/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * 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 2
+ * as published by the Free Software Foundation, either version 3
* 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import java.io.*;
-import java.net.*;
+import java.io.IOException;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
public class IdentifyFile
{
+ public static final String FeaturesFile = "GFF or Jalview features";
+
/**
* Identify a datasource's file content.
- *
+ *
* @note Do not use this method for stream sources - create a FileParse object
* instead.
- *
+ *
* @param file
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param protocol
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @return ID String
*/
- public String Identify(String file, String protocol)
+ public String identify(String file, String protocol)
{
String emessage = "UNIDENTIFIED FILE PARSING ERROR";
FileParse parser = null;
parser = new FileParse(file, protocol);
if (parser.isValid())
{
- return Identify(parser);
+ return identify(parser);
}
} catch (Exception e)
{
emessage = e.getMessage();
}
if (parser != null)
+ {
return parser.errormessage;
+ }
return emessage;
}
- public String Identify(FileParse source)
+ public String identify(FileParse source)
{
- return Identify(source, true); // preserves original behaviour prior to
- // version 2.3
+ 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)
+ public String identify(FileParse source, boolean closeSource)
{
String reply = "PFAM";
String data;
- int length = 0;
+ int bytesRead = 0;
+ int trimmedLength = 0;
boolean lineswereskipped = false;
boolean isBinary = false; // true if length is non-zero and non-printable
- // characters are encountered
+ // characters are encountered
try
{
if (!closeSource)
}
while ((data = source.nextLine()) != null)
{
- length += data.length();
+ bytesRead += data.length();
+ trimmedLength += data.trim().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
+ // excluding CR, LF, tab,DEL and ^E
+ // for certain blast ids
}
}
if (isBinary)
}
data = data.toUpperCase();
- if ((data.indexOf("# STOCKHOLM") > -1))
+ if (data.startsWith("##GFF-VERSION"))
+ {
+ // GFF - possibly embedded in a Jalview features file!
+ reply = FeaturesFile;
+ break;
+ }
+ if (looksLikeFeatureData(data))
+ {
+ reply = FeaturesFile;
+ break;
+ }
+ if (data.indexOf("# STOCKHOLM") > -1)
{
reply = "STH";
+ break;
+ }
+ // if (data.indexOf(">") > -1)
+ if (data.startsWith(">"))
+ {
+ // 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();
+ int c1;
+ if (checkPIR)
+ {
+ starterm = (data1 != null && data1.indexOf("*") > -1)
+ || (data2 != null && data2.indexOf("*") > -1);
+ }
+ if (data2 != null && (c1 = data.indexOf("*")) > -1)
+ {
+ if (c1 == 0 && c1 == data2.indexOf("*"))
+ {
+ reply = "BLC";
+ }
+ else
+ {
+ reply = "FASTA"; // possibly a bad choice - may be recognised as
+ // PIR
+ }
+ // 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;
}
+ if ((data.indexOf("<") > -1)) // possible Markup Language data i.e HTML,
+ // RNAML, XML
+ {
+ // FIXME this is nuts - it consumes the rest of the file if no match
+ boolean identified = false;
+ do
+ {
+ if (data.matches("<(?i)html(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
+ {
+ reply = HtmlFile.FILE_DESC;
+ identified = true;
+ break;
+ }
+
+ if (data.matches("<(?i)rnaml (\"[^\"]*\"|'[^']*'|[^'\">])*>"))
+ {
+ reply = "RNAML";
+ identified = true;
+ break;
+ }
+ } while ((data = source.nextLine()) != null);
+ if (identified)
+ {
+ break;
+ }
+ if (data == null)
+ {
+ break;
+ }
+ }
+
+ if (data.indexOf("{\"") > -1)
+ {
+ reply = JSONFile.FILE_DESC;
+ break;
+ }
if ((data.length() < 1) || (data.indexOf("#") == 0))
{
lineswereskipped = true;
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 = source.nextLine();
-
- if (data.indexOf(">") > -1)
- {
- reply = "BLC";
- }
- else
- {
- // Is this a single line BLC file?
- source.nextLine();
- String data2 = source.nextLine();
- 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.
- }
- }
- break;
- }
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 (data.matches("\\s*\\d+\\s+\\d+\\s*"))
{
- // file looks like a concise JNet file
- reply = "JnetFile";
+ reply = PhylipFile.FILE_DESC;
break;
}
+ else
+ {
+ if (!lineswereskipped && looksLikeJnetData(data))
+ {
+ reply = "JnetFile";
+ break;
+ }
+ }
lineswereskipped = true; // this means there was some junk before any
- // key file signature
+ // key file signature
}
if (closeSource)
{
}
else
{
- source.reset(); // so the file can be parsed from the beginning again.
+ source.reset(bytesRead); // so the file can be parsed from the mark
}
} catch (Exception ex)
{
System.err.println("File Identification failed!\n" + ex);
return source.errormessage;
}
- if (length == 0)
+ if (trimmedLength == 0)
{
System.err
.println("File Identification failed! - Empty file was read.");
return reply;
}
+ /**
+ * Returns true if the data appears to be Jnet concise annotation format
+ *
+ * @param data
+ * @return
+ */
+ protected boolean looksLikeJnetData(String data)
+ {
+ char firstChar = data.charAt(0);
+ int colonPos = data.indexOf(":");
+ int commaPos = data.indexOf(",");
+ boolean isJnet = firstChar != '*' && firstChar != ' ' && colonPos > -1
+ && commaPos > -1 && colonPos < commaPos;
+ // && data.indexOf(",")<data.indexOf(",", data.indexOf(","))) / ??
+ return isJnet;
+ }
+
+ /**
+ * Returns true if the data has at least 6 tab-delimited fields _and_
+ * fields 4 and 5 are integer (start/end)
+ * @param data
+ * @return
+ */
+ protected boolean looksLikeFeatureData(String data)
+ {
+ if (data == null)
+ {
+ return false;
+ }
+ String[] columns = data.split("\t");
+ if (columns.length < 6) {
+ return false;
+ }
+ for (int col = 3; col < 5; col++)
+ {
+ try {
+ Integer.parseInt(columns[col]);
+ } catch (NumberFormatException e) {
+ return false;
+ }
+ }
+ return true;
+ }
+
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);
+ String type = ider.identify(args[i], AppletFormatAdapter.FILE);
System.out.println("Type of " + args[i] + " is " + type);
}
if (args == null || args.length == 0)
git://source.jalview.org / jalview.git / blobdiff