org.gbif.api.vocabulary

Enum NameType

java.lang.Object

java.lang.Enum<NameType>

org.gbif.api.vocabulary.NameType

All Implemented Interfaces:

Serializable, Comparable<NameType>

public enum NameType
extends Enum<NameType>

A short classification of scientific name strings used in Checklist Bank.

Enum Constant Summary

Enum Constants

Enum Constant and Description
BLACKLISTED A name that has been flagged by the name parser due to the use of blacklisted epithets/words.
CANDIDATUS Candidatus is a component of the taxonomic name for a bacterium that cannot be maintained in a Bacteriology Culture Collection.
CULTIVAR A cultivated plant name.
DOUBTFUL Doubtful whether this is a scientific name at all.
HYBRID A hybrid formula (not a hybrid name).
INFORMAL A scientific name with some informal addition like "cf." or indetermined like Abies spec.
NO_NAME Surely not a scientific name of any kind.
OTU Operational Taxonomic Unit.
PLACEHOLDER A placeholder name like "incertae sedis" or "unknown genus".
SCIENTIFIC A scientific latin name that might contain authorship but is not any of the other name types below (virus, hybrid, cultivar, etc).
VIRUS A virus name.

Method Summary

Modifier and Type	Method and Description
static NameType	fromString(String nameType) Case insensitive lookup of a name type by its name that does not throw an exception but returns null for not found name types.
boolean	isBackboneType()
boolean	isParsable()
static NameType	valueOf(String name) Returns the enum constant of this type with the specified name.
static NameType[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

SCIENTIFIC

public static final NameType SCIENTIFIC

A scientific latin name that might contain authorship but is not any of the other name types below (virus, hybrid, cultivar, etc).

VIRUS

public static final NameType VIRUS

A virus name.

HYBRID

public static final NameType HYBRID

A hybrid formula (not a hybrid name).

INFORMAL

public static final NameType INFORMAL

A scientific name with some informal addition like "cf." or indetermined like Abies spec.

CULTIVAR

public static final NameType CULTIVAR

A cultivated plant name.

CANDIDATUS

public static final NameType CANDIDATUS

Candidatus is a component of the taxonomic name for a bacterium that cannot be maintained in a Bacteriology Culture Collection. It is an interim taxonomic status for noncultivable organisms. An example would be "Candidatus Phytoplasma allocasuarinae". This can be abbreviated to "Ca. Phytoplasma allocasuarinae".

See Also:

wikipedia, J.P. Euzéby

OTU

public static final NameType OTU

Operational Taxonomic Unit. An OTU is a pragmatic definition to group individuals by similarity, equivalent to but not necessarily in line with classical Linnaean taxonomy or modern Evolutionary taxonomy. A OTU usually refers to clusters of organisms, grouped by DNA sequence similarity of a specific taxonomic marker gene. In other words, OTUs are pragmatic proxies for "species" at different taxonomic levels. Sequences can be clustered according to their similarity to one another, and operational taxonomic units are defined based on the similarity threshold (usually 97% similarity) set by the researcher. Typically, OTU's are based on similar 16S rRNA sequences.

DOUBTFUL

public static final NameType DOUBTFUL

Doubtful whether this is a scientific name at all.

PLACEHOLDER

public static final NameType PLACEHOLDER

A placeholder name like "incertae sedis" or "unknown genus".

NO_NAME

public static final NameType NO_NAME

Surely not a scientific name of any kind.

BLACKLISTED

public static final NameType BLACKLISTED

A name that has been flagged by the name parser due to the use of blacklisted epithets/words.

Method Detail

values

public static NameType[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (NameType c : NameType.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static NameType valueOf(String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

IllegalArgumentException - if this enum type has no constant with the specified name

NullPointerException - if the argument is null

fromString

public static NameType fromString(String nameType)

Case insensitive lookup of a name type by its name that does not throw an exception but returns null for not found name types.

Parameters:

nameType - case insensitive name of name type

Returns:

the matching NameType or null

isBackboneType

public boolean isBackboneType()

Returns:

true if the type of name is included in the GBIF backbone

isParsable

public boolean isParsable()

Returns:

true if the GBIF name parser can parse such a name into a ParsedName instance