-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
- * AM Waterhouse\r
- *******************/\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
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.io;\r
\r
import java.io.*;\r
import java.net.*;\r
\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
public class IdentifyFile\r
{\r
- public static String Identify(String file, String protocol)\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
- try{\r
-\r
+ String error = "FILE NOT FOUND";\r
+ try\r
+ {\r
BufferedReader reader = null;\r
\r
- if(protocol.equals("File"))\r
+ if (protocol.equals(AppletFormatAdapter.FILE))\r
+ {\r
reader = new BufferedReader(new FileReader(file));\r
-\r
- else if (protocol.equals("URL"))\r
+ }\r
+ else if (protocol.equals(AppletFormatAdapter.URL))\r
{\r
- reply = "URL NOT FOUND";\r
+ error = "URL NOT FOUND";\r
URL url = new URL(file);\r
- reader = new BufferedReader(new InputStreamReader( url.openStream() ) );\r
- reply = "error";\r
- }\r
- else if( protocol.equals("Paste"))\r
- reader = new BufferedReader( new StringReader(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(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
- while( (data=reader.readLine())!=null)\r
+\r
+ while ( (data = reader.readLine()) != null)\r
{\r
data = data.toUpperCase();\r
- if(data.indexOf("#")==0 || data.length()<1)\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
+ }\r
+\r
+ if (data.indexOf("PILEUP") > -1)\r
+ {\r
+ reply = "PileUp";\r
+\r
+ break;\r
+ }\r
\r
- if(data.indexOf("PILEUP")>-1)\r
+ if ( (data.indexOf("//") == 0) ||\r
+ ( (data.indexOf("!!") > -1) &&\r
+ (data.indexOf("!!") < data.indexOf(\r
+ "_MULTIPLE_ALIGNMENT "))))\r
{\r
reply = "MSF";\r
+\r
break;\r
}\r
- else if(data.indexOf("CLUSTAL")>-1)\r
+ else if (data.indexOf("CLUSTAL") > -1)\r
{\r
reply = "CLUSTAL";\r
+\r
break;\r
}\r
- else if(data.indexOf(">P1;")>-1 || data.indexOf(">DL;")>-1)\r
+ else if ( (data.indexOf(">P1;") > -1) ||\r
+ (data.indexOf(">DL;") > -1))\r
{\r
reply = "PIR";\r
+\r
break;\r
}\r
- else if(data.indexOf(">")>-1)\r
+ else if (data.indexOf(">") > -1)\r
{\r
// could be BLC file, read next line to confirm\r
data = reader.readLine();\r
- if(data.indexOf(">")>-1)\r
+\r
+ if (data.indexOf(">") > -1)\r
+ {\r
reply = "BLC";\r
+ }\r
else\r
- reply = "FASTA";\r
+ {\r
+ //Is this a single line BLC file?\r
+ reader.readLine();\r
+ String data2 = reader.readLine();\r
+ if (data2 != null\r
+ && data.indexOf("*") > -1\r
+ && data.indexOf("*") == data2.indexOf("*"))\r
+ {\r
+ reply = "BLC";\r
+ }\r
+ else\r
+ {\r
+ reply = "FASTA";\r
+ }\r
+ }\r
\r
- break;\r
+ break;\r
+ }\r
+ else if (data.indexOf("HEADER") == 0 ||\r
+ data.indexOf("ATOM") == 0)\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
}\r
- catch(Exception ex){\r
- System.err.println("File Identification failed!"); ex.printStackTrace();}\r
+ catch (Exception ex)\r
+ {\r
+ System.err.println("File Identification failed!\n" + ex);\r
+ return error;\r
+ }\r
\r
return reply;\r
}\r
-\r
-\r
}\r
git://source.jalview.org / jalview.git / blobdiff