X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FIdentifyFile.java;h=baee5314c0f4193245b0aecce67610eb108b0b1c;hb=a9177efb4097815d9a8031aa22700c61a7d6260a;hp=f1f51b15c845d921dbbddce67efbf9378630eacc;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index f1f51b1..baee531 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,99 +1,158 @@
/*
- * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import java.io.*;
-import java.net.*;
+import java.io.File;
+import java.io.IOException;
+import java.util.Locale;
+
+import jalview.bin.Console;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
public class IdentifyFile
{
+
+ private static final String XMLHEADER = "";
+
+ public FileFormatI identify(Object file, DataSourceType protocol)
+ throws FileFormatException
+ {
+ // BH 2018
+ return (file instanceof File ? identify((File) file, protocol)
+ : identify((String) file, protocol));
+
+ }
+
+ public FileFormatI identify(File file, DataSourceType sourceType)
+ throws FileFormatException
+ {
+ // BH 2018
+ String emessage = "UNIDENTIFIED FILE PARSING ERROR";
+ FileParse parser = null;
+ try
+ {
+ parser = new FileParse(file, sourceType);
+ if (parser.isValid())
+ {
+ return identify(parser);
+ }
+ } catch (Exception e)
+ {
+ Console.error("Error whilst identifying " + file, e);
+ emessage = e.getMessage();
+ }
+ if (parser != null)
+ {
+ throw new FileFormatException(parser.errormessage);
+ }
+ throw new FileFormatException(emessage);
+ }
+
/**
* 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
+ * @param sourceType
+ * @return
+ * @throws FileFormatException
*/
- public String Identify(String file, String protocol)
+ public FileFormatI identify(String file, DataSourceType sourceType)
+ throws FileFormatException
{
String emessage = "UNIDENTIFIED FILE PARSING ERROR";
FileParse parser = null;
try
{
- parser = new FileParse(file, protocol);
+ parser = new FileParse(file, sourceType);
if (parser.isValid())
{
- return Identify(parser);
+ return identify(parser);
}
} catch (Exception e)
{
- System.err.println("Error whilst identifying");
- e.printStackTrace(System.err);
+ Console.error("Error whilst identifying " + file, e);
emessage = e.getMessage();
}
if (parser != null)
- return parser.errormessage;
- return emessage;
+ {
+ throw new FileFormatException(parser.errormessage);
+ }
+ throw new FileFormatException(emessage);
}
- public String Identify(FileParse source)
+ public FileFormatI identify(FileParse source) throws FileFormatException
{
- return Identify(source, true); // preserves original behaviour prior to
- // version 2.3
+ return identify(source, true);
+ // preserves original behaviour prior to version 2.3
+ }
+
+ public FileFormatI identify(AlignmentFileReaderI file,
+ boolean closeSource) throws IOException
+ {
+ FileParse fp = new FileParse(file.getInFile(),
+ file.getDataSourceType());
+ return identify(fp, closeSource);
}
/**
* Identify contents of source, closing it or resetting source to start
* afterwards.
- *
+ *
* @param source
* @param closeSource
- * @return filetype string
+ * @return (best guess at) file format
+ * @throws FileFormatException
*/
- public String Identify(FileParse source, boolean closeSource)
+ public FileFormatI identify(FileParse source, boolean closeSource)
+ throws FileFormatException
{
- String reply = "PFAM";
+ FileFormatI reply = FileFormat.Pfam;
String data;
- int length = 0;
+ int bytesRead = 0;
+ int trimmedLength = 0;
+ boolean isXml = false; // set true if first line is XMLHEADER
boolean lineswereskipped = false;
boolean isBinary = false; // true if length is non-zero and non-printable
- // characters are encountered
+ // characters are encountered
+
try
{
if (!closeSource)
{
source.mark();
}
+ boolean aaIndexHeaderRead = false;
+
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++)
@@ -101,8 +160,8 @@ public class IdentifyFile
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)
@@ -112,108 +171,244 @@ public class IdentifyFile
if (source.inFile != null)
{
String fileStr = source.inFile.getName();
- // possibly a Jalview archive.
- if (fileStr.lastIndexOf(".jar") > -1
- || fileStr.lastIndexOf(".zip") > -1)
+ if (fileStr.contains(".jar") || fileStr.contains(".zip")
+ || fileStr.contains(".jvp"))
{
- reply = "Jalview";
+ // possibly a Jalview archive (but check further)
+ reply = FileFormat.Jalview;
}
}
if (!lineswereskipped && data.startsWith("PK"))
{
- reply = "Jalview"; // archive.
+ reply = FileFormat.Jalview; // archive
break;
}
}
- data = data.toUpperCase();
+ data = data.toUpperCase(Locale.ROOT);
- if ((data.indexOf("# STOCKHOLM") > -1))
+ if (data.startsWith(ScoreMatrixFile.SCOREMATRIX))
{
- reply = "STH";
-
+ reply = FileFormat.ScoreMatrix;
break;
}
-
- if ((data.length() < 1) || (data.indexOf("#") == 0))
+ if (data.startsWith(XMLHEADER) && !lineswereskipped)
{
- lineswereskipped = true;
- continue;
+ isXml = true;
}
-
- if (data.indexOf("PILEUP") > -1)
+ if (data.startsWith("LOCUS"))
{
- reply = "PileUp";
-
+ reply = FileFormat.GenBank;
break;
}
-
- if ((data.indexOf("//") == 0)
- || ((data.indexOf("!!") > -1) && (data.indexOf("!!") < data
- .indexOf("_MULTIPLE_ALIGNMENT "))))
+ if (data.startsWith("ID "))
{
- reply = "MSF";
-
+ if (data.substring(2).trim().split(";").length == 7)
+ {
+ reply = FileFormat.Embl;
+ break;
+ }
+ }
+ if (data.startsWith("H ") && !aaIndexHeaderRead)
+ {
+ aaIndexHeaderRead = true;
+ }
+ if (data.startsWith("D ") && aaIndexHeaderRead)
+ {
+ reply = FileFormat.ScoreMatrix;
break;
}
- else if (data.indexOf("CLUSTAL") > -1)
+ if (data.startsWith("##GFF-VERSION"))
{
- reply = "CLUSTAL";
-
+ // GFF - possibly embedded in a Jalview features file!
+ reply = FileFormat.Features;
break;
}
- else if ((data.indexOf(">P1;") > -1) || (data.indexOf(">DL;") > -1))
+ if (looksLikeFeatureData(data))
{
- reply = "PIR";
-
+ reply = FileFormat.Features;
break;
}
- else if (data.indexOf(">") > -1)
+ if (data.indexOf("# STOCKHOLM") > -1)
{
- // could be BLC file, read next line to confirm
+ reply = FileFormat.Stockholm;
+ break;
+ }
+ if (data.indexOf("_ENTRY.ID") > -1
+ || data.indexOf("_AUDIT_AUTHOR.NAME") > -1
+ || data.indexOf("_ATOM_SITE.") > -1)
+ {
+ reply = FileFormat.MMCif;
+ 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 = FileFormat.PIR;
+ }
+ // could also be BLC file, read next line to confirm
data = source.nextLine();
if (data.indexOf(">") > -1)
{
- reply = "BLC";
+ reply = FileFormat.BLC;
}
else
{
// Is this a single line BLC file?
- source.nextLine();
+ String data1 = source.nextLine();
String data2 = source.nextLine();
- if (data2 != null && data.indexOf("*") > -1
- && data.indexOf("*") == data2.indexOf("*"))
+ int c1;
+ if (checkPIR)
+ {
+ starterm = (data1 != null && data1.indexOf("*") > -1)
+ || (data2 != null && data2.indexOf("*") > -1);
+ }
+ if (data2 != null && (c1 = data.indexOf("*")) > -1)
{
- reply = "BLC";
+ if (c1 == 0 && c1 == data2.indexOf("*"))
+ {
+ reply = FileFormat.BLC;
+ }
+ else
+ {
+ reply = FileFormat.Fasta; // possibly a bad choice - may be
+ // recognised as
+ // PIR
+ }
+ // otherwise can still possibly be a PIR file
}
else
{
- reply = "FASTA";
+ reply = FileFormat.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\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 = FileFormat.PIR;
+ break;
+ }
+ else
+ {
+ reply = FileFormat.Fasta; // probably a bad choice!
}
}
+ // read as a FASTA (probably)
+ break;
+ }
+ if (data.indexOf("{\"") > -1)
+ {
+ reply = FileFormat.Json;
+ break;
+ }
+ int lessThan = data.indexOf("<");
+ if ((lessThan > -1)) // possible Markup Language data i.e HTML,
+ // RNAML, XML
+ {
+ String upper = data.toUpperCase(Locale.ROOT);
+ if (upper.substring(lessThan).startsWith(""))
+ {
+ reply = FileFormat.FeatureSettings;
+ break;
+ }
+ }
+
+ if ((data.length() < 1) || (data.indexOf("#") == 0))
+ {
+ lineswereskipped = true;
+ continue;
+ }
+
+ if (data.indexOf("PILEUP") > -1)
+ {
+ reply = FileFormat.Pileup;
+
+ break;
+ }
+
+ if ((data.indexOf("//") == 0) || ((data.indexOf("!!") > -1) && (data
+ .indexOf("!!") < data.indexOf("_MULTIPLE_ALIGNMENT "))))
+ {
+ reply = FileFormat.MSF;
+
+ break;
+ }
+ else if (data.indexOf("CLUSTAL") > -1)
+ {
+ reply = FileFormat.Clustal;
+
break;
}
+
else if (data.indexOf("HEADER") == 0 || data.indexOf("ATOM") == 0)
{
- reply = "PDB";
+ reply = FileFormat.PDB;
break;
}
- else if (!lineswereskipped && data.charAt(0) != '*'
- && data.charAt(0) != ' '
- && data.indexOf(":") < data.indexOf(",")) // &&
- // data.indexOf(",") -1
+ && commaPos > -1 && colonPos < commaPos;
+ // && data.indexOf(",") [ ...]");
+ Console.error("Usage: [ ...]");
}
}
+
}