/*\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
import java.net.*;\r
\r
\r
-public class IdentifyFile {\r
- public static String Identify(String file, String protocol) {\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class IdentifyFile\r
+{\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param file DOCUMENT ME!\r
+ * @param protocol DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String Identify(String file, String protocol)\r
+ {\r
String reply = "PFAM";\r
-\r
- try {\r
+ String error = "FILE NOT FOUND";\r
+ try\r
+ {\r
BufferedReader reader = null;\r
\r
- if (protocol.equals("File")) {\r
- reader = new BufferedReader(new FileReader(file));\r
+ if (protocol.equals(AppletFormatAdapter.FILE))\r
+ {\r
+ reader = new BufferedReader(new FileReader(file));\r
+ }\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
+\r
+ }\r
+ else if (protocol.equals(AppletFormatAdapter.PASTE))\r
+ {\r
+ reader = new BufferedReader(new StringReader(file));\r
}\r
- else if (protocol.equals("URL")) {\r
- reply = "URL NOT FOUND";\r
-\r
- URL url = new URL(file);\r
- reader = new BufferedReader(new InputStreamReader(\r
- url.openStream()));\r
- reply = "error";\r
- } else if (protocol.equals("Paste")) {\r
- reader = new BufferedReader(new StringReader(file));\r
+ else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))\r
+ {\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
- while ((data = reader.readLine()) != null) {\r
+ while ((data = reader.readLine()) != null)\r
+ {\r
data = data.toUpperCase();\r
\r
- if ((data.indexOf("#") == 0) || (data.length() < 1)) {\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
}\r
\r
- if (data.indexOf("PILEUP") > -1) {\r
+ if (data.indexOf("PILEUP") > -1)\r
+ {\r
reply = "PileUp";\r
\r
break;\r
if ((data.indexOf("//") == 0) ||\r
((data.indexOf("!!") > -1) &&\r
(data.indexOf("!!") < data.indexOf(\r
- "_MULTIPLE_ALIGNMENT ")))) {\r
+ "_MULTIPLE_ALIGNMENT "))))\r
+ {\r
reply = "MSF";\r
\r
break;\r
- } else if (data.indexOf("CLUSTAL") > -1) {\r
+ }\r
+ else if (data.indexOf("CLUSTAL") > -1)\r
+ {\r
reply = "CLUSTAL";\r
\r
break;\r
- } else if ((data.indexOf(">P1;") > -1) ||\r
- (data.indexOf(">DL;") > -1)) {\r
+ }\r
+ else if ((data.indexOf(">P1;") > -1) ||\r
+ (data.indexOf(">DL;") > -1))\r
+ {\r
reply = "PIR";\r
\r
break;\r
- } else if (data.indexOf(">") > -1) {\r
+ }\r
+ else if (data.indexOf(">") > -1)\r
+ {\r
// could be BLC file, read next line to confirm\r
data = reader.readLine();\r
\r
- if (data.indexOf(">") > -1) {\r
+ if (data.indexOf(">") > -1 || data.indexOf("*") >-1 )\r
+ {\r
reply = "BLC";\r
- } else {\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
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
System.err.println("File Identification failed!\n" + ex);\r
+ return error;\r
}\r
\r
return reply;\r