Package org.biojavax.bio.seq.io

Class EMBLFormat

java.lang.Object

org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat

org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat

org.biojavax.bio.seq.io.EMBLFormat

All Implemented Interfaces:

SequenceFormat, RichSequenceFormat

public class EMBLFormat
extends RichSequenceFormat.HeaderlessFormat

Format reader for EMBL files. This version of EMBL format will generate and write RichSequence objects. Loosely Based on code from the old, deprecated, org.biojava.bio.seq.io.EmblLikeFormat object.

This format will read both Pre-87 and 87+ versions of EMBL. It will also write them both. By default, it will write the most recent version. If you want an earlier one, you must specify the format by passing one of the constants defined in this class to writeSequence(Sequence, String, Namespace).

Since:

1.5

Author:

Richard Holland, Jolyon Holdstock, Mark Schreiber

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	EMBLFormat.Terms	Implements some EMBL-specific terms.

Nested classes/interfaces inherited from interface org.biojavax.bio.seq.io.RichSequenceFormat

RichSequenceFormat.BasicFormat, RichSequenceFormat.HeaderlessFormat

Field Summary

Fields

Modifier and Type	Field	Description
protected static String	ACCESSION_TAG
protected static String	AUTHORS_TAG
protected static String	COMMENT_TAG
protected static String	CONSORTIUM_TAG
protected static String	CONTIG_TAG
protected static String	DATABASE_XREF_TAG
protected static String	DATE_TAG
protected static Pattern	dbxp
protected static String	DEFINITION_TAG
protected static String	DELIMITER_TAG
protected static Pattern	dp
static String	EMBL_FORMAT	The name of the current format
static String	EMBL_PRE87_FORMAT	The name of the Pre-87 format
protected static String	END_SEQUENCE_TAG
protected static String	FEATURE_HEADER_TAG
protected static String	FEATURE_TAG
protected static Pattern	headerLine
protected static String	KEYWORDS_TAG
protected static String	LOCATOR_TAG
protected static String	LOCUS_TAG
protected static Pattern	lp
protected static Pattern	lpPre87
protected static String	ORGANELLE_TAG
protected static String	ORGANISM_TAG
protected static Pattern	readableFileNames
protected static String	REFERENCE_POSITION_TAG
protected static String	REFERENCE_TAG
protected static String	REFERENCE_XREF_TAG
protected static String	REMARK_TAG
protected static Pattern	rpp
protected static String	SOURCE_TAG
protected static String	START_SEQUENCE_TAG
protected static String	TITLE_TAG
protected static String	TPA_TAG
protected static String	VERSION_TAG
protected static Pattern	vp

Constructor Summary

Constructors

Constructor	Description
EMBLFormat()

Method Summary

Modifier and Type	Method	Description
boolean	canRead(BufferedInputStream stream)	Check to see if a given stream is in our format.
boolean	canRead(File file)	Check to see if a given file is in our format.
String	getDefaultFormat()	getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
SymbolTokenization	guessSymbolTokenization(BufferedInputStream stream)	On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
SymbolTokenization	guessSymbolTokenization(File file)	On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
boolean	readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns)	Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
boolean	readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)	Read a sequence and pass data on to a SeqIOListener.
void	writeSequence(Sequence seq, PrintStream os)	writeSequence writes a sequence to the specified PrintStream, using the default format.
void	writeSequence(Sequence seq, String format, PrintStream os)	writeSequence writes a sequence to the specified PrintStream, using the specified format.
void	writeSequence(Sequence seq, String format, Namespace ns)	As per writeSequence(Sequence, Namespace), except that it also takes a format parameter.
void	writeSequence(Sequence seq, Namespace ns)	Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.

Methods inherited from class org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat

beginWriting, finishWriting

Methods inherited from class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat

getElideComments, getElideFeatures, getElideReferences, getElideSymbols, getLineWidth, getPrintStream, setElideComments, setElideFeatures, setElideReferences, setElideSymbols, setLineWidth, setPrintStream

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

EMBL_PRE87_FORMAT

public static final String EMBL_PRE87_FORMAT

The name of the Pre-87 format

See Also:

Constant Field Values

EMBL_FORMAT

public static final String EMBL_FORMAT

The name of the current format

See Also:

Constant Field Values

LOCUS_TAG

protected static final String LOCUS_TAG

See Also:

Constant Field Values

ACCESSION_TAG

protected static final String ACCESSION_TAG

See Also:

Constant Field Values

VERSION_TAG

protected static final String VERSION_TAG

See Also:

Constant Field Values

DEFINITION_TAG

protected static final String DEFINITION_TAG

See Also:

Constant Field Values

DATE_TAG

protected static final String DATE_TAG

See Also:

Constant Field Values

DATABASE_XREF_TAG

protected static final String DATABASE_XREF_TAG

See Also:

Constant Field Values

SOURCE_TAG

protected static final String SOURCE_TAG

See Also:

Constant Field Values

ORGANISM_TAG

protected static final String ORGANISM_TAG

See Also:

Constant Field Values

ORGANELLE_TAG

protected static final String ORGANELLE_TAG

See Also:

Constant Field Values

REFERENCE_TAG

protected static final String REFERENCE_TAG

See Also:

Constant Field Values

REFERENCE_POSITION_TAG

protected static final String REFERENCE_POSITION_TAG

See Also:

Constant Field Values

REFERENCE_XREF_TAG

protected static final String REFERENCE_XREF_TAG

See Also:

Constant Field Values

AUTHORS_TAG

protected static final String AUTHORS_TAG

See Also:

Constant Field Values

CONSORTIUM_TAG

protected static final String CONSORTIUM_TAG

See Also:

Constant Field Values

TITLE_TAG

protected static final String TITLE_TAG

See Also:

Constant Field Values

LOCATOR_TAG

protected static final String LOCATOR_TAG

See Also:

Constant Field Values

REMARK_TAG

protected static final String REMARK_TAG

See Also:

Constant Field Values

KEYWORDS_TAG

protected static final String KEYWORDS_TAG

See Also:

Constant Field Values

COMMENT_TAG

protected static final String COMMENT_TAG

See Also:

Constant Field Values

FEATURE_HEADER_TAG

protected static final String FEATURE_HEADER_TAG

See Also:

Constant Field Values

FEATURE_TAG

protected static final String FEATURE_TAG

See Also:

Constant Field Values

CONTIG_TAG

protected static final String CONTIG_TAG

See Also:

Constant Field Values

TPA_TAG

protected static final String TPA_TAG

See Also:

Constant Field Values

START_SEQUENCE_TAG

protected static final String START_SEQUENCE_TAG

See Also:

Constant Field Values

DELIMITER_TAG

protected static final String DELIMITER_TAG

See Also:

Constant Field Values

END_SEQUENCE_TAG

protected static final String END_SEQUENCE_TAG

See Also:

Constant Field Values

dp

protected static final Pattern dp

lp

protected static final Pattern lp

lpPre87

protected static final Pattern lpPre87

vp

protected static final Pattern vp

rpp

protected static final Pattern rpp

dbxp

protected static final Pattern dbxp

readableFileNames

protected static final Pattern readableFileNames

headerLine

protected static final Pattern headerLine

Constructor Detail

EMBLFormat

public EMBLFormat()

Method Detail

canRead

public boolean canRead(File file)
                throws IOException

Check to see if a given file is in our format. Some formats may be able to determine this by filename, whilst others may have to open the file and read it to see what format it is in. A file is in EMBL format if its name contains the word eem or edat, or the first line matches the EMBL format for the ID line.

Specified by:

canRead in interface RichSequenceFormat

Overrides:

canRead in class RichSequenceFormat.BasicFormat

Parameters:

file - the File to check.

Returns:

true if the file is readable by this format, false if not.

Throws:

IOException - in case the file is inaccessible.

guessSymbolTokenization

public SymbolTokenization guessSymbolTokenization(File file)
                                           throws IOException

On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. For formats that only accept one tokenization, just return it without checking the file. For formats that accept multiple tokenizations, its up to you how you do it. Always returns a DNA tokenizer.

Specified by:

guessSymbolTokenization in interface RichSequenceFormat

Overrides:

guessSymbolTokenization in class RichSequenceFormat.BasicFormat

Parameters:

file - the File object to guess the format of.

Returns:

a SymbolTokenization to read the file with.

Throws:

IOException - if the file is unrecognisable or inaccessible.

canRead

public boolean canRead(BufferedInputStream stream)
                throws IOException

Check to see if a given stream is in our format. A stream is in EMBL format if its first line matches the EMBL format for the ID line.

Parameters:

stream - the BufferedInputStream to check.

Returns:

true if the stream is readable by this format, false if not.

Throws:

IOException - in case the stream is inaccessible.

guessSymbolTokenization

public SymbolTokenization guessSymbolTokenization(BufferedInputStream stream)
                                           throws IOException

On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. For formats that only accept one tokenization, just return it without checking the stream. For formats that accept multiple tokenizations, its up to you how you do it. Always returns a DNA tokenizer.

Parameters:

stream - the BufferedInputStream object to guess the format of.

Returns:

a SymbolTokenization to read the stream with.

Throws:

IOException - if the stream is unrecognisable or inaccessible.

readSequence

public boolean readSequence(BufferedReader reader,
                            SymbolTokenization symParser,
                            SeqIOListener listener)
                     throws IllegalSymbolException,
                            IOException,
                            ParseException

Read a sequence and pass data on to a SeqIOListener.

Parameters:

reader - The stream of data to parse.

symParser - A SymbolParser defining a mapping from character data to Symbols.

listener - A listener to notify when data is extracted from the stream.

Returns:

a boolean indicating whether or not the stream contains any more sequences.

Throws:

IllegalSymbolException - if it is not possible to translate character data from the stream into valid BioJava symbols.

IOException - if an error occurs while reading from the stream.

ParseException

readRichSequence

public boolean readRichSequence(BufferedReader reader,
                                SymbolTokenization symParser,
                                RichSeqIOListener rlistener,
                                Namespace ns)
                         throws IllegalSymbolException,
                                IOException,
                                ParseException

Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. Events are passed to the listener, and the namespace used for sequences read is the one given. If the namespace is null, then the default namespace for the parser is used, which may depend on individual implementations of this interface.

Parameters:

reader - the input source

symParser - the tokenizer which understands the sequence being read

rlistener - the listener to send sequence events to

ns - the namespace to read sequences into.

Returns:

true if there is more to read after this, false otherwise.

Throws:

IllegalSymbolException - if the tokenizer couldn't understand one of the sequence symbols in the file.

IOException - if there was a read error.

ParseException

writeSequence

public void writeSequence(Sequence seq,
                          PrintStream os)
                   throws IOException

writeSequence writes a sequence to the specified PrintStream, using the default format.

Parameters:

seq - the sequence to write out.

os - the printstream to write to.

Throws:

IOException

writeSequence

public void writeSequence(Sequence seq,
                          String format,
                          PrintStream os)
                   throws IOException

writeSequence writes a sequence to the specified PrintStream, using the specified format.

Parameters:

seq - a Sequence to write out.

format - a String indicating which sub-format of those available from a particular SequenceFormat implemention to use when writing.

os - a PrintStream object.

Throws:

IOException - if an error occurs.

writeSequence

public void writeSequence(Sequence seq,
                          Namespace ns)
                   throws IOException

Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. If namespace is given, sequences will be written with that namespace, otherwise they will be written with the default namespace of the implementing class (which is usually the namespace of the sequence itself). If you pass this method a sequence which is not a RichSequence, it will attempt to convert it using RichSequence.Tools.enrich(). Obviously this is not going to guarantee a perfect conversion, so it's better if you just use RichSequences to start with! Namespace is ignored as EMBL has no concept of it.

Parameters:

seq - the sequence to write

ns - the namespace to write it with

Throws:

IOException - in case it couldn't write something

writeSequence

public void writeSequence(Sequence seq,
                          String format,
                          Namespace ns)
                   throws IOException

As per writeSequence(Sequence, Namespace), except that it also takes a format parameter. This can be any of the formats defined as constants in this class.

Parameters:

seq - see writeSequence(Sequence, Namespace)

format - the format to use.

ns - see writeSequence(Sequence, Namespace)

Throws:

IOException - see writeSequence(Sequence, Namespace)

getDefaultFormat

public String getDefaultFormat()

getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.

Returns:

a String.