Package org.biojava.bio.seq.io

Class OrganismParser

java.lang.Object

org.biojava.bio.seq.io.SequenceBuilderFilter

org.biojava.bio.seq.io.OrganismParser

All Implemented Interfaces:

SeqIOListener, SequenceBuilder

public class OrganismParser
extends SequenceBuilderFilter

Deprecated.

Use org.biojavax.bio.taxa framework instead

A parser that is able to generate Taxon entries for sequence builder event streams.

Author:

Matthew Pocock

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	OrganismParser.Factory	Deprecated. Factory which wraps SequenceBuilders in an OrganismParser.

Field Summary

Fields

Modifier and Type	Field	Description
static String	PROPERTY_ORGANISM	Deprecated.

Constructor Summary

Constructors

Constructor	Description
OrganismParser(SequenceBuilder delegate, TaxonFactory taxonFactory, TaxonParser taxonParser, String sciNameKey, String commonNameKey, String ncbiTaxonKey)	Deprecated.

Method Summary

Modifier and Type	Method	Description
void	addSequenceProperty(Object sciNameKey, Object value)	Deprecated. Notify the listener of a sequence-wide property.
void	endSequence()	Deprecated. Notify the listener that processing of the sequence is complete.

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

addFeatureProperty, addSymbols, endFeature, getDelegate, makeSequence, setName, setURI, startFeature, startSequence

Methods inherited from class java.lang.Object

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

Field Detail

PROPERTY_ORGANISM

public static final String PROPERTY_ORGANISM

Deprecated.

Constructor Detail

OrganismParser

public OrganismParser(SequenceBuilder delegate,
                      TaxonFactory taxonFactory,
                      TaxonParser taxonParser,
                      String sciNameKey,
                      String commonNameKey,
                      String ncbiTaxonKey)

Deprecated.

Method Detail

addSequenceProperty

public void addSequenceProperty(Object sciNameKey,
                                Object value)
                         throws ParseException

Deprecated.

Description copied from interface: SeqIOListener

Notify the listener of a sequence-wide property. This might be stored as an entry in the sequence's annotation bundle.

Specified by:

addSequenceProperty in interface SeqIOListener

Overrides:

addSequenceProperty in class SequenceBuilderFilter

Throws:

ParseException

endSequence

public void endSequence()
                 throws ParseException

Deprecated.

Description copied from interface: SeqIOListener

Notify the listener that processing of the sequence is complete.

Specified by:

endSequence in interface SeqIOListener

Overrides:

endSequence in class SequenceBuilderFilter

Throws:

ParseException