Modifier and Type | Method and Description |
---|---|
<S extends TaxonBase> |
TaxonServiceImpl.findByIdentifier(java.lang.Class<S> clazz,
java.lang.String identifier,
DefinedTerm identifierType,
TaxonNode subtreeFilter,
MatchMode matchmode,
boolean includeEntity,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
<S extends TaxonBase> |
ITaxonService.findByIdentifier(java.lang.Class<S> clazz,
java.lang.String identifier,
DefinedTerm identifierType,
TaxonNode subtreeFilter,
MatchMode matchmode,
boolean includeEntity,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
<S extends TaxonBase> |
TaxonServiceImpl.findByMarker(java.lang.Class<S> clazz,
MarkerType markerType,
java.lang.Boolean markerValue,
TaxonNode subtreeFilter,
boolean includeEntity,
TaxonTitleType titleType,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
<S extends TaxonBase> |
ITaxonService.findByMarker(java.lang.Class<S> clazz,
MarkerType markerType,
java.lang.Boolean markerValue,
TaxonNode subtreeFilter,
boolean includeEntity,
TaxonTitleType titleType,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
|
<T extends TaxonBase> |
TaxonServiceImpl.getUuidAndTitleCache(java.lang.Class<T> clazz,
java.lang.Integer limit,
java.lang.String pattern) |
<S extends TaxonBase> |
TaxonServiceImpl.page(java.lang.Class<S> clazz,
java.util.List<Restriction<?>> restrictions,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
<S extends TaxonBase> |
TaxonServiceImpl.page(java.lang.Class<S> clazz,
java.util.List<Restriction<?>> restrictions,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths,
boolean includeUnpublished) |
<S extends TaxonBase> |
ITaxonService.page(java.lang.Class<S> clazz,
java.util.List<Restriction<?>> restrictions,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths,
boolean includeUnpublished) |
Modifier and Type | Method and Description |
---|---|
TaxonBase |
TaxonServiceImpl.findTaxonByUuid(java.util.UUID uuid,
java.util.List<java.lang.String> propertyPaths) |
TaxonBase |
ITaxonService.findTaxonByUuid(java.util.UUID uuid,
java.util.List<java.lang.String> propertyPaths)
Returns the TaxonBase with the given UUID
using the given match mode and initialization strategy
|
TaxonBase |
TaxonServiceImpl.load(java.util.UUID uuid,
boolean includeUnpublished,
java.util.List<java.lang.String> propertyPaths)
Like
#load(int, List) but allows loading unpublished taxa |
TaxonBase |
ITaxonService.load(java.util.UUID uuid,
java.util.List<java.lang.String> propertyPaths)
Finds the cdm entity specified by the
uuid parameter and
recursively initializes all bean properties given in the
propertyPaths parameter. |
Modifier and Type | Method and Description |
---|---|
Pager<SearchResult<TaxonBase>> |
TaxonServiceImpl.findByDescriptionElementFullText(java.lang.Class<? extends DescriptionElementBase> clazz,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
java.util.List<Feature> features,
java.util.List<Language> languages,
boolean highlightFragments,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Pager<SearchResult<TaxonBase>> |
ITaxonService.findByDescriptionElementFullText(java.lang.Class<? extends DescriptionElementBase> clazz,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
java.util.List<Feature> features,
java.util.List<Language> languages,
boolean highlightFragments,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Searches for TaxonBase instances by using the DescriptionElement free text index.
|
Pager<SearchResult<TaxonBase>> |
TaxonServiceImpl.findByDistribution(java.util.List<NamedArea> areaFilter,
java.util.List<PresenceAbsenceTerm> statusFilter,
Classification classification,
TaxonNode subtree,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Pager<SearchResult<TaxonBase>> |
ITaxonService.findByDistribution(java.util.List<NamedArea> areaFilter,
java.util.List<PresenceAbsenceTerm> statusFilter,
Classification classification,
TaxonNode subtree,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Pager<SearchResult<TaxonBase>> |
TaxonServiceImpl.findByEverythingFullText(java.lang.String queryString,
Classification classification,
TaxonNode subtree,
boolean includeUnpublished,
java.util.List<Language> languages,
boolean highlightFragments,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Pager<SearchResult<TaxonBase>> |
ITaxonService.findByEverythingFullText(java.lang.String queryString,
Classification classification,
TaxonNode subtree,
boolean includeUnpublished,
java.util.List<Language> languages,
boolean highlightFragments,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Deprecated.
this search should fully be covered by the new method
#findTaxaAndNamesByFullText(EnumSet, String, Classification, Set, List, boolean, Integer, Integer, List, List)
, maybe we should rename this latter method to give it a more meaningful name |
Pager<SearchResult<TaxonBase>> |
TaxonServiceImpl.findByFullText(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
boolean includeUnpublished,
java.util.List<Language> languages,
boolean highlightFragments,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Pager<SearchResult<TaxonBase>> |
ITaxonService.findByFullText(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
boolean includeUnpublished,
java.util.List<Language> languages,
boolean highlightFragments,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Searches for TaxonBase instances using the TaxonBase free text index.
|
Pager<SearchResult<TaxonBase>> |
TaxonServiceImpl.findTaxaAndNamesByFullText(java.util.EnumSet<TaxaAndNamesSearchMode> searchModes,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
java.util.Set<NamedArea> namedAreas,
java.util.Set<PresenceAbsenceTerm> distributionStatus,
java.util.List<Language> languages,
boolean highlightFragments,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Pager<SearchResult<TaxonBase>> |
ITaxonService.findTaxaAndNamesByFullText(java.util.EnumSet<TaxaAndNamesSearchMode> searchModes,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
java.util.Set<NamedArea> namedAreas,
java.util.Set<PresenceAbsenceTerm> distributionStatus,
java.util.List<Language> languages,
boolean highlightFragments,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Searches for TaxonBase instances using the TaxonBase free text index.
|
java.util.List<TaxonBase> |
TaxonServiceImpl.findTaxaByID(java.util.Set<java.lang.Integer> listOfIDs) |
java.util.List<TaxonBase> |
ITaxonService.findTaxaByID(java.util.Set<java.lang.Integer> listOfIDs) |
Pager<TaxonBase> |
TaxonServiceImpl.findTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String uninomial,
java.lang.String infragenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
java.lang.String authorshipCache,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
Pager<TaxonBase> |
ITaxonService.findTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String uninomial,
java.lang.String infragenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
java.lang.String authorshipCache,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a list of TaxonBase instances where the
taxon.name properties match the parameters passed.
|
java.util.List<TaxonBase> |
TaxonServiceImpl.findTaxaByName(MatchingTaxonConfigurator config) |
java.util.List<TaxonBase> |
ITaxonService.findTaxaByName(MatchingTaxonConfigurator config) |
java.util.List<UuidAndTitleCache<TaxonBase>> |
TaxonServiceImpl.getTaxonUuidAndTitleCache(java.lang.Integer limit,
java.lang.String pattern) |
java.util.Collection<TaxonBase<?>> |
IOccurrenceService.listAssociatedTaxa(SpecimenOrObservationBase<?> specimen,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Retrieves all associated taxa for the given specimen (via type designations, determination, individuals associations)
|
java.util.Collection<TaxonBase<?>> |
OccurrenceServiceImpl.listAssociatedTaxa(SpecimenOrObservationBase<?> specimen,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.Collection<TaxonBase<?>> |
IOccurrenceService.listAssociatedTaxa(SpecimenOrObservationBase<?> specimen,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.Collection<TaxonBase<?>> |
OccurrenceServiceImpl.listAssociatedTaxa(SpecimenOrObservationBase<?> specimen,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonBase> |
ReferenceServiceImpl.listCoveredTaxa(Reference reference,
boolean includeSubordinateReferences,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonBase> |
IReferenceService.listCoveredTaxa(Reference reference,
boolean includeSubordinateReferences,
java.util.List<java.lang.String> propertyPaths)
returns
all taxa directly covered by this reference
all taxa covered by the according in references of this reference
searches for taxa using the following relations:
taxon.name.nomenclaturalreference
taxon.descriptions.descriptionElement.sources.citation
taxon.descriptions.descriptionSources
taxon.name.descriptions.descriptionElement.sources
taxon.name.descriptions.descriptionSources
|
java.util.Collection<TaxonBase<?>> |
IOccurrenceService.listDeterminedTaxa(SpecimenOrObservationBase<?> specimen,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Retrieves all taxa that the given specimen is determined as
|
java.util.Collection<TaxonBase<?>> |
OccurrenceServiceImpl.listDeterminedTaxa(SpecimenOrObservationBase<?> specimen,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.Collection<TaxonBase<?>> |
IOccurrenceService.listDeterminedTaxa(SpecimenOrObservationBase<?> specimen,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.Collection<TaxonBase<?>> |
OccurrenceServiceImpl.listDeterminedTaxa(SpecimenOrObservationBase<?> specimen,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.Collection<TaxonBase<?>> |
IOccurrenceService.listIndividualsAssociationTaxa(SpecimenOrObservationBase<?> specimen,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.Collection<TaxonBase<?>> |
OccurrenceServiceImpl.listIndividualsAssociationTaxa(SpecimenOrObservationBase<?> specimen,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.Collection<TaxonBase<?>> |
IOccurrenceService.listIndividualsAssociationTaxa(SpecimenOrObservationBase<?> specimen,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Retrieves all taxa linked via
IndividualsAssociation with the given specimen. |
java.util.Collection<TaxonBase<?>> |
OccurrenceServiceImpl.listIndividualsAssociationTaxa(SpecimenOrObservationBase<?> specimen,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Retrieves all taxa linked via
IndividualsAssociation with the given specimen. |
java.util.List<TaxonBase> |
TaxonServiceImpl.listTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String uninomial,
java.lang.String infragenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
java.lang.String authorshipCache,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonBase> |
ITaxonService.listTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String uninomial,
java.lang.String infragenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
java.lang.String authorshipCache,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a list of TaxonBase instances where the
taxon.name properties match the parameters passed.
|
java.util.Collection<TaxonBase<?>> |
IOccurrenceService.listTypeDesignationTaxa(DerivedUnit specimen,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.Collection<TaxonBase<?>> |
OccurrenceServiceImpl.listTypeDesignationTaxa(DerivedUnit specimen,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.Collection<TaxonBase<?>> |
IOccurrenceService.listTypeDesignationTaxa(DerivedUnit specimen,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Retrieves all taxa with a
SpecimenTypeDesignation with the given specimen as a type specimen. |
java.util.Collection<TaxonBase<?>> |
OccurrenceServiceImpl.listTypeDesignationTaxa(DerivedUnit specimen,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Retrieves all taxa with a
SpecimenTypeDesignation with the given specimen as a type specimen. |
Pager<TaxonBase> |
ITaxonService.search(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String queryString,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Returns a Paged List of TaxonBase instances where the default field matches the String queryString (as interpreted by the Lucene QueryParser)
|
java.util.List<TaxonBase> |
TaxonServiceImpl.searchByName(java.lang.String name,
boolean includeUnpublished,
Reference sec) |
java.util.List<TaxonBase> |
ITaxonService.searchByName(java.lang.String name,
boolean includeUnpublished,
Reference sec)
Returns a list of taxa that matches the name string and the sec reference
|
Modifier and Type | Method and Description |
---|---|
long |
IOccurrenceService.countDeterminations(SpecimenOrObservationBase occurence,
TaxonBase taxonbase)
Returns a count of determinations that have been made for a given occurence and for a given taxon concept
|
long |
OccurrenceServiceImpl.countDeterminations(SpecimenOrObservationBase occurence,
TaxonBase taxonbase) |
Pager<PolytomousKey> |
PolytomousKeyServiceImpl.findByTaxonomicScope(TaxonBase taxon,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths,
java.util.List<java.lang.String> nodePaths) |
Pager<PolytomousKey> |
IPolytomousKeyService.findByTaxonomicScope(TaxonBase taxon,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths,
java.util.List<java.lang.String> nodePaths) |
<T extends IIdentificationKey> |
IIdentificationKeyService.findKeysConvering(TaxonBase taxon,
java.lang.Class<T> type,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Finds IdentificationKeys which cover the Taxon given as parameter
|
<T extends IIdentificationKey> |
IdentificationKeyServiceImpl.findKeysConvering(TaxonBase taxon,
java.lang.Class<T> type,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
Pager<DeterminationEvent> |
IOccurrenceService.getDeterminations(SpecimenOrObservationBase occurence,
TaxonBase taxonBase,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a List of determinations that have been made for a given occurence
|
Pager<DeterminationEvent> |
OccurrenceServiceImpl.getDeterminations(SpecimenOrObservationBase occurrence,
TaxonBase taxonBase,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
Pager<SpecimenOrObservationBase> |
IOccurrenceService.list(java.lang.Class<? extends SpecimenOrObservationBase> type,
TaxonBase determinedAs,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Returns a paged list of occurrences that have been determined to belong
to the taxon concept determinedAs, optionally restricted to objects
belonging to a class that that extends SpecimenOrObservationBase.
|
Pager<SpecimenOrObservationBase> |
OccurrenceServiceImpl.list(java.lang.Class<? extends SpecimenOrObservationBase> type,
TaxonBase determinedAs,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<Classification> |
TaxonServiceImpl.listClassifications(TaxonBase taxonBase,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<Classification> |
ITaxonService.listClassifications(TaxonBase taxonBase,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<java.lang.String> propertyPaths)
Lists all classifications the given taxon/synonym is used in
Synonym |
java.util.List<TaxonNodeDto> |
TaxonNodeServiceImpl.taxonNodeDtoParentRank(Classification classification,
Rank rank,
TaxonBase<?> taxonBase) |
java.util.List<TaxonNodeDto> |
ITaxonNodeService.taxonNodeDtoParentRank(Classification classification,
Rank rank,
TaxonBase<?> taxonBase) |
Modifier and Type | Method and Description |
---|---|
Pager<SearchResult<TaxonBase>> |
TaxonServiceImpl.findByFullText(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
boolean includeUnpublished,
java.util.List<Language> languages,
boolean highlightFragments,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Pager<SearchResult<TaxonBase>> |
ITaxonService.findByFullText(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
boolean includeUnpublished,
java.util.List<Language> languages,
boolean highlightFragments,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Searches for TaxonBase instances using the TaxonBase free text index.
|
Pager<TaxonBase> |
TaxonServiceImpl.findTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String uninomial,
java.lang.String infragenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
java.lang.String authorshipCache,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
Pager<TaxonBase> |
ITaxonService.findTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String uninomial,
java.lang.String infragenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
java.lang.String authorshipCache,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a list of TaxonBase instances where the
taxon.name properties match the parameters passed.
|
java.util.List<TaxonBase> |
TaxonServiceImpl.listTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String uninomial,
java.lang.String infragenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
java.lang.String authorshipCache,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonBase> |
ITaxonService.listTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String uninomial,
java.lang.String infragenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
java.lang.String authorshipCache,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a list of TaxonBase instances where the
taxon.name properties match the parameters passed.
|
Pager<TaxonBase> |
ITaxonService.search(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String queryString,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Returns a Paged List of TaxonBase instances where the default field matches the String queryString (as interpreted by the Lucene QueryParser)
|
UpdateResult |
TaxonServiceImpl.updateCaches(java.lang.Class<? extends TaxonBase> clazz,
java.lang.Integer stepSize,
IIdentifiableEntityCacheStrategy<TaxonBase> cacheStrategy,
IProgressMonitor monitor) |
UpdateResult |
TaxonServiceImpl.updateCaches(java.lang.Class<? extends TaxonBase> clazz,
java.lang.Integer stepSize,
IIdentifiableEntityCacheStrategy<TaxonBase> cacheStrategy,
IProgressMonitor monitor) |
Modifier and Type | Method and Description |
---|---|
protected java.lang.String |
DescriptionAggregationBase.taxonToString(TaxonBase<?> taxon) |
Modifier and Type | Method and Description |
---|---|
static java.lang.Integer |
BerlinModelTransformer.taxonBase2statusFk(TaxonBase<?> taxonBase) |
Modifier and Type | Method and Description |
---|---|
protected <T extends TaxonBase> |
Cdm2CdmImportBase.handlePersisted(TaxonBase taxonBase) |
Modifier and Type | Method and Description |
---|---|
protected <T extends TaxonBase> |
Cdm2CdmImportBase.handlePersisted(TaxonBase taxonBase) |
Modifier and Type | Method and Description |
---|---|
protected TaxonBase<?> |
CdmLightExportState.getActualTaxonBase() |
Modifier and Type | Method and Description |
---|---|
protected void |
CdmLightExportState.setActualTaxonBase(TaxonBase<?> actualTaxonBase) |
Modifier and Type | Method and Description |
---|---|
protected Taxon |
CdmImportBase.getAcceptedTaxon(TaxonBase<?> taxonBase)
Returns the accepted taxon of a
taxon base . |
Modifier and Type | Method and Description |
---|---|
TaxonBase |
DbImportImageGalleryMapper.invoke(java.sql.ResultSet rs,
TaxonBase taxonBase) |
Modifier and Type | Method and Description |
---|---|
TaxonBase |
DbImportImageGalleryMapper.invoke(java.sql.ResultSet rs,
TaxonBase taxonBase) |
Modifier and Type | Method and Description |
---|---|
protected java.lang.String |
CsvDemoBase.getTaxonLogString(TaxonBase<?> taxon) |
protected void |
CsvDemoBase.handleArea(ICsvAreaRecord record,
NamedArea area,
TaxonBase<?> taxon,
boolean required)
Creates the locationId, locality, countryCode triple
|
Modifier and Type | Method and Description |
---|---|
protected java.lang.String |
CsvExportBaseRedlist.getTaxonLogString(TaxonBase<?> taxon) |
protected void |
CsvExportBaseRedlist.handleArea(ICsvAreaRecord record,
NamedArea area,
TaxonBase<?> taxon,
boolean required)
Creates the locationId, locality, countryCode triple
|
Modifier and Type | Method and Description |
---|---|
protected java.lang.String |
DwcaDataExportBase.getTaxonLogString(TaxonBase<?> taxon) |
protected void |
DwcaDataExportBase.handleArea(DwcaTaxExportState state,
IDwcaAreaRecord record,
NamedArea area,
TaxonBase<?> taxon,
boolean required)
Creates the locationId, locality, countryCode triple
|
Modifier and Type | Method and Description |
---|---|
protected <T extends TaxonBase<?>> |
ExcelImportBase.getTaxonByCdmId(STATE state,
java.lang.String colTaxonUuid,
java.lang.String colNameCache,
java.lang.String colNameTitleCache,
java.lang.String colTaxonTitleCache,
java.lang.Class<T> clazz,
java.lang.String line)
Returns the taxon for the given CDM uuid.
|
Modifier and Type | Method and Description |
---|---|
protected void |
ExcelImportBase.verifyName(STATE state,
java.lang.String colNameCache,
java.lang.String colNameTitleCache,
java.lang.String colTaxonTitleCache,
java.lang.String line,
java.util.Map<java.lang.String,java.lang.String> record,
TaxonBase<?> result) |
Modifier and Type | Method and Description |
---|---|
TaxonBase |
TaxonExcelImportState.getTaxonBase(java.lang.String taxonId) |
Modifier and Type | Method and Description |
---|---|
java.util.Map<java.lang.String,TaxonBase> |
TaxonExcelImportState.getTaxonMap() |
Modifier and Type | Method and Description |
---|---|
void |
TaxonExcelImportState.putTaxon(java.lang.String taxonId,
TaxonBase taxonBase) |
Modifier and Type | Method and Description |
---|---|
void |
TaxonExcelImportState.setTaxonMap(java.util.Map<java.lang.String,TaxonBase> taxonMap) |
Modifier and Type | Field and Description |
---|---|
protected java.util.List<TaxonBase<?>> |
DataSet.taxonBases |
Modifier and Type | Method and Description |
---|---|
java.util.List<TaxonBase<?>> |
DataSet.getTaxonBases() |
Modifier and Type | Method and Description |
---|---|
void |
DataSet.addTaxonBase(TaxonBase value) |
Modifier and Type | Method and Description |
---|---|
void |
DataSet.addTaxonBases(java.util.Collection<TaxonBase<?>> value) |
void |
DataSet.setTaxonBases(java.util.List<TaxonBase<?>> value) |
Modifier and Type | Method and Description |
---|---|
java.util.Collection<? extends TaxonBase> |
SDDDataSet.getTaxa() |
java.util.Collection<TaxonBase> |
SDDDataSet.getTaxonBases() |
Modifier and Type | Method and Description |
---|---|
Taxon |
SpecimenUserInteraction.askWhereToFixData(java.lang.String scientificName,
java.util.List<TaxonBase> taxonList,
Classification classification)
Look if the same name already exists in the ALL classifications and ask the user to select one or none.
|
Taxon |
SpecimenUserInteraction.lookForTaxaIntoCurrentClassification(java.util.List<TaxonBase> taxonBaseList,
Classification classification)
Look if the same TaxonBase already exists in the SAME classification
|
Modifier and Type | Method and Description |
---|---|
protected <T extends TaxonBase<?>> |
PartitionableConverterBase.getTaxonBase(java.lang.String id,
StreamItem item,
java.lang.Class<T> clazz,
STATE state) |
Modifier and Type | Field and Description |
---|---|
protected TaxonBase<?> |
CdmLinkBase.taxon |
Modifier and Type | Method and Description |
---|---|
java.util.Set<TaxonBase> |
TaxonName.getTaxonBases()
Returns the set of
taxon bases that refer to this taxon name. |
java.util.Set<TaxonBase> |
ITaxonNameBase.getTaxonBases()
Returns the set of
taxon bases that refer to this taxon name. |
Modifier and Type | Method and Description |
---|---|
void |
TaxonName.addTaxonBase(TaxonBase taxonBase)
Adds a new
taxon base
to the set of taxon bases using this taxon name. |
void |
ITaxonNameBase.addTaxonBase(TaxonBase taxonBase)
Adds a new
taxon base
to the set of taxon bases using this taxon name. |
void |
TaxonName.removeTaxonBase(TaxonBase taxonBase)
Removes one element from the set of
taxon bases that refer to this taxon name. |
void |
ITaxonNameBase.removeTaxonBase(TaxonBase taxonBase)
Removes one element from the set of
taxon bases that refer to this taxon name. |
Modifier and Type | Method and Description |
---|---|
TaxonBase |
DeterminationEvent.getTaxon() |
Modifier and Type | Method and Description |
---|---|
void |
DeterminationEvent.setTaxon(TaxonBase taxon) |
Modifier and Type | Class and Description |
---|---|
class |
Synonym
|
class |
Taxon
|
Modifier and Type | Method and Description |
---|---|
int |
HomotypicGroupTaxonComparator.compare(TaxonBase taxonBase1,
TaxonBase taxonBase2) |
int |
HomotypicGroupTaxonComparator.compare(TaxonBase taxonBase1,
TaxonBase taxonBase2) |
int |
TaxonComparator.compare(TaxonBase taxonBase1,
TaxonBase taxonBase2)
Returns an integer generated by comparing first the nomenclatural status and then the
publication years
of both taxon names
used in the given taxa . |
int |
TaxonComparator.compare(TaxonBase taxonBase1,
TaxonBase taxonBase2)
Returns an integer generated by comparing first the nomenclatural status and then the
publication years
of both taxon names
used in the given taxa . |
int |
TaxonBase.compareToTaxon(TaxonBase otherTaxon)
This method compares 2 taxa on it's name titles and caches.
|
java.lang.String |
TaxonNodeByRankAndNameComparator.getTaxonTitle(TaxonBase<?> taxon,
TaxonNode node) |
Constructor and Description |
---|
HomotypicGroupTaxonComparator(TaxonBase firstTaxonInGroup) |
HomotypicGroupTaxonComparator(TaxonBase firstTaxonInGroup,
boolean includeRanks) |
Modifier and Type | Method and Description |
---|---|
long |
OccurrenceDaoHibernateImpl.count(java.lang.Class<? extends SpecimenOrObservationBase> clazz,
TaxonBase determinedAs) |
long |
OccurrenceDaoHibernateImpl.countDeterminations(SpecimenOrObservationBase occurrence,
TaxonBase taxonBase) |
java.util.List<DeterminationEvent> |
OccurrenceDaoHibernateImpl.getDeterminations(SpecimenOrObservationBase occurrence,
TaxonBase taxonBase,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<SpecimenOrObservationBase> |
OccurrenceDaoHibernateImpl.list(java.lang.Class<? extends SpecimenOrObservationBase> clazz,
TaxonBase determinedAs,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Modifier and Type | Method and Description |
---|---|
java.util.List<TaxonBase> |
ReferenceDaoHibernateImpl.listCoveredTaxa(Reference reference,
boolean includeSubordinateReferences,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Modifier and Type | Method and Description |
---|---|
java.lang.Long |
StatisticsDaoHibernateImpl.countTaxaInClassification(java.lang.Class<? extends TaxonBase> clazz,
Classification classification) |
Modifier and Type | Method and Description |
---|---|
<S extends TaxonBase> |
TaxonDaoHibernateImpl.countByIdentifier(java.lang.Class<S> clazz,
java.lang.String identifier,
DefinedTerm identifierType,
TaxonNode subtreeFilter,
MatchMode matchmode) |
<S extends TaxonBase> |
TaxonDaoHibernateImpl.countByMarker(java.lang.Class<S> clazz,
MarkerType markerType,
java.lang.Boolean markerValue,
TaxonNode subtreeFilter)
Counts all taxa which have the given marker of type markerType and with value markerValue.
|
<S extends TaxonBase> |
TaxonDaoHibernateImpl.findByIdentifier(java.lang.Class<S> clazz,
java.lang.String identifier,
DefinedTerm identifierType,
TaxonNode subtreeFilter,
MatchMode matchmode,
boolean includeEntity,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
<S extends TaxonBase> |
TaxonDaoHibernateImpl.findByMarker(java.lang.Class<S> clazz,
MarkerType markerType,
java.lang.Boolean markerValue,
TaxonNode subtreeFilter,
boolean includeEntity,
TaxonTitleType titleType,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
<S extends TaxonBase> |
TaxonDaoHibernateImpl.list(java.lang.Class<S> type,
java.util.List<Restriction<?>> restrictions,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
<S extends TaxonBase> |
TaxonDaoHibernateImpl.list(java.lang.Class<S> type,
java.util.List<Restriction<?>> restrictions,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths,
boolean includePublished) |
Modifier and Type | Method and Description |
---|---|
TaxonBase |
TaxonDaoHibernateImpl.find(LSID lsid) |
TaxonBase |
TaxonDaoHibernateImpl.findByUuid(java.util.UUID uuid,
java.util.List<org.hibernate.criterion.Criterion> criteria,
java.util.List<java.lang.String> propertyPaths) |
TaxonBase |
TaxonDaoHibernateImpl.load(java.util.UUID uuid,
boolean includeUnpublished,
java.util.List<java.lang.String> propertyPaths) |
TaxonBase |
TaxonDaoHibernateImpl.load(java.util.UUID uuid,
java.util.List<java.lang.String> propertyPaths) |
Modifier and Type | Method and Description |
---|---|
java.util.List<TaxonBase> |
TaxonDaoHibernateImpl.findByNameTitleCache(boolean doTaxa,
boolean doSynonyms,
boolean includeUnpublished,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
NameSearchOrder order,
java.lang.Integer pageNumber,
java.lang.Integer pageSize,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<? extends TaxonBase> |
TaxonDaoHibernateImpl.findByUuids(java.util.List<java.util.UUID> uuids,
java.util.List<org.hibernate.criterion.Criterion> criteria,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonBase> |
TaxonDaoHibernateImpl.findTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String genusOrUninomial,
java.lang.String infraGenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraSpecificEpithet,
java.lang.String authorship,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonBase> |
TaxonDaoHibernateImpl.getTaxaByName(boolean doTaxa,
boolean doSynonyms,
boolean doMisappliedNames,
boolean doCommonNames,
boolean includeAuthors,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
boolean includeUnpublished,
NameSearchOrder order,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonBase> |
TaxonDaoHibernateImpl.getTaxaByName(boolean doTaxa,
boolean doSynonyms,
boolean includeUnpublished,
java.lang.String queryString,
MatchMode matchMode,
java.lang.Integer pageSize,
java.lang.Integer pageNumber) |
java.util.List<TaxonBase> |
TaxonDaoHibernateImpl.getTaxaByName(java.lang.String queryString,
java.lang.Boolean accepted,
boolean includeUnpublished,
Reference sec) |
java.util.List<TaxonBase> |
TaxonDaoHibernateImpl.getTaxaByName(java.lang.String queryString,
boolean includeUnpublished,
Reference sec) |
java.util.List<TaxonBase> |
TaxonDaoHibernateImpl.getTaxaByName(java.lang.String queryString,
MatchMode matchMode,
java.lang.Boolean accepted,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageNumber) |
java.util.List<UuidAndTitleCache<TaxonBase>> |
TaxonDaoHibernateImpl.getUuidAndTitleCache(java.lang.Integer limit,
java.lang.String pattern) |
protected java.util.List<UuidAndTitleCache<TaxonBase>> |
TaxonDaoHibernateImpl.getUuidAndTitleCache(org.hibernate.Query query) |
java.util.Set<TaxonBase> |
TaxonNodeDaoHibernateImpl.setPublishForSubtreeAcceptedTaxa(TreeIndex subTreeIndex,
boolean publish,
boolean includeSharedTaxa,
boolean includeHybrids,
IProgressMonitor monitor) |
java.util.Set<TaxonBase> |
TaxonNodeDaoHibernateImpl.setPublishForSubtreeRelatedTaxa(TreeIndex subTreeIndex,
boolean publish,
java.util.Set<java.util.UUID> relationTypes,
boolean includeSharedTaxa,
boolean includeHybrids,
IProgressMonitor monitor) |
java.util.Set<TaxonBase> |
TaxonNodeDaoHibernateImpl.setPublishForSubtreeSynonyms(TreeIndex subTreeIndex,
boolean publish,
boolean includeSharedTaxa,
boolean includeHybrids,
IProgressMonitor monitor) |
java.util.Set<TaxonBase> |
TaxonNodeDaoHibernateImpl.setSecundumForSubtreeAcceptedTaxa(TreeIndex subTreeIndex,
Reference newSec,
boolean overwriteExisting,
boolean includeSharedTaxa,
boolean emptyDetail,
IProgressMonitor monitor) |
java.util.Set<TaxonBase> |
TaxonNodeDaoHibernateImpl.setSecundumForSubtreeSynonyms(TreeIndex subTreeIndex,
Reference newSec,
boolean overwriteExisting,
boolean includeSharedTaxa,
boolean emptyDetail,
IProgressMonitor monitor) |
Modifier and Type | Method and Description |
---|---|
java.util.UUID |
TaxonDaoHibernateImpl.delete(TaxonBase taxonBase) |
java.util.List<TaxonNodeDto> |
TaxonNodeDaoHibernateImpl.getParentTaxonNodeDtoForRank(Classification classification,
Rank rank,
TaxonBase<?> taxonBase) |
Modifier and Type | Method and Description |
---|---|
long |
TaxonDaoHibernateImpl.count(java.lang.Class<? extends TaxonBase> type,
java.util.List<Restriction<?>> restrictions) |
long |
TaxonDaoHibernateImpl.count(java.lang.Class<? extends TaxonBase> type,
java.util.List<Restriction<?>> restrictions,
boolean includePublished) |
long |
TaxonDaoHibernateImpl.countTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String genusOrUninomial,
java.lang.String infraGenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraSpecificEpithet,
java.lang.String authorshipCache,
Rank rank) |
java.util.List<TaxonBase> |
TaxonDaoHibernateImpl.findTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String genusOrUninomial,
java.lang.String infraGenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraSpecificEpithet,
java.lang.String authorship,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
Modifier and Type | Method and Description |
---|---|
long |
IOccurrenceDao.count(java.lang.Class<? extends SpecimenOrObservationBase> clazz,
TaxonBase determinedAs)
Returns the number of occurences belonging to a certain subclass - which must extend SpecimenOrObservationBase
|
long |
IOccurrenceDao.countDeterminations(SpecimenOrObservationBase occurence,
TaxonBase taxonbase)
Returns a count of determinations that have been made for a given occurence and for a given taxon concept
|
java.util.List<DeterminationEvent> |
IOccurrenceDao.getDeterminations(SpecimenOrObservationBase occurence,
TaxonBase taxonbase,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a List of determinations that have been made for a given occurence and for a given taxon concept
|
java.util.List<SpecimenOrObservationBase> |
IOccurrenceDao.list(java.lang.Class<? extends SpecimenOrObservationBase> type,
TaxonBase determinedAs,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Returns a sublist of SpecimenOrObservationBase instances stored in the database.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<TaxonBase> |
IReferenceDao.listCoveredTaxa(Reference reference,
boolean includeSubordinateReferences,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
searches for taxa using the following relations:
taxon.name.nomenclaturalreference
taxon.descriptions.descriptionElement.sources.citation
taxon.descriptions.descriptionSources
taxon.name.descriptions.descriptionElement.sources
taxon.name.descriptions.descriptionSources
|
Modifier and Type | Method and Description |
---|---|
java.lang.Long |
IStatisticsDao.countTaxaInClassification(java.lang.Class<? extends TaxonBase> clazz,
Classification classification)
counts items of the type Taxon, Synonym or TaxonBase (Taxon & Synonym)
|
Modifier and Type | Method and Description |
---|---|
<S extends TaxonBase> |
ITaxonDao.countByIdentifier(java.lang.Class<S> clazz,
java.lang.String identifier,
DefinedTerm identifierType,
TaxonNode subtreeFilter,
MatchMode matchmode)
Counts all taxa which match the given identifier (identifier type, identifier string and match mode).
|
<S extends TaxonBase> |
ITaxonDao.countByMarker(java.lang.Class<S> clazz,
MarkerType markerType,
java.lang.Boolean markerValue,
TaxonNode subtreeFilter)
Counts all taxa which have the given marker of type markerType and with value markerValue.
|
<S extends TaxonBase> |
ITaxonDao.findByIdentifier(java.lang.Class<S> clazz,
java.lang.String identifier,
DefinedTerm identifierType,
TaxonNode subtreeFilter,
MatchMode matchmode,
boolean includeEntity,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
<S extends TaxonBase> |
ITaxonDao.findByMarker(java.lang.Class<S> clazz,
MarkerType markerType,
java.lang.Boolean markerValue,
TaxonNode subtreeFilter,
boolean includeEntity,
TaxonTitleType titleType,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
<S extends TaxonBase> |
ITaxonDao.list(java.lang.Class<S> type,
java.util.List<Restriction<?>> restrictions,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths,
boolean includePublished) |
Modifier and Type | Method and Description |
---|---|
TaxonBase |
ITaxonDao.findByUuid(java.util.UUID uuid,
java.util.List<org.hibernate.criterion.Criterion> criteria,
java.util.List<java.lang.String> propertyPaths)
Returns a taxon corresponding to the given uuid
|
TaxonBase |
ITaxonDao.load(java.util.UUID uuid,
java.util.List<java.lang.String> propertyPaths)
Finds the cdm entity specified by the
uuid parameter and
recursively initializes all bean properties given in the
propertyPaths parameter. |
Modifier and Type | Method and Description |
---|---|
java.util.List<TaxonBase> |
ITaxonDao.findByNameTitleCache(boolean doTaxa,
boolean doSynonyms,
boolean includeUnpublished,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
NameSearchOrder order,
java.lang.Integer pageNumber,
java.lang.Integer pageSize,
java.util.List<java.lang.String> propertyPaths)
Find taxa by searching for Taxa and Synonyms where the
TaxonName .titleCache matches
the name specified as queryString taxonName |
java.util.List<? extends TaxonBase> |
ITaxonDao.findByUuids(java.util.List<java.util.UUID> uuids,
java.util.List<org.hibernate.criterion.Criterion> criteria,
java.util.List<java.lang.String> propertyPaths)
Returns a list of Taxon entities corresponding to the given uuid list.
|
java.util.List<TaxonBase> |
ITaxonDao.findTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String uninomial,
java.lang.String infragenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
java.lang.String authorshipCache,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a list of TaxonBase instances where the
taxon.name properties match the parameters passed.
|
java.util.List<TaxonBase> |
ITaxonDao.getTaxaByName(boolean doTaxa,
boolean doSynonyms,
boolean doMisappliedNames,
boolean doCommonNames,
boolean includeAuthors,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
boolean includeUnpublished,
NameSearchOrder order,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a list of TaxonBase instances (or Taxon instances, if accepted == true, or Synonym instance, if accepted == false)
where the taxonBase.name.nameCache property matches the String queryString.
|
java.util.List<TaxonBase> |
ITaxonDao.getTaxaByName(java.lang.String queryString,
java.lang.Boolean accepted,
boolean includeUnpublished,
Reference sec)
Returns a list of TaxonBase instances (or Taxon instances, if accepted == true, or Synonym instance, if accepted == false)
where the taxonBase.name.nameCache property matches the String queryString, and taxon.sec matches the sec parameter.
|
java.util.List<TaxonBase> |
ITaxonDao.getTaxaByName(java.lang.String name,
boolean includeUnpublished,
Reference sec)
Returns a list of TaxonBase instances where the taxon.titleCache property matches the name parameter,
and taxon.sec matches the sec parameter.
|
java.util.List<TaxonBase> |
ITaxonDao.getTaxaByName(java.lang.String queryString,
MatchMode matchMode,
java.lang.Boolean accepted,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageNumber)
Returns a list of TaxonBase instances (or Taxon instances, if accepted == true, or Synonym instance, if accepted == false)
where the taxonBase.name.nameCache property matches the String queryString.
|
java.util.Set<TaxonBase> |
ITaxonNodeDao.setPublishForSubtreeAcceptedTaxa(TreeIndex subTreeIndex,
boolean publish,
boolean includeSharedTaxa,
boolean includeHybrids,
IProgressMonitor monitor) |
java.util.Set<TaxonBase> |
ITaxonNodeDao.setPublishForSubtreeRelatedTaxa(TreeIndex subTreeIndex,
boolean publish,
java.util.Set<java.util.UUID> relationTypes,
boolean includeSharedTaxa,
boolean includeHybrids,
IProgressMonitor monitor) |
java.util.Set<TaxonBase> |
ITaxonNodeDao.setPublishForSubtreeSynonyms(TreeIndex subTreeIndex,
boolean publish,
boolean includeSharedTaxa,
boolean includeHybrids,
IProgressMonitor monitor) |
java.util.Set<TaxonBase> |
ITaxonNodeDao.setSecundumForSubtreeAcceptedTaxa(TreeIndex subTreeIndex,
Reference newSec,
boolean overwriteExisting,
boolean includeSharedTaxa,
boolean emptyDetail,
IProgressMonitor monitor) |
java.util.Set<TaxonBase> |
ITaxonNodeDao.setSecundumForSubtreeSynonyms(TreeIndex subTreeIndex,
Reference newSec,
boolean overwriteExisting,
boolean includeSharedTaxa,
boolean emptyDetail,
IProgressMonitor monitor) |
Modifier and Type | Method and Description |
---|---|
java.util.List<TaxonNodeDto> |
ITaxonNodeDao.getParentTaxonNodeDtoForRank(Classification classification,
Rank rank,
TaxonBase<?> taxonBase) |
Modifier and Type | Method and Description |
---|---|
long |
ITaxonDao.count(java.lang.Class<? extends TaxonBase> type,
java.util.List<Restriction<?>> restrictions,
boolean includePublished) |
long |
ITaxonDao.countTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String uninomial,
java.lang.String infragenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
java.lang.String authorshipCache,
Rank rank)
Returns a count of TaxonBase instances where the
taxon.name properties match the parameters passed.
|
java.util.List<TaxonBase> |
ITaxonDao.findTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String uninomial,
java.lang.String infragenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
java.lang.String authorshipCache,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a list of TaxonBase instances where the
taxon.name properties match the parameters passed.
|
Modifier and Type | Method and Description |
---|---|
java.lang.String |
TaxonNodeDtoByRankAndNameComparator.getTaxonTitle(TaxonBase<?> taxon,
TaxonNode node) |
Modifier and Type | Method and Description |
---|---|
protected <S extends TaxonBase<?>> |
TaxonController.checkExistsSubtreeAndAccess(S taxonBase,
TaxonNode subtree,
boolean includeUnpublished,
javax.servlet.http.HttpServletResponse response)
|
<T extends TaxonBase> |
TaxonListController.doFindByIdentifier(java.lang.Class<T> type,
java.util.UUID identifierType,
java.lang.String identifier,
java.lang.Integer pageNumber,
java.lang.Integer pageSize,
MatchMode matchMode,
java.lang.Boolean includeEntity,
java.util.UUID subtreeUuid,
javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response)
list IdentifiableEntity objects by identifiers
|
<T extends TaxonBase> |
TaxonListController.doFindByMarker(java.lang.Class<T> type,
java.util.UUID markerTypeUuid,
java.lang.Boolean value,
java.lang.Integer pageNumber,
java.lang.Integer pageSize,
java.lang.Boolean includeEntity,
java.util.UUID subtreeUuid,
TaxonTitleType titleType,
javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response)
List taxa by markers using a subtree filter
|
Modifier and Type | Method and Description |
---|---|
TaxonBase |
TaxonListController.doFindBestMatchingTaxon(java.lang.String taxonName,
javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response) |
TaxonBase<?> |
TaxonController.doGet(java.util.UUID uuid,
java.util.UUID subtreeUuid,
javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response) |
TaxonBase |
TaxonNodePrintAppController.doGetTaxon(java.util.UUID taxonNodeUuid)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
Pager<SearchResult<TaxonBase>> |
TaxonListController.doFindByDescriptionElementFullText(java.lang.Class<? extends DescriptionElementBase> clazz,
java.lang.String queryString,
java.util.UUID treeUuid,
java.util.UUID subtreeUuid,
UuidList featureUuids,
java.util.List<Language> languages,
java.lang.Boolean highlighting,
java.lang.Integer pageNumber,
java.lang.Integer pageSize,
javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response) |
Pager<SearchResult<TaxonBase>> |
TaxonListController.doFindByEverythingFullText(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String queryString,
java.util.UUID treeUuid,
java.util.UUID subtreeUuid,
java.util.List<Language> languages,
java.lang.Boolean highlighting,
java.lang.Integer pageNumber,
java.lang.Integer pageSize,
javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response)
Deprecated.
see
ITaxonService#findByEverythingFullText(String, Classification, boolean, List, boolean, Integer, Integer, List, List) |
Pager<SearchResult<TaxonBase>> |
TaxonListController.doFindByFullText(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String queryString,
java.util.UUID classificationUuid,
java.util.UUID subtreeUuid,
java.util.List<Language> languages,
java.lang.Boolean highlighting,
java.lang.Integer pageNumber,
java.lang.Integer pageSize,
javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response) |
Pager<TaxonBase> |
TaxonListController.doFindByNameParts(java.lang.String genusOrUninomial,
java.lang.String infragenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
java.lang.String authorshipCache,
java.util.UUID rankUuid,
java.lang.Integer pageNumber,
java.lang.Integer pageSize,
javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response) |
Pager<SearchResult<TaxonBase>> |
TaxonListController.doSearch(java.lang.String query,
java.util.UUID classificationUuid,
java.util.UUID subtreeUuid,
DefinedTermBaseList<NamedArea> areaList,
PresenceAbsenceTerm[] status,
java.lang.Integer pageNumber,
java.lang.Integer pageSize,
java.lang.Boolean doTaxa,
java.lang.Boolean doSynonyms,
java.lang.Boolean doMisappliedNames,
java.lang.Boolean doTaxaByCommonNames,
javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response)
Find Taxa, Synonyms, Common Names by name, either globally or in a specific geographic area.
|
protected Pager<TaxonBase> |
TaxonListController.pageByRestrictions(java.lang.Class<TaxonBase> type,
java.util.List<java.lang.String> initStrategy,
eu.etaxonomy.cdm.remote.controller.OrderHintPreset orderBy,
PagerParameters pagerParameters,
java.util.ArrayList<Restriction<?>> restrictions) |
Modifier and Type | Method and Description |
---|---|
Pager<SearchResult<TaxonBase>> |
TaxonListController.doFindByEverythingFullText(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String queryString,
java.util.UUID treeUuid,
java.util.UUID subtreeUuid,
java.util.List<Language> languages,
java.lang.Boolean highlighting,
java.lang.Integer pageNumber,
java.lang.Integer pageSize,
javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response)
Deprecated.
see
ITaxonService#findByEverythingFullText(String, Classification, boolean, List, boolean, Integer, Integer, List, List) |
Pager<SearchResult<TaxonBase>> |
TaxonListController.doFindByFullText(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String queryString,
java.util.UUID classificationUuid,
java.util.UUID subtreeUuid,
java.util.List<Language> languages,
java.lang.Boolean highlighting,
java.lang.Integer pageNumber,
java.lang.Integer pageSize,
javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response) |
protected Pager<TaxonBase> |
TaxonListController.pageByRestrictions(java.lang.Class<TaxonBase> type,
java.util.List<java.lang.String> initStrategy,
eu.etaxonomy.cdm.remote.controller.OrderHintPreset orderBy,
PagerParameters pagerParameters,
java.util.ArrayList<Restriction<?>> restrictions) |
Modifier and Type | Method and Description |
---|---|
void |
NameSearch.addToResponseList(java.lang.String title,
java.lang.String name,
float score,
java.lang.String nameUuid,
java.util.Set<TaxonBase> taxonBases,
java.util.Set<TaxonBase> accTaxonBases) |
void |
NameSearch.addToResponseList(java.lang.String title,
java.lang.String name,
float score,
java.lang.String nameUuid,
java.util.Set<TaxonBase> taxonBases,
java.util.Set<TaxonBase> accTaxonBases) |
void |
NameInformation.addToResponseTaxonInfo(java.util.Set<TaxonBase> taxonBases) |
void |
NameInformation.setResponse(java.lang.String title,
java.lang.String name,
java.lang.String rank,
java.util.Set<NomenclaturalStatus> nomenclatureStatus,
java.lang.String citation,
java.util.Set<NameRelationship> relationsFromThisName,
java.util.Set<NameRelationship> relationsToThisName,
java.util.Set<TaxonBase> taxonBases) |
Modifier and Type | Method and Description |
---|---|
net.sf.json.JSONObject |
TaxonBaseBeanProcessor.processBeanSecondStep(TaxonBase bean,
net.sf.json.JSONObject json,
net.sf.json.JsonConfig jsonConfig) |
Modifier and Type | Interface and Description |
---|---|
interface |
ITaxonCacheStrategy<T extends TaxonBase>
A name cache rendering strategy for all TaxonName subclasses.
|
class |
TaxonBaseDefaultCacheStrategy<T extends TaxonBase> |
class |
TaxonBaseShortSecCacheStrategy<T extends TaxonBase> |
Modifier and Type | Method and Description |
---|---|
boolean |
TaxonNameCannotBeAcceptedAndSynonymValidator.isValid(TaxonBase<?> taxon,
javax.validation.ConstraintValidatorContext constraintContext) |
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