X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=a3f75316676f9b7d21547a6f6b5a4c22d73ff344;hb=3cea1ee2c1c9a2ad0a3b2c76bac165b1b6a3ff2a;hp=cff328b040d35d7cb99db90779b53cc1c3c30928;hpb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;p=jalview.git

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index cff328b..a3f7531 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -90,7 +90,7 @@ public class StockholmFile extends AlignFile
   // use the following regex to decide an annotations (whole) line is NOT an RNA
   // SS (it contains only E,H,e,h and other non-brace/non-alpha chars)
   private static final Regex NOT_RNASS = new Regex(
-          "^[^<>[\\](){}A-DF-Za-df-z]*$");
+          "^[^<>[\\](){}ADFJ-RUVWYZadfj-ruvwyz]*$");
 
   StringBuffer out; // output buffer
 
@@ -219,7 +219,7 @@ public class StockholmFile extends AlignFile
     if (!r.search(nextLine()))
     {
       throw new IOException(MessageManager
-              .getString("exception.stockholm_invalid_format"));
+			    .getString("exception.stockholm_invalid_format") +" ("+r+")");
     }
     else
     {