eu.etaxonomy.cdm.model.name
Class NameRelationshipType

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<IIdentifiableEntityCacheStrategy>
                  eu.etaxonomy.cdm.model.common.TermBase
                      eu.etaxonomy.cdm.model.common.DefinedTermBase<T>
                          eu.etaxonomy.cdm.model.common.OrderedTermBase<T>
                              eu.etaxonomy.cdm.model.common.RelationshipTermBase<NameRelationshipType>
                                  eu.etaxonomy.cdm.model.name.NameRelationshipType

All Implemented Interfaces:

IAnnotatableEntity, ICdmBase, IDefinedTerm<NameRelationshipType>, IIdentifiableEntity, ILoadableTerm<NameRelationshipType>, ISourceable<IdentifiableSource>, IVersionableEntity, Serializable, Cloneable, Comparable<NameRelationshipType>

@Entity
@Indexed(index="eu.etaxonomy.cdm.model.common.DefinedTermBase")
public class NameRelationshipType
extends RelationshipTermBase<NameRelationshipType>

The class representing the categories of taxon name relationships between two taxon names. These name relationship types are based on the concrete nomenclatural code governing the taxon names involved in the name relationship or on decisions taken by the competent authorities; they do not depend on the use made of these taxon names in a particular reference or in a particular taxonomic treatment. Most relationships are to be understood as 'is .... of': for instance Linum radiola L. is a replaced synonym of Radiola linoides Roth or Astragalus rhizanthus Boiss. is a later homonym of Astragalus rhizanthus Royle.

A standard (ordered) list of name relationship type instances will be automatically created as the project starts. But this class allows to extend this standard list by creating new instances of additional name relationship types if needed.

This class corresponds partially to:

• TaxonRelationshipTerm and NomenclaturalNoteTypeTerm according to the TDWG ontology
• RelationshipType and NomenclaturalNoteType according to the TCS

Version:

1.0

Author:

m.doering

See Also:

Serialized Form

Field Summary

protected static Map<UUID,NameRelationshipType>

termMap

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

orderIndex

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

partOf, vocabulary

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

NameRelationshipType()
Class constructor: creates a new empty name relationship type instance.

NameRelationshipType(String term, String label, String labelAbbrev, boolean symmetric, boolean transitive)
Class constructor: creates an additional name relationship type instance with a description, a label, a label abbreviation and the flags indicating whether this new name relationship type is symmetric and/or transitive.

Method Summary

static NameRelationshipType	ALTERNATIVE_NAME() Returns the "alternative name" name relationship type.
static NameRelationshipType	BASIONYM() Returns the "basionym" name relationship type.
static NameRelationshipType	BLOCKING_NAME_FOR() Returns the "blocking name" name relationship type.
static NameRelationshipType	CONSERVED_AGAINST() Returns the "conserved against" name relationship type.
static NameRelationshipType	EMENDATION() Returns the "emendation" name relationship type.
protected static NameRelationshipType	findTermByUuid(UUID uuid)
boolean	isBasionymRelation()
boolean	isIllegitimateType() Returns the boolean value indicating whether the nomenclatural status type of the first taxon name involved in a name relationship with this name relationship type should be "illegitimate" (true) or not (false).
boolean	isInvalidType() Returns the boolean value indicating whether the nomenclatural status type of the first taxon name involved in a name relationship with this name relationship type should be "invalid" (true) or not (false).
boolean	isLegitimateType() Returns the boolean value indicating whether the nomenclatural status type of the first taxon name involved in a name relationship with this name relationship type should be "legitimate" (true) or not (false).
boolean	isReplacedSynonymRelation()
static NameRelationshipType	LATER_HOMONYM() Returns the "later homonym" name relationship type.
static NameRelationshipType	LATER_VALIDATED_BY_NAME() Returns the "later validated by name" name relationship type.
static NameRelationshipType	MISSPELLING() Returns the "misspelling" name relationship type.
static NameRelationshipType	ORTHOGRAPHIC_VARIANT() Returns the "orthographic variant" name relationship type.
NameRelationshipType	readCsvLine(Class<NameRelationshipType> termClass, List<String> csvLine, Map<UUID,DefinedTermBase> terms) Fills the term with contents from a csvLine.
static NameRelationshipType	REPLACED_SYNONYM() Returns the "replaced synonym" name relationship type.
void	resetTerms()
protected void	setDefaultTerms(TermVocabulary<NameRelationshipType> termVocabulary)
static NameRelationshipType	TREATED_AS_LATER_HOMONYM() Returns the "treated as later homonym" name relationship type.
static NameRelationshipType	VALIDATED_BY_NAME() Returns the "validated by name" name relationship type.

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

addInverseRepresentation, addRepresentation, clone, getInverseDescription, getInverseDescription, getInverseLabel, getInverseLabel, getInverseRepresentation, getInverseRepresentations, getPreferredInverseRepresentation, isSymmetric, isTransitive, removeInverseRepresentation, setSymmetric, setTransitive, writeCsvLine

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

compareTo, decreaseIndex, equals, getOrderIndex, incrementIndex, isHigher, isLower, performCompareTo

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

addGeneralizationOf, addIncludes, addMedia, getByUuid, getGeneralizationOf, getIncludes, getKindOf, getMedia, getPartOf, getVocabulary, readCsvLine, removeGeneralization, removeIncludes, removeMedia, setGeneralizationOf, setIncludes, setKindOf, setPartOf, setVocabulary

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

addRepresentation, getDescription, getDescription, getLabel, getLabel, getPreferredRepresentation, getPreferredRepresentation, getRepresentation, getRepresentations, getUri, removeRepresentation, setLabel, setLabel, setUri, toString

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, getTitleCache, getTruncatedCache, initListener, isProtectedTitleCache, regenerateTitleCache, removeCredit, removeCredit, removeExtension, removeRights, removeSource, setCacheStrategy, setLsid, setProtectedTitleCache, setTitleCache, setTitleCache

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

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.IDefinedTerm

getUuid

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

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

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

Field Detail

termMap

protected static Map<UUID,NameRelationshipType> termMap

Constructor Detail

NameRelationshipType

public NameRelationshipType()

Class constructor: creates a new empty name relationship type instance.

See Also:

NameRelationshipType(String, String, String, boolean, boolean)

NameRelationshipType

public NameRelationshipType(String term,
                            String label,
                            String labelAbbrev,
                            boolean symmetric,
                            boolean transitive)

Class constructor: creates an additional name relationship type instance with a description, a label, a label abbreviation and the flags indicating whether this new name relationship type is symmetric and/or transitive.

Parameters:

term - the string (in the default language) describing the new name relationship type to be created

label - the string identifying the new name relationship type to be created

labelAbbrev - the string identifying (in abbreviated form) the new name relationship type to be created

symmetric - the boolean indicating whether the new name relationship type to be created is symmetric

transitive - the boolean indicating whether the new name relationship type to be created is transitive

See Also:

NameRelationshipType()

Method Detail

findTermByUuid

protected static NameRelationshipType findTermByUuid(UUID uuid)

resetTerms

public void resetTerms()

Specified by:

resetTerms in class DefinedTermBase<NameRelationshipType>

isInvalidType

public boolean isInvalidType()

Returns the boolean value indicating whether the nomenclatural status type of the first taxon name involved in a name relationship with this name relationship type should be "invalid" (true) or not (false). Returns false if this name relationship status type is null.

See Also:

isLegitimateType(), isIllegitimateType(), NomenclaturalStatusType.isInvalidType(), RelationshipBase.getRelatedFrom()

isLegitimateType

public boolean isLegitimateType()

Returns the boolean value indicating whether the nomenclatural status type of the first taxon name involved in a name relationship with this name relationship type should be "legitimate" (true) or not (false). Returns false if this name relationship status type is null.

See Also:

isInvalidType(), isIllegitimateType(), NomenclaturalStatusType.isLegitimateType(), RelationshipBase.getRelatedFrom()

isIllegitimateType

public boolean isIllegitimateType()

Returns the boolean value indicating whether the nomenclatural status type of the first taxon name involved in a name relationship with this name relationship type should be "illegitimate" (true) or not (false). Returns false if this name relationship status type is null.

See Also:

isInvalidType(), isLegitimateType(), NomenclaturalStatusType.isIllegitimateType(), RelationshipBase.getRelatedFrom()

isBasionymRelation

public boolean isBasionymRelation()

isReplacedSynonymRelation

public boolean isReplacedSynonymRelation()

ORTHOGRAPHIC_VARIANT

public static final NameRelationshipType ORTHOGRAPHIC_VARIANT()

Returns the "orthographic variant" name relationship type. The first taxon name involved in such a relationship is an orthographic variant of the second taxon name. The two taxon names involved in such a relationship must have the same authorship and rank, belong to the same homotypical group and their name parts must be almost identical (so one usually does not differentiate them).
For instance Angelica silvestris L. is an orthographic variant of Angelica sylvestris L.
This type is symmetric and transitive but usually orthographic variant relationships should be organized in a star schema with the correct variant in the middle and other variants pointing to it.

MISSPELLING

public static final NameRelationshipType MISSPELLING()

Returns the "misspelling" name relationship type. The first taxon name involved in such a relationship is a misspelling of the second taxon name. The two taxon names involved in such a relationship must have the same authorship and rank, belong to the same homotypical group and their name parts must be almost identical (so one usually does not differentiate them).
For instance Anhelica silvestris L. is a misspelling of Angelica silvestris L.
A misspelling is always accicentally (not on purpose). Therefore misspellings are a subset of orthographic variants and are complementary to emendations. A misspelling is always an orthographic variant, too. This type is symmetric and transitive but usually the misspelling relationships should be organized in a star schema with the correct variant in the middle and the misspellings pointing to it.

EMENDATION

public static final NameRelationshipType EMENDATION()

Returns the "emendation" name relationship type. The first taxon name involved in such a relationship is a misspelling of the second taxon name. The two taxon names involved in such a relationship must have the same authorship and rank, belong to the same homotypical group and their name parts must be almost identical (so one usually does not differentiate them).
For instance Angelica silvestris L. is a emendation of Angelica sylvestris L.
The name corrected by an emendation has originally been used on purpose (not accidentially) Therefore emendations are a subset of orthographic variants and are complementary to missepllings. An emendation is always an orthographic variant, too.
This type is symmetric and transitive but usually the misspelling relationships should be organized in a star schema with the correct variant in the middle and the misspellings pointing to it.

LATER_HOMONYM

public static final NameRelationshipType LATER_HOMONYM()

Returns the "later homonym" name relationship type. The first taxon name involved in such a relationship should have been published after the second taxon name. The two taxon names involved in such a relationship must belong to different homotypical groups, have in general different authorship and their name parts (excluding infraspecific ranks) must be (almost) identical, so one could be mistaken for the other one. The first taxon name is "illegitimate" and the second one is "legitimate" (this corresponds to "invalid" and "valid" in case of zoological names).
For instance Astragalus rhizanthus Boiss. is a later homonym of Astragalus rhizanthus Royle.
This type is not symmetric but transitive.

See Also:

NomenclaturalStatusType.isIllegitimateType(), NomenclaturalStatusType.isLegitimateType()

TREATED_AS_LATER_HOMONYM

public static final NameRelationshipType TREATED_AS_LATER_HOMONYM()

Returns the "treated as later homonym" name relationship type. The first taxon name involved in such a relationship is treated as an homonym although it has been published before the second taxon name. The two taxon names involved must belong to different homotypical groups and their name parts (excluding infraspecific ranks and authorship) must be almost identical (so one could be mistaken for the other). The first taxon name is "illegitimate" and the second one is "legitimate" (this corresponds to "invalid" and "valid" in case of zoological names).
This type is not symmetric but transitive.

See Also:

LATER_HOMONYM(), NomenclaturalStatusType.isIllegitimateType(), NomenclaturalStatusType.isLegitimateType()

ALTERNATIVE_NAME

public static final NameRelationshipType ALTERNATIVE_NAME()

Returns the "alternative name" name relationship type. Both taxon names involved in such a relationship are family names. The first one is a classical name long in use, in some cases, even before 1753 and is considered as valid and also legitimate although it does not follow the rules for family names (see Article 18 of the ICBN). An alternative name is typified by the type of the name it is alternative to (so both must belong to the same homotypical group).
For instance Cruciferae Adans is an alternative name to Brassicaceae Lindl.
This type is neither symmetric nor transitive.

BASIONYM

public static final NameRelationshipType BASIONYM()

Returns the "basionym" name relationship type. The first taxon name involved in such a relationship is the "basionym" of the second taxon name. Both taxon names belong to the same homotypical group). The basionym is the epithet-bringing taxon name (first taxon name ever validly published given to the same infrageneric taxon, the epithet of which is the same as in the second taxon name originated through a reclassification).
According to the ICBN the author of the basionym must be mentioned in the later taxon name (by placing it in parentheses before the authority of the new combination). For instance Pinus abies L. is the basionym of Picea abies (L.) H. Karst.
This type is neither symmetric nor transitive.

REPLACED_SYNONYM

public static final NameRelationshipType REPLACED_SYNONYM()

Returns the "replaced synonym" name relationship type. The first taxon name involved in such a relationship is the "replaced synonym" of the second taxon name. Both taxon names belong to the same homotypical group. The replaced synonym is the first taxon name ever validly published given to the same infrageneric taxon that is either itself a "later homonym" or the epithet of which could not be used in the new taxon name originated through a reclassification. A new epithet must be proposed if the use of the original epithet leads to an already existing taxon name (for another taxon) or in botany to autonyms (since the ICBN does not allow such names where epithet and genus name are the same).
For instance Spartium biflorum Desf. is the replaced synonym of of Cytisus fontanesii Spach ("novum" taxon name) because at the time of reclassification a taxon name Cytisus biflorum had been already published by L'H�r.
This type is neither symmetric nor transitive.

See Also:

BASIONYM(), LATER_HOMONYM(), NomenclaturalStatusType.NOVUM()

CONSERVED_AGAINST

public static final NameRelationshipType CONSERVED_AGAINST()

Returns the "conserved against" name relationship type. Both taxon names involved in such a relationship belong to the same homotypical group. Competent authorities decided, regardless of the general nomenclatural rules, to handle the first one as the "legitimate" one and the second taxon name as "illegitimate" (this corresponds to "valid" and "invalid" in case of zoological names).
For instance Cephaloziella (Spruce) Schiffn. is conserved against Dichiton Mont.
This type is neither symmetric nor transitive.

See Also:

NomenclaturalStatusType.CONSERVED(), NomenclaturalStatusType.REJECTED(), NomenclaturalStatusType.isLegitimateType(), NomenclaturalStatusType.isIllegitimateType()

VALIDATED_BY_NAME

public static final NameRelationshipType VALIDATED_BY_NAME()

Returns the "validated by name" name relationship type. The two taxon names involved in such a relationship were published in order to define the same taxonomical group but the first (earlier) taxon name was invalidly published whereas the second (later) taxon name is the one which was validly published for the first time.
This type is neither symmetric nor transitive.

See Also:

NomenclaturalStatusType.isInvalidType(), NomenclaturalStatusType.VALID()

LATER_VALIDATED_BY_NAME

public static final NameRelationshipType LATER_VALIDATED_BY_NAME()

Returns the "later validated by name" name relationship type. The two taxon names involved in such a relationship were published in order to define the same taxonomical group but the first (earlier) taxon name was invalidly published whereas the second (later) taxon name is the one which was validly published for the first time.
This type is neither symmetric nor transitive.

See Also:

NomenclaturalStatusType.isInvalidType(), NomenclaturalStatusType.VALID()

BLOCKING_NAME_FOR

public static final NameRelationshipType BLOCKING_NAME_FOR()

Returns the "blocking name" name relationship type. The first taxon name involved in such a relationship is the "blocking name" for the second taxon name. Both taxon names belong to different homotypical groups). The blocking taxon name is the infrageneric taxon name, already published at the time of reclassification, which makes illegitim (because of homonymy) the use of the epithet in the second taxon name originated through a reclassification. Therefore a "replaced synonym" name relationship arises.
For instance Cytisus biflorum L'H�r. is the blocking name for Cytisus fontanesii Spach ("novum" taxon name) when reclassifying Spartium biflorum Desf. from Spartium to Cytisus.
This type is neither symmetric nor transitive.

See Also:

REPLACED_SYNONYM(), LATER_HOMONYM(), NomenclaturalStatusType.NOVUM()

setDefaultTerms

protected void setDefaultTerms(TermVocabulary<NameRelationshipType> termVocabulary)

Specified by:

setDefaultTerms in class DefinedTermBase<NameRelationshipType>

readCsvLine

public NameRelationshipType readCsvLine(Class<NameRelationshipType> termClass,
                                        List<String> csvLine,
                                        Map<UUID,DefinedTermBase> terms)

Description copied from interface: ILoadableTerm

Fills the term with contents from a csvLine. If the csvLine represents the default language the csvLine attributes are merged into the existing default language and the default Language is returned.

Specified by:

readCsvLine in interface ILoadableTerm<NameRelationshipType>

Overrides:

readCsvLine in class RelationshipTermBase<NameRelationshipType>

Returns: