/*
- * 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
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 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
+ * 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/>.
+ *
+ * You should have received a copy of the GNU General Public License
+ * 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 GFF3File = "GFF v2 or v3";
+
/**
* 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
emessage = e.getMessage();
}
if (parser != null)
+ {
return parser.errormessage;
+ }
return emessage;
}
/**
* Identify contents of source, closing it or resetting source to start
* afterwards.
- *
+ *
* @param source
* @param closeSource
* @return filetype string
}
while ((data = source.nextLine()) != null)
{
- length += data.length();
+ length += data.trim().length();
if (!lineswereskipped)
{
for (int i = 0; !isBinary && i < data.length(); i++)
}
data = data.toUpperCase();
- if ((data.indexOf("# STOCKHOLM") > -1))
- {
- reply = "STH";
-
- break;
- }
-
- if ((data.indexOf(">") > -1))
- {
- reply = "RNAML";
- System.out.println("This is a RNAML format");
- 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 "))))
+ if (data.startsWith("##GFF-VERSION"))
{
- reply = "MSF";
-
+ reply = GFF3File;
break;
}
- else if (data.indexOf("CLUSTAL") > -1)
+ if (data.indexOf("# STOCKHOLM") > -1)
{
- reply = "CLUSTAL";
-
+ reply = "STH";
break;
}
-
-
- else if (data.indexOf(">") > -1)
+ // if (data.indexOf(">") > -1)
+ if (data.startsWith(">"))
{
// FASTA, PIR file or BLC file
- boolean checkPIR = false,starterm=false;
+ boolean checkPIR = false, starterm = false;
if ((data.indexOf(">P1;") > -1) || (data.indexOf(">DL;") > -1))
{
// watch for PIR file attributes
// 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);
+ starterm = (data1 != null && data1.indexOf("*") > -1)
+ || (data2 != null && data2.indexOf("*") > -1);
}
- if (data2 != null && data.indexOf("*") > -1)
+ if (data2 != null && (c1 = data.indexOf("*")) > -1)
{
- if (data.indexOf("*") == data2.indexOf("*"))
+ 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
// TODO : AMSA File is indicated if there is annotation in the
// FASTA file - but FASTA will automatically generate this at the
// mo.
- if (!checkPIR) {
+ 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
+ // 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;
+ String dta = null;
if (!starterm)
{
- do {
- try {
+ do
+ {
+ try
+ {
dta = source.nextLine();
- } catch(IOException ex) {};
- if (dta!=null && dta.indexOf("*")>-1)
+ } catch (IOException ex)
+ {
+ }
+ ;
+ if (dta != null && dta.indexOf("*") > -1)
{
starterm = true;
}
- } while (dta!=null && !starterm);
+ } while (dta != null && !starterm);
}
if (starterm)
{
- reply="PIR";
+ reply = "PIR";
break;
- } else {
- reply="FASTA"; // probably a bad choice!
+ }
+ 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
+ {
+ 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.indexOf("{\"") > -1)
+ {
+ reply = JSONFile.FILE_DESC;
+ 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("HEADER") == 0 || data.indexOf("ATOM") == 0)
{
reply = "PDB";
break;
}
+ else if (data.matches("\\s*\\d+\\s+\\d+\\s*"))
+ {
+ reply = PhylipFile.FILE_DESC;
+ break;
+ }
+
/*
* // TODO comment out SimpleBLAST identification for Jalview 2.4.1 else
* if (!lineswereskipped && data.indexOf("BLAST")<4) { reply =
public static void main(String[] args)
{
-
+
for (int i = 0; args != null && i < args.length; i++)
{
IdentifyFile ider = new IdentifyFile();
git://source.jalview.org / jalview.git / blobdiff