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. 
 

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

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

Constructors in org.biojava.bio.seq.db with parameters of type SequenceBuilderFactory
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.
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.
TabIndexStore(java.io.File storeFile, java.io.File indexFile, java.lang.String name, SequenceFormat format, SequenceBuilderFactory sbFactory, SymbolTokenization symbolParser)
           
 

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

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

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

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

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