org.biojava.bio.seq.io

Class GenbankXmlFormat

java.lang.Object

org.biojava.bio.seq.io.GenbankFormat

org.biojava.bio.seq.io.GenbankXmlFormat

All Implemented Interfaces:

Serializable, EventListener, SequenceFormat, ParseErrorListener, ParseErrorSource

Deprecated.

Use org.biojavax.bio.seq.io.INSDseqFormat

public class GenbankXmlFormat
extends GenbankFormat

Format reader for GenBank XML files.

Author:

Alan Li - alanli[at]xyworks.com

See Also:

Serialized Form

Field Summary

Fields inherited from class org.biojava.bio.seq.io.GenbankFormat

ACCESSION_TAG, AUTHORS_TAG, BASE_COUNT_TAG, CIRCULAR_TAG, COMMENT_TAG, COORDINATE_TAG, DATE_TAG, DEFAULT, DEFINITION_TAG, DIVISION_TAG, END_SEQUENCE_TAG, FEATURE_FLAG, FEATURE_LINE_PREFIX, FEATURE_TAG, GI_TAG, JOURNAL_TAG, KEYWORDS_TAG, LOCUS_TAG, MEDLINE_TAG, ORGANISM_TAG, PUBMED_TAG, REF_ACCESSION_TAG, REFERENCE_TAG, SIZE_TAG, SOURCE_TAG, START_SEQUENCE_TAG, STRAND_NUMBER_TAG, TITLE_TAG, TYPE_TAG, VERSION_TAG

Constructor Summary

Constructors

Constructor and Description
GenbankXmlFormat() Deprecated.

Method Summary

Methods

Modifier and Type	Method and Description
String	getDefaultFormat() Deprecated. getDefaultFormat returns the String identifier for the default format.
boolean	readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Deprecated. Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided.

Methods inherited from class org.biojava.bio.seq.io.GenbankFormat

addParseErrorListener, BadLineParsed, getElideSymbols, notifyParseErrorEvent, removeParseErrorListener, setElideSymbols, writeSequence, writeSequence

Methods inherited from class java.lang.Object

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

Constructor Detail

GenbankXmlFormat

public GenbankXmlFormat()

Deprecated.

Method Detail

readSequence

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

Deprecated.

Description copied from class: GenbankFormat

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

Overrides:

readSequence in class GenbankFormat

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

getDefaultFormat

public String getDefaultFormat()

Deprecated.

Description copied from class: GenbankFormat

getDefaultFormat returns the String identifier for the default format.

Specified by:

getDefaultFormat in interface SequenceFormat

Overrides:

getDefaultFormat in class GenbankFormat

Returns:

a String.