Uses of Interface
org.biojava.bio.seq.io.SequenceBuilder

Packages that use SequenceBuilder
org.biojava.bio.seq.io Classes and interfaces for processing and producing flat-file representations of sequences. 
org.biojava.bio.seq.ragbag The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code. 
 

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

Classes in org.biojava.bio.seq.io that implement SequenceBuilder
 class EmblProcessor
          Simple filter which handles attribute lines from an EMBL file.
 class FastaDescriptionLineParser
          Simple filter which performs a default extraction of data from the description lines of FASTA files.
 class GenbankProcessor
          Simple filter which handles attribute lines from a Genbank file
 class OrganismParser
          A parser that is able to generate Taxon entries for sequence builder event streams.
 class ProteinRefSeqProcessor
          Class description
 class SequenceBuilderBase
          Basic SequenceBuilder implementation which accumulates all notified information.
 class SequenceBuilderFilter
          Base-class for builders that pass filtered events onto another builder.
 class SequenceDBSequenceBuilder
          This SequenceBuilder has a variety of modes of operation.
 class SimpleAssemblyBuilder
          Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleAssembly.
 class SimpleSequenceBuilder
          Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleSequence.
 class SmartSequenceBuilder
          Basic SequenceBuilder implementation which accumulates all notified information and chooses a sequence implementation suited to the size of the sequence.
 class SwissprotProcessor
          Simple filter which handles attribute lines from an Swissprot entry.
 

Methods in org.biojava.bio.seq.io that return SequenceBuilder
 SequenceBuilder SequenceBuilderFilter.getDelegate()
          Retrieve the delegate that is wrapped.
 SequenceBuilder FastaDescriptionLineParser.Factory.makeSequenceBuilder()
           
 SequenceBuilder EmblProcessor.Factory.makeSequenceBuilder()
           
 SequenceBuilder SwissprotProcessor.Factory.makeSequenceBuilder()
           
 SequenceBuilder SwissprotProcessor.Factory.makeSequenceBuilder(java.lang.String theSource)
           
 SequenceBuilder GenbankProcessor.Factory.makeSequenceBuilder()
           
 SequenceBuilder GenbankProcessor.Factory.makeSequenceBuilder(java.lang.String theSource)
           
 SequenceBuilder OrganismParser.Factory.makeSequenceBuilder()
           
 SequenceBuilder SequenceBuilderFactory.makeSequenceBuilder()
           
 SequenceBuilder ProteinRefSeqProcessor.Factory.makeSequenceBuilder()
           
 

Constructors in org.biojava.bio.seq.io with parameters of type SequenceBuilder
SequenceBuilderFilter(SequenceBuilder delegate)
          Create a new SeqIOFilter that will forward events on to another listener.
FastaDescriptionLineParser(SequenceBuilder delegate)
           
EmblProcessor(SequenceBuilder delegate)
           
SwissprotProcessor(SequenceBuilder delegate, java.lang.String theSource)
          Constructor that sets the source of the feature to theSource.
SwissprotProcessor(SequenceBuilder delegate)
           
GenbankProcessor(SequenceBuilder theDelegate, java.lang.String theSource)
           
GenbankProcessor(SequenceBuilder theDelegate)
           
OrganismParser(SequenceBuilder delegate, TaxonFactory taxonFactory, TaxonParser taxonParser, java.lang.String sciNameKey, java.lang.String commonNameKey, java.lang.String ncbiTaxonKey)
           
ProteinRefSeqProcessor(SequenceBuilder theDelegate)
           
 

Uses of SequenceBuilder in org.biojava.bio.seq.ragbag
 

Classes in org.biojava.bio.seq.ragbag that implement SequenceBuilder
 class RagbagIdleSequenceBuilder
          A breakfast cereal of a SequenceBuilder, jes' sits there soakin' up all those events and doin' absolutely nuffin'.
 

Methods in org.biojava.bio.seq.ragbag that return SequenceBuilder
 SequenceBuilder RagbagFeatureTypeCatcher.wrap(SequenceBuilder delegate)
           
 SequenceBuilder RagbagFilterFactory.wrap(SequenceBuilder delegate)
          returns a SequenceBuilder object wrapped with an a filter.
 

Methods in org.biojava.bio.seq.ragbag with parameters of type SequenceBuilder
 SequenceBuilder RagbagFeatureTypeCatcher.wrap(SequenceBuilder delegate)
           
 SequenceBuilder RagbagFilterFactory.wrap(SequenceBuilder delegate)
          returns a SequenceBuilder object wrapped with an a filter.