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 AnnotationChanger.getWrapped()
          getWrapped returns the Annotation being remapped.
 Annotation AnnotationRenamer.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 SequenceDBSearchSubHit.getAnnotation()
          Deprecated.  
 Annotation SimpleSeqSimilaritySearchResult.getAnnotation()
          getAnnotation returns the Annotation associated with this hit.
 Annotation SimpleSeqSimilaritySearchHit.getAnnotation()
          getAnnotation returns the Annotation associated with this hit.
 Annotation SequenceDBSearchHit.getAnnotation()
          Deprecated. getAnnotation returns the Annotation associated with this hit.
 Annotation SequenceDBSearchResult.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 NewSimpleAssembly.getAnnotation()
           
 Annotation SimpleAssembly.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 SimpleSequence.getAnnotation()
           
 Annotation SimpleFeature.getAnnotation()
           
 Annotation SimpleGappedSequence.getAnnotation()
           
 Annotation SubSequence.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 AGAVEAnnotFilter.getAccession(Annotation annot)
           
 String SimpleAnnotFilter.getAccession(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getAccession(Annotation annot)
           
 String Embl2AgaveAnnotFilter.getAccession(Annotation annot)
           
 String AGAVEAnnotFilter.getAlignLength(Annotation annot)
           
 String SimpleAnnotFilter.getAlignLength(Annotation annot)
           
 String AGAVEAnnotFilter.getAlignUnits(Annotation annot)
           
 String SimpleAnnotFilter.getAlignUnits(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getAlignUnits(Annotation annot)
           
 AGAVEDbId[] AGAVEAnnotFilter.getAltIds(Annotation annot)
           
 AGAVEDbId[] SimpleAnnotFilter.getAltIds(Annotation annot)
           
 AGAVEDbId[] Agave2AgaveAnnotFilter.getAltIds(Annotation annot)
           
 String AGAVEAnnotFilter.getChromNum(Annotation annot)
           
 String SimpleAnnotFilter.getChromNum(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getChromNum(Annotation annot)
           
 String AGAVEAnnotFilter.getChromosome(Annotation annot)
           
 String SimpleAnnotFilter.getChromosome(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getChromosome(Annotation annot)
           
 String AGAVEAnnotFilter.getClassifyId(Annotation annot)
           
 String SimpleAnnotFilter.getClassifyId(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getClassifyId(Annotation annot)
           
 String AGAVEAnnotFilter.getClassifySystem(Annotation annot)
           
 String SimpleAnnotFilter.getClassifySystem(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getClassifySystem(Annotation annot)
           
 String AGAVEAnnotFilter.getClassifyType(Annotation annot)
           
 String SimpleAnnotFilter.getClassifyType(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getClassifyType(Annotation annot)
           
 String AGAVEAnnotFilter.getCloneId(Annotation annot)
           
 String SimpleAnnotFilter.getCloneId(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getCloneId(Annotation annot)
           
 String AGAVEAnnotFilter.getCloneLibrary(Annotation annot)
           
 String SimpleAnnotFilter.getCloneLibrary(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getCloneLibrary(Annotation annot)
           
 String AGAVEAnnotFilter.getConfidence(Annotation annot)
           
 String SimpleAnnotFilter.getConfidence(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getConfidence(Annotation annot)
           
 String AGAVEAnnotFilter.getCreateDate(Annotation annot)
           
 String SimpleAnnotFilter.getCreateDate(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getCreateDate(Annotation annot)
           
 AGAVEDbId AGAVEAnnotFilter.getDbId(Annotation annot)
           
 AGAVEDbId SimpleAnnotFilter.getDbId(Annotation annot)
           
 AGAVEDbId Agave2AgaveAnnotFilter.getDbId(Annotation annot)
           
 AGAVEDbId Embl2AgaveAnnotFilter.getDbId(Annotation annot)
           
 String AGAVEAnnotFilter.getDescription(Annotation annot)
           
 String SimpleAnnotFilter.getDescription(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getDescription(Annotation annot)
           
 String Embl2AgaveAnnotFilter.getDescription(Annotation annot)
           
 String AGAVEAnnotFilter.getEcNumber(Annotation annot)
           
 String SimpleAnnotFilter.getEcNumber(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getEcNumber(Annotation annot)
           
 String AGAVEAnnotFilter.getElementId(Annotation annot)
           
 String SimpleAnnotFilter.getElementId(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getElementId(Annotation annot)
           
 String[] AGAVEAnnotFilter.getElementIds(Annotation annot)
           
 String[] SimpleAnnotFilter.getElementIds(Annotation annot)
           
 String[] Agave2AgaveAnnotFilter.getElementIds(Annotation annot)
           
 String[] AGAVEAnnotFilter.getExonIds(Annotation annot)
           
 String[] SimpleAnnotFilter.getExonIds(Annotation annot)
           
 String[] Agave2AgaveAnnotFilter.getExonIds(Annotation annot)
           
 String AGAVEAnnotFilter.getFeatureType(Annotation annot)
           
 String SimpleAnnotFilter.getFeatureType(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getFeatureType(Annotation annot)
           
 String AGAVEAnnotFilter.getGroupOrder(Annotation annot)
           
 String SimpleAnnotFilter.getGroupOrder(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getGroupOrder(Annotation annot)
           
 AGAVEIdAlias[] AGAVEAnnotFilter.getIdAlias(Annotation annot)
           
 AGAVEIdAlias[] SimpleAnnotFilter.getIdAlias(Annotation annot)
           
 AGAVEIdAlias[] Agave2AgaveAnnotFilter.getIdAlias(Annotation annot)
           
 String AGAVEAnnotFilter.getKeyword(Annotation annot)
           
 String SimpleAnnotFilter.getKeyword(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getKeyword(Annotation annot)
           
 String Embl2AgaveAnnotFilter.getKeyword(Annotation annot)
           
 String AGAVEAnnotFilter.getLabel(Annotation annot)
           
 String SimpleAnnotFilter.getLabel(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getLabel(Annotation annot)
           
 AGAVEMapLocation[] AGAVEAnnotFilter.getMapLocation(Annotation annot)
           
 AGAVEMapLocation[] SimpleAnnotFilter.getMapLocation(Annotation annot)
           
 AGAVEMapLocation[] Agave2AgaveAnnotFilter.getMapLocation(Annotation annot)
           
 String AGAVEAnnotFilter.getMapPosition(Annotation annot)
           
 String SimpleAnnotFilter.getMapPosition(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getMapPosition(Annotation annot)
           
 String AGAVEAnnotFilter.getMatchAlign(Annotation annot)
           
 String SimpleAnnotFilter.getMatchAlign(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getMatchAlign(Annotation annot)
           
 String AGAVEAnnotFilter.getMatchDesc(Annotation annot)
           
 String SimpleAnnotFilter.getMatchDesc(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getMatchDesc(Annotation annot)
           
 AGAVEMatchRegion AGAVEAnnotFilter.getMatchRegion(Annotation annot)
           
 AGAVEMatchRegion SimpleAnnotFilter.getMatchRegion(Annotation annot)
           
 AGAVEMatchRegion Agave2AgaveAnnotFilter.getMatchRegion(Annotation annot)
           
 String AGAVEAnnotFilter.getMolType(Annotation annot)
           
 String SimpleAnnotFilter.getMolType(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getMolType(Annotation annot)
           
 String Embl2AgaveAnnotFilter.getMolType(Annotation annot)
           
 String AGAVEAnnotFilter.getNote(Annotation annot)
           
 String SimpleAnnotFilter.getNote(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getNote(Annotation annot)
           
 String Embl2AgaveAnnotFilter.getNote(Annotation annot)
           
 String AGAVEAnnotFilter.getOrganism(Annotation annot)
           
 String SimpleAnnotFilter.getOrganism(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getOrganism(Annotation annot)
           
 String Embl2AgaveAnnotFilter.getOrganism(Annotation annot)
           
 String AGAVEAnnotFilter.getOS(Annotation annot)
           
 String SimpleAnnotFilter.getOS(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getOS(Annotation annot)
           
 String Embl2AgaveAnnotFilter.getOS(Annotation annot)
           
 AGAVEProperty[] AGAVEAnnotFilter.getProperty(Annotation annot, String type)
           
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[] Agave2AgaveAnnotFilter.getProperty(Annotation annot, String type)
           
 AGAVEQueryRegion AGAVEAnnotFilter.getQueryRegion(Annotation annot)
           
 AGAVEQueryRegion SimpleAnnotFilter.getQueryRegion(Annotation annot)
           
 AGAVEQueryRegion Agave2AgaveAnnotFilter.getQueryRegion(Annotation annot)
           
 AGAVERelatedAnnot[] AGAVEAnnotFilter.getRelatedAnnot(Annotation annot)
           
 AGAVERelatedAnnot[] SimpleAnnotFilter.getRelatedAnnot(Annotation annot)
           
 AGAVERelatedAnnot[] Agave2AgaveAnnotFilter.getRelatedAnnot(Annotation annot)
           
 String AGAVEAnnotFilter.getResultType(Annotation annot)
           
 String SimpleAnnotFilter.getResultType(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getResultType(Annotation annot)
           
 String AGAVEAnnotFilter.getSequenceId(Annotation annot)
           
 String SimpleAnnotFilter.getSequenceId(Annotation annot)
           
 String AGAVEAnnotFilter.getTaxonId(Annotation annot)
           
 String SimpleAnnotFilter.getTaxonId(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getTaxonId(Annotation annot)
           
 String AGAVEAnnotFilter.getUpdateDate(Annotation annot)
           
 String SimpleAnnotFilter.getUpdateDate(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getUpdateDate(Annotation annot)
           
 String AGAVEAnnotFilter.getVersion(Annotation annot)
           
 String SimpleAnnotFilter.getVersion(Annotation annot)
           
 String Agave2AgaveAnnotFilter.getVersion(Annotation annot)
           
 String Embl2AgaveAnnotFilter.getVersion(Annotation annot)
           
 AGAVEXrefs[] AGAVEAnnotFilter.getXrefs(Annotation annot)
           
 AGAVEXrefs[] SimpleAnnotFilter.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 Chain.getAnnotation()
          get/set the Annotation of a Chain.
 Annotation ChainImpl.getAnnotation()
          get/set the Annotation of a Chain.
 

Methods in org.biojava.bio.structure with parameters of type Annotation
 void Chain.setAnnotation(Annotation anno)
          get/set the Annotation of a Chain.
 void ChainImpl.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 FundamentalAtomicSymbol.getAnnotation()
           
 Annotation DoubleAlphabet.getAnnotation()
           
 Annotation DoubleAlphabet.DoubleSymbol.getAnnotation()
           
 Annotation DoubleAlphabet.DoubleRange.getAnnotation()
           
 Annotation DoubleAlphabet.SubDoubleAlphabet.getAnnotation()
           
 Annotation SimpleAlphabet.getAnnotation()
           
 Annotation IntegerAlphabet.getAnnotation()
           
 Annotation IntegerAlphabet.IntegerSymbol.getAnnotation()
           
 Annotation IntegerAlphabet.SubIntegerAlphabet.getAnnotation()
           
 Annotation SoftMaskedAlphabet.getAnnotation()
          The SoftMaskedAlphabet has no annotation
 Annotation SoftMaskedAlphabet.CaseSensitiveTokenization.getAnnotation()
           
 Annotation SingletonAlphabet.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 IntegerOntology.IntTerm.getAnnotation()
           
 Annotation Triple.Impl.getAnnotation()
           
 Annotation Term.Impl.getAnnotation()
           
 Annotation OntologyTerm.Impl.getAnnotation()
           
 Annotation RemoteTerm.Impl.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 CompoundRichLocation.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.
 

Uses of Annotation in org.biojavax.ontology
 

Methods in org.biojavax.ontology that return Annotation
 Annotation SimpleComparableTriple.getAnnotation()
          Should return the associated annotation object.
 Annotation SimpleComparableTerm.getAnnotation()
          Should return the associated annotation object.