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| Uses of Taxon in eu.etaxonomy.cdm.api.service |
|---|
| Methods in eu.etaxonomy.cdm.api.service that return Taxon | |
|---|---|
Taxon |
TaxonServiceImpl.changeSynonymToAcceptedTaxon(Synonym synonym,
Taxon acceptedTaxon,
boolean deleteSynonym,
boolean copyCitationInfo,
Reference citation,
String microCitation)
|
Taxon |
ITaxonService.changeSynonymToAcceptedTaxon(Synonym synonym,
Taxon acceptedTaxon,
boolean deleteSynonym,
boolean copyCitationInfo,
Reference citation,
String microCitation)
Changes a synonym into an accepted taxon and removes the synonym relationship to the given accepted taxon. |
Taxon |
TaxonServiceImpl.changeSynonymToRelatedTaxon(Synonym synonym,
Taxon toTaxon,
TaxonRelationshipType taxonRelationshipType,
Reference citation,
String microcitation)
|
Taxon |
ITaxonService.changeSynonymToRelatedTaxon(Synonym synonym,
Taxon toTaxon,
TaxonRelationshipType taxonRelationshipType,
Reference reference,
String microReference)
TODO still needed and correct? Change a synonym into a related concept |
Taxon |
TaxonServiceImpl.findBestMatchingTaxon(MatchingTaxonConfigurator config)
|
Taxon |
ITaxonService.findBestMatchingTaxon(MatchingTaxonConfigurator config)
|
Taxon |
TaxonServiceImpl.findBestMatchingTaxon(String taxonName)
|
Taxon |
ITaxonService.findBestMatchingTaxon(String taxonName)
|
| Methods in eu.etaxonomy.cdm.api.service that return types with arguments of type Taxon | |
|---|---|
List<Taxon> |
TaxonServiceImpl.getAllTaxa(int limit,
int start)
FIXME Candidate for harmonization list(Taxon.class, ...) (non-Javadoc) |
List<Taxon> |
ITaxonService.getAllTaxa(int limit,
int start)
Computes all taxon bases. |
List<Taxon> |
TaxonServiceImpl.getRootTaxa(Rank rank,
Reference sec,
boolean onlyWithChildren,
boolean withMisapplications,
List<String> propertyPaths)
|
List<Taxon> |
ITaxonService.getRootTaxa(Rank rank,
Reference sec,
boolean onlyWithChildren,
boolean withMisapplications,
List<String> propertyPaths)
Deprecated. obsolete when using classification |
List<Taxon> |
TaxonServiceImpl.getRootTaxa(Reference sec,
CdmFetch cdmFetch,
boolean onlyWithChildren)
FIXME Candidate for harmonization merge with getRootTaxa(Reference sec, ..., ...) (non-Javadoc) |
List<Taxon> |
ITaxonService.getRootTaxa(Reference sec,
CdmFetch cdmFetch,
boolean onlyWithChildren)
Deprecated. obsolete when using classification |
Set<Taxon> |
TaxonServiceImpl.listRelatedTaxa(Taxon taxon,
Set<TaxonRelationshipEdge> includeRelationships,
Integer maxDepth,
Integer limit,
Integer start,
List<String> propertyPaths)
|
Set<Taxon> |
ITaxonService.listRelatedTaxa(Taxon taxon,
Set<TaxonRelationshipEdge> includeRelationships,
Integer maxDepth,
Integer limit,
Integer start,
List<String> propertyPaths)
lists all taxa which are related to the taxon given as
parameter. |
| Methods in eu.etaxonomy.cdm.api.service with parameters of type Taxon | ||
|---|---|---|
void |
TaxonServiceImpl.changeHomotypicalGroupOfSynonym(Synonym synonym,
HomotypicalGroup newHomotypicalGroup,
Taxon targetTaxon,
boolean removeFromOtherTaxa,
boolean setBasionymRelationIfApplicable)
|
|
void |
ITaxonService.changeHomotypicalGroupOfSynonym(Synonym synonym,
HomotypicalGroup newHomotypicalGroup,
Taxon targetTaxon,
boolean removeFromOtherTaxa,
boolean setBasionymRelationIfApplicable)
Changes the homotypic group of a synonym into the new homotypic group. |
|
Taxon |
TaxonServiceImpl.changeSynonymToAcceptedTaxon(Synonym synonym,
Taxon acceptedTaxon,
boolean deleteSynonym,
boolean copyCitationInfo,
Reference citation,
String microCitation)
|
|
Taxon |
ITaxonService.changeSynonymToAcceptedTaxon(Synonym synonym,
Taxon acceptedTaxon,
boolean deleteSynonym,
boolean copyCitationInfo,
Reference citation,
String microCitation)
Changes a synonym into an accepted taxon and removes the synonym relationship to the given accepted taxon. |
|
Taxon |
TaxonServiceImpl.changeSynonymToRelatedTaxon(Synonym synonym,
Taxon toTaxon,
TaxonRelationshipType taxonRelationshipType,
Reference citation,
String microcitation)
|
|
Taxon |
ITaxonService.changeSynonymToRelatedTaxon(Synonym synonym,
Taxon toTaxon,
TaxonRelationshipType taxonRelationshipType,
Reference reference,
String microReference)
TODO still needed and correct? Change a synonym into a related concept |
|
List<Synonym> |
TaxonServiceImpl.createAllInferredSynonyms(Taxon taxon,
Classification tree,
boolean doWithMisappliedNames)
|
|
List<Synonym> |
ITaxonService.createAllInferredSynonyms(Taxon taxon,
Classification tree,
boolean doWithMisappliedNames)
Creates all inferred synonyms for the taxon in the classification, but do not insert it to the database |
|
List<Synonym> |
TaxonServiceImpl.createInferredSynonyms(Taxon taxon,
Classification classification,
SynonymRelationshipType type,
boolean doWithMisappliedNames)
|
|
List<Synonym> |
ITaxonService.createInferredSynonyms(Taxon taxon,
Classification tree,
SynonymRelationshipType type,
boolean doWithMisappliedNames)
Creates the specified inferred synonyms for the taxon in the classification, but do not insert it to the database |
|
void |
TaxonServiceImpl.deleteSynonym(Synonym synonym,
Taxon taxon,
boolean removeNameIfPossible,
boolean newHomotypicGroupIfNeeded)
|
|
void |
ITaxonService.deleteSynonym(Synonym synonym,
Taxon taxon,
boolean removeNameIfPossible,
boolean newHomotypicGroupIfNeeded)
Removes a synonym. In detail it removes all synonym relationship to the given taxon or to all taxa if taxon is null
the synonym concept if it is not referenced by any synonym relationship anymore
If removeNameIfPossible is true
it also removes the synonym name if it is not used in any other context
(part of a concept, in DescriptionElementSource, part of a name relationship, used inline, ...)If newHomotypicGroupIfNeeded is true and the synonym name is not deleted and
the name is homotypic to the taxon the name is moved to a new homotypical group.If synonym is null the method has no effect. |
|
long |
TaxonServiceImpl.deleteSynonymRelationships(Synonym syn,
Taxon taxon)
|
|
long |
ITaxonService.deleteSynonymRelationships(Synonym syn,
Taxon taxon)
Deletes all synonym relationships of a given synonym. |
|
void |
TaxonServiceImpl.deleteTaxon(Taxon taxon,
TaxonDeletionConfigurator config)
|
|
void |
ITaxonService.deleteTaxon(Taxon taxon,
TaxonDeletionConfigurator config)
Deletes a taxon from the underlying database according to the given configurator. |
|
List<MediaRepresentation> |
TaxonServiceImpl.getAllMedia(Taxon taxon,
int size,
int height,
int widthOrDuration,
String[] mimeTypes)
|
|
List<MediaRepresentation> |
ITaxonService.getAllMedia(Taxon taxon,
int size,
int height,
int widthOrDuration,
String[] mimeTypes)
Deprecated. use #listMedia(Taxon, Set, boolean, boolean, List) instead |
|
Map<UUID,List<MediaRepresentation>> |
ClassificationServiceImpl.getAllMediaForChildNodes(Taxon taxon,
Classification taxTree,
List<String> propertyPaths,
int size,
int height,
int widthOrDuration,
String[] mimeTypes)
|
|
Map<UUID,List<MediaRepresentation>> |
IClassificationService.getAllMediaForChildNodes(Taxon taxon,
Classification taxTree,
List<String> propertyPaths,
int size,
int height,
int widthOrDuration,
String[] mimeTypes)
Deprecated. use getAllMediaForChildNodes(TaxonNode taxonNode, ...) instead if you have a classification and a taxon that is in it, you should also have the according taxonNode |
|
|
DescriptionServiceImpl.getDescriptionElementsForTaxon(Taxon taxon,
Set<Feature> features,
Class<T> type,
Integer pageSize,
Integer pageNumber,
List<String> propertyPaths)
FIXME Candidate for harmonization descriptionElementService.listDescriptionElementsForTaxon |
|
|
IDescriptionService.getDescriptionElementsForTaxon(Taxon taxon,
Set<Feature> features,
Class<T> type,
Integer pageSize,
Integer pageNumber,
List<String> propertyPaths)
|
|
List<List<Synonym>> |
TaxonServiceImpl.getHeterotypicSynonymyGroups(Taxon taxon,
List<String> propertyPaths)
|
|
List<List<Synonym>> |
ITaxonService.getHeterotypicSynonymyGroups(Taxon taxon,
List<String> propertyPaths)
Returns the ordered list of all homotypical groups
that contain synonyms that are heterotypic to the given taxon. |
|
List<Synonym> |
TaxonServiceImpl.getHomotypicSynonymsByHomotypicGroup(Taxon taxon,
List<String> propertyPaths)
|
|
List<Synonym> |
ITaxonService.getHomotypicSynonymsByHomotypicGroup(Taxon taxon,
List<String> propertyPaths)
Returns the list of all synonyms that share the same homotypical group with the given taxon. |
|
Pager<SynonymRelationship> |
TaxonServiceImpl.getSynonyms(Taxon taxon,
SynonymRelationshipType type,
Integer pageSize,
Integer pageNumber,
List<OrderHint> orderHints,
List<String> propertyPaths)
|
|
Pager<SynonymRelationship> |
ITaxonService.getSynonyms(Taxon taxon,
SynonymRelationshipType type,
Integer pageSize,
Integer pageNumber,
List<OrderHint> orderHints,
List<String> propertyPaths)
Returns the SynonymRelationships (of where relationship.type == type, if this argument is supplied) where the supplied taxon is relatedTo. |
|
|
OccurrenceServiceImpl.listByAssociatedTaxon(Class<T> type,
Set<TaxonRelationshipEdge> includeRelationships,
Taxon associatedTaxon,
Integer maxDepth,
Integer pageSize,
Integer pageNumber,
List<OrderHint> orderHints,
List<String> propertyPaths)
|
|
|
IOccurrenceService.listByAssociatedTaxon(Class<T> type,
Set<TaxonRelationshipEdge> includeRelationships,
Taxon associatedTaxon,
Integer maxDepth,
Integer pageSize,
Integer pageNumber,
List<OrderHint> orderHints,
List<String> propertyPaths)
Lists all instances of SpecimenOrObservationBase which are
associated with the taxon specified as parameter. |
|
List<TaxonRelationship> |
TaxonServiceImpl.listFromTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
Integer pageSize,
Integer pageNumber,
List<OrderHint> orderHints,
List<String> propertyPaths)
|
|
List<TaxonRelationship> |
ITaxonService.listFromTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
Integer pageSize,
Integer pageNumber,
List<OrderHint> orderHints,
List<String> propertyPaths)
Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied) where the supplied taxon is relatedFrom. |
|
List<Media> |
TaxonServiceImpl.listMedia(Taxon taxon,
Set<TaxonRelationshipEdge> includeRelationships,
Boolean limitToGalleries,
Boolean includeTaxonDescriptions,
Boolean includeOccurrences,
Boolean includeTaxonNameDescriptions,
List<String> propertyPath)
|
|
List<Media> |
ITaxonService.listMedia(Taxon taxon,
Set<TaxonRelationshipEdge> includeRelationships,
Boolean limitToGalleries,
Boolean includeTaxonDescriptions,
Boolean includeOccurrences,
Boolean includeTaxonNameDescriptions,
List<String> propertyPath)
Lists all Media found in an any TaxonDescription, NameDescription, SpecimenOrObservationBase, DnaSample Chromatograms, etc. |
|
Set<Taxon> |
TaxonServiceImpl.listRelatedTaxa(Taxon taxon,
Set<TaxonRelationshipEdge> includeRelationships,
Integer maxDepth,
Integer limit,
Integer start,
List<String> propertyPaths)
|
|
Set<Taxon> |
ITaxonService.listRelatedTaxa(Taxon taxon,
Set<TaxonRelationshipEdge> includeRelationships,
Integer maxDepth,
Integer limit,
Integer start,
List<String> propertyPaths)
lists all taxa which are related to the taxon given as
parameter. |
|
List<Media> |
TaxonServiceImpl.listTaxonDescriptionMedia(Taxon taxon,
Set<TaxonRelationshipEdge> includeRelationships,
boolean limitToGalleries,
List<String> propertyPath)
|
|
List<Media> |
ITaxonService.listTaxonDescriptionMedia(Taxon taxon,
Set<TaxonRelationshipEdge> includeRelationships,
boolean limitToGalleries,
List<String> propertyPath)
Deprecated. use #listMedia(Taxon, Set, boolean, boolean, List) instead |
|
List<TaxonDescription> |
DescriptionServiceImpl.listTaxonDescriptions(Taxon taxon,
Set<Scope> scopes,
Set<NamedArea> geographicalScope,
Integer pageSize,
Integer pageNumber,
List<String> propertyPaths)
|
|
List<TaxonDescription> |
IDescriptionService.listTaxonDescriptions(Taxon taxon,
Set<Scope> scopes,
Set<NamedArea> geographicalScope,
Integer pageSize,
Integer pageNumber,
List<String> propertyPaths)
|
|
List<TaxonDescription> |
DescriptionServiceImpl.listTaxonDescriptions(Taxon taxon,
Set<Scope> scopes,
Set<NamedArea> geographicalScope,
Set<MarkerType> markerTypes,
Integer pageSize,
Integer pageNumber,
List<String> propertyPaths)
|
|
List<TaxonDescription> |
IDescriptionService.listTaxonDescriptions(Taxon taxon,
Set<Scope> scopes,
Set<NamedArea> geographicalScope,
Set<MarkerType> markerTypes,
Integer pageSize,
Integer pageNumber,
List<String> propertyPaths)
|
|
List<TaxonRelationship> |
TaxonServiceImpl.listToTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
Integer pageSize,
Integer pageNumber,
List<OrderHint> orderHints,
List<String> propertyPaths)
|
|
List<TaxonRelationship> |
ITaxonService.listToTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
Integer pageSize,
Integer pageNumber,
List<OrderHint> orderHints,
List<String> propertyPaths)
Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied) where the supplied taxon is relatedTo. |
|
List<TaxonNode> |
ClassificationServiceImpl.loadChildNodesOfTaxon(Taxon taxon,
Classification classification,
List<String> propertyPaths)
|
|
List<TaxonNode> |
IClassificationService.loadChildNodesOfTaxon(Taxon taxon,
Classification classification,
List<String> propertyPaths)
Although this method seems to be a redundant alternative to IClassificationService.loadChildNodesOfTaxonNode(TaxonNode, List) it is an important
alternative from which web services benefit. |
|
TaxonNode |
ClassificationServiceImpl.loadTaxonNodeByTaxon(Taxon taxon,
UUID classificationUuid,
List<String> propertyPaths)
|
|
TaxonNode |
IClassificationService.loadTaxonNodeByTaxon(Taxon taxon,
UUID classificationUuid,
List<String> propertyPaths)
Deprecated. use loadTaxonNode(TaxonNode taxonNode, ...) instead if you have a classification and a taxon that is in it, you should also have the according taxonNode |
|
List<TaxonNode> |
ClassificationServiceImpl.loadTreeBranchToTaxon(Taxon taxon,
Classification classification,
Rank baseRank,
List<String> propertyPaths)
|
|
List<TaxonNode> |
IClassificationService.loadTreeBranchToTaxon(Taxon taxon,
Classification classification,
Rank baseRank,
List<String> propertyPaths)
Although this method seems to be a redundant alternative to IClassificationService.loadChildNodesOfTaxonNode(TaxonNode, List) it is an important
alternative from which web services benefit. |
|
SynonymRelationship |
TaxonServiceImpl.moveSynonymToAnotherTaxon(SynonymRelationship oldSynonymRelation,
Taxon newTaxon,
boolean moveHomotypicGroup,
SynonymRelationshipType newSynonymRelationshipType,
Reference reference,
String referenceDetail,
boolean keepReference)
|
|
SynonymRelationship |
ITaxonService.moveSynonymToAnotherTaxon(SynonymRelationship oldSynonymRelation,
Taxon newTaxon,
boolean moveHomotypicGroup,
SynonymRelationshipType newSynonymRelationshipType,
Reference newReference,
String newReferenceDetail,
boolean keepReference)
Moves a synonym to another taxon and removes the old synonym relationship. |
|
|
OccurrenceServiceImpl.pageByAssociatedTaxon(Class<T> type,
Set<TaxonRelationshipEdge> includeRelationships,
Taxon associatedTaxon,
Integer maxDepth,
Integer pageSize,
Integer pageNumber,
List<OrderHint> orderHints,
List<String> propertyPaths)
|
|
|
IOccurrenceService.pageByAssociatedTaxon(Class<T> type,
Set<TaxonRelationshipEdge> includeRelationships,
Taxon associatedTaxon,
Integer maxDepth,
Integer pageSize,
Integer pageNumber,
List<OrderHint> orderHints,
List<String> propertyPaths)
See IOccurrenceService.listByAssociatedTaxon(Class, Set, Taxon, Integer, Integer, Integer, List, List) |
|
Pager<TaxonRelationship> |
TaxonServiceImpl.pageFromTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
Integer pageSize,
Integer pageNumber,
List<OrderHint> orderHints,
List<String> propertyPaths)
|
|
Pager<TaxonRelationship> |
ITaxonService.pageFromTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
Integer pageSize,
Integer pageNumber,
List<OrderHint> orderHints,
List<String> propertyPaths)
Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied) where the supplied taxon is relatedFrom. |
|
Pager<TaxonDescription> |
DescriptionServiceImpl.pageTaxonDescriptions(Taxon taxon,
Set<Scope> scopes,
Set<NamedArea> geographicalScope,
Integer pageSize,
Integer pageNumber,
List<String> propertyPaths)
|
|
Pager<TaxonDescription> |
IDescriptionService.pageTaxonDescriptions(Taxon taxon,
Set<Scope> scopes,
Set<NamedArea> geographicalScope,
Integer pageSize,
Integer pageNumber,
List<String> propertyPaths)
Returns a List of TaxonDescription instances, optionally filtered by parameters passed to this method |
|
Pager<TaxonDescription> |
DescriptionServiceImpl.pageTaxonDescriptions(Taxon taxon,
Set<Scope> scopes,
Set<NamedArea> geographicalScope,
Set<MarkerType> markerTypes,
Integer pageSize,
Integer pageNumber,
List<String> propertyPaths)
|
|
Pager<TaxonDescription> |
IDescriptionService.pageTaxonDescriptions(Taxon taxon,
Set<Scope> scopes,
Set<NamedArea> geographicalScope,
Set<MarkerType> markerTypes,
Integer pageSize,
Integer pageNumber,
List<String> propertyPaths)
Returns a List of TaxonDescription instances, optionally filtered by parameters passed to this method |
|
Pager<TaxonRelationship> |
TaxonServiceImpl.pageToTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
Integer pageSize,
Integer pageNumber,
List<OrderHint> orderHints,
List<String> propertyPaths)
|
|
Pager<TaxonRelationship> |
ITaxonService.pageToTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
Integer pageSize,
Integer pageNumber,
List<OrderHint> orderHints,
List<String> propertyPaths)
Returns the TaxonRelationships (of where relationship.type == type, if this arguement is supplied) where the supplied taxon is relatedTo. |
|
void |
TaxonServiceImpl.swapSynonymAndAcceptedTaxon(Synonym synonym,
Taxon acceptedTaxon)
|
|
void |
ITaxonService.swapSynonymAndAcceptedTaxon(Synonym synonym,
Taxon acceptedTaxon)
Swaps given synonym and accepted taxon. |
|
| Method parameters in eu.etaxonomy.cdm.api.service with type arguments of type Taxon | |
|---|---|
Pager<MediaKey> |
IMediaService.getMediaKeys(Set<Taxon> taxonomicScope,
Set<NamedArea> geoScopes,
Integer pageSize,
Integer pageNumber,
List<String> propertyPaths)
Return a List of MediaKeys, optionally filtered by the parameters passed. |
Pager<MediaKey> |
MediaServiceImpl.getMediaKeys(Set<Taxon> taxonomicScope,
Set<NamedArea> geoScopes,
Integer pageSize,
Integer pageNumber,
List<String> propertyPaths)
|
| Uses of Taxon in eu.etaxonomy.cdm.api.utility |
|---|
| Methods in eu.etaxonomy.cdm.api.utility with parameters of type Taxon | |
|---|---|
static void |
ImagesUtility.addTaxonImage(Taxon taxon,
DescriptionBase<?> imageGallery,
ImageFile imageFile)
Deprecated. not used by EDITor anymore |
static DescriptionElementBase |
ImagesUtility.findImageElement(ImageFile image,
Taxon taxon)
Deprecated. not used by EDITor anymore |
static void |
ImagesUtility.removeTaxonImage(Taxon taxon,
DescriptionBase<?> imageGallery,
ImageFile imageFile)
Deprecated. not used by EDITor anymore |
| Uses of Taxon in eu.etaxonomy.cdm.hibernate.search |
|---|
| Methods in eu.etaxonomy.cdm.hibernate.search that return Taxon | |
|---|---|
protected Taxon |
GroupByTaxonClassBridge.getAssociatedTaxon(Object entity)
|
| Uses of Taxon in eu.etaxonomy.cdm.io.berlinModel.in |
|---|
| Methods in eu.etaxonomy.cdm.io.berlinModel.in that return Taxon | |
|---|---|
protected Taxon |
BerlinModelImportBase.getTaxon(BerlinModelImportState state,
int taxonId,
Map<String,TaxonBase> taxonMap,
int factId)
|
| Uses of Taxon in eu.etaxonomy.cdm.io.common |
|---|
| Methods in eu.etaxonomy.cdm.io.common that return Taxon | |
|---|---|
protected Taxon |
CdmImportBase.getAcceptedTaxon(TaxonBase<?> taxonBase)
Returns the accepted taxon of a taxon base. |
| Methods in eu.etaxonomy.cdm.io.common with parameters of type Taxon | |
|---|---|
protected void |
CdmImportBase.fillMissingEpithetsForTaxa(Taxon parentTaxon,
Taxon childTaxon)
If the child taxon is missing genus or species epithet information and the rank is below genus or species respectively the according epithets are taken from the parent taxon. |
TaxonDescription |
CdmImportBase.getTaxonDescription(Taxon taxon,
boolean isImageGallery,
boolean createNewIfNotExists)
Returns the taxon description for a taxon. |
TaxonDescription |
CdmImportBase.getTaxonDescription(Taxon taxon,
Reference ref,
boolean isImageGallery,
boolean createNewIfNotExists)
Like CdmImportBase.getTaxonDescription(Taxon, boolean, boolean)
Only matches a description if the given reference is a source of the description.If a new description is created the given reference will be added as a source. |
| Uses of Taxon in eu.etaxonomy.cdm.io.common.mapping |
|---|
| Methods in eu.etaxonomy.cdm.io.common.mapping that return Taxon | |
|---|---|
protected Taxon |
DbImportDescriptionElementCreationMapperBase.getAcceptedTaxon(ResultSet rs)
|
| Methods in eu.etaxonomy.cdm.io.common.mapping with parameters of type Taxon | |
|---|---|
protected ELEMENT |
DbImportDescriptionElementCreationMapperBase.addDescriptionElement(Taxon taxon,
ELEMENT element)
Adds a description element to the taxon's first description which is not an image gallery. |
protected TextData |
DbImportImageCreationMapper.addDescriptionElement(Taxon taxon,
TextData element)
|
protected TaxonDescription |
DbImportDescriptionElementCreationMapperBase.getTaxonDescription(Taxon taxon,
boolean isImageGallery)
|
| Uses of Taxon in eu.etaxonomy.cdm.io.dwca.in |
|---|
| Methods in eu.etaxonomy.cdm.io.dwca.in with parameters of type Taxon | |
|---|---|
protected TaxonDescription |
PartitionableConverterBase.getTaxonDescription(Taxon taxon,
boolean isImageGallery)
|
| Uses of Taxon in eu.etaxonomy.cdm.io.markup |
|---|
| Methods in eu.etaxonomy.cdm.io.markup that return Taxon | |
|---|---|
Taxon |
MarkupImportState.getCurrentTaxon()
|
| Methods in eu.etaxonomy.cdm.io.markup with parameters of type Taxon | |
|---|---|
protected void |
MarkupImportBase.fillMissingEpithetsForTaxa(Taxon parentTaxon,
Taxon childTaxon)
|
void |
MarkupDocumentImport.fillMissingEpithetsForTaxa(Taxon parentTaxon,
Taxon childTaxon)
|
TaxonDescription |
MarkupImportBase.getTaxonDescription(Taxon taxon,
Reference ref,
boolean isImageGallery,
boolean createNewIfNotExists)
|
void |
MarkupImportState.setCurrentTaxon(Taxon currentTaxon)
|
| Uses of Taxon in eu.etaxonomy.cdm.io.pilotOutputHtml |
|---|
| Methods in eu.etaxonomy.cdm.io.pilotOutputHtml with parameters of type Taxon | |
|---|---|
String |
PilotOutputDocumentBuilder.writeTaxonDescriptionsToHTML(Taxon taxon,
String texte)
Write the HTML part for one taxon. |
| Uses of Taxon in eu.etaxonomy.cdm.io.sdd.out |
|---|
| Fields in eu.etaxonomy.cdm.io.sdd.out with type parameters of type Taxon | |
|---|---|
protected List<Taxon> |
SDDDataSet.taxa
|
| Methods in eu.etaxonomy.cdm.io.sdd.out with parameters of type Taxon | |
|---|---|
void |
SDDDataSet.addTaxon(Taxon value)
Adds the taxon in value to the taxa property list. |
| Method parameters in eu.etaxonomy.cdm.io.sdd.out with type arguments of type Taxon | |
|---|---|
void |
SDDDataSet.addTaxa(Collection<Taxon> value)
Adds the taxa in value to the taxa property list. |
void |
SDDDataSet.setTaxa(List<Taxon> value)
Sets the value of the taxa property. |
| Uses of Taxon in eu.etaxonomy.cdm.model.description |
|---|
| Methods in eu.etaxonomy.cdm.model.description that return Taxon | |
|---|---|
Taxon |
PolytomousKeyNode.getTaxon()
Returns the taxon this node links to. |
Taxon |
TaxonDescription.getTaxon()
|
Taxon |
TaxonInteraction.getTaxon2()
Returns the second taxon involved in this taxon interaction. |
| Methods in eu.etaxonomy.cdm.model.description that return types with arguments of type Taxon | |
|---|---|
Set<Taxon> |
IIdentificationKey.getCoveredTaxa()
Covered taxa are the tips of the key. |
Set<Taxon> |
PolytomousKey.getCoveredTaxa()
Returns the set of possible taxa corresponding to
this identification key. |
Set<Taxon> |
MediaKey.getCoveredTaxa()
Returns the set of possible taxa corresponding to
this identification key. |
Set<Taxon> |
MultiAccessKey.getCoveredTaxa()
Returns the set of possible taxa corresponding to
this identification key. |
Set<Taxon> |
IIdentificationKey.getTaxonomicScope()
Taxonomic Scope is the taxon which you want the key to be attached to e.g. |
Set<Taxon> |
PolytomousKey.getTaxonomicScope()
Returns the set of taxa that define the taxonomic scope of
this identification key |
Set<Taxon> |
MediaKey.getTaxonomicScope()
Returns the set of taxa that define the taxonomic
scope of this identification key |
Set<Taxon> |
MultiAccessKey.getTaxonomicScope()
Returns the set of taxa that define the taxonomic
scope of this identification key |
| Methods in eu.etaxonomy.cdm.model.description with parameters of type Taxon | |
|---|---|
void |
IIdentificationKey.addCoveredTaxon(Taxon taxon)
|
void |
PolytomousKey.addCoveredTaxon(Taxon taxon)
Adds a taxa to the set of covered
taxa corresponding to this identification key. |
void |
MediaKey.addCoveredTaxon(Taxon taxon)
Adds a taxa to the set of covered taxa
corresponding to this identification key. |
void |
MultiAccessKey.addCoveredTaxon(Taxon taxon)
Adds a taxa to the set of covered taxa
corresponding to this identification key. |
void |
IIdentificationKey.addTaxonomicScope(Taxon taxon)
|
void |
PolytomousKey.addTaxonomicScope(Taxon taxon)
Adds a taxa to the set of taxonomic scopes corresponding to this identification key. |
void |
MediaKey.addTaxonomicScope(Taxon taxon)
Adds a taxa to the set of taxonomic scopes
corresponding to this identification key. |
void |
MultiAccessKey.addTaxonomicScope(Taxon taxon)
Adds a taxa to the set of taxonomic scopes
corresponding to this identification key. |
static PolytomousKeyNode |
PolytomousKeyNode.NewInstance(String statement,
String question,
Taxon taxon,
Feature feature)
Creates a new polytomous key node instance. |
static TaxonDescription |
TaxonDescription.NewInstance(Taxon taxon)
Creates a new taxon description instance for the given taxon. |
static TaxonDescription |
TaxonDescription.NewInstance(Taxon taxon,
boolean isImageGallery)
Creates a new taxon description instance for the given taxon. |
void |
IIdentificationKey.removeCoveredTaxon(Taxon taxon)
|
void |
PolytomousKey.removeCoveredTaxon(Taxon taxon)
Removes one element from the set of covered
taxa corresponding to this identification key. |
void |
MediaKey.removeCoveredTaxon(Taxon taxon)
Removes one element from the set of covered taxa
corresponding to this identification key. |
void |
MultiAccessKey.removeCoveredTaxon(Taxon taxon)
Removes one element from the set of covered taxa
corresponding to this identification key. |
void |
IIdentificationKey.removeTaxonomicScope(Taxon taxon)
|
void |
PolytomousKey.removeTaxonomicScope(Taxon taxon)
Removes one element from the set of taxonomic
scopes corresponding to this identification key. |
void |
MediaKey.removeTaxonomicScope(Taxon taxon)
Removes one element from the set of taxonomic scopes
corresponding to this identification key. |
void |
MultiAccessKey.removeTaxonomicScope(Taxon taxon)
Removes one element from the set of taxonomic scopes
corresponding to this identification key. |
void |
PolytomousKeyNode.setTaxon(Taxon taxon)
Sets the taxon this node links to. |
void |
TaxonDescription.setTaxon(Taxon taxon)
|
void |
TaxonInteraction.setTaxon2(Taxon taxon2)
|
| Method parameters in eu.etaxonomy.cdm.model.description with type arguments of type Taxon | |
|---|---|
protected void |
PolytomousKey.setCoveredTaxa(Set<Taxon> coveredTaxa)
|
protected void |
MediaKey.setCoveredTaxa(Set<Taxon> coveredTaxa)
|
protected void |
MultiAccessKey.setCoveredTaxa(Set<Taxon> coveredTaxa)
|
| Uses of Taxon in eu.etaxonomy.cdm.model.name |
|---|
| Methods in eu.etaxonomy.cdm.model.name that return types with arguments of type Taxon | |
|---|---|
Set<Taxon> |
TaxonNameBase.getTaxa()
Returns the set of taxa ("accepted/correct" names according to any
reference) that are based on this taxon name. |
| Uses of Taxon in eu.etaxonomy.cdm.model.occurrence |
|---|
| Methods in eu.etaxonomy.cdm.model.occurrence with parameters of type Taxon | |
|---|---|
static DeterminationEvent |
DeterminationEvent.NewInstance(Taxon taxon,
SpecimenOrObservationBase identifiedUnit)
Factory method |
| Uses of Taxon in eu.etaxonomy.cdm.model.taxon |
|---|
| Methods in eu.etaxonomy.cdm.model.taxon that return Taxon | |
|---|---|
Taxon |
SynonymRelationship.getAcceptedTaxon()
Returns the ("accepted/correct") taxon involved in this
synonym relationship. |
Taxon |
TaxonRelationship.getFromTaxon()
Returns the taxon involved as a source in this
taxon relationship. |
protected Taxon |
TaxonRelationship.getRelatedFrom()
|
protected Taxon |
TaxonRelationship.getRelatedTo()
|
protected Taxon |
SynonymRelationship.getRelatedTo()
|
Taxon |
TaxonNode.getTaxon()
|
Taxon |
Taxon.getTaxonomicParent()
Deprecated. |
Taxon |
TaxonRelationship.getToTaxon()
Returns the taxon involved as a target in this
taxon relationship. |
static Taxon |
Taxon.NewInstance(TaxonNameBase taxonNameBase,
Reference sec)
Creates a new (accepted/correct) taxon instance with the taxon name used and the reference
using it. |
static Taxon |
Taxon.NewUnknownStatusInstance(TaxonNameBase taxonNameBase,
Reference sec)
Creates a new taxon instance with an unknown status (accepted/synonym) and with the taxon name used and the reference
using it. |
| Methods in eu.etaxonomy.cdm.model.taxon that return types with arguments of type Taxon | |
|---|---|
Set<Taxon> |
Synonym.getAcceptedTaxa()
Returns the set of all ("accepted/correct") taxa involved in the same
synonym relationships as this synonym. |
Set<Taxon> |
Taxon.getMisappliedNames()
Returns the set of taxa playing the source role in taxon relationships
(with taxon relationship type "misapplied name for") where
this taxon plays the target role. |
Set<Taxon> |
Taxon.getTaxonForMisappliedName()
Returns the set of taxa playing the target role in taxon relationships
(with taxon relationship type "misapplied name for") where
this taxon plays the source role. |
Set<Taxon> |
Taxon.getTaxonomicChildren()
Deprecated. |
| Methods in eu.etaxonomy.cdm.model.taxon with parameters of type Taxon | |
|---|---|
TaxonNode |
ITreeNode.addChildTaxon(Taxon taxon,
Reference citation,
String microCitation,
Synonym synonymToBeUsed)
Adds a taxon as a child of the ITreeNode |
TaxonNode |
Classification.addChildTaxon(Taxon taxon,
Reference citation,
String microCitation,
Synonym synonymToBeUsed)
|
TaxonNode |
TaxonNode.addChildTaxon(Taxon taxon,
Reference citation,
String microCitation,
Synonym synonymToBeUsed)
|
TaxonRelationship |
Taxon.addMisappliedName(Taxon misappliedNameTaxon,
Reference citation,
String microcitation)
Creates a new taxon relationship (with taxon relationship type
"misapplied name for") instance where this taxon plays the target role
and adds it to the set of taxon relationships to this taxon. |
TaxonNode |
Classification.addParentChild(Taxon parent,
Taxon child,
Reference citation,
String microCitation)
Relates two taxa as parent-child nodes within a classification. |
void |
Taxon.addTaxonomicChild(Taxon child,
Reference citation,
String microcitation)
Deprecated. |
TaxonRelationship |
Taxon.addTaxonRelation(Taxon toTaxon,
TaxonRelationshipType type,
Reference citation,
String microcitation)
Creates a new taxon relationship instance where this taxon
plays the source role and adds it to the set of
"taxon relationships from" belonging to this taxon. |
TaxonNode |
Classification.getNode(Taxon taxon)
Checks if the given taxon is part of this tree. |
Set<SynonymRelationshipType> |
Synonym.getRelationType(Taxon taxon)
Returns the set of synonym relationship types of the
synonym relationships where the synonym
is this synonym and the taxon
is the given one. |
Set<TaxonRelationship> |
Taxon.getTaxonRelations(Taxon possiblyRelatedTaxon)
If a relationships between this and the given taxon exists they will be returned. |
TaxonNode |
Classification.getTopmostNode(Taxon taxon)
Checks if the taxon is a direct child of this tree and returns the according node if true. |
boolean |
Synonym.isSynonymOf(Taxon taxon)
Returns true if this is a synonym of the given taxon. |
boolean |
Classification.isTaxonInTree(Taxon taxon)
Checks if the given taxon is part of this tree. |
boolean |
Classification.isTopmostInTree(Taxon taxon)
Checks if the given taxon is one of the topmost taxa in this tree. |
void |
Taxon.removeTaxon(Taxon taxon,
TaxonRelationshipType taxonRelType)
TODO update documentation Removes one taxon relationship with taxon relationship type
taxonRelType and with the given child taxon playing the
source role from the set of "taxon relationships to" belonging
to this taxon. |
void |
Taxon.removeTaxonomicChild(Taxon child)
Deprecated. |
void |
Synonym.replaceAcceptedTaxon(Taxon newAcceptedTaxon,
SynonymRelationshipType relType,
boolean copyCitationInfo,
Reference citation,
String microCitation)
Replaces ALL accepted taxa of this synonym by the new accepted taxon. |
void |
SynonymRelationship.setAcceptedTaxon(Taxon acceptedTaxon)
Sets the given ("accepted/valid") taxon to this
synonym relationship. |
void |
TaxonRelationship.setFromTaxon(Taxon fromTaxon)
Sets the given taxon as a source in this taxon relationship. |
protected void |
TaxonRelationship.setRelatedFrom(Taxon relatedFrom)
|
protected void |
TaxonRelationship.setRelatedTo(Taxon relatedTo)
|
protected void |
SynonymRelationship.setRelatedTo(Taxon relatedTo)
|
protected void |
TaxonNode.setTaxon(Taxon taxon)
|
void |
Taxon.setTaxonomicParent(Taxon newParent,
Reference citation,
String microcitation)
Deprecated. |
void |
TaxonRelationship.setToTaxon(Taxon toTaxon)
Sets the given taxon as a target in this taxon relationship. |
| Constructors in eu.etaxonomy.cdm.model.taxon with parameters of type Taxon | |
|---|---|
SynonymRelationship(Synonym synonym,
Taxon taxon,
SynonymRelationshipType type,
Reference citation,
String citationMicroReference)
Class constructor: creates a new synonym relationship instance (with the given synonym, the given "accepted/correct" taxon,
the given synonym relationship type and with the
reference source on which the relationship assertion is based). |
|
TaxonNode(Taxon taxon)
to create nodes either use Classification.addChildTaxon(Taxon, Reference, String, Synonym)
or TaxonNode.addChildTaxon(Taxon, Reference, String, Synonym) |
|
TaxonNode(Taxon taxon,
Classification classification)
Deprecated. setting of classification is handled in the addTaxonNode() method, use TaxonNode(taxon) instead |
|
TaxonRelationship(Taxon from,
Taxon to,
TaxonRelationshipType type,
Reference citation,
String citationMicroReference)
Class constructor: creates a new taxon relationship instance (with the given "accepted/correct" taxa, the given synonym relationship type
and with the reference source on which the relationship
assertion is based). |
|
| Uses of Taxon in eu.etaxonomy.cdm.persistence.dao.description |
|---|
| Methods in eu.etaxonomy.cdm.persistence.dao.description with parameters of type Taxon | ||
|---|---|---|
int |
IDescriptionDao.countTaxonDescriptions(Taxon taxon,
Set<Scope> scopes,
Set<NamedArea> geographicalScope,
Set<MarkerType> markerType)
Returns a count of TaxonDescription instances, optionally filtered by parameters passed to this method |
|
|
IDescriptionDao.getDescriptionElementForTaxon(Taxon taxon,
Set<Feature> features,
Class<T> type,
Integer pageSize,
Integer pageNumber,
List<String> propertyPaths)
|
|
List<TaxonDescription> |
IDescriptionDao.listTaxonDescriptions(Taxon taxon,
Set<Scope> scopes,
Set<NamedArea> geographicalScope,
Set<MarkerType> markerTypes,
Integer pageSize,
Integer pageNumber,
List<String> propertyPaths)
Returns a List of TaxonDescription instances, optionally filtered by parameters passed to this method |
|
| Uses of Taxon in eu.etaxonomy.cdm.persistence.dao.hibernate.description |
|---|
| Methods in eu.etaxonomy.cdm.persistence.dao.hibernate.description with parameters of type Taxon | ||
|---|---|---|
int |
DescriptionDaoImpl.countTaxonDescriptions(Taxon taxon,
Set<Scope> scopes,
Set<NamedArea> geographicalScopes,
Set<MarkerType> markerTypes)
|
|
|
DescriptionDaoImpl.getDescriptionElementForTaxon(Taxon taxon,
Set<Feature> features,
Class<T> type,
Integer pageSize,
Integer pageNumber,
List<String> propertyPaths)
|
|
List<TaxonDescription> |
DescriptionDaoImpl.listTaxonDescriptions(Taxon taxon,
Set<Scope> scopes,
Set<NamedArea> geographicalScopes,
Set<MarkerType> markerTypes,
Integer pageSize,
Integer pageNumber,
List<String> propertyPaths)
|
|
| Uses of Taxon in eu.etaxonomy.cdm.persistence.dao.hibernate.media |
|---|
| Method parameters in eu.etaxonomy.cdm.persistence.dao.hibernate.media with type arguments of type Taxon | |
|---|---|
int |
MediaDaoHibernateImpl.countMediaKeys(Set<Taxon> taxonomicScope,
Set<NamedArea> geoScopes)
|
List<MediaKey> |
MediaDaoHibernateImpl.getMediaKeys(Set<Taxon> taxonomicScope,
Set<NamedArea> geoScopes,
Integer pageSize,
Integer pageNumber,
List<String> propertyPaths)
|
| Uses of Taxon in eu.etaxonomy.cdm.persistence.dao.hibernate.occurrence |
|---|
| Methods in eu.etaxonomy.cdm.persistence.dao.hibernate.occurrence with parameters of type Taxon | ||
|---|---|---|
|
OccurrenceDaoHibernateImpl.listByAssociatedTaxon(Class<T> type,
Taxon associatedTaxon,
Integer limit,
Integer start,
List<OrderHint> orderHints,
List<String> propertyPaths)
|
|
| Uses of Taxon in eu.etaxonomy.cdm.persistence.dao.hibernate.taxon |
|---|
| Methods in eu.etaxonomy.cdm.persistence.dao.hibernate.taxon that return types with arguments of type Taxon | |
|---|---|
List<Taxon> |
TaxonDaoHibernateImpl.getAllTaxa(Integer limit,
Integer start)
|
List<Taxon> |
TaxonDaoHibernateImpl.getRootTaxa(Rank rank,
Reference sec,
CdmFetch cdmFetch,
Boolean onlyWithChildren,
Boolean withMisapplications,
List<String> propertyPaths)
|
List<Taxon> |
TaxonDaoHibernateImpl.getRootTaxa(Reference sec)
|
List<Taxon> |
TaxonDaoHibernateImpl.getRootTaxa(Reference sec,
CdmFetch cdmFetch,
Boolean onlyWithChildren,
Boolean withMisapplications)
|
| Methods in eu.etaxonomy.cdm.persistence.dao.hibernate.taxon with parameters of type Taxon | |
|---|---|
int |
TaxonDaoHibernateImpl.countSynonyms(Taxon taxon,
SynonymRelationshipType type)
|
int |
TaxonDaoHibernateImpl.countTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
RelationshipBase.Direction direction)
|
long |
TaxonDaoHibernateImpl.deleteSynonymRelationships(Synonym synonym,
Taxon taxon)
|
List<SynonymRelationship> |
TaxonDaoHibernateImpl.getSynonyms(Taxon taxon,
SynonymRelationshipType type,
Integer pageSize,
Integer pageNumber,
List<OrderHint> orderHints,
List<String> propertyPaths)
|
List<TaxonRelationship> |
TaxonDaoHibernateImpl.getTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
Integer pageSize,
Integer pageNumber,
List<OrderHint> orderHints,
List<String> propertyPaths,
RelationshipBase.Direction direction)
|
| Uses of Taxon in eu.etaxonomy.cdm.persistence.dao.media |
|---|
| Method parameters in eu.etaxonomy.cdm.persistence.dao.media with type arguments of type Taxon | |
|---|---|
int |
IMediaDao.countMediaKeys(Set<Taxon> taxonomicScope,
Set<NamedArea> geoScopes)
Return a count of MediaKeys, optionally filtered by the parameters passed. |
List<MediaKey> |
IMediaDao.getMediaKeys(Set<Taxon> taxonomicScope,
Set<NamedArea> geoScopes,
Integer pageSize,
Integer pageNumber,
List<String> propertyPaths)
Return a List of MediaKeys, optionally filtered by the parameters passed. |
| Uses of Taxon in eu.etaxonomy.cdm.persistence.dao.occurrence |
|---|
| Methods in eu.etaxonomy.cdm.persistence.dao.occurrence with parameters of type Taxon | ||
|---|---|---|
|
IOccurrenceDao.listByAssociatedTaxon(Class<T> type,
Taxon associatedTaxon,
Integer limit,
Integer start,
List<OrderHint> orderHints,
List<String> propertyPaths)
Lists all instances of SpecimenOrObservationBase which are associated with the taxon specified as parameter. |
|
| Uses of Taxon in eu.etaxonomy.cdm.persistence.dao.taxon |
|---|
| Methods in eu.etaxonomy.cdm.persistence.dao.taxon that return types with arguments of type Taxon | |
|---|---|
List<Taxon> |
ITaxonDao.getAllTaxa(Integer limit,
Integer start)
|
List<Taxon> |
ITaxonDao.getRootTaxa(Rank rank,
Reference sec,
CdmFetch cdmFetch,
Boolean onlyWithChildren,
Boolean withMisapplications,
List<String> propertyPaths)
Deprecated. obsolete when using classification |
List<Taxon> |
ITaxonDao.getRootTaxa(Reference sec)
Deprecated. obsolete when using classification |
List<Taxon> |
ITaxonDao.getRootTaxa(Reference sec,
CdmFetch cdmFetch,
Boolean onlyWithChildren,
Boolean withMisapplications)
Deprecated. obsolete when using classification |
| Methods in eu.etaxonomy.cdm.persistence.dao.taxon with parameters of type Taxon | |
|---|---|
int |
ITaxonDao.countSynonyms(Taxon taxon,
SynonymRelationshipType type)
Returns a count of the SynonymRelationships (of where relationship.type == type, if this arguement is supplied) where the supplied taxon is relatedTo. |
int |
ITaxonDao.countTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
RelationshipBase.Direction direction)
Returns a count of the TaxonRelationships (of where relationship.type == type, if this argument is supplied) where the supplied taxon either is relatedFrom or relatedTo depending on the direction
parameter. |
long |
ITaxonDao.deleteSynonymRelationships(Synonym syn,
Taxon taxon)
Deletes all synonym relationships of a given synonym. |
List<SynonymRelationship> |
ITaxonDao.getSynonyms(Taxon taxon,
SynonymRelationshipType type,
Integer pageSize,
Integer pageNumber,
List<OrderHint> orderHints,
List<String> propertyPaths)
Returns the SynonymRelationships (of where relationship.type == type, if this arguement is supplied) where the supplied taxon is relatedTo. |
List<TaxonRelationship> |
ITaxonDao.getTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
Integer pageSize,
Integer pageNumber,
List<OrderHint> orderHints,
List<String> propertyPaths,
RelationshipBase.Direction direction)
Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied) where the supplied taxon either is relatedFrom or relatedTo depending on the direction
parameter. |
| Uses of Taxon in eu.etaxonomy.cdm.remote.json.processor.bean |
|---|
| Methods in eu.etaxonomy.cdm.remote.json.processor.bean with parameters of type Taxon | |
|---|---|
net.sf.json.JSONObject |
TaxonBeanProcessor.processBeanSecondStep(Taxon bean,
net.sf.json.JSONObject json,
net.sf.json.JsonConfig jsonConfig)
|
|
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