From: Jim Procter <jprocter@dundee.ac.uk>
Date: Mon, 1 Dec 2014 21:49:16 +0000 (+0000)
Subject: JAL-1199 JAL-1569 incremental patch allow non-standard annotation to be output
X-Git-Tag: Release_2_8_2~1^2~4^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=78c75d17d486be63f023a9eed386a0b40954d95b;hp=1852685ff3c86b4939b4e7fcc0233b420f711dde;p=jalview.git

JAL-1199 JAL-1569 incremental patch allow non-standard annotation to be output
---

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 96c462c..3b9fb00 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -1027,13 +1027,21 @@ public class StockholmFile extends AlignFile
         }
         else
         {
-          label = (key = type2id(aa.label.toLowerCase())) + "_cons";
+          key = type2id(aa.label.toLowerCase());
+          if (key == null)
+          {
+            label = aa.label;
+          }
+          else
+          {
+            label = key + "_cons";
+          }
         }
-
         if (label == null)
         {
           label = aa.label;
         }
+        label = label.replace(" ", "_");
 
         out.append(new Format("%-" + maxid + "s").form("#=GC " + label
                 + " "));
@@ -1067,7 +1075,7 @@ public class StockholmFile extends AlignFile
     String ch = (annot == null) ? ((sequenceI == null) ? "-" : Character
             .toString(sequenceI.getCharAt(k)))
             : annot.displayCharacter;
-    if (key.equals("SS"))
+    if (key != null && key.equals("SS"))
     {
       if (annot == null)
       {