@Entity public class Rank extends OrderedTermBase<Rank>
taxon names
across all nomenclatural codes
for bacteria (ICNB), viruses (ICVCN), plants and fungi (ICBN),
cultivars (ICNCP) and animals (ICZN).
A standard (ordered) list of taxonomical rank instances will be automatically created as the project starts. But this class allows to extend this standard list by creating new instances of additional taxonomical ranks if needed.
This class corresponds to:
Modifier and Type | Field and Description |
---|---|
protected static java.util.Map<java.util.UUID,Rank> |
termMap |
static java.util.UUID |
uuidCohort |
static java.util.UUID |
uuidCollSpecies |
static java.util.UUID |
uuidGenus |
static java.util.UUID |
uuidHyporder |
static java.util.UUID |
uuidInfragenericTaxon |
static java.util.UUID |
uuidInfraspecificTaxon |
static java.util.UUID |
uuidProles |
static java.util.UUID |
uuidRace |
static java.util.UUID |
uuidSpecies |
static java.util.UUID |
uuidSublusus |
orderIndex
partOf, vocabulary
cacheStrategy, NOT_PROTECTED, PROTECTED, protectedTitleCache, titleCache
annotations, markers
CLOB_LENGTH, uuid
Modifier | Constructor and Description |
---|---|
protected |
Rank()
Deprecated.
|
protected |
Rank(RankClass rankClass,
java.lang.String term,
java.lang.String label,
java.lang.String labelAbbrev)
Class constructor: creates an additional rank instance with a description
(in the
default language ), a label and a label abbreviation. |
Modifier and Type | Method and Description |
---|---|
static Rank |
BIOVARIETY() |
static Rank |
CANDIDATE() |
static Rank |
CLASS() |
int |
compareTo(Rank orderedTerm)
It is necessary to skip the vocabulary check, otherwise we would have
problems in some CacheStrategies, due to uninitialized Vocabularies.
|
static Rank |
CONVAR() |
static Rank |
CULTIVAR() |
static Rank |
CULTIVARGROUP() |
static Rank |
DENOMINATIONCLASS() |
static Rank |
DIVISION() |
static Rank |
DOMAIN() |
static Rank |
EMPIRE() |
static Rank |
FAMILY() |
static Rank |
FORM() |
static Rank |
GENUS() |
java.lang.String |
getAbbreviation()
Returns the abbreviated rank name for this rank according to the English representation
abbreviated label.
|
java.lang.String |
getInfraGenericMarker() |
static Rank |
getRankByEnglishName(java.lang.String rankName,
NomenclaturalCode nc,
boolean useUnknown)
Defines the rank according to the English name.
|
static Rank |
getRankByIdInVoc(java.lang.String abbrev)
Returns the rank identified through the vocabulary identifier.
|
static Rank |
getRankByIdInVoc(java.lang.String idInVoc,
boolean useUnknown)
Returns the rank identified through an abbreviated representation.
|
static Rank |
getRankByIdInVoc(java.lang.String abbrev,
NomenclaturalCode nc)
Returns the rank identified through an abbreviated name for a given nomenclatural code.
|
static Rank |
getRankByIdInVoc(java.lang.String abbrev,
NomenclaturalCode nc,
boolean useUnknown)
Returns the rank identified through an abbreviated name for a given nomenclatural code.
|
static Rank |
getRankByName(java.lang.String rankName)
Returns the rank identified through a name.
|
static Rank |
getRankByName(java.lang.String rankName,
boolean useUnknown)
Returns the rank identified through a name.
|
static Rank |
getRankByName(java.lang.String rankName,
NomenclaturalCode nc)
Returns the rank identified through a name for a given nomenclatural code.
|
static Rank |
getRankByName(java.lang.String rankName,
NomenclaturalCode nc,
boolean useUnknown) |
static Rank |
getRankByNameOrIdInVoc(java.lang.String strRank)
Returns the rank identified through a label or the identifier within the vocabulary
Preliminary implementation for BotanicalNameParser.
|
static Rank |
getRankByNameOrIdInVoc(java.lang.String strRank,
boolean useUnknown)
Returns the rank identified through a label or the identifier within the vocabulary.
|
static Rank |
getRankByNameOrIdInVoc(java.lang.String strRank,
NomenclaturalCode nc)
Returns the rank identified through a label or the identifier within the vocabulary
for a given nomenclatural code.
|
static Rank |
getRankByNameOrIdInVoc(java.lang.String strRank,
NomenclaturalCode nc,
boolean useUnknown)
Returns the rank identified through a label or the identifier within the vocabulary.
|
RankClass |
getRankClass() |
protected static Rank |
getTermByUuid(java.util.UUID uuid) |
static Rank |
GRAFTCHIMAERA() |
static Rank |
GREX() |
static Rank |
INFRACLASS() |
static Rank |
INFRADIVISION() |
static Rank |
INFRAFAMILY() |
static Rank |
INFRAGENERICTAXON()
'Unranked infrageneric'.
|
static Rank |
INFRAGENUS() |
static Rank |
INFRAKINGDOM() |
static Rank |
INFRAORDER() |
static Rank |
INFRAPHYLUM() |
static Rank |
INFRASPECIES() |
static Rank |
INFRASPECIFICTAXON()
'Unranked infraspecific'.
|
static Rank |
INFRATRIBE() |
static void |
initDefaultTerms() |
boolean |
isGenus()
Returns the boolean value indicating whether this rank is the genus rank
(true) or not (false).
|
boolean |
isInfraGeneric()
Returns the boolean value indicating whether this rank is higher than the
species rank and lower than the genus rank (true) or not (false).
|
boolean |
isInfraGenericButNotSpeciesGroup()
Returns the boolean value indicating whether this rank is higher than the
species aggregate/group rank and lower than the genus rank (true) or not (false).
|
boolean |
isInfraSpecific()
Returns the boolean value indicating whether this rank is lower than the
species rank (true) or not (false).
|
boolean |
isSpecies()
Returns the boolean value indicating whether this rank is the species
rank (true) or not (false).
|
boolean |
isSpeciesAggregate()
Returns true if this rank indicates a rank that aggregates species
like species aggregates or species groups, false otherwise.
|
boolean |
isSupraGeneric()
Returns the boolean value indicating whether this rank is higher than
the genus rank (true) or not (false).
|
static Rank |
KINGDOM() |
static Rank |
NATIO() |
static Rank |
NewInstance(RankClass rankClass,
java.lang.String term,
java.lang.String label,
java.lang.String labelAbbrev)
Creates an additional rank with a description (in the
default language ),
a label and a label abbreviation. |
static Rank |
ORDER() |
static Rank |
PATHOVARIETY() |
static Rank |
PHYLUM() |
static Rank |
PROLES() |
static Rank |
RACE() |
Rank |
readCsvLine(java.lang.Class<Rank> termClass,
java.util.List<java.lang.String> csvLine,
TermType termType,
java.util.Map<java.util.UUID,DefinedTermBase> terms,
boolean abbrevAsId)
Fills the
term with contents from a csvLine. |
void |
resetTerms() |
static Rank |
SECTION_BOTANY() |
static Rank |
SECTION_ZOOLOGY() |
static Rank |
SERIES() |
protected void |
setDefaultTerms(TermVocabulary<Rank> termVocabulary) |
void |
setRankClass(RankClass rankClass) |
static Rank |
SPECIALFORM() |
static Rank |
SPECIES() |
static Rank |
SPECIESAGGREGATE() |
static Rank |
SPECIESGROUP() |
static Rank |
SUBCLASS() |
static Rank |
SUBDIVISION() |
static Rank |
SUBFAMILY() |
static Rank |
SUBFORM() |
static Rank |
SUBGENUS() |
static Rank |
SUBKINGDOM() |
static Rank |
SUBLUSUS() |
static Rank |
SUBORDER() |
static Rank |
SUBPHYLUM() |
static Rank |
SUBSECTION_BOTANY() |
static Rank |
SUBSECTION_ZOOLOGY() |
static Rank |
SUBSERIES() |
static Rank |
SUBSPECIES() |
static Rank |
SUBSPECIFICAGGREGATE() |
static Rank |
SUBSUBFORM() |
static Rank |
SUBSUBVARIETY() |
static Rank |
SUBTRIBE() |
static Rank |
SUBVARIETY() |
static Rank |
SUPERCLASS() |
static Rank |
SUPERDIVISION() |
static Rank |
SUPERFAMILY() |
static Rank |
SUPERKINGDOM() |
static Rank |
SUPERORDER() |
static Rank |
SUPERPHYLUM() |
static Rank |
SUPERTRIBE() |
static Rank |
SUPRAGENERICTAXON() |
static Rank |
TRIBE() |
static Rank |
UNKNOWN_RANK() |
static Rank |
UNRANKED_INFRAGENERIC() |
static Rank |
UNRANKED_INFRASPECIFIC() |
static Rank |
VARIETY() |
clone, decreaseIndex, getNextHigherTerm, getNextLowerTerm, getOrderIndex, incrementIndex, isHigher, isLower, performCompareTo
addGeneralizationOf, addIncludes, addMedia, getByUuid, getCacher, getGeneralizationOf, getGeneralizationOf, getIdInVocabulary, getIncludes, getKindOf, getMedia, getPartOf, getSymbol, getSymbol2, getTermByClassAndUUID, getVocabulary, isKindOf, partOfCsvLineIndex, readCsvLine, readIsPartOf, removeGeneralization, removeIncludes, removeMedia, setCacher, setGeneralizationOf, setIdInVocabulary, setIncludes, setKindOf, setPartOf, setSymbol, setSymbol2, setVocabulary, writeCsvLine
addRepresentation, getDescription, getDescription, getLabel, getLabel, getPreferredRepresentation, getPreferredRepresentation, getRepresentation, getRepresentations, getTermType, getUri, removeRepresentation, setLabel, setLabel, setTermType, setUri, toString
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, 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
getUuid
checkTermTypeEqualOrDescendant, checkTermTypeNull, checkTermTypes
removeSources
addAggregationSource, addImportSource, addPrimaryTaxonomicSource, addPrimaryTaxonomicSource, addSource, addSource, getSources, removeSource
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
public static final java.util.UUID uuidGenus
public static final java.util.UUID uuidInfragenericTaxon
public static final java.util.UUID uuidSpecies
public static final java.util.UUID uuidProles
public static final java.util.UUID uuidRace
public static final java.util.UUID uuidSublusus
public static final java.util.UUID uuidInfraspecificTaxon
public static final java.util.UUID uuidCohort
public static final java.util.UUID uuidHyporder
public static java.util.UUID uuidCollSpecies
protected static java.util.Map<java.util.UUID,Rank> termMap
@Deprecated protected Rank()
protected Rank(RankClass rankClass, java.lang.String term, java.lang.String label, java.lang.String labelAbbrev)
default language
), a label and a label abbreviation.term
- the string (in the default language) describing the
new rank to be createdlabel
- the string identifying the new rank to be createdlabelAbbrev
- the string identifying (in abbreviated form) the
new rank to be createdRank()
public static Rank NewInstance(RankClass rankClass, java.lang.String term, java.lang.String label, java.lang.String labelAbbrev)
default language
),
a label and a label abbreviation.term
- the string (in the default language) describing the
new rank to be createdlabel
- the string identifying the new rank to be createdlabelAbbrev
- the string identifying (in abbreviated form) the
new rank to be created#NewInstance()
public void resetTerms()
resetTerms
in class DefinedTermBase<Rank>
protected static Rank getTermByUuid(java.util.UUID uuid)
public static final Rank EMPIRE()
public static final Rank DOMAIN()
public static final Rank SUPERKINGDOM()
public static final Rank KINGDOM()
public static final Rank SUBKINGDOM()
public static final Rank INFRAKINGDOM()
public static final Rank SUPERPHYLUM()
public static final Rank PHYLUM()
public static final Rank SUBPHYLUM()
public static final Rank INFRAPHYLUM()
public static final Rank SUPERDIVISION()
public static final Rank DIVISION()
public static final Rank SUBDIVISION()
public static final Rank INFRADIVISION()
public static final Rank SUPERCLASS()
public static final Rank CLASS()
public static final Rank SUBCLASS()
public static final Rank INFRACLASS()
public static final Rank SUPERORDER()
public static final Rank ORDER()
public static final Rank SUBORDER()
public static final Rank INFRAORDER()
public static final Rank SUPERFAMILY()
public static final Rank FAMILY()
public static final Rank SUBFAMILY()
public static final Rank INFRAFAMILY()
public static final Rank SUPERTRIBE()
public static final Rank TRIBE()
public static final Rank SUBTRIBE()
public static final Rank INFRATRIBE()
public static final Rank SUPRAGENERICTAXON()
public static final Rank GENUS()
public static final Rank SUBGENUS()
public static final Rank INFRAGENUS()
public static final Rank SECTION_BOTANY()
public static final Rank SUBSECTION_BOTANY()
public static final Rank SECTION_ZOOLOGY()
public static final Rank SUBSECTION_ZOOLOGY()
public static final Rank SERIES()
public static final Rank SUBSERIES()
public static final Rank SPECIESAGGREGATE()
public static final Rank SPECIESGROUP()
public static final Rank INFRAGENERICTAXON()
public static final Rank SPECIES()
public static final Rank SUBSPECIFICAGGREGATE()
public static final Rank SUBSPECIES()
public static final Rank INFRASPECIES()
public static final Rank VARIETY()
public static final Rank BIOVARIETY()
public static final Rank PATHOVARIETY()
public static final Rank SUBVARIETY()
public static final Rank SUBSUBVARIETY()
public static final Rank PROLES()
public static final Rank RACE()
public static final Rank SUBLUSUS()
public static final Rank CONVAR()
public static final Rank FORM()
public static final Rank SPECIALFORM()
public static final Rank SUBFORM()
public static final Rank SUBSUBFORM()
public static final Rank INFRASPECIFICTAXON()
public static final Rank CANDIDATE()
public static final Rank DENOMINATIONCLASS()
public static final Rank GREX()
public static final Rank GRAFTCHIMAERA()
public static final Rank CULTIVARGROUP()
public static final Rank CULTIVAR()
public static final Rank UNKNOWN_RANK()
public static final Rank NATIO()
public static final Rank UNRANKED_INFRASPECIFIC()
INFRASPECIFICTAXON()
public static final Rank UNRANKED_INFRAGENERIC()
INFRAGENERICTAXON()
public RankClass getRankClass()
public void setRankClass(RankClass rankClass)
public boolean isSupraGeneric()
isGenus()
,
isInfraGeneric()
,
isSpecies()
,
isInfraSpecific()
public boolean isGenus()
isSupraGeneric()
,
isInfraGeneric()
,
isSpecies()
,
isInfraSpecific()
public boolean isInfraGeneric()
public boolean isInfraGenericButNotSpeciesGroup()
public boolean isSpeciesAggregate()
public boolean isSpecies()
isSupraGeneric()
,
isGenus()
,
isInfraGeneric()
,
isInfraSpecific()
public boolean isInfraSpecific()
isSupraGeneric()
,
isGenus()
,
isInfraGeneric()
,
isSpecies()
public static Rank getRankByNameOrIdInVoc(java.lang.String strRank) throws UnknownCdmTypeException
strRank
- the string identifying the rankUnknownCdmTypeException
public static Rank getRankByNameOrIdInVoc(java.lang.String strRank, NomenclaturalCode nc) throws UnknownCdmTypeException
strRank
- the string identifying the ranknc
- the nomenclatural codeUnknownCdmTypeException
public static Rank getRankByNameOrIdInVoc(java.lang.String strRank, boolean useUnknown) throws UnknownCdmTypeException
strRank
- the string identifying the rankuseUnknown
- if true the rank UNKNOWN_RANK is returned if the abbrev is
unknown or not yet implementedUnknownCdmTypeException
public static Rank getRankByNameOrIdInVoc(java.lang.String strRank, NomenclaturalCode nc, boolean useUnknown) throws UnknownCdmTypeException
strRank
- the string identifying the ranknc
- the nomenclatural codeuseUnknown
- if true the rank UNKNOWN_RANK is returned if the abbrev is
unknown or not yet implementedUnknownCdmTypeException
public static Rank getRankByIdInVoc(java.lang.String abbrev) throws UnknownCdmTypeException
abbrev
- the string for the name abbreviationUnknownCdmTypeException
public static Rank getRankByIdInVoc(java.lang.String abbrev, NomenclaturalCode nc) throws UnknownCdmTypeException
getRankByIdInVoc(String, boolean)
abbrev
- the string for the name abbreviationnc
- the nomenclatural codeUnknownCdmTypeException
public static Rank getRankByIdInVoc(java.lang.String idInVoc, boolean useUnknown) throws UnknownCdmTypeException
idInVoc
- the string for the name abbreviationuseUnknown
- if true the rank UNKNOWN_RANK is returned if the abbrev is
unknown or not yet existentUnknownCdmTypeException
public static Rank getRankByIdInVoc(java.lang.String abbrev, NomenclaturalCode nc, boolean useUnknown) throws UnknownCdmTypeException
getRankByIdInVoc(String, boolean)
abbrev
- the string for the name abbreviationnc
- the nomenclatural codeuseUnknown
- if true the rank UNKNOWN_RANK is returned if the abbrev is
unknown or not yet implementedUnknownCdmTypeException
public static Rank getRankByName(java.lang.String rankName) throws UnknownCdmTypeException
rankName
- the string for the name of the rankUnknownCdmTypeException
public static Rank getRankByName(java.lang.String rankName, NomenclaturalCode nc) throws UnknownCdmTypeException
rankName
- the string for the name of the ranknc
- the nomenclatural codeUnknownCdmTypeException
public static Rank getRankByName(java.lang.String rankName, boolean useUnknown) throws UnknownCdmTypeException
rankName
- the string for the name of the rankuseUnknown
- if true the rank UNKNOWN_RANK is returned if the rank name is
unknown or not yet implementedUnknownCdmTypeException
public static Rank getRankByEnglishName(java.lang.String rankName, NomenclaturalCode nc, boolean useUnknown) throws UnknownCdmTypeException
rankName
- English rank name.nc
- Defines the handling of the section and subsection ranks. These are in different orders depending on the
nomenclatural code.useUnknown
- if true, the "Unknown" rank is returned as a placeholder.UnknownCdmTypeException
- never thrown if useUnknown is truepublic static Rank getRankByName(java.lang.String rankName, NomenclaturalCode nc, boolean useUnknown) throws UnknownCdmTypeException
UnknownCdmTypeException
public java.lang.String getAbbreviation()
public java.lang.String getInfraGenericMarker() throws UnknownCdmTypeException
UnknownCdmTypeException
public Rank readCsvLine(java.lang.Class<Rank> termClass, java.util.List<java.lang.String> csvLine, TermType termType, java.util.Map<java.util.UUID,DefinedTermBase> terms, boolean abbrevAsId)
ILoadableTerm
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.readCsvLine
in interface ILoadableTerm<Rank>
readCsvLine
in class DefinedTermBase<Rank>
protected void setDefaultTerms(TermVocabulary<Rank> termVocabulary)
setDefaultTerms
in class DefinedTermBase<Rank>
public static void initDefaultTerms()
public int compareTo(Rank orderedTerm)
compareTo
in interface java.lang.Comparable<Rank>
compareTo
in class OrderedTermBase<Rank>
orderedTerm
- the OrderedTermBase to be comparedOrderedTermBase.compareTo(eu.etaxonomy.cdm.model.term.OrderedTermBase)
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