X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=348b085fe01176e6b8d1b974caa64f0f4c35aaf7;hb=72baa5e02d3f71f1c0259072fdbd0b2bf8250e6c;hp=f4beccb42d77ccad84cbd77cd53c9c17d981fe59;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index f4beccb..348b085 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -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;
@@ -120,7 +125,19 @@ 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();
@@ -130,6 +147,7 @@ public class IdentifyFile
             System.err.println("File Identification failed!\n" + ex);
             return error;
         }
+
         return reply;
     }
 }