Uses of Interface
org.biojava.bio.seq.io.SequenceBuilderFactory
Packages that use SequenceBuilderFactory
Package
Description
Collections of biological sequence data.
Classes and interfaces for processing and producing flat-file representations
of sequences.
Classes to support the I/O of RichSequence and
Bioentry objects.
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Uses of SequenceBuilderFactory in org.biojava.bio.seq.db
Methods in org.biojava.bio.seq.db that return SequenceBuilderFactoryModifier and TypeMethodDescriptionBioIndex.getSBFactory()
EmblCDROMIndexStore.getSBFactory()
IndexStore.getSBFactory()
Retrieve the SequenceBuilderFactory used to build Sequence instances.TabIndexStore.getSBFactory()
Constructors in org.biojava.bio.seq.db with parameters of type SequenceBuilderFactoryModifierConstructorDescriptionEmblCDROMIndexStore
(File pathPrefix, File divisionLkp, File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser) Creates a newEmblCDROMIndexStore
backed by a random access binary index.EmblCDROMIndexStore
(File divisionLkp, File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser) Creates a newEmblCDROMIndexStore
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 SequenceBuilderFactoryModifier and TypeClassDescriptionstatic class
Deprecated.Factory which wraps SequenceBuilders in an EmblProcessorstatic class
Deprecated.Factory which wraps SequenceBuilders in a FastaDescriptionLineParserstatic class
Deprecated.Factory which wraps sequence builders in a GenbankProcessorstatic class
Deprecated.Factory which wraps SequenceBuilders in an OrganismParser.static class
Deprecated.Factory which wraps sequence builders in a ProteinRefSeqProcessorstatic class
Deprecated.Factory which wraps SequenceBuilders in a SwissprotProcessorFields in org.biojava.bio.seq.io declared as SequenceBuilderFactoryModifier and TypeFieldDescriptionstatic final SequenceBuilderFactory
SmartSequenceBuilder.BIT_PACKED
static final SequenceBuilderFactory
SimpleAssemblyBuilder.FACTORY
static final SequenceBuilderFactory
SimpleSequenceBuilder.FACTORY
static final SequenceBuilderFactory
SmartSequenceBuilder.FACTORY
Methods in org.biojava.bio.seq.io that return SequenceBuilderFactoryModifier and TypeMethodDescriptionstatic SequenceBuilderFactory
SeqIOTools.formatToFactory
(SequenceFormat format, Alphabet alpha) Deprecated.static SequenceBuilderFactory
SeqIOTools.getBuilderFactory
(int identifier) Deprecated.getBuilderFactory
accepts a value which represents a sequence format and returns the relevantSequenceBuilderFactory
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 SequenceBuilderFactoryModifier and TypeMethodDescriptionstatic 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 SequenceBuilderFactoryModifierConstructorDescriptionFactory
(SequenceBuilderFactory delegateFactory) Factory
(SequenceBuilderFactory delegateFactory) Factory
(SequenceBuilderFactory theDelegate) Factory
(SequenceBuilderFactory delegateFactory, TaxonFactory taxonFactory, TaxonParser taxonParser, String sciNameKey, String commonNameKey, String ncbiTaxonKey) Factory
(SequenceBuilderFactory theDelegate) Factory
(SequenceBuilderFactory delegateFactory) StreamReader
(BufferedReader reader, SequenceFormat format, SymbolTokenization symParser, SequenceBuilderFactory sf) StreamReader
(InputStream is, SequenceFormat format, SymbolTokenization symParser, SequenceBuilderFactory sf) -
Uses of SequenceBuilderFactory in org.biojavax.bio.seq.io
Subinterfaces of SequenceBuilderFactory in org.biojavax.bio.seq.ioModifier and TypeInterfaceDescriptioninterface
Simple factory for constructing new RichSequenceBuilder objects.Classes in org.biojavax.bio.seq.io that implement SequenceBuilderFactoryModifier and TypeClassDescriptionclass
Generates RichSequenceBuilder objects.
identifyBuilderFactory
.