X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=e97ec40941ff4061ce7e2718535ac750c08f29dc;hb=a7bec763a3e4f17a549115f8f9f19ee4c742c26b;hp=729a86040aab30234553b705008803d08c1d5da9;hpb=25db325e1dbc879140d059522af353a199045646;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 729a860..e97ec40 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
@@ -39,30 +39,35 @@ public class IdentifyFile
      *
      * @return DOCUMENT ME!
      */
-    public static String Identify(String file, String protocol)
+    public String Identify(String file, String protocol)
     {
         String reply = "PFAM";
         String error =  "FILE NOT FOUND";
-
         try
         {
             BufferedReader reader = null;
 
-            if (protocol.equalsIgnoreCase("File"))
+            if (protocol.equals(AppletFormatAdapter.FILE))
             {
-                reader = new BufferedReader(new FileReader(file));
+              reader = new BufferedReader(new FileReader(file));
             }
-            else if (protocol.equalsIgnoreCase("URL"))
+            else if (protocol.equals(AppletFormatAdapter.URL))
             {
-                error = "URL NOT FOUND";
-                URL url = new URL(file);
-                reader = new BufferedReader(new InputStreamReader(
-                            url.openStream()));
+              error = "URL NOT FOUND";
+              URL url = new URL(file);
+              reader = new BufferedReader(new InputStreamReader(
+                  url.openStream()));
 
             }
-            else if (protocol.equalsIgnoreCase("Paste"))
+            else if (protocol.equals(AppletFormatAdapter.PASTE))
+            {
+              reader = new BufferedReader(new StringReader(file));
+            }
+            else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
             {
-                reader = new BufferedReader(new StringReader(file));
+              java.io.InputStream is = getClass().getResourceAsStream("/" +
+                  file);
+              reader = new BufferedReader(new java.io.InputStreamReader(is));
             }
 
             String data;
@@ -71,6 +76,13 @@ public class IdentifyFile
             {
                 data = data.toUpperCase();
 
+                if ( (data.indexOf("# STOCKHOLM") > -1))
+                {
+                  reply = "STH";
+
+                  break;
+                }
+
                 if ((data.indexOf("#") == 0) || (data.length() < 1))
                 {
                     continue;
@@ -116,11 +128,35 @@ public class IdentifyFile
                     }
                     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)
+                  {
+                    reply = "PDB";
+                    break;
+                  }
+                  else if (data.indexOf(":") < data.indexOf(",")) //  && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))
+                  {
+                    // file looks like a concise JNet file
+                    reply = "JnetFile";
+                    break;
+                  }
             }
 
             reader.close();
@@ -130,6 +166,7 @@ public class IdentifyFile
             System.err.println("File Identification failed!\n" + ex);
             return error;
         }
+
         return reply;
     }
 }