OrganismParser (biojava-legacy 1.9.7 API)

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 final 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 Details
- PROPERTY_ORGANISM
  
  public static final String PROPERTY_ORGANISM
  
  Deprecated.
Constructor Details
- OrganismParser
  
  public OrganismParser(SequenceBuilder delegate, TaxonFactory taxonFactory, TaxonParser taxonParser, String sciNameKey, String commonNameKey, String ncbiTaxonKey)
  
  Deprecated.
Method Details
- 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