/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
- *
+ * 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 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.util.Locale;
+
+import java.io.File;
+import java.io.IOException;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
public class IdentifyFile
{
+
+ 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)
+ {
+ System.err.println("Error whilst identifying " + file);
+ e.printStackTrace(System.err);
+ 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");
+ System.err.println("Error whilst identifying " + file);
e.printStackTrace(System.err);
emessage = e.getMessage();
}
if (parser != null)
- return parser.errormessage;
- return emessage;
+ {
+ throw new FileFormatException(parser.errormessage);
+ }
+ throw new FileFormatException(emessage);
+ }
+
+ public FileFormatI identify(FileParse source) throws FileFormatException
+ {
+ return identify(source, true);
+ // preserves original behaviour prior to version 2.3
}
- public String Identify(FileParse source)
+ public FileFormatI identify(AlignmentFileReaderI file,
+ boolean closeSource) throws IOException
{
- return Identify(source, true); // preserves original behaviour prior to
- // version 2.3
+ 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 lineswereskipped = false;
boolean isBinary = false; // true if length is non-zero and non-printable
// 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++)
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("LOCUS"))
{
- lineswereskipped = true;
- continue;
+ reply = FileFormat.GenBank;
+ break;
}
-
- if (data.indexOf("PILEUP") > -1)
+ if (data.startsWith("ID "))
{
- reply = "PileUp";
-
+ 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;
}
-
- if ((data.indexOf("//") == 0)
- || ((data.indexOf("!!") > -1) && (data.indexOf("!!") < data
- .indexOf("_MULTIPLE_ALIGNMENT "))))
+ if (data.startsWith("##GFF-VERSION"))
{
- reply = "MSF";
-
+ // GFF - possibly embedded in a Jalview features file!
+ reply = FileFormat.Features;
break;
}
- else if (data.indexOf("CLUSTAL") > -1)
+ if (looksLikeFeatureData(data))
{
- reply = "CLUSTAL";
-
+ reply = FileFormat.Features;
+ break;
+ }
+ if (data.indexOf("# STOCKHOLM") > -1)
+ {
+ 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;
}
- else if (data.indexOf(">") > -1)
+ // if (data.indexOf(">") > -1)
+ if (data.startsWith(">"))
{
// FASTA, PIR file or BLC file
boolean checkPIR = false, starterm = false;
{
// watch for PIR file attributes
checkPIR = true;
- reply = "PIR";
+ 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?
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 && data.indexOf("*") > -1)
+ if (data2 != null && (c1 = data.indexOf("*")) > -1)
{
- if (data.indexOf("*") == data2.indexOf("*"))
+ if (c1 == 0 && c1 == data2.indexOf("*"))
+ {
+ reply = FileFormat.BLC;
+ }
+ else
{
- reply = "BLC";
+ 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.
} catch (IOException ex)
{
}
- ;
if (dta != null && dta.indexOf("*") > -1)
{
starterm = true;
}
if (starterm)
{
- reply = "PIR";
+ reply = FileFormat.PIR;
break;
}
else
{
- reply = "FASTA"; // probably a bad choice!
+ 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("<HTML"))
+ {
+ reply = FileFormat.Html;
+ break;
+ }
+ if (upper.substring(lessThan).startsWith("<RNAML"))
+ {
+ reply = FileFormat.Rnaml;
+ 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;
}
- /*
- * // TODO comment out SimpleBLAST identification for Jalview 2.4.1 else
- * if (!lineswereskipped && data.indexOf("BLAST")<4) { reply =
- * "SimpleBLAST"; break;
- *
- * } // end comments for Jalview 2.4.1
- */
- 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 = FileFormat.Phylip;
break;
}
+ else if (!lineswereskipped && looksLikeJnetData(data))
+ {
+ reply = FileFormat.Jnet;
+ break;
+
+ }
+ else // phylogenetic file
+ {
+ // may also have a <xml header before hand, probably need to check it
+ if (data.toLowerCase(Locale.ROOT).startsWith("<phyloxml"))
+ {
+ reply = FileFormat.PhyloXML;
+ break;
+ }
+ // commented out, nexus parser is troublesome
+ // else if (((identifier.startsWith("nexus"))
+ // || (identifier.startsWith("#nexus"))
+ // || (identifier.startsWith("# nexus"))
+ // || (identifier.startsWith("begin"))))
+ // {
+ // reply = FileFormat.Nexus;
+ // break;
+ // }
+ }
lineswereskipped = true; // this means there was some junk before any
// key file signature
}
}
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;
+ throw new FileFormatException(source.errormessage);
}
- if (length == 0)
+ if (trimmedLength == 0)
{
- System.err
- .println("File Identification failed! - Empty file was read.");
- return "EMPTY DATA FILE";
+ System.err.println(
+ "File Identification failed! - Empty file was read.");
+ throw new FileFormatException("EMPTY DATA FILE");
}
+ System.out.println("File format identified as " + reply.toString());
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;
+ }
+
+ /**
+ *
+ * @param args
+ * @j2sIgnore
+ */
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);
+ FileFormatI type = null;
+ try
+ {
+ type = ider.identify(args[i], DataSourceType.FILE);
+ } catch (FileFormatException e)
+ {
+ System.err.println(
+ String.format("Error '%s' identifying file type for %s",
+ args[i], e.getMessage()));
+ }
System.out.println("Type of " + args[i] + " is " + type);
}
if (args == null || args.length == 0)
System.err.println("Usage: <Filename> [<Filename> ...]");
}
}
+
}
git://source.jalview.org / jalview.git / blobdiff