public interface ITaxonNameBase extends IIdentifiableEntity, IParsable, IRelated, IMatchable, java.lang.Cloneable
This class corresponds partially to:
TaxonName
instances. It should not be used to interface
instances of any other classModifier and Type | Method and Description |
---|---|
NameRelationship |
addBasionym(TaxonName basionym)
Assigns a taxon name as
basionym of this taxon name. |
NameRelationship |
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. |
void |
addDescription(TaxonNameDescription description)
Adds a new
taxon name description
to the set of taxon name descriptions assigned to this taxon name. |
NameTypeDesignation |
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 |
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 |
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
|
void |
addParsingProblems(int problems) |
NameRelationship |
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 |
addRelationshipFromName(TaxonName fromName,
NameRelationshipType type,
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 |
addRelationshipToName(TaxonName toName,
NameRelationshipType type)
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 . |
NameRelationship |
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 . |
NameRelationship |
addRelationshipToName(TaxonName toName,
NameRelationshipType type,
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 |
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 |
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. |
void |
addStatus(NomenclaturalStatus nomStatus)
Adds a new
nomenclatural status
to this taxon name's set of nomenclatural status. |
NomenclaturalStatus |
addStatus(NomenclaturalStatusType statusType,
Reference citation,
java.lang.String microCitation) |
void |
addTaxonBase(TaxonBase taxonBase)
Adds a new
taxon base
to the set of taxon bases using this taxon name. |
TextualTypeDesignation |
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. |
boolean |
addTypeDesignation(TypeDesignationBase<?> typeDesignation,
boolean addToAllNames)
Adds a
type designation to this taxon name's set of type designations |
java.lang.Object |
clone() |
int |
compareToName(TaxonName otherName)
This method compares 2 taxon names on it's name titles and caches.
|
java.lang.String |
generateFullTitle() |
java.lang.String |
getAppendedPhrase()
Returns the appended phrase string assigned to this taxon name.
|
TaxonName |
getBasionym()
Returns the taxon name which is the
basionym of this taxon name. |
java.util.Set<TaxonName> |
getBasionyms()
Returns the set of taxon names which are the
basionyms of this taxon name. |
java.lang.String |
getCitationString()
Returns the complete string containing the
nomenclatural reference citation
and the details assigned to this taxon name. |
java.util.Set<TaxonNameDescription> |
getDescriptions()
Returns the set of
taxon name descriptions assigned
to this taxon name. |
java.lang.String |
getFullTitleCache() |
HomotypicalGroup |
getHomotypicalGroup()
Returns the
homotypical group to which
this taxon name belongs. |
java.util.Set<NameRelationship> |
getNameRelations()
Returns the set of all
name relationships
in which this taxon name is involved. |
NomenclaturalCode |
getNameType() |
java.util.Set<NameTypeDesignation> |
getNameTypeDesignations()
Returns the set of
name type designations assigned
to this taxon name the rank of which must be above "species". |
java.lang.String |
getNomenclaturalMicroReference()
Returns the details string of the
nomenclatural reference assigned
to this taxon name. |
Reference |
getNomenclaturalReference()
Returns the
nomenclatural reference of this taxon name. |
DescriptionElementSource |
getNomenclaturalSource()
Sets the nomenclatural source which is a combination of the nomenclatural reference
and the detail information (exact page, table, figure, ...) where to find this name
for the first time.
|
Rank |
getRank()
Returns the taxonomic
rank of this taxon name. |
java.lang.String |
getReferenceYear()
Returns the string containing the publication date (generally only year)
of the
nomenclatural reference for this taxon name, null if there is
no nomenclatural reference. |
java.util.Set<Registration> |
getRegistrations()
This method returns als
registrations for the given name. |
java.util.Set<NameRelationship> |
getRelationsFromThisName()
Returns the set of all
name relationships
in which this taxon name is involved as a source ("from"-side). |
java.util.Set<NameRelationship> |
getRelationsToThisName()
Returns the set of all
name relationships
in which this taxon name is involved as a target ("to"-side). |
java.util.Set<TaxonName> |
getReplacedSynonyms()
Returns the set of taxon names which are the
replaced synonyms of this taxon name. |
java.util.Set<SpecimenTypeDesignation> |
getSpecimenTypeDesignations()
Returns the set of
specimen type designations
that typify this taxon name. |
java.util.Set<SpecimenTypeDesignation> |
getSpecimenTypeDesignationsOfHomotypicalGroup()
Returns the set of
specimen type designations assigned
to this taxon name. |
java.util.Set<NomenclaturalStatus> |
getStatus()
Returns the set of
nomenclatural status assigned
to this taxon name according to its corresponding nomenclature code. |
java.util.Set<Synonym> |
getSynonyms()
Returns the set of
(junior) synonyms (according to any
reference) that are based on this taxon name. |
java.util.List<TaggedText> |
getTaggedFullTitle() |
java.util.List<TaggedText> |
getTaggedName() |
java.util.Set<Taxon> |
getTaxa()
Returns the set of
taxa ("accepted/correct" names according to any
reference) that are based on this taxon name. |
java.util.Set<TaxonBase> |
getTaxonBases()
Returns the set of
taxon bases that refer to this taxon name. |
java.util.Set<TypeDesignationBase> |
getTypeDesignations()
Returns the set of
type designations assigned
to this taxon name. |
boolean |
isBacterial()
Returns
true if this name is of type NomenclaturalCode.ICNB or
any sub type and is supposed to be handled via IBacterialName |
boolean |
isBasionymFor(TaxonName newCombinationName)
Checks whether a basionym relationship exists between fromName and toName.
|
boolean |
isBotanical()
Returns
true if this name is of type NomenclaturalCode.ICNAFP or
any sub type and is supposed to be handled via IBotanicalName |
boolean |
isCultivar()
Returns
true if this name is of type NomenclaturalCode.ICNCP or
any sub type and is supposed to be handled via ICultivarPlantName |
boolean |
isGenus()
Returns the boolean value indicating whether the taxonomic
rank of this
taxon name is the genus rank (true) or not (false). |
boolean |
isGenusOrSupraGeneric()
Returns the boolean value indicating whether the taxonomic
rank of this
taxon name is the genus rank or higher (true ) or not (false ). |
boolean |
isGroupsBasionym()
Checks whether name is a basionym for ALL names
in its homotypical group.
|
boolean |
isHomotypic(TaxonName homoTypicName)
Returns the boolean value indicating whether a given taxon name belongs
to the same
homotypical group as this taxon name (true)
or not (false). |
boolean |
isInfraGeneric()
Returns the boolean value indicating whether the taxonomic
rank of this
taxon name is higher than the species rank and lower than the
genus rank (true) or not (false). |
boolean |
isInfraSpecific()
Returns the boolean value indicating whether the taxonomic
rank of this
taxon name is lower than the species rank (true) or not (false). |
boolean |
isNonViral()
Returns
true if this name is of type NomenclaturalCode.NonViral or
any sub type and is supposed to be handled via INonViralName |
boolean |
isOriginalCombination()
Indicates whether this taxon name is a
basionym
or a replaced synonym
of any other taxon name. |
boolean |
isProtectedFullTitleCache() |
boolean |
isReplacedSynonym()
Indicates this taxon name is a
replaced synonym
of any other taxon name. |
boolean |
isSpecies()
Returns the boolean value indicating whether the taxonomic
rank of this
taxon name is the species rank (true) or not (false). |
boolean |
isSpeciesAggregate()
Returns true if this name's rank indicates a rank that aggregates species like species
aggregates or species groups, false otherwise.
|
boolean |
isSupraGeneric()
Returns the boolean value indicating whether the taxonomic
rank of this
taxon name is higher than the genus rank (true) or not (false). |
boolean |
isSupraSpecific()
Returns the boolean value indicating whether the taxonomic
rank of this
taxon name is higher than the species rank (true) or not (false). |
boolean |
isViral()
Returns
true if this name is of type NomenclaturalCode.ICVCN or
any sub type and is supposed to be handled via IViralName |
boolean |
isZoological()
Returns
true if this name is of type NomenclaturalCode.ICZN or
any sub type and is supposed to be handled via IZoologicalName |
void |
makeGroupsBasionym()
Creates a basionym relationship to all other names in this names homotypical
group.
|
void |
mergeHomotypicGroups(TaxonName name) |
void |
removeAsGroupsBasionym()
Removes basionym relationship between this name and
each name in its homotypic group.
|
void |
removeBasionyms()
|
void |
removeDescription(TaxonNameDescription description)
Removes one element from the set of
taxon name descriptions assigned
to this taxon name. |
void |
removeNameRelationship(NameRelationship nameRelation)
Removes one
name relationship from one of both sets of
name relationships in which this taxon name is involved. |
void |
removeRelationToTaxonName(TaxonName toTaxonName) |
void |
removeStatus(NomenclaturalStatus nomStatus)
Removes one element from the set of nomenclatural status of this taxon name.
|
void |
removeTaxonBase(TaxonBase taxonBase)
Removes one element from the set of
taxon bases that refer to this taxon name. |
void |
removeTypeDesignation(TypeDesignationBase<?> typeDesignation)
Removes one element from the set of
type designations assigned to
this taxon name. |
void |
setAppendedPhrase(java.lang.String appendedPhrase) |
void |
setAsGroupsBasionym()
Creates a basionym relationship between this name and
each name in its homotypic group.
|
void |
setFullTitleCache(java.lang.String fullTitleCache) |
void |
setFullTitleCache(java.lang.String fullTitleCache,
boolean protectCache) |
void |
setHomotypicalGroup(HomotypicalGroup homotypicalGroup) |
void |
setNameType(NomenclaturalCode nameType) |
void |
setNomenclaturalMicroReference(java.lang.String nomenclaturalMicroReference) |
void |
setNomenclaturalReference(INomenclaturalReference nomenclaturalReference)
Same as setNomenclaturalReferences, to also allow interfaces to be used.
|
void |
setNomenclaturalReference(Reference nomenclaturalReference)
Assigns a
nomenclatural reference to this taxon name. |
void |
setNomenclaturalSource(DescriptionElementSource nomenclaturalSource)
Sets the nomenclatural source
|
void |
setProtectedFullTitleCache(boolean protectedFullTitleCache) |
void |
setRank(Rank rank) |
addCredit, addCredit, addExtension, addExtension, addIdentifier, addIdentifier, addIdentifier, addRights, generateTitle, getCredits, getCredits, getData, getExtensions, getIdentifiers, getLsid, getRights, getTitleCache, isProtectedTitleCache, removeCredit, removeCredit, removeExtension, removeIdentifier, removeIdentifier, removeRights, removeSources, replaceCredit, replaceIdentifier, resetTitleCache, setLsid, setProtectedTitleCache, setTitleCache, setTitleCache, toString
addAggregationSource, addImportSource, addPrimaryTaxonomicSource, addPrimaryTaxonomicSource, addSource, addSource, addSource, addSources, getSources, removeSource
addAnnotation, addMarker, getAnnotations, getMarkers, getMarkers, hasMarker, hasMarker, markerValue, removeAnnotation, removeMarker, removeMarker
getUpdated, getUpdatedBy, setUpdated, setUpdatedBy
getCreated, getCreatedBy, getId, getUuid, isInstanceOf, isPersited, setCreated, setCreatedBy, setId, setUuid
addParsingProblem, getParsingProblem, getParsingProblems, getProblemEnds, getProblemStarts, hasProblem, hasProblem, removeParsingProblem, setParsingProblem, setProblemEnds, setProblemStarts
addRelationship, getUuid
NomenclaturalCode getNameType()
void setNameType(NomenclaturalCode nameType)
java.lang.Object clone()
java.lang.String generateFullTitle()
java.lang.String getFullTitleCache()
java.util.List<TaggedText> getTaggedName()
java.util.List<TaggedText> getTaggedFullTitle()
void setFullTitleCache(java.lang.String fullTitleCache)
void setFullTitleCache(java.lang.String fullTitleCache, boolean protectCache)
boolean isProtectedFullTitleCache()
void setProtectedFullTitleCache(boolean protectedFullTitleCache)
java.util.Set<NameRelationship> getNameRelations()
name relationships
in which this taxon name is involved. A taxon name can be both source
in some name relationships or target in some others.getRelationsToThisName()
,
getRelationsFromThisName()
,
#addNameRelationship(NameRelationship)
,
#addRelationshipToName(TaxonName, NameRelationshipType, String)
,
#addRelationshipFromName(TaxonName, NameRelationshipType, String)
NameRelationship addRelationshipToName(TaxonName toName, NameRelationshipType type, java.lang.String ruleConsidered, NomenclaturalCodeEdition codeEdition)
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
.toName
- the taxon name of the target for this new name relationshiptype
- the type of this new name relationshipruleConsidered
- the string which specifies the rule on which this name relationship is basedgetRelationsToThisName()
,
getNameRelations()
,
#addRelationshipFromName(TaxonName, NameRelationshipType, String)
,
#addNameRelationship(NameRelationship)
NameRelationship addRelationshipToName(TaxonName toName, NameRelationshipType type)
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
.toName
- the taxon name of the target for this new name relationshiptype
- the type of this new name relationshipruleConsidered
- the string which specifies the rule on which this name relationship is basedcodeEdition
- the edition of the nomenclatural code where the ruleConsidered
has been published.getRelationsToThisName()
,
getNameRelations()
,
#addRelationshipFromName(TaxonName, NameRelationshipType, String)
,
#addNameRelationship(NameRelationship)
NameRelationship addRelationshipToName(TaxonName toName, NameRelationshipType type, Reference citation, java.lang.String microCitation, java.lang.String ruleConsidered, NomenclaturalCodeEdition codeEdition)
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
.toName
- the taxon name of the target for this new name relationshiptype
- the type of this new name relationshipruleConsidered
- the string which specifies the rule on which this name relationship is basedgetRelationsToThisName()
,
getNameRelations()
,
#addRelationshipFromName(TaxonName, NameRelationshipType, String)
,
#addNameRelationship(NameRelationship)
NameRelationship addRelationshipFromName(TaxonName fromName, NameRelationshipType type, java.lang.String ruleConsidered, NomenclaturalCodeEdition codeEdition)
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
.fromName
- the taxon name of the source for this new name relationshiptype
- the type of this new name relationshipruleConsidered
- the string which specifies the rule on which this name relationship is basedcitation
- the reference in which this relation was describedmicroCitation
- the reference detail for this relation (e.g. page)getRelationsFromThisName()
,
getNameRelations()
,
#addRelationshipToName(TaxonName, NameRelationshipType, String)
,
#addNameRelationship(NameRelationship)
NameRelationship addRelationshipFromName(TaxonName fromName, NameRelationshipType type, Reference citation, java.lang.String microCitation, java.lang.String ruleConsidered, NomenclaturalCodeEdition codeEdition)
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
.fromName
- the taxon name of the source for this new name relationshiptype
- the type of this new name relationshipruleConsidered
- the string which specifies the rule on which this name relationship is basedcitation
- the reference in which this relation was describedmicroCitation
- the reference detail for this relation (e.g. page)codeEditrion
- the nomenclatural code used for the considered rulegetRelationsFromThisName()
,
getNameRelations()
,
#addRelationshipToName(TaxonName, NameRelationshipType, String)
,
#addNameRelationship(NameRelationship)
void removeNameRelationship(NameRelationship nameRelation)
name relationship
from one of both sets of
name relationships
in which this taxon name is involved.
The name relationship will also be removed from one of both sets belonging
to the second taxon name involved. Furthermore the fromName and toName
attributes of the name relationship object will be nullified.nameRelation
- the name relationship which should be deleted from one of both setsgetNameRelations()
void removeRelationToTaxonName(TaxonName toTaxonName)
java.util.Set<NameRelationship> getRelationsFromThisName()
name relationships
in which this taxon name is involved as a source ("from"-side).getNameRelations()
,
getRelationsToThisName()
,
#addRelationshipFromName(TaxonName, NameRelationshipType, String)
java.util.Set<NameRelationship> getRelationsToThisName()
name relationships
in which this taxon name is involved as a target ("to"-side).getNameRelations()
,
getRelationsFromThisName()
,
#addRelationshipToName(TaxonName, NameRelationshipType, String)
java.util.Set<NomenclaturalStatus> getStatus()
nomenclatural status
assigned
to this taxon name according to its corresponding nomenclature code.
This includes the type
of the nomenclatural status
and the nomenclatural code rule considered.NomenclaturalStatus
,
NomenclaturalStatusType
void addStatus(NomenclaturalStatus nomStatus)
nomenclatural status
to this taxon name's set of nomenclatural status.nomStatus
- the nomenclatural status to be addedgetStatus()
NomenclaturalStatus addStatus(NomenclaturalStatusType statusType, Reference citation, java.lang.String microCitation)
void removeStatus(NomenclaturalStatus nomStatus)
nomStatus
- the nomenclatural status of this taxon name which should be deletedgetStatus()
boolean isOriginalCombination()
basionym
or a replaced synonym
of any other taxon name. Returns "true", if a basionym or a replaced
synonym relationship
from this taxon name to another taxon name exists,
false otherwise (also in case this taxon name is the only one in the
homotypical group).boolean isReplacedSynonym()
replaced synonym
of any other taxon name. Returns "true", if a replaced
synonym relationship
from this taxon name to another taxon name exists,
false otherwise (also in case this taxon name is the only one in the
homotypical group).TaxonName getBasionym()
basionym
of this taxon name.
The basionym of a taxon name is its epithet-bringing synonym.
For instance Pinus abies L. was published by Linnaeus and the botanist
Karsten transferred later this taxon to the genus Picea. Therefore,
Pinus abies L. is the basionym of the new combination Picea abies (L.) H. Karst.
If more than one basionym exists one is choosen at radom.
If no basionym exists null is returned.java.util.Set<TaxonName> getBasionyms()
basionyms
of this taxon name.
The basionym of a taxon name is its epithet-bringing synonym.
For instance Pinus abies L. was published by Linnaeus and the botanist
Karsten transferred later this taxon to the genus Picea. Therefore,
Pinus abies L. is the basionym of the new combination Picea abies (L.) H. Karst.NameRelationship addBasionym(TaxonName basionym)
basionym
of this taxon name.
The basionym relationship
will be added to this taxon name
and to the basionym. The basionym cannot have itself a basionym.
The homotypical groups
of this taxon name and of the basionym
will be merged
.basionym
- the taxon name to be set as the basionym of this taxon namegetBasionym()
,
#addBasionym(TaxonName, String)
NameRelationship addBasionym(TaxonName basionym, Reference citation, java.lang.String microcitation, java.lang.String ruleConsidered, NomenclaturalCodeEdition codeEdition)
basionym
of this taxon name
and keeps the nomenclatural rule considered for it. The basionym
relationship
will be added to this taxon name and to the basionym.
The basionym cannot have itself a basionym.
The homotypical groups
of this taxon name and of the basionym
will be merged
.basionym
- the taxon name to be set as the basionym of this taxon nameruleConsidered
- the string identifying the nomenclatural rulegetBasionym()
,
addBasionym(TaxonName)
void removeBasionyms()
basionym
relationship
from the set of
name relationships to
this taxon name. The same relationhip will be
removed from the set of name relationships from
the taxon name
previously used as basionym.getBasionym()
,
addBasionym(TaxonName)
java.util.Set<TaxonName> getReplacedSynonyms()
replaced synonyms
of this taxon name.void addReplacedSynonym(TaxonName replacedSynonym, Reference citation, java.lang.String microcitation, java.lang.String ruleConsidered, NomenclaturalCodeEdition codeEdition)
replaced synonym
of this taxon name
and keeps the nomenclatural rule considered for it. The replaced synonym
relationship
will be added to this taxon name and to the replaced synonym.
The homotypical groups
of this taxon name and of the replaced synonym
will be merged
.basionym
- the taxon name to be set as the basionym of this taxon nameruleConsidered
- the string identifying the nomenclatural rulegetBasionym()
,
addBasionym(TaxonName)
@Deprecated NameRelationship addOriginalSpelling(TaxonName originalSpelling, Reference citation, java.lang.String microcitation)
Reference getNomenclaturalReference()
nomenclatural reference
of this taxon name.
The nomenclatural reference is here meant to be the one publication
this taxon name was originally published in while fulfilling the formal
requirements as specified by the corresponding nomenclatural code
.Reference
,
getNomenclaturalSource()
void setNomenclaturalReference(Reference nomenclaturalReference)
nomenclatural reference
to this taxon name.
The corresponding nomenclaturally relevant flag
will be set to true
as it is obviously used for nomenclatural purposes.getNomenclaturalReference()
void setNomenclaturalReference(INomenclaturalReference nomenclaturalReference)
nomenclaturalReference
- setNomenclaturalReference(Reference)
java.lang.String getNomenclaturalMicroReference()
nomenclatural reference
assigned
to this taxon name. The details describe the exact localisation within
the publication used as nomenclature reference. These are mostly
(implicitly) pages but can also be figures or tables or any other
element of a publication. A nomenclatural micro reference (details)
requires the existence of a nomenclatural reference.void setNomenclaturalMicroReference(java.lang.String nomenclaturalMicroReference)
getNomenclaturalMicroReference()
DescriptionElementSource getNomenclaturalSource()
void setNomenclaturalSource(DescriptionElementSource nomenclaturalSource)
nomenclaturalSource
- java.lang.String getAppendedPhrase()
void setAppendedPhrase(java.lang.String appendedPhrase)
getAppendedPhrase()
void addParsingProblems(int problems)
warnings
- java.util.Set<TypeDesignationBase> getTypeDesignations()
type designations
assigned
to this taxon name.NameTypeDesignation
,
SpecimenTypeDesignation
void removeTypeDesignation(TypeDesignationBase<?> typeDesignation)
type designations
assigned to
this taxon name. The type designation itself will be nullified.typeDesignation
- the type designation which should be deletedjava.util.Set<SpecimenTypeDesignation> getSpecimenTypeDesignationsOfHomotypicalGroup()
specimen type designations
assigned
to this taxon name. The rank
of this taxon name is generally
"species" or below. The specimen type designations include all the
specimens on which the typification of this name is based (which are
exclusively used to typify taxon names belonging to the same
homotypical group
to which this taxon name
belongs) and eventually the status of these designations.java.util.Set<NameTypeDesignation> getNameTypeDesignations()
name type designations
assigned
to this taxon name the rank of which must be above "species".
The name type designations include all the taxon names used to typify
this taxon name and eventually the rejected or conserved status
of these designations.NameTypeDesignation
,
SpecimenTypeDesignation
NameTypeDesignation addNameTypeDesignation(TaxonName typeSpecies, Reference citation, java.lang.String citationMicroReference, java.lang.String originalNameString, NameTypeDesignationStatus status, boolean isRejectedType, boolean isConservedType, boolean isNotDesignated, boolean addToAllHomotypicNames)
name type designation
to this taxon name's set of type designations.typeSpecies
- the taxon name to be used as type of this taxon namecitation
- the reference for this new designationcitationMicroReference
- the string with the details (generally pages) within the referenceoriginalNameString
- the taxon name string used in the reference to assert this designationisRejectedType
- the boolean status for a rejected name type designationisConservedType
- the boolean status for a conserved name type designationisLectoType
- the boolean status for a lectotype name type designationisNotDesignated
- the boolean status for a name type designation without name typeaddToAllHomotypicNames
- the boolean indicating whether the name type designation should be
added to all taxon names of the homotypical group this taxon name belongs togetNameTypeDesignations()
,
NameTypeDesignation
,
TypeDesignationBase.isNotDesignated()
NameTypeDesignation addNameTypeDesignation(TaxonName typeSpecies, Reference citation, java.lang.String citationMicroReference, java.lang.String originalNameString, NameTypeDesignationStatus status, boolean addToAllHomotypicNames)
name type designation
to this taxon name's set of type designations.typeSpecies
- the taxon name to be used as type of this taxon namecitation
- the reference for this new designationcitationMicroReference
- the string with the details (generally pages) within the referenceoriginalNameString
- the taxon name string used in the reference to assert this designationstatus
- the name type designation statusaddToAllHomotypicNames
- the boolean indicating whether the name type designation should be
added to all taxon names of the homotypical group this taxon name belongs togetNameTypeDesignations()
,
NameTypeDesignation
,
TypeDesignationBase.isNotDesignated()
java.util.Set<SpecimenTypeDesignation> getSpecimenTypeDesignations()
specimen type designations
that typify this taxon name.SpecimenTypeDesignation addSpecimenTypeDesignation(DerivedUnit typeSpecimen, SpecimenTypeDesignationStatus status, Reference citation, java.lang.String citationMicroReference, java.lang.String originalNameString, boolean isNotDesignated, boolean addToAllHomotypicNames)
specimen type designation
to this taxon name's set of type designations.typeSpecimen
- the specimen to be used as a type for this taxon namestatus
- the specimen type designation statuscitation
- the reference for this new specimen type designationcitationMicroReference
- the string with the details (generally pages) within the referenceoriginalNameString
- the taxon name used in the reference to assert this designationisNotDesignated
- the boolean status for a specimen type designation without specimen typeaddToAllHomotypicNames
- the boolean indicating whether the specimen type designation should be
added to all taxon names of the homotypical group the typified
taxon name belongs togetSpecimenTypeDesignations()
,
SpecimenTypeDesignationStatus
,
SpecimenTypeDesignation
,
TypeDesignationBase.isNotDesignated()
TextualTypeDesignation addTextualTypeDesignation(java.lang.String text, Language language, boolean isVerbatim, Reference citation, java.lang.String citationMicroReference, java.lang.String originalNameString, boolean addToAllHomotypicNames)
textual type designation
to this taxon name's set of type designations.text
- the textlanguage
- the language of the text, if no language is defined Language.UNDETERMINED()
is usedisVerbatim
- wether or not this the text is a verbatim text from a referencecitation
- the reference for this new specimen type designationcitationMicroReference
- the string with the details (generally pages) within the referenceoriginalNameString
- the taxon name used in the reference to assert this designationaddToAllHomotypicNames
- the boolean indicating whether the specimen type designation should beboolean addTypeDesignation(TypeDesignationBase<?> typeDesignation, boolean addToAllNames)
type designation
to this
taxon name's set of type designationstypeDesignation
- the typeDesignation to be added to this
taxon nameaddToAllNames
- the boolean indicating whether the type designation should be
added to all taxon names of the homotypical group the typified
taxon name belongs tojava.lang.IllegalArgumentException
- if the type designation already has typified names, an exception
is thrown. We do this to prevent a type designation to be used for multiple taxon names.HomotypicalGroup getHomotypicalGroup()
homotypical group
to which
this taxon name belongs. A homotypical group represents all taxon names
that share the same types.HomotypicalGroup
void setHomotypicalGroup(HomotypicalGroup homotypicalGroup)
getHomotypicalGroup()
java.lang.String getCitationString()
nomenclatural reference citation
and the details
assigned to this taxon name.eu.etaxonomy.cdm.model.reference.INomenclaturalReference#getNomenclaturalCitation()
,
getNomenclaturalReference()
,
getNomenclaturalMicroReference()
java.lang.String getReferenceYear()
nomenclatural reference
for this taxon name, null if there is
no nomenclatural reference.INomenclaturalReference.getYear()
java.util.Set<TaxonBase> getTaxonBases()
taxon bases
that refer to this taxon name.
In this context a taxon base means the use of a taxon name by a reference
either as a taxon
("accepted/correct" name) or
as a (junior) synonym
.
A taxon name can be used by several distinct references
but only once
within a taxonomic treatment (identified by one reference).getTaxa()
,
getSynonyms()
void addTaxonBase(TaxonBase taxonBase)
taxon base
to the set of taxon bases using this taxon name.taxonBase
- the taxon base to be addedgetTaxonBases()
,
removeTaxonBase(TaxonBase)
void removeTaxonBase(TaxonBase taxonBase)
taxon bases
that refer to this taxon name.taxonBase
- the taxon base which should be removed from the corresponding setgetTaxonBases()
,
addTaxonBase(TaxonBase)
java.util.Set<Taxon> getTaxa()
taxa
("accepted/correct" names according to any
reference) that are based on this taxon name. This set is a subset of
the set returned by getTaxonBases().Taxon
,
getTaxonBases()
,
getSynonyms()
java.util.Set<Synonym> getSynonyms()
(junior) synonyms
(according to any
reference) that are based on this taxon name. This set is a subset of
the set returned by getTaxonBases().Synonym
,
getTaxonBases()
,
getTaxa()
java.util.Set<TaxonNameDescription> getDescriptions()
taxon name descriptions
assigned
to this taxon name. A taxon name description is a piece of information
concerning the taxon name like for instance the content of its first
publication (protolog) or a picture of this publication.void addDescription(TaxonNameDescription description)
taxon name description
to the set of taxon name descriptions assigned to this taxon name. The
content of the taxonName attribute
of the
taxon name description itself will be replaced with this taxon name.description
- the taxon name description to be addedgetDescriptions()
,
removeDescription(TaxonNameDescription)
void removeDescription(TaxonNameDescription description)
taxon name descriptions
assigned
to this taxon name. The content of the taxonName attribute
of the description itself will be set to "null".description
- the taxon name description which should be removedgetDescriptions()
,
addDescription(TaxonNameDescription)
,
TaxonNameDescription.getTaxonName()
void mergeHomotypicGroups(TaxonName name)
boolean isHomotypic(TaxonName homoTypicName)
homotypical group
as this taxon name (true)
or not (false). Returns "true" only if the homotypical groups of both
taxon names exist and if they are identical.homoTypicName
- the taxon name the homotypical group of which is to be checkedHomotypicalGroup
boolean isGroupsBasionym()
false
if there are no other names in the groupname
- boolean isBasionymFor(TaxonName newCombinationName)
fromName
- toName
- void makeGroupsBasionym()
HomotypicalGroup.setGroupBasionym(TaxonName basionymName)
boolean isSupraGeneric()
rank
of this
taxon name is higher than the genus rank (true) or not (false).
Suprageneric non viral names are monomials.
Returns false if rank is null.boolean isGenus()
rank
of this
taxon name is the genus rank (true) or not (false). Non viral names with
genus rank are monomials. Returns false if rank is null.boolean isGenusOrSupraGeneric()
rank
of this
taxon name is the genus rank or higher (true
) or not (false
).
Non viral names with
genus rank or higher are monomials. Returns false if rank is null.isGenus()
|| isSupraGeneric()
isGenus()
,
isSupraGeneric()
,
isInfraGeneric()
,
isSpecies()
,
isInfraSpecific()
boolean isInfraGeneric()
rank
of this
taxon name is higher than the species rank and lower than the
genus rank (true) or not (false). Infrageneric non viral names are
binomials. Returns false if rank is null.isSupraGeneric()
,
isGenus()
,
isSpecies()
,
isInfraSpecific()
boolean isSupraSpecific()
rank
of this
taxon name is higher than the species rank (true) or not (false).
Returns false if rank is null.isGenus()
,
isInfraGeneric()
,
isSpecies()
,
isInfraSpecific()
boolean isSpecies()
rank
of this
taxon name is the species rank (true) or not (false). Non viral names
with species rank are binomials.
Returns false if rank is null.isSupraGeneric()
,
isGenus()
,
isInfraGeneric()
,
isInfraSpecific()
boolean isInfraSpecific()
rank
of this
taxon name is lower than the species rank (true) or not (false).
Infraspecific non viral names are trinomials.
Returns false if rank is null.isSupraGeneric()
,
isGenus()
,
isInfraGeneric()
,
isSpecies()
boolean isSpeciesAggregate()
Rank.isSpeciesAggregate()
void setAsGroupsBasionym()
basionymName
- void removeAsGroupsBasionym()
basionymName
- int compareToName(TaxonName otherName)
TaxonNameComparator
.
Historically it was a compareTo method in IdentifiableEntity
but did not fulfill the Comparable
contract.
https://dev.e-taxonomy.eu/redmine/issues/922
https://dev.e-taxonomy.eu/redmine/issues/6311
otherTaxon
- Comparable.compareTo(Object)
java.lang.NullPointerException
- if otherTaxon is null
TaxonName.compareToName(TaxonName)
,
TaxonNameComparator
,
TaxonComparator
java.util.Set<Registration> getRegistrations()
registrations
for the given name.boolean isZoological()
true
if this name is of type NomenclaturalCode.ICZN
or
any sub type and is supposed to be handled via IZoologicalName
boolean isNonViral()
true
if this name is of type NomenclaturalCode.NonViral
or
any sub type and is supposed to be handled via INonViralName
boolean isBotanical()
true
if this name is of type NomenclaturalCode.ICNAFP
or
any sub type and is supposed to be handled via IBotanicalName
boolean isCultivar()
true
if this name is of type NomenclaturalCode.ICNCP
or
any sub type and is supposed to be handled via ICultivarPlantName
boolean isBacterial()
true
if this name is of type NomenclaturalCode.ICNB
or
any sub type and is supposed to be handled via IBacterialName
boolean isViral()
true
if this name is of type NomenclaturalCode.ICVCN
or
any sub type and is supposed to be handled via IViralName
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