From: jprocter <Jim Procter>
Date: Mon, 14 Jun 2010 11:21:34 +0000 (+0000)
Subject: patch for JAL-572
X-Git-Tag: Release_2_6~181
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d46053ba40ebbaf5a8b8867cdc770673228b4721;p=jalview.git

patch for JAL-572
---

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 764a3d4..b407463 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