Package org.biojavax.bio.seq.io

Class GenbankFormat

java.lang.Object

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

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

org.biojavax.bio.seq.io.GenbankFormat

All Implemented Interfaces:

SequenceFormat, RichSequenceFormat

public class GenbankFormat
extends RichSequenceFormat.HeaderlessFormat

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

Since:

1.5

Author:

Richard Holland, Mark Schreiber, David Scott, Bubba Puryear, George Waldon, Deepak Sheoran

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	GenbankFormat.Terms	Implements some GenBank-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	BASE_COUNT_TAG
protected static String	BASE_COUNT_TAG_FULL
protected static String	COMMENT_TAG
protected static String	CONSORTIUM_TAG
protected static Pattern	dbxp
protected static String	DEFINITION_TAG
protected static String	END_SEQUENCE_TAG
protected static String	FEATURE_TAG
static String	GENBANK_FORMAT	The name of this format
protected static Pattern	headerLine
protected static String	JOURNAL_TAG
protected static String	KEYWORDS_TAG
protected static String	LOCUS_TAG
protected static Pattern	lp
protected static String	MEDLINE_TAG
protected static String	ORGANISM_TAG
protected static String	PUBMED_TAG
protected static Pattern	readableFiles
protected static String	REFERENCE_TAG
protected static Pattern	refp
protected static Pattern	refRange
protected static String	REMARK_TAG
protected static Pattern	sectp
protected static String	SOURCE_TAG
protected static String	START_SEQUENCE_TAG
protected static String	TITLE_TAG
protected static String	VERSION_TAG
protected static Pattern	vp

Constructor Summary

Constructors

Constructor	Description
GenbankFormat()

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, 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

GENBANK_FORMAT

public static final String GENBANK_FORMAT

The name of this format

See Also:

Constant Field Values

LOCUS_TAG

protected static final String LOCUS_TAG

See Also:

Constant Field Values

DEFINITION_TAG

protected static final String DEFINITION_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

KEYWORDS_TAG

protected static final String KEYWORDS_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

REFERENCE_TAG

protected static final String REFERENCE_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

JOURNAL_TAG

protected static final String JOURNAL_TAG

See Also:

Constant Field Values

PUBMED_TAG

protected static final String PUBMED_TAG

See Also:

Constant Field Values

MEDLINE_TAG

protected static final String MEDLINE_TAG

See Also:

Constant Field Values

REMARK_TAG

protected static final String REMARK_TAG

See Also:

Constant Field Values

COMMENT_TAG

protected static final String COMMENT_TAG

See Also:

Constant Field Values

FEATURE_TAG

protected static final String FEATURE_TAG

See Also:

Constant Field Values

BASE_COUNT_TAG_FULL

protected static final String BASE_COUNT_TAG_FULL

See Also:

Constant Field Values

BASE_COUNT_TAG

protected static final String BASE_COUNT_TAG

See Also:

Constant Field Values

START_SEQUENCE_TAG

protected static final String START_SEQUENCE_TAG

See Also:

Constant Field Values

END_SEQUENCE_TAG

protected static final String END_SEQUENCE_TAG

See Also:

Constant Field Values

lp

protected static final Pattern lp

vp

protected static final Pattern vp

refRange

protected static final Pattern refRange

refp

protected static final Pattern refp

dbxp

protected static final Pattern dbxp

sectp

protected static final Pattern sectp

readableFiles

protected static final Pattern readableFiles

headerLine

protected static final Pattern headerLine

Constructor Detail

GenbankFormat

public GenbankFormat()

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 GenBank format if the name ends with gbk, contains the letters egb, or the first line of the file starts with the word LOCUS

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. Returns an dna parser if the letters DNA or RNA appear in the first line of the file. Otherwise 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 GenBank format if the first line of the stream starts with the word LOCUS

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. Returns an dna parser if the letters DNA or RNA appear in the first line of the stream. Otherwise 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 Genbank 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

getDefaultFormat

public String getDefaultFormat()

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

Returns:

a String.