Package | Description |
---|---|
eu.etaxonomy.cdm.api.service | |
eu.etaxonomy.cdm.api.service.dto | |
eu.etaxonomy.cdm.io.cdm2cdm | |
eu.etaxonomy.cdm.io.common | |
eu.etaxonomy.cdm.io.sdd.out | |
eu.etaxonomy.cdm.io.taxonx2013 | |
eu.etaxonomy.cdm.model.name |
Provides classes for nomenclature and typification.
|
eu.etaxonomy.cdm.model.taxon |
Provides classes for taxonomy including synonymy and concept synonymy.
|
eu.etaxonomy.cdm.persistence.dao.hibernate.taxon | |
eu.etaxonomy.cdm.persistence.dao.taxon | |
eu.etaxonomy.cdm.persistence.dto | |
eu.etaxonomy.cdm.validation.constraint |
Modifier and Type | Method and Description |
---|---|
Synonym |
TaxonServiceImpl.findBestMatchingSynonym(java.lang.String taxonName,
boolean includeUnpublished) |
Synonym |
ITaxonService.findBestMatchingSynonym(java.lang.String taxonName,
boolean includeUnpublished) |
Modifier and Type | Method and Description |
---|---|
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
|
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.
|
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.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
|
DeleteResult |
TaxonServiceImpl.deleteSynonym(Synonym synonym,
SynonymDeletionConfigurator config) |
DeleteResult |
ITaxonService.deleteSynonym(Synonym synonym,
SynonymDeletionConfigurator config)
Removes a synonym.
In detail it removes the synonym concept If removeNameIfPossible is true
it also removes the synonym name if it is not used in any other context
(part of a concept, in DescriptionElementSource, part of a name relationship, used inline, ...)If newHomotypicGroupIfNeeded is true and the synonym name
is not deleted and the name is homotypic to the taxon
the name is moved to a new homotypic group.If synonym is null the method has no effect. |
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 |
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) |
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 |
---|---|
java.util.List<EntityDTO<Synonym>> |
TaxonInContextDTO.getSynonyms() |
Modifier and Type | Method and Description |
---|---|
void |
TaxonInContextDTO.addSynonym(EntityDTO<Synonym> synonymDto) |
void |
TaxonInContextDTO.setSynonyms(java.util.List<EntityDTO<Synonym>> synonyms) |
Modifier and Type | Method and Description |
---|---|
protected Synonym |
Cdm2CdmImportBase.handlePersistedSynonym(Synonym synonym) |
Modifier and Type | Method and Description |
---|---|
protected Synonym |
Cdm2CdmImportBase.handlePersistedSynonym(Synonym synonym) |
Modifier and Type | Method and Description |
---|---|
protected boolean |
CdmExportBase.isUnpublished(CONFIG config,
Synonym synonym)
true if neither synonym has state publish nor
taxon node filter includes unpublished taxa. |
Modifier and Type | Field and Description |
---|---|
protected java.util.List<Synonym> |
SDDDataSet.synonyms |
Modifier and Type | Method and Description |
---|---|
java.util.List<Synonym> |
SDDDataSet.getSynonyms() |
Modifier and Type | Method and Description |
---|---|
void |
SDDDataSet.addSynonym(Synonym value) |
Modifier and Type | Method and Description |
---|---|
void |
SDDDataSet.addSynonyms(java.util.Collection<Synonym> value) |
void |
SDDDataSet.setSynonyms(java.util.List<Synonym> value) |
Modifier and Type | Method and Description |
---|---|
Synonym |
TaxonXTreatmentExtractor.MyName.getSyno() |
Modifier and Type | Method and Description |
---|---|
protected void |
TaxonXAddSources.addSource(Reference refMods,
Synonym synonym) |
void |
TaxonXTreatmentExtractor.MyName.setSyno(Synonym syno) |
Modifier and Type | Method and Description |
---|---|
java.util.Set<Synonym> |
TaxonName.getSynonyms()
Returns the set of
(junior) synonyms (according to any
reference) that are based on this taxon name. |
java.util.Set<Synonym> |
ITaxonNameBase.getSynonyms()
Returns the set of
(junior) synonyms (according to any
reference) that are based on this taxon name. |
Modifier and Type | Method and Description |
---|---|
Synonym |
Taxon.addHeterotypicSynonymName(TaxonName synonymName)
|
Synonym |
Taxon.addHeterotypicSynonymName(TaxonName synonymName,
Reference secReference,
java.lang.String secDetail,
HomotypicalGroup homotypicalGroup)
|
Synonym |
Taxon.addHomotypicSynonymName(TaxonName synonymName)
|
Synonym |
Taxon.addSynonymName(TaxonName synonymName,
Reference secReference,
java.lang.String secMicroReference,
SynonymType synonymType)
|
Synonym |
Taxon.addSynonymName(TaxonName synonymName,
SynonymType synonymType)
|
Synonym |
TaxonNode.getSynonymToBeUsed() |
static Synonym |
Synonym.NewInstance(ITaxonNameBase taxonName,
Reference sec) |
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 Synonym |
Synonym.NewInstance(TaxonName taxonName,
Reference sec,
java.lang.String secDetail) |
Modifier and Type | Method and Description |
---|---|
java.util.List<Synonym> |
Taxon.getHomotypicSynonymsByHomotypicGroup() |
java.util.List<Synonym> |
Taxon.getHomotypicSynonymsByHomotypicGroup(TaxonComparator comparator)
Retrieves the ordered list (depending on the date of publication) of
homotypic
synonyms (according to the same reference
as for this taxon) under the condition that the taxon names
of these synonyms and the taxon name of this taxon belong to the
same homotypical group . |
java.util.List<Synonym> |
Taxon.getHomotypicSynonymsByHomotypicSynonymType()
Deprecated.
as the method currently returns data not matching the original description of the method
as an ordered list (according to date of publication) of synonyms with same secundum as this taxon.
In future this method will either be removed or semantics may change.
|
java.util.Set<Synonym> |
Taxon.getSynonyms()
Returns the set of all
synonyms
for which this ("accepted/valid") taxon is the accepted taxon. |
java.util.List<Synonym> |
Taxon.getSynonymsInGroup(HomotypicalGroup homotypicGroup)
Retrieves the ordered list (depending on the rules defined for
the
HomotypicGroupTaxonComparator ) of
synonyms (according to a given reference)
the taxon names of which belong to the homotypical group. |
java.util.List<Synonym> |
Taxon.getSynonymsInGroup(HomotypicalGroup homotypicGroup,
TaxonComparator comparator) |
Modifier and Type | Method and Description |
---|---|
void |
Taxon.addHomotypicSynonym(Synonym synonym)
Adds the given
synonym to this taxon,
with the "is homotypic synonym of"
relationship type and returns it. |
protected void |
Taxon.addSynonym(Synonym synonym)
Might be public in future.
|
void |
Taxon.addSynonym(Synonym synonym,
SynonymType synonymType)
|
void |
Taxon.removeSynonym(Synonym synonym)
Like
Taxon.removeSynonym(Synonym, boolean) with removeSynonymNameFromHomotypicalGroup set to true. |
void |
Taxon.removeSynonym(Synonym synonym,
boolean removeSynonymNameFromHomotypicalGroup)
Removes one element from the set of
synonyms assigned
to this (accepted/valid) taxon. |
void |
TaxonNode.setSynonymToBeUsed(Synonym synonymToBeUsed) |
Modifier and Type | Method and Description |
---|---|
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) |
Modifier and Type | Method and Description |
---|---|
Taxon |
TaxonDaoHibernateImpl.acceptedTaxonFor(Synonym synonym,
Classification classificationFilter,
java.util.List<java.lang.String> propertyPaths) |
long |
TaxonDaoHibernateImpl.countAcceptedTaxonFor(Synonym synonym,
Classification classificationFilter) |
long |
TaxonDaoHibernateImpl.countSynonyms(Synonym synonym,
SynonymType type) |
Modifier and Type | Method and Description |
---|---|
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.
|
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.
|
long |
ITaxonDao.countAcceptedTaxonFor(Synonym synonym,
Classification classificationFilter)
This method was originally required when synonyms still had a synonym relationship
to taxa and could belong to multiple taxa.
|
long |
ITaxonDao.countSynonyms(Synonym synonym,
SynonymType type)
Returns a count of the synonyms (where relationship.type == type,
if this argument is supplied) which do have an accepted taxon.
|
Constructor and Description |
---|
TaxonNodeDto(Synonym synonym,
boolean isHomotypic) |
Modifier and Type | Method and Description |
---|---|
boolean |
HomotypicSynonymsShouldBelongToGroupValidator.isValid(Synonym synonym,
javax.validation.ConstraintValidatorContext constraintContext) |
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