JAL-1620 version bump and release notes

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

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index ed4001e..beb1385 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,27 +1,30 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
- * 
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * 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.
- *  
- * 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 
+ * 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.
+ *
+ * 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.io.IOException;
 
 /**
  * DOCUMENT ME!
- * 
+ *
  * @author $author$
  * @version $Revision$
  */
@@ -29,10 +32,10 @@ public class IdentifyFile
 {
   /**
    * Identify a datasource's file content.
-   * 
+   *
    * @note Do not use this method for stream sources - create a FileParse object
    *       instead.
-   * 
+   *
    * @param file
    *          DOCUMENT ME!
    * @param protocol
@@ -57,7 +60,9 @@ public class IdentifyFile
       emessage = e.getMessage();
     }
     if (parser != null)
+    {
       return parser.errormessage;
+    }
     return emessage;
   }
 
@@ -70,7 +75,7 @@ public class IdentifyFile
   /**
    * Identify contents of source, closing it or resetting source to start
    * afterwards.
-   * 
+   *
    * @param source
    * @param closeSource
    * @return filetype string
@@ -131,11 +136,11 @@ public class IdentifyFile
 
           break;
         }
-        
+
         if ((data.indexOf("<") > -1))
         {
           reply = "RNAML";
-          
+
           break;
         }
 
@@ -166,8 +171,7 @@ public class IdentifyFile
 
           break;
         }
-        
-        
+
         else if (data.indexOf(">") > -1)
         {
           // FASTA, PIR file or BLC file
@@ -190,17 +194,23 @@ 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
@@ -259,18 +269,24 @@ public class IdentifyFile
           reply = "PDB";
           break;
         }
+        else if (data.matches("\\s*\\d+\\s+\\d+\\s*"))
+        {
+          reply = PhylipFile.FILE_DESC;
+          break;
+        }
+
         /*
          * // TODO comment out SimpleBLAST identification for Jalview 2.4.1 else
          * if (!lineswereskipped && data.indexOf("BLAST")<4) { reply =
          * "SimpleBLAST"; break;
-         * 
+         *
          * } // end comments for Jalview 2.4.1
          */
         else if (!lineswereskipped && data.charAt(0) != '*'
                 && data.charAt(0) != ' '
                 && data.indexOf(":") < data.indexOf(",")) // &&
-        // data.indexOf(",")<data.indexOf(",",
-        // data.indexOf(",")))
+          // data.indexOf(",")<data.indexOf(",",
+          // data.indexOf(",")))
         {
           // file looks like a concise JNet file
           reply = "JnetFile";
@@ -296,7 +312,7 @@ public class IdentifyFile
     if (length == 0)
     {
       System.err
-              .println("File Identification failed! - Empty file was read.");
+      .println("File Identification failed! - Empty file was read.");
       return "EMPTY DATA FILE";
     }
     return reply;
@@ -304,7 +320,6 @@ public class IdentifyFile
 
   public static void main(String[] args)
   {
-        
     for (int i = 0; args != null && i < args.length; i++)
     {
       IdentifyFile ider = new IdentifyFile();