patch for JAL-572

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 470cc37..b70636f 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -98,7 +98,7 @@ public class StockholmFile extends AlignFile
     }\r
 \r
     // We define some Regexes here that will be used regularily later\r
-    rend = new Regex("\\/\\/"); // Find the end of an alignment\r
+    rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment\r
     p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in\r
     // id/from/to\r
     s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype\r