Uses of Interface org.biojava.bio.seq.io.SequenceBuilderFactory (BioJava-1.5-beta API)

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## Uses of Interface
org.biojava.bio.seq.io.SequenceBuilderFactory

Packages that use SequenceBuilderFactory
org.biojava.bio.seq.db | Collections of biological sequence data.
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 SequenceBuilderFactory in org.biojava.bio.seq.db

Methods in org.biojava.bio.seq.db that return SequenceBuilderFactory
`SequenceBuilderFactory` | `BioIndex.getSBFactory()`
`SequenceBuilderFactory` | `EmblCDROMIndexStore.getSBFactory()`
`SequenceBuilderFactory` | `IndexStore.getSBFactory()` Retrieve the SequenceBuilderFactory used to build Sequence instances.
`SequenceBuilderFactory` | `TabIndexStore.getSBFactory()`

Constructors in org.biojava.bio.seq.db with parameters of type SequenceBuilderFactory
`EmblCDROMIndexStore(File pathPrefix, File divisionLkp, File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser)` Creates a new `EmblCDROMIndexStore` backed by a random access binary index.
`EmblCDROMIndexStore(File divisionLkp, File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser)` Creates a new `EmblCDROMIndexStore` backed by a random access binary index.
`TabIndexStore(File storeFile, File indexFile, String name, SequenceFormat format, SequenceBuilderFactory sbFactory, SymbolTokenization symbolParser)` Create a new TabIndexStore.

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

Classes in org.biojava.bio.seq.io that implement SequenceBuilderFactory
`static class` | `EmblProcessor.Factory` Deprecated. Factory which wraps SequenceBuilders in an EmblProcessor
`static class` | `FastaDescriptionLineParser.Factory` Deprecated. Factory which wraps SequenceBuilders in a FastaDescriptionLineParser
`static class` | `GenbankProcessor.Factory` Deprecated. Factory which wraps sequence builders in a GenbankProcessor
`static class` | `OrganismParser.Factory` Deprecated. Factory which wraps SequenceBuilders in an OrganismParser.
`static class` | `ProteinRefSeqProcessor.Factory` Deprecated. Factory which wraps sequence builders in a ProteinRefSeqProcessor
`static class` | `SwissprotProcessor.Factory` Deprecated. Factory which wraps SequenceBuilders in a SwissprotProcessor

Fields in org.biojava.bio.seq.io declared as SequenceBuilderFactory
`static SequenceBuilderFactory` | `SmartSequenceBuilder.BIT_PACKED`
`static SequenceBuilderFactory` | `SmartSequenceBuilder.FACTORY`
`static SequenceBuilderFactory` | `SimpleSequenceBuilder.FACTORY`
`static SequenceBuilderFactory` | `SimpleAssemblyBuilder.FACTORY`

Methods in org.biojava.bio.seq.io that return SequenceBuilderFactory
`static SequenceBuilderFactory` | `SeqIOTools.formatToFactory(SequenceFormat format, Alphabet alpha)` Deprecated. as this essentially duplicates the operation available in the method `identifyBuilderFactory`.
`static SequenceBuilderFactory` | `SeqIOTools.getBuilderFactory(int identifier)` Deprecated. `getBuilderFactory` accepts a value which represents a sequence format and returns the relevant `SequenceBuilderFactory` object.
`static SequenceBuilderFactory` | `SeqIOTools.getEmblBuilderFactory()` Deprecated. Get a default SequenceBuilderFactory for handling EMBL files.
`static SequenceBuilderFactory` | `SeqIOTools.getFastaBuilderFactory()` Deprecated. Get a default SequenceBuilderFactory for handling FASTA files.
`static SequenceBuilderFactory` | `SeqIOTools.getGenbankBuilderFactory()` Deprecated. Get a default SequenceBuilderFactory for handling GenBank files.
`static SequenceBuilderFactory` | `SeqIOTools.getGenpeptBuilderFactory()` Deprecated. Get a default SequenceBuilderFactory for handling Genpept files.
`static SequenceBuilderFactory` | `SeqIOTools.getSwissprotBuilderFactory()` Deprecated. Get a default SequenceBuilderFactory for handling Swissprot files.

Methods in org.biojava.bio.seq.io with parameters of type SequenceBuilderFactory
`static SequenceIterator` | `SeqIOTools.readFasta(BufferedReader br, SymbolTokenization sTok, SequenceBuilderFactory seqFactory)` Deprecated. Read a fasta file using a custom type of SymbolList.

Constructors in org.biojava.bio.seq.io with parameters of type SequenceBuilderFactory
`EmblProcessor.Factory(SequenceBuilderFactory delegateFactory)`
`FastaDescriptionLineParser.Factory(SequenceBuilderFactory delegateFactory)`
`GenbankProcessor.Factory(SequenceBuilderFactory theDelegate)`
`OrganismParser.Factory(SequenceBuilderFactory delegateFactory, TaxonFactory taxonFactory, TaxonParser taxonParser, String sciNameKey, String commonNameKey, String ncbiTaxonKey)`
`ProteinRefSeqProcessor.Factory(SequenceBuilderFactory theDelegate)`
`StreamReader(BufferedReader reader, SequenceFormat format, SymbolTokenization symParser, SequenceBuilderFactory sf)`
`StreamReader(InputStream is, SequenceFormat format, SymbolTokenization symParser, SequenceBuilderFactory sf)`
`SwissprotProcessor.Factory(SequenceBuilderFactory delegateFactory)`

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

Subinterfaces of SequenceBuilderFactory in org.biojavax.bio.seq.io
`interface` | `RichSequenceBuilderFactory` Simple factory for constructing new RichSequenceBuilder objects.

Classes in org.biojavax.bio.seq.io that implement SequenceBuilderFactory
`class` | `SimpleRichSequenceBuilderFactory` Generates RichSequenceBuilder objects.

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