X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=34ce3bf99db93a2bdc75743c6ef4c5da66361096;hb=6aae80a714d6cf5c2d28d02f74fbbf5296a0b71a;hp=764a3d48506b9a825bf2bd341f51dae5ffdf7bee;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 764a3d4..34ce3bf 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -98,7 +98,7 @@ public class StockholmFile extends AlignFile
     }
 
     // We define some Regexes here that will be used regularily later
-    rend = new Regex("\\/\\/"); // Find the end of an alignment
+    rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment
     p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
     // id/from/to
     s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype
@@ -363,8 +363,8 @@ public class StockholmFile extends AlignFile
           if (x.search(annContent))
           {
             // parse out and create alignment annotation directly.
-            parseAnnotationRow(annotations, x.stringMatched(1), x
-                    .stringMatched(2));
+            parseAnnotationRow(annotations, x.stringMatched(1),
+                    x.stringMatched(2));
           }
         }
         else if (annType.equals("GR"))