@Entity @TaxonNameCannotBeAcceptedAndSynonym(groups=Level3.class) @ClassBridge(name="classInfo",index=YES,store=YES,impl=ClassInfoBridge.class) @ClassBridge(name="accTaxon",index=YES,store=YES,impl=AcceptedTaxonBridge.class) @ClassBridge(impl=NomenclaturalSortOrderBrigde.class) public abstract class TaxonBase<S extends ITaxonCacheStrategy> extends IdentifiableEntity<S> implements IPublishable, IIntextReferenceTarget
taxon name
in a reference
or within a taxonomic view/treatment either as a taxon
("accepted" respectively "correct" name) or as a (junior) synonym
.
Within a taxonomic view/treatment or a reference a taxon name can be used
only in one of both described meanings. The reference using the taxon name
is generally cited with "sec." (secundum, sensu). For instance:
"Juncus longirostris Kuvaev sec. Kirschner, J. et al. 2002".
This class corresponds to:
Modifier and Type | Field and Description |
---|---|
static java.lang.String |
ACC_TAXON_BRIDGE_PREFIX |
cacheStrategy, NOT_PROTECTED, PROTECTED, protectedTitleCache, titleCache
annotations, markers
CLOB_LENGTH, uuid
Modifier | Constructor and Description |
---|---|
protected |
TaxonBase()
Class constructor: creates a new empty (abstract) taxon.
|
protected |
TaxonBase(TaxonName taxonName,
Reference sec,
java.lang.String secDetail)
Class constructor: creates a new (abstract) taxon with the
taxon name used and the reference
using it. |
Modifier and Type | Method and Description |
---|---|
java.lang.Object |
clone()
Clones this taxon.
|
int |
compareToTaxon(TaxonBase otherTaxon)
This method compares 2 taxa on it's name titles and caches.
|
java.lang.String |
getAppendedPhrase()
An appended phrase is a phrase that is added to the
taxon name
's title cache to be used just in this taxon. |
HomotypicalGroup |
getHomotypicGroup()
Returns the
homotypical group of the
taxon name used in this (abstract) taxon. |
TaxonName |
getName()
Returns the
taxon name used in this (abstract) taxon. |
Rank |
getNullSafeRank() |
Reference |
getSec()
Returns the
reference of this (abstract) taxon. |
java.lang.String |
getSecMicroReference() |
java.util.List<TaggedText> |
getTaggedTitle()
Generates and returns the string with the full scientific name (including
authorship) of the
taxon name used in this
(abstract) taxon as well as the title of the reference using
this taxon name. |
boolean |
isDoubtful()
|
abstract boolean |
isOrphaned()
Returns
true if this
taxon base is not part of any classification. |
boolean |
isPublish()
Returns the boolean value indicating if this taxon should be withheld (
publish=false ) or not
(publish=true ) during any publication process to the general public. |
boolean |
isUseNameCache() |
void |
setAppendedPhrase(java.lang.String appendedPhrase) |
void |
setDoubtful(boolean doubtful) |
void |
setName(TaxonName name) |
void |
setPublish(boolean publish) |
void |
setSec(Reference sec) |
void |
setSecMicroReference(java.lang.String secMicroReference) |
void |
setUseNameCache(boolean useNameCache) |
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
getCreated, getCreatedBy, getId, getUuid, isInstanceOf, isPersited, setCreated, setCreatedBy, setId, setUuid
removeSources
addAggregationSource, addImportSource, addPrimaryTaxonomicSource, addPrimaryTaxonomicSource, addSource, addSource, getSources, removeSource
addAnnotation, addMarker, getAnnotations, getMarkers, getMarkers, hasMarker, hasMarker, markerValue, removeAnnotation, removeMarker, removeMarker
getUpdated, getUpdatedBy, setUpdated, setUpdatedBy
public static final java.lang.String ACC_TAXON_BRIDGE_PREFIX
protected TaxonBase()
#TaxonBase(TaxonName, Reference)
protected TaxonBase(TaxonName taxonName, Reference sec, java.lang.String secDetail)
taxon name
used and the reference
using it.taxonName
- the taxon name usedsec
- the reference using the taxon nameTaxonBase()
public java.util.List<TaggedText> getTaggedTitle()
taxon name
used in this
(abstract) taxon as well as the title of the reference
using
this taxon name. This string may be stored in the inherited
titleCache
attribute.
This method overrides the generic and inherited generateTitle() method
from IdentifiableEntity
.IdentifiableEntity.generateTitle()
,
IdentifiableEntity.getTitleCache()
public TaxonName getName()
taxon name
used in this (abstract) taxon.public void setName(TaxonName name)
public HomotypicalGroup getHomotypicGroup()
homotypical group
of the
taxon name
used in this (abstract) taxon.public boolean isDoubtful()
Taxon
or to the Synonym
class
is definitive (false) or not (true). If this flag is set the use of this (abstract)
taxon as an "accepted/correct" name or as a (junior) "synonym" might
still change in the course of taxonomical working process.public void setDoubtful(boolean doubtful)
isDoubtful()
public boolean isPublish()
publish=false
) or not
(publish=true
) during any publication process to the general public.
This publish flag implementation is preliminary and may be replaced by a more general
implementation of READ rights in future.true
.isPublish
in interface IPublishable
public void setPublish(boolean publish)
setPublish
in interface IPublishable
public Reference getSec()
reference
of this (abstract) taxon.
This is the reference or the treatment using the taxon name
in this (abstract) taxon.public java.lang.String getSecMicroReference()
getSec()
public void setSecMicroReference(java.lang.String secMicroReference)
getSecMicroReference()
,
getSec()
public java.lang.String getAppendedPhrase()
taxon name
's title cache to be used just in this taxon. E.g. the phrase "sensu latu" may be added
to the name to describe this taxon more precisely.
If isUseNameCache()
public void setAppendedPhrase(java.lang.String appendedPhrase)
appendedPhrase
- the appendedPhrase to setpublic boolean isUseNameCache()
public void setUseNameCache(boolean useNameCache)
useNameCache
- the useNameCache to setpublic abstract boolean isOrphaned()
true
if this
taxon base is not part of any classification.
False otherwisepublic Rank getNullSafeRank()
public int compareToTaxon(TaxonBase otherTaxon)
TaxonComparator
. The later
currently uses this method.
Historically it was a compareTo method in IdentifiableEntity
but did not fulfill the Comparable
contract.
https://dev.e-taxonomy.eu/redmine/issues/922
https://dev.e-taxonomy.eu/redmine/issues/6311
otherTaxon
- Comparable.compareTo(Object)
java.lang.NullPointerException
- if otherTaxon is null
ITaxonNameBase.compareToName(TaxonName)
,
TaxonComparator
,
TaxonNaturalComparator
,
TaxonNodeByNameComparator
,
TaxonNodeByRankAndNameComparator
public java.lang.Object clone()
clone
in class IdentifiableEntity<S extends ITaxonCacheStrategy>
eu.etaxonomy.cdm.model.media.IdentifiableEntity#clone()
,
Object.clone()
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