X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=08d4dca897efd371f81db835f045e782354280b1;hb=ad5029edaf36ceaafb4e269f2e00b0e1e0d7ffc4;hp=d30ed202e8ad00ef01e8bd49914cf5e8a7211036;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index d30ed20..08d4dca 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,24 +1,26 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
 import java.io.*;
-import java.net.*;
 
 /**
  * DOCUMENT ME!
@@ -133,6 +135,13 @@ public class IdentifyFile
           break;
         }
 
+        if ((data.indexOf("<") > -1))
+        {
+          reply = "RNAML";
+
+          break;
+        }
+
         if ((data.length() < 1) || (data.indexOf("#") == 0))
         {
           lineswereskipped = true;
@@ -160,6 +169,7 @@ public class IdentifyFile
 
           break;
         }
+
         else if (data.indexOf(">") > -1)
         {
           // FASTA, PIR file or BLC file
@@ -182,17 +192,23 @@ public class IdentifyFile
             // Is this a single line BLC file?
             String data1 = source.nextLine();
             String data2 = source.nextLine();
+            int c1;
             if (checkPIR)
             {
               starterm = (data1 != null && data1.indexOf("*") > -1)
                       || (data2 != null && data2.indexOf("*") > -1);
             }
-            if (data2 != null && data.indexOf("*") > -1)
+            if (data2 != null && (c1 = data.indexOf("*")) > -1)
             {
-              if (data.indexOf("*") == data2.indexOf("*"))
+              if (c1 == 0 && c1 == data2.indexOf("*"))
               {
                 reply = "BLC";
               }
+              else
+              {
+                reply = "FASTA"; // possibly a bad choice - may be recognised as
+                                 // PIR
+              }
               // otherwise can still possibly be a PIR file
             }
             else