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Packages that use SequenceBuilderFactory | |
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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 |
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Methods in org.biojava.bio.seq.db that return SequenceBuilderFactory | |
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SequenceBuilderFactory |
BioIndex.getSBFactory()
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SequenceBuilderFactory |
EmblCDROMIndexStore.getSBFactory()
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SequenceBuilderFactory |
IndexStore.getSBFactory()
Retrieve the SequenceBuilderFactory used to build Sequence instances. |
SequenceBuilderFactory |
TabIndexStore.getSBFactory()
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Constructors in org.biojava.bio.seq.db with parameters of type SequenceBuilderFactory | |
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EmblCDROMIndexStore(java.io.File pathPrefix,
java.io.File divisionLkp,
java.io.File entryNamIdx,
SequenceFormat format,
SequenceBuilderFactory factory,
SymbolTokenization parser)
Creates a new EmblCDROMIndexStore backed by a
random access binary index. |
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EmblCDROMIndexStore(java.io.File divisionLkp,
java.io.File entryNamIdx,
SequenceFormat format,
SequenceBuilderFactory factory,
SymbolTokenization parser)
Creates a new EmblCDROMIndexStore backed by a
random access binary index. |
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TabIndexStore(java.io.File storeFile,
java.io.File indexFile,
java.lang.String name,
SequenceFormat format,
SequenceBuilderFactory sbFactory,
SymbolTokenization symbolParser)
Create a new TabIndexStore. |
Uses of SequenceBuilderFactory in org.biojava.bio.seq.io |
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Classes in org.biojava.bio.seq.io that implement SequenceBuilderFactory | |
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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 | |
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static SequenceBuilderFactory |
SmartSequenceBuilder.BIT_PACKED
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static SequenceBuilderFactory |
SmartSequenceBuilder.FACTORY
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static SequenceBuilderFactory |
SimpleSequenceBuilder.FACTORY
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static SequenceBuilderFactory |
SimpleAssemblyBuilder.FACTORY
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Methods in org.biojava.bio.seq.io that return SequenceBuilderFactory | |
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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 | |
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static SequenceIterator |
SeqIOTools.readFasta(java.io.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 | |
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EmblProcessor.Factory(SequenceBuilderFactory delegateFactory)
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FastaDescriptionLineParser.Factory(SequenceBuilderFactory delegateFactory)
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GenbankProcessor.Factory(SequenceBuilderFactory theDelegate)
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OrganismParser.Factory(SequenceBuilderFactory delegateFactory,
TaxonFactory taxonFactory,
TaxonParser taxonParser,
java.lang.String sciNameKey,
java.lang.String commonNameKey,
java.lang.String ncbiTaxonKey)
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ProteinRefSeqProcessor.Factory(SequenceBuilderFactory theDelegate)
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StreamReader(java.io.BufferedReader reader,
SequenceFormat format,
SymbolTokenization symParser,
SequenceBuilderFactory sf)
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StreamReader(java.io.InputStream is,
SequenceFormat format,
SymbolTokenization symParser,
SequenceBuilderFactory sf)
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SwissprotProcessor.Factory(SequenceBuilderFactory delegateFactory)
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Uses of SequenceBuilderFactory in org.biojavax.bio.seq.io |
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Subinterfaces of SequenceBuilderFactory in org.biojavax.bio.seq.io | |
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interface |
RichSequenceBuilderFactory
Simple factory for constructing new RichSequenceBuilder objects. |
Classes in org.biojavax.bio.seq.io that implement SequenceBuilderFactory | |
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class |
SimpleRichSequenceBuilderFactory
Generates RichSequenceBuilder objects. |
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