Package org.biojava.bio.seq.io
Class SequenceDBSequenceBuilder
java.lang.Object
org.biojava.bio.seq.io.SequenceBuilderBase
org.biojava.bio.seq.io.SequenceDBSequenceBuilder
- All Implemented Interfaces:
SeqIOListener
,SequenceBuilder
This SequenceBuilder has a variety of modes of operation.
It can take a sequence from an existing SequenceDB and
apply annotations to it.
If the SequenceDB has persistence, then it can also create a sequence in the sequenceDB and apply the annotation to that. However, performance under those circumstances can vary depending on how well the persistent SequenceDB handles this.
Following the introduction of biojavax persistence is handled by
Hibernate refer to
BioSQLRichObjectBuilder
- Author:
- David Huen
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final int
static final int
static final int
Fields inherited from class org.biojava.bio.seq.io.SequenceBuilderBase
annotation, ERROR_FEATURES_PROPERTY, name, seq, uri
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addSymbols
(Alphabet alpha, Symbol[] syms, int pos, int len) does nothing for now.create the sequenceMethods inherited from class org.biojava.bio.seq.io.SequenceBuilderBase
addFeatureProperty, addProperty, addSequenceProperty, endFeature, endSequence, setName, setURI, startFeature, startSequence
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Field Details
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ANNOTATE_EXISTING
- See Also:
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CREATE_DUMMYSEQ
- See Also:
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CREATE_REALSEQ
- See Also:
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Constructor Details
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SequenceDBSequenceBuilder
constructor
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Method Details
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addSymbols
does nothing for now.- Specified by:
addSymbols
in interfaceSeqIOListener
- Specified by:
addSymbols
in classSequenceBuilderBase
- Parameters:
alpha
- The alphabet of the symbol datasyms
- An array containing symbolspos
- The start offset of valid data within the arraylen
- The number of valid symbols in the array
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makeSequence
create the sequence- Specified by:
makeSequence
in interfaceSequenceBuilder
- Overrides:
makeSequence
in classSequenceBuilderBase
- Throws:
BioException
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