/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
/**
* 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!
+ * 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 {
+ try
+ {
parser = new FileParse(file, protocol);
- if (parser.isValid()) {
+ if (parser.isValid())
+ {
return Identify(parser);
}
- } catch (Exception e) {
+ } catch (Exception e)
+ {
System.err.println("Error whilst identifying");
e.printStackTrace(System.err);
emessage = e.getMessage();
}
- if (parser!=null)
+ 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
+
+ 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.
+ * 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) {
+ 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 {
+ 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)
+ while ((data = source.nextLine()) != null)
{
- length+=data.length();
+ length += data.length();
if (!lineswereskipped)
{
- for (int i=0;!isBinary && i<data.length(); i++)
+ 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
+ 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)
+ // 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.
+ 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))
+ if ((data.indexOf("# STOCKHOLM") > -1))
{
reply = "STH";
if ((data.length() < 1) || (data.indexOf("#") == 0))
{
- lineswereskipped=true;
+ lineswereskipped = true;
continue;
}
break;
}
- if ( (data.indexOf("//") == 0) ||
- ( (data.indexOf("!!") > -1) &&
- (data.indexOf("!!") < data.indexOf(
- "_MULTIPLE_ALIGNMENT "))))
+ if ((data.indexOf("//") == 0)
+ || ((data.indexOf("!!") > -1) && (data.indexOf("!!") < data
+ .indexOf("_MULTIPLE_ALIGNMENT "))))
{
reply = "MSF";
break;
}
- else if ( (data.indexOf(">P1;") > -1) ||
- (data.indexOf(">DL;") > -1))
+ else if ((data.indexOf(">P1;") > -1) || (data.indexOf(">DL;") > -1))
{
reply = "PIR";
}
else
{
- //Is this a single line BLC file?
+ // Is this a single line BLC file?
source.nextLine();
String data2 = source.nextLine();
- if (data2 != null
- && data.indexOf("*") > -1
- && data.indexOf("*") == data2.indexOf("*"))
+ if (data2 != null && data.indexOf("*") > -1
+ && data.indexOf("*") == data2.indexOf("*"))
{
reply = "BLC";
}
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.
+ reply = "FASTA";
+ // TODO : AMSA File is indicated if there is annotation in the
+ // FASTA file - but FASTA will automatically generate this at the
+ // mo.
}
}
break;
}
- else if (data.indexOf("HEADER") == 0 ||
- data.indexOf("ATOM") == 0)
+ else if (data.indexOf("HEADER") == 0 || data.indexOf("ATOM") == 0)
{
reply = "PDB";
break;
}
- else if (!lineswereskipped
- && data.charAt(0)!='*'
- && data.charAt(0)!=' '
- && data.indexOf(":") < data.indexOf(",")) // && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))
+ 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
+
+ lineswereskipped = true; // this means there was some junk before any
+ // key file signature
}
- if (closeSource) {
+ if (closeSource)
+ {
source.close();
- } else {
+ }
+ else
+ {
source.reset(); // so the file can be parsed from the beginning again.
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
System.err.println("File Identification failed!\n" + ex);
return source.errormessage;
}
- if (length==0)
+ if (length == 0)
{
- System.err.println("File Identification failed! - Empty file was read.");
+ 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++)
+
+ 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);
+ System.out.println("Type of " + args[i] + " is " + type);
}
- if (args==null || args.length==0)
+ if (args == null || args.length == 0)
{
System.err.println("Usage: <Filename> [<Filename> ...]");
}
git://source.jalview.org / jalview.git / blobdiff