Uses of Interface
org.biojava.bio.seq.io.SequenceBuilder
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Packages that use SequenceBuilder Package Description 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. -
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Uses of SequenceBuilder in org.biojava.bio.seq.io
Classes in org.biojava.bio.seq.io that implement SequenceBuilder Modifier and Type Class Description class
EmblProcessor
Deprecated.Use org.biojavax.bio.seq.io framework insteadclass
FastaDescriptionLineParser
Deprecated.Use org.biojavax.bio.seq.io.FastaFormatclass
GenbankProcessor
Deprecated.Use org.biojavax.bio.seq.io framework insteadclass
OrganismParser
Deprecated.Use org.biojavax.bio.taxa framework insteadclass
ProteinRefSeqProcessor
Deprecated.Use org.biojavax.bio.seq.io framework insteadclass
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 insteadMethods in org.biojava.bio.seq.io that return SequenceBuilder Modifier and Type Method Description SequenceBuilder
SequenceBuilderFilter. getDelegate()
Retrieve the delegate that is wrapped.SequenceBuilder
EmblProcessor.Factory. makeSequenceBuilder()
SequenceBuilder
FastaDescriptionLineParser.Factory. makeSequenceBuilder()
SequenceBuilder
GenbankProcessor.Factory. makeSequenceBuilder()
SequenceBuilder
GenbankProcessor.Factory. makeSequenceBuilder(String theSource)
SequenceBuilder
OrganismParser.Factory. makeSequenceBuilder()
SequenceBuilder
ProteinRefSeqProcessor.Factory. makeSequenceBuilder()
SequenceBuilder
SequenceBuilderFactory. makeSequenceBuilder()
SequenceBuilder
SwissprotProcessor.Factory. makeSequenceBuilder()
SequenceBuilder
SwissprotProcessor.Factory. makeSequenceBuilder(String theSource)
Constructors in org.biojava.bio.seq.io with parameters of type SequenceBuilder Constructor Description 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 Modifier and Type Interface Description interface
RichSequenceBuilder
An interface for objects that can build RichSequences.Classes in org.biojavax.bio.seq.io that implement SequenceBuilder Modifier and Type Class Description class
SimpleRichSequenceBuilder
Constructs BioEntry objects by listening to events.Methods in org.biojavax.bio.seq.io that return SequenceBuilder Modifier and Type Method Description SequenceBuilder
SimpleRichSequenceBuilderFactory. makeSequenceBuilder()
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