From: jprocter <Jim Procter>
Date: Fri, 22 Feb 2008 16:28:47 +0000 (+0000)
Subject: possible fix for stockhom ss-annotation re-creation after it is saved to Jalview... 
X-Git-Tag: Release_2_4~129
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=77e9dc41516acc93470931bcc5f344c67e819e70;p=jalview.git

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 8cfe728..f68786b 100755
--- 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("-")