Modifier and Type | Method and Description |
---|---|
IdentifiableSource |
DerivedUnitFacade.addSource(OriginalSourceType type,
Reference reference,
java.lang.String microReference,
java.lang.String originalNameString)
Creates an
orignal source or type ,
adds it to the specimen and returns it. |
Modifier and Type | Method and Description |
---|---|
java.util.List<Reference> |
ReferenceServiceImpl.findByTitleAndAbbrevTitle(IIdentifiableEntityServiceConfigurator<Reference> config) |
java.util.List<Reference> |
IReferenceService.findByTitleAndAbbrevTitle(IIdentifiableEntityServiceConfigurator<Reference> config) |
java.util.List<UuidAndTitleCache<Reference>> |
ReferenceServiceImpl.getUuidAndAbbrevTitleCache(java.lang.Integer limit,
java.lang.String pattern) |
java.util.List<UuidAndTitleCache<Reference>> |
IReferenceService.getUuidAndAbbrevTitleCache(java.lang.Integer limit,
java.lang.String pattern) |
java.util.List<UuidAndTitleCache<Reference>> |
ReferenceServiceImpl.getUuidAndAbbrevTitleCache(java.lang.Integer limit,
java.lang.String pattern,
ReferenceType type) |
java.util.List<UuidAndTitleCache<Reference>> |
IReferenceService.getUuidAndAbbrevTitleCache(java.lang.Integer limit,
java.lang.String pattern,
ReferenceType type) |
java.util.List<UuidAndTitleCache<Reference>> |
ReferenceServiceImpl.getUuidAndAbbrevTitleCacheForAuthor(java.lang.Integer limit,
java.lang.String pattern,
ReferenceType type) |
java.util.List<UuidAndTitleCache<Reference>> |
IReferenceService.getUuidAndAbbrevTitleCacheForAuthor(java.lang.Integer limit,
java.lang.String pattern,
ReferenceType type) |
java.util.List<UuidAndTitleCache<Reference>> |
ReferenceServiceImpl.getUuidAndTitle() |
java.util.List<UuidAndTitleCache<Reference>> |
IReferenceService.getUuidAndTitle()
Returns a map that holds uuid, titleCache pairs of all references in the current database
|
java.util.List<UuidAndTitleCache<Reference>> |
ReferenceServiceImpl.getUuidAndTitleCache(java.lang.Integer limit,
java.lang.String pattern,
ReferenceType type) |
java.util.List<UuidAndTitleCache<Reference>> |
IReferenceService.getUuidAndTitleCache(java.lang.Integer limit,
java.lang.String pattern,
ReferenceType type) |
java.util.List<UuidAndTitleCache<Reference>> |
ReferenceServiceImpl.getUuidAndTitleCacheForUUIDS(java.util.Set<java.util.UUID> uuids) |
java.util.List<UuidAndTitleCache<Reference>> |
IReferenceService.getUuidAndTitleCacheForUUIDS(java.util.Set<java.util.UUID> uuids) |
java.util.List<UuidAndTitleCache<Reference>> |
ReferenceServiceImpl.getUuidAndTitleCacheForUUIDS(java.util.Set<java.util.UUID> uuids,
ReferenceType refType) |
java.util.List<UuidAndTitleCache<Reference>> |
IReferenceService.getUuidAndTitleCacheForUUIDS(java.util.Set<java.util.UUID> uuids,
ReferenceType refType) |
java.util.List<IdentifiedEntityDTO<Reference>> |
ReferenceServiceImpl.listByIdentifierAbbrev(java.lang.String identifier,
DefinedTerm identifierType,
MatchMode matchmode,
java.lang.Integer limit) |
java.util.List<IdentifiedEntityDTO<Reference>> |
IReferenceService.listByIdentifierAbbrev(java.lang.String identifier,
DefinedTerm identifierType,
MatchMode matchmode,
java.lang.Integer limit) |
java.util.List<IdentifiedEntityDTO<Reference>> |
ReferenceServiceImpl.listByIdentifierAndTitleCacheAbbrev(java.lang.String identifier,
DefinedTerm identifierType,
MatchMode matchmode,
java.lang.Integer limit) |
java.util.List<IdentifiedEntityDTO<Reference>> |
IReferenceService.listByIdentifierAndTitleCacheAbbrev(java.lang.String identifier,
DefinedTerm identifierType,
MatchMode matchmode,
java.lang.Integer limit) |
java.util.List<Reference> |
ReferenceServiceImpl.listNomenclaturalReferences() |
java.util.List<Reference> |
IReferenceService.listNomenclaturalReferences()
Lists all references used as nomenclatural references in at least 1
TaxonName |
java.util.List<Reference> |
ReferenceServiceImpl.listReferencesForPublishing() |
java.util.List<Reference> |
IReferenceService.listReferencesForPublishing()
lists all references marked as "publish" and not used as nomenclatural references
|
Pager<Reference> |
IReferenceService.search(java.lang.Class<? extends Reference> 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 Reference instances where the default field matches the String queryString (as interpreted by the Lucene QueryParser)
|
Modifier and Type | Method and Description |
---|---|
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
|
UpdateResult |
TaxonServiceImpl.changeSynonymToRelatedTaxon(java.util.UUID synonymUuid,
java.util.UUID toTaxonUuid,
TaxonRelationshipType taxonRelationshipType,
Reference citation,
java.lang.String microcitation) |
UpdateResult |
ITaxonService.changeSynonymToRelatedTaxon(java.util.UUID synonymUuid,
java.util.UUID toTaxonUuid,
TaxonRelationshipType taxonRelationshipType,
Reference citation,
java.lang.String microcitation) |
UpdateResult |
IClassificationService.cloneClassification(java.util.UUID classificationUuid,
java.lang.String name,
Reference sec,
TaxonRelationshipType relationshipType)
Clones an existing classification including all taxa and taxon nodes.
|
UpdateResult |
ClassificationServiceImpl.cloneClassification(java.util.UUID classificationUuid,
java.lang.String name,
Reference sec,
TaxonRelationshipType relationshipType) |
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) |
UpdateResult |
TaxonNodeServiceImpl.createNewTaxonNode(java.util.UUID parentNodeUuid,
java.util.UUID taxonUuid,
Reference ref,
java.lang.String microref) |
UpdateResult |
ITaxonNodeService.createNewTaxonNode(java.util.UUID parentNodeUuid,
java.util.UUID taxonUuid,
Reference ref,
java.lang.String microref) |
DeleteResult |
ReferenceServiceImpl.delete(Reference reference) |
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
|
DeleteResult |
TaxonNodeServiceImpl.makeTaxonNodeASynonymOfAnotherTaxonNode(TaxonNode oldTaxonNode,
TaxonNode newAcceptedTaxonNode,
SynonymType synonymType,
Reference citation,
java.lang.String citationMicroReference,
boolean setNameInSource) |
DeleteResult |
ITaxonNodeService.makeTaxonNodeASynonymOfAnotherTaxonNode(TaxonNode oldTaxonNode,
TaxonNode newAcceptedTaxonNode,
SynonymType synonymType,
Reference citation,
java.lang.String citationMicroReference,
boolean setNameInSource)
Changes the taxon associated with the given taxon node into a synonym of the new accepted taxon node.
|
UpdateResult |
TaxonNodeServiceImpl.makeTaxonNodeASynonymOfAnotherTaxonNode(java.util.UUID oldTaxonNodeUuid,
java.util.UUID newAcceptedTaxonNodeUUID,
SynonymType synonymType,
Reference citation,
java.lang.String citationMicroReference,
boolean setNameInSource) |
UpdateResult |
ITaxonNodeService.makeTaxonNodeASynonymOfAnotherTaxonNode(java.util.UUID oldTaxonNodeUuid,
java.util.UUID newAcceptedTaxonNodeUUID,
SynonymType synonymType,
Reference citation,
java.lang.String citationMicroReference,
boolean setNameInSource) |
UpdateResult |
TaxonNodeServiceImpl.makeTaxonNodeSynonymsOfAnotherTaxonNode(java.util.Set<java.util.UUID> oldTaxonNodeUuids,
java.util.UUID newAcceptedTaxonNodeUUIDs,
SynonymType synonymType,
Reference citation,
java.lang.String citationMicroReference,
boolean setNameInSource) |
UpdateResult |
ITaxonNodeService.makeTaxonNodeSynonymsOfAnotherTaxonNode(java.util.Set<java.util.UUID> oldTaxonNodeUuids,
java.util.UUID newAcceptedTaxonNodeUUIDs,
SynonymType synonymType,
Reference citation,
java.lang.String citationMicroReference,
boolean setNameInSource)
Changes the taxa associated with the given taxon nodes into synonyms of the new accepted taxon node.
|
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 |
TaxonServiceImpl.moveSynonymToAnotherTaxon(Synonym oldSynonym,
java.util.UUID newTaxonUUID,
boolean moveHomotypicGroup,
SynonymType newSynonymType,
Reference newSecundum,
java.lang.String newSecundumDetail,
boolean keepSecundumIfUndefined) |
UpdateResult |
ITaxonService.moveSynonymToAnotherTaxon(Synonym oldSynonym,
java.util.UUID newTaxonUUID,
boolean moveHomotypicGroup,
SynonymType newSynonymType,
Reference newSecundum,
java.lang.String newSecundumDetail,
boolean keepSecundumIfUndefined) |
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 |
---|---|
java.util.List<Reference> |
ReferenceServiceImpl.findByTitleAndAbbrevTitle(IIdentifiableEntityServiceConfigurator<Reference> config) |
java.util.List<Reference> |
IReferenceService.findByTitleAndAbbrevTitle(IIdentifiableEntityServiceConfigurator<Reference> config) |
Pager<Registration> |
IRegistrationService.page(java.util.Optional<Reference> reference,
java.util.Collection<RegistrationStatus> includedStatus,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths)
Returns a sublist of Registration instances stored in the database.
|
Pager<Registration> |
RegistrationServiceImpl.page(java.util.Optional<Reference> reference,
java.util.Collection<RegistrationStatus> includedStatus,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths)
Returns a sublist of Registration instances stored in the database.
|
Pager<Reference> |
IReferenceService.search(java.lang.Class<? extends Reference> 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 Reference instances where the default field matches the String queryString (as interpreted by the Lucene QueryParser)
|
UpdateResult |
ReferenceServiceImpl.updateCaches(java.lang.Class<? extends Reference> clazz,
java.lang.Integer stepSize,
IIdentifiableEntityCacheStrategy<Reference> cacheStrategy,
IProgressMonitor monitor) |
UpdateResult |
ReferenceServiceImpl.updateCaches(java.lang.Class<? extends Reference> clazz,
java.lang.Integer stepSize,
IIdentifiableEntityCacheStrategy<Reference> cacheStrategy,
IProgressMonitor monitor) |
Modifier and Type | Method and Description |
---|---|
Reference |
SecundumForSubtreeConfigurator.getNewSecundum() |
Modifier and Type | Method and Description |
---|---|
void |
SecundumForSubtreeConfigurator.setNewSecundum(Reference newSecundum) |
Constructor and Description |
---|
SecundumForSubtreeConfigurator(java.util.UUID subtreeUuid,
Reference newSecundum,
IRemotingProgressMonitor monitor) |
Modifier and Type | Method and Description |
---|---|
Reference |
RegistrationDTO.getCitation() |
protected Reference |
RegistrationWorkingSet.publicationUnit(RegistrationDTO regDto) |
Modifier and Type | Method and Description |
---|---|
java.util.Set<Reference> |
SequenceDTO.getCitations() |
Modifier and Type | Method and Description |
---|---|
void |
RegistrationDTO.setCitation(Reference citation) |
Constructor and Description |
---|
RegistrationDTO(Registration reg,
TaxonName typifiedName,
Reference publication)
To create an initially empty DTO for which only the
typifiedName and the publication are defined. |
RegistrationWorkingSet(Reference citation)
Creates an empty working set
|
Modifier and Type | Method and Description |
---|---|
protected Reference |
RegistrationWorkingSetService.resolveSection(Reference reference) |
Modifier and Type | Method and Description |
---|---|
boolean |
RegistrationWorkingSetService.checkReferencePublished(Reference reference) |
boolean |
RegistrationWorkingSetService.isPermissionDenied(Reference reference) |
protected Reference |
RegistrationWorkingSetService.resolveSection(Reference reference) |
Modifier and Type | Method and Description |
---|---|
void |
TaxonGraphBeforeTransactionCompleteProcess.onNomReferenceChange(TaxonName taxonName,
Reference oldNomReference) |
Modifier and Type | Method and Description |
---|---|
java.util.List<Reference> |
BciSchemaAdapter.getCmdEntities(java.io.InputStream inputStream) |
Modifier and Type | Method and Description |
---|---|
java.util.List<Reference> |
DublinCoreSchemaAdapter.getCmdEntities(java.io.InputStream inputStream) |
Modifier and Type | Method and Description |
---|---|
java.util.List<Reference> |
IpniService.getPublications(java.lang.String title,
java.lang.String abbreviation,
ICdmRepository services,
IpniServicePublicationConfigurator config) |
java.util.List<Reference> |
IIpniService.getPublications(java.lang.String title,
java.lang.String abbreviation,
ICdmRepository services,
IpniServicePublicationConfigurator config)
Returns a list of publications matching the title and/or the abbreviation parameter according to the IPNI Publication search function.
|
Modifier and Type | Class and Description |
---|---|
class |
OpenUrlReference |
Modifier and Type | Method and Description |
---|---|
java.util.List<Reference> |
MobotOpenUrlResponseSchemaAdapter.getCmdEntities(java.io.InputStream inputStream) |
Modifier and Type | Method and Description |
---|---|
static MobotOpenUrlServiceWrapper.ReferenceType |
MobotOpenUrlServiceWrapper.ReferenceType.getReferenceType(Reference reference) |
Modifier and Type | Method and Description |
---|---|
java.util.List<Reference> |
SruServiceWrapper.doSearchRetrieve(java.lang.String cqlQuery,
java.lang.String recordSchema)
The GRIB sru service is available at "http://gso.gbv.de/sru/DB=1.83/"
The documentation is found at http://bhleurope.gbv.de/#sru from where the following text has been retrieved:
|
Modifier and Type | Method and Description |
---|---|
protected AbstractEllypsisFormatter.EllipsisData |
ReferenceEllypsisFormatter.entityEllypsis(Reference entity,
java.lang.String preserveString) |
Modifier and Type | Method and Description |
---|---|
static java.lang.Integer |
BerlinModelTransformer.ref2refCategoryId(Reference ref) |
Modifier and Type | Method and Description |
---|---|
Reference |
Cdm2CdmImportConfigurator.getSourceReference()
Deprecated.
|
protected Reference |
Cdm2CdmImportBase.handlePersistedReference(Reference reference) |
Modifier and Type | Method and Description |
---|---|
protected Reference |
Cdm2CdmImportBase.handlePersistedReference(Reference reference) |
Modifier and Type | Method and Description |
---|---|
protected void |
CdmLightExportState.addReferenceToStore(Reference ref) |
Modifier and Type | Field and Description |
---|---|
protected Reference |
ImportConfiguratorBase.sourceReference |
Modifier and Type | Method and Description |
---|---|
Reference |
DbImportConfiguratorBase.getSourceReference() |
abstract Reference |
ImportConfiguratorBase.getSourceReference() |
Reference |
IImportConfigurator.getSourceReference()
The reference that represents the source.
|
Reference |
DbImportStateBase.getTransactionalSourceReference()
Stores the source reference for the time of a transaction.
|
Reference |
IPartitionedState.getTransactionalSourceReference() |
Modifier and Type | Method and Description |
---|---|
void |
CdmImportBase.addOriginalSource(ICdmBase cdmBase,
java.lang.Object idAttributeValue,
java.lang.String namespace,
Reference citation)
Adds an orginal source to a sourceable objects (implemented for Identifiable entity and description element.
|
void |
CdmImportBase.addOriginalSource(java.sql.ResultSet rs,
CdmBase cdmBase,
java.lang.String dbIdAttribute,
java.lang.String namespace,
Reference citation) |
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. |
SpecimenDescription |
CdmImportBase.getSpecimenDescription(SpecimenOrObservationBase specimen,
Reference ref,
boolean isImageGallery,
boolean createNewIfNotExists)
Like
CdmImportBase.getSpecimenDescription(SpecimenOrObservationBase, 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. |
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. |
TaxonNameDescription |
CdmImportBase.getTaxonNameDescription(TaxonName name,
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. |
java.util.UUID |
ImportStateBase.getTreeUuid(Reference ref) |
protected Classification |
CdmImportBase.makeTree(STATE state,
Reference reference) |
protected Classification |
CdmImportBase.makeTreeMemSave(STATE state,
Reference ref)
Alternative memory saving method variant of
#makeTree(STATE state, Reference ref) which stores only the
UUID instead of the full tree in the ImportStateBase by
using state.putTreeUuid(ref, tree); |
void |
ImportStateBase.putTreeUuid(Reference ref,
Classification tree) |
static boolean |
ImportHelper.setOriginalSource(ISourceable<?> sourceable,
Reference sourceReference,
long sourceId,
java.lang.String namespace) |
static boolean |
ImportHelper.setOriginalSource(ISourceable sourceable,
Reference sourceReference,
java.lang.String sourceId,
java.lang.String namespace)
Adds an original source object to the identifiable entity.
|
void |
ImportConfiguratorBase.setSourceReference(Reference sourceReference) |
void |
IImportConfigurator.setSourceReference(Reference sourceReference) |
Modifier and Type | Method and Description |
---|---|
Reference |
ImportDeduplicationHelper.getExistingReference(STATE state,
Reference ref) |
Modifier and Type | Method and Description |
---|---|
Reference |
ImportDeduplicationHelper.getExistingReference(STATE state,
Reference ref) |
Modifier and Type | Method and Description |
---|---|
Reference |
CsvImportConfiguratorBase.getSourceReference() |
Reference |
CsvImportState.getSourceReference() |
protected Reference |
CsvImportBase.getTransactionalSourceReference(STATE state)
Transaction save method to retrieve the source reference
if either existent or not in the database (uses check for uuid).
|
Modifier and Type | Method and Description |
---|---|
void |
CsvImportState.setSourceReference(Reference sourceReference) |
Modifier and Type | Method and Description |
---|---|
Reference |
StructureTreeOwlImportConfigurator.getSourceReference() |
Modifier and Type | Method and Description |
---|---|
Reference |
ExcelDistributionUpdateConfigurator.getSourceReference() |
Modifier and Type | Method and Description |
---|---|
java.util.List<Reference> |
DwcaEmlRecord.getReferences() |
Modifier and Type | Method and Description |
---|---|
void |
DwcaEmlRecord.setReferences(java.util.List<Reference> references) |
Modifier and Type | Method and Description |
---|---|
Reference |
ExcelImportState.getSourceReference() |
Reference |
ExcelImportConfiguratorBase.getSourceReference() |
protected Reference |
ExcelImportBase.getSourceReference(STATE state)
Non transaction save method to retrieve the source reference
if either existent or not in the database (uses check for uuid).
|
Modifier and Type | Method and Description |
---|---|
void |
ExcelRowBase.putSourceReference(int key,
Reference reference) |
void |
ExcelImportState.setSourceReference(Reference sourceReference) |
Modifier and Type | Method and Description |
---|---|
Reference |
DistributionImportConfigurator.getSourceReference() |
Modifier and Type | Method and Description |
---|---|
Reference |
TaxonExcelImportState.getReference(java.lang.String key) |
Reference |
NormalExplicitImportConfigurator.getSourceReference() |
Modifier and Type | Method and Description |
---|---|
void |
TaxonExcelImportState.putReference(java.lang.String key,
Reference reference) |
Modifier and Type | Method and Description |
---|---|
Reference |
IdentifierImportConfigurator.getSourceReference()
The reference that represents the source.
|
Modifier and Type | Field and Description |
---|---|
protected java.util.List<Reference> |
DataSet.references |
Modifier and Type | Method and Description |
---|---|
Reference |
JaxbImportConfigurator.getSourceReference() |
Modifier and Type | Method and Description |
---|---|
java.util.List<Reference> |
DataSet.getReferences() |
Modifier and Type | Method and Description |
---|---|
void |
DataSet.setReferences(java.util.List<Reference> value) |
Modifier and Type | Field and Description |
---|---|
protected Reference |
MarkupImportBase.LabeledReference.ref |
Modifier and Type | Method and Description |
---|---|
Reference |
MarkupImportState.getLatestReferenceInHomotype() |
Reference |
MarkupImportConfigurator.getSourceReference() |
protected Reference |
MarkupImportBase.handleNonCitationSpecific(MarkupImportState state,
java.lang.String type,
java.lang.String authorStr,
java.lang.String titleStr,
java.lang.String titleCache,
java.lang.String volume,
java.lang.String issue,
java.lang.String edition,
java.lang.String editors,
java.lang.String pubName,
java.lang.String appendix,
java.lang.String pages,
javax.xml.stream.events.XMLEvent parentEvent)
Create reference for non nomenclatural references
|
Reference |
MarkupNomenclatureImport.handleReference(MarkupImportState state,
javax.xml.stream.XMLEventReader reader,
javax.xml.stream.events.XMLEvent parentEvent) |
Modifier and Type | Method and Description |
---|---|
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) |
DescriptionElementBase |
MarkupFeatureImport.makeFeatureFigureRef(MarkupImportState state,
javax.xml.stream.XMLEventReader reader,
TaxonDescription taxonDescription,
boolean isDescription,
DescriptionElementBase lastDescriptionElement,
Reference sourceReference,
javax.xml.stream.events.XMLEvent next) |
void |
MarkupImportState.setLatestReferenceInHomotype(Reference latestReferenceInHomotype) |
Constructor and Description |
---|
LabeledReference(Reference ref,
java.lang.String detail,
java.lang.String label) |
Modifier and Type | Method and Description |
---|---|
Reference |
DeleteNonReferencedReferencesConfigurator.getSourceReference() |
Modifier and Type | Method and Description |
---|---|
Reference |
EndnoteImportConfigurator.getSourceReference() |
Modifier and Type | Method and Description |
---|---|
boolean |
IEndnotePlaceholderClass.makePublicationDetailed(TcsXmlImportConfigurator tcsConfig,
org.jdom.Element elPublicationDetailed,
Reference publication) |
Modifier and Type | Method and Description |
---|---|
Reference |
RisReferenceImportConfigurator.getSourceReference()
The reference that represents the source.
|
Modifier and Type | Method and Description |
---|---|
Reference |
IkeyPlusImportConfigurator.getSourceReference() |
Modifier and Type | Method and Description |
---|---|
Reference |
SDDImportConfigurator.getSourceReference() |
Modifier and Type | Field and Description |
---|---|
protected java.util.List<Reference> |
SDDDataSet.references |
Modifier and Type | Method and Description |
---|---|
java.util.List<Reference> |
SDDDataSet.getReferences() |
Modifier and Type | Method and Description |
---|---|
void |
SDDDataSet.setReferences(java.util.List<Reference> value) |
Modifier and Type | Method and Description |
---|---|
Reference |
SpecimenUserInteraction.askForReference(java.util.Map<java.lang.String,Reference> refMap) |
Reference |
SpecimenImportStateBase.getImportReference(java.net.URI accessPoint) |
Reference |
SpecimenImportStateBase.getRef() |
Modifier and Type | Method and Description |
---|---|
void |
SpecimenImportStateBase.addImportReference(Reference ref) |
protected IdentifiableSource |
SpecimenImportBase.getIdentifiableSource(Reference reference,
java.lang.String citationDetail) |
void |
SpecimenImportStateBase.setRef(Reference ref) |
Modifier and Type | Method and Description |
---|---|
Reference |
SpecimenUserInteraction.askForReference(java.util.Map<java.lang.String,Reference> refMap) |
Modifier and Type | Method and Description |
---|---|
Reference |
Abcd206ImportConfigurator.getSourceReference() |
static Reference |
AbcdParseUtility.parseFirstReference(org.w3c.dom.NodeList referenceNodeList,
ICdmRepository cdmAppController) |
Modifier and Type | Method and Description |
---|---|
Reference |
SpecimenSynthesysExcelImportConfigurator.getDataReference() |
Reference |
SpecimenCdmExcelImportState.getReference(java.lang.String key) |
Reference |
SpecimenSynthesysExcelImportConfigurator.getSourceReference() |
Reference |
SpecimenCdmExcelImportConfigurator.getSourceReference() |
Reference |
SpecimenSynthesysExcelImportConfigurator.getTaxonReference() |
Reference |
SpecimenCdmExcelImportConfigurator.getTaxonReference() |
Reference |
SpecimenCdmExcelImportState.putReference(java.lang.String key,
Reference value) |
Modifier and Type | Method and Description |
---|---|
Reference |
SpecimenCdmExcelImportState.putReference(java.lang.String key,
Reference value) |
void |
SpecimenRow.putSourceReference(int key,
Reference reference) |
void |
SpecimenSynthesysExcelImportConfigurator.setDataReference(Reference ref) |
Modifier and Type | Method and Description |
---|---|
Reference |
GbifImportState.getRef() |
Reference |
GbifImportConfigurator.getSourceReference() |
Modifier and Type | Method and Description |
---|---|
void |
GbifImportState.setRef(Reference ref) |
Modifier and Type | Method and Description |
---|---|
Reference |
StreamImportConfiguratorBase.getSourceReference() |
Reference |
StreamImportStateBase.getTransactionalSourceReference()
Returns the source reference object that is attached to the current transaction.
|
Modifier and Type | Method and Description |
---|---|
Reference |
TaxonXImportState.getModsReference() |
Reference |
TaxonXImportConfigurator.getSourceReference() |
Modifier and Type | Method and Description |
---|---|
void |
TaxonXImportState.setModsReference(Reference modsReference) |
Modifier and Type | Method and Description |
---|---|
Reference |
TaxonXModsExtractor.extractMods(org.w3c.dom.Node node) |
Reference |
TaxonXImportConfigurator.getOriginalSourceURL() |
protected Reference |
TaxonXExtractor.getReferenceWithType(int reftype) |
Reference |
TaxonXImportConfigurator.getSecundum() |
Reference |
TaxonXImportConfigurator.getSourceReference() |
Reference |
TaxonXAddSources.getSourceUrlRef() |
Reference |
TaxonXXMLFieldGetter.parseMods()
parse the Mods from the TaxonX file
|
Modifier and Type | Method and Description |
---|---|
protected void |
TaxonXAddSources.addAndSaveSource(Reference refMods,
DerivedUnit derivedUnitBase) |
protected void |
TaxonXAddSources.addAndSaveSource(Reference refMods,
TaxonDescription taxonDescription,
Reference currentRef) |
void |
TaxonXImportConfigurator.addOriginalSource(Reference referenceUrl) |
protected IndividualsAssociation |
TaxonXAddSources.addSource(Reference refMods,
IndividualsAssociation indAssociation) |
protected void |
TaxonXAddSources.addSource(Reference refMods,
Synonym synonym) |
protected void |
TaxonXAddSources.addSource(Reference refMods,
Taxon acceptedTaxon) |
void |
TaxonXAddSources.addSource(Reference refMods,
TaxonDescription taxonDescription) |
protected void |
TaxonXAddSources.addSource(Reference refMods,
TaxonName nameToBeFilled) |
protected void |
TaxonXAddSources.addSource(Reference refMods,
TextData textData) |
void |
TaxonXAddSources.addSource(Reference reference,
TextData textData,
TaxonName name,
Reference refMods) |
protected boolean |
TaxonXExtractor.askIfReuseBestMatchingTaxon(INonViralName taxonname2,
Taxon bestMatchingTaxon,
Reference refMods,
double similarityScore,
double similarityAuthor) |
void |
TaxonXExtractor.ReferenceBuilder.builReference(java.lang.String mref,
java.lang.String treatmentMainName,
NomenclaturalCode nomenclaturalCode,
Taxon acceptedTaxon,
Reference refMods) |
protected void |
TaxonXTreatmentExtractor.extractTreatment(org.w3c.dom.Node treatmentnode,
Reference refMods,
java.net.URI sourceName)
extracts all the treament information and save them
|
protected DescriptionElementSource |
TaxonXAddSources.getDescriptionElementSource(Reference reference,
java.util.Set<DescriptionElementSource> sources,
boolean original) |
protected IdentifiableSource |
TaxonXAddSources.getIdentifiableSource(Reference reference,
java.util.Set<IdentifiableSource> sources,
boolean original) |
void |
TaxonXTreatmentExtractor.lookForParentNode(INonViralName taxonName,
Taxon tax,
Reference ref,
TaxonXTreatmentExtractor.MyName myName) |
void |
TaxonXXMLFieldGetter.parseTreatment(Reference ref,
java.net.URI sourceName)
Foreach treatment section, launches the treatment "extractor"
|
void |
TaxonXImportConfigurator.setSecundum(Reference reference) |
void |
TaxonXTreatmentExtractor.MyName.setSource(Reference re) |
static void |
TaxonXImportConfigurator.setSourceRef(Reference reference) |
void |
TaxonXAddSources.setSourceUrlRef(Reference sourceUrlRef) |
Constructor and Description |
---|
TaxonXTreatmentExtractor(NomenclaturalCode nomenclaturalCode,
Classification classification,
TaxonXImport importer,
TaxonXImportState configState,
java.util.Map<java.lang.String,Feature> featuresMap,
Reference urlSource) |
Modifier and Type | Method and Description |
---|---|
Reference |
TcsRdfImportConfigurator.getSourceReference() |
static Reference |
TcsRdfTransformer.pubTypeStr2PubType(java.lang.String strPubType)
Creates an cdm-Rank by the tcs rank
|
Modifier and Type | Method and Description |
---|---|
static Reference |
TcsXmlTransformer.pubTypeStr2PubType(java.lang.String strPubType)
Creates an cdm-Rank by the tcs rank
|
Modifier and Type | Method and Description |
---|---|
boolean |
ITcsXmlPlaceholderClass.makePublicationDetailed(TcsXmlImportConfigurator tcsConfig,
org.jdom.Element elPublicationDetailed,
Reference publication) |
boolean |
DefaultTcsXmlPlaceholders.makePublicationDetailed(TcsXmlImportConfigurator config,
org.jdom.Element elPublicationDetailed,
Reference publication) |
Modifier and Type | Method and Description |
---|---|
Reference |
TcsXmlImportConfigurator.getSourceReference() |
protected Reference |
TcsXmlImportBase.makeAccordingTo(org.jdom.Element elAccordingTo,
MapWrapper<Reference> referenceMap,
ResultWrapper<java.lang.Boolean> success) |
protected static Reference |
TcsXmlImportBase.unknownSec() |
Modifier and Type | Method and Description |
---|---|
protected Reference |
TcsXmlImportBase.makeAccordingTo(org.jdom.Element elAccordingTo,
MapWrapper<Reference> referenceMap,
ResultWrapper<java.lang.Boolean> success) |
Modifier and Type | Method and Description |
---|---|
Reference |
RepresentationCsvImportConfigurator.getSourceReference()
The reference that represents the source.
|
Modifier and Type | Method and Description |
---|---|
Reference |
ReferencedEntityBase.getCitation() |
Reference |
IReferencedEntity.getCitation() |
Modifier and Type | Method and Description |
---|---|
SOURCE |
SourcedEntityBase.addImportSource(java.lang.String id,
java.lang.String idNamespace,
Reference citation,
java.lang.String microCitation) |
SOURCE |
SourcedEntityBase.addPrimaryTaxonomicSource(Reference citation) |
SOURCE |
SourcedEntityBase.addPrimaryTaxonomicSource(Reference citation,
java.lang.String microCitation) |
SOURCE |
SourcedEntityBase.addSource(OriginalSourceType type,
Reference reference,
java.lang.String microReference,
java.lang.String originalInformation) |
SOURCE |
SourcedEntityBase.addSource(OriginalSourceType type,
java.lang.String id,
java.lang.String idNamespace,
Reference citation,
java.lang.String microCitation) |
protected IdentifiableSource |
IdentifiableEntity.createNewSource(OriginalSourceType type,
java.lang.String idInSource,
java.lang.String idNamespace,
Reference reference,
java.lang.String microReference,
java.lang.String originalInfo,
ICdmTarget target) |
protected abstract SOURCE |
SourcedEntityBase.createNewSource(OriginalSourceType type,
java.lang.String idInSource,
java.lang.String idNamespace,
Reference citation,
java.lang.String microReference,
java.lang.String originalInformation,
ICdmTarget target) |
static IdentifiableSource |
IdentifiableSource.NewDataImportInstance(java.lang.String id,
java.lang.String idNamespace,
Reference ref) |
static IdentifiableSource |
IdentifiableSource.NewInstance(OriginalSourceType type,
java.lang.String id,
java.lang.String idNamespace,
Reference reference,
java.lang.String microReference) |
static IdentifiableSource |
IdentifiableSource.NewInstance(OriginalSourceType type,
java.lang.String id,
java.lang.String idNamespace,
Reference reference,
java.lang.String microReference,
java.lang.String originalInfo) |
static IdentifiableSource |
IdentifiableSource.NewInstance(OriginalSourceType type,
java.lang.String id,
java.lang.String idNamespace,
Reference reference,
java.lang.String microReference,
java.lang.String originalInfo,
ICdmTarget target) |
static IdentifiableSource |
IdentifiableSource.NewPrimaryMediaSourceInstance(Reference citation,
java.lang.String microCitation) |
static IdentifiableSource |
IdentifiableSource.NewPrimarySourceInstance(Reference citation,
java.lang.String microCitation) |
void |
ReferencedEntityBase.setCitation(Reference citation) |
Constructor and Description |
---|
ReferencedEntityBase(Reference citation,
java.lang.String citationMicroReference,
java.lang.String originalNameString) |
RelationshipBase(FROM from,
TO to,
TYPE type,
Reference citation,
java.lang.String citationMicroReference)
Creates a relationship between 2 objects and adds it to the respective
relation sets of both objects.
|
Modifier and Type | Method and Description |
---|---|
java.util.Set<Reference> |
DescriptionBase.getDescriptionSources()
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
void |
DescriptionBase.addDescriptionSource(Reference descriptionSource)
Deprecated.
|
DescriptionElementSource |
DescriptionElementBase.addImportSource(java.lang.String id,
java.lang.String idNamespace,
Reference reference,
java.lang.String microReference) |
DescriptionElementSource |
DescriptionElementBase.addPrimaryTaxonomicSource(Reference reference) |
DescriptionElementSource |
DescriptionElementBase.addPrimaryTaxonomicSource(Reference reference,
java.lang.String microReference) |
DescriptionElementSource |
DescriptionElementBase.addSource(OriginalSourceType type,
Reference reference,
java.lang.String microReference,
java.lang.String originalInformation) |
DescriptionElementSource |
DescriptionElementBase.addSource(OriginalSourceType type,
java.lang.String id,
java.lang.String idNamespace,
Reference reference,
java.lang.String microReference) |
DescriptionElementSource |
DescriptionElementBase.addSource(OriginalSourceType type,
java.lang.String idInSource,
java.lang.String idNamespace,
Reference reference,
java.lang.String microReference,
TaxonName nameUsedInSource,
java.lang.String originalNameString)
Adds a
source to this description element. |
static DescriptionElementSource |
DescriptionElementSource.NewDataImportInstance(java.lang.String id,
java.lang.String idNamespace,
Reference ref) |
static DescriptionElementSource |
DescriptionElementSource.NewInstance(OriginalSourceType type,
java.lang.String id,
java.lang.String idNamespace,
Reference citation) |
static DescriptionElementSource |
DescriptionElementSource.NewInstance(OriginalSourceType type,
java.lang.String id,
java.lang.String idNamespace,
Reference citation,
java.lang.String microCitation) |
static DescriptionElementSource |
DescriptionElementSource.NewInstance(OriginalSourceType type,
java.lang.String id,
java.lang.String idNamespace,
Reference citation,
java.lang.String microReference,
TaxonName nameUsedInSource,
java.lang.String originalNameString) |
static DescriptionElementSource |
DescriptionElementSource.NewInstance(OriginalSourceType type,
java.lang.String id,
java.lang.String idNamespace,
Reference citation,
java.lang.String microReference,
TaxonName nameUsedInSource,
java.lang.String originalNameString,
ICdmTarget target) |
static DescriptionElementSource |
DescriptionElementSource.NewPrimarySourceInstance(Reference citation,
java.lang.String microCitation) |
static DescriptionElementSource |
DescriptionElementSource.NewPrimarySourceInstance(Reference citation,
java.lang.String microReference,
TaxonName nameUsedInSource,
java.lang.String originalNameString) |
void |
DescriptionBase.removeDescriptionSource(Reference descriptionSource)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
IdentifiableSource |
Media.addPrimaryMediaSource(Reference citation,
java.lang.String microCitation) |
Modifier and Type | Method and Description |
---|---|
Reference |
Primer.getPublishedIn()
The reference in which this primer was published and described
for the first time.
|
Modifier and Type | Method and Description |
---|---|
java.util.Set<Reference> |
Sequence.getCitations()
Citations are the set of references in which this sequence was published.
|
Modifier and Type | Method and Description |
---|---|
void |
Sequence.addCitation(Reference citation) |
void |
Sequence.removeCitation(Reference citation) |
void |
Primer.setPublishedIn(Reference publishedIn) |
Modifier and Type | Method and Description |
---|---|
protected void |
Sequence.setCitations(java.util.Set<Reference> citations) |
Modifier and Type | Method and Description |
---|---|
Reference |
TypeDesignationBase.getCitation() |
Reference |
TaxonName.getNomenclaturalReference() |
Reference |
ITaxonNameBase.getNomenclaturalReference()
Returns the
nomenclatural reference of this taxon name. |
Modifier and Type | Method and Description |
---|---|
NameRelationship |
TaxonName.addBasionym(TaxonName basionym,
Reference citation,
java.lang.String microcitation,
java.lang.String ruleConsidered,
NomenclaturalCodeEdition codeEdition)
Assigns a taxon name as
basionym of this taxon name
and keeps the nomenclatural rule considered for it. |
NameRelationship |
ITaxonNameBase.addBasionym(TaxonName basionym,
Reference citation,
java.lang.String microcitation,
java.lang.String ruleConsidered,
NomenclaturalCodeEdition codeEdition)
Assigns a taxon name as
basionym of this taxon name
and keeps the nomenclatural rule considered for it. |
HybridRelationship |
INonViralName.addHybridParent(INonViralName parentName,
HybridRelationshipType type,
Reference reference,
java.lang.String microReference,
java.lang.String ruleConsidered,
NomenclaturalCodeEdition codeEdition)
Creates a new
hybrid relationship
to this non viral name. |
HybridRelationship |
TaxonName.addHybridParent(INonViralName parentName,
HybridRelationshipType type,
Reference reference,
java.lang.String microReference,
java.lang.String ruleConsidered,
NomenclaturalCodeEdition codeEdition) |
NameTypeDesignation |
TaxonName.addNameTypeDesignation(TaxonName typeSpecies,
Reference citation,
java.lang.String citationMicroReference,
java.lang.String originalNameString,
NameTypeDesignationStatus status,
boolean addToAllHomotypicNames)
Creates and adds a new
name type designation
to this taxon name's set of type designations. |
NameTypeDesignation |
ITaxonNameBase.addNameTypeDesignation(TaxonName typeSpecies,
Reference citation,
java.lang.String citationMicroReference,
java.lang.String originalNameString,
NameTypeDesignationStatus status,
boolean addToAllHomotypicNames)
Creates and adds a new
name type designation
to this taxon name's set of type designations. |
NameTypeDesignation |
TaxonName.addNameTypeDesignation(TaxonName typeSpecies,
Reference citation,
java.lang.String citationMicroReference,
java.lang.String originalNameString,
NameTypeDesignationStatus status,
boolean isRejectedType,
boolean isConservedType,
boolean isNotDesignated,
boolean addToAllHomotypicNames)
Creates and adds a new
name type designation
to this taxon name's set of type designations. |
NameTypeDesignation |
ITaxonNameBase.addNameTypeDesignation(TaxonName typeSpecies,
Reference citation,
java.lang.String citationMicroReference,
java.lang.String originalNameString,
NameTypeDesignationStatus status,
boolean isRejectedType,
boolean isConservedType,
boolean isNotDesignated,
boolean addToAllHomotypicNames)
Creates and adds a new
name type designation
to this taxon name's set of type designations. |
NameRelationship |
TaxonName.addOriginalSpelling(TaxonName originalSpelling,
Reference citation,
java.lang.String microcitation)
Deprecated.
|
NameRelationship |
ITaxonNameBase.addOriginalSpelling(TaxonName originalSpelling,
Reference citation,
java.lang.String microcitation)
Deprecated.
in future original spellings will be stored with nomenclatural source
so this method may be deleted then
|
NameRelationship |
TaxonName.addRelationshipFromName(TaxonName fromName,
NameRelationshipType type,
Reference citation,
java.lang.String microCitation,
java.lang.String ruleConsidered,
NomenclaturalCodeEdition codeEdition) |
NameRelationship |
ITaxonNameBase.addRelationshipFromName(TaxonName fromName,
NameRelationshipType type,
Reference citation,
java.lang.String microCitation,
java.lang.String ruleConsidered,
NomenclaturalCodeEdition codeEdition)
Creates a new
name relationship from another taxon name to this taxon name
and adds it both to the set of relations to this taxon name and
to the set of relations from the other taxon name . |
NameRelationship |
TaxonName.addRelationshipToName(TaxonName toName,
NameRelationshipType type,
Reference citation,
java.lang.String microCitation,
java.lang.String ruleConsidered,
NomenclaturalCodeEdition codeEdition) |
NameRelationship |
ITaxonNameBase.addRelationshipToName(TaxonName toName,
NameRelationshipType type,
Reference citation,
java.lang.String microCitation,
java.lang.String ruleConsidered,
NomenclaturalCodeEdition codeEdition)
Creates a new
name relationship from this taxon name to another taxon name
and adds it both to the set of relations from this taxon name and
to the set of relations to the other taxon name . |
void |
TaxonName.addReplacedSynonym(TaxonName replacedSynonym,
Reference citation,
java.lang.String microcitation,
java.lang.String ruleConsidered,
NomenclaturalCodeEdition codeEdition)
Assigns a taxon name as
replaced synonym of this taxon name
and keeps the nomenclatural rule considered for it. |
void |
ITaxonNameBase.addReplacedSynonym(TaxonName replacedSynonym,
Reference citation,
java.lang.String microcitation,
java.lang.String ruleConsidered,
NomenclaturalCodeEdition codeEdition)
Assigns a taxon name as
replaced synonym of this taxon name
and keeps the nomenclatural rule considered for it. |
SpecimenTypeDesignation |
TaxonName.addSpecimenTypeDesignation(DerivedUnit typeSpecimen,
SpecimenTypeDesignationStatus status,
Reference citation,
java.lang.String citationMicroReference,
java.lang.String originalNameString,
boolean isNotDesignated,
boolean addToAllHomotypicNames)
Creates and adds a new
specimen type designation
to this taxon name's set of type designations. |
SpecimenTypeDesignation |
ITaxonNameBase.addSpecimenTypeDesignation(DerivedUnit typeSpecimen,
SpecimenTypeDesignationStatus status,
Reference citation,
java.lang.String citationMicroReference,
java.lang.String originalNameString,
boolean isNotDesignated,
boolean addToAllHomotypicNames)
Creates and adds a new
specimen type designation
to this taxon name's set of type designations. |
NomenclaturalStatus |
TaxonName.addStatus(NomenclaturalStatusType statusType,
Reference citation,
java.lang.String microCitation) |
NomenclaturalStatus |
ITaxonNameBase.addStatus(NomenclaturalStatusType statusType,
Reference citation,
java.lang.String microCitation) |
TextualTypeDesignation |
TaxonName.addTextualTypeDesignation(java.lang.String text,
Language language,
boolean isVerbatim,
Reference citation,
java.lang.String citationMicroReference,
java.lang.String originalNameString,
boolean addToAllHomotypicNames) |
TextualTypeDesignation |
ITaxonNameBase.addTextualTypeDesignation(java.lang.String text,
Language language,
boolean isVerbatim,
Reference citation,
java.lang.String citationMicroReference,
java.lang.String originalNameString,
boolean addToAllHomotypicNames)
Creates and adds a new
textual type designation
to this taxon name's set of type designations. |
protected IdentifiableSource |
TypeDesignationBase.createNewSource(OriginalSourceType type,
java.lang.String idInSource,
java.lang.String idNamespace,
Reference reference,
java.lang.String microReference,
java.lang.String originalInfo,
ICdmTarget target) |
static TaxonName |
TaxonNameFactory.NewBotanicalInstance(Rank rank,
java.lang.String genusOrUninomial,
java.lang.String infraGenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraSpecificEpithet,
TeamOrPersonBase combinationAuthorship,
Reference nomenclaturalReference,
java.lang.String nomenclMicroRef,
HomotypicalGroup homotypicalGroup)
Creates a new botanical taxon name instance
containing its
rank ,
its homotypical group ,
its scientific name components, its author(team) ,
its nomenclatural reference and
the default cache strategy . |
static TaxonName |
TaxonName.NewInstance(NomenclaturalCode code,
Rank rank,
java.lang.String genusOrUninomial,
java.lang.String infraGenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraSpecificEpithet,
TeamOrPersonBase combinationAuthorship,
Reference nomenclaturalReference,
java.lang.String nomenclMicroRef,
HomotypicalGroup homotypicalGroup) |
static NomenclaturalStatus |
NomenclaturalStatus.NewInstance(NomenclaturalStatusType nomStatusType,
Reference citation,
java.lang.String microCitation)
Creates a new nomenclatural status instance with a given
nomenclatural status type . |
static TextualTypeDesignation |
TextualTypeDesignation.NewInstance(java.lang.String text,
Language language,
boolean isVerbatim,
Reference citation,
java.lang.String citationMicroReference,
java.lang.String originalNameString) |
static INonViralName |
TaxonNameFactory.NewNonViralInstance(Rank rank,
java.lang.String genusOrUninomial,
java.lang.String infraGenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraSpecificEpithet,
TeamOrPersonBase combinationAuthorship,
Reference nomenclaturalReference,
java.lang.String nomenclMicroRef,
HomotypicalGroup homotypicalGroup) |
static TaxonName |
TaxonNameFactory.NewZoologicalInstance(Rank rank,
java.lang.String genusOrUninomial,
java.lang.String infraGenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraSpecificEpithet,
TeamOrPersonBase combinationAuthorship,
Reference nomenclaturalReference,
java.lang.String nomenclMicroRef,
HomotypicalGroup homotypicalGroup)
Creates a new zoological taxon name instance
containing its
rank ,
its homotypical group ,
its scientific name components, its author(team) ,
its nomenclatural reference and
the default cache strategy . |
void |
TextualTypeDesignation.setCitation(Reference citation)
Deprecated.
not relevant for
TextualTypeDesignation throws Exception |
void |
TypeDesignationBase.setCitation(Reference citation) |
void |
HomotypicalGroup.setGroupBasionym(TaxonName basionymName,
Reference citation,
java.lang.String microCitation,
java.lang.String ruleConsidered,
NomenclaturalCodeEdition codeEdition) |
void |
TaxonName.setNomenclaturalReference(Reference nomenclaturalReference)
Assigns a
nomenclatural reference to this taxon name. |
void |
ITaxonNameBase.setNomenclaturalReference(Reference nomenclaturalReference)
Assigns a
nomenclatural reference to this taxon name. |
Constructor and Description |
---|
HybridRelationship(INonViralName hybridName,
INonViralName parentName,
HybridRelationshipType type,
Reference citation,
java.lang.String citationMicroReference,
java.lang.String ruleConsidered,
NomenclaturalCodeEdition codeEdition)
Class constructor: creates a new hybrid relationship instance including
its
reference source and adds it to the respective
botanical taxon name relation sets of both involved names. |
NameRelationship(TaxonName toName,
TaxonName fromName,
NameRelationshipType type,
Reference citation,
java.lang.String citationMicroReference,
java.lang.String ruleConsidered,
NomenclaturalCodeEdition codeEdition)
Class constructor: creates a new name relationship instance including
its
reference source and adds it to the respective
taxon name relation sets of both involved names. |
NameTypeDesignation(TaxonName typeName,
NameTypeDesignationStatus status,
Reference citation,
java.lang.String citationMicroReference,
java.lang.String originalNameString)
Class constructor: creates a new name type designation instance
(including its
reference source and eventually
the taxon name string originally used by this reference when establishing
the former designation). |
NameTypeDesignation(TaxonName typeName,
Reference citation,
java.lang.String citationMicroReference,
java.lang.String originalNameString,
NameTypeDesignationStatus status,
boolean rejectedType,
boolean conservedType,
boolean isNotDesignated)
Class constructor: creates a new name type designation instance
(including its
reference source and eventually
the taxon name string originally used by this reference when establishing
the former designation). |
SpecimenTypeDesignation(DerivedUnit specimen,
SpecimenTypeDesignationStatus status,
Reference citation,
java.lang.String citationMicroReference,
java.lang.String originalNameString,
boolean isNotDesignated)
Class constructor: creates a new specimen type designation instance
(including its
reference source and
eventually the taxon name string originally used by this reference when
establishing the former designation). |
TaxonName(NomenclaturalCode type,
Rank rank,
java.lang.String genusOrUninomial,
java.lang.String infraGenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraSpecificEpithet,
TeamOrPersonBase combinationAuthorship,
Reference nomenclaturalReference,
java.lang.String nomenclMicroRef,
HomotypicalGroup homotypicalGroup)
Class constructor: creates a new non viral taxon name instance
containing its
rank ,
its homotypical group ,
its scientific name components, its author(team) ,
its nomenclatural reference and
the default cache strategy . |
TextualTypeDesignation(java.lang.String text,
Language language,
boolean isVerbatim,
Reference citation,
java.lang.String citationMicroReference,
java.lang.String originalNameString) |
TypeDesignationBase(Reference citation,
java.lang.String citationMicroReference,
java.lang.String originalNameString)
Class constructor: creates a new type designation
(including its
reference source and eventually
the taxon name string originally used by this reference when establishing
the former designation). |
TypeDesignationBase(Reference citation,
java.lang.String citationMicroReference,
java.lang.String originalNameString,
boolean notDesignated)
Class constructor: creates a new type designation
(including its
reference source and eventually
the taxon name string originally used by this reference when establishing
the former designation). |
Modifier and Type | Method and Description |
---|---|
java.util.Set<Reference> |
DeterminationEvent.getReferences() |
Modifier and Type | Method and Description |
---|---|
void |
DeterminationEvent.addReference(Reference reference) |
Modifier and Type | Method and Description |
---|---|
void |
DeterminationEvent.setReferences(java.util.Set<Reference> references) |
Modifier and Type | Field and Description |
---|---|
protected Reference |
Reference.inReference |
Modifier and Type | Method and Description |
---|---|
Reference |
IOriginalSource.getCitation()
Returns the citation.
|
Reference |
ISection.getInReference()
Returns the in-reference of this reference.
|
Reference |
IWebPage.getInReference()
Returns this websites inReference (e.g.
|
Reference |
Reference.getInReference() |
static Reference |
ReferenceFactory.newArticle() |
static Reference |
ReferenceFactory.newArticle(Reference inJournal,
TeamOrPersonBase partAuthor,
java.lang.String title,
java.lang.String pages,
java.lang.String seriesPart,
java.lang.String volume,
VerbatimTimePeriod datePublished) |
static Reference |
ReferenceFactory.newBook() |
static Reference |
ReferenceFactory.newBookSection() |
static Reference |
ReferenceFactory.newBookSection(Reference book,
TeamOrPersonBase partAuthor,
java.lang.String sectionTitle,
java.lang.String pages) |
static Reference |
ReferenceFactory.newCdDvd() |
static Reference |
ReferenceFactory.newDatabase() |
static Reference |
ReferenceFactory.newGeneric() |
static Reference |
ReferenceFactory.newInProceedings() |
static Reference |
ReferenceFactory.newJournal() |
static Reference |
ReferenceFactory.newMap() |
static Reference |
ReferenceFactory.newPatent() |
static Reference |
ReferenceFactory.newPersonalCommunication() |
static Reference |
ReferenceFactory.newPrintSeries() |
static Reference |
ReferenceFactory.newPrintSeries(java.lang.String series)
Creates a new print series instance with a given title string.
|
static Reference |
ReferenceFactory.newProceedings() |
static Reference |
ReferenceFactory.newReference(ReferenceType referenceType)
Returns a new reference for the according reference type.
|
static Reference |
ReferenceFactory.newReport() |
static Reference |
ReferenceFactory.newSection() |
static Reference |
ReferenceFactory.newThesis() |
static Reference |
ReferenceFactory.newWebPage() |
Modifier and Type | Method and Description |
---|---|
T |
ISourceable.addImportSource(java.lang.String id,
java.lang.String idNamespace,
Reference reference,
java.lang.String microReference)
Adds a
source of type OriginalSourceType.Import
to this object. |
T |
ISourceable.addPrimaryTaxonomicSource(Reference reference)
Adds a
source of type
OriginalSourceType.PrimaryTaxonomicSource
to this object. |
T |
ISourceable.addPrimaryTaxonomicSource(Reference reference,
java.lang.String microReference)
Adds a
source of type OriginalSourceType.PrimaryTaxonomicSource
to this object. |
T |
ISourceable.addSource(OriginalSourceType type,
Reference reference,
java.lang.String microReference,
java.lang.String originalInformation) |
T |
ISourceable.addSource(OriginalSourceType type,
java.lang.String id,
java.lang.String idNamespace,
Reference reference,
java.lang.String microReference)
Adds a source that is newly created by its components.
|
static Reference |
ReferenceFactory.newArticle(Reference inJournal,
TeamOrPersonBase partAuthor,
java.lang.String title,
java.lang.String pages,
java.lang.String seriesPart,
java.lang.String volume,
VerbatimTimePeriod datePublished) |
static Reference |
ReferenceFactory.newBookSection(Reference book,
TeamOrPersonBase partAuthor,
java.lang.String sectionTitle,
java.lang.String pages) |
void |
IOriginalSource.setCitation(Reference citation) |
void |
ISection.setInReference(Reference reference)
Sets the in-reference of this reference.
|
void |
IWebPage.setInReference(Reference inReference)
Sets this websites inreference (e.g.
|
void |
Reference.setInReference(Reference inReference) |
void |
IGeneric.setInReference(Reference inReference)
Sets the inreference.
|
Modifier and Type | Method and Description |
---|---|
Reference |
Classification.getCitation() |
Reference |
Classification.getReference() |
Reference |
ITaxonTreeNode.getReference() |
Reference |
TaxonNode.getReference() |
Reference |
TaxonBase.getSec()
Returns the
reference of this (abstract) taxon. |
Modifier and Type | Method and Description |
---|---|
TaxonNode |
Classification.addChildNode(TaxonNode childNode,
int index,
Reference citation,
java.lang.String microCitation) |
TaxonNode |
ITaxonTreeNode.addChildNode(TaxonNode childNode,
int index,
Reference citation,
java.lang.String microCitation)
Adds a taxon node as a child of this
ITreeNode at the index position. |
TaxonNode |
TaxonNode.addChildNode(TaxonNode child,
int index,
Reference reference,
java.lang.String microReference)
Inserts the given taxon node in the list of children of this taxon node
at the given (index + 1) position.
|
TaxonNode |
Classification.addChildNode(TaxonNode childNode,
Reference citation,
java.lang.String microCitation) |
TaxonNode |
ITaxonTreeNode.addChildNode(TaxonNode childNode,
Reference citation,
java.lang.String microCitation)
Adds a taxon node as a child of the ITreeNode at the last position.
|
TaxonNode |
TaxonNode.addChildNode(TaxonNode childNode,
Reference reference,
java.lang.String microReference)
Moves a taxon node to a new parent.
|
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) |
Synonym |
Taxon.addHeterotypicSynonymName(TaxonName synonymName,
Reference secReference,
java.lang.String secDetail,
HomotypicalGroup homotypicalGroup)
|
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 . |
Synonym |
Taxon.addSynonymName(TaxonName synonymName,
Reference secReference,
java.lang.String secMicroReference,
SynonymType synonymType)
|
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. |
void |
Classification.makeTopmostNodeChildOfOtherNode(TaxonNode topmostNode,
TaxonNode otherNode,
Reference ref,
java.lang.String microReference)
Appends an existing topmost node to another node of this tree.
|
static Synonym |
Synonym.NewInstance(ITaxonNameBase taxonName,
Reference sec) |
static Taxon |
Taxon.NewInstance(ITaxonNameBase taxonName,
Reference sec) |
static Classification |
Classification.NewInstance(java.lang.String name,
Reference reference) |
static Classification |
Classification.NewInstance(java.lang.String name,
Reference reference,
Language language) |
static Synonym |
Synonym.NewInstance(TaxonName taxonName,
Reference sec)
Creates a new synonym instance with
the
taxon name used and the reference
using it as a synonym and not as an ("accepted/correct") taxon . |
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 Synonym |
Synonym.NewInstance(TaxonName taxonName,
Reference sec,
java.lang.String secDetail) |
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. |
void |
Classification.setReference(Reference reference) |
void |
TaxonNode.setReference(Reference reference) |
void |
TaxonBase.setSec(Reference sec) |
Constructor and Description |
---|
AlternativeTreeRoot(TaxonNode oldRoot,
TaxonNode replacedTaxonNodeFromParentView,
Reference reference,
java.lang.String microReference) |
Classification(java.lang.String name,
Reference reference,
Language language) |
TaxonBase(TaxonName taxonName,
Reference sec,
java.lang.String secDetail)
Class constructor: creates a new (abstract) taxon with the
taxon name used and the reference
using it. |
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 |
---|---|
java.lang.Long |
RegistrationDaoHibernateImpl.count(java.util.Optional<Reference> reference,
java.util.Collection<RegistrationStatus> includedStatus)
Counts the Registration instances stored in the database.
|
java.util.List<Registration> |
RegistrationDaoHibernateImpl.list(java.util.Optional<Reference> reference,
java.util.Collection<RegistrationStatus> includedStatus,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<java.lang.String> propertyPaths)
Returns a sublist of Registration instances stored in the database.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<Reference> |
ReferenceDaoHibernateImpl.findByTitleAndAbbrevTitle(java.lang.Class clazz,
java.lang.String queryString,
MatchMode matchmode,
java.util.List<org.hibernate.criterion.Criterion> criterion,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<Reference> |
ReferenceDaoHibernateImpl.getAllNomenclaturalReferences() |
java.util.List<Reference> |
ReferenceDaoHibernateImpl.getAllNotNomenclaturalReferencesForPublishing() |
java.util.List<Reference> |
ReferenceDaoHibernateImpl.getAllReferencesForPublishing() |
java.util.List<Reference> |
ReferenceDaoHibernateImpl.getSubordinateReferences(Reference reference) |
java.util.List<UuidAndTitleCache<Reference>> |
ReferenceDaoHibernateImpl.getUuidAndAbbrevTitleCache(java.lang.Integer limit,
java.lang.String pattern,
ReferenceType refType) |
java.util.List<UuidAndTitleCache<Reference>> |
ReferenceDaoHibernateImpl.getUuidAndAbbrevTitleCacheForAuthor(java.lang.Integer limit,
java.lang.String pattern,
ReferenceType refType) |
java.util.List<UuidAndTitleCache<Reference>> |
ReferenceDaoHibernateImpl.getUuidAndTitle() |
java.util.List<UuidAndTitleCache<Reference>> |
ReferenceDaoHibernateImpl.getUuidAndTitle(java.util.Set<java.util.UUID> uuids) |
java.util.List<UuidAndTitleCache<Reference>> |
ReferenceDaoHibernateImpl.getUuidAndTitle(java.util.Set<java.util.UUID> uuids,
ReferenceType refType) |
java.util.List<UuidAndTitleCache<Reference>> |
ReferenceDaoHibernateImpl.getUuidAndTitleCache(java.lang.Integer limit,
java.lang.String pattern,
ReferenceType refType) |
Modifier and Type | Method and Description |
---|---|
java.util.List<Reference> |
ReferenceDaoHibernateImpl.getSubordinateReferences(Reference reference) |
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 |
---|---|
int |
TaxonNodeDaoHibernateImpl.countSecundumForSubtreeAcceptedTaxa(TreeIndex subTreeIndex,
Reference newSec,
boolean overwriteExisting,
boolean includeSharedTaxa,
boolean emptySecundumDetail) |
int |
TaxonNodeDaoHibernateImpl.countSecundumForSubtreeSynonyms(TreeIndex subTreeIndex,
Reference newSec,
boolean overwriteExisting,
boolean includeSharedTaxa,
boolean emptySecundumDetail) |
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.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 |
---|---|
protected Reference |
AbstractHibernateTaxonGraphProcessor.conceptReference(Reference nomenclaturalReference) |
Reference |
AbstractHibernateTaxonGraphProcessor.secReference() |
Modifier and Type | Method and Description |
---|---|
protected Reference |
AbstractHibernateTaxonGraphProcessor.conceptReference(Reference nomenclaturalReference) |
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) |
protected void |
AbstractHibernateTaxonGraphProcessor.updateReferenceInEdges(Taxon taxon,
Reference conceptReference,
Reference oldConceptReference) |
Modifier and Type | Method and Description |
---|---|
java.lang.Long |
IRegistrationDao.count(java.util.Optional<Reference> reference,
java.util.Collection<RegistrationStatus> includedStatus)
Counts the Registration instances stored in the database.
|
java.util.List<Registration> |
IRegistrationDao.list(java.util.Optional<Reference> reference,
java.util.Collection<RegistrationStatus> includedStatus,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<java.lang.String> propertyPaths)
Returns a sublist of Registration instances stored in the database.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<Reference> |
IReferenceDao.findByTitleAndAbbrevTitle(java.lang.Class clazz,
java.lang.String queryString,
MatchMode matchmode,
java.util.List<org.hibernate.criterion.Criterion> criterion,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<Reference> |
IReferenceDao.getAllNomenclaturalReferences()
TODO candidate for harmonization: rename to listNomenclaturalReferences
|
java.util.List<Reference> |
IReferenceDao.getAllNotNomenclaturalReferencesForPublishing()
TODO candidate for harmonization: rename to listAllNotNomenclaturalReferencesForPublishing
|
java.util.List<Reference> |
IReferenceDao.getAllReferencesForPublishing()
TODO candidate for harmonization: rename to listAllReferencesForPublishing
|
java.util.List<Reference> |
IReferenceDao.getSubordinateReferences(Reference reference)
recursively finds all references where the
referenceBase given as parameter
is the inReference . |
java.util.List<UuidAndTitleCache<Reference>> |
IReferenceDao.getUuidAndAbbrevTitleCache(java.lang.Integer limit,
java.lang.String pattern,
ReferenceType refType) |
java.util.List<UuidAndTitleCache<Reference>> |
IReferenceDao.getUuidAndAbbrevTitleCacheForAuthor(java.lang.Integer limit,
java.lang.String pattern,
ReferenceType refType) |
java.util.List<UuidAndTitleCache<Reference>> |
IReferenceDao.getUuidAndTitle() |
java.util.List<UuidAndTitleCache<Reference>> |
IReferenceDao.getUuidAndTitle(java.util.Set<java.util.UUID> uuids) |
java.util.List<UuidAndTitleCache<Reference>> |
IReferenceDao.getUuidAndTitle(java.util.Set<java.util.UUID> uuids,
ReferenceType refType) |
java.util.List<UuidAndTitleCache<Reference>> |
IReferenceDao.getUuidAndTitleCache(java.lang.Integer limit,
java.lang.String pattern,
ReferenceType refType) |
Modifier and Type | Method and Description |
---|---|
java.util.List<Reference> |
IReferenceDao.getSubordinateReferences(Reference reference)
recursively finds all references where the
referenceBase given as parameter
is the inReference . |
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 |
---|---|
int |
ITaxonNodeDao.countSecundumForSubtreeAcceptedTaxa(TreeIndex subTreeIndex,
Reference newSec,
boolean overwriteExistingAccepted,
boolean includeSharedTaxa,
boolean emptySecundumDetail) |
int |
ITaxonNodeDao.countSecundumForSubtreeSynonyms(TreeIndex subTreeIndex,
Reference newSec,
boolean overwriteExistingSynonyms,
boolean includeSharedTaxa,
boolean emptySecundumDetail) |
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.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 |
---|---|
net.sf.json.JSONObject |
ReferenceBaseBeanProcessor.processBeanSecondStep(Reference bean,
net.sf.json.JSONObject json,
net.sf.json.JsonConfig jsonConfig) |
Modifier and Type | Method and Description |
---|---|
java.lang.String |
DefaultReferenceCacheStrategy.createShortCitation(Reference reference) |
java.lang.String |
IReferenceCacheStrategy.getCitation(Reference reference)
Returns a short version of the reference, suitable for citation (e.g.
|
java.lang.String |
DefaultReferenceCacheStrategy.getCitation(Reference reference) |
java.lang.String |
IReferenceCacheStrategy.getFullAbbrevTitleString(Reference reference)
Returns the full abbreviated title string which
is a string representation of Reference which
preferably uses the
abbrev title
of the reference instead of the title. |
java.lang.String |
DefaultReferenceCacheStrategy.getFullAbbrevTitleString(Reference reference) |
java.lang.String |
DefaultReferenceCacheStrategy.getNomenclaturalCache(Reference reference) |
java.lang.String |
INomenclaturalReferenceCacheStrategy.getNomenclaturalCache(Reference reference)
Computes the nomenclatural cache.
|
java.lang.String |
DefaultReferenceCacheStrategy.getNomenclaturalCitation(Reference reference,
java.lang.String microReference) |
java.lang.String |
INomenclaturalReferenceCacheStrategy.getNomenclaturalCitation(Reference nomenclaturalReference,
java.lang.String microReference)
Returns a formatted string containing the entire citation used for
nomenclatural purposes based on the
reference supplied - including
(abbreviated) title but not authors - and on the given details.The returned string is build according to the corresponding cache strategy . |
java.lang.String |
DefaultReferenceCacheStrategy.getTitleCache(Reference reference) |
static java.lang.String |
TitleWithoutYearAndAuthorHelper.getTitleWithoutYearAndAuthor(Reference ref,
boolean isAbbrev) |
static java.lang.String |
TitleWithoutYearAndAuthorHelper.getTitleWithoutYearAndAuthorGeneric(Reference genericReference,
boolean isAbbrev) |
Modifier and Type | Method and Description |
---|---|
boolean |
ReferenceCheckValidator.isValid(Reference value,
javax.validation.ConstraintValidatorContext constraintValidatorContext) |
boolean |
InReferenceValidator.isValid(Reference value,
javax.validation.ConstraintValidatorContext constraintValidatorContext) |
boolean |
NoRecursiveInReferenceValidator.isValid(Reference value,
javax.validation.ConstraintValidatorContext constraintValidatorContext) |
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