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Packages that use SequenceBuilder | |
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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 |
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Classes in org.biojava.bio.seq.io that implement SequenceBuilder | |
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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 | |
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SequenceBuilder |
SequenceBuilderFilter.getDelegate()
Retrieve the delegate that is wrapped. |
SequenceBuilder |
EmblProcessor.Factory.makeSequenceBuilder()
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SequenceBuilder |
FastaDescriptionLineParser.Factory.makeSequenceBuilder()
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SequenceBuilder |
GenbankProcessor.Factory.makeSequenceBuilder()
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SequenceBuilder |
OrganismParser.Factory.makeSequenceBuilder()
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SequenceBuilder |
ProteinRefSeqProcessor.Factory.makeSequenceBuilder()
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SequenceBuilder |
SequenceBuilderFactory.makeSequenceBuilder()
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SequenceBuilder |
SwissprotProcessor.Factory.makeSequenceBuilder()
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SequenceBuilder |
GenbankProcessor.Factory.makeSequenceBuilder(String theSource)
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SequenceBuilder |
SwissprotProcessor.Factory.makeSequenceBuilder(String theSource)
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Constructors in org.biojava.bio.seq.io with parameters of type SequenceBuilder | |
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EmblProcessor(SequenceBuilder delegate)
Deprecated. |
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FastaDescriptionLineParser(SequenceBuilder delegate)
Deprecated. |
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GenbankProcessor(SequenceBuilder theDelegate)
Deprecated. |
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GenbankProcessor(SequenceBuilder theDelegate,
String theSource)
Deprecated. |
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OrganismParser(SequenceBuilder delegate,
TaxonFactory taxonFactory,
TaxonParser taxonParser,
String sciNameKey,
String commonNameKey,
String ncbiTaxonKey)
Deprecated. |
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ProteinRefSeqProcessor(SequenceBuilder theDelegate)
Deprecated. |
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SequenceBuilderFilter(SequenceBuilder delegate)
Create a new SeqIOFilter that will forward events on to another listener. |
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SwissprotProcessor(SequenceBuilder delegate)
Deprecated. |
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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 |
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Subinterfaces of SequenceBuilder in org.biojavax.bio.seq.io | |
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interface |
RichSequenceBuilder
An interface for objects that can build RichSequences. |
Classes in org.biojavax.bio.seq.io that implement SequenceBuilder | |
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class |
SimpleRichSequenceBuilder
Constructs BioEntry objects by listening to events. |
Methods in org.biojavax.bio.seq.io that return SequenceBuilder | |
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SequenceBuilder |
SimpleRichSequenceBuilderFactory.makeSequenceBuilder()
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