X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=9a248e5abe40694c229844e40d6ec84c9e00889a;hb=fbb18baad3919cbf94fcb5159bbd5269d6af18b4;hp=dbee007fd4b5289f88228d71db3e61c4416f22ab;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index dbee007..9a248e5 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.equals("File"))
+            if (protocol.equals(AppletFormatAdapter.FILE))
             {
-                reader = new BufferedReader(new FileReader(file));
+              reader = new BufferedReader(new FileReader(file));
             }
-            else if (protocol.equals("URL"))
+            else if (protocol.equals(AppletFormatAdapter.URL))
             {
-                reply = "URL NOT FOUND";
+              error = "URL NOT FOUND";
+              URL url = new URL(file);
+              reader = new BufferedReader(new InputStreamReader(
+                  url.openStream()));
 
-                URL url = new URL(file);
-                reader = new BufferedReader(new InputStreamReader(
-                            url.openStream()));
-                reply = "error";
             }
-            else if (protocol.equals("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;
@@ -110,7 +122,7 @@ public class IdentifyFile
                     // could be BLC file, read next line to confirm
                     data = reader.readLine();
 
-                    if (data.indexOf(">") > -1)
+                    if (data.indexOf(">") > -1 || data.indexOf("*") >-1 )
                     {
                         reply = "BLC";
                     }
@@ -120,7 +132,19 @@ public class IdentifyFile
                     }
 
                     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();
@@ -128,6 +152,7 @@ public class IdentifyFile
         catch (Exception ex)
         {
             System.err.println("File Identification failed!\n" + ex);
+            return error;
         }
 
         return reply;