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. 
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
 SequenceBuilderFactory BioIndex.getSBFactory()
           
 SequenceBuilderFactory EmblCDROMIndexStore.getSBFactory()
           
 SequenceBuilderFactory IndexStore.getSBFactory()
          Retrieve the SequenceBuilderFactory used to build Sequence instances.
 SequenceBuilderFactory TabIndexStore.getSBFactory()
           
 

Constructors in org.biojava.bio.seq.db with parameters of type SequenceBuilderFactory
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
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
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
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
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
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
 interface RichSequenceBuilderFactory
          Simple factory for constructing new RichSequenceBuilder objects.
 

Classes in org.biojavax.bio.seq.io that implement SequenceBuilderFactory
 class SimpleRichSequenceBuilderFactory
          Generates RichSequenceBuilder objects.