@Entity @Indexed(index="eu.etaxonomy.cdm.model.taxon.TaxonBase") @Configurable @ClassBridge(impl=GroupByTaxonClassBridge.class) @ClassBridge(impl=TaxonRelationshipClassBridge.class) public class Taxon extends TaxonBase<ITaxonCacheStrategy<Taxon>> implements IRelated<RelationshipBase>, IDescribable<TaxonDescription>, ICdmTarget
taxa
(only these taxa according to
the opinion of the reference
can build a classification).
An interface
is supported to iterate through taxonomic children."synonyms"
makes it easier to handle
particular relationships between ("accepted/correct") taxa on the one hand
and between ("synonym") taxa and ("accepted/correct") taxa on the other.ACC_TAXON_BRIDGE_PREFIX
cacheStrategy, NOT_PROTECTED, PROTECTED, protectedTitleCache, titleCache
annotations, markers
CLOB_LENGTH, uuid
Constructor and Description |
---|
Taxon()
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
void |
addDescription(TaxonDescription description)
Adds a new
taxon description to the set
of taxon descriptions assigned to this (accepted/correct) taxon. |
Synonym |
addHeterotypicSynonymName(TaxonName synonymName)
|
Synonym |
addHeterotypicSynonymName(TaxonName synonymName,
Reference secReference,
java.lang.String secDetail,
HomotypicalGroup homotypicalGroup)
|
void |
addHomotypicSynonym(Synonym synonym)
Adds the given
synonym to this taxon,
with the "is homotypic synonym of"
relationship type and returns it. |
Synonym |
addHomotypicSynonymName(TaxonName synonymName)
|
TaxonRelationship |
addMisappliedName(Taxon misappliedNameTaxon,
Reference citation,
java.lang.String microcitation)
Creates a new
taxon relationship (with taxon relationship type
"misapplied name for") instance where this taxon plays the target role
and adds it to the set of taxon relationships to this taxon . |
TaxonRelationship |
addPartialMisappliedName(Taxon partialMisappliedNameTaxon,
Reference citation,
java.lang.String microcitation)
Creates a new
taxon relationship (with taxon relationship type
"partial misapplied name for") instance where this taxon plays the target role
and adds it to the set of taxon relationships to this taxon . |
TaxonRelationship |
addPartialSynonym(Taxon partialTaxon,
Reference citation,
java.lang.String microcitation)
Creates a new
taxon relationship instance with
taxon relationship type partial synonym for where this taxon plays the target role
and adds it to the set of taxon relationships to this taxon . |
TaxonRelationship |
addProParteMisappliedName(Taxon proParteMisappliedNameTaxon,
Reference citation,
java.lang.String microcitation)
Creates a new
taxon relationship (with taxon relationship type
"pro parte misapplied name for") instance where this taxon plays the target role
and adds it to the set of taxon relationships to this taxon . |
TaxonRelationship |
addProparteSynonym(Taxon proParteTaxon,
Reference citation,
java.lang.String microcitation)
Creates a new
taxon relationship (with taxon relationship type
"pro parte synonym for") instance where this taxon plays the target role
and adds it to the set of taxon relationships to this taxon . |
void |
addRelationship(RelationshipBase rel)
Deprecated.
|
protected void |
addSynonym(Synonym synonym)
Might be public in future.
|
void |
addSynonym(Synonym synonym,
SynonymType synonymType)
|
Synonym |
addSynonymName(TaxonName synonymName,
Reference secReference,
java.lang.String secMicroReference,
SynonymType synonymType)
|
Synonym |
addSynonymName(TaxonName synonymName,
SynonymType synonymType)
|
protected void |
addTaxonNode(TaxonNode taxonNode) |
void |
addTaxonRelation(TaxonRelationship rel)
Adds an existing
taxon relationship either to the set of
taxon relationships to this taxon or to the set of
taxon relationships from this taxon . |
TaxonRelationship |
addTaxonRelation(Taxon toTaxon,
TaxonRelationshipType type,
Reference citation,
java.lang.String microcitation)
Creates a new
taxon relationship instance where this taxon
plays the source role and adds it to the set of
"taxon relationships from" belonging to this taxon. |
void |
clearDescriptions() |
java.lang.Object |
clone()
Clones this taxon.
|
java.util.List<Taxon> |
getAllMisappliedNames() |
java.util.List<Taxon> |
getAllProParteSynonyms() |
<T extends DescriptionElementBase> |
getDescriptionItems(Feature feature,
java.lang.Class<T> clazz)
Compiles all description items attached to this taxon having the given feature
and being of the given class.
|
java.util.Set<TaxonDescription> |
getDescriptions()
Returns the set of
taxon descriptions
concerning this taxon. |
java.util.Set<TaxonDescription> |
getDescriptions(DescriptionType type) |
java.util.List<HomotypicalGroup> |
getHeterotypicSynonymyGroups()
Returns the ordered list of all
homotypical groups
that contain synonyms that are heterotypic to this taxon.Taxon names of heterotypic synonyms
belong to a homotypical group which cannot be the homotypical group to which the
taxon name of this taxon belongs. |
java.util.List<Synonym> |
getHomotypicSynonymsByHomotypicGroup() |
java.util.List<Synonym> |
getHomotypicSynonymsByHomotypicGroup(TaxonComparator comparator)
Retrieves the ordered list (depending on the date of publication) of
homotypic
synonyms (according to the same reference
as for this taxon) under the condition that the taxon names
of these synonyms and the taxon name of this taxon belong to the
same homotypical group . |
java.util.List<Synonym> |
getHomotypicSynonymsByHomotypicSynonymType()
Deprecated.
as the method currently returns data not matching the original description of the method
as an ordered list (according to date of publication) of synonyms with same secundum as this taxon.
In future this method will either be removed or semantics may change.
|
java.util.List<HomotypicalGroup> |
getHomotypicSynonymyGroups()
Returns the ordered list of all
homotypical groups synonyms of
this taxon belong to. |
TaxonDescription |
getImageGallery(boolean createNewIfNotExists)
Returns the image gallery for a taxon.
|
java.util.List<Taxon> |
getInvalidDesignations() |
java.util.Set<TaxonRelationship> |
getMisappliedNameRelations()
Returns the set of misapplied name relationships in which this taxon
plays the role of the correctly accepted taxon (target).
|
java.util.Set<Taxon> |
getMisappliedNames(boolean includeNonCongruent)
Returns the set of taxa playing the source role in
taxon relationships
(with taxon relationship type "misapplied name for") where
this taxon plays the target role. |
TaxonDescription |
getOrCreateImageGallery(java.lang.String title)
Returns the image gallery description.
|
TaxonDescription |
getOrCreateImageGallery(java.lang.String title,
boolean addImageGalleryToTitle,
boolean onlyTitle)
Returns the image gallery description.
|
java.util.Set<TaxonRelationship> |
getProParteAndPartialSynonymRelations()
Returns the set of pro parte or partial synonym relationships in which this taxon
plays the role of the "correctly" accepted taxon (target).
|
java.util.Set<Taxon> |
getProParteAndPartialSynonyms()
Returns the set of pro parte or partial synonyms in which this taxon
plays the role of the "correctly" accepted taxon (target).
|
java.util.Set<TaxonRelationship> |
getRelationsFromThisTaxon()
Returns the set of all
taxon relationships
between two taxa in which this taxon is involved as a source. |
java.util.Set<TaxonRelationship> |
getRelationsToThisTaxon()
Returns the set of all
taxon relationships
between two taxa in which this taxon is involved as a target. |
java.util.Set<TaxonName> |
getSynonymNames()
Returns the set of all
taxon names used as synonyms
of this ("accepted/valid") taxon. |
java.util.Set<Synonym> |
getSynonyms()
Returns the set of all
synonyms
for which this ("accepted/valid") taxon is the accepted taxon. |
java.util.List<Synonym> |
getSynonymsInGroup(HomotypicalGroup homotypicGroup)
Retrieves the ordered list (depending on the rules defined for
the
HomotypicGroupTaxonComparator ) of
synonyms (according to a given reference)
the taxon names of which belong to the homotypical group. |
java.util.List<Synonym> |
getSynonymsInGroup(HomotypicalGroup homotypicGroup,
TaxonComparator comparator) |
java.util.Set<Taxon> |
getTaxaForMisappliedName(boolean includeNonCongruent)
Returns the set of taxa playing the target role in
taxon relationships
(with taxon relationship type "misapplied name for"
or "pro parte misapplied name for") where
this taxon plays the source role. |
TaxonNode |
getTaxonNode(Classification classification) |
java.util.Set<TaxonNode> |
getTaxonNodes() |
java.util.Set<TaxonRelationship> |
getTaxonRelations()
Returns the set of all
taxon relationships
between two taxa in which this taxon is involved either as a source or
as a target. |
java.util.Set<TaxonRelationship> |
getTaxonRelations(Taxon possiblyRelatedTaxon)
If a relationships between this and the given taxon exists they will be returned.
|
boolean |
hasSynonyms()
Returns the boolean value indicating whether this taxon has at least one
synonym (true) or not (false). |
boolean |
hasTaxonRelationships()
Returns the boolean value indicating whether this taxon is at least
involved in one
taxon relationship between
two taxa (true), either as a source or as a target, or not (false). |
boolean |
isInvalidDesignation()
Returns the boolean value indicating whether this taxon is a invalid designation
for at least one other taxon.
|
boolean |
isMisapplication()
Returns the boolean value indicating whether this taxon is a misapplication
(misapplied name) for at least one other taxon.
|
boolean |
isOrphaned()
Returns
true if this
taxon base is not part of any classification. |
boolean |
isProparteSynonym()
Returns the boolean value indicating whether this taxon is a misapplication
(misapplied name) for at least one other taxon.
|
boolean |
isRelatedConcept()
Returns the boolean value indicating whether this taxon is a related
concept for at least one other taxon.
|
boolean |
isTaxonStatusUnknown()
The status of this taxon is unknown it could also be some kind of synonym.
|
static Taxon |
NewInstance(ITaxonNameBase taxonName,
Reference sec) |
static Taxon |
NewInstance(TaxonName taxonName,
Reference sec)
Creates a new (accepted/valid) taxon instance with
the
taxon name used and the reference
using it. |
static Taxon |
NewInstance(TaxonName taxonName,
Reference sec,
java.lang.String secMicroReference)
Creates a new Taxon for the given name, secundum reference and secundum detail
|
static Taxon |
NewUnknownStatusInstance(TaxonName taxonName,
Reference sec)
Creates a new taxon instance with an unknown status (accepted/synonym) and with
the
taxon name used and the reference
using it. |
void |
removeDescription(TaxonDescription description)
Removes one element from the set of
taxon descriptions assigned
to this (accepted/correct) taxon. |
void |
removeDescription(TaxonDescription description,
boolean removeElements) |
void |
removeSynonym(Synonym synonym)
Like
removeSynonym(Synonym, boolean) with removeSynonymNameFromHomotypicalGroup set to true. |
void |
removeSynonym(Synonym synonym,
boolean removeSynonymNameFromHomotypicalGroup)
Removes one element from the set of
synonyms assigned
to this (accepted/valid) taxon. |
void |
removeTaxon(Taxon taxon,
TaxonRelationshipType taxonRelType)
TODO update documentation
Removes one
taxon relationship with taxon relationship type
taxonRelType and with the given child taxon playing the
source role from the set of "taxon relationships to" belonging
to this taxon. |
boolean |
removeTaxonNode(TaxonNode taxonNode) |
boolean |
removeTaxonNode(TaxonNode taxonNode,
boolean deleteChildren) |
boolean |
removeTaxonNodes(boolean deleteChildren) |
void |
removeTaxonRelation(TaxonRelationship rel)
Removes one
taxon relationship from one of both sets of
taxon relationships in which this taxon is involved
either as a source or as a target . |
protected void |
setRelationsFromThisTaxon(java.util.Set<TaxonRelationship> relationsFromThisTaxon) |
protected void |
setRelationsToThisTaxon(java.util.Set<TaxonRelationship> relationsToThisTaxon) |
void |
setTaxonStatusUnknown(boolean taxonStatusUnknown) |
compareToTaxon, getAppendedPhrase, getHomotypicGroup, getName, getNullSafeRank, getSec, getSecMicroReference, getTaggedTitle, isDoubtful, isPublish, isUseNameCache, setAppendedPhrase, setDoubtful, setName, setPublish, setSec, setSecMicroReference, setUseNameCache
addCredit, addCredit, addExtension, addExtension, addIdentifier, addIdentifier, addIdentifier, addRights, addSource, addSources, createNewSource, generateTitle, getCacheStrategy, getCredits, getCredits, getData, getExtensions, getExtensions, getExtensions, getExtensionsConcat, getExtensionsConcat, getFilteredExtensions, getIdentifiers, getIdentifiers, getIdentifiers, getLsid, getRights, getTitleCache, getTruncatedCache, hasEmptyTitleCache, hasExtension, hasExtension, initListener, isProtectedTitleCache, removeCredit, removeCredit, removeExtension, removeIdentifier, removeIdentifier, removeRights, replaceCredit, replaceIdentifier, resetTitleCache, setCacheStrategy, setLsid, setProtectedTitleCache, setTitleCache, setTitleCache, toString, updateCaches, updateCaches
addAggregationSource, addImportSource, addPrimaryTaxonomicSource, addPrimaryTaxonomicSource, addSource, addSource, getSources, removeSource, removeSources
addAnnotation, addMarker, addMarker, getAnnotations, getAnnotations, getMarkers, getMarkers, hasMarker, hasMarker, markerValue, removeAnnotation, removeMarker, removeMarker, setAnnotations
cloneLanguageString, equals, getUpdated, getUpdatedBy, setUpdated, setUpdatedBy
addPropertyChangeListener, addPropertyChangeListener, addToSetWithChangeEvent, deproxy, deproxy, fireOnCreateEvent, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getCreated, getCreatedBy, getId, getUserFriendlyDescription, getUserFriendlyFieldName, getUserFriendlyTypeName, getUuid, hashCode, hasListeners, instanceToString, invokeSetMethod, invokeSetMethodWithNull, isBlank, isInstanceOf, isNotBlank, isPersited, removeFromSetWithChangeEvent, removePropertyChangeListener, removePropertyChangeListener, replaceInList, setCreated, setCreatedBy, setId, setNewEntityListener, setUuid
finalize, getClass, notify, notifyAll, wait, wait, wait
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
removeSources
addAggregationSource, addImportSource, addPrimaryTaxonomicSource, addPrimaryTaxonomicSource, addSource, addSource, getSources, removeSource
public boolean isTaxonStatusUnknown()
public void setTaxonStatusUnknown(boolean taxonStatusUnknown)
isTaxonStatusUnknown()
public static Taxon NewInstance(ITaxonNameBase taxonName, Reference sec)
taxonName
- sec
- NewInstance(TaxonName, Reference)
public static Taxon NewInstance(TaxonName taxonName, Reference sec)
taxon name
used and the reference
using it.taxonName
- the taxon name usedsec
- the reference using the taxon nameTaxon(TaxonName, Reference)
public static Taxon NewInstance(TaxonName taxonName, Reference sec, java.lang.String secMicroReference)
taxonName
- sec
- secMicroReference
- #
public static Taxon NewUnknownStatusInstance(TaxonName taxonName, Reference sec)
taxon name
used and the reference
using it.taxonName
- the taxon name usedsec
- the reference using the taxon nameTaxon(TaxonName, Reference)
public java.util.Set<TaxonDescription> getDescriptions()
taxon descriptions
concerning this taxon.getDescriptions
in interface IDescribable<TaxonDescription>
removeDescription(TaxonDescription)
,
addDescription(TaxonDescription)
,
TaxonDescription.getTaxon()
public java.util.Set<TaxonDescription> getDescriptions(DescriptionType type)
public void addDescription(TaxonDescription description)
taxon description
to the set
of taxon descriptions assigned to this (accepted/correct) taxon.
Due to bidirectionality the content of the taxon attribute
of the
taxon description itself will be replaced with this taxon. The taxon
description will also be removed from the set of taxon descriptions
assigned to its previous taxon.addDescription
in interface IDescribable<TaxonDescription>
description
- the taxon description to be added for this taxongetDescriptions()
,
removeDescription(TaxonDescription)
,
TaxonDescription.getTaxon()
public void removeDescription(TaxonDescription description)
taxon descriptions
assigned
to this (accepted/correct) taxon. Due to bidirectionality the content of
the taxon attribute
of the taxon description
itself will be set to "null".removeDescription
in interface IDescribable<TaxonDescription>
description
- the taxon description which should be removedgetDescriptions()
,
addDescription(TaxonDescription)
,
TaxonDescription.getTaxon()
public void removeDescription(TaxonDescription description, boolean removeElements)
public TaxonDescription getImageGallery(boolean createNewIfNotExists)
createNewIfNotExists
is true
.createNewIfNotExists
- public java.util.Set<TaxonNode> getTaxonNodes()
protected void addTaxonNode(TaxonNode taxonNode)
public boolean removeTaxonNode(TaxonNode taxonNode)
public boolean removeTaxonNode(TaxonNode taxonNode, boolean deleteChildren)
public boolean removeTaxonNodes(boolean deleteChildren)
public TaxonNode getTaxonNode(Classification classification)
public java.util.Set<Synonym> getSynonyms()
synonyms
for which this ("accepted/valid") taxon is the accepted taxon.public java.util.Set<TaxonRelationship> getRelationsFromThisTaxon()
taxon relationships
between two taxa in which this taxon is involved as a source.getRelationsToThisTaxon()
,
getTaxonRelations()
public java.util.Set<TaxonRelationship> getRelationsToThisTaxon()
taxon relationships
between two taxa in which this taxon is involved as a target.getRelationsFromThisTaxon()
,
getTaxonRelations()
public java.util.Set<TaxonRelationship> getTaxonRelations()
taxon relationships
between two taxa in which this taxon is involved either as a source or
as a target.protected void setRelationsToThisTaxon(java.util.Set<TaxonRelationship> relationsToThisTaxon)
getRelationsToThisTaxon()
protected void setRelationsFromThisTaxon(java.util.Set<TaxonRelationship> relationsFromThisTaxon)
getRelationsFromThisTaxon()
public java.util.Set<TaxonRelationship> getTaxonRelations(Taxon possiblyRelatedTaxon)
null
if no relations exist between the two taxa.possiblyRelatedTaxon
- a taxon to check for a relationshipTaxonRelationship
s or null if none exists.
public void removeTaxonRelation(TaxonRelationship rel)
taxon relationship
from one of both sets of
taxon relationships
in which this taxon is involved
either as a source
or as a target
.
The taxon relationship will also be removed from one of both sets
belonging to the second taxon involved. Furthermore the inherited RelatedFrom and
RelatedTo attributes of the given taxon relationship will be nullified.rel
- the taxon relationship which should be removed from one
of both setsgetTaxonRelations()
,
RelationshipBase.getRelatedFrom()
,
RelationshipBase.getRelatedTo()
public void addTaxonRelation(TaxonRelationship rel)
taxon relationship
either to the set of
taxon relationships to this taxon
or to the set of
taxon relationships from this taxon
. If neither the
source nor the target of the taxon relationship match with this taxon
no addition will be carried out. The taxon relationship will also be
added to the second taxon involved in the given relationship.rel
- the taxon relationship to be added to one of this taxon's taxon relationships setsaddTaxonRelation(Taxon, TaxonRelationshipType, Reference, String)
,
getTaxonRelations()
,
getRelationsFromThisTaxon()
,
getRelationsToThisTaxon()
@Deprecated public void addRelationship(RelationshipBase rel)
addRelationship
in interface IRelated<RelationshipBase>
public TaxonRelationship addTaxonRelation(Taxon toTaxon, TaxonRelationshipType type, Reference citation, java.lang.String microcitation)
taxon relationship
instance where this taxon
plays the source role and adds it to the set of
"taxon relationships from"
belonging to this taxon.
The taxon relationship will also be added to the set of taxon
relationships to the second taxon involved in the created relationship.toTaxon
- the taxon which plays the target role in the new taxon relationshiptype
- the taxon relationship type for the new taxon relationshipcitation
- the reference source for the new taxon relationshipmicrocitation
- the string with the details describing the exact localisation within the referenceaddTaxonRelation(TaxonRelationship)
,
getTaxonRelations()
,
getRelationsFromThisTaxon()
,
getRelationsToThisTaxon()
public TaxonRelationship addMisappliedName(Taxon misappliedNameTaxon, Reference citation, java.lang.String microcitation)
taxon relationship
(with taxon relationship type
"misapplied name for") instance where this taxon plays the target role
and adds it to the set of taxon relationships to this taxon
.
The taxon relationship will also be added to the set of taxon
relationships to the other (misapplied name) taxon involved in the created relationship.misappliedNameTaxon
- the taxon which plays the source role in the new taxon relationshipcitation
- the reference source for the new taxon relationshipmicrocitation
- the string with the details describing the exact localisation within the reference#getMisappliedNames()
,
addProParteMisappliedName(Taxon, Reference, String)
,
addTaxonRelation(Taxon, TaxonRelationshipType, Reference, String)
,
addTaxonRelation(TaxonRelationship)
,
getTaxonRelations()
,
getRelationsFromThisTaxon()
,
getRelationsToThisTaxon()
public TaxonRelationship addProParteMisappliedName(Taxon proParteMisappliedNameTaxon, Reference citation, java.lang.String microcitation)
taxon relationship
(with taxon relationship type
"pro parte misapplied name for") instance where this taxon plays the target role
and adds it to the set of taxon relationships to this taxon
.
The taxon relationship will also be added to the set of taxon
relationships to the other (pro parte misapplied name) taxon involved in the created relationship.proParteMisappliedNameTaxon
- the taxon which plays the source role in the new taxon relationshipcitation
- the reference source for the new taxon relationshipmicrocitation
- the string with the details describing the exact localisation within the referenceaddMisappliedName(Taxon, Reference, String)
,
#getMisappliedNames()
,
addTaxonRelation(Taxon, TaxonRelationshipType, Reference, String)
,
addTaxonRelation(TaxonRelationship)
,
getTaxonRelations()
,
getRelationsFromThisTaxon()
,
getRelationsToThisTaxon()
public TaxonRelationship addPartialMisappliedName(Taxon partialMisappliedNameTaxon, Reference citation, java.lang.String microcitation)
taxon relationship
(with taxon relationship type
"partial misapplied name for") instance where this taxon plays the target role
and adds it to the set of taxon relationships to this taxon
.
The taxon relationship will also be added to the set of taxon
relationships to the other (pro parte misapplied name) taxon involved in the created relationship.partialMisappliedNameTaxon
- the taxon which plays the source role in the new taxon relationshipcitation
- the reference source for the new taxon relationshipmicrocitation
- the string with the details describing the exact localization within the referenceaddMisappliedName(Taxon, Reference, String)
,
addProParteMisappliedName(Taxon, Reference, String)
,
#getMisappliedNames()
,
addTaxonRelation(Taxon, TaxonRelationshipType, Reference, String)
,
addTaxonRelation(TaxonRelationship)
,
getTaxonRelations()
,
getRelationsFromThisTaxon()
,
getRelationsToThisTaxon()
public TaxonRelationship addProparteSynonym(Taxon proParteTaxon, Reference citation, java.lang.String microcitation)
taxon relationship
(with taxon relationship type
"pro parte synonym for") instance where this taxon plays the target role
and adds it to the set of taxon relationships to this taxon
.
The taxon relationship will also be added to the set of taxon
relationships to the other (pro parte synonym) taxon involved in the created relationship.proParteTaxon
- the taxon which plays the source role in the new taxon relationshipcitation
- the reference source for the new taxon relationshipmicrocitation
- the string with the details describing the exact localisation within the reference#getMisappliedNames()
,
addProParteMisappliedName(Taxon, Reference, String)
,
addTaxonRelation(Taxon, TaxonRelationshipType, Reference, String)
,
addTaxonRelation(TaxonRelationship)
,
getTaxonRelations()
,
getRelationsFromThisTaxon()
,
getRelationsToThisTaxon()
public TaxonRelationship addPartialSynonym(Taxon partialTaxon, Reference citation, java.lang.String microcitation)
taxon relationship
instance with
taxon relationship type
partial synonym for
where this taxon plays the target role
and adds it to the set of taxon relationships to this taxon
.
The taxon relationship will also be added to the set of taxon
relationships to the other (partial synonym) taxon involved in the created relationship.partialTaxon
- the taxon which plays the source role in the new taxon relationshipcitation
- the reference source for the new taxon relationshipmicrocitation
- the string with the details describing the exact localisation within the referenceaddProparteSynonym(Taxon, Reference, String)
,
addTaxonRelation(Taxon, TaxonRelationshipType, Reference, String)
,
addTaxonRelation(TaxonRelationship)
,
getTaxonRelations()
,
getRelationsFromThisTaxon()
,
getRelationsToThisTaxon()
public void removeTaxon(Taxon taxon, TaxonRelationshipType taxonRelType)
taxon relationship
with taxon relationship type
taxonRelType and with the given child taxon playing the
source role from the set of "taxon relationships to"
belonging
to this taxon. The taxon relationship will also be removed from the set
of "taxon relationships from"
belonging to the other side taxon.
Furthermore, the inherited RelatedFrom and RelatedTo attributes of the
taxon relationship will be nullified.taxon
- the taxon which plays the source role in the taxon relationshiptaxonRelType
- the taxon relationship typepublic boolean isMisapplication()
public boolean isProparteSynonym()
public boolean isInvalidDesignation()
public boolean isRelatedConcept()
public boolean hasSynonyms()
synonym
(true) or not (false). If true the set of synonyms
belonging to this ("accepted/valid") taxon is not empty .getSynonyms()
,
getSynonymNames()
,
removeSynonym(Synonym)
public boolean hasTaxonRelationships()
taxon relationship
between
two taxa (true), either as a source or as a target, or not (false).public java.util.Set<Taxon> getMisappliedNames(boolean includeNonCongruent)
taxon relationships
(with taxon relationship type
"misapplied name for") where
this taxon plays the target role. A misapplied name is a taxon the
taxon name
of which has been erroneously used
by its taxon reference
to denominate the same real taxon
as the one meant by this ("accepted/correct") taxon.includeNonCongruent
- if true
also those taxa are returned that are related
via a non congruent relationship like pro parte misapplied name
getTaxonRelations()
,
getRelationsToThisTaxon()
,
addMisappliedName(Taxon, Reference, String)
public java.util.Set<TaxonRelationship> getMisappliedNameRelations()
taxon name
of which has been erroneously used
by its taxon reference
to denominate the same real taxon
as the one meant by this ("accepted/correct") taxon.public java.util.Set<Taxon> getTaxaForMisappliedName(boolean includeNonCongruent)
taxon relationships
(with taxon relationship type
"misapplied name for"
or "pro parte misapplied name for") where
this taxon plays the source role. A misapplied name is a taxon the
taxon name
of which has been erroneously used
by its taxon reference
to denominate the same real taxon
as the one meant by this ("accepted/correct") taxon.includeNonCongruent
- if true
also those taxa are returned that are related
via a non congruent relationship like pro parte misapplied name
getTaxonRelations()
,
getRelationsToThisTaxon()
,
addMisappliedName(Taxon, Reference, String)
,
addProParteMisappliedName(Taxon, Reference, String)
public java.util.Set<TaxonRelationship> getProParteAndPartialSynonymRelations()
public java.util.Set<Taxon> getProParteAndPartialSynonyms()
public java.util.Set<TaxonName> getSynonymNames()
taxon names
used as synonyms
of this ("accepted/valid") taxon.getSynonyms()
,
#getSynonymsSortedByType()
,
addSynonymName(TaxonName, SynonymType)
,
addSynonym(Synonym, SynonymType, Reference, String)
,
removeSynonym(Synonym)
protected void addSynonym(Synonym synonym)
synonym
- public void addSynonym(Synonym synonym, SynonymType synonymType)
synonym
- the synonym to be addedsynonymType
- the synonym type of the synonym to be added. If not null
and if the synonym already has a type the existing type will be overwritten.SynonymType.HOMOTYPIC_SYNONYM_OF()
the homotypic group of the synonym is changed to that of this
taxon.null
use Synonym.setType(SynonymType)
addSynonym(Synonym)
,
addSynonym(Synonym, SynonymType, Reference, String)
,
addSynonymName(TaxonName, SynonymType)
,
#addSynonymName(TaxonName, SynonymType, Reference, String)
,
#addHomotypicSynonymName(TaxonName, Reference, String)
,
addHeterotypicSynonymName(TaxonName)
,
addHeterotypicSynonymName(TaxonName, Reference, String, HomotypicalGroup)
,
getSynonyms()
,
removeSynonym(Synonym)
,
Synonym.getAcceptedTaxon()
public Synonym addSynonymName(TaxonName synonymName, SynonymType synonymType)
synonym
to this
taxon
) using the
given synonym name
and with the given
synonym type
. If the later is
homotypic synonym
the name will be added to the same homotypical group
as the this
accepted taxon.this
taxon.
A secundum detail is not set.synonymName
- the taxon name to be used as a synonym to be added
to this taxon's set of synonymssynonymType
- the synonym type of the synonym
relationship to be added#addSynonymName(TaxonName, SynonymType, Reference, String)
,
addSynonym(Synonym, SynonymType)
,
addSynonym(Synonym, SynonymType, Reference, String)
,
#addHomotypicSynonym(Synonym, Reference, String)
,
#addHomotypicSynonymName(TaxonName, Reference, String)
,
addHeterotypicSynonymName(TaxonName)
,
#addHeterotypicSynonymName(TaxonName, HomotypicalGroup, Reference, String)
,
getSynonyms()
,
removeSynonym(Synonym)
public Synonym addSynonymName(TaxonName synonymName, Reference secReference, java.lang.String secMicroReference, SynonymType synonymType)
synonym
to this
taxon
) using the
given synonym name
and with the given
synonym type
. If the later is
homotypic synonym
the name will be added to the same homotypical group
as the this
accepted taxon.null
, the new synonym will have this as
secundum reference. Otherwise this
taxons sec reference is taken
as secundum reference for the synonym. SecDetail will be the secMicroReference of the
new synonym.synonymName
- the taxon name to be used as a synonym to be added
to this taxon's set of synonymssecReference
- the secundum reference for the new synonym (if null
this
taxon's secundum reference is taken.secMicroReference
- the secundum micro reference of the new synonymsynonymType
- the synonym type of the synonym to be added#addSynonymName(TaxonName, SynonymType, Reference, String)
,
addSynonym(Synonym, SynonymType)
,
addSynonym(Synonym, SynonymType, Reference, String)
,
#addHomotypicSynonym(Synonym, Reference, String)
,
#addHomotypicSynonymName(TaxonName, Reference, String)
,
addHeterotypicSynonymName(TaxonName)
,
#addHeterotypicSynonymName(TaxonName, HomotypicalGroup, Reference, String)
,
getSynonyms()
,
removeSynonym(Synonym)
public Synonym addHeterotypicSynonymName(TaxonName synonymName)
synonym
to this
taxon
) using the given
synonym name
. The synonym will have the synonym type
"is heterotypic synonym of"
.this
taxon.
No secMicroReference will be set for the new synonym.synonymName
- the taxon name to be used as an heterotypic synonym
to be added to this taxon's set of synonymsaddHeterotypicSynonymName(TaxonName, Reference, String, HomotypicalGroup)
,
addSynonymName(TaxonName, SynonymType)
,
#addSynonymName(TaxonName, SynonymType, Reference, String)
,
addSynonym(Synonym, SynonymType)
,
addSynonym(Synonym, SynonymType, Reference, String)
,
#addHomotypicSynonym(Synonym, Reference, String)
,
#addHomotypicSynonymName(TaxonName, Reference, String)
,
getSynonyms()
,
removeSynonym(Synonym)
public Synonym addHeterotypicSynonymName(TaxonName synonymName, Reference secReference, java.lang.String secDetail, HomotypicalGroup homotypicalGroup)
synonym
to this
taxon
) using the given
synonym name
. The synonym will have the synonym type
"is heterotypic synonym of"
.null
, the new synonym will have this as
secundum reference. Otherwise this
taxons sec reference is taken
as secundum reference for the synonym. SecDetail will be the secMicroReference of the
new synonym.homotypical group
(if not null
).synonymName
- the taxon name to be used as an heterotypic synonym
to be added to this taxon's set of synonymssecReference
- the secundum reference for the new synonymsecDetail
- the secundum detil for the new synonymhomotypicalGroup
- the homotypical group to which the taxon name
of the synonym will be added. If null
the homotypical group of synonymName is not changedaddHeterotypicSynonymName(TaxonName)
,
#addSynonymName(TaxonName, SynonymType, Reference, String)
,
addSynonymName(TaxonName, SynonymType)
,
addSynonym(Synonym, SynonymType)
,
addSynonym(Synonym, SynonymType, Reference, String)
,
#addHomotypicSynonym(Synonym, Reference, String)
,
#addHomotypicSynonymName(TaxonName, Reference, String)
,
getSynonyms()
,
removeSynonym(Synonym)
public Synonym addHomotypicSynonymName(TaxonName synonymName)
synonym
to this
taxon
) using the given
synonym name
. The synonym will have the synonym type
"is homotypic synonym of"
.this
taxon.
No secMicroReference will be set for the new synonym.this
taxon's group.synonymName
- the taxon name to be used as an homotypic synonym
to be added to this taxon's set of synonyms#addHomotypicSynonym(Synonym, Reference, String)
,
#addSynonymName(TaxonName, SynonymType, Reference, String)
,
addSynonymName(TaxonName, SynonymType)
,
addSynonym(Synonym, SynonymType)
,
addSynonym(Synonym, SynonymType, Reference, String)
,
addHeterotypicSynonymName(TaxonName)
,
addHeterotypicSynonymName(TaxonName, Reference, String, HomotypicalGroup)
,
getSynonyms()
,
removeSynonym(Synonym)
public void addHomotypicSynonym(Synonym synonym)
synonym
to this
taxon,
with the "is homotypic synonym of"
relationship type
and returns it.
Furthermore the taxon name
used as synonym will be added to the same homotypic group
to which the taxon name of this taxon belongs.synonym
- the synonym added to this taxon's synonym set#addHomotypicSynonymName(TaxonName, Reference, String)
,
addSynonym(Synonym, SynonymType)
,
addSynonym(Synonym, SynonymType, Reference, String)
,
#addSynonymName(TaxonName, SynonymType, Reference, String)
,
addSynonymName(TaxonName, SynonymType)
,
addHeterotypicSynonymName(TaxonName)
,
addHeterotypicSynonymName(TaxonName, Reference, String, HomotypicalGroup)
,
getSynonyms()
,
removeSynonym(Synonym)
public void removeSynonym(Synonym synonym)
removeSynonym(Synonym, boolean)
with removeSynonymNameFromHomotypicalGroup
set to true.removeSynonym(Synonym, boolean)
public void removeSynonym(Synonym synonym, boolean removeSynonymNameFromHomotypicalGroup)
synonyms
assigned
to this (accepted/valid) taxon.synonym
- the synonym to be removedremoveSynonymNameFromHomotypicalGroup
- if true
the synonym name will also be deleted from its homotypical group if the
group contains other namesgetSynonyms()
,
removeSynonym(Synonym)
public java.util.List<Synonym> getHomotypicSynonymsByHomotypicGroup()
public java.util.List<Synonym> getHomotypicSynonymsByHomotypicGroup(TaxonComparator comparator)
synonyms
(according to the same reference
as for this taxon) under the condition that the taxon names
of these synonyms and the taxon name of this taxon belong to the
same homotypical group
.comparator
- the taxon comparator to use, if null
the default comparator is taken.getHomotypicSynonymsByHomotypicSynonymType()
,
getSynonyms()
,
getHomotypicSynonymyGroups()
,
HomotypicalGroup
,
eu.etaxonomy.cdm.model.name.HomotypicalGroup#getSynonymsInGroup(Reference)
@Deprecated public java.util.List<Synonym> getHomotypicSynonymsByHomotypicSynonymType()
synonyms
(according to the same reference
as for this taxon) under the condition that these synonyms and
this taxon are involved in synonym relationships
with an
"is homotypic synonym of" synonym relationship type
.getHomotypicSynonymsByHomotypicGroup()
,
getSynonyms()
,
getHomotypicSynonymyGroups()
,
SynonymType
public java.util.List<HomotypicalGroup> getHomotypicSynonymyGroups()
homotypical groups
synonyms
of
this taxon belong to. Taxon names
of homotypic synonyms
belong to the same homotypical group as the taxon name of this
taxon. Taxon names of heterotypic synonyms belong to at least one other
homotypical group. public boolean isOrphaned()
true
if this
taxon base is not part of any classification.
False otherwise.
false
if it is a misapplied name or has a similar concept relationship that
is similar to synonym relationship (shows up in the synonymy of applications)isOrphaned
in class TaxonBase<ITaxonCacheStrategy<Taxon>>
public java.util.List<HomotypicalGroup> getHeterotypicSynonymyGroups()
homotypical groups
that contain synonyms
that are heterotypic to this taxon.Taxon names
of heterotypic synonyms
belong to a homotypical group which cannot be the homotypical group to which the
taxon name of this taxon belongs.
This method returns the same
list as the getHomotypicSynonymyGroups
method
but without the homotypical group to which the taxon name of this taxon
belongs.HomotypicGroupTaxonComparator
which includes 1) grouping of
basionym groups, 2) replaced synonym relationships, 3) publication date,
4) ranks and 5) alphabetical order.public java.util.List<Synonym> getSynonymsInGroup(HomotypicalGroup homotypicGroup)
HomotypicGroupTaxonComparator
) of
synonyms
(according to a given reference)
the taxon names
of which belong to the homotypical group.
If other names are part of the group that are not considered synonyms of
this taxon, then they will not be included in
the result set.homotypicGroup
- getHeterotypicSynonymyGroups()
,
TaxonName.getSynonyms()
,
TaxonName.getTaxa()
,
taxon.Synonym
public java.util.List<Synonym> getSynonymsInGroup(HomotypicalGroup homotypicGroup, TaxonComparator comparator)
homotypicGroup
- comparator
- getSynonymsInGroup(HomotypicalGroup)
,
getHeterotypicSynonymyGroups()
public java.util.List<Taxon> getAllMisappliedNames()
#getSynonymsGroups()
public java.util.List<Taxon> getInvalidDesignations()
#getSynonymsGroups()
public java.util.List<Taxon> getAllProParteSynonyms()
#getSynonymsGroups()
public TaxonDescription getOrCreateImageGallery(java.lang.String title)
title
- public TaxonDescription getOrCreateImageGallery(java.lang.String title, boolean addImageGalleryToTitle, boolean onlyTitle)
title
- onlyTitle
- if
- true, the String "Image Gallerypublic void clearDescriptions()
public <T extends DescriptionElementBase> java.util.Set<T> getDescriptionItems(Feature feature, java.lang.Class<T> clazz)
public java.lang.Object clone()
clone
in class TaxonBase<ITaxonCacheStrategy<Taxon>>
TaxonBase.clone()
,
eu.etaxonomy.cdm.model.media.IdentifiableEntity#clone()
,
Object.clone()
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