Uses of Interface
org.biojava.bio.seq.io.SequenceBuilder

Packages that use SequenceBuilder

Package	Description
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojavax.bio.seq.io	Classes to support the I/O of RichSequence and Bioentry objects.

Uses of SequenceBuilder in org.biojava.bio.seq.io

Classes in org.biojava.bio.seq.io that implement SequenceBuilder

Modifier and Type	Class and Description
class	EmblProcessor Deprecated. Use org.biojavax.bio.seq.io framework instead
class	FastaDescriptionLineParser Deprecated. Use org.biojavax.bio.seq.io.FastaFormat
class	GenbankProcessor Deprecated. Use org.biojavax.bio.seq.io framework instead
class	OrganismParser Deprecated. Use org.biojavax.bio.taxa framework instead
class	ProteinRefSeqProcessor Deprecated. Use org.biojavax.bio.seq.io framework instead
class	SequenceBuilderBase Basic SequenceBuilder implementation which accumulates all notified information.
class	SequenceBuilderFilter Base-class for builders that pass filtered events onto another builder.
class	SequenceDBSequenceBuilder This SequenceBuilder has a variety of modes of operation.
class	SimpleAssemblyBuilder Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleAssembly.
class	SimpleSequenceBuilder Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleSequence.
class	SmartSequenceBuilder Basic SequenceBuilder implementation which accumulates all notified information and chooses a sequence implementation suited to the size of the sequence.
class	SwissprotProcessor Deprecated. Use org.biojavax.bio.seq.io framework instead

Methods in org.biojava.bio.seq.io that return SequenceBuilder

Modifier and Type	Method and Description
SequenceBuilder	SequenceBuilderFilter.getDelegate() Retrieve the delegate that is wrapped.
SequenceBuilder	SwissprotProcessor.Factory.makeSequenceBuilder()
SequenceBuilder	OrganismParser.Factory.makeSequenceBuilder()
SequenceBuilder	GenbankProcessor.Factory.makeSequenceBuilder()
SequenceBuilder	FastaDescriptionLineParser.Factory.makeSequenceBuilder()
SequenceBuilder	SequenceBuilderFactory.makeSequenceBuilder()
SequenceBuilder	EmblProcessor.Factory.makeSequenceBuilder()
SequenceBuilder	ProteinRefSeqProcessor.Factory.makeSequenceBuilder()
SequenceBuilder	SwissprotProcessor.Factory.makeSequenceBuilder(String theSource)
SequenceBuilder	GenbankProcessor.Factory.makeSequenceBuilder(String theSource)

Constructors in org.biojava.bio.seq.io with parameters of type SequenceBuilder

Constructor and Description
EmblProcessor(SequenceBuilder delegate) Deprecated.
FastaDescriptionLineParser(SequenceBuilder delegate) Deprecated.
GenbankProcessor(SequenceBuilder theDelegate) Deprecated.
GenbankProcessor(SequenceBuilder theDelegate, String theSource) Deprecated.
OrganismParser(SequenceBuilder delegate, TaxonFactory taxonFactory, TaxonParser taxonParser, String sciNameKey, String commonNameKey, String ncbiTaxonKey) Deprecated.
ProteinRefSeqProcessor(SequenceBuilder theDelegate) Deprecated.
SequenceBuilderFilter(SequenceBuilder delegate) Create a new SeqIOFilter that will forward events on to another listener.
SwissprotProcessor(SequenceBuilder delegate) Deprecated.
SwissprotProcessor(SequenceBuilder delegate, String theSource) Deprecated. Constructor that sets the source of the feature to theSource.

Uses of SequenceBuilder in org.biojavax.bio.seq.io

Subinterfaces of SequenceBuilder in org.biojavax.bio.seq.io

Modifier and Type	Interface and Description
interface	RichSequenceBuilder An interface for objects that can build RichSequences.

Classes in org.biojavax.bio.seq.io that implement SequenceBuilder

Modifier and Type	Class and Description
class	SimpleRichSequenceBuilder Constructs BioEntry objects by listening to events.

Methods in org.biojavax.bio.seq.io that return SequenceBuilder

Modifier and Type	Method and Description
SequenceBuilder	SimpleRichSequenceBuilderFactory.makeSequenceBuilder()