X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=b70636fdfa6570e4bd7305fd52acdb4e7f244684;hb=a4a4122f1a7b0c615d6780197456c811db6b8a2f;hp=470cc371a6cef848b764c6e89d88d8e868158a96;hpb=93642d621a7f86318a7777b0a70f6113dcd299dc;p=jalview.git

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 470cc37..b70636f 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -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