X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=01282ea1f353930f03d92ed64d728c30b8f7c401;hb=6a44f113099e7ee83deada4d8426cd98757c2425;hp=348b085fe01176e6b8d1b974caa64f0f4c35aaf7;hpb=a6afc82877599e6ad2c52f01249c36338f251983;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 348b085..01282ea 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
@@ -76,6 +76,13 @@ public class IdentifyFile
             {
                 data = data.toUpperCase();
 
+                if ( (data.indexOf("# STOCKHOLM") > -1))
+                {
+                  reply = "STH";
+
+                  break;
+                }
+
                 if ((data.indexOf("#") == 0) || (data.length() < 1))
                 {
                     continue;
@@ -115,19 +122,31 @@ public class IdentifyFile
                     // could be BLC file, read next line to confirm
                     data = reader.readLine();
 
-                    if (data.indexOf(">") > -1 || data.indexOf("*") >-1 )
+                    if (data.indexOf(">") > -1)
                     {
                         reply = "BLC";
                     }
                     else
                     {
+                      //Is this a single line BLC file?
+                      reader.readLine();
+                      String data2 = reader.readLine();
+                      if ( data2 != null
+                           && data.indexOf("*")>-1
+                           && data.indexOf("*")==data2.indexOf("*"))
+                      {
+                        reply = "BLC";
+                      }
+                      else
+                      {
                         reply = "FASTA";
+                      }
                     }
 
                     break;
                   }
-                  else if (data.indexOf("HEADER") > -1 ||
-                           data.indexOf("ATOM") > -1)
+                  else if (data.indexOf("HEADER") == 0 ||
+                           data.indexOf("ATOM") == 0)
                   {
                     reply = "PDB";
                     break;