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
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
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic class
Deprecated.Factory which wraps SequenceBuilders in an OrganismParser. -
Field Summary
Fields -
Constructor Summary
ConstructorsConstructorDescriptionOrganismParser
(SequenceBuilder delegate, TaxonFactory taxonFactory, TaxonParser taxonParser, String sciNameKey, String commonNameKey, String ncbiTaxonKey) Deprecated. -
Method Summary
Modifier and TypeMethodDescriptionvoid
addSequenceProperty
(Object sciNameKey, Object value) Deprecated.Notify the listener of a sequence-wide property.void
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
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Field Details
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PROPERTY_ORGANISM
Deprecated.
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Constructor Details
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OrganismParser
public OrganismParser(SequenceBuilder delegate, TaxonFactory taxonFactory, TaxonParser taxonParser, String sciNameKey, String commonNameKey, String ncbiTaxonKey) Deprecated.
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Method Details
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addSequenceProperty
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 interfaceSeqIOListener
- Overrides:
addSequenceProperty
in classSequenceBuilderFilter
- Throws:
ParseException
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endSequence
Deprecated.Description copied from interface:SeqIOListener
Notify the listener that processing of the sequence is complete.- Specified by:
endSequence
in interfaceSeqIOListener
- Overrides:
endSequence
in classSequenceBuilderFilter
- Throws:
ParseException
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