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

Packages that use SequenceBuilderFactory

Package	Description
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

Modifier and Type	Method and Description
SequenceBuilderFactory	TabIndexStore.getSBFactory()
SequenceBuilderFactory	IndexStore.getSBFactory() Retrieve the SequenceBuilderFactory used to build Sequence instances.
SequenceBuilderFactory	EmblCDROMIndexStore.getSBFactory()
SequenceBuilderFactory	BioIndex.getSBFactory()

Constructors in org.biojava.bio.seq.db with parameters of type SequenceBuilderFactory

Constructor and Description
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

Modifier and Type	Class and Description
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

Modifier and Type	Field and Description
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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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

Constructor and Description
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

Modifier and Type	Interface and Description
interface	RichSequenceBuilderFactory Simple factory for constructing new RichSequenceBuilder objects.

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

Modifier and Type	Class and Description
class	SimpleRichSequenceBuilderFactory Generates RichSequenceBuilder objects.