Dont add group if seqs not found

[jalview.git] / src / jalview / io / IdentifyFile.java

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