-/*\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.equalsIgnoreCase("File"))\r
- {\r
- reader = new BufferedReader(new FileReader(file));\r
- }\r
- else if (protocol.equalsIgnoreCase("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.equalsIgnoreCase("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 || 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 (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.io;
+
+import java.io.*;
+import java.net.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdentifyFile
+{
+ /**
+ * Identify a datasource's file content.
+ *
+ * @note Do not use this method for stream sources - create a FileParse object
+ * instead.
+ *
+ * @param file
+ * DOCUMENT ME!
+ * @param protocol
+ * DOCUMENT ME!
+ * @return ID String
+ */
+ public String Identify(String file, String protocol)
+ {
+ String emessage = "UNIDENTIFIED FILE PARSING ERROR";
+ FileParse parser = null;
+ try
+ {
+ parser = new FileParse(file, protocol);
+ if (parser.isValid())
+ {
+ return Identify(parser);
+ }
+ } catch (Exception e)
+ {
+ System.err.println("Error whilst identifying");
+ e.printStackTrace(System.err);
+ emessage = e.getMessage();
+ }
+ if (parser != null)
+ return parser.errormessage;
+ return emessage;
+ }
+
+ public String Identify(FileParse source)
+ {
+ return Identify(source, true); // preserves original behaviour prior to
+ // version 2.3
+ }
+
+ /**
+ * Identify contents of source, closing it or resetting source to start
+ * afterwards.
+ *
+ * @param source
+ * @param closeSource
+ * @return filetype string
+ */
+ public String Identify(FileParse source, boolean closeSource)
+ {
+ String reply = "PFAM";
+ String data;
+ int length = 0;
+ boolean lineswereskipped = false;
+ boolean isBinary = false; // true if length is non-zero and non-printable
+ // characters are encountered
+ try
+ {
+ if (!closeSource)
+ {
+ source.mark();
+ }
+ while ((data = source.nextLine()) != null)
+ {
+ length += data.length();
+ if (!lineswereskipped)
+ {
+ for (int i = 0; !isBinary && i < data.length(); i++)
+ {
+ char c = data.charAt(i);
+ isBinary = (c < 32 && c != '\t' && c != '\n' && c != '\r'
+ && c != 5 && c != 27); // nominal binary character filter
+ // excluding CR, LF, tab,DEL and ^E
+ // for certain blast ids
+ }
+ }
+ if (isBinary)
+ {
+ // jar files are special - since they contain all sorts of random
+ // characters.
+ if (source.inFile != null)
+ {
+ String fileStr = source.inFile.getName();
+ // possibly a Jalview archive.
+ if (fileStr.lastIndexOf(".jar") > -1
+ || fileStr.lastIndexOf(".zip") > -1)
+ {
+ reply = "Jalview";
+ }
+ }
+ if (!lineswereskipped && data.startsWith("PK"))
+ {
+ reply = "Jalview"; // archive.
+ break;
+ }
+ }
+ data = data.toUpperCase();
+
+ if ((data.indexOf("# STOCKHOLM") > -1))
+ {
+ reply = "STH";
+
+ break;
+ }
+
+ if ((data.length() < 1) || (data.indexOf("#") == 0))
+ {
+ lineswereskipped = true;
+ 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(">") > -1)
+ {
+ // FASTA, PIR file or BLC file
+ boolean checkPIR = false,starterm=false;
+ if ((data.indexOf(">P1;") > -1) || (data.indexOf(">DL;") > -1))
+ {
+ // watch for PIR file attributes
+ checkPIR = true;
+ reply = "PIR";
+ }
+ // could also be BLC file, read next line to confirm
+ data = source.nextLine();
+
+ if (data.indexOf(">") > -1)
+ {
+ reply = "BLC";
+ }
+ else
+ {
+ // Is this a single line BLC file?
+ String data1 = source.nextLine();
+ String data2 = source.nextLine();
+ if (checkPIR)
+ {
+ starterm = (data1!=null && data1.indexOf("*")>-1) || (data2!=null && data2.indexOf("*")>-1);
+ }
+ if (data2 != null && data.indexOf("*") > -1)
+ {
+ if (data.indexOf("*") == data2.indexOf("*"))
+ {
+ reply = "BLC";
+ }
+ // otherwise can still possibly be a PIR file
+ }
+ else
+ {
+ reply = "FASTA";
+ // TODO : AMSA File is indicated if there is annotation in the
+ // FASTA file - but FASTA will automatically generate this at the
+ // mo.
+ if (!checkPIR) {
+ break;
+ }
+ }
+ }
+ // final check for PIR content. require
+ // >P1;title\n<blah>\nterminated sequence to occur at least once.
+
+ // TODO the PIR/fasta ambiguity may be the use case that is needed to have
+ // a 'Parse as type XXX' parameter for the applet/application.
+ if (checkPIR)
+ {
+ String dta=null;
+ if (!starterm)
+ {
+ do {
+ try {
+ dta = source.nextLine();
+ } catch(IOException ex) {};
+ if (dta!=null && dta.indexOf("*")>-1)
+ {
+ starterm = true;
+ }
+ } while (dta!=null && !starterm);
+ }
+ if (starterm)
+ {
+ reply="PIR";
+ break;
+ } else {
+ reply="FASTA"; // probably a bad choice!
+ }
+ }
+ // read as a FASTA (probably)
+ break;
+ }
+ else if (data.indexOf("HEADER") == 0 || data.indexOf("ATOM") == 0)
+ {
+ reply = "PDB";
+ break;
+ }
+ /*
+ * // TODO comment out SimpleBLAST identification for Jalview 2.4.1 else
+ * if (!lineswereskipped && data.indexOf("BLAST")<4) { reply =
+ * "SimpleBLAST"; break;
+ *
+ * } // end comments for Jalview 2.4.1
+ */
+ else if (!lineswereskipped && data.charAt(0) != '*'
+ && data.charAt(0) != ' '
+ && data.indexOf(":") < data.indexOf(",")) // &&
+ // data.indexOf(",")<data.indexOf(",",
+ // data.indexOf(",")))
+ {
+ // file looks like a concise JNet file
+ reply = "JnetFile";
+ break;
+ }
+
+ lineswereskipped = true; // this means there was some junk before any
+ // key file signature
+ }
+ if (closeSource)
+ {
+ source.close();
+ }
+ else
+ {
+ source.reset(); // so the file can be parsed from the beginning again.
+ }
+ } catch (Exception ex)
+ {
+ System.err.println("File Identification failed!\n" + ex);
+ return source.errormessage;
+ }
+ if (length == 0)
+ {
+ System.err
+ .println("File Identification failed! - Empty file was read.");
+ return "EMPTY DATA FILE";
+ }
+ return reply;
+ }
+
+ public static void main(String[] args)
+ {
+ for (int i = 0; args != null && i < args.length; i++)
+ {
+ IdentifyFile ider = new IdentifyFile();
+ String type = ider.Identify(args[i], AppletFormatAdapter.FILE);
+ System.out.println("Type of " + args[i] + " is " + type);
+ }
+ if (args == null || args.length == 0)
+ {
+ System.err.println("Usage: <Filename> [<Filename> ...]");
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff