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 newEmblCDROMIndexStorebacked by a random access binary index.EmblCDROMIndexStore(File divisionLkp, File entryNamIdx, SequenceFormat format, SequenceBuilderFactory factory, SymbolTokenization parser) Creates a newEmblCDROMIndexStorebacked 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 classDeprecated.Factory which wraps SequenceBuilders in an EmblProcessorstatic classDeprecated.Factory which wraps SequenceBuilders in a FastaDescriptionLineParserstatic classDeprecated.Factory which wraps sequence builders in a GenbankProcessorstatic classDeprecated.Factory which wraps SequenceBuilders in an OrganismParser.static classDeprecated.Factory which wraps sequence builders in a ProteinRefSeqProcessorstatic classDeprecated.Factory which wraps SequenceBuilders in a SwissprotProcessorFields in org.biojava.bio.seq.io declared as SequenceBuilderFactoryModifier and TypeFieldDescriptionstatic final SequenceBuilderFactorySmartSequenceBuilder.BIT_PACKEDstatic final SequenceBuilderFactorySimpleAssemblyBuilder.FACTORYstatic final SequenceBuilderFactorySimpleSequenceBuilder.FACTORYstatic final SequenceBuilderFactorySmartSequenceBuilder.FACTORYMethods in org.biojava.bio.seq.io that return SequenceBuilderFactoryModifier and TypeMethodDescriptionstatic SequenceBuilderFactorySeqIOTools.formatToFactory(SequenceFormat format, Alphabet alpha) Deprecated.static SequenceBuilderFactorySeqIOTools.getBuilderFactory(int identifier) Deprecated.getBuilderFactoryaccepts a value which represents a sequence format and returns the relevantSequenceBuilderFactoryobject.static SequenceBuilderFactorySeqIOTools.getEmblBuilderFactory()Deprecated.Get a default SequenceBuilderFactory for handling EMBL files.static SequenceBuilderFactorySeqIOTools.getFastaBuilderFactory()Deprecated.Get a default SequenceBuilderFactory for handling FASTA files.static SequenceBuilderFactorySeqIOTools.getGenbankBuilderFactory()Deprecated.Get a default SequenceBuilderFactory for handling GenBank files.static SequenceBuilderFactorySeqIOTools.getGenpeptBuilderFactory()Deprecated.Get a default SequenceBuilderFactory for handling Genpept files.static SequenceBuilderFactorySeqIOTools.getSwissprotBuilderFactory()Deprecated.Get a default SequenceBuilderFactory for handling Swissprot files.Methods in org.biojava.bio.seq.io with parameters of type SequenceBuilderFactoryModifier and TypeMethodDescriptionstatic SequenceIteratorSeqIOTools.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 TypeInterfaceDescriptioninterfaceSimple factory for constructing new RichSequenceBuilder objects.Classes in org.biojavax.bio.seq.io that implement SequenceBuilderFactoryModifier and TypeClassDescriptionclassGenerates RichSequenceBuilder objects.
identifyBuilderFactory.