Uses of Interface
org.biojava.bio.seq.io.SequenceBuilder
Packages that use SequenceBuilder
Package
Description
Classes and interfaces for processing and producing flat-file representations
of sequences.
Classes to support the I/O of RichSequence and
Bioentry objects.
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Uses of SequenceBuilder in org.biojava.bio.seq.io
Classes in org.biojava.bio.seq.io that implement SequenceBuilderModifier and TypeClassDescriptionclassDeprecated.Use org.biojavax.bio.seq.io framework insteadclassDeprecated.Use org.biojavax.bio.seq.io.FastaFormatclassDeprecated.Use org.biojavax.bio.seq.io framework insteadclassDeprecated.Use org.biojavax.bio.taxa framework insteadclassDeprecated.Use org.biojavax.bio.seq.io framework insteadclassBasic SequenceBuilder implementation which accumulates all notified information.classBase-class for builders that pass filtered events onto another builder.classThis SequenceBuilder has a variety of modes of operation.classBasic SequenceBuilder implementation which accumulates all notified information and creates a SimpleAssembly.classBasic SequenceBuilder implementation which accumulates all notified information and creates a SimpleSequence.classBasic SequenceBuilder implementation which accumulates all notified information and chooses a sequence implementation suited to the size of the sequence.classDeprecated.Use org.biojavax.bio.seq.io framework insteadMethods in org.biojava.bio.seq.io that return SequenceBuilderModifier and TypeMethodDescriptionSequenceBuilderFilter.getDelegate()Retrieve the delegate that is wrapped.EmblProcessor.Factory.makeSequenceBuilder()FastaDescriptionLineParser.Factory.makeSequenceBuilder()GenbankProcessor.Factory.makeSequenceBuilder()GenbankProcessor.Factory.makeSequenceBuilder(String theSource) OrganismParser.Factory.makeSequenceBuilder()ProteinRefSeqProcessor.Factory.makeSequenceBuilder()SequenceBuilderFactory.makeSequenceBuilder()SwissprotProcessor.Factory.makeSequenceBuilder()SwissprotProcessor.Factory.makeSequenceBuilder(String theSource) Constructors in org.biojava.bio.seq.io with parameters of type SequenceBuilderModifierConstructorDescriptionEmblProcessor(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.ioModifier and TypeInterfaceDescriptioninterfaceAn interface for objects that can build RichSequences.Classes in org.biojavax.bio.seq.io that implement SequenceBuilderModifier and TypeClassDescriptionclassConstructs BioEntry objects by listening to events.Methods in org.biojavax.bio.seq.io that return SequenceBuilder