possible fix for stockhom ss-annotation re-creation after it is saved to Jalview...

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 8cfe728..f68786b 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -154,8 +154,11 @@ Loading...
       {
         continue;
       }
-
+      
       if (annotations[i].displayCharacter.length() == 1
+              // Uncomment to only catch case where displayCharacter==secondary Structure 
+              // to correctly redisplay SS annotation imported from Stockholm, exported to JalviewXML and read back in again.
+          // && annotations[i].displayCharacter.charAt(0)==annotations[i].secondaryStructure
           && !annotations[i].displayCharacter.equals("H")
           && !annotations[i].displayCharacter.equals("E")
           && !annotations[i].displayCharacter.equals("-")