Uses of Interface
org.biojava.bio.Annotation

Packages that use Annotation

Package	Description
org.biojava.bio	The core classes that will be used throughout the bio packages.
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.molbio	The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR.
org.biojava.bio.program.gff3	Support for reading and writing GFF3.
org.biojava.bio.program.hmmer	Tools for working with profile Hidden Markov Models from the HMMer package.
org.biojava.bio.program.indexdb	A flat-file ascii index of ascii flat files as per the OBDA specification.
org.biojava.bio.program.phred	Parser for Phred output
org.biojava.bio.program.ssbind	Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
org.biojava.bio.program.tagvalue	Process files as streams of records, each with tags with values.
org.biojava.bio.program.xff	Event-driven parsing system for the Extensible Feature Format (XFF).
org.biojava.bio.search	Interfaces and classes for representing sequence similarity search results.
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.impl	Standard in-memory implementations of Sequence and Feature.
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.seq.io.agave	Classes for converting between AGAVE XML and BioJava objects.
org.biojava.bio.symbol	Representation of the Symbols that make up a sequence, and locations within them.
org.biojava.bio.taxa	Taxonomy object for representing species information.
org.biojava.ontology	A general-purpose API for ontologies.
org.biojavax	The Biojava extensions packages, classes that extend the core biojava functionality The biojavax packages contain a number of extensions to the core biojava interfaces.
org.biojavax.bio	Classes to represent biological entities and their relationships.
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.
org.biojavax.ontology	Extensions to the biojava ontology model that represent BioSQL ontology.

Uses of Annotation in org.biojava.bio

Classes in org.biojava.bio that implement Annotation

Modifier and Type	Class and Description
class	AbstractAnnotation A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.
class	AnnotationChanger AnnotationChanger remaps the values of an Annotation to new values specified by a ValueChanger.
class	AnnotationRenamer AnnotationRenamer remaps the keys of an Annotation to new keys specified by a TagMapper.
class	BeanAsAnnotation Create an Annotation with properties matching those of a JavaBean instance.
class	MergeAnnotation Merged view onto a list of underlying Annotation objects.
class	OverlayAnnotation Annotation implementation which allows new key-value pairs to be layered on top of an underlying Annotation.
class	SimpleAnnotation A no-frills implementation of Annotation that is just a wrapper around a LinkedHashMap.
class	SmallAnnotation Annotation that is optimized for memory usage.

Fields in org.biojava.bio declared as Annotation

Modifier and Type	Field and Description
static Annotation	Annotation.EMPTY_ANNOTATION A really useful empty and immutable annotation object.

Methods in org.biojava.bio that return Annotation

Modifier and Type	Method and Description
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 new Annotation containing only those values in the Annotation argument which are not of a type specified by the AnnotationType.
Annotation	Annotatable.getAnnotation() Should return the associated annotation object.
Annotation	AnnotationRenamer.getWrapped() getWrapped returns the Annotation being remapped.
Annotation	AnnotationChanger.getWrapped() getWrapped returns the Annotation being remapped.

Methods in org.biojava.bio with parameters of type Annotation

Modifier and Type	Method and Description
void	MergeAnnotation.addAnnotation(Annotation ann) Add a new Annotation to to the end of the list to be merged.
void	AnnotationType.addProperty(Annotation ann, Object property, Object value) Add a value to the specified property slot.
void	AnnotationType.Abstract.addProperty(Annotation ann, Object key, Object value)
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 new Annotation containing only those values in the Annotation argument which are not of a type specified by the AnnotationType.
Collection	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.
Collection	AnnotationType.Abstract.getProperty(Annotation ann, Object property)
boolean	AnnotationType.instanceOf(Annotation ann) Validate an Annotation against this AnnotationType.
boolean	AnnotationType.Abstract.instanceOf(Annotation ann)
void	MergeAnnotation.removeAnnotation(Annotation ann) Remove an Annotation from the list.
void	AnnotationType.removeProperty(Annotation ann, Object property, Object value) Remove a value from the specified property slot.
void	AnnotationType.Abstract.removeProperty(Annotation ann, Object key, Object value)
static Set	AnnotationTools.searchAnnotation(Annotation ann, AnnotationType query) Scans an Annotation with an AnnotationType and returns all Annotation instances matching a Type.
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.
void	AnnotationType.Abstract.setProperty(Annotation ann, Object property, Object value)

Constructors in org.biojava.bio with parameters of type Annotation

Constructor and Description
AbstractAnnotation(Annotation ann) Copy-constructor.
AnnotationChanger(Annotation wrapped, ChangeTable changer) Creates a new AnnotationChanger using the specified ValueChanger to remap its values.
AnnotationRenamer(Annotation wrapped, PropertyChanger mapper) Creates a new AnnotationRenamer using the specified TagMapper to remap its keys.
OverlayAnnotation(Annotation par) Construct an annotation which can overlay new key-value pairs onto an underlying annotation.
SimpleAnnotation(Annotation ann) Create a new SimpleAnnotation by copying the properties from another one.
SmallAnnotation(Annotation ann) 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 Annotation

Modifier and Type	Method and Description
Annotation	SimpleEmissionState.getAnnotation()

Methods in org.biojava.bio.dp with parameters of type Annotation

Modifier and Type	Method and Description
void	SimpleEmissionState.setAnnotation(Annotation ann)

Constructors in org.biojava.bio.dp with parameters of type Annotation

Constructor and Description
SimpleDotState(char token, String name, Annotation annotation) Deprecated. token is ignored since 1.2. Use the 2-arg constructor instead.
SimpleDotState(String name, Annotation annotation) Construct a new state with the specified name and annotation
SimpleEmissionState(String name, Annotation ann, int[] advance, Distribution dis)

Uses of Annotation in org.biojava.bio.molbio

Methods in org.biojava.bio.molbio that return Annotation

Modifier and Type	Method and Description
static 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 Annotation

Modifier and Type	Method and Description
Annotation	GFF3Record.Impl.getAnnotation()

Methods in org.biojava.bio.program.gff3 with parameters of type Annotation

Modifier and Type	Method and Description
protected 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 Annotation

Modifier and Type	Method and Description
protected 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 Annotation

Constructor and Description
ProfileEmissionState(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 Annotation

Modifier and Type	Method and Description
Annotation	IndexStore.getMetaData() getMetaData returns a data structure which represents an OBDA "config.dat" flatfile indexing configuration file.
Annotation	BioStore.getMetaData()

Uses of Annotation in org.biojava.bio.program.phred

Constructors in org.biojava.bio.program.phred with parameters of type Annotation

Constructor and Description
PhredSequence(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 Annotation

Modifier and Type	Method and Description
static 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 Annotation

Modifier and Type	Method and Description
Annotation	AnnotationBuilder.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 Annotation

Modifier and Type	Method and Description
Annotation	XFFFeatureSetHandler.getMergeAnnotation()

Methods in org.biojava.bio.program.xff with parameters of type Annotation

Modifier and Type	Method and Description
static 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 Annotation

Modifier and Type	Method and Description
Annotation	SimpleSeqSimilaritySearchSubHit.getAnnotation() getAnnotation returns the Annotation associated with this sub-hit.
Annotation	SimpleSeqSimilaritySearchResult.getAnnotation() getAnnotation returns the Annotation associated with this hit.
Annotation	SimpleSeqSimilaritySearchHit.getAnnotation() getAnnotation returns the Annotation associated with this hit.
Annotation	SequenceDBSearchSubHit.getAnnotation() Deprecated.
Annotation	SequenceDBSearchResult.getAnnotation() Deprecated. getAnnotation returns the Annotation associated with this hit.
Annotation	SequenceDBSearchHit.getAnnotation() Deprecated. getAnnotation returns the Annotation associated with this hit.

Constructors in org.biojava.bio.search with parameters of type Annotation

Constructor and Description
SequenceDBSearchHit(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 new SequenceDBSearchHit object.
SequenceDBSearchResult(Sequence querySequence, SequenceDB sequenceDB, Map searchParameters, List hits, Annotation annotation) Deprecated. Creates a new SequenceDBSearchResult.
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 new SequenceDBSearchSubHit 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 new SimpleSeqSimilaritySearchHit object.
SimpleSeqSimilaritySearchResult(Sequence querySequence, SequenceDB sequenceDB, Map searchParameters, List hits, Annotation annotation) Creates a new SimpleSeqSimilaritySearchResult.
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 new SimpleSeqSimilaritySearchSubHit object.

Uses of Annotation in org.biojava.bio.seq

Fields in org.biojava.bio.seq declared as Annotation

Modifier and Type	Field and Description
Annotation	Feature.Template.annotation

Methods in org.biojava.bio.seq that return Annotation

Modifier and Type	Method and Description
Annotation	SimpleAssembly.getAnnotation()
Annotation	NewSimpleAssembly.getAnnotation()
Annotation	FeatureTypes.RepositoryImpl.getAnnotation()

Methods in org.biojava.bio.seq with parameters of type Annotation

Modifier and Type	Method and Description
static Sequence	SequenceTools.createSequence(SymbolList syms, String uri, String name, Annotation ann)
Sequence	SequenceFactory.createSequence(SymbolList symList, String uri, String name, Annotation annotation) Deprecated. Creates a sequence using these parameters.

Uses of Annotation in org.biojava.bio.seq.impl

Methods in org.biojava.bio.seq.impl that return Annotation

Modifier and Type	Method and Description
Annotation	ViewSequence.getAnnotation()
Annotation	SubSequence.getAnnotation()
Annotation	SimpleSequence.getAnnotation()
Annotation	SimpleGappedSequence.getAnnotation()
Annotation	SimpleFeature.getAnnotation()
Annotation	DummySequence.getAnnotation()

Methods in org.biojava.bio.seq.impl with parameters of type Annotation

Modifier and Type	Method and Description
Sequence	SimpleSequenceFactory.createSequence(SymbolList symList, String uri, String name, Annotation annotation)

Constructors in org.biojava.bio.seq.impl with parameters of type Annotation

Constructor and Description
RevCompSequence(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 Annotation

Modifier and Type	Class and Description
class	ReferenceAnnotation Deprecated. Use org.biojavax.bio.seq.io framework instead

Fields in org.biojava.bio.seq.io declared as Annotation

Modifier and Type	Field and Description
protected Annotation	SequenceBuilderBase.annotation

Methods in org.biojava.bio.seq.io that return Annotation

Modifier and Type	Method and Description
Annotation	WordTokenization.getAnnotation()
Annotation	CharacterTokenization.getAnnotation()
Annotation	AlternateTokenization.getAnnotation()

Methods in org.biojava.bio.seq.io with parameters of type Annotation

Modifier and Type	Method and Description
protected 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 Annotation

Modifier and Type	Method and Description
String	SimpleAnnotFilter.getAccession(Annotation annot)
String	Embl2AgaveAnnotFilter.getAccession(Annotation annot)
String	AGAVEAnnotFilter.getAccession(Annotation annot)
String	Agave2AgaveAnnotFilter.getAccession(Annotation annot)
String	SimpleAnnotFilter.getAlignLength(Annotation annot)
String	AGAVEAnnotFilter.getAlignLength(Annotation annot)
String	SimpleAnnotFilter.getAlignUnits(Annotation annot)
String	AGAVEAnnotFilter.getAlignUnits(Annotation annot)
String	Agave2AgaveAnnotFilter.getAlignUnits(Annotation annot)
AGAVEDbId[]	SimpleAnnotFilter.getAltIds(Annotation annot)
AGAVEDbId[]	AGAVEAnnotFilter.getAltIds(Annotation annot)
AGAVEDbId[]	Agave2AgaveAnnotFilter.getAltIds(Annotation annot)
String	SimpleAnnotFilter.getChromNum(Annotation annot)
String	AGAVEAnnotFilter.getChromNum(Annotation annot)
String	Agave2AgaveAnnotFilter.getChromNum(Annotation annot)
String	SimpleAnnotFilter.getChromosome(Annotation annot)
String	AGAVEAnnotFilter.getChromosome(Annotation annot)
String	Agave2AgaveAnnotFilter.getChromosome(Annotation annot)
String	SimpleAnnotFilter.getClassifyId(Annotation annot)
String	AGAVEAnnotFilter.getClassifyId(Annotation annot)
String	Agave2AgaveAnnotFilter.getClassifyId(Annotation annot)
String	SimpleAnnotFilter.getClassifySystem(Annotation annot)
String	AGAVEAnnotFilter.getClassifySystem(Annotation annot)
String	Agave2AgaveAnnotFilter.getClassifySystem(Annotation annot)
String	SimpleAnnotFilter.getClassifyType(Annotation annot)
String	AGAVEAnnotFilter.getClassifyType(Annotation annot)
String	Agave2AgaveAnnotFilter.getClassifyType(Annotation annot)
String	SimpleAnnotFilter.getCloneId(Annotation annot)
String	AGAVEAnnotFilter.getCloneId(Annotation annot)
String	Agave2AgaveAnnotFilter.getCloneId(Annotation annot)
String	SimpleAnnotFilter.getCloneLibrary(Annotation annot)
String	AGAVEAnnotFilter.getCloneLibrary(Annotation annot)
String	Agave2AgaveAnnotFilter.getCloneLibrary(Annotation annot)
String	SimpleAnnotFilter.getConfidence(Annotation annot)
String	AGAVEAnnotFilter.getConfidence(Annotation annot)
String	Agave2AgaveAnnotFilter.getConfidence(Annotation annot)
String	SimpleAnnotFilter.getCreateDate(Annotation annot)
String	AGAVEAnnotFilter.getCreateDate(Annotation annot)
String	Agave2AgaveAnnotFilter.getCreateDate(Annotation annot)
AGAVEDbId	SimpleAnnotFilter.getDbId(Annotation annot)
AGAVEDbId	Embl2AgaveAnnotFilter.getDbId(Annotation annot)
AGAVEDbId	AGAVEAnnotFilter.getDbId(Annotation annot)
AGAVEDbId	Agave2AgaveAnnotFilter.getDbId(Annotation annot)
String	SimpleAnnotFilter.getDescription(Annotation annot)
String	Embl2AgaveAnnotFilter.getDescription(Annotation annot)
String	AGAVEAnnotFilter.getDescription(Annotation annot)
String	Agave2AgaveAnnotFilter.getDescription(Annotation annot)
String	SimpleAnnotFilter.getEcNumber(Annotation annot)
String	AGAVEAnnotFilter.getEcNumber(Annotation annot)
String	Agave2AgaveAnnotFilter.getEcNumber(Annotation annot)
String	SimpleAnnotFilter.getElementId(Annotation annot)
String	AGAVEAnnotFilter.getElementId(Annotation annot)
String	Agave2AgaveAnnotFilter.getElementId(Annotation annot)
String[]	SimpleAnnotFilter.getElementIds(Annotation annot)
String[]	AGAVEAnnotFilter.getElementIds(Annotation annot)
String[]	Agave2AgaveAnnotFilter.getElementIds(Annotation annot)
String[]	SimpleAnnotFilter.getExonIds(Annotation annot)
String[]	AGAVEAnnotFilter.getExonIds(Annotation annot)
String[]	Agave2AgaveAnnotFilter.getExonIds(Annotation annot)
String	SimpleAnnotFilter.getFeatureType(Annotation annot)
String	AGAVEAnnotFilter.getFeatureType(Annotation annot)
String	Agave2AgaveAnnotFilter.getFeatureType(Annotation annot)
String	SimpleAnnotFilter.getGroupOrder(Annotation annot)
String	AGAVEAnnotFilter.getGroupOrder(Annotation annot)
String	Agave2AgaveAnnotFilter.getGroupOrder(Annotation annot)
AGAVEIdAlias[]	SimpleAnnotFilter.getIdAlias(Annotation annot)
AGAVEIdAlias[]	AGAVEAnnotFilter.getIdAlias(Annotation annot)
AGAVEIdAlias[]	Agave2AgaveAnnotFilter.getIdAlias(Annotation annot)
String	SimpleAnnotFilter.getKeyword(Annotation annot)
String	Embl2AgaveAnnotFilter.getKeyword(Annotation annot)
String	AGAVEAnnotFilter.getKeyword(Annotation annot)
String	Agave2AgaveAnnotFilter.getKeyword(Annotation annot)
String	SimpleAnnotFilter.getLabel(Annotation annot)
String	AGAVEAnnotFilter.getLabel(Annotation annot)
String	Agave2AgaveAnnotFilter.getLabel(Annotation annot)
AGAVEMapLocation[]	SimpleAnnotFilter.getMapLocation(Annotation annot)
AGAVEMapLocation[]	AGAVEAnnotFilter.getMapLocation(Annotation annot)
AGAVEMapLocation[]	Agave2AgaveAnnotFilter.getMapLocation(Annotation annot)
String	SimpleAnnotFilter.getMapPosition(Annotation annot)
String	AGAVEAnnotFilter.getMapPosition(Annotation annot)
String	Agave2AgaveAnnotFilter.getMapPosition(Annotation annot)
String	SimpleAnnotFilter.getMatchAlign(Annotation annot)
String	AGAVEAnnotFilter.getMatchAlign(Annotation annot)
String	Agave2AgaveAnnotFilter.getMatchAlign(Annotation annot)
String	SimpleAnnotFilter.getMatchDesc(Annotation annot)
String	AGAVEAnnotFilter.getMatchDesc(Annotation annot)
String	Agave2AgaveAnnotFilter.getMatchDesc(Annotation annot)
AGAVEMatchRegion	SimpleAnnotFilter.getMatchRegion(Annotation annot)
AGAVEMatchRegion	AGAVEAnnotFilter.getMatchRegion(Annotation annot)
AGAVEMatchRegion	Agave2AgaveAnnotFilter.getMatchRegion(Annotation annot)
String	SimpleAnnotFilter.getMolType(Annotation annot)
String	Embl2AgaveAnnotFilter.getMolType(Annotation annot)
String	AGAVEAnnotFilter.getMolType(Annotation annot)
String	Agave2AgaveAnnotFilter.getMolType(Annotation annot)
String	SimpleAnnotFilter.getNote(Annotation annot)
String	Embl2AgaveAnnotFilter.getNote(Annotation annot)
String	AGAVEAnnotFilter.getNote(Annotation annot)
String	Agave2AgaveAnnotFilter.getNote(Annotation annot)
String	SimpleAnnotFilter.getOrganism(Annotation annot)
String	Embl2AgaveAnnotFilter.getOrganism(Annotation annot)
String	AGAVEAnnotFilter.getOrganism(Annotation annot)
String	Agave2AgaveAnnotFilter.getOrganism(Annotation annot)
String	SimpleAnnotFilter.getOS(Annotation annot)
String	Embl2AgaveAnnotFilter.getOS(Annotation annot)
String	AGAVEAnnotFilter.getOS(Annotation annot)
String	Agave2AgaveAnnotFilter.getOS(Annotation annot)
static Object	UtilHelper.getProperty(Annotation annot, String key) inhibit the getProperty(key) of Annotation from throw exception when key does not exist.
AGAVEProperty[]	SimpleAnnotFilter.getProperty(Annotation annot, String type) ThomasD made this a bit safer...
AGAVEProperty[]	AGAVEAnnotFilter.getProperty(Annotation annot, String type)
AGAVEProperty[]	Agave2AgaveAnnotFilter.getProperty(Annotation annot, String type)
AGAVEQueryRegion	SimpleAnnotFilter.getQueryRegion(Annotation annot)
AGAVEQueryRegion	AGAVEAnnotFilter.getQueryRegion(Annotation annot)
AGAVEQueryRegion	Agave2AgaveAnnotFilter.getQueryRegion(Annotation annot)
AGAVERelatedAnnot[]	SimpleAnnotFilter.getRelatedAnnot(Annotation annot)
AGAVERelatedAnnot[]	AGAVEAnnotFilter.getRelatedAnnot(Annotation annot)
AGAVERelatedAnnot[]	Agave2AgaveAnnotFilter.getRelatedAnnot(Annotation annot)
String	SimpleAnnotFilter.getResultType(Annotation annot)
String	AGAVEAnnotFilter.getResultType(Annotation annot)
String	Agave2AgaveAnnotFilter.getResultType(Annotation annot)
String	SimpleAnnotFilter.getSequenceId(Annotation annot)
String	AGAVEAnnotFilter.getSequenceId(Annotation annot)
String	SimpleAnnotFilter.getTaxonId(Annotation annot)
String	AGAVEAnnotFilter.getTaxonId(Annotation annot)
String	Agave2AgaveAnnotFilter.getTaxonId(Annotation annot)
String	SimpleAnnotFilter.getUpdateDate(Annotation annot)
String	AGAVEAnnotFilter.getUpdateDate(Annotation annot)
String	Agave2AgaveAnnotFilter.getUpdateDate(Annotation annot)
String	SimpleAnnotFilter.getVersion(Annotation annot)
String	Embl2AgaveAnnotFilter.getVersion(Annotation annot)
String	AGAVEAnnotFilter.getVersion(Annotation annot)
String	Agave2AgaveAnnotFilter.getVersion(Annotation annot)
AGAVEXrefs[]	SimpleAnnotFilter.getXrefs(Annotation annot)
AGAVEXrefs[]	AGAVEAnnotFilter.getXrefs(Annotation annot)
AGAVEXrefs[]	Agave2AgaveAnnotFilter.getXrefs(Annotation annot)

Uses of Annotation in org.biojava.bio.symbol

Methods in org.biojava.bio.symbol that return Annotation

Modifier and Type	Method and Description
Annotation	SoftMaskedAlphabet.getAnnotation() The SoftMaskedAlphabet has no annotation
Annotation	SoftMaskedAlphabet.CaseSensitiveTokenization.getAnnotation()
Annotation	SingletonAlphabet.getAnnotation()
Annotation	SimpleAlphabet.getAnnotation()
Annotation	IntegerAlphabet.getAnnotation()
Annotation	IntegerAlphabet.IntegerSymbol.getAnnotation()
Annotation	IntegerAlphabet.SubIntegerAlphabet.getAnnotation()
Annotation	FundamentalAtomicSymbol.getAnnotation()
Annotation	DoubleAlphabet.getAnnotation()
Annotation	DoubleAlphabet.DoubleSymbol.getAnnotation()
Annotation	DoubleAlphabet.DoubleRange.getAnnotation()
Annotation	DoubleAlphabet.SubDoubleAlphabet.getAnnotation()

Methods in org.biojava.bio.symbol with parameters of type Annotation

Modifier and Type	Method and Description
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.
static Symbol	AlphabetManager.createSymbol(char token, Annotation annotation, List symList, Alphabet alpha) Deprecated. use the new version, without the token argument
static 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(char token, String name, Annotation annotation) Deprecated. Use the two-arg version of this method instead.
static AtomicSymbol	AlphabetManager.createSymbol(String name, Annotation annotation) Generate a new AtomicSymbol instance with a name and Annotation.

Constructors in org.biojava.bio.symbol with parameters of type Annotation

Constructor and Description
FundamentalAtomicSymbol(String name, Annotation annotation)
SimpleAtomicSymbol(Annotation annotation, List syms)

Uses of Annotation in org.biojava.bio.taxa

Methods in org.biojava.bio.taxa that return Annotation

Modifier and Type	Method and Description
Annotation	AbstractTaxon.getAnnotation() Deprecated.

Uses of Annotation in org.biojava.ontology

Methods in org.biojava.ontology that return Annotation

Modifier and Type	Method and Description
Annotation	Triple.Impl.getAnnotation()
Annotation	Term.Impl.getAnnotation()
Annotation	RemoteTerm.Impl.getAnnotation()
Annotation	OntologyTerm.Impl.getAnnotation()
Annotation	IntegerOntology.IntTerm.getAnnotation()

Methods in org.biojava.ontology with parameters of type Annotation

Modifier and Type	Method and Description
void	Term.Impl.setAnnotation(Annotation annotation)

Uses of Annotation in org.biojavax

Subinterfaces of Annotation in org.biojavax

Modifier and Type	Interface and Description
interface	RichAnnotation An annotation collection which stores annotations as Note objects.

Classes in org.biojavax that implement Annotation

Modifier and Type	Class and Description
class	EmptyRichAnnotation A place holder for a RichAnnotation that prevents null having to be used
class	SimpleRichAnnotation Simple annotation wrapper.

Methods in org.biojavax that return Annotation

Modifier and Type	Method and Description
Annotation	SimpleCrossRef.getAnnotation() Should return the associated annotation object.

Uses of Annotation in org.biojavax.bio

Methods in org.biojavax.bio that return Annotation

Modifier and Type	Method and Description
Annotation	SimpleBioEntry.getAnnotation() Should return the associated annotation object.

Uses of Annotation in org.biojavax.bio.seq

Methods in org.biojavax.bio.seq that return Annotation

Modifier and Type	Method and Description
Annotation	SimpleRichLocation.getAnnotation() Should return the associated annotation object.
Annotation	SimpleRichFeature.getAnnotation() Should return the associated annotation object.
Annotation	EmptyRichLocation.getAnnotation() Should return the associated annotation object.
Annotation	CompoundRichLocation.getAnnotation() Should return the associated annotation object.

Uses of Annotation in org.biojavax.ontology

Methods in org.biojavax.ontology that return Annotation

Modifier and Type	Method and Description
Annotation	SimpleComparableTriple.getAnnotation() Should return the associated annotation object.
Annotation	SimpleComparableTerm.getAnnotation() Should return the associated annotation object.