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.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.

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 Map.
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	AnnotationRenamer.getWrapped() getWrapped returns the Annotation being remapped.
Annotation	AnnotationChanger.getWrapped() getWrapped returns the Annotation being remapped.
Annotation	Annotatable.getAnnotation() Should return the associated annotation object.

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	MergeAnnotation.removeAnnotation(Annotation ann) Remove an Annotation from the list.
boolean	AnnotationType.instanceOf(Annotation ann) Validate an Annotation against this AnnotationType.
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.addProperty(Annotation ann, Object property, Object value) Add a value to the specified property slot.
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.
void	AnnotationType.removeProperty(Annotation ann, Object property, Object value) Remove a value from the specified property slot.
boolean	AnnotationType.Abstract.instanceOf(Annotation ann)
void	AnnotationType.Abstract.setProperty(Annotation ann, Object property, Object value)
Collection	AnnotationType.Abstract.getProperty(Annotation ann, Object property)
void	AnnotationType.Abstract.addProperty(Annotation ann, Object key, Object value)
void	AnnotationType.Abstract.removeProperty(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.
static Set	AnnotationTools.searchAnnotation(Annotation ann, AnnotationType query) Scans an Annotation with an AnnotationType and returns all Annotation instances matching a Type.

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

SmallAnnotation(Annotation ann)
Return a new SmallAnnotation that copies all values from another annoation.

SimpleAnnotation(Annotation ann)
Create a new SimpleAnnotation by copying the properties from another one.

OverlayAnnotation(Annotation par)
Construct an annotation which can overlay new key-value pairs onto an underlying annotation.

AnnotationRenamer(Annotation wrapped, PropertyChanger mapper)
Creates a new AnnotationRenamer using the specified TagMapper to remap its keys.

AnnotationChanger(Annotation wrapped, ChangeTable changer)
Creates a new AnnotationChanger using the specified ValueChanger to remap its values.

AbstractAnnotation(Annotation ann)
Copy-constructor.

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

SimpleEmissionState(String name, Annotation ann, int[] advance, Distribution dis)

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

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.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

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.

SimpleSeqSimilaritySearchResult(Sequence querySequence, SequenceDB sequenceDB, Map searchParameters, List hits, Annotation annotation)
Creates a new SimpleSeqSimilaritySearchResult.

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.

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.

SequenceDBSearchResult(Sequence querySequence, SequenceDB sequenceDB, Map searchParameters, List hits, Annotation annotation)
Deprecated. Creates a new SequenceDBSearchResult.

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.

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) 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

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.

RevCompSequence(Sequence seq, String urn, String name, Annotation annotation)

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

Classes in org.biojava.bio.seq.io that implement Annotation

class

ReferenceAnnotation

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()

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

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

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 AtomicSymbol	AlphabetManager.createSymbol(String name, Annotation annotation) Generate a new AtomicSymbol instance with a name and Annotation.
static 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 argument
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(char token, Annotation annotation, Set symSet, Alphabet alpha) Deprecated. use the three-arg version of this method instead.
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 Annotation

SimpleAtomicSymbol(Annotation annotation, List syms)

FundamentalAtomicSymbol(String name, Annotation annotation)

Uses of Annotation in org.biojava.bio.taxa

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

Annotation

AbstractTaxon.getAnnotation()

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()