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 TypeClassDescriptionclassA utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.classAnnotationChangerremaps the values of anAnnotationto new values specified by aValueChanger.classAnnotationRenamerremaps the keys of anAnnotationto new keys specified by aTagMapper.classCreate an Annotation with properties matching those of a JavaBean instance.classMerged view onto a list of underlying Annotation objects.classAnnotation implementation which allows new key-value pairs to be layered on top of an underlying Annotation.classA no-frills implementation of Annotation that is just a wrapper around aLinkedHashMap.classAnnotation that is optimized for memory usage.Fields in org.biojava.bio declared as AnnotationModifier and TypeFieldDescriptionstatic final AnnotationAnnotation.EMPTY_ANNOTATIONA really useful empty and immutable annotation object.Methods in org.biojava.bio that return AnnotationModifier and TypeMethodDescriptionstatic AnnotationAnnotationTools.allIn(Annotation annotation, AnnotationType annType) Destructive down-cast an annotation to a type.static AnnotationAnnotationTools.allOut(Annotation annotation, AnnotationType annType) allOutreturns a newAnnotationcontaining only those values in theAnnotationargument which are not of a type specified by theAnnotationType.Annotatable.getAnnotation()Should return the associated annotation object.AnnotationChanger.getWrapped()getWrappedreturns theAnnotationbeing remapped.AnnotationRenamer.getWrapped()getWrappedreturns theAnnotationbeing remapped.Methods in org.biojava.bio with parameters of type AnnotationModifier and TypeMethodDescriptionvoidMergeAnnotation.addAnnotation(Annotation ann) Add a new Annotation to to the end of the list to be merged.final voidAnnotationType.Abstract.addProperty(Annotation ann, Object key, Object value) voidAnnotationType.addProperty(Annotation ann, Object property, Object value) Add a value to the specified property slot.static AnnotationAnnotationTools.allIn(Annotation annotation, AnnotationType annType) Destructive down-cast an annotation to a type.static AnnotationAnnotationTools.allOut(Annotation annotation, AnnotationType annType) allOutreturns a newAnnotationcontaining only those values in theAnnotationargument which are not of a type specified by theAnnotationType.final CollectionAnnotationType.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.booleanAnnotationType.Abstract.instanceOf(Annotation ann) booleanAnnotationType.instanceOf(Annotation ann) Validate an Annotation against this AnnotationType.voidMergeAnnotation.removeAnnotation(Annotation ann) Remove an Annotation from the list.final voidAnnotationType.Abstract.removeProperty(Annotation ann, Object key, Object value) voidAnnotationType.removeProperty(Annotation ann, Object property, Object value) Remove a value from the specified property slot.static SetAnnotationTools.searchAnnotation(Annotation ann, AnnotationType query) Scans an Annotation with an AnnotationType and returns all Annotation instances matching a Type.final voidAnnotationType.Abstract.setProperty(Annotation ann, Object property, Object value) voidAnnotationType.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 AnnotationModifierConstructorDescriptionprotectedCopy-constructor.AnnotationChanger(Annotation wrapped, ChangeTable changer) Creates a newAnnotationChangerusing the specifiedValueChangerto remap its values.AnnotationRenamer(Annotation wrapped, PropertyChanger mapper) Creates a newAnnotationRenamerusing the specifiedTagMapperto 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 AnnotationRestrictionEnzymeManager.getAnnotation(RestrictionEnzyme enzyme) getAnnotationreturns 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 voidGFF3Parser.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 EmissionStateHmmerProfileHMM.makeNewInsertState(String str, Annotation ann, int[] adv, Distribution dis) protected EmissionStateHmmerProfileHMM.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()getMetaDatareturns 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 AnnotationAnnotationFactory.makeAnnotation(Map m) makeAnnotationcreates 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 voidXFFTools.annotateXFF(File xffFile, Sequence sequence, Annotation ann) voidXFFFeatureSetHandler.setMergeAnnotation(Annotation ann) -
Uses of Annotation in org.biojava.bio.search
Methods in org.biojava.bio.search that return AnnotationModifier and TypeMethodDescriptionSequenceDBSearchHit.getAnnotation()Deprecated.getAnnotationreturns the Annotation associated with this hit.SequenceDBSearchResult.getAnnotation()Deprecated.getAnnotationreturns the Annotation associated with this hit.SequenceDBSearchSubHit.getAnnotation()Deprecated.SimpleSeqSimilaritySearchHit.getAnnotation()getAnnotationreturns the Annotation associated with this hit.SimpleSeqSimilaritySearchResult.getAnnotation()getAnnotationreturns the Annotation associated with this hit.SimpleSeqSimilaritySearchSubHit.getAnnotation()getAnnotationreturns 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 newSequenceDBSearchHitobject.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 newSequenceDBSearchSubHitobject.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 newSimpleSeqSimilaritySearchHitobject.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 newSimpleSeqSimilaritySearchSubHitobject. -
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 SequenceSequenceTools.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 TypeClassDescriptionclassDeprecated.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 voidSequenceBuilderBase.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 ObjectUtilHelper.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 AtomicSymbolAlphabetManager.createSymbol(char token, String name, Annotation annotation) Deprecated.Use the two-arg version of this method instead.static SymbolAlphabetManager.createSymbol(char token, Annotation annotation, List symList, Alphabet alpha) Deprecated.use the new version, without the token argumentstatic SymbolAlphabetManager.createSymbol(char token, Annotation annotation, Set symSet, Alphabet alpha) Deprecated.use the three-arg version of this method instead.static AtomicSymbolAlphabetManager.createSymbol(String name, Annotation annotation) Generate a new AtomicSymbol instance with a name and Annotation.static SymbolAlphabetManager.createSymbol(Annotation annotation, List symList, Alphabet alpha) Generates a new Symbol instance that represents the tuple of Symbols in symList.static SymbolAlphabetManager.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) protectedSimpleAtomicSymbol(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 TypeInterfaceDescriptioninterfaceAn annotation collection which stores annotations as Note objects.Classes in org.biojavax that implement AnnotationModifier and TypeClassDescriptionclassA place holder for a RichAnnotation that prevents null having to be usedclassSimple 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.