eu.etaxonomy.cdm.model.name
Class NonViralName<T extends NonViralName>

java.lang.Object
  eu.etaxonomy.cdm.model.common.CdmBase
      eu.etaxonomy.cdm.model.common.VersionableEntity
          eu.etaxonomy.cdm.model.common.AnnotatableEntity
              eu.etaxonomy.cdm.model.common.IdentifiableEntity<S>
                  eu.etaxonomy.cdm.model.name.TaxonNameBase<T,INonViralNameCacheStrategy>
                      eu.etaxonomy.cdm.model.name.NonViralName<T>

All Implemented Interfaces:

IAnnotatableEntity, ICdmBase, IIdentifiableEntity, IParsable, IReferencedEntity, IRelated, ISourceable<IdentifiableSource>, IVersionableEntity, IMatchable, Serializable, Cloneable

Direct Known Subclasses:

BacterialName, BotanicalName, ZoologicalName

@Entity
@Indexed(index="eu.etaxonomy.cdm.model.name.TaxonNameBase")
@Configurable
@CorrectEpithetsForRank(groups=Level2.class)
@MustHaveAuthority(groups=Level2.class)
@NoDuplicateNames(groups=Level3.class)
public class NonViralName<T extends NonViralName>
extends TaxonNameBase<T,INonViralNameCacheStrategy>
implements Cloneable

The taxon name class for all non viral taxa. Parenthetical authorship is derived from basionym relationship. The scientific name including author strings and maybe year can be stored as a string in the inherited titleCache attribute. The year itself is an information obtained from the nomenclatural reference. The scientific name string without author strings and year can be stored in the nameCache attribute.

This class corresponds partially to:

• TaxonName according to the TDWG ontology
• ScientificName and CanonicalName according to the TCS
• ScientificName according to the ABCD schema

Version:

1.0

Author:

m.doering

See Also:

Serialized Form

Field Summary

protected boolean	protectedAuthorshipCache
protected boolean	protectedNameCache

Fields inherited from class eu.etaxonomy.cdm.model.name.TaxonNameBase

fullTitleCache

Fields inherited from class eu.etaxonomy.cdm.model.common.IdentifiableEntity

cacheStrategy, NOT_PROTECTED, PROTECTED, protectedTitleCache, titleCache

Fields inherited from class eu.etaxonomy.cdm.model.common.AnnotatableEntity

annotations, markers

Fields inherited from class eu.etaxonomy.cdm.model.common.CdmBase

uuid

Constructor Summary

protected	NonViralName() Class constructor: creates a new non viral taxon name instance only containing the default cache strategy.
protected	NonViralName(Rank rank, HomotypicalGroup homotypicalGroup) Class constructor: creates a new non viral taxon name instance only containing its rank, its homotypical group and the default cache strategy.
protected	NonViralName(Rank rank, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, TeamOrPersonBase combinationAuthorTeam, INomenclaturalReference nomenclaturalReference, 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.

Method Summary

HybridRelationship	addHybridChild(NonViralName childName, HybridRelationshipType type, String ruleConsidered) Creates a new hybrid relationship to this botanical name.
HybridRelationship	addHybridParent(NonViralName parentName, HybridRelationshipType type, String ruleConsidered) Creates a new hybrid relationship to this botanical name.
protected void	addHybridRelationship(HybridRelationship rel) Adds the given hybrid relationship to the set of hybrid relationships of both non-viral names involved in this hybrid relationship.
void	addRelationship(RelationshipBase relation) Deprecated. to be used by RelationshipBase only
Object	clone() Clones this non-viral name.
String	computeBasionymAuthorNomenclaturalTitle() Shortcut.
String	computeCombinationAuthorNomenclaturalTitle() Shortcut.
String	computeExBasionymAuthorNomenclaturalTitle() Shortcut.
String	computeExCombinationAuthorNomenclaturalTitle() Shortcut.
String	generateAuthorship() Generates and returns a concatenated and formated authorteams string including basionym and combination authors of this non viral taxon name according to the strategy defined in INonViralNameCacheStrategy.
String	generateFullTitle() Generates and returns the string with the scientific name of this non viral taxon name including author strings and maybe year according to the strategy defined in INonViralNameCacheStrategy.
protected String	generateNameCache() Generates the composed name string of this non viral taxon name without author strings or year according to the strategy defined in INonViralNameCacheStrategy.
protected Map<String,Field>	getAllFields()
String	getAuthorshipCache() Returns the concatenated and formated authorteams string including basionym and combination authors of this non viral taxon name.
INomenclaturalAuthor	getBasionymAuthorTeam() Returns the author (team) that published the original combination on which this non viral taxon name is nomenclaturally based.
Set<HybridRelationship>	getChildRelationships() Deprecated. use getHybridChildRelations() instead. Will be removed in higher versions.
INomenclaturalAuthor	getCombinationAuthorTeam() Returns the author (team) that published this non viral taxon name.
INomenclaturalAuthor	getExBasionymAuthorTeam() Returns the author (team) that contributed to the publication of the original combination this non viral taxon name is based on.
INomenclaturalAuthor	getExCombinationAuthorTeam() Returns the author (team) that contributed to the publication of this non viral taxon name as generally stated by the combination author (team) itself. An ex-author(-team) is an author(-team) to whom a taxon name was ascribed although it is not the author(-team) of a valid publication (for instance without the validating description or diagnosis in case of a name for a new taxon).
String	getFullTitleCache()
String	getGenusOrUninomial() Returns either the scientific name string (without authorship) for this non viral taxon name if its rank is genus or higher (monomial) or the string for the genus part of it if its rank is lower than genus (bi- or trinomial).
Set<HybridRelationship>	getHybridChildRelations() Returns the set of all hybrid relationships in which this taxon name is involved as a child.
Set<HybridRelationship>	getHybridParentRelations() Returns the set of all hybrid relationships in which this taxon name is involved as a parent.
String	getInfraGenericEpithet() Returns the genus subdivision epithet string (infrageneric part) for this non viral taxon name if its rank is infrageneric (lower than genus and higher than species aggregate: binomial).
String	getInfraSpecificEpithet() Returns the species subdivision epithet string (infraspecific part) for this non viral taxon name if its rank is infraspecific (lower than species: trinomial).
String	getNameCache() Returns or generates the nameCache (scientific name without author strings and year) string for this non viral taxon name.
NomenclaturalCode	getNomenclaturalCode() Returns null as nomenclatural code that governs the construction of this non viral taxon name since there is no specific nomenclatural code defined.
List<HybridRelationship>	getOrderedChildRelationships() Returns the hybrid child relationships ordered by relationship type, or if equal by title cache of the related names.
Set<HybridRelationship>	getParentRelationships() Deprecated. use getHybridParentRelations() instead. Will be removed in higher versions.
String	getSpecificEpithet() Returns the species epithet string for this non viral taxon name if its rank is species aggregate or lower (bi- or trinomial).
String	getTitleCache()
boolean	hasAuthors() Tests if the given name has any authors.
protected void	initListener()
boolean	isAutonym() Needs to be implemented by those classes that handle autonyms (e.g.
boolean	isBinomHybrid() Returns the boolean value of the flag indicating whether this botanical taxon name is the name of an interspecific hybrid (true) or not (false).
boolean	isCodeCompliant() Returns the boolean value "false" since the components of this taxon name cannot follow the rules of a corresponding nomenclatural code which is not defined for this class.
boolean	isHybridFormula() Returns the boolean value of the flag indicating whether the name of this botanical taxon name is a hybrid formula (true) or not (false).
boolean	isMonomHybrid() Returns the boolean value of the flag indicating whether this botanical taxon name is the name of an intergeneric hybrid (true) or not (false).
boolean	isProtectedAuthorshipCache() Returns the boolean value of the flag intended to protect (true) or not (false) the authorshipCache (complete authorship string) of this non viral taxon name.
boolean	isProtectedNameCache() Returns the boolean value of the flag intended to protect (true) or not (false) the nameCache (scientific name without author strings and year) string of this non viral taxon name.
boolean	isTrinomHybrid() Returns the boolean value of the flag indicating whether this botanical taxon name is the name of an infraspecific hybrid (true) or not (false).
static NonViralName	NewInstance(Rank rank) Creates a new non viral taxon name instance only containing its rank and the default cache strategy.
static NonViralName	NewInstance(Rank rank, HomotypicalGroup homotypicalGroup) Creates a new non viral taxon name instance only containing its rank, its homotypical group and the default cache strategy.
void	removeHybridChild(NonViralName child)
void	removeHybridParent(NonViralName parent)
void	removeHybridRelationship(HybridRelationship hybridRelation) Removes one hybrid relationship from the set of hybrid relationships in which this botanical taxon name is involved.
void	setAuthorshipCache(String authorshipCache) Assigns an authorshipCache string to this non viral taxon name.
void	setAuthorshipCache(String authorshipCache, boolean protectedAuthorshipCache) Assigns an authorshipCache string to this non viral taxon name.
void	setBasionymAuthorTeam(INomenclaturalAuthor basionymAuthorTeam)
void	setBinomHybrid(boolean binomHybrid)
void	setCombinationAuthorTeam(INomenclaturalAuthor combinationAuthorTeam)
void	setExBasionymAuthorTeam(INomenclaturalAuthor exBasionymAuthorTeam)
void	setExCombinationAuthorTeam(INomenclaturalAuthor exCombinationAuthorTeam)
void	setGenusOrUninomial(String genusOrUninomial)
void	setHybridFormula(boolean hybridFormula)
void	setInfraGenericEpithet(String infraGenericEpithet)
void	setInfraSpecificEpithet(String infraSpecificEpithet)
void	setMonomHybrid(boolean monomHybrid)
void	setNameCache(String nameCache) Assigns a nameCache string to this non viral taxon name and protects it from being overwritten.
void	setNameCache(String nameCache, boolean protectedNameCache) Assigns a nameCache string to this non viral taxon name and protects it from being overwritten.
void	setProtectedAuthorshipCache(boolean protectedAuthorshipCache)
void	setProtectedNameCache(boolean protectedNameCache)
void	setSpecificEpithet(String specificEpithet)
void	setTitleCache(String titleCache, boolean protectCache)
void	setTrinomHybrid(boolean trinomHybrid)

Methods inherited from class eu.etaxonomy.cdm.model.name.TaxonNameBase

addBasionym, addBasionym, addDescription, addNameRelationship, addNameTypeDesignation, addNameTypeDesignation, addParsingProblem, addParsingProblems, addRelationshipFromName, addRelationshipFromName, addRelationshipToName, addRelationshipToName, addReplacedSynonym, addSpecimenTypeDesignation, addStatus, addTaxonBase, addTypeDesignation, getAppendedPhrase, getBasionym, getBasionyms, getCitation, getCitationString, getDescriptions, getHomotypicalGroup, getNameRelations, getNameTypeDesignations, getNomenclaturalMicroReference, getNomenclaturalReference, getParsingProblem, getParsingProblems, getProblemEnds, getProblemStarts, getRank, getReferenceYear, getRelationsFromThisName, getRelationsToThisName, getSpecimenTypeDesignations, getSpecimenTypeDesignationsOfHomotypicalGroup, getStatus, getSynonyms, getTaggedName, getTaxa, getTaxonBases, getTypeDesignations, hasProblem, hasProblem, isBasionymFor, isGenus, isGroupsBasionym, isHomotypic, isInfraGeneric, isInfraSpecific, isOriginalCombination, isProtectedFullTitleCache, isSpecies, isSupraGeneric, isSupraSpecific, makeGroupsBasionym, mergeHomotypicGroups, removeAsGroupsBasionym, removeBasionyms, removeDescription, removeNameRelationship, removeParsingProblem, removeRelationToTaxonName, removeStatus, removeTaxonBase, removeTypeDesignation, setAppendedPhrase, setAsGroupsBasionym, setFullTitleCache, setFullTitleCache, setHomotypicalGroup, setNomenclaturalMicroReference, setNomenclaturalReference, setParsingProblem, setProblemEnds, setProblemStarts, setProtectedFullTitleCache, setRank

Methods inherited from class eu.etaxonomy.cdm.model.common.IdentifiableEntity

addCredit, addCredit, addExtension, addExtension, addRights, addSource, addSource, compareTo, generateTitle, getCacheStrategy, getCredits, getCredits, getData, getExtensions, getExtensions, getExtensions, getLsid, getRights, getSources, getTruncatedCache, isProtectedTitleCache, regenerateTitleCache, removeCredit, removeCredit, removeExtension, removeRights, removeSource, setCacheStrategy, setLsid, setProtectedTitleCache, setTitleCache, toString

Methods inherited from class eu.etaxonomy.cdm.model.common.AnnotatableEntity

addAnnotation, addMarker, getAnnotations, getMarkers, hasMarker, hasMarker, removeAnnotation, removeMarker

Methods inherited from class eu.etaxonomy.cdm.model.common.VersionableEntity

equals, getUpdated, getUpdatedBy, setUpdated, setUpdatedBy

Methods inherited from class eu.etaxonomy.cdm.model.common.CdmBase

addPropertyChangeListener, addPropertyChangeListener, clone, deproxy, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getCreated, getCreatedBy, getId, getUuid, hashCode, hasListeners, instanceToString, invokeSetMethod, invokeSetMethodWithNull, isInstanceOf, removePropertyChangeListener, removePropertyChangeListener, setCreated, setCreatedBy, setId, setUuid

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface eu.etaxonomy.cdm.model.common.IRelated

getUuid

Methods inherited from interface eu.etaxonomy.cdm.model.common.ICdmBase

getCreated, getCreatedBy, getId, getUuid, setCreated, setCreatedBy, setId, setUuid

Methods inherited from interface eu.etaxonomy.cdm.model.common.IAnnotatableEntity

addAnnotation, addMarker, getAnnotations, getMarkers, hasMarker, hasMarker, removeAnnotation, removeMarker

Methods inherited from interface eu.etaxonomy.cdm.model.common.IVersionableEntity

getUpdated, getUpdatedBy, setUpdated, setUpdatedBy

Field Detail

protectedNameCache

protected boolean protectedNameCache

protectedAuthorshipCache

protected boolean protectedAuthorshipCache

Constructor Detail

NonViralName

protected NonViralName()

Class constructor: creates a new non viral taxon name instance only containing the default cache strategy.

See Also:

NonViralName(Rank, HomotypicalGroup), #NonViralName(Rank, String, String, String, String, TeamOrPersonBase, Reference, String, HomotypicalGroup), INonViralNameCacheStrategy, INameCacheStrategy, IIdentifiableEntityCacheStrategy

NonViralName

protected NonViralName(Rank rank,
                       HomotypicalGroup homotypicalGroup)

Class constructor: creates a new non viral taxon name instance only containing its rank, its homotypical group and the default cache strategy. The new non viral taxon name instance will be also added to the set of non viral taxon names belonging to this homotypical group.

Parameters:

rank - the rank to be assigned to this non viral taxon name

homotypicalGroup - the homotypical group to which this non viral taxon name belongs

See Also:

NonViralName(), #NonViralName(Rank, String, String, String, String, TeamOrPersonBase, Reference, String, HomotypicalGroup), NewInstance(Rank, HomotypicalGroup), INonViralNameCacheStrategy, INameCacheStrategy, IIdentifiableEntityCacheStrategy

NonViralName

protected NonViralName(Rank rank,
                       String genusOrUninomial,
                       String infraGenericEpithet,
                       String specificEpithet,
                       String infraSpecificEpithet,
                       TeamOrPersonBase combinationAuthorTeam,
                       INomenclaturalReference nomenclaturalReference,
                       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. The new non viral taxon name instance will be also added to the set of non viral taxon names belonging to this homotypical group.

Parameters:

rank - the rank to be assigned to this non viral taxon name

genusOrUninomial - the string for this non viral taxon name if its rank is genus or higher or for the genus part if its rank is lower than genus

infraGenericEpithet - the string for the first epithet of this non viral taxon name if its rank is lower than genus and higher than species aggregate

specificEpithet - the string for the first epithet of this non viral taxon name if its rank is species aggregate or lower

infraSpecificEpithet - the string for the second epithet of this non viral taxon name if its rank is lower than species

combinationAuthorTeam - the author or the team who published this non viral taxon name

nomenclaturalReference - the nomenclatural reference where this non viral taxon name was published

nomenclMicroRef - the string with the details for precise location within the nomenclatural reference

homotypicalGroup - the homotypical group to which this non viral taxon name belongs

See Also:

NonViralName(), NonViralName(Rank, HomotypicalGroup), NewInstance(Rank, HomotypicalGroup), INonViralNameCacheStrategy, INameCacheStrategy, IIdentifiableEntityCacheStrategy

Method Detail

NewInstance

public static NonViralName NewInstance(Rank rank)

Creates a new non viral taxon name instance only containing its rank and the default cache strategy.

Parameters:

rank - the rank to be assigned to this non viral taxon name

See Also:

NewInstance(Rank, HomotypicalGroup), NonViralName(Rank, HomotypicalGroup), NonViralName(), #NonViralName(Rank, String, String, String, String, TeamOrPersonBase, Reference, String, HomotypicalGroup), INonViralNameCacheStrategy, INameCacheStrategy, IIdentifiableEntityCacheStrategy

NewInstance

public static NonViralName NewInstance(Rank rank,
                                       HomotypicalGroup homotypicalGroup)

Creates a new non viral taxon name instance only containing its rank, its homotypical group and the default cache strategy. The new non viral taxon name instance will be also added to the set of non viral taxon names belonging to this homotypical group.

Parameters:

rank - the rank to be assigned to this non viral taxon name

homotypicalGroup - the homotypical group to which this non viral taxon name belongs

See Also:

NewInstance(Rank), NonViralName(Rank, HomotypicalGroup), NonViralName(), #NonViralName(Rank, String, String, String, String, TeamOrPersonBase, Reference, String, HomotypicalGroup), INonViralNameCacheStrategy, INameCacheStrategy, IIdentifiableEntityCacheStrategy

initListener

protected void initListener()

Overrides:

initListener in class IdentifiableEntity<INonViralNameCacheStrategy>

getAllFields

protected Map<String,Field> getAllFields()

Specified by:

getAllFields in class TaxonNameBase<T extends NonViralName,INonViralNameCacheStrategy>

getCombinationAuthorTeam

public INomenclaturalAuthor getCombinationAuthorTeam()

Returns the author (team) that published this non viral taxon name.

Returns:

the nomenclatural author (team) of this non viral taxon name

See Also:

INomenclaturalAuthor, TeamOrPersonBase.getNomenclaturalTitle()

setCombinationAuthorTeam

public void setCombinationAuthorTeam(INomenclaturalAuthor combinationAuthorTeam)

See Also:

getCombinationAuthorTeam()

getExCombinationAuthorTeam

public INomenclaturalAuthor getExCombinationAuthorTeam()

Returns the author (team) that contributed to the publication of this non viral taxon name as generally stated by the combination author (team) itself.
An ex-author(-team) is an author(-team) to whom a taxon name was ascribed although it is not the author(-team) of a valid publication (for instance without the validating description or diagnosis in case of a name for a new taxon). The name of this ascribed authorship, followed by "ex", may be inserted before the name(s) of the publishing author(s) of the validly published name:
Lilium tianschanicum was described by Grubov (1977) as a new species and its name was ascribed to Ivanova; since there is no indication that Ivanova provided the validating description, the name may be cited as Lilium tianschanicum N. A. Ivanova ex Grubov or Lilium tianschanicum Grubov.

The presence of an author (team) of this non viral taxon name is a condition for the existence of an ex author (team) for this same name.

Returns:

the nomenclatural ex author (team) of this non viral taxon name

See Also:

getCombinationAuthorTeam(), INomenclaturalAuthor, TeamOrPersonBase.getNomenclaturalTitle()

setExCombinationAuthorTeam

public void setExCombinationAuthorTeam(INomenclaturalAuthor exCombinationAuthorTeam)

See Also:

getExCombinationAuthorTeam()

getBasionymAuthorTeam

public INomenclaturalAuthor getBasionymAuthorTeam()

Returns the author (team) that published the original combination on which this non viral taxon name is nomenclaturally based. Such an author (team) can only exist if this non viral taxon name is a new combination due to a taxonomical revision.

Returns:

the nomenclatural basionym author (team) of this non viral taxon name

See Also:

getCombinationAuthorTeam(), INomenclaturalAuthor, TeamOrPersonBase.getNomenclaturalTitle()

setBasionymAuthorTeam

public void setBasionymAuthorTeam(INomenclaturalAuthor basionymAuthorTeam)

See Also:

getBasionymAuthorTeam()

getExBasionymAuthorTeam

public INomenclaturalAuthor getExBasionymAuthorTeam()

Returns the author (team) that contributed to the publication of the original combination this non viral taxon name is based on. This should have been generally stated by the basionym author (team) itself. The presence of a basionym author (team) of this non viral taxon name is a condition for the existence of an ex basionym author (team) for this same name.

Returns:

the nomenclatural ex basionym author (team) of this non viral taxon name

See Also:

getBasionymAuthorTeam(), getExCombinationAuthorTeam(), getCombinationAuthorTeam(), INomenclaturalAuthor, TeamOrPersonBase.getNomenclaturalTitle()

setExBasionymAuthorTeam

public void setExBasionymAuthorTeam(INomenclaturalAuthor exBasionymAuthorTeam)

See Also:

getExBasionymAuthorTeam()

getGenusOrUninomial

public String getGenusOrUninomial()

Returns either the scientific name string (without authorship) for this non viral taxon name if its rank is genus or higher (monomial) or the string for the genus part of it if its rank is lower than genus (bi- or trinomial). Genus or uninomial strings begin with an upper case letter.

Returns:

the string containing the suprageneric name, the genus name or the genus part of this non viral taxon name

See Also:

getNameCache()

setGenusOrUninomial

public void setGenusOrUninomial(String genusOrUninomial)

See Also:

getGenusOrUninomial()

getInfraGenericEpithet

public String getInfraGenericEpithet()

Returns the genus subdivision epithet string (infrageneric part) for this non viral taxon name if its rank is infrageneric (lower than genus and higher than species aggregate: binomial). Genus subdivision epithet strings begin with an upper case letter.

Returns:

the string containing the infrageneric part of this non viral taxon name

See Also:

getNameCache()

setInfraGenericEpithet

public void setInfraGenericEpithet(String infraGenericEpithet)

See Also:

getInfraGenericEpithet()

getSpecificEpithet

public String getSpecificEpithet()

Returns the species epithet string for this non viral taxon name if its rank is species aggregate or lower (bi- or trinomial). Species epithet strings begin with a lower case letter.

Returns:

the string containing the species epithet of this non viral taxon name

See Also:

getNameCache()

setSpecificEpithet

public void setSpecificEpithet(String specificEpithet)

See Also:

getSpecificEpithet()

getInfraSpecificEpithet

public String getInfraSpecificEpithet()

Returns the species subdivision epithet string (infraspecific part) for this non viral taxon name if its rank is infraspecific (lower than species: trinomial). Species subdivision epithet strings begin with a lower case letter.

Returns:

the string containing the infraspecific part of this non viral taxon name

See Also:

getNameCache()

setInfraSpecificEpithet

public void setInfraSpecificEpithet(String infraSpecificEpithet)

See Also:

getInfraSpecificEpithet()

generateFullTitle

public String generateFullTitle()

Generates and returns the string with the scientific name of this non viral taxon name including author strings and maybe year according to the strategy defined in INonViralNameCacheStrategy. This string may be stored in the inherited titleCache attribute. This method overrides the generic and inherited TaxonNameBase#generateTitle() method.

Specified by:

generateFullTitle in class TaxonNameBase<T extends NonViralName,INonViralNameCacheStrategy>

Returns:

the string with the composed name of this non viral taxon name with authorship (and maybe year)

See Also:

IdentifiableEntity.generateTitle(), IdentifiableEntity.getTitleCache(), IdentifiableEntity.generateTitle()

generateNameCache

protected String generateNameCache()

Generates the composed name string of this non viral taxon name without author strings or year according to the strategy defined in INonViralNameCacheStrategy. The result might be stored in nameCache if the flag protectedNameCache is not set.

Returns:

the string with the composed name of this non viral taxon name without authors or year

See Also:

getNameCache()

getNameCache

public String getNameCache()

Returns or generates the nameCache (scientific name without author strings and year) string for this non viral taxon name. If the protectedNameCache flag is not set (False) the string will be generated according to a defined strategy, otherwise the value of the actual nameCache string will be returned.

Returns:

the string which identifies this non viral taxon name (without authors or year)

See Also:

generateNameCache()

setNameCache

public void setNameCache(String nameCache)

Assigns a nameCache string to this non viral taxon name and protects it from being overwritten. Sets the protectedNameCache flag to true.

Parameters:

nameCache - the string which identifies this non viral taxon name (without authors or year)

See Also:

getNameCache()

setNameCache

public void setNameCache(String nameCache,
                         boolean protectedNameCache)

Assigns a nameCache string to this non viral taxon name and protects it from being overwritten. Sets the protectedNameCache flag to true.

Parameters:

nameCache - the string which identifies this non viral taxon name (without authors or year)

protectedNameCache - if true teh protectedNameCache is set to true or otherwise set to false

See Also:

getNameCache()

isProtectedNameCache

public boolean isProtectedNameCache()

Returns the boolean value of the flag intended to protect (true) or not (false) the nameCache (scientific name without author strings and year) string of this non viral taxon name.

Returns:

the boolean value of the protectedNameCache flag

See Also:

getNameCache()

setProtectedNameCache

public void setProtectedNameCache(boolean protectedNameCache)

See Also:

isProtectedNameCache()

generateAuthorship

public String generateAuthorship()

Generates and returns a concatenated and formated authorteams string including basionym and combination authors of this non viral taxon name according to the strategy defined in INonViralNameCacheStrategy.

Returns:

the string with the concatenated and formated authorteams for this non viral taxon name

See Also:

INonViralNameCacheStrategy.getAuthorshipCache(NonViralName)

getAuthorshipCache

public String getAuthorshipCache()

Returns the concatenated and formated authorteams string including basionym and combination authors of this non viral taxon name. If the protectedAuthorshipCache flag is set this method returns the string stored in the the authorshipCache attribute, otherwise it generates the complete authorship string, returns it and stores it in the authorshipCache attribute.

Returns:

the string with the concatenated and formated authorteams for this non viral taxon name

See Also:

generateAuthorship()

setAuthorshipCache

public void setAuthorshipCache(String authorshipCache)

Assigns an authorshipCache string to this non viral taxon name. Sets the isProtectedAuthorshipCache flag to true.

Parameters:

authorshipCache - the string which identifies the complete authorship of this non viral taxon name

See Also:

getAuthorshipCache()

getFullTitleCache

public String getFullTitleCache()

Overrides:

getFullTitleCache in class TaxonNameBase<T extends NonViralName,INonViralNameCacheStrategy>

getTitleCache

public String getTitleCache()

Specified by:

getTitleCache in interface IIdentifiableEntity

Overrides:

getTitleCache in class IdentifiableEntity<INonViralNameCacheStrategy>

setAuthorshipCache

public void setAuthorshipCache(String authorshipCache,
                               boolean protectedAuthorshipCache)

Assigns an authorshipCache string to this non viral taxon name.

Parameters:

authorshipCache - the string which identifies the complete authorship of this non viral taxon name

protectedAuthorshipCache - if true the isProtectedAuthorshipCache flag is set to true, otherwise the flag is set to false.

See Also:

getAuthorshipCache()

setTitleCache

public void setTitleCache(String titleCache,
                          boolean protectCache)

Specified by:

setTitleCache in interface IIdentifiableEntity

Overrides:

setTitleCache in class IdentifiableEntity<INonViralNameCacheStrategy>

isCodeCompliant

public boolean isCodeCompliant()

Returns the boolean value "false" since the components of this taxon name cannot follow the rules of a corresponding nomenclatural code which is not defined for this class. The nomenclature code depends on the concrete name subclass (BacterialName, BotanicalName, CultivarPlantName or ZoologicalName to which this non viral taxon name belongs. This method overrides the isCodeCompliant method from the abstract TaxonNameBase class.

Specified by:

isCodeCompliant in class TaxonNameBase<T extends NonViralName,INonViralNameCacheStrategy>

Returns:

false

See Also:

TaxonNameBase.isCodeCompliant()

getNomenclaturalCode

public NomenclaturalCode getNomenclaturalCode()

Returns null as nomenclatural code that governs the construction of this non viral taxon name since there is no specific nomenclatural code defined. The real implementention takes place in the subclasses BacterialName, BotanicalName, CultivarPlantName and ZoologicalName. This method overrides the getNomeclaturalCode method from TaxonNameBase.

Specified by:

getNomenclaturalCode in class TaxonNameBase<T extends NonViralName,INonViralNameCacheStrategy>

Returns:

null

See Also:

isCodeCompliant(), TaxonNameBase#getHasProblem()

isProtectedAuthorshipCache

public boolean isProtectedAuthorshipCache()

Returns the boolean value of the flag intended to protect (true) or not (false) the authorshipCache (complete authorship string) of this non viral taxon name.

Returns:

the boolean value of the protectedAuthorshipCache flag

See Also:

getAuthorshipCache()

setProtectedAuthorshipCache

public void setProtectedAuthorshipCache(boolean protectedAuthorshipCache)

See Also:

isProtectedAuthorshipCache(), getAuthorshipCache()

isHybridFormula

public boolean isHybridFormula()

Returns the boolean value of the flag indicating whether the name of this botanical taxon name is a hybrid formula (true) or not (false). A hybrid named by a hybrid formula (composed with its parent names by placing the multiplication sign between them) does not have an own published name and therefore has neither an autorship nor other name components. If this flag is set no other hybrid flags may be set.

Returns:

the boolean value of the isHybridFormula flag

See Also:

isMonomHybrid(), isBinomHybrid(), isTrinomHybrid()

setHybridFormula

public void setHybridFormula(boolean hybridFormula)

See Also:

isHybridFormula()

isMonomHybrid

public boolean isMonomHybrid()

Returns the boolean value of the flag indicating whether this botanical taxon name is the name of an intergeneric hybrid (true) or not (false). In this case the multiplication sign is placed before the scientific name. If this flag is set no other hybrid flags may be set.

Returns:

the boolean value of the isMonomHybrid flag

See Also:

isHybridFormula(), isBinomHybrid(), isTrinomHybrid()

setMonomHybrid

public void setMonomHybrid(boolean monomHybrid)

See Also:

isMonomHybrid(), isBinomHybrid(), isTrinomHybrid()

isBinomHybrid

public boolean isBinomHybrid()

Returns the boolean value of the flag indicating whether this botanical taxon name is the name of an interspecific hybrid (true) or not (false). In this case the multiplication sign is placed before the species epithet. If this flag is set no other hybrid flags may be set.

Returns:

the boolean value of the isBinomHybrid flag

See Also:

isHybridFormula(), isMonomHybrid(), isTrinomHybrid()

setBinomHybrid

public void setBinomHybrid(boolean binomHybrid)

See Also:

isBinomHybrid(), isMonomHybrid(), isTrinomHybrid()

isTrinomHybrid

public boolean isTrinomHybrid()

Returns the boolean value of the flag indicating whether this botanical taxon name is the name of an infraspecific hybrid (true) or not (false). In this case the term "notho-" (optionally abbreviated "n-") is used as a prefix to the term denoting the infraspecific rank of this botanical taxon name. If this flag is set no other hybrid flags may be set.

Returns:

the boolean value of the isTrinomHybrid flag

See Also:

isHybridFormula(), isMonomHybrid(), isBinomHybrid()

setTrinomHybrid

public void setTrinomHybrid(boolean trinomHybrid)

See Also:

isTrinomHybrid(), isBinomHybrid(), isMonomHybrid()

getHybridParentRelations

public Set<HybridRelationship> getHybridParentRelations()

Returns the set of all hybrid relationships in which this taxon name is involved as a parent.

See Also:

#getHybridRelationships(), getChildRelationships(), HybridRelationshipType

getHybridChildRelations

public Set<HybridRelationship> getHybridChildRelations()

Returns the set of all hybrid relationships in which this taxon name is involved as a child.

See Also:

#getHybridRelationships(), getParentRelationships(), HybridRelationshipType

getParentRelationships

@Deprecated
public Set<HybridRelationship> getParentRelationships()

Deprecated. use getHybridParentRelations() instead. Will be removed in higher versions.

Returns the set of all hybrid relationships in which this taxon name is involved as a parent.

See Also:

getHybridParentRelations(), #getHybridRelationships(), getChildRelationships(), HybridRelationshipType

getOrderedChildRelationships

public List<HybridRelationship> getOrderedChildRelationships()

Returns the hybrid child relationships ordered by relationship type, or if equal by title cache of the related names.

See Also:

getHybridParentRelations()

getChildRelationships

@Deprecated
public Set<HybridRelationship> getChildRelationships()

Deprecated. use getHybridChildRelations() instead. Will be removed in higher versions.

See Also:

getHybridChildRelations()

addHybridRelationship

protected void addHybridRelationship(HybridRelationship rel)

Adds the given hybrid relationship to the set of hybrid relationships of both non-viral names involved in this hybrid relationship. One of both non-viral names must be this non-viral name otherwise no addition will be carried out. The child non viral taxon name must be a hybrid, which means that one of its four hybrid flags must be set.

Parameters:

relationship - the hybrid relationship to be added

Throws:

IllegalArgumentException

See Also:

isHybridFormula(), isMonomHybrid(), isBinomHybrid(), isTrinomHybrid(), #getHybridRelationships(), getParentRelationships(), getChildRelationships(), addRelationship(RelationshipBase)

addRelationship

@Deprecated
public void addRelationship(RelationshipBase relation)

Deprecated. to be used by RelationshipBase only

Does the same as the addHybridRelationship method if the given relation is also a hybrid relationship. Otherwise this method does the same as the overwritten addRelationship method from TaxonNameBase.

Specified by:

addRelationship in interface IRelated

Overrides:

addRelationship in class TaxonNameBase<T extends NonViralName,INonViralNameCacheStrategy>

Parameters:

relation - the relationship to be added to some of this taxon name's relationships sets

See Also:

addHybridRelationship(HybridRelationship), TaxonNameBase.addRelationship(RelationshipBase), TaxonNameBase.addNameRelationship(NameRelationship)

addHybridParent

public HybridRelationship addHybridParent(NonViralName parentName,
                                          HybridRelationshipType type,
                                          String ruleConsidered)

Creates a new hybrid relationship to this botanical name. A HybridRelationship may be of type "is first/second parent" or "is male/female parent". By invoking this method this botanical name becomes a hybrid child of the parent botanical name.

Parameters:

parentName - the botanical name of the parent for this new hybrid name relationship

type - the type of this new name relationship

ruleConsidered - the string which specifies the rule on which this name relationship is based

Returns:

See Also:

#addHybridChild(BotanicalName, HybridRelationshipType,String ), TaxonNameBase.getRelationsToThisName(), TaxonNameBase.getNameRelations(), TaxonNameBase.addRelationshipFromName(TaxonNameBase, NameRelationshipType, String), TaxonNameBase.addNameRelationship(NameRelationship)

addHybridChild

public HybridRelationship addHybridChild(NonViralName childName,
                                         HybridRelationshipType type,
                                         String ruleConsidered)

Creates a new hybrid relationship to this botanical name. A HybridRelationship may be of type "is first/second parent" or "is male/female parent". By invoking this method this botanical name becomes a parent of the hybrid child botanical name.

Parameters:

childName - the botanical name of the child for this new hybrid name relationship

type - the type of this new name relationship

ruleConsidered - the string which specifies the rule on which this name relationship is based

Returns:

See Also:

#addHybridParent(BotanicalName, HybridRelationshipType,String ), TaxonNameBase.getRelationsToThisName(), TaxonNameBase.getNameRelations(), TaxonNameBase.addRelationshipFromName(TaxonNameBase, NameRelationshipType, String), TaxonNameBase.addNameRelationship(NameRelationship)

removeHybridRelationship

public void removeHybridRelationship(HybridRelationship hybridRelation)

Removes one hybrid relationship from the set of hybrid relationships in which this botanical taxon name is involved. The hybrid relationship will also be removed from the set belonging to the second botanical taxon name involved.

Parameters:

relationship - the hybrid relationship which should be deleted from the corresponding sets

See Also:

#getHybridRelationships()

removeHybridChild

public void removeHybridChild(NonViralName child)

removeHybridParent

public void removeHybridParent(NonViralName parent)

isAutonym

public boolean isAutonym()

Needs to be implemented by those classes that handle autonyms (e.g. botanical names).

hasAuthors

public boolean hasAuthors()

Tests if the given name has any authors.

Returns:

false if no author ((ex)combination or (ex)basionym) exists, true otherwise

computeCombinationAuthorNomenclaturalTitle

public String computeCombinationAuthorNomenclaturalTitle()

Shortcut. Returns the combination authors title cache. Returns null if no combination author exists.

Returns:

computeBasionymAuthorNomenclaturalTitle

public String computeBasionymAuthorNomenclaturalTitle()

Shortcut. Returns the basionym authors title cache. Returns null if no basionym author exists.

Returns:

computeExCombinationAuthorNomenclaturalTitle

public String computeExCombinationAuthorNomenclaturalTitle()

Shortcut. Returns the ex-combination authors title cache. Returns null if no ex-combination author exists.

Returns:

computeExBasionymAuthorNomenclaturalTitle

public String computeExBasionymAuthorNomenclaturalTitle()

Shortcut. Returns the ex-basionym authors title cache. Returns null if no exbasionym author exists.

Returns:

clone

public Object clone()

Clones this non-viral name. This is a shortcut that enables to create a new instance that differs only slightly from this non-viral name by modifying only some of the attributes.

Overrides:

clone in class TaxonNameBase<T extends NonViralName,INonViralNameCacheStrategy>

See Also:

TaxonNameBase.clone(), Object.clone()