X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=6b32fe1a867d4214efd90b7a08e5943bfedbd72f;hb=4f24ef0848cf3c43ba0467f31fce1baa5c57aad5;hp=729a86040aab30234553b705008803d08c1d5da9;hpb=25db325e1dbc879140d059522af353a199045646;p=jalview.git

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 729a860..6b32fe1 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;
@@ -110,7 +115,7 @@ 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";
                     }
@@ -121,6 +126,12 @@ public class IdentifyFile
 
                     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();