/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public static String Identify(String file, String protocol)\r
+ public String Identify(String file, String protocol)\r
{\r
String reply = "PFAM";\r
String error = "FILE NOT FOUND";\r
-\r
try\r
{\r
BufferedReader reader = null;\r
\r
- if (protocol.equalsIgnoreCase("File"))\r
+ if (protocol.equals(AppletFormatAdapter.FILE))\r
{\r
- reader = new BufferedReader(new FileReader(file));\r
+ reader = new BufferedReader(new FileReader(file));\r
}\r
- else if (protocol.equalsIgnoreCase("URL"))\r
+ else if (protocol.equals(AppletFormatAdapter.URL))\r
{\r
- error = "URL NOT FOUND";\r
- URL url = new URL(file);\r
- reader = new BufferedReader(new InputStreamReader(\r
- url.openStream()));\r
+ error = "URL NOT FOUND";\r
+ URL url = new URL(file);\r
+ reader = new BufferedReader(new InputStreamReader(\r
+ url.openStream()));\r
\r
}\r
- else if (protocol.equalsIgnoreCase("Paste"))\r
+ else if (protocol.equals(AppletFormatAdapter.PASTE))\r
+ {\r
+ reader = new BufferedReader(new StringReader(file));\r
+ }\r
+ else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))\r
{\r
- reader = new BufferedReader(new StringReader(file));\r
+ java.io.InputStream is = getClass().getResourceAsStream("/" +\r
+ file);\r
+ reader = new BufferedReader(new java.io.InputStreamReader(is));\r
}\r
\r
String data;\r
{\r
data = data.toUpperCase();\r
\r
+ if ( (data.indexOf("# STOCKHOLM") > -1))\r
+ {\r
+ reply = "STH";\r
+\r
+ break;\r
+ }\r
+\r
if ((data.indexOf("#") == 0) || (data.length() < 1))\r
{\r
continue;\r
// could be BLC file, read next line to confirm\r
data = reader.readLine();\r
\r
- if (data.indexOf(">") > -1 || data.indexOf("*") >-1 )\r
+ if (data.indexOf(">") > -1)\r
{\r
reply = "BLC";\r
}\r
+ //Is this a single line BLC file?\r
+ data = reader.readLine();\r
+ if(data!=null && data.length()==1)\r
+ {\r
+ reply = "BLC";\r
+ }\r
else\r
{\r
reply = "FASTA";\r
}\r
\r
break;\r
- }\r
+ }\r
+ else if (data.indexOf("HEADER") > -1 ||\r
+ data.indexOf("ATOM") > -1)\r
+ {\r
+ reply = "PDB";\r
+ break;\r
+ }\r
+ else if (data.indexOf(":") < data.indexOf(",")) // && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))\r
+ {\r
+ // file looks like a concise JNet file\r
+ reply = "JnetFile";\r
+ break;\r
+ }\r
}\r
\r
reader.close();\r
System.err.println("File Identification failed!\n" + ex);\r
return error;\r
}\r
+\r
return reply;\r
}\r
}\r