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.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.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.seq.projection Code for projecting Feature objects into alternate coordinate systems. 
org.biojava.bio.seq.ragbag The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code. 
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. 
 

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 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
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 java.util.Set AnnotationTools.searchAnnotation(Annotation ann, AnnotationType query)
           Scans an Annotation with an AnnotationType and returns all Annotation instances matching a Type.
 boolean AnnotationType.instanceOf(Annotation ann)
          Validate an Annotation against this AnnotationType.
 void AnnotationType.setProperty(Annotation ann, java.lang.Object property, java.lang.Object value)
          Set the property in an annotation bundle according to the type we believe it should be.
 void AnnotationType.addProperty(Annotation ann, java.lang.Object property, java.lang.Object value)
          Add a value to the specified property slot.
 java.util.Collection AnnotationType.getProperty(Annotation ann, java.lang.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, java.lang.Object property, java.lang.Object value)
          Remove a value from the specified property slot.
 boolean AnnotationType.Abstract.instanceOf(Annotation ann)
           
 void AnnotationType.Abstract.setProperty(Annotation ann, java.lang.Object property, java.lang.Object value)
           
 java.util.Collection AnnotationType.Abstract.getProperty(Annotation ann, java.lang.Object property)
           
 void AnnotationType.Abstract.addProperty(Annotation ann, java.lang.Object key, java.lang.Object value)
           
 void AnnotationType.Abstract.removeProperty(Annotation ann, java.lang.Object key, java.lang.Object value)
           
 void MergeAnnotation.addAnnotation(Annotation ann)
          Add a new Annotation to the list to be merged.
 

Constructors in org.biojava.bio with parameters of type Annotation
OverlayAnnotation(Annotation par)
          Construct an annotation which can overlay new key-value pairs onto an underlying annotation.
SmallAnnotation(Annotation ann)
           
AbstractAnnotation(Annotation ann)
           
AnnotationChanger(Annotation wrapped, ChangeTable changer)
          Creates a new AnnotationChanger using the specified ValueChanger to remap its values.
AnnotationRenamer(Annotation wrapped, TagMapper mapper)
          Creates a new AnnotationRenamer using the specified TagMapper to remap its keys.
SimpleAnnotation(Annotation ann)
          Create a new SimpleAnnotation by copying the properties from another one.
 

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(java.lang.String name, Annotation ann, int[] advance, Distribution dis)
           
SimpleDotState(char token, java.lang.String name, Annotation annotation)
          Deprecated. token is ignored since 1.2. Use the 2-arg constructor instead.
SimpleDotState(java.lang.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.hmmer
 

Methods in org.biojava.bio.program.hmmer with parameters of type Annotation
protected  EmissionState HmmerProfileHMM.makeNewInsertState(java.lang.String str, Annotation ann, int[] adv, Distribution dis)
           
protected  EmissionState HmmerProfileHMM.makeNewMatchState(java.lang.String str, Annotation ann, int[] adv, Distribution dis)
           
 

Constructors in org.biojava.bio.program.hmmer with parameters of type Annotation
ProfileEmissionState(java.lang.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 BioStore.getMetaData()
           
 Annotation IndexStore.getMetaData()
          getMetaData returns 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 Annotation
PhredSequence(SymbolList phredSequence, java.lang.String name, java.lang.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(java.util.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.search
 

Methods in org.biojava.bio.search that return Annotation
 Annotation SequenceDBSearchHit.getAnnotation()
          Deprecated. getAnnotation returns the Annotation associated with this hit.
 Annotation SimpleSeqSimilaritySearchSubHit.getAnnotation()
          getAnnotation returns the Annotation associated with this sub-hit.
 Annotation SimpleSeqSimilaritySearchHit.getAnnotation()
          getAnnotation returns the Annotation associated with this hit.
 Annotation SequenceDBSearchSubHit.getAnnotation()
          Deprecated.  
 Annotation SimpleSeqSimilaritySearchResult.getAnnotation()
          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, java.lang.String subjectID, Annotation annotation, java.util.List subHits)
          Deprecated. Creates a new SequenceDBSearchHit object.
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.
SimpleSeqSimilaritySearchHit(double score, double eValue, double pValue, int queryStart, int queryEnd, StrandedFeature.Strand queryStrand, int subjectStart, int subjectEnd, StrandedFeature.Strand subjectStrand, java.lang.String subjectID, Annotation annotation, java.util.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.
SimpleSeqSimilaritySearchResult(Sequence querySequence, SequenceDB sequenceDB, java.util.Map searchParameters, java.util.List hits, Annotation annotation)
          Creates a new SimpleSeqSimilaritySearchResult.
SequenceDBSearchResult(Sequence querySequence, SequenceDB sequenceDB, java.util.Map searchParameters, java.util.List hits, Annotation annotation)
          Deprecated. Creates a new SequenceDBSearchResult.
 

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 FeatureTypes.RepositoryImpl.getAnnotation()
           
 Annotation ViewSequence.getAnnotation()
           
 Annotation SimpleAssembly.getAnnotation()
           
 Annotation SimpleGappedSequence.getAnnotation()
           
 Annotation ProjectedFeatureHolder.getAnnotation(Feature f)
           
 Annotation SubSequence.getAnnotation()
           
 Annotation DummySequence.getAnnotation()
           
 

Methods in org.biojava.bio.seq with parameters of type Annotation
 Sequence SequenceFactory.createSequence(SymbolList symList, java.lang.String uri, java.lang.String name, Annotation annotation)
          Creates a sequence using these parameters.
static Sequence SequenceTools.createSequence(SymbolList syms, java.lang.String uri, java.lang.String name, Annotation ann)
           
 

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

Methods in org.biojava.bio.seq.impl that return Annotation
 Annotation SimpleSequence.getAnnotation()
           
 Annotation SimpleFeature.getAnnotation()
           
 

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

Constructors in org.biojava.bio.seq.impl with parameters of type Annotation
SimpleSequence(SymbolList sym, java.lang.String urn, java.lang.String name, Annotation annotation)
          Create a SimpleSequence with the symbols and alphabet of sym, and the sequence properties listed.
SimpleSequence(SymbolList sym, java.lang.String urn, java.lang.String name, Annotation annotation, FeatureRealizer realizer)
          Create a SimpleSequence using a specified FeatureRealizer.
RevCompSequence(Sequence seq, java.lang.String urn, java.lang.String name, Annotation annotation)
           
 

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

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 CharacterTokenization.getAnnotation()
           
 Annotation WordTokenization.getAnnotation()
           
 

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

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

Methods in org.biojava.bio.seq.projection that return Annotation
 Annotation ProjectedFeature.getAnnotation()
           
 Annotation ProjectionContext.getAnnotation(Feature f)
          Get the annotation bundle of the projected feature.
 

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

Methods in org.biojava.bio.seq.ragbag with parameters of type Annotation
 void RagbagIdleSequenceBuilder.addProperty(Annotation ann, java.lang.Object key, java.lang.Object value)
           
 

Uses of Annotation in org.biojava.bio.symbol
 

Methods in org.biojava.bio.symbol that return Annotation
 Annotation SingletonAlphabet.getAnnotation()
           
 Annotation DoubleAlphabet.getAnnotation()
           
 Annotation DoubleAlphabet.DoubleSymbol.getAnnotation()
           
 Annotation DoubleAlphabet.DoubleRange.getAnnotation()
           
 Annotation DoubleAlphabet.SubDoubleAlphabet.getAnnotation()
           
 Annotation FundamentalAtomicSymbol.getAnnotation()
           
 Annotation SimpleAlphabet.getAnnotation()
           
 Annotation IntegerAlphabet.getAnnotation()
           
 Annotation IntegerAlphabet.IntegerSymbol.getAnnotation()
           
 Annotation IntegerAlphabet.SubIntegerAlphabet.getAnnotation()
           
 

Methods in org.biojava.bio.symbol with parameters of type Annotation
static AtomicSymbol AlphabetManager.createSymbol(java.lang.String name, Annotation annotation)
           Generate a new AtomicSymbol instance with a name and Annotation.
static AtomicSymbol AlphabetManager.createSymbol(char token, java.lang.String name, Annotation annotation)
          Deprecated. Use the two-arg version of this method instead.
static Symbol AlphabetManager.createSymbol(char token, Annotation annotation, java.util.List symList, Alphabet alpha)
          Deprecated. use the new version, without the token argument
static Symbol AlphabetManager.createSymbol(Annotation annotation, java.util.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, java.util.Set symSet, Alphabet alpha)
          Deprecated. use the three-arg version of this method instead.
static Symbol AlphabetManager.createSymbol(Annotation annotation, java.util.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, java.util.List syms)
           
FundamentalAtomicSymbol(java.lang.String name, Annotation annotation)
           
 

Uses of Annotation in org.biojava.bio.taxa
 

Methods in org.biojava.bio.taxa that return Annotation
 Annotation AbstractTaxon.getAnnotation()