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Packages that use Annotation | |
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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 | |
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 |
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Classes in org.biojava.bio that implement Annotation | |
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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 | |
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static Annotation |
Annotation.EMPTY_ANNOTATION
A really useful empty and immutable annotation object. |
Methods in org.biojava.bio that return Annotation | |
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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 | |
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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 | |
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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 |
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Methods in org.biojava.bio.dp that return Annotation | |
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Annotation |
SimpleEmissionState.getAnnotation()
|
Methods in org.biojava.bio.dp with parameters of type Annotation | |
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void |
SimpleEmissionState.setAnnotation(Annotation ann)
|
Constructors in org.biojava.bio.dp with parameters of type Annotation | |
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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 |
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Methods in org.biojava.bio.molbio that return Annotation | |
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static Annotation |
RestrictionEnzymeManager.getAnnotation(RestrictionEnzyme enzyme)
getAnnotation returns an immutable, static
annotation describing the enzyme. |
Uses of Annotation in org.biojava.bio.program.das |
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Methods in org.biojava.bio.program.das that return Annotation | |
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Annotation |
DASSequence.getAnnotation()
|
Uses of Annotation in org.biojava.bio.program.das.dasalignment |
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Methods in org.biojava.bio.program.das.dasalignment that return Annotation | |
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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 |
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Methods in org.biojava.bio.program.gff3 that return Annotation | |
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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 |
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Methods in org.biojava.bio.program.hmmer with parameters of type Annotation | |
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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 |
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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 |
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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 |
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Methods in org.biojava.bio.program.ssbind that return Annotation | |
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static Annotation |
AnnotationFactory.makeAnnotation(Map m)
makeAnnotation creates the annotation. |
Uses of Annotation in org.biojava.bio.program.tagvalue |
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Methods in org.biojava.bio.program.tagvalue that return Annotation | |
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Annotation |
AnnotationBuilder.getLast()
Get the last complete annotation built. |
Uses of Annotation in org.biojava.bio.program.xff |
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Methods in org.biojava.bio.program.xff that return Annotation | |
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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 |
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Methods in org.biojava.bio.search that return Annotation | |
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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 |
SequenceDBSearchResult.getAnnotation()
Deprecated. getAnnotation returns the Annotation associated
with this hit. |
Annotation |
SimpleSeqSimilaritySearchResult.getAnnotation()
getAnnotation returns the Annotation associated
with this hit. |
Annotation |
SequenceDBSearchSubHit.getAnnotation()
Deprecated. |
Annotation |
SimpleSeqSimilaritySearchHit.getAnnotation()
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 |
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Fields in org.biojava.bio.seq declared as Annotation | |
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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 | |
---|---|
Sequence |
SequenceFactory.createSequence(SymbolList symList,
String uri,
String name,
Annotation annotation)
Deprecated. Creates a sequence using these parameters. |
static Sequence |
SequenceTools.createSequence(SymbolList syms,
String uri,
String name,
Annotation ann)
|
Uses of Annotation in org.biojava.bio.seq.impl |
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Methods in org.biojava.bio.seq.impl that return Annotation | |
---|---|
Annotation |
SimpleGappedSequence.getAnnotation()
|
Annotation |
SimpleSequence.getAnnotation()
|
Annotation |
SimpleFeature.getAnnotation()
|
Annotation |
DummySequence.getAnnotation()
|
Annotation |
ViewSequence.getAnnotation()
|
Annotation |
SubSequence.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 |
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Classes in org.biojava.bio.seq.io that implement Annotation | |
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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()
|
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 |
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Methods in org.biojava.bio.seq.io.agave with parameters of type Annotation | |
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String |
Agave2AgaveAnnotFilter.getAccession(Annotation annot)
|
String |
Embl2AgaveAnnotFilter.getAccession(Annotation annot)
|
String |
SimpleAnnotFilter.getAccession(Annotation annot)
|
String |
AGAVEAnnotFilter.getAccession(Annotation annot)
|
String |
SimpleAnnotFilter.getAlignLength(Annotation annot)
|
String |
AGAVEAnnotFilter.getAlignLength(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getAlignUnits(Annotation annot)
|
String |
SimpleAnnotFilter.getAlignUnits(Annotation annot)
|
String |
AGAVEAnnotFilter.getAlignUnits(Annotation annot)
|
AGAVEDbId[] |
Agave2AgaveAnnotFilter.getAltIds(Annotation annot)
|
AGAVEDbId[] |
SimpleAnnotFilter.getAltIds(Annotation annot)
|
AGAVEDbId[] |
AGAVEAnnotFilter.getAltIds(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getChromNum(Annotation annot)
|
String |
SimpleAnnotFilter.getChromNum(Annotation annot)
|
String |
AGAVEAnnotFilter.getChromNum(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getChromosome(Annotation annot)
|
String |
SimpleAnnotFilter.getChromosome(Annotation annot)
|
String |
AGAVEAnnotFilter.getChromosome(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getClassifyId(Annotation annot)
|
String |
SimpleAnnotFilter.getClassifyId(Annotation annot)
|
String |
AGAVEAnnotFilter.getClassifyId(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getClassifySystem(Annotation annot)
|
String |
SimpleAnnotFilter.getClassifySystem(Annotation annot)
|
String |
AGAVEAnnotFilter.getClassifySystem(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getClassifyType(Annotation annot)
|
String |
SimpleAnnotFilter.getClassifyType(Annotation annot)
|
String |
AGAVEAnnotFilter.getClassifyType(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getCloneId(Annotation annot)
|
String |
SimpleAnnotFilter.getCloneId(Annotation annot)
|
String |
AGAVEAnnotFilter.getCloneId(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getCloneLibrary(Annotation annot)
|
String |
SimpleAnnotFilter.getCloneLibrary(Annotation annot)
|
String |
AGAVEAnnotFilter.getCloneLibrary(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getConfidence(Annotation annot)
|
String |
SimpleAnnotFilter.getConfidence(Annotation annot)
|
String |
AGAVEAnnotFilter.getConfidence(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getCreateDate(Annotation annot)
|
String |
SimpleAnnotFilter.getCreateDate(Annotation annot)
|
String |
AGAVEAnnotFilter.getCreateDate(Annotation annot)
|
AGAVEDbId |
Agave2AgaveAnnotFilter.getDbId(Annotation annot)
|
AGAVEDbId |
Embl2AgaveAnnotFilter.getDbId(Annotation annot)
|
AGAVEDbId |
SimpleAnnotFilter.getDbId(Annotation annot)
|
AGAVEDbId |
AGAVEAnnotFilter.getDbId(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getDescription(Annotation annot)
|
String |
Embl2AgaveAnnotFilter.getDescription(Annotation annot)
|
String |
SimpleAnnotFilter.getDescription(Annotation annot)
|
String |
AGAVEAnnotFilter.getDescription(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getEcNumber(Annotation annot)
|
String |
SimpleAnnotFilter.getEcNumber(Annotation annot)
|
String |
AGAVEAnnotFilter.getEcNumber(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getElementId(Annotation annot)
|
String |
SimpleAnnotFilter.getElementId(Annotation annot)
|
String |
AGAVEAnnotFilter.getElementId(Annotation annot)
|
String[] |
Agave2AgaveAnnotFilter.getElementIds(Annotation annot)
|
String[] |
SimpleAnnotFilter.getElementIds(Annotation annot)
|
String[] |
AGAVEAnnotFilter.getElementIds(Annotation annot)
|
String[] |
Agave2AgaveAnnotFilter.getExonIds(Annotation annot)
|
String[] |
SimpleAnnotFilter.getExonIds(Annotation annot)
|
String[] |
AGAVEAnnotFilter.getExonIds(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getFeatureType(Annotation annot)
|
String |
SimpleAnnotFilter.getFeatureType(Annotation annot)
|
String |
AGAVEAnnotFilter.getFeatureType(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getGroupOrder(Annotation annot)
|
String |
SimpleAnnotFilter.getGroupOrder(Annotation annot)
|
String |
AGAVEAnnotFilter.getGroupOrder(Annotation annot)
|
AGAVEIdAlias[] |
Agave2AgaveAnnotFilter.getIdAlias(Annotation annot)
|
AGAVEIdAlias[] |
SimpleAnnotFilter.getIdAlias(Annotation annot)
|
AGAVEIdAlias[] |
AGAVEAnnotFilter.getIdAlias(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getKeyword(Annotation annot)
|
String |
Embl2AgaveAnnotFilter.getKeyword(Annotation annot)
|
String |
SimpleAnnotFilter.getKeyword(Annotation annot)
|
String |
AGAVEAnnotFilter.getKeyword(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getLabel(Annotation annot)
|
String |
SimpleAnnotFilter.getLabel(Annotation annot)
|
String |
AGAVEAnnotFilter.getLabel(Annotation annot)
|
AGAVEMapLocation[] |
Agave2AgaveAnnotFilter.getMapLocation(Annotation annot)
|
AGAVEMapLocation[] |
SimpleAnnotFilter.getMapLocation(Annotation annot)
|
AGAVEMapLocation[] |
AGAVEAnnotFilter.getMapLocation(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getMapPosition(Annotation annot)
|
String |
SimpleAnnotFilter.getMapPosition(Annotation annot)
|
String |
AGAVEAnnotFilter.getMapPosition(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getMatchAlign(Annotation annot)
|
String |
SimpleAnnotFilter.getMatchAlign(Annotation annot)
|
String |
AGAVEAnnotFilter.getMatchAlign(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getMatchDesc(Annotation annot)
|
String |
SimpleAnnotFilter.getMatchDesc(Annotation annot)
|
String |
AGAVEAnnotFilter.getMatchDesc(Annotation annot)
|
AGAVEMatchRegion |
Agave2AgaveAnnotFilter.getMatchRegion(Annotation annot)
|
AGAVEMatchRegion |
SimpleAnnotFilter.getMatchRegion(Annotation annot)
|
AGAVEMatchRegion |
AGAVEAnnotFilter.getMatchRegion(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getMolType(Annotation annot)
|
String |
Embl2AgaveAnnotFilter.getMolType(Annotation annot)
|
String |
SimpleAnnotFilter.getMolType(Annotation annot)
|
String |
AGAVEAnnotFilter.getMolType(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getNote(Annotation annot)
|
String |
Embl2AgaveAnnotFilter.getNote(Annotation annot)
|
String |
SimpleAnnotFilter.getNote(Annotation annot)
|
String |
AGAVEAnnotFilter.getNote(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getOrganism(Annotation annot)
|
String |
Embl2AgaveAnnotFilter.getOrganism(Annotation annot)
|
String |
SimpleAnnotFilter.getOrganism(Annotation annot)
|
String |
AGAVEAnnotFilter.getOrganism(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getOS(Annotation annot)
|
String |
Embl2AgaveAnnotFilter.getOS(Annotation annot)
|
String |
SimpleAnnotFilter.getOS(Annotation annot)
|
String |
AGAVEAnnotFilter.getOS(Annotation annot)
|
AGAVEProperty[] |
Agave2AgaveAnnotFilter.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[] |
AGAVEAnnotFilter.getProperty(Annotation annot,
String type)
|
AGAVEQueryRegion |
Agave2AgaveAnnotFilter.getQueryRegion(Annotation annot)
|
AGAVEQueryRegion |
SimpleAnnotFilter.getQueryRegion(Annotation annot)
|
AGAVEQueryRegion |
AGAVEAnnotFilter.getQueryRegion(Annotation annot)
|
AGAVERelatedAnnot[] |
Agave2AgaveAnnotFilter.getRelatedAnnot(Annotation annot)
|
AGAVERelatedAnnot[] |
SimpleAnnotFilter.getRelatedAnnot(Annotation annot)
|
AGAVERelatedAnnot[] |
AGAVEAnnotFilter.getRelatedAnnot(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getResultType(Annotation annot)
|
String |
SimpleAnnotFilter.getResultType(Annotation annot)
|
String |
AGAVEAnnotFilter.getResultType(Annotation annot)
|
String |
SimpleAnnotFilter.getSequenceId(Annotation annot)
|
String |
AGAVEAnnotFilter.getSequenceId(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getTaxonId(Annotation annot)
|
String |
SimpleAnnotFilter.getTaxonId(Annotation annot)
|
String |
AGAVEAnnotFilter.getTaxonId(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getUpdateDate(Annotation annot)
|
String |
SimpleAnnotFilter.getUpdateDate(Annotation annot)
|
String |
AGAVEAnnotFilter.getUpdateDate(Annotation annot)
|
String |
Agave2AgaveAnnotFilter.getVersion(Annotation annot)
|
String |
Embl2AgaveAnnotFilter.getVersion(Annotation annot)
|
String |
SimpleAnnotFilter.getVersion(Annotation annot)
|
String |
AGAVEAnnotFilter.getVersion(Annotation annot)
|
AGAVEXrefs[] |
Agave2AgaveAnnotFilter.getXrefs(Annotation annot)
|
AGAVEXrefs[] |
SimpleAnnotFilter.getXrefs(Annotation annot)
|
AGAVEXrefs[] |
AGAVEAnnotFilter.getXrefs(Annotation annot)
|
Uses of Annotation in org.biojava.bio.structure |
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Methods in org.biojava.bio.structure that return Annotation | |
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Annotation |
Chain.getAnnotation()
get/set the Annotation of a Chain. |
Annotation |
ChainImpl.getAnnotation()
|
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)
|
Uses of Annotation in org.biojava.bio.symbol |
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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 |
IntegerAlphabet.getAnnotation()
|
Annotation |
IntegerAlphabet.IntegerSymbol.getAnnotation()
|
Annotation |
IntegerAlphabet.SubIntegerAlphabet.getAnnotation()
|
Annotation |
DoubleAlphabet.getAnnotation()
|
Annotation |
DoubleAlphabet.DoubleSymbol.getAnnotation()
|
Annotation |
DoubleAlphabet.DoubleRange.getAnnotation()
|
Annotation |
DoubleAlphabet.SubDoubleAlphabet.getAnnotation()
|
Annotation |
FundamentalAtomicSymbol.getAnnotation()
|
Annotation |
SimpleAlphabet.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 |
RemoteTerm.Impl.getAnnotation()
|
Annotation |
IntegerOntology.IntTerm.getAnnotation()
|
Annotation |
Term.Impl.getAnnotation()
|
Annotation |
Triple.Impl.getAnnotation()
|
Annotation |
OntologyTerm.Impl.getAnnotation()
|
Uses of Annotation in org.biojavax |
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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 |
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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 |
SimpleRichFeature.getAnnotation()
Should return the associated annotation object. |
Annotation |
SimpleRichLocation.getAnnotation()
Should return the associated annotation object. |
Annotation |
EmptyRichLocation.getAnnotation()
Should return the associated annotation object. ALWAYS RETURNS THE EMPTY ANNOTATION |
Annotation |
CompoundRichLocation.getAnnotation()
Should return the associated annotation object. ALWAYS RETURNS THE EMPTY ANNOTATION |
Uses of Annotation in org.biojavax.ontology |
---|
Methods in org.biojavax.ontology that return Annotation | |
---|---|
Annotation |
SimpleComparableTriple.getAnnotation()
Should return the associated annotation object. ALWAYS RETURNS THE EMPTY ANNOTATION |
Annotation |
SimpleComparableTerm.getAnnotation()
Should return the associated annotation object. ALWAYS RETURNS AN EMPTY ANNOTATION OBJECT |
|
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