/*
- * 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
*/
public String Identify(String file, String protocol)
{
+ String emessage = "UNIDENTIFIED FILE PARSING ERROR";
FileParse parser = null;
try {
parser = new FileParse(file, protocol);
} catch (Exception e) {
System.err.println("Error whilst identifying");
e.printStackTrace(System.err);
+ emessage = e.getMessage();
}
if (parser!=null)
return parser.errormessage;
- return "UNIDENTIFIED FILE PARSING ERROR";
+ return emessage;
}
public String Identify(FileParse source) {
return Identify(source, true); // preserves original behaviour prior to version 2.3
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))
}
else
{
- reply = "FASTA";
+ 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 ||
reply = "JnetFile";
break;
}
- else if (source.inFile!=null)
- {
- String fileStr=source.inFile.getName();
- // possibly a Jalview archive.
- if (fileStr.lastIndexOf(".jar")>-1 || fileStr.lastIndexOf(".zip")>-1)
- {
- reply = "Jalview";
- }
- } else if (data.startsWith("PK")) {
- reply="Jalview"; // archive.
- break;
- }
lineswereskipped=true; // this means there was some junk before any key file signature
}
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> ...]");
+ }
+ }
}