Modifier and Type | Method and Description |
---|---|
Taxon |
TaxonServiceImpl.findAcceptedTaxonFor(java.util.UUID synonymUuid,
java.util.UUID classificationUuid,
boolean includeUnpublished,
java.util.List<java.lang.String> propertyPaths) |
Taxon |
ITaxonService.findAcceptedTaxonFor(java.util.UUID synonymUuid,
java.util.UUID classificationUuid,
boolean includeUnpublished,
java.util.List<java.lang.String> propertyPaths) |
Taxon |
TaxonServiceImpl.findBestMatchingTaxon(MatchingTaxonConfigurator config) |
Taxon |
ITaxonService.findBestMatchingTaxon(MatchingTaxonConfigurator config) |
Taxon |
TaxonServiceImpl.findBestMatchingTaxon(java.lang.String taxonName) |
Taxon |
ITaxonService.findBestMatchingTaxon(java.lang.String taxonName) |
Modifier and Type | Method and Description |
---|---|
java.util.Set<Taxon> |
TaxonServiceImpl.listRelatedTaxa(Taxon taxon,
java.util.Set<TaxonRelationshipEdge> includeRelationships,
java.lang.Integer maxDepth,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<java.lang.String> propertyPaths) |
java.util.Set<Taxon> |
ITaxonService.listRelatedTaxa(Taxon taxon,
java.util.Set<TaxonRelationshipEdge> includeRelationships,
java.lang.Integer maxDepth,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<java.lang.String> propertyPaths)
lists all taxa which are related to the
taxon given as
parameter. |
Modifier and Type | Method and Description |
---|---|
void |
TaxonServiceImpl.changeHomotypicalGroupOfSynonym(Synonym synonym,
HomotypicalGroup newHomotypicalGroup,
Taxon targetTaxon,
boolean setBasionymRelationIfApplicable) |
void |
ITaxonService.changeHomotypicalGroupOfSynonym(Synonym synonym,
HomotypicalGroup newHomotypicalGroup,
Taxon targetTaxon,
boolean setBasionymRelationIfApplicable)
Changes the homotypic group of a synonym into the new homotypic group.
|
UpdateResult |
TaxonServiceImpl.changeRelatedTaxonToSynonym(Taxon fromTaxon,
Taxon toTaxon,
TaxonRelationshipType oldRelationshipType,
SynonymType synonymType) |
UpdateResult |
ITaxonService.changeRelatedTaxonToSynonym(Taxon fromTaxon,
Taxon toTaxon,
TaxonRelationshipType oldRelationshipType,
SynonymType synonymType)
Change a related concept into synonym
|
UpdateResult |
TaxonServiceImpl.changeSynonymToAcceptedTaxon(Synonym synonym,
Taxon acceptedTaxon,
boolean deleteSynonym) |
UpdateResult |
ITaxonService.changeSynonymToAcceptedTaxon(Synonym synonym,
Taxon acceptedTaxon,
boolean deleteSynonym)
Changes a synonym into an accepted taxon and removes
the synonym relationship to the given accepted taxon.
|
UpdateResult |
TaxonServiceImpl.changeSynonymToRelatedTaxon(Synonym synonym,
Taxon toTaxon,
TaxonRelationshipType taxonRelationshipType,
Reference citation,
java.lang.String microcitation) |
UpdateResult |
ITaxonService.changeSynonymToRelatedTaxon(Synonym synonym,
Taxon toTaxon,
TaxonRelationshipType taxonRelationshipType,
Reference reference,
java.lang.String microReference)
Change a synonym into a related concept
|
java.util.List<Synonym> |
TaxonServiceImpl.createAllInferredSynonyms(Taxon taxon,
Classification tree,
boolean doWithMisappliedNames) |
java.util.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
|
java.util.List<Synonym> |
TaxonServiceImpl.createInferredSynonyms(Taxon taxon,
Classification classification,
SynonymType type,
boolean doWithMisappliedNames) |
java.util.List<Synonym> |
ITaxonService.createInferredSynonyms(Taxon taxon,
Classification tree,
SynonymType type,
boolean doWithMisappliedNames)
Creates the specified inferred synonyms for the taxon in the classification, but do not insert it to the database
|
UpdateResult |
TaxonNodeServiceImpl.createNewTaxonNode(java.util.UUID parentNodeUuid,
Taxon newTaxon,
Reference ref,
java.lang.String microref) |
UpdateResult |
ITaxonNodeService.createNewTaxonNode(java.util.UUID parentNodeUuid,
Taxon newTaxon,
Reference ref,
java.lang.String microref) |
<T extends DescriptionElementBase> |
IDescriptionService.getDescriptionElementsForTaxon(Taxon taxon,
java.util.Set<Feature> features,
java.lang.Class<T> type,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Deprecated.
|
<T extends DescriptionElementBase> |
DescriptionServiceImpl.getDescriptionElementsForTaxon(Taxon taxon,
java.util.Set<Feature> features,
java.lang.Class<T> type,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Deprecated.
|
java.util.List<java.util.List<Synonym>> |
TaxonServiceImpl.getHeterotypicSynonymyGroups(Taxon taxon,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<java.util.List<Synonym>> |
ITaxonService.getHeterotypicSynonymyGroups(Taxon taxon,
java.util.List<java.lang.String> propertyPaths)
Returns the ordered list of all
homotypical groups
that contain synonyms that are heterotypic to the given taxon. |
java.util.List<Synonym> |
TaxonServiceImpl.getHomotypicSynonymsByHomotypicGroup(Taxon taxon,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<Synonym> |
ITaxonService.getHomotypicSynonymsByHomotypicGroup(Taxon taxon,
java.util.List<java.lang.String> propertyPaths)
Returns the list of all synonyms that share the same homotypical group with the given taxon.
|
Pager<Synonym> |
TaxonServiceImpl.getSynonyms(Taxon taxon,
SynonymType type,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Pager<Synonym> |
ITaxonService.getSynonyms(Taxon taxon,
SynonymType type,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Returns the Synonyms (with the given synonym relationship type, if this argument is supplied)
that do have the supplied taxon as accepted taxon.
|
java.util.List<java.util.List<Synonym>> |
TaxonServiceImpl.getSynonymsByHomotypicGroup(Taxon taxon,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<java.util.List<Synonym>> |
ITaxonService.getSynonymsByHomotypicGroup(Taxon taxon,
java.util.List<java.lang.String> propertyPaths)
This method returns in the first entry the list of synonyms of the
homotypic group of the accepted taxon.
|
<T extends SpecimenOrObservationBase> |
IOccurrenceService.listByAssociatedTaxon(java.lang.Class<T> type,
java.util.Set<TaxonRelationshipEdge> includeRelationships,
Taxon associatedTaxon,
java.lang.Integer maxDepth,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Lists all instances of
SpecimenOrObservationBase which are
associated with the taxon specified as parameter. |
<T extends SpecimenOrObservationBase> |
OccurrenceServiceImpl.listByAssociatedTaxon(java.lang.Class<T> type,
java.util.Set<TaxonRelationshipEdge> includeRelationships,
Taxon associatedTaxon,
java.lang.Integer maxDepth,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
<T extends DescriptionElementBase> |
IDescriptionService.listDescriptionElementsForTaxon(Taxon taxon,
java.util.Set<Feature> features,
java.lang.Class<T> type,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Provides access to all DescriptionElements associated with the given Taxon
via a TaxonDescrition.
|
<T extends DescriptionElementBase> |
DescriptionServiceImpl.listDescriptionElementsForTaxon(Taxon taxon,
java.util.Set<Feature> features,
java.lang.Class<T> type,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
java.util.Collection<SpecimenOrObservationBase> |
IOccurrenceService.listFieldUnitsByAssociatedTaxon(Taxon associatedTaxon,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Lists all instances of
FieldUnit which are
associated directly or indirectlywith the taxon specified
as parameter. |
java.util.Collection<SpecimenOrObservationBase> |
OccurrenceServiceImpl.listFieldUnitsByAssociatedTaxon(Taxon associatedTaxon,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonRelationship> |
TaxonServiceImpl.listFromTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonRelationship> |
ITaxonService.listFromTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
where the supplied taxon is relatedFrom.
|
java.util.List<Media> |
TaxonServiceImpl.listMedia(Taxon taxon,
java.util.Set<TaxonRelationshipEdge> includeRelationships,
java.lang.Boolean limitToGalleries,
java.lang.Boolean includeTaxonDescriptions,
java.lang.Boolean includeOccurrences,
java.lang.Boolean includeTaxonNameDescriptions,
java.util.List<java.lang.String> propertyPath) |
java.util.List<Media> |
ITaxonService.listMedia(Taxon taxon,
java.util.Set<TaxonRelationshipEdge> includeRelationships,
java.lang.Boolean limitToGalleries,
java.lang.Boolean includeTaxonDescriptions,
java.lang.Boolean includeOccurrences,
java.lang.Boolean includeTaxonNameDescriptions,
java.util.List<java.lang.String> propertyPath)
Lists all Media found in an any TaxonDescription, NameDescription,
SpecimenOrObservationBase, DnaSample Chromatograms, etc.
|
java.util.Set<Taxon> |
TaxonServiceImpl.listRelatedTaxa(Taxon taxon,
java.util.Set<TaxonRelationshipEdge> includeRelationships,
java.lang.Integer maxDepth,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<java.lang.String> propertyPaths) |
java.util.Set<Taxon> |
ITaxonService.listRelatedTaxa(Taxon taxon,
java.util.Set<TaxonRelationshipEdge> includeRelationships,
java.lang.Integer maxDepth,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<java.lang.String> propertyPaths)
lists all taxa which are related to the
taxon given as
parameter. |
java.util.List<Media> |
TaxonServiceImpl.listTaxonDescriptionMedia(Taxon taxon,
java.util.Set<TaxonRelationshipEdge> includeRelationships,
boolean limitToGalleries,
java.util.List<java.lang.String> propertyPath) |
java.util.List<Media> |
ITaxonService.listTaxonDescriptionMedia(Taxon taxon,
java.util.Set<TaxonRelationshipEdge> includeRelationships,
boolean limitToGalleries,
java.util.List<java.lang.String> propertyPath)
Deprecated.
use
#listMedia(Taxon, Set, boolean, boolean, List) instead |
java.util.List<TaxonDescription> |
IDescriptionService.listTaxonDescriptions(Taxon taxon,
java.util.Set<DefinedTerm> scopes,
java.util.Set<NamedArea> geographicalScope,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonDescription> |
DescriptionServiceImpl.listTaxonDescriptions(Taxon taxon,
java.util.Set<DefinedTerm> scopes,
java.util.Set<NamedArea> geographicalScope,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonDescription> |
IDescriptionService.listTaxonDescriptions(Taxon taxon,
java.util.Set<DefinedTerm> scopes,
java.util.Set<NamedArea> geographicalScope,
java.util.Set<MarkerType> markerTypes,
java.util.Set<DescriptionType> descriptionTypes,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonDescription> |
DescriptionServiceImpl.listTaxonDescriptions(Taxon taxon,
java.util.Set<DefinedTerm> scopes,
java.util.Set<NamedArea> geographicalScope,
java.util.Set<MarkerType> markerTypes,
java.util.Set<DescriptionType> descriptionTypes,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonRelationship> |
TaxonServiceImpl.listToTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonRelationship> |
ITaxonService.listToTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
where the supplied taxon is relatedTo.
|
TaxonNode |
IClassificationService.loadTaxonNodeByTaxon(Taxon taxon,
java.util.UUID classificationUuid,
java.util.List<java.lang.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
|
TaxonNode |
ClassificationServiceImpl.loadTaxonNodeByTaxon(Taxon taxon,
java.util.UUID classificationUuid,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonNode> |
IClassificationService.loadTreeBranchToTaxon(Taxon taxon,
Classification classification,
Rank baseRank,
boolean includeUnpublished,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonNode> |
ClassificationServiceImpl.loadTreeBranchToTaxon(Taxon taxon,
Classification classification,
Rank baseRank,
boolean includeUnpublished,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonNode> |
IClassificationService.loadTreeBranchToTaxon(Taxon taxon,
Classification classification,
TaxonNode subtree,
Rank baseRank,
boolean includeUnpublished,
java.util.List<java.lang.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. |
java.util.List<TaxonNode> |
ClassificationServiceImpl.loadTreeBranchToTaxon(Taxon taxon,
Classification classification,
TaxonNode subtree,
Rank baseRank,
boolean includeUnpublished,
java.util.List<java.lang.String> propertyPaths) |
UpdateResult |
TaxonServiceImpl.moveSynonymToAnotherTaxon(Synonym oldSynonym,
Taxon newTaxon,
boolean moveHomotypicGroup,
SynonymType newSynonymType) |
UpdateResult |
ITaxonService.moveSynonymToAnotherTaxon(Synonym oldSynonym,
Taxon newTaxon,
boolean moveHomotypicGroup,
SynonymType newSynonymType)
|
UpdateResult |
TaxonServiceImpl.moveSynonymToAnotherTaxon(Synonym oldSynonym,
Taxon newTaxon,
boolean moveHomotypicGroup,
SynonymType newSynonymType,
Reference newSecundum,
java.lang.String newSecundumDetail,
boolean keepSecundumIfUndefined) |
UpdateResult |
ITaxonService.moveSynonymToAnotherTaxon(Synonym oldSynonym,
Taxon newTaxon,
boolean moveHomotypicGroup,
SynonymType newSynonymType,
Reference newSecundum,
java.lang.String newSecundumDetail,
boolean keepSecundumIfUndefined)
Moves a synonym to another taxon and removes the old synonym relationship.
|
UpdateResult |
IDescriptionService.moveTaxonDescriptions(Taxon sourceTaxon,
Taxon targetTaxon,
boolean setNameInSource) |
UpdateResult |
DescriptionServiceImpl.moveTaxonDescriptions(Taxon sourceTaxon,
Taxon targetTaxon,
boolean setNameInSource) |
<T extends SpecimenOrObservationBase> |
IOccurrenceService.pageByAssociatedTaxon(java.lang.Class<T> type,
java.util.Set<TaxonRelationshipEdge> includeRelationships,
Taxon associatedTaxon,
java.lang.Integer maxDepth,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
|
<T extends SpecimenOrObservationBase> |
OccurrenceServiceImpl.pageByAssociatedTaxon(java.lang.Class<T> type,
java.util.Set<TaxonRelationshipEdge> includedRelationships,
Taxon associatedTaxon,
java.lang.Integer maxDepth,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
<T extends DescriptionElementBase> |
IDescriptionService.pageDescriptionElementsForTaxon(Taxon taxon,
java.util.Set<Feature> features,
java.lang.Class<T> type,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Provides access to all DescriptionElements associated with the given Taxon
via a TaxonDescrition.
|
<T extends DescriptionElementBase> |
DescriptionServiceImpl.pageDescriptionElementsForTaxon(Taxon taxon,
java.util.Set<Feature> features,
java.lang.Class<T> type,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
Pager<SpecimenOrObservationBase> |
IOccurrenceService.pageFieldUnitsByAssociatedTaxon(java.util.Set<TaxonRelationshipEdge> includeRelationships,
Taxon associatedTaxon,
java.lang.Integer maxDepth,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
See
#listFieldUnitsByAssociatedTaxon(Set, Taxon, Integer, Integer, Integer, List, List) |
Pager<SpecimenOrObservationBase> |
OccurrenceServiceImpl.pageFieldUnitsByAssociatedTaxon(java.util.Set<TaxonRelationshipEdge> includeRelationships,
Taxon associatedTaxon,
java.lang.Integer maxDepth,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Pager<TaxonRelationship> |
TaxonServiceImpl.pageFromTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Pager<TaxonRelationship> |
ITaxonService.pageFromTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
where the supplied taxon is relatedFrom.
|
Pager<TaxonDescription> |
IDescriptionService.pageTaxonDescriptions(Taxon taxon,
java.util.Set<DefinedTerm> scopes,
java.util.Set<NamedArea> geographicalScope,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a List of TaxonDescription instances, optionally filtered by parameters passed to this method
|
Pager<TaxonDescription> |
DescriptionServiceImpl.pageTaxonDescriptions(Taxon taxon,
java.util.Set<DefinedTerm> scopes,
java.util.Set<NamedArea> geographicalScope,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
Pager<TaxonDescription> |
IDescriptionService.pageTaxonDescriptions(Taxon taxon,
java.util.Set<DefinedTerm> scopes,
java.util.Set<NamedArea> geographicalScope,
java.util.Set<MarkerType> markerTypes,
java.util.Set<DescriptionType> descriptionTypes,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a List of TaxonDescription instances, optionally filtered by parameters passed to this method
|
Pager<TaxonDescription> |
DescriptionServiceImpl.pageTaxonDescriptions(Taxon taxon,
java.util.Set<DefinedTerm> scopes,
java.util.Set<NamedArea> geographicalScope,
java.util.Set<MarkerType> markerTypes,
java.util.Set<DescriptionType> descriptionTypes,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
Pager<TaxonRelationship> |
TaxonServiceImpl.pageToTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Pager<TaxonRelationship> |
ITaxonService.pageToTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Returns the TaxonRelationships (of where relationship.type == type, if this arguement is supplied)
where the supplied taxon is relatedTo.
|
UpdateResult |
TaxonServiceImpl.swapSynonymAndAcceptedTaxon(Synonym synonym,
Taxon acceptedTaxon,
boolean setNameInSource) |
UpdateResult |
ITaxonService.swapSynonymAndAcceptedTaxon(Synonym synonym,
Taxon acceptedTaxon,
boolean setNameInSource)
Swaps given synonym and accepted taxon.
|
Modifier and Type | Method and Description |
---|---|
Pager<MediaKey> |
MediaServiceImpl.getMediaKeys(java.util.Set<Taxon> taxonomicScope,
java.util.Set<NamedArea> geoScopes,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
Pager<MediaKey> |
IMediaService.getMediaKeys(java.util.Set<Taxon> taxonomicScope,
java.util.Set<NamedArea> geoScopes,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Return a List of MediaKeys, optionally filtered by the parameters passed.
|
Modifier and Type | Method and Description |
---|---|
protected abstract void |
DescriptionAggregationBase.aggregateWithinSingleTaxon(Taxon taxon,
DescriptionAggregationBase.ResultHolder resultHolder,
java.util.Set<TaxonDescription> excludedDescriptions) |
protected void |
DistributionAggregation.aggregateWithinSingleTaxon(Taxon taxon,
DescriptionAggregationBase.ResultHolder resultHolder,
java.util.Set<TaxonDescription> excludedDescriptions) |
protected void |
StructuredDescriptionAggregation.aggregateWithinSingleTaxon(Taxon taxon,
DescriptionAggregationBase.ResultHolder resultHolder,
java.util.Set<TaxonDescription> excludedDescriptions) |
protected abstract TaxonDescription |
DescriptionAggregationBase.createNewDescription(Taxon taxon) |
protected TaxonDescription |
DistributionAggregation.createNewDescription(Taxon taxon) |
protected TaxonDescription |
StructuredDescriptionAggregation.createNewDescription(Taxon taxon) |
protected abstract void |
DescriptionAggregationBase.setDescriptionTitle(TaxonDescription description,
Taxon taxon) |
protected void |
DistributionAggregation.setDescriptionTitle(TaxonDescription description,
Taxon taxon) |
protected void |
StructuredDescriptionAggregation.setDescriptionTitle(TaxonDescription description,
Taxon taxon) |
Modifier and Type | Method and Description |
---|---|
java.util.List<EntityDTO<Taxon>> |
TaxonInContextDTO.getChildren() |
java.util.List<MarkedEntityDTO<Taxon>> |
TaxonInContextDTO.getMarkedAncestors() |
Modifier and Type | Method and Description |
---|---|
void |
PreservedSpecimenDTO.addAssociatedTaxon(Taxon taxon) |
Modifier and Type | Method and Description |
---|---|
void |
TaxonInContextDTO.addChild(EntityDTO<Taxon> childDto) |
void |
TaxonInContextDTO.addMarkedAncestor(MarkedEntityDTO<Taxon> markedAncestor) |
void |
TaxonInContextDTO.setChildren(java.util.List<EntityDTO<Taxon>> children) |
void |
TaxonInContextDTO.setMarkedAncestors(java.util.List<MarkedEntityDTO<Taxon>> markedAncestors) |
Constructor and Description |
---|
TaxonDescriptionDTO(Taxon taxon) |
TaxonDistributionDTO(Taxon taxon) |
Modifier and Type | Method and Description |
---|---|
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
|
Modifier and Type | Method and Description |
---|---|
java.util.List<LogicFilter<Taxon>> |
TaxonNodeFilter.getTaxonFilter() |
Modifier and Type | Method and Description |
---|---|
static TaxonNodeFilter |
TaxonNodeFilter.NewTaxonInstance(Taxon taxon) |
TaxonNodeFilter |
TaxonNodeFilter.notTaxon(Taxon taxon) |
TaxonNodeFilter |
TaxonNodeFilter.orTaxon(Taxon taxon) |
Constructor and Description |
---|
TaxonNodeFilter(Taxon taxon) |
Modifier and Type | Method and Description |
---|---|
protected Taxon |
GroupByTaxonClassBridge.getAssociatedTaxon(java.lang.Object entity) |
Modifier and Type | Method and Description |
---|---|
protected Taxon |
Cdm2CdmImportBase.handlePersistedTaxon(Taxon taxon) |
Modifier and Type | Method and Description |
---|---|
protected Taxon |
Cdm2CdmImportBase.handlePersistedTaxon(Taxon taxon) |
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 |
---|---|
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.getDefaultTaxonDescription(Taxon taxon,
boolean isImageGallery,
boolean createNewIfNotExists,
Reference source)
Returns the default taxon description.
|
TaxonDescription |
CdmImportBase.getMarkedTaxonDescription(Taxon taxon,
MarkerType markerType,
boolean isImageGallery,
boolean createNewIfNotExists,
Reference source,
java.lang.String title)
Returns the taxon description with marked as
true with the given marker type. |
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. |
protected boolean |
CdmExportBase.isUnpublished(CONFIG config,
Taxon relatedSynonymOrMisappliedName)
true if neither pro parte synonym or misapplied name has state publish nor
taxon node filter includes unpublished taxa. |
Modifier and Type | Method and Description |
---|---|
protected Taxon |
DbImportDescriptionElementCreationMapperBase.getAcceptedTaxon(java.sql.ResultSet rs) |
Modifier and Type | Method and Description |
---|---|
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) |
Modifier and Type | Method and Description |
---|---|
Taxon |
TaxonExcelImportState.getParent() |
Modifier and Type | Method and Description |
---|---|
void |
TaxonExcelImportState.setParent(Taxon parent) |
Modifier and Type | Method and Description |
---|---|
Taxon |
MarkupImportState.getCurrentTaxon() |
Modifier and Type | Method and Description |
---|---|
protected void |
MarkupImportBase.fillMissingEpithetsForTaxa(Taxon parentTaxon,
Taxon childTaxon) |
void |
MarkupDocumentImport.fillMissingEpithetsForTaxa(Taxon parentTaxon,
Taxon childTaxon) |
protected TaxonDescription |
MarkupImportBase.getDefaultTaxonDescription(Taxon taxon,
boolean isImageGallery,
boolean createNewIfNotExists,
Reference source) |
protected TaxonDescription |
MarkupImportBase.getExtractedMarkupMarkedDescription(MarkupImportState state,
Taxon taxon,
Reference sourceReference) |
protected TaxonDescription |
MarkupImportBase.getMarkedTaxonDescription(Taxon taxon,
MarkerType markerType,
boolean isImageGallery,
boolean createNewIfNotExists,
Reference source,
java.lang.String title)
Returns the taxon description with marked as
true with the given marker type. |
protected TaxonDescription |
MarkupImportBase.getTaxonDescription(Taxon taxon,
Reference ref,
boolean isImageGallery,
boolean createNewIfNotExists) |
void |
MarkupImportState.setCurrentTaxon(Taxon currentTaxon) |
Modifier and Type | Method and Description |
---|---|
java.lang.String |
PilotOutputDocumentBuilder.writeTaxonDescriptionsToHTML(Taxon taxon,
java.lang.String texte)
Write the HTML part for one taxon.
|
Modifier and Type | Field and Description |
---|---|
protected java.util.List<Taxon> |
SDDDataSet.taxa |
Modifier and Type | Method and Description |
---|---|
void |
SDDDataSet.addTaxon(Taxon value) |
Modifier and Type | Method and Description |
---|---|
void |
SDDDataSet.addTaxa(java.util.Collection<Taxon> value) |
void |
SDDDataSet.setTaxa(java.util.List<Taxon> value) |
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.
|
protected Taxon |
SpecimenImportBase.getOrCreateTaxonForName(TaxonName taxonName,
STATE state) |
protected Taxon |
SpecimenImportBase.linkParentChildNode(Taxon parent,
Taxon child,
Classification classification,
STATE state)
Link a parent to a child and save it in the current classification
|
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 void |
SpecimenImportBase.addParentTaxon(Taxon taxon,
STATE state,
boolean preferredFlag,
Classification classification)
Add the hierarchy for a Taxon(add higher taxa)
|
protected void |
SpecimenImportBase.addTaxonNode(Taxon taxon,
STATE state,
boolean preferredFlag) |
protected void |
SpecimenImportBase.linkDeterminationEvent(STATE state,
Taxon taxon,
boolean preferredFlag,
DerivedUnitFacade derivedFacade,
java.lang.String identifierStr,
java.lang.String dateStr,
java.lang.String modifier)
join DeterminationEvent to the Taxon Object
|
protected Taxon |
SpecimenImportBase.linkParentChildNode(Taxon parent,
Taxon child,
Classification classification,
STATE state)
Link a parent to a child and save it in the current classification
|
protected void |
SpecimenImportBase.makeIndividualsAssociation(STATE state,
Taxon taxon,
DeterminationEvent determinationEvent)
create and link each association (specimen, observation..) to the accepted taxon
|
Modifier and Type | Method and Description |
---|---|
void |
SpecimenImportReport.addIndividualAssociation(Taxon taxon,
java.lang.String derivedUnitId,
DerivedUnit derivedUnitBase) |
void |
SpecimenImportReport.addTaxon(Taxon taxon) |
Modifier and Type | Method and Description |
---|---|
protected TaxonDescription |
PartitionableConverterBase.getTaxonDescription(Taxon taxon,
boolean isImageGallery) |
Modifier and Type | Method and Description |
---|---|
protected Taxon |
TaxonXExtractor.askParent(Taxon taxon,
Classification classification)
asks for the hierarchical parent, based on the current classification
|
Taxon |
TaxonXTreatmentExtractor.MyName.findOrCreateTaxon(java.lang.String partialname,
java.lang.String fullname,
Rank rank,
Rank globalrank) |
Taxon |
TaxonXTreatmentExtractor.MyName.getFamily() |
Taxon |
TaxonXTreatmentExtractor.MyName.getGenus() |
Taxon |
TaxonXTreatmentExtractor.MyName.getHigherTaxa() |
Taxon |
TaxonXTreatmentExtractor.MyName.getSpecies() |
Taxon |
TaxonXTreatmentExtractor.MyName.getSubfamily() |
Taxon |
TaxonXTreatmentExtractor.MyName.getSubgenus() |
Taxon |
TaxonXTreatmentExtractor.MyName.getSubspecies() |
Taxon |
TaxonXTreatmentExtractor.MyName.getSubtribe() |
Taxon |
TaxonXTreatmentExtractor.MyName.getTaxon() |
Taxon |
TaxonXTreatmentExtractor.MyName.getTribe() |
Modifier and Type | Method and Description |
---|---|
protected void |
TaxonXAddSources.addSource(Reference refMods,
Taxon acceptedTaxon) |
protected boolean |
TaxonXExtractor.askIfReuseBestMatchingTaxon(INonViralName taxonname2,
Taxon bestMatchingTaxon,
Reference refMods,
double similarityScore,
double similarityAuthor) |
protected Taxon |
TaxonXExtractor.askParent(Taxon taxon,
Classification classification)
asks for the hierarchical parent, based on the current classification
|
void |
TaxonXExtractor.ReferenceBuilder.builReference(java.lang.String mref,
java.lang.String treatmentMainName,
NomenclaturalCode nomenclaturalCode,
Taxon acceptedTaxon,
Reference refMods) |
void |
TaxonXTreatmentExtractor.lookForParentNode(INonViralName taxonName,
Taxon tax,
Reference ref,
TaxonXTreatmentExtractor.MyName myName) |
void |
TaxonXTreatmentExtractor.MyName.setFamily(Taxon family) |
void |
TaxonXTreatmentExtractor.MyName.setForm(Taxon form) |
void |
TaxonXTreatmentExtractor.MyName.setGenus(Taxon genus) |
void |
TaxonXTreatmentExtractor.MyName.setHigherTaxa(Taxon higherTaxa) |
void |
TaxonXTreatmentExtractor.MyName.setSpecies(Taxon species) |
void |
TaxonXTreatmentExtractor.MyName.setSubfamily(Taxon subfamily) |
void |
TaxonXTreatmentExtractor.MyName.setSubgenus(Taxon subgenus) |
void |
TaxonXTreatmentExtractor.MyName.setSubspecies(Taxon subspecies) |
void |
TaxonXTreatmentExtractor.MyName.setSubtribe(Taxon subtribe) |
void |
TaxonXTreatmentExtractor.MyName.setTribe(Taxon tribe) |
void |
TaxonXTreatmentExtractor.MyName.setVariety(Taxon variety) |
Modifier and Type | Method and Description |
---|---|
Taxon |
TaxonDescription.getTaxon() |
Taxon |
PolytomousKeyNode.getTaxon()
Returns the taxon this node links to.
|
Taxon |
TaxonInteraction.getTaxon2()
Returns the second
taxon involved in this taxon interaction. |
Taxon |
PolytomousKeyNode.removeTaxon() |
Modifier and Type | Method and Description |
---|---|
java.util.Set<Taxon> |
MediaKey.getCoveredTaxa()
Returns the set of possible
taxa corresponding to
this identification key. |
java.util.Set<Taxon> |
MultiAccessKey.getCoveredTaxa()
Returns the set of possible
taxa corresponding to
this identification key. |
java.util.Set<Taxon> |
IIdentificationKey.getCoveredTaxa()
Covered taxa are the tips of the key.
|
java.util.Set<Taxon> |
PolytomousKey.getCoveredTaxa()
Returns the set of possible
taxa corresponding to
this identification key. |
java.util.Set<Taxon> |
MediaKey.getTaxonomicScope()
Returns the set of
taxa that define the taxonomic
scope of this identification key |
java.util.Set<Taxon> |
MultiAccessKey.getTaxonomicScope()
Returns the set of
taxa that define the taxonomic
scope of this identification key |
java.util.Set<Taxon> |
IIdentificationKey.getTaxonomicScope()
Taxonomic Scope is the taxon which you want the key to be attached to e.g.
|
java.util.Set<Taxon> |
PolytomousKey.getTaxonomicScope()
Returns the set of
taxa that define the taxonomic scope of
this identification key |
Modifier and Type | Method and Description |
---|---|
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.addCoveredTaxon(Taxon taxon) |
void |
PolytomousKey.addCoveredTaxon(Taxon taxon)
Adds a
taxa to the set of covered
taxa 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. |
void |
IIdentificationKey.addTaxonomicScope(Taxon taxon) |
void |
PolytomousKey.addTaxonomicScope(Taxon taxon)
Adds a
taxa to the set of taxonomic scopes corresponding to this identification key. |
static PolytomousKeyNode |
PolytomousKeyNode.NewInstance(java.lang.String statement,
java.lang.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 |
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.removeCoveredTaxon(Taxon taxon) |
void |
PolytomousKey.removeCoveredTaxon(Taxon taxon)
Removes one element from the set of
covered
taxa 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 |
IIdentificationKey.removeTaxonomicScope(Taxon taxon) |
void |
PolytomousKey.removeTaxonomicScope(Taxon taxon)
Removes one element from the set of
taxonomic
scopes corresponding to this identification key. |
PolytomousKeyNode |
PolytomousKeyNode.setOrAddTaxon(Taxon taxon)
Sets the taxon of this
PolytomousKeyNode . |
protected void |
TaxonDescription.setTaxon(Taxon taxon) |
void |
PolytomousKeyNode.setTaxon(Taxon taxon)
Sets the taxon this node links to.
|
void |
TaxonInteraction.setTaxon2(Taxon taxon2) |
Modifier and Type | Method and Description |
---|---|
protected void |
MediaKey.setCoveredTaxa(java.util.Set<Taxon> coveredTaxa) |
protected void |
MultiAccessKey.setCoveredTaxa(java.util.Set<Taxon> coveredTaxa) |
protected void |
PolytomousKey.setCoveredTaxa(java.util.Set<Taxon> coveredTaxa) |
Modifier and Type | Method and Description |
---|---|
java.util.Set<Taxon> |
TaxonName.getTaxa()
Returns the set of
taxa ("accepted/correct" names according to any
reference) that are based on this taxon name. |
java.util.Set<Taxon> |
ITaxonNameBase.getTaxa()
Returns the set of
taxa ("accepted/correct" names according to any
reference) that are based on this taxon name. |
Modifier and Type | Method and Description |
---|---|
static DeterminationEvent |
DeterminationEvent.NewInstance(Taxon taxon,
SpecimenOrObservationBase identifiedUnit)
Factory method
|
Modifier and Type | Method and Description |
---|---|
Taxon |
Synonym.getAcceptedTaxon()
Returns the "accepted/valid"
taxon |
Taxon |
TaxonRelationship.getFromTaxon()
Returns the
taxon involved as a source in this
taxon relationship. |
protected Taxon |
TaxonRelationship.getRelatedFrom() |
protected Taxon |
TaxonRelationship.getRelatedTo() |
Taxon |
TaxonNode.getTaxon() |
Taxon |
TaxonRelationship.getToTaxon()
Returns the
taxon involved as a target in this
taxon relationship. |
static Taxon |
Taxon.NewInstance(ITaxonNameBase taxonName,
Reference sec) |
static Taxon |
Taxon.NewInstance(TaxonName taxonName,
Reference sec)
Creates a new (accepted/valid) taxon instance with
the
taxon name used and the reference
using it. |
static Taxon |
Taxon.NewInstance(TaxonName taxonName,
Reference sec,
java.lang.String secMicroReference)
Creates a new Taxon for the given name, secundum reference and secundum detail
|
static Taxon |
Taxon.NewUnknownStatusInstance(TaxonName taxonName,
Reference sec)
Creates a new taxon instance with an unknown status (accepted/synonym) and with
the
taxon name used and the reference
using it. |
Modifier and Type | Method and Description |
---|---|
java.util.List<Taxon> |
Taxon.getAllMisappliedNames() |
java.util.List<Taxon> |
Taxon.getAllProParteSynonyms() |
java.util.List<Taxon> |
TaxonNode.getAncestorTaxaList()
Returns the ancestor taxa, starting with the highest (e.g.
|
java.util.List<Taxon> |
Taxon.getInvalidDesignations() |
java.util.Set<Taxon> |
Taxon.getMisappliedNames(boolean includeNonCongruent)
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. |
java.util.Set<Taxon> |
Taxon.getProParteAndPartialSynonyms()
Returns the set of pro parte or partial synonyms in which this taxon
plays the role of the "correctly" accepted taxon (target).
|
java.util.Set<Taxon> |
Taxon.getTaxaForMisappliedName(boolean includeNonCongruent)
Returns the set of taxa playing the target role in
taxon relationships
(with taxon relationship type "misapplied name for"
or "pro parte misapplied name for") where
this taxon plays the source role. |
Modifier and Type | Method and Description |
---|---|
TaxonNode |
Classification.addChildTaxon(Taxon taxon,
int index,
Reference citation,
java.lang.String microCitation) |
TaxonNode |
ITaxonTreeNode.addChildTaxon(Taxon taxon,
int index,
Reference citation,
java.lang.String microCitation)
Adds a taxon as a child of the ITreeNode at the index position.
|
TaxonNode |
TaxonNode.addChildTaxon(Taxon taxon,
int index,
Reference citation,
java.lang.String microCitation) |
TaxonNode |
Classification.addChildTaxon(Taxon taxon,
Reference citation,
java.lang.String microCitation) |
TaxonNode |
ITaxonTreeNode.addChildTaxon(Taxon taxon,
Reference citation,
java.lang.String microCitation)
Adds a taxon as a child of the ITreeNode at the last position.
|
TaxonNode |
TaxonNode.addChildTaxon(Taxon taxon,
Reference citation,
java.lang.String microCitation) |
TaxonRelationship |
Taxon.addMisappliedName(Taxon misappliedNameTaxon,
Reference citation,
java.lang.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,
java.lang.String microCitation)
Relates two taxa as parent-child nodes within a classification.
|
TaxonRelationship |
Taxon.addPartialMisappliedName(Taxon partialMisappliedNameTaxon,
Reference citation,
java.lang.String microcitation)
Creates a new
taxon relationship (with taxon relationship type
"partial misapplied name for") instance where this taxon plays the target role
and adds it to the set of taxon relationships to this taxon . |
TaxonRelationship |
Taxon.addPartialSynonym(Taxon partialTaxon,
Reference citation,
java.lang.String microcitation)
Creates a new
taxon relationship instance with
taxon relationship type partial synonym for where this taxon plays the target role
and adds it to the set of taxon relationships to this taxon . |
TaxonRelationship |
Taxon.addProParteMisappliedName(Taxon proParteMisappliedNameTaxon,
Reference citation,
java.lang.String microcitation)
Creates a new
taxon relationship (with taxon relationship type
"pro parte misapplied name for") instance where this taxon plays the target role
and adds it to the set of taxon relationships to this taxon . |
TaxonRelationship |
Taxon.addProparteSynonym(Taxon proParteTaxon,
Reference citation,
java.lang.String microcitation)
Creates a new
taxon relationship (with taxon relationship type
"pro parte synonym for") instance where this taxon plays the target role
and adds it to the set of taxon relationships to this taxon . |
TaxonRelationship |
Taxon.addTaxonRelation(Taxon toTaxon,
TaxonRelationshipType type,
Reference citation,
java.lang.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.
|
java.util.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 the root 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. |
protected void |
Synonym.setAcceptedTaxon(Taxon acceptedTaxon) |
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) |
void |
TaxonNode.setTaxon(Taxon taxon) |
void |
TaxonRelationship.setToTaxon(Taxon toTaxon)
Sets the given
taxon as a target in this taxon relationship. |
Constructor and Description |
---|
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,
java.lang.String citationMicroReference)
Class constructor: creates a new taxon relationship instance (with the
given "accepted/valid"
taxa , the given taxon relationship type
and with the reference source on which the relationship
assertion is based). |
Modifier and Type | Method and Description |
---|---|
long |
IDescriptionDao.countTaxonDescriptions(Taxon taxon,
java.util.Set<DefinedTerm> scopes,
java.util.Set<NamedArea> geographicalScope,
java.util.Set<MarkerType> markerType,
java.util.Set<DescriptionType> descriptionTypes)
Returns a count of TaxonDescription instances, optionally filtered by parameters passed to this method
|
java.util.List<TaxonDescription> |
IDescriptionDao.listTaxonDescriptions(Taxon taxon,
java.util.Set<DefinedTerm> scopes,
java.util.Set<NamedArea> geographicalScope,
java.util.Set<MarkerType> markerTypes,
java.util.Set<DescriptionType> descriptionTypes,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a List of TaxonDescription instances, optionally filtered by parameters passed to this method
|
Modifier and Type | Method and Description |
---|---|
long |
DescriptionDaoImpl.countTaxonDescriptions(Taxon taxon,
java.util.Set<DefinedTerm> scopes,
java.util.Set<NamedArea> geographicalScopes,
java.util.Set<MarkerType> markerTypes,
java.util.Set<DescriptionType> descriptionTypes) |
java.util.List<TaxonDescription> |
DescriptionDaoImpl.listTaxonDescriptions(Taxon taxon,
java.util.Set<DefinedTerm> scopes,
java.util.Set<NamedArea> geographicalScopes,
java.util.Set<MarkerType> markerTypes,
java.util.Set<DescriptionType> descriptionTypes,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
Modifier and Type | Method and Description |
---|---|
long |
MediaDaoHibernateImpl.countMediaKeys(java.util.Set<Taxon> taxonomicScope,
java.util.Set<NamedArea> geoScopes) |
java.util.List<MediaKey> |
MediaDaoHibernateImpl.getMediaKeys(java.util.Set<Taxon> taxonomicScope,
java.util.Set<NamedArea> geoScopes,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
Modifier and Type | Method and Description |
---|---|
<T extends SpecimenOrObservationBase> |
OccurrenceDaoHibernateImpl.countOccurrences(java.lang.Class<T> clazz,
java.lang.String queryString,
java.lang.String significantIdentifier,
SpecimenOrObservationType recordBasis,
Taxon associatedTaxon,
TaxonName associatedTaxonName,
MatchMode matchmode,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
<T extends SpecimenOrObservationBase> |
OccurrenceDaoHibernateImpl.findOccurrences(java.lang.Class<T> clazz,
java.lang.String queryString,
java.lang.String significantIdentifier,
SpecimenOrObservationType recordBasis,
Taxon associatedTaxon,
TaxonName associatedTaxonName,
MatchMode matchmode,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
<T extends SpecimenOrObservationBase> |
OccurrenceDaoHibernateImpl.findOccurrencesUuidAndTitleCache(java.lang.Class<T> clazz,
java.lang.String queryString,
java.lang.String significantIdentifier,
SpecimenOrObservationType recordBasis,
Taxon associatedTaxon,
TaxonName associatedTaxonName,
MatchMode matchmode,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints) |
<T extends SpecimenOrObservationBase> |
OccurrenceDaoHibernateImpl.listByAssociatedTaxon(java.lang.Class<T> clazz,
Taxon associatedTaxon,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
<T extends SpecimenOrObservationBase> |
OccurrenceDaoHibernateImpl.listUuidAndTitleCacheByAssociatedTaxon(java.lang.Class<T> clazz,
Taxon associatedTaxon,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints) |
Modifier and Type | Method and Description |
---|---|
Taxon |
TaxonDaoHibernateImpl.acceptedTaxonFor(Synonym synonym,
Classification classificationFilter,
java.util.List<java.lang.String> propertyPaths) |
Modifier and Type | Method and Description |
---|---|
java.util.List<Taxon> |
TaxonDaoHibernateImpl.getTaxaByCommonName(java.lang.String queryString,
Classification classification,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<UuidAndTitleCache<Taxon>> |
TaxonDaoHibernateImpl.getTaxaByCommonNameForEditor(java.lang.String titleSearchStringSqlized,
Classification classification,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas) |
Modifier and Type | Method and Description |
---|---|
java.lang.Long |
ClassificationDaoHibernateImpl.countChildrenOf(Taxon taxon,
Classification classification,
TaxonNode subtree,
boolean includeUnpublished) |
java.lang.Long |
ClassificationDaoHibernateImpl.countSiblingsOf(Taxon taxon,
Classification classification,
boolean includeUnpublished) |
long |
TaxonDaoHibernateImpl.countSynonyms(Taxon taxon,
SynonymType type) |
long |
TaxonDaoHibernateImpl.countTaxonRelationships(Taxon taxon,
java.util.Set<TaxonRelationshipType> types,
boolean includeUnpublished,
RelationshipBase.Direction direction) |
long |
TaxonDaoHibernateImpl.countTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
boolean includeUnpublished,
RelationshipBase.Direction direction) |
java.util.List<Synonym> |
TaxonDaoHibernateImpl.getSynonyms(Taxon taxon,
SynonymType type,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonRelationship> |
TaxonDaoHibernateImpl.getTaxonRelationships(Taxon taxon,
java.util.Set<TaxonRelationshipType> types,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths,
RelationshipBase.Direction direction) |
java.util.List<TaxonRelationship> |
TaxonDaoHibernateImpl.getTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths,
RelationshipBase.Direction direction) |
java.util.List<TaxonNode> |
ClassificationDaoHibernateImpl.listChildrenOf(Taxon taxon,
Classification classification,
TaxonNode subtree,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonNode> |
ClassificationDaoHibernateImpl.listSiblingsOf(Taxon taxon,
Classification classification,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths) |
Modifier and Type | Method and Description |
---|---|
Taxon |
AbstractHibernateTaxonGraphProcessor.assureSingleTaxon(TaxonName taxonName) |
Taxon |
AbstractHibernateTaxonGraphProcessor.assureSingleTaxon(TaxonName taxonName,
boolean createMissing) |
Modifier and Type | Method and Description |
---|---|
protected java.util.List<TaxonRelationship> |
AbstractHibernateTaxonGraphProcessor.getTaxonRelationships(Taxon relatedTaxon,
TaxonRelationshipType type,
Reference citation,
RelationshipBase.Direction direction) |
void |
AbstractHibernateTaxonGraphProcessor.removeEdges(Taxon taxon,
Reference conceptReference)
Remove all edges from the
taxon having the conceptReference |
protected java.util.List<TaxonRelationship> |
AbstractHibernateTaxonGraphProcessor.taxonGraphRelationsFrom(Taxon taxon,
Reference citation) |
protected java.util.List<TaxonRelationship> |
AbstractHibernateTaxonGraphProcessor.taxonGraphRelationsTo(Taxon taxon,
Reference citation) |
void |
AbstractHibernateTaxonGraphProcessor.updateConceptReferenceInEdges(Taxon taxon,
Reference oldNomReference) |
void |
AbstractHibernateTaxonGraphProcessor.updateEdges(Taxon taxon)
Create all missing edges from the
taxon . |
protected void |
AbstractHibernateTaxonGraphProcessor.updateReferenceInEdges(Taxon taxon,
Reference conceptReference,
Reference oldConceptReference) |
Modifier and Type | Method and Description |
---|---|
long |
IMediaDao.countMediaKeys(java.util.Set<Taxon> taxonomicScope,
java.util.Set<NamedArea> geoScopes)
Return a count of MediaKeys, optionally filtered by the parameters passed.
|
java.util.List<MediaKey> |
IMediaDao.getMediaKeys(java.util.Set<Taxon> taxonomicScope,
java.util.Set<NamedArea> geoScopes,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Return a List of MediaKeys, optionally filtered by the parameters passed.
|
Modifier and Type | Method and Description |
---|---|
<T extends SpecimenOrObservationBase> |
IOccurrenceDao.countOccurrences(java.lang.Class<T> clazz,
java.lang.String queryString,
java.lang.String significantIdentifier,
SpecimenOrObservationType recordBasis,
Taxon associatedTaxon,
TaxonName associatedTaxonName,
MatchMode matchmode,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Returns the number of specimens that match the given parameters
Note: Specifying a taxon will already check the name of this
taxon, its synonymy and the synonym names for determinations of the
specimen.
|
<T extends SpecimenOrObservationBase> |
IOccurrenceDao.findOccurrences(java.lang.Class<T> clazz,
java.lang.String queryString,
java.lang.String significantIdentifier,
SpecimenOrObservationType type,
Taxon determinedAs,
TaxonName associatedTaxonName,
MatchMode matchmode,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Queries the database for specimens which match the given criteria
Note: Specifying a taxon will already check the name of this taxon, its synonymy and the synonym names for determinations of the specimen. |
<T extends SpecimenOrObservationBase> |
IOccurrenceDao.findOccurrencesUuidAndTitleCache(java.lang.Class<T> clazz,
java.lang.String queryString,
java.lang.String significantIdentifier,
SpecimenOrObservationType type,
Taxon determinedAs,
TaxonName associatedTaxonName,
MatchMode matchmode,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints) |
<T extends SpecimenOrObservationBase> |
IOccurrenceDao.listByAssociatedTaxon(java.lang.Class<T> type,
Taxon associatedTaxon,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Lists all instances of
SpecimenOrObservationBase which are associated with the taxon specified as parameter. |
<T extends SpecimenOrObservationBase> |
IOccurrenceDao.listUuidAndTitleCacheByAssociatedTaxon(java.lang.Class<T> type,
Taxon associatedTaxon,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints) |
Modifier and Type | Method and Description |
---|---|
Taxon |
ITaxonDao.acceptedTaxonFor(Synonym synonym,
Classification classificationFilter,
java.util.List<java.lang.String> propertyPaths)
This method was originally required when synonyms still had a synonym relationship
to taxa and could belong to multiple taxa.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<Taxon> |
ITaxonDao.getTaxaByCommonName(java.lang.String queryString,
Classification classification,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<UuidAndTitleCache<Taxon>> |
ITaxonDao.getTaxaByCommonNameForEditor(java.lang.String titleSearchStringSqlized,
Classification classification,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas) |
Modifier and Type | Method and Description |
---|---|
java.lang.Long |
IClassificationDao.countChildrenOf(Taxon taxon,
Classification classification,
TaxonNode subtree,
boolean includeUnpublished) |
java.lang.Long |
IClassificationDao.countSiblingsOf(Taxon taxon,
Classification classification,
boolean includeUnpublished) |
long |
ITaxonDao.countSynonyms(Taxon taxon,
SynonymType type)
Returns a count of the Synonyms (where relationship.type == type,
if this argument is supplied) where the supplied taxon is relatedTo.
|
long |
ITaxonDao.countTaxonRelationships(Taxon taxon,
java.util.Set<TaxonRelationshipType> types,
boolean includeUnpublished,
RelationshipBase.Direction direction) |
long |
ITaxonDao.countTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
boolean includeUnpublished,
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. |
java.util.List<Synonym> |
ITaxonDao.getSynonyms(Taxon taxon,
SynonymType type,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Returns the Synonyms (of where relationship.type == type, if this argument is supplied)
that do have the supplied taxon as accepted taxon.
|
java.util.List<TaxonRelationship> |
ITaxonDao.getTaxonRelationships(Taxon taxon,
java.util.Set<TaxonRelationshipType> type,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths,
RelationshipBase.Direction direction) |
java.util.List<TaxonRelationship> |
ITaxonDao.getTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.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. |
java.util.List<TaxonNode> |
IClassificationDao.listChildrenOf(Taxon taxon,
Classification classification,
TaxonNode subtree,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonNode> |
IClassificationDao.listSiblingsOf(Taxon taxon,
Classification classification,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths) |
Modifier and Type | Method and Description |
---|---|
Taxon |
ITaxonGraphDao.assureSingleTaxon(TaxonName taxonName) |
Taxon |
ITaxonGraphDao.assureSingleTaxon(TaxonName taxonName,
boolean createMissing) |
Modifier and Type | Method and Description |
---|---|
Taxon |
TaxonController.doGetAcceptedFor(java.util.UUID uuid,
java.util.UUID classification_uuid,
javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response)
|
Modifier and Type | Method and Description |
---|---|
TaxonPortalController.EntityMediaContext<Taxon> |
TaxonPortalController.loadMediaForTaxonAndRelated(java.util.UUID uuid,
UuidList relationshipUuids,
UuidList relationshipInversUuids,
java.lang.Boolean includeTaxonDescriptions,
java.lang.Boolean includeOccurrences,
java.lang.Boolean includeTaxonNameDescriptions,
javax.servlet.http.HttpServletResponse response,
java.util.List<java.lang.String> taxonInitStrategy)
Deprecated.
|
TaxonPortalController.EntityMediaContext<Taxon> |
TaxonPortalController.loadMediaForTaxonAndRelated(java.util.UUID uuid,
UuidList relationshipUuids,
UuidList relationshipInversUuids,
java.lang.Boolean includeTaxonDescriptions,
java.lang.Boolean includeOccurrences,
java.lang.Boolean includeTaxonNameDescriptions,
javax.servlet.http.HttpServletResponse response,
java.util.List<java.lang.String> taxonInitStrategy,
java.util.List<java.lang.String> mediaInitStrategy) |
Modifier and Type | Method and Description |
---|---|
java.util.List<Media> |
TaxonPortalController.addTaxonomicChildrenMedia(java.lang.Boolean includeTaxonDescriptions,
java.lang.Boolean includeOccurrences,
java.lang.Boolean includeTaxonNameDescriptions,
Taxon taxon,
java.util.Set<TaxonRelationshipEdge> includeRelationships,
java.util.List<Media> media) |
Modifier and Type | Method and Description |
---|---|
void |
BasionymRelationCreator.invoke(Taxon taxon) |
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