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.biojavax.bio.seq.io Classes to support the I/O of RichSequence and Bioentry objects. 
 

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

Classes in org.biojava.bio.seq.io that implement SequenceBuilder
 class EmblProcessor
          Deprecated. Use org.biojavax.bio.seq.io framework instead
 class FastaDescriptionLineParser
          Deprecated. Use org.biojavax.bio.seq.io.FastaFormat
 class GenbankProcessor
          Deprecated. Use org.biojavax.bio.seq.io framework instead
 class OrganismParser
          Deprecated. Use org.biojavax.bio.taxa framework instead
 class ProteinRefSeqProcessor
          Deprecated. Use org.biojavax.bio.seq.io framework instead
 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
          Deprecated. Use org.biojavax.bio.seq.io framework instead
 

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

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

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

Subinterfaces of SequenceBuilder in org.biojavax.bio.seq.io
 interface RichSequenceBuilder
          An interface for objects that can build RichSequences.
 

Classes in org.biojavax.bio.seq.io that implement SequenceBuilder
 class SimpleRichSequenceBuilder
          Constructs BioEntry objects by listening to events.
 

Methods in org.biojavax.bio.seq.io that return SequenceBuilder
 SequenceBuilder SimpleRichSequenceBuilderFactory.makeSequenceBuilder()