Uses of Interface
org.biojava.bio.Annotation
Packages that use Annotation
Package
Description
The core classes that will be used throughout the bio packages.
HMM and Dynamic Programming Algorithms.
The classes and interfaces in this package cover common molecular
biological techniques such as restriction digests and PCR.
Support for reading and writing GFF3.
Tools for working with profile Hidden Markov Models from the HMMer package.
A flat-file ascii index of ascii flat files as per the OBDA specification.
Parser for Phred output
Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
Process files as streams of records, each with tags with values.
Event-driven parsing system for the Extensible Feature Format (XFF).
Interfaces and classes for representing sequence similarity search results.
Classes and interfaces for defining biological sequences and informatics
objects.
Standard in-memory implementations of
Sequence
and
Feature
.Classes and interfaces for processing and producing flat-file representations
of sequences.
Classes for converting between AGAVE XML and BioJava objects.
Representation of the Symbols that make up a sequence, and locations within
them.
Taxonomy object for representing species information.
A general-purpose API for ontologies.
The Biojava extensions packages, classes that extend the core biojava
functionality
Classes to represent biological entities and their relationships.
Rich implementations of Sequences, Locations and Features.
Extensions to the biojava ontology model that represent BioSQL ontology.
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Uses of Annotation in org.biojava.bio
Classes in org.biojava.bio that implement AnnotationModifier and TypeClassDescriptionclass
A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.class
AnnotationChanger
remaps the values of anAnnotation
to new values specified by aValueChanger
.class
AnnotationRenamer
remaps the keys of anAnnotation
to new keys specified by aTagMapper
.class
Create an Annotation with properties matching those of a JavaBean instance.class
Merged view onto a list of underlying Annotation objects.class
Annotation implementation which allows new key-value pairs to be layered on top of an underlying Annotation.class
A no-frills implementation of Annotation that is just a wrapper around aLinkedHashMap
.class
Annotation that is optimized for memory usage.Fields in org.biojava.bio declared as AnnotationModifier and TypeFieldDescriptionstatic final Annotation
Annotation.EMPTY_ANNOTATION
A really useful empty and immutable annotation object.Methods in org.biojava.bio that return AnnotationModifier and TypeMethodDescriptionstatic Annotation
AnnotationTools.allIn
(Annotation annotation, AnnotationType annType) Destructive down-cast an annotation to a type.static Annotation
AnnotationTools.allOut
(Annotation annotation, AnnotationType annType) allOut
returns a newAnnotation
containing only those values in theAnnotation
argument which are not of a type specified by theAnnotationType
.Annotatable.getAnnotation()
Should return the associated annotation object.AnnotationChanger.getWrapped()
getWrapped
returns theAnnotation
being remapped.AnnotationRenamer.getWrapped()
getWrapped
returns theAnnotation
being remapped.Methods in org.biojava.bio with parameters of type AnnotationModifier and TypeMethodDescriptionvoid
MergeAnnotation.addAnnotation
(Annotation ann) Add a new Annotation to to the end of the list to be merged.final void
AnnotationType.Abstract.addProperty
(Annotation ann, Object key, Object value) void
AnnotationType.addProperty
(Annotation ann, Object property, Object value) Add a value to the specified property slot.static Annotation
AnnotationTools.allIn
(Annotation annotation, AnnotationType annType) Destructive down-cast an annotation to a type.static Annotation
AnnotationTools.allOut
(Annotation annotation, AnnotationType annType) allOut
returns a newAnnotation
containing only those values in theAnnotation
argument which are not of a type specified by theAnnotationType
.final Collection
AnnotationType.Abstract.getProperty
(Annotation ann, Object property) AnnotationType.getProperty
(Annotation ann, Object property) Get the Collection of values associated with an Annotation bundle according to the type we believe it to be.boolean
AnnotationType.Abstract.instanceOf
(Annotation ann) boolean
AnnotationType.instanceOf
(Annotation ann) Validate an Annotation against this AnnotationType.void
MergeAnnotation.removeAnnotation
(Annotation ann) Remove an Annotation from the list.final void
AnnotationType.Abstract.removeProperty
(Annotation ann, Object key, Object value) void
AnnotationType.removeProperty
(Annotation ann, Object property, Object value) Remove a value from the specified property slot.static Set
AnnotationTools.searchAnnotation
(Annotation ann, AnnotationType query) Scans an Annotation with an AnnotationType and returns all Annotation instances matching a Type.final void
AnnotationType.Abstract.setProperty
(Annotation ann, Object property, Object value) void
AnnotationType.setProperty
(Annotation ann, Object property, Object value) Set the property in an annotation bundle according to the type we believe it should be.Constructors in org.biojava.bio with parameters of type AnnotationModifierConstructorDescriptionprotected
Copy-constructor.AnnotationChanger
(Annotation wrapped, ChangeTable changer) Creates a newAnnotationChanger
using the specifiedValueChanger
to remap its values.AnnotationRenamer
(Annotation wrapped, PropertyChanger mapper) Creates a newAnnotationRenamer
using the specifiedTagMapper
to remap its keys.Construct an annotation which can overlay new key-value pairs onto an underlying annotation.Create a new SimpleAnnotation by copying the properties from another one.Return a new SmallAnnotation that copies all values from another annoation. -
Uses of Annotation in org.biojava.bio.dp
Methods in org.biojava.bio.dp that return AnnotationMethods in org.biojava.bio.dp with parameters of type AnnotationConstructors in org.biojava.bio.dp with parameters of type AnnotationModifierConstructorDescriptionSimpleDotState
(char token, String name, Annotation annotation) Deprecated.token is ignored since 1.2.SimpleDotState
(String name, Annotation annotation) Construct a new state with the specified name and annotationSimpleEmissionState
(String name, Annotation ann, int[] advance, Distribution dis) -
Uses of Annotation in org.biojava.bio.molbio
Methods in org.biojava.bio.molbio that return AnnotationModifier and TypeMethodDescriptionstatic Annotation
RestrictionEnzymeManager.getAnnotation
(RestrictionEnzyme enzyme) getAnnotation
returns an immutable, static annotation describing the enzyme. -
Uses of Annotation in org.biojava.bio.program.gff3
Methods in org.biojava.bio.program.gff3 that return AnnotationMethods in org.biojava.bio.program.gff3 with parameters of type AnnotationModifier and TypeMethodDescriptionprotected void
GFF3Parser.parseAttribute
(String attValList, Annotation anno, Ontology onto, Ontology fallBack) Parse attValList into a Map of attributes and value lists. -
Uses of Annotation in org.biojava.bio.program.hmmer
Methods in org.biojava.bio.program.hmmer with parameters of type AnnotationModifier and TypeMethodDescriptionprotected EmissionState
HmmerProfileHMM.makeNewInsertState
(String str, Annotation ann, int[] adv, Distribution dis) protected EmissionState
HmmerProfileHMM.makeNewMatchState
(String str, Annotation ann, int[] adv, Distribution dis) Constructors in org.biojava.bio.program.hmmer with parameters of type AnnotationModifierConstructorDescriptionProfileEmissionState
(String str, Annotation ann, int[] adv, Distribution dis) -
Uses of Annotation in org.biojava.bio.program.indexdb
Methods in org.biojava.bio.program.indexdb that return AnnotationModifier and TypeMethodDescriptionBioStore.getMetaData()
IndexStore.getMetaData()
getMetaData
returns a data structure which represents an OBDA "config.dat" flatfile indexing configuration file. -
Uses of Annotation in org.biojava.bio.program.phred
Constructors in org.biojava.bio.program.phred with parameters of type AnnotationModifierConstructorDescriptionPhredSequence
(SymbolList phredSequence, String name, String urn, Annotation anno) Constructs a new PhredSequence. -
Uses of Annotation in org.biojava.bio.program.ssbind
Methods in org.biojava.bio.program.ssbind that return AnnotationModifier and TypeMethodDescriptionstatic Annotation
AnnotationFactory.makeAnnotation
(Map m) makeAnnotation
creates the annotation. -
Uses of Annotation in org.biojava.bio.program.tagvalue
Methods in org.biojava.bio.program.tagvalue that return AnnotationModifier and TypeMethodDescriptionAnnotationBuilder.getLast()
Get the last complete annotation built. -
Uses of Annotation in org.biojava.bio.program.xff
Methods in org.biojava.bio.program.xff that return AnnotationMethods in org.biojava.bio.program.xff with parameters of type AnnotationModifier and TypeMethodDescriptionstatic void
XFFTools.annotateXFF
(File xffFile, Sequence sequence, Annotation ann) void
XFFFeatureSetHandler.setMergeAnnotation
(Annotation ann) -
Uses of Annotation in org.biojava.bio.search
Methods in org.biojava.bio.search that return AnnotationModifier and TypeMethodDescriptionSequenceDBSearchHit.getAnnotation()
Deprecated.getAnnotation
returns the Annotation associated with this hit.SequenceDBSearchResult.getAnnotation()
Deprecated.getAnnotation
returns the Annotation associated with this hit.SequenceDBSearchSubHit.getAnnotation()
Deprecated.SimpleSeqSimilaritySearchHit.getAnnotation()
getAnnotation
returns the Annotation associated with this hit.SimpleSeqSimilaritySearchResult.getAnnotation()
getAnnotation
returns the Annotation associated with this hit.SimpleSeqSimilaritySearchSubHit.getAnnotation()
getAnnotation
returns the Annotation associated with this sub-hit.Constructors in org.biojava.bio.search with parameters of type AnnotationModifierConstructorDescriptionSequenceDBSearchHit
(double score, double eValue, double pValue, int queryStart, int queryEnd, StrandedFeature.Strand queryStrand, int subjectStart, int subjectEnd, StrandedFeature.Strand subjectStrand, String subjectID, Annotation annotation, List subHits) Deprecated.Creates a newSequenceDBSearchHit
object.SequenceDBSearchResult
(Sequence querySequence, SequenceDB sequenceDB, Map searchParameters, List hits, Annotation annotation) Deprecated.Creates a newSequenceDBSearchResult
.SequenceDBSearchSubHit
(double score, double eValue, double pValue, int queryStart, int queryEnd, StrandedFeature.Strand queryStrand, int subjectStart, int subjectEnd, StrandedFeature.Strand subjectStrand, Alignment alignment, Annotation annotation) Deprecated.Creates a newSequenceDBSearchSubHit
object.SimpleSeqSimilaritySearchHit
(double score, double eValue, double pValue, int queryStart, int queryEnd, StrandedFeature.Strand queryStrand, int subjectStart, int subjectEnd, StrandedFeature.Strand subjectStrand, String subjectID, Annotation annotation, List subHits) Creates a newSimpleSeqSimilaritySearchHit
object.SimpleSeqSimilaritySearchResult
(Sequence querySequence, SequenceDB sequenceDB, Map searchParameters, List hits, Annotation annotation) Creates a newSimpleSeqSimilaritySearchResult
.SimpleSeqSimilaritySearchSubHit
(double score, double eValue, double pValue, int queryStart, int queryEnd, StrandedFeature.Strand queryStrand, int subjectStart, int subjectEnd, StrandedFeature.Strand subjectStrand, Alignment alignment, Annotation annotation) Creates a newSimpleSeqSimilaritySearchSubHit
object. -
Uses of Annotation in org.biojava.bio.seq
Fields in org.biojava.bio.seq declared as AnnotationMethods in org.biojava.bio.seq that return AnnotationModifier and TypeMethodDescriptionFeatureTypes.RepositoryImpl.getAnnotation()
NewSimpleAssembly.getAnnotation()
SimpleAssembly.getAnnotation()
Methods in org.biojava.bio.seq with parameters of type AnnotationModifier and TypeMethodDescriptionSequenceFactory.createSequence
(SymbolList symList, String uri, String name, Annotation annotation) Deprecated.Creates a sequence using these parameters.static Sequence
SequenceTools.createSequence
(SymbolList syms, String uri, String name, Annotation ann) -
Uses of Annotation in org.biojava.bio.seq.impl
Methods in org.biojava.bio.seq.impl that return AnnotationModifier and TypeMethodDescriptionDummySequence.getAnnotation()
SimpleFeature.getAnnotation()
SimpleGappedSequence.getAnnotation()
SimpleSequence.getAnnotation()
SubSequence.getAnnotation()
ViewSequence.getAnnotation()
Methods in org.biojava.bio.seq.impl with parameters of type AnnotationModifier and TypeMethodDescriptionSimpleSequenceFactory.createSequence
(SymbolList symList, String uri, String name, Annotation annotation) Constructors in org.biojava.bio.seq.impl with parameters of type AnnotationModifierConstructorDescriptionRevCompSequence
(Sequence seq, String urn, String name, Annotation annotation) SimpleSequence
(SymbolList sym, String urn, String name, Annotation annotation) Create a SimpleSequence with the symbols and alphabet of sym, and the sequence properties listed.SimpleSequence
(SymbolList sym, String urn, String name, Annotation annotation, FeatureRealizer realizer) Create a SimpleSequence using a specified FeatureRealizer. -
Uses of Annotation in org.biojava.bio.seq.io
Classes in org.biojava.bio.seq.io that implement AnnotationModifier and TypeClassDescriptionclass
Deprecated.Use org.biojavax.bio.seq.io framework insteadFields in org.biojava.bio.seq.io declared as AnnotationMethods in org.biojava.bio.seq.io that return AnnotationModifier and TypeMethodDescriptionAlternateTokenization.getAnnotation()
CharacterTokenization.getAnnotation()
WordTokenization.getAnnotation()
Methods in org.biojava.bio.seq.io with parameters of type AnnotationModifier and TypeMethodDescriptionprotected void
SequenceBuilderBase.addProperty
(Annotation ann, Object key, Object value) -
Uses of Annotation in org.biojava.bio.seq.io.agave
Methods in org.biojava.bio.seq.io.agave with parameters of type AnnotationModifier and TypeMethodDescriptionAgave2AgaveAnnotFilter.getAccession
(Annotation annot) AGAVEAnnotFilter.getAccession
(Annotation annot) Embl2AgaveAnnotFilter.getAccession
(Annotation annot) SimpleAnnotFilter.getAccession
(Annotation annot) AGAVEAnnotFilter.getAlignLength
(Annotation annot) SimpleAnnotFilter.getAlignLength
(Annotation annot) Agave2AgaveAnnotFilter.getAlignUnits
(Annotation annot) AGAVEAnnotFilter.getAlignUnits
(Annotation annot) SimpleAnnotFilter.getAlignUnits
(Annotation annot) Agave2AgaveAnnotFilter.getAltIds
(Annotation annot) AGAVEAnnotFilter.getAltIds
(Annotation annot) SimpleAnnotFilter.getAltIds
(Annotation annot) Agave2AgaveAnnotFilter.getChromNum
(Annotation annot) AGAVEAnnotFilter.getChromNum
(Annotation annot) SimpleAnnotFilter.getChromNum
(Annotation annot) Agave2AgaveAnnotFilter.getChromosome
(Annotation annot) AGAVEAnnotFilter.getChromosome
(Annotation annot) SimpleAnnotFilter.getChromosome
(Annotation annot) Agave2AgaveAnnotFilter.getClassifyId
(Annotation annot) AGAVEAnnotFilter.getClassifyId
(Annotation annot) SimpleAnnotFilter.getClassifyId
(Annotation annot) Agave2AgaveAnnotFilter.getClassifySystem
(Annotation annot) AGAVEAnnotFilter.getClassifySystem
(Annotation annot) SimpleAnnotFilter.getClassifySystem
(Annotation annot) Agave2AgaveAnnotFilter.getClassifyType
(Annotation annot) AGAVEAnnotFilter.getClassifyType
(Annotation annot) SimpleAnnotFilter.getClassifyType
(Annotation annot) Agave2AgaveAnnotFilter.getCloneId
(Annotation annot) AGAVEAnnotFilter.getCloneId
(Annotation annot) SimpleAnnotFilter.getCloneId
(Annotation annot) Agave2AgaveAnnotFilter.getCloneLibrary
(Annotation annot) AGAVEAnnotFilter.getCloneLibrary
(Annotation annot) SimpleAnnotFilter.getCloneLibrary
(Annotation annot) Agave2AgaveAnnotFilter.getConfidence
(Annotation annot) AGAVEAnnotFilter.getConfidence
(Annotation annot) SimpleAnnotFilter.getConfidence
(Annotation annot) Agave2AgaveAnnotFilter.getCreateDate
(Annotation annot) AGAVEAnnotFilter.getCreateDate
(Annotation annot) SimpleAnnotFilter.getCreateDate
(Annotation annot) Agave2AgaveAnnotFilter.getDbId
(Annotation annot) AGAVEAnnotFilter.getDbId
(Annotation annot) Embl2AgaveAnnotFilter.getDbId
(Annotation annot) SimpleAnnotFilter.getDbId
(Annotation annot) Agave2AgaveAnnotFilter.getDescription
(Annotation annot) AGAVEAnnotFilter.getDescription
(Annotation annot) Embl2AgaveAnnotFilter.getDescription
(Annotation annot) SimpleAnnotFilter.getDescription
(Annotation annot) Agave2AgaveAnnotFilter.getEcNumber
(Annotation annot) AGAVEAnnotFilter.getEcNumber
(Annotation annot) SimpleAnnotFilter.getEcNumber
(Annotation annot) Agave2AgaveAnnotFilter.getElementId
(Annotation annot) AGAVEAnnotFilter.getElementId
(Annotation annot) SimpleAnnotFilter.getElementId
(Annotation annot) String[]
Agave2AgaveAnnotFilter.getElementIds
(Annotation annot) String[]
AGAVEAnnotFilter.getElementIds
(Annotation annot) String[]
SimpleAnnotFilter.getElementIds
(Annotation annot) String[]
Agave2AgaveAnnotFilter.getExonIds
(Annotation annot) String[]
AGAVEAnnotFilter.getExonIds
(Annotation annot) String[]
SimpleAnnotFilter.getExonIds
(Annotation annot) Agave2AgaveAnnotFilter.getFeatureType
(Annotation annot) AGAVEAnnotFilter.getFeatureType
(Annotation annot) SimpleAnnotFilter.getFeatureType
(Annotation annot) Agave2AgaveAnnotFilter.getGroupOrder
(Annotation annot) AGAVEAnnotFilter.getGroupOrder
(Annotation annot) SimpleAnnotFilter.getGroupOrder
(Annotation annot) Agave2AgaveAnnotFilter.getIdAlias
(Annotation annot) AGAVEAnnotFilter.getIdAlias
(Annotation annot) SimpleAnnotFilter.getIdAlias
(Annotation annot) Agave2AgaveAnnotFilter.getKeyword
(Annotation annot) AGAVEAnnotFilter.getKeyword
(Annotation annot) Embl2AgaveAnnotFilter.getKeyword
(Annotation annot) SimpleAnnotFilter.getKeyword
(Annotation annot) Agave2AgaveAnnotFilter.getLabel
(Annotation annot) AGAVEAnnotFilter.getLabel
(Annotation annot) SimpleAnnotFilter.getLabel
(Annotation annot) Agave2AgaveAnnotFilter.getMapLocation
(Annotation annot) AGAVEAnnotFilter.getMapLocation
(Annotation annot) SimpleAnnotFilter.getMapLocation
(Annotation annot) Agave2AgaveAnnotFilter.getMapPosition
(Annotation annot) AGAVEAnnotFilter.getMapPosition
(Annotation annot) SimpleAnnotFilter.getMapPosition
(Annotation annot) Agave2AgaveAnnotFilter.getMatchAlign
(Annotation annot) AGAVEAnnotFilter.getMatchAlign
(Annotation annot) SimpleAnnotFilter.getMatchAlign
(Annotation annot) Agave2AgaveAnnotFilter.getMatchDesc
(Annotation annot) AGAVEAnnotFilter.getMatchDesc
(Annotation annot) SimpleAnnotFilter.getMatchDesc
(Annotation annot) Agave2AgaveAnnotFilter.getMatchRegion
(Annotation annot) AGAVEAnnotFilter.getMatchRegion
(Annotation annot) SimpleAnnotFilter.getMatchRegion
(Annotation annot) Agave2AgaveAnnotFilter.getMolType
(Annotation annot) AGAVEAnnotFilter.getMolType
(Annotation annot) Embl2AgaveAnnotFilter.getMolType
(Annotation annot) SimpleAnnotFilter.getMolType
(Annotation annot) Agave2AgaveAnnotFilter.getNote
(Annotation annot) AGAVEAnnotFilter.getNote
(Annotation annot) Embl2AgaveAnnotFilter.getNote
(Annotation annot) SimpleAnnotFilter.getNote
(Annotation annot) Agave2AgaveAnnotFilter.getOrganism
(Annotation annot) AGAVEAnnotFilter.getOrganism
(Annotation annot) Embl2AgaveAnnotFilter.getOrganism
(Annotation annot) SimpleAnnotFilter.getOrganism
(Annotation annot) Agave2AgaveAnnotFilter.getOS
(Annotation annot) AGAVEAnnotFilter.getOS
(Annotation annot) Embl2AgaveAnnotFilter.getOS
(Annotation annot) SimpleAnnotFilter.getOS
(Annotation annot) Agave2AgaveAnnotFilter.getProperty
(Annotation annot, String type) AGAVEAnnotFilter.getProperty
(Annotation annot, String type) SimpleAnnotFilter.getProperty
(Annotation annot, String type) ThomasD made this a bit safer...static Object
UtilHelper.getProperty
(Annotation annot, String key) inhibit the getProperty(key) of Annotation from throw exception when key does not exist.Agave2AgaveAnnotFilter.getQueryRegion
(Annotation annot) AGAVEAnnotFilter.getQueryRegion
(Annotation annot) SimpleAnnotFilter.getQueryRegion
(Annotation annot) Agave2AgaveAnnotFilter.getRelatedAnnot
(Annotation annot) AGAVEAnnotFilter.getRelatedAnnot
(Annotation annot) SimpleAnnotFilter.getRelatedAnnot
(Annotation annot) Agave2AgaveAnnotFilter.getResultType
(Annotation annot) AGAVEAnnotFilter.getResultType
(Annotation annot) SimpleAnnotFilter.getResultType
(Annotation annot) AGAVEAnnotFilter.getSequenceId
(Annotation annot) SimpleAnnotFilter.getSequenceId
(Annotation annot) Agave2AgaveAnnotFilter.getTaxonId
(Annotation annot) AGAVEAnnotFilter.getTaxonId
(Annotation annot) SimpleAnnotFilter.getTaxonId
(Annotation annot) Agave2AgaveAnnotFilter.getUpdateDate
(Annotation annot) AGAVEAnnotFilter.getUpdateDate
(Annotation annot) SimpleAnnotFilter.getUpdateDate
(Annotation annot) Agave2AgaveAnnotFilter.getVersion
(Annotation annot) AGAVEAnnotFilter.getVersion
(Annotation annot) Embl2AgaveAnnotFilter.getVersion
(Annotation annot) SimpleAnnotFilter.getVersion
(Annotation annot) Agave2AgaveAnnotFilter.getXrefs
(Annotation annot) AGAVEAnnotFilter.getXrefs
(Annotation annot) SimpleAnnotFilter.getXrefs
(Annotation annot) -
Uses of Annotation in org.biojava.bio.symbol
Methods in org.biojava.bio.symbol that return AnnotationModifier and TypeMethodDescriptionDoubleAlphabet.DoubleRange.getAnnotation()
DoubleAlphabet.DoubleSymbol.getAnnotation()
DoubleAlphabet.getAnnotation()
DoubleAlphabet.SubDoubleAlphabet.getAnnotation()
FundamentalAtomicSymbol.getAnnotation()
IntegerAlphabet.getAnnotation()
IntegerAlphabet.IntegerSymbol.getAnnotation()
IntegerAlphabet.SubIntegerAlphabet.getAnnotation()
SimpleAlphabet.getAnnotation()
SingletonAlphabet.getAnnotation()
SoftMaskedAlphabet.CaseSensitiveTokenization.getAnnotation()
SoftMaskedAlphabet.getAnnotation()
The SoftMaskedAlphabet has no annotationMethods in org.biojava.bio.symbol with parameters of type AnnotationModifier and TypeMethodDescriptionstatic AtomicSymbol
AlphabetManager.createSymbol
(char token, String name, Annotation annotation) Deprecated.Use the two-arg version of this method instead.static Symbol
AlphabetManager.createSymbol
(char token, Annotation annotation, List symList, Alphabet alpha) Deprecated.use the new version, without the token argumentstatic Symbol
AlphabetManager.createSymbol
(char token, Annotation annotation, Set symSet, Alphabet alpha) Deprecated.use the three-arg version of this method instead.static AtomicSymbol
AlphabetManager.createSymbol
(String name, Annotation annotation) Generate a new AtomicSymbol instance with a name and Annotation.static Symbol
AlphabetManager.createSymbol
(Annotation annotation, List symList, Alphabet alpha) Generates a new Symbol instance that represents the tuple of Symbols in symList.static Symbol
AlphabetManager.createSymbol
(Annotation annotation, Set symSet, Alphabet alpha) Generates a new Symbol instance that represents the tuple of Symbols in symList.Constructors in org.biojava.bio.symbol with parameters of type AnnotationModifierConstructorDescriptionFundamentalAtomicSymbol
(String name, Annotation annotation) protected
SimpleAtomicSymbol
(Annotation annotation, List syms) -
Uses of Annotation in org.biojava.bio.taxa
Methods in org.biojava.bio.taxa that return Annotation -
Uses of Annotation in org.biojava.ontology
Methods in org.biojava.ontology that return AnnotationModifier and TypeMethodDescriptionIntegerOntology.IntTerm.getAnnotation()
OntologyTerm.Impl.getAnnotation()
RemoteTerm.Impl.getAnnotation()
Term.Impl.getAnnotation()
Triple.Impl.getAnnotation()
Methods in org.biojava.ontology with parameters of type Annotation -
Uses of Annotation in org.biojavax
Subinterfaces of Annotation in org.biojavaxModifier and TypeInterfaceDescriptioninterface
An annotation collection which stores annotations as Note objects.Classes in org.biojavax that implement AnnotationModifier and TypeClassDescriptionclass
A place holder for a RichAnnotation that prevents null having to be usedclass
Simple annotation wrapper.Methods in org.biojavax that return AnnotationModifier and TypeMethodDescriptionSimpleCrossRef.getAnnotation()
Should return the associated annotation object. -
Uses of Annotation in org.biojavax.bio
Methods in org.biojavax.bio that return AnnotationModifier and TypeMethodDescriptionSimpleBioEntry.getAnnotation()
Should return the associated annotation object. -
Uses of Annotation in org.biojavax.bio.seq
Methods in org.biojavax.bio.seq that return AnnotationModifier and TypeMethodDescriptionCompoundRichLocation.getAnnotation()
Should return the associated annotation object.EmptyRichLocation.getAnnotation()
Should return the associated annotation object.SimpleRichFeature.getAnnotation()
Should return the associated annotation object.SimpleRichLocation.getAnnotation()
Should return the associated annotation object. -
Uses of Annotation in org.biojavax.ontology
Methods in org.biojavax.ontology that return AnnotationModifier and TypeMethodDescriptionSimpleComparableTerm.getAnnotation()
Should return the associated annotation object.SimpleComparableTriple.getAnnotation()
Should return the associated annotation object.