-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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
-* 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
-\r
-import java.net.*;\r
-\r
-\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 static 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.equals("File"))\r
- {\r
- reader = new BufferedReader(new FileReader(file));\r
- }\r
- else if (protocol.equals("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("Paste"))\r
- {\r
- reader = new BufferedReader(new StringReader(file));\r
- }\r
-\r
- String data;\r
-\r
- while ((data = reader.readLine()) != null)\r
- {\r
- data = data.toUpperCase();\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("//") == 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
- {\r
- reply = "CLUSTAL";\r
-\r
- break;\r
- }\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
- {\r
- // could be BLC file, read next line to confirm\r
- data = reader.readLine();\r
-\r
- if (data.indexOf(">") > -1)\r
- {\r
- reply = "BLC";\r
- }\r
- else\r
- {\r
- reply = "FASTA";\r
- }\r
-\r
- break;\r
- }\r
- }\r
-\r
- reader.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- System.err.println("File Identification failed!\n" + ex);\r
- return error;\r
- }\r
- return reply;\r
- }\r
-}\r
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+package jalview.io;
+
+import java.io.*;
+
+import java.net.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdentifyFile
+{
+ /**
+ * DOCUMENT ME!
+ *
+ * @param file DOCUMENT ME!
+ * @param protocol DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String Identify(String file, String protocol)
+ {
+ String reply = "PFAM";
+ String error = "FILE NOT FOUND";
+ try
+ {
+ BufferedReader reader = null;
+
+ if (protocol.equals(AppletFormatAdapter.FILE))
+ {
+ reader = new BufferedReader(new FileReader(file));
+ }
+ else if (protocol.equals(AppletFormatAdapter.URL))
+ {
+ error = "URL NOT FOUND";
+ URL url = new URL(file);
+ reader = new BufferedReader(new InputStreamReader(
+ url.openStream()));
+
+ }
+ else if (protocol.equals(AppletFormatAdapter.PASTE))
+ {
+ reader = new BufferedReader(new StringReader(file));
+ }
+ else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
+ {
+ java.io.InputStream is = getClass().getResourceAsStream("/" +
+ file);
+ reader = new BufferedReader(new java.io.InputStreamReader(is));
+ }
+
+ String data;
+
+ while ((data = reader.readLine()) != null)
+ {
+ data = data.toUpperCase();
+
+ if ( (data.indexOf("# STOCKHOLM") > -1))
+ {
+ reply = "STH";
+
+ break;
+ }
+
+ if ((data.indexOf("#") == 0) || (data.length() < 1))
+ {
+ continue;
+ }
+
+ if (data.indexOf("PILEUP") > -1)
+ {
+ reply = "PileUp";
+
+ break;
+ }
+
+ if ((data.indexOf("//") == 0) ||
+ ((data.indexOf("!!") > -1) &&
+ (data.indexOf("!!") < data.indexOf(
+ "_MULTIPLE_ALIGNMENT "))))
+ {
+ reply = "MSF";
+
+ break;
+ }
+ else if (data.indexOf("CLUSTAL") > -1)
+ {
+ reply = "CLUSTAL";
+
+ break;
+ }
+ else if ((data.indexOf(">P1;") > -1) ||
+ (data.indexOf(">DL;") > -1))
+ {
+ reply = "PIR";
+
+ break;
+ }
+ else if (data.indexOf(">") > -1)
+ {
+ // could be BLC file, read next line to confirm
+ data = reader.readLine();
+
+ if (data.indexOf(">") > -1 || data.indexOf("*") >-1 )
+ {
+ reply = "BLC";
+ }
+ else
+ {
+ reply = "FASTA";
+ }
+
+ 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();
+ }
+ catch (Exception ex)
+ {
+ System.err.println("File Identification failed!\n" + ex);
+ return error;
+ }
+
+ return reply;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff