eu.etaxonomy.cdm.model.name
Class HomotypicalGroup

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.name.HomotypicalGroup

All Implemented Interfaces:

IAnnotatableEntity, ICdmBase, IVersionableEntity, Serializable, Cloneable

@Entity
public class HomotypicalGroup
extends AnnotatableEntity

The homotypical group class represents a set of taxon names associated on the base of their typifications. Since it can be asserted that two taxon names are typified by the same type without mentioning the type itself, even taxon names without explicit type designation can belong to an homotypical group.
Taxon names belonging to an homotypical group and the taxon names or specimens used as types for their type designations have the following properties:

• A taxon name belongs exactly to one homotypical group
• A type specimen or a type name can be used as a type only for taxon names belonging to the same homotypical group
  - therefore an homotypical group circumscribes a set of types
  - each taxon name shares a subset of these types
  - each type is used by a subset of these taxon names within the homotypical group
• Names that share at least one common type must belong to the same homotypical group
• Names that share the same basionym or replaced synonym must belong to the same homotypical group

Version:

1.0

Author:

m.doering

See Also:

TypeDesignationBase, NameTypeDesignation, SpecimenTypeDesignation, Serialized Form

Field Summary

protected Set<TaxonNameBase>

typifiedNames

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

HomotypicalGroup()
Class constructor: creates a new homotypical group instance with an empty set of typified taxon names.

Method Summary

void	addTypifiedName(TaxonNameBase typifiedName) Adds a new taxon name to the set of taxon names that belong to this homotypical group.
Set<NameRelationship>	getBasionymAndReplacedSynonymRelations() Returns the name relationships that represent either a basionym (original combination) relationship or a replaced synonym relationship.
Set<TaxonNameBase>	getBasionyms() Returns all taxon names in the homotypical group that have a 'is_basionym_for' (zool.: 'is_original_combination_for') relationship.
Set<TaxonNameBase>	getBasionymsOrReplacedSynonyms() Returns all taxon names in the homotypical group that have an 'is_basionym_for' (zool.: 'is_original_combination_for') or a replaced synonym relationship.
Set<NameTypeDesignation>	getNameTypeDesignations() Returns the set of name type designations that typify the taxon names belonging to this homotypical group including the status of these designations.
Set<TaxonNameBase>	getNewCombinations() Returns all taxon names in the homotypical group that are new combinations (have a basionym/original combination or a replaced synonym).
Set<TaxonNameBase>	getReplacedSynonym() Returns all taxon names in the homotypical group that have a 'is_replaced_synonym_for' relationship.
Set<SpecimenTypeDesignation>	getSpecimenTypeDesignations() Returns the set of specimen type designations that typify the taxon names belonging to this homotypical group including the status of these designations.
List<Synonym>	getSynonymsInGroup(Reference sec) Deprecated. synonyms should not depend on the sec. Therefore this method will be removed in version 3.1 or higher. Use Taxon#getSynonymsInGroup(HomotypicalGroup) instead. But be aware that the semantics is slightly different.
Set<TypeDesignationBase>	getTypeDesignations() Returns the set of all type designations that typify the taxon names belonging to this homotypical group (this includes either name type designations or specimen type designations).
Set<TaxonNameBase>	getTypifiedNames() Returns the set of taxon names that belong to this homotypical group.
Set<TaxonNameBase>	getUnrelatedNames() Returns all taxon names in the homotypical group that do not have an 'is_basionym_for' (zool.: 'is_original_combination_for') or a replaced synonym relationship.
void	merge(HomotypicalGroup homotypicalGroupToMerge) Merges the typified taxon names from one homotypical group into the set of typified taxon names of this homotypical group.
static HomotypicalGroup	NewInstance() Creates a new homotypical group instance with an empty set of typified taxon names.
static void	removeGroupBasionym(TaxonNameBase basionymName) Removes all basionym relationships between basionymName and any other name in its homotypic group
void	removeTypifiedName(TaxonNameBase typifiedName) Removes one element from the set of taxon names that belong to this homotypical group.
void	setGroupBasionym(TaxonNameBase basionymName) Creates a basionym relationship to all other names in this names homotypical group.
void	setGroupBasionym(TaxonNameBase basionymName, Reference citation, String microCitation, String ruleConsidered)

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

addAnnotation, addMarker, clone, 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, toString

Methods inherited from class java.lang.Object

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

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

typifiedNames

protected Set<TaxonNameBase> typifiedNames

Constructor Detail

HomotypicalGroup

public HomotypicalGroup()

Class constructor: creates a new homotypical group instance with an empty set of typified taxon names.

Method Detail

NewInstance

public static HomotypicalGroup NewInstance()

Creates a new homotypical group instance with an empty set of typified taxon names.

See Also:

HomotypicalGroup()

getTypifiedNames

public Set<TaxonNameBase> getTypifiedNames()

Returns the set of taxon names that belong to this homotypical group.

See Also:

getSpecimenTypeDesignations()

addTypifiedName

public void addTypifiedName(TaxonNameBase typifiedName)

Adds a new taxon name to the set of taxon names that belong to this homotypical group.

Parameters:

typifiedName - the taxon name to be added to this group

See Also:

getTypifiedNames(), removeTypifiedName(TaxonNameBase)

removeTypifiedName

public void removeTypifiedName(TaxonNameBase typifiedName)

Removes one element from the set of taxon names that belong to this homotypical group.

Parameters:

taxonBase - the taxon name which should be removed from the corresponding set

See Also:

addTypifiedName(TaxonNameBase)

merge

public void merge(HomotypicalGroup homotypicalGroupToMerge)

Merges the typified taxon names from one homotypical group into the set of typified taxon names of this homotypical group.

Parameters:

homotypicalGroupToMerge - the homotypical group the typified names of which are to be transferred to this homotypical group

getSpecimenTypeDesignations

public Set<SpecimenTypeDesignation> getSpecimenTypeDesignations()

Returns the set of specimen type designations that typify the taxon names belonging to this homotypical group including the status of these designations.

See Also:

getTypifiedNames(), getNameTypeDesignations(), getTypeDesignations(), TaxonNameBase.getSpecimenTypeDesignations()

getNameTypeDesignations

public Set<NameTypeDesignation> getNameTypeDesignations()

Returns the set of name type designations that typify the taxon names belonging to this homotypical group including the status of these designations.

See Also:

getTypifiedNames(), getSpecimenTypeDesignations(), getTypeDesignations(), TaxonNameBase.getNameTypeDesignations()

getTypeDesignations

public Set<TypeDesignationBase> getTypeDesignations()

Returns the set of all type designations that typify the taxon names belonging to this homotypical group (this includes either name type designations or specimen type designations).

See Also:

getTypifiedNames(), getNameTypeDesignations(), getSpecimenTypeDesignations(), TaxonNameBase.getTypeDesignations()

getSynonymsInGroup

@Deprecated
public List<Synonym> getSynonymsInGroup(Reference sec)

Deprecated. synonyms should not depend on the sec. Therefore this method will be removed in version 3.1 or higher. Use Taxon#getSynonymsInGroup(HomotypicalGroup) instead. But be aware that the semantics is slightly different.

Retrieves the ordered list (depending on the date of publication) of synonyms (according to a given reference) the taxon names of which belong to this homotypical group. If other names are part of this group that are not considered synonyms according to the respective reference, then they will not be included in the result set.

Parameters:

sec - the reference whose treatment is to be considered

Returns:

the ordered list of synonyms

See Also:

TaxonNameBase.getSynonyms(), TaxonNameBase.getTaxa(), taxon.Synonym

setGroupBasionym

public void setGroupBasionym(TaxonNameBase basionymName)
                      throws IllegalArgumentException

Creates a basionym relationship to all other names in this names homotypical group.

Parameters:

basionymName -

Throws:

IllegalArgumentException - if basionymName is not member in this homotypical group

See Also:

HomotypicalGroup.setGroupBasionym(TaxonNameBase basionymName)

setGroupBasionym

public void setGroupBasionym(TaxonNameBase basionymName,
                             Reference citation,
                             String microCitation,
                             String ruleConsidered)
                      throws IllegalArgumentException

Throws:

IllegalArgumentException

removeGroupBasionym

public static void removeGroupBasionym(TaxonNameBase basionymName)

Removes all basionym relationships between basionymName and any other name in its homotypic group

Parameters:

basionymName -

getUnrelatedNames

public Set<TaxonNameBase> getUnrelatedNames()

Returns all taxon names in the homotypical group that do not have an 'is_basionym_for' (zool.: 'is_original_combination_for') or a replaced synonym relationship.

Returns:

getNewCombinations

public Set<TaxonNameBase> getNewCombinations()

Returns all taxon names in the homotypical group that are new combinations (have a basionym/original combination or a replaced synonym).

Returns:

getBasionymsOrReplacedSynonyms

public Set<TaxonNameBase> getBasionymsOrReplacedSynonyms()

Returns all taxon names in the homotypical group that have an 'is_basionym_for' (zool.: 'is_original_combination_for') or a replaced synonym relationship.

Returns:

getBasionyms

public Set<TaxonNameBase> getBasionyms()

Returns all taxon names in the homotypical group that have a 'is_basionym_for' (zool.: 'is_original_combination_for') relationship.

Returns:

getReplacedSynonym

public Set<TaxonNameBase> getReplacedSynonym()

Returns all taxon names in the homotypical group that have a 'is_replaced_synonym_for' relationship.

Returns:

getBasionymAndReplacedSynonymRelations

public Set<NameRelationship> getBasionymAndReplacedSynonymRelations()

Returns the name relationships that represent either a basionym (original combination) relationship or a replaced synonym relationship.

Returns: