org.biojava.bio.seq.io

Class GenbankFormat

java.lang.Object

org.biojava.bio.seq.io.GenbankFormat

All Implemented Interfaces:

Serializable, EventListener, SequenceFormat, ParseErrorListener, ParseErrorSource

Direct Known Subclasses:

GenbankXmlFormat, GenpeptFormat

Deprecated.

Use org.biojavax.bio.seq.io.GenbankFormat

public class GenbankFormat
extends Object
implements SequenceFormat, Serializable, ParseErrorListener, ParseErrorSource

Format reader for GenBank files. Converted from the old style io to the new by working from EmblLikeFormat.

Author:

Thomas Down, Thad Welch Added GenBank header info to the sequence annotation. The ACCESSION header tag is not included. Stored in sequence.getName()., Greg Cox, Keith James, Matthew Pocock, Ron Kuhn

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	ACCESSION_TAG Deprecated.
protected static String	AUTHORS_TAG Deprecated.
protected static String	BASE_COUNT_TAG Deprecated.
protected static String	CIRCULAR_TAG Deprecated.
protected static String	COMMENT_TAG Deprecated.
protected static String	COORDINATE_TAG Deprecated.
protected static String	DATE_TAG Deprecated.
static String	DEFAULT Deprecated.
protected static String	DEFINITION_TAG Deprecated.
protected static String	DIVISION_TAG Deprecated.
protected static String	END_SEQUENCE_TAG Deprecated.
protected static String	FEATURE_FLAG Deprecated.
protected static String	FEATURE_LINE_PREFIX Deprecated.
protected static String	FEATURE_TAG Deprecated.
protected static String	GI_TAG Deprecated.
protected static String	JOURNAL_TAG Deprecated.
protected static String	KEYWORDS_TAG Deprecated.
protected static String	LOCUS_TAG Deprecated.
protected static String	MEDLINE_TAG Deprecated.
protected static String	ORGANISM_TAG Deprecated.
protected static String	PUBMED_TAG Deprecated.
protected static String	REF_ACCESSION_TAG Deprecated.
protected static String	REFERENCE_TAG Deprecated.
protected static String	SIZE_TAG Deprecated.
protected static String	SOURCE_TAG Deprecated.
protected static String	START_SEQUENCE_TAG Deprecated.
protected static String	STRAND_NUMBER_TAG Deprecated.
protected static String	TITLE_TAG Deprecated.
protected static String	TYPE_TAG Deprecated.
protected static String	VERSION_TAG Deprecated.

Constructor Summary

Constructors

Constructor and Description
GenbankFormat() Deprecated.

Method Summary

Methods

Modifier and Type	Method and Description
void	addParseErrorListener(ParseErrorListener theListener) Deprecated. Adds a parse error listener to the list of listeners if it isn't already included.
void	BadLineParsed(ParseErrorEvent theEvent) Deprecated. This method determines the behaviour when a bad line is processed.
String	getDefaultFormat() Deprecated.
boolean	getElideSymbols() Deprecated.
protected void	notifyParseErrorEvent(ParseErrorEvent theEvent) Deprecated. Passes the event on to all the listeners registered for ParseErrorEvents.
boolean	readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Deprecated. Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided.
void	removeParseErrorListener(ParseErrorListener theListener) Deprecated. Removes a parse error listener from the list of listeners if it is included.
void	setElideSymbols(boolean elideSymbols) Deprecated. Use this method to toggle reading of sequence data.
void	writeSequence(Sequence seq, PrintStream os) Deprecated. writeSequence writes a sequence to the specified PrintStream, using the default format.
void	writeSequence(Sequence seq, String format, PrintStream os) Deprecated. use writeSequence(Sequence seq, PrintStream os)

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT

public static final String DEFAULT

Deprecated.

See Also:

Constant Field Values

LOCUS_TAG

protected static final String LOCUS_TAG

Deprecated.

See Also:

Constant Field Values

SIZE_TAG

protected static final String SIZE_TAG

Deprecated.

See Also:

Constant Field Values

STRAND_NUMBER_TAG

protected static final String STRAND_NUMBER_TAG

Deprecated.

See Also:

Constant Field Values

TYPE_TAG

protected static final String TYPE_TAG

Deprecated.

See Also:

Constant Field Values

CIRCULAR_TAG

protected static final String CIRCULAR_TAG

Deprecated.

See Also:

Constant Field Values

DIVISION_TAG

protected static final String DIVISION_TAG

Deprecated.

See Also:

Constant Field Values

DATE_TAG

protected static final String DATE_TAG

Deprecated.

See Also:

Constant Field Values

ACCESSION_TAG

protected static final String ACCESSION_TAG

Deprecated.

See Also:

Constant Field Values

VERSION_TAG

protected static final String VERSION_TAG

Deprecated.

See Also:

Constant Field Values

GI_TAG

protected static final String GI_TAG

Deprecated.

See Also:

Constant Field Values

KEYWORDS_TAG

protected static final String KEYWORDS_TAG

Deprecated.

See Also:

Constant Field Values

DEFINITION_TAG

protected static final String DEFINITION_TAG

Deprecated.

See Also:

Constant Field Values

SOURCE_TAG

protected static final String SOURCE_TAG

Deprecated.

See Also:

Constant Field Values

ORGANISM_TAG

protected static final String ORGANISM_TAG

Deprecated.

See Also:

Constant Field Values

REFERENCE_TAG

protected static final String REFERENCE_TAG

Deprecated.

See Also:

Constant Field Values

COORDINATE_TAG

protected static final String COORDINATE_TAG

Deprecated.

See Also:

Constant Field Values

REF_ACCESSION_TAG

protected static final String REF_ACCESSION_TAG

Deprecated.

See Also:

Constant Field Values

AUTHORS_TAG

protected static final String AUTHORS_TAG

Deprecated.

See Also:

Constant Field Values

TITLE_TAG

protected static final String TITLE_TAG

Deprecated.

See Also:

Constant Field Values

JOURNAL_TAG

protected static final String JOURNAL_TAG

Deprecated.

See Also:

Constant Field Values

PUBMED_TAG

protected static final String PUBMED_TAG

Deprecated.

See Also:

Constant Field Values

MEDLINE_TAG

protected static final String MEDLINE_TAG

Deprecated.

See Also:

Constant Field Values

COMMENT_TAG

protected static final String COMMENT_TAG

Deprecated.

See Also:

Constant Field Values

FEATURE_TAG

protected static final String FEATURE_TAG

Deprecated.

See Also:

Constant Field Values

BASE_COUNT_TAG

protected static final String BASE_COUNT_TAG

Deprecated.

See Also:

Constant Field Values

FEATURE_FLAG

protected static final String FEATURE_FLAG

Deprecated.

See Also:

Constant Field Values

START_SEQUENCE_TAG

protected static final String START_SEQUENCE_TAG

Deprecated.

See Also:

Constant Field Values

END_SEQUENCE_TAG

protected static final String END_SEQUENCE_TAG

Deprecated.

See Also:

Constant Field Values

FEATURE_LINE_PREFIX

protected static final String FEATURE_LINE_PREFIX

Deprecated.

See Also:

Constant Field Values

Constructor Detail

GenbankFormat

public GenbankFormat()

Deprecated.

Method Detail

readSequence

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

Deprecated.

Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided. The sequence read in must be in Genbank format.

Specified by:

readSequence in interface SequenceFormat

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:

boolean True if there is another sequence in the file; false otherwise

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

writeSequence

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

Deprecated.

Description copied from interface: SequenceFormat

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

Specified by:

writeSequence in interface SequenceFormat

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

Deprecated. use writeSequence(Sequence seq, PrintStream os)

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

Specified by:

writeSequence in interface SequenceFormat

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.

getDefaultFormat

public String getDefaultFormat()

Deprecated.

getDefaultFormat returns the String identifier for the default format.

Specified by:

getDefaultFormat in interface SequenceFormat

Returns:

a String.

addParseErrorListener

public void addParseErrorListener(ParseErrorListener theListener)

Deprecated.

Adds a parse error listener to the list of listeners if it isn't already included.

Specified by:

addParseErrorListener in interface ParseErrorSource

Parameters:

theListener - Listener to be added.

removeParseErrorListener

public void removeParseErrorListener(ParseErrorListener theListener)

Deprecated.

Removes a parse error listener from the list of listeners if it is included.

Specified by:

removeParseErrorListener in interface ParseErrorSource

Parameters:

theListener - Listener to be removed.

BadLineParsed

public void BadLineParsed(ParseErrorEvent theEvent)

Deprecated.

This method determines the behaviour when a bad line is processed. Some options are to log the error, throw an exception, ignore it completely, or pass the event through.

This method should be overwritten when different behavior is desired.

Specified by:

BadLineParsed in interface ParseErrorListener

Parameters:

theEvent - The event that contains the bad line and token.

notifyParseErrorEvent

protected void notifyParseErrorEvent(ParseErrorEvent theEvent)

Deprecated.

Passes the event on to all the listeners registered for ParseErrorEvents.

Parameters:

theEvent - The event to be handed to the listeners.

getElideSymbols

public boolean getElideSymbols()

Deprecated.

setElideSymbols

public void setElideSymbols(boolean elideSymbols)

Deprecated.

Use this method to toggle reading of sequence data. If you're only interested in header data set to true.

Parameters:

elideSymbols - set to true if you don't want the sequence data.