[i].secondaryStructure == 'F'
         		|| annotations[i].secondaryStructure == 'G'
-        		|| annotations[i].secondaryStructure == '2'
+        		|| annotations[i].secondaryStructure == 'H'
         		|| annotations[i].secondaryStructure == 'I'
         		|| annotations[i].secondaryStructure == 'J'
         		|| annotations[i].secondaryStructure == 'K'
@@ -315,8 +316,8 @@ public class AlignmentAnnotation
                 // &&
                 // annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
                 firstChar != ' '
-                && firstChar != 'H'
-                && firstChar != 'E'
+                && firstChar != '$'
+                && firstChar != '�' // JBPNote should explicitly express as unicode number to avoid source code translation problems
                 && firstChar != '('
                 && firstChar != '['
                 && firstChar != '>'
@@ -325,10 +326,10 @@ public class AlignmentAnnotation
                 && firstChar != 'B'
                 && firstChar != 'C'
                 && firstChar != 'D'
-                && firstChar != '1'
+                && firstChar != 'E'
                 && firstChar != 'F'
                 && firstChar != 'G'
-                && firstChar != '2'
+                && firstChar != 'H'
                 && firstChar != 'I'
                 && firstChar != 'J'
                 && firstChar != 'K'