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

Packages that use SequenceBuilder

org.biojava.bio.seq.io

Classes and interfaces for processing and producing flat-file representations of sequences.

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

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

class	EmblProcessor Simple filter which handles attribute lines from an EMBL file.
class	FastaDescriptionLineParser Simple filter which performs a default extraction of data from the description lines of FASTA files.
class	GenbankProcessor Simple filter which handles attribute lines from a Genbank file
class	OrganismParser A parser that is able to generate Taxon entries for sequence builder event streams.
class	ProteinRefSeqProcessor Class description
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 Simple filter which handles attribute lines from an Swissprot entry.

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

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

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

SwissprotProcessor(SequenceBuilder delegate, String theSource)
Constructor that sets the source of the feature to theSource.

SwissprotProcessor(SequenceBuilder delegate)

SequenceBuilderFilter(SequenceBuilder delegate)
Create a new SeqIOFilter that will forward events on to another listener.

ProteinRefSeqProcessor(SequenceBuilder theDelegate)

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

GenbankProcessor(SequenceBuilder theDelegate, String theSource)

GenbankProcessor(SequenceBuilder theDelegate)

FastaDescriptionLineParser(SequenceBuilder delegate)

EmblProcessor(SequenceBuilder delegate)