## Uses of Interface
org.biojava.bio.Annotation

Packages that use Annotation
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.das: Development client for the Distributed Annotation System.
org.biojava.bio.program.das.dasalignment: request alignments via DAS
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.structure: Interfaces and classes for protein structure (PDB).
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
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
`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
`static Annotation` `Annotation.EMPTY_ANNOTATION` A really useful empty and immutable annotation object.

Methods in org.biojava.bio that return Annotation
`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
`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
`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
`Annotation` `SimpleEmissionState.getAnnotation()`

Methods in org.biojava.bio.dp with parameters of type Annotation
`void` `SimpleEmissionState.setAnnotation(Annotation ann)`

Constructors in org.biojava.bio.dp with parameters of type Annotation
`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
`static Annotation` `RestrictionEnzymeManager.getAnnotation(RestrictionEnzyme enzyme)` `getAnnotation` returns an immutable, static annotation describing the enzyme.

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

Methods in org.biojava.bio.program.das that return Annotation
`Annotation` `DASSequence.getAnnotation()`

Uses of Annotation in org.biojava.bio.program.das.dasalignment

Methods in org.biojava.bio.program.das.dasalignment that return Annotation
`Annotation[]` `Alignment.getBlocks()` get all Annotations of type "Block".
`Annotation[]` `Alignment.getMatrices()` Returns the matrices.
`Annotation[]` `Alignment.getObjects()` Returns the Annotation of all objects in this Alignment.
`Annotation[]` `Alignment.getScores()` get all "Score" Annotations.
`Annotation[]` `Alignment.getVectors()` Returns the shift vectors.

Methods in org.biojava.bio.program.das.dasalignment with parameters of type Annotation
`void` `Alignment.addBlock(Annotation block)` Add a "Block" Annotation.
`void` `Alignment.addMatrix(Annotation matrix)` add Annotation of DAS alignment "matrix" type.
`void` `Alignment.addObject(Annotation object)` add Annotation of DAS alignment "object" type.
`void` `Alignment.addScore(Annotation score)` adds a "Score" Annotation.
`void` `Alignment.addVector(Annotation vector)` add Annotation of DAS alignment "vector" type.

Uses of Annotation in org.biojava.bio.program.gff3

Methods in org.biojava.bio.program.gff3 that return Annotation
`Annotation` `GFF3Record.Impl.getAnnotation()`

Methods in org.biojava.bio.program.gff3 with parameters of type Annotation
`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
`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
`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
`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
`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
`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
`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
`Annotation` `XFFFeatureSetHandler.getMergeAnnotation()`

Methods in org.biojava.bio.program.xff with parameters of type Annotation
`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
`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
`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
`Annotation` `Feature.Template.annotation`

Methods in org.biojava.bio.seq that return Annotation
`Annotation` `SimpleAssembly.getAnnotation()`
`Annotation` `NewSimpleAssembly.getAnnotation()`
`Annotation` `FeatureTypes.RepositoryImpl.getAnnotation()`

Methods in org.biojava.bio.seq with parameters of type Annotation
`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
`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
`Sequence` `SimpleSequenceFactory.createSequence(SymbolList symList, String uri, String name, Annotation annotation)`

Constructors in org.biojava.bio.seq.impl with parameters of type Annotation
`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
`class` `ReferenceAnnotation` Deprecated. Use org.biojavax.bio.seq.io framework instead

Fields in org.biojava.bio.seq.io declared as Annotation
`protected Annotation` `SequenceBuilderBase.annotation`

Methods in org.biojava.bio.seq.io that return Annotation
`Annotation` `WordTokenization.getAnnotation()`
`Annotation` `CharacterTokenization.getAnnotation()`
`Annotation` `AlternateTokenization.getAnnotation()`

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

Methods in org.biojava.bio.structure that return Annotation
`Annotation` `ChainImpl.getAnnotation()` get/set the Annotation of a Chain.
`Annotation` `Chain.getAnnotation()` get/set the Annotation of a Chain.

Methods in org.biojava.bio.structure with parameters of type Annotation
`void` `ChainImpl.setAnnotation(Annotation anno)` get/set the Annotation of a Chain.
`void` `Chain.setAnnotation(Annotation anno)` get/set the Annotation of a Chain.

Uses of Annotation in org.biojava.bio.symbol

Methods in org.biojava.bio.symbol that return Annotation
`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
`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
`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
`Annotation` `AbstractTaxon.getAnnotation()` Deprecated.

Uses of Annotation in org.biojava.ontology

Methods in org.biojava.ontology that return Annotation
`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
`void` `Term.Impl.setAnnotation(Annotation annotation)`

Uses of Annotation in org.biojavax

Subinterfaces of Annotation in org.biojavax
`interface` `RichAnnotation` An annotation collection which stores annotations as Note objects.

Classes in org.biojavax that implement Annotation
`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
`Annotation` `SimpleCrossRef.getAnnotation()` Should return the associated annotation object.

Uses of Annotation in org.biojavax.bio

Methods in org.biojavax.bio that return Annotation
`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
`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. ALWAYS RETURNS THE EMPTY ANNOTATION
`Annotation` `CompoundRichLocation.getAnnotation()` Should return the associated annotation object. ALWAYS RETURNS THE EMPTY ANNOTATION

Uses of Annotation in org.biojavax.ontology

Methods in org.biojavax.ontology that return Annotation
`Annotation` `SimpleComparableTriple.getAnnotation()` Should return the associated annotation object. ALWAYS RETURNS THE EMPTY ANNOTATION
`Annotation` `SimpleComparableTerm.getAnnotation()` Should return the associated annotation object. ALWAYS RETURNS AN EMPTY ANNOTATION OBJECT