## 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.
org.biojava.bio.seq.ragbag: The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code.

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

Constructors in org.biojava.bio.seq.io with parameters of type SequenceBuilder
`SequenceBuilderFilter(SequenceBuilder delegate)` Create a new SeqIOFilter that will forward events on to another listener.
`FastaDescriptionLineParser(SequenceBuilder delegate)`
`EmblProcessor(SequenceBuilder delegate)`
`SwissprotProcessor(SequenceBuilder delegate, java.lang.String theSource)` Constructor that sets the source of the feature to theSource.
`SwissprotProcessor(SequenceBuilder delegate)`
`GenbankProcessor(SequenceBuilder theDelegate, java.lang.String theSource)`
`GenbankProcessor(SequenceBuilder theDelegate)`
`OrganismParser(SequenceBuilder delegate, TaxonFactory taxonFactory, TaxonParser taxonParser, java.lang.String sciNameKey, java.lang.String commonNameKey, java.lang.String ncbiTaxonKey)`
`ProteinRefSeqProcessor(SequenceBuilder theDelegate)`

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

Classes in org.biojava.bio.seq.ragbag that implement SequenceBuilder
`class` `RagbagIdleSequenceBuilder` A breakfast cereal of a SequenceBuilder, jes' sits there soakin' up all those events and doin' absolutely nuffin'.

Methods in org.biojava.bio.seq.ragbag that return SequenceBuilder
`SequenceBuilder` `RagbagFeatureTypeCatcher.wrap(SequenceBuilder delegate)`
`SequenceBuilder` `RagbagFilterFactory.wrap(SequenceBuilder delegate)` returns a SequenceBuilder object wrapped with an a filter.

Methods in org.biojava.bio.seq.ragbag with parameters of type SequenceBuilder
`SequenceBuilder` `RagbagFeatureTypeCatcher.wrap(SequenceBuilder delegate)`
`SequenceBuilder` `RagbagFilterFactory.wrap(SequenceBuilder delegate)` returns a SequenceBuilder object wrapped with an a filter.