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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()
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SequenceBuilder |
EmblProcessor.Factory.makeSequenceBuilder()
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SequenceBuilder |
SwissprotProcessor.Factory.makeSequenceBuilder()
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SequenceBuilder |
SwissprotProcessor.Factory.makeSequenceBuilder(java.lang.String theSource)
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SequenceBuilder |
GenbankProcessor.Factory.makeSequenceBuilder()
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SequenceBuilder |
GenbankProcessor.Factory.makeSequenceBuilder(java.lang.String theSource)
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SequenceBuilder |
OrganismParser.Factory.makeSequenceBuilder()
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SequenceBuilder |
SequenceBuilderFactory.makeSequenceBuilder()
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SequenceBuilder |
ProteinRefSeqProcessor.Factory.makeSequenceBuilder()
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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. |
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FastaDescriptionLineParser(SequenceBuilder delegate)
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EmblProcessor(SequenceBuilder delegate)
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SwissprotProcessor(SequenceBuilder delegate,
java.lang.String theSource)
Constructor that sets the source of the feature to theSource. |
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SwissprotProcessor(SequenceBuilder delegate)
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GenbankProcessor(SequenceBuilder theDelegate,
java.lang.String theSource)
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GenbankProcessor(SequenceBuilder theDelegate)
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OrganismParser(SequenceBuilder delegate,
TaxonFactory taxonFactory,
TaxonParser taxonParser,
java.lang.String sciNameKey,
java.lang.String commonNameKey,
java.lang.String ncbiTaxonKey)
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ProteinRefSeqProcessor(SequenceBuilder theDelegate)
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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)
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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)
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SequenceBuilder |
RagbagFilterFactory.wrap(SequenceBuilder delegate)
returns a SequenceBuilder object wrapped with an a filter. |
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