net.maizegenetics.taxa

Class Taxon

net.maizegenetics.taxa.Taxon

public class Taxon

An identifier for some sampled data. This will most often be for example, the accession number of a DNA sequence, or the taxonomic name that the sequence represents, et cetera. The generally used class for defining a taxon. Contains its name, plus a series of optional annotations. Use the builder to create immutable instances.

Field Detail

DELIMITER

public static java.lang.String DELIMITER

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Constant Field Values

ANONYMOUS

public static Taxon ANONYMOUS

FatherKey

public static java.lang.String FatherKey

Standard key for the father of the taxon

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Constant Field Values

MotherKey

public static java.lang.String MotherKey

Standard key for the mother of the taxon

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Constant Field Values

PedigreeKey

public static java.lang.String PedigreeKey

Standard key for the pedigree of the taxon

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Constant Field Values

SexKey

public static java.lang.String SexKey

Standard key for the sex of the taxon

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Constant Field Values

InbreedFKey

public static java.lang.String InbreedFKey

Standard key for inbreeding coefficient of the taxon

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Constant Field Values

SynonymKey

public static java.lang.String SynonymKey

Standard key for a synonym of the taxon

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Constant Field Values

LatitudeKey

public static java.lang.String LatitudeKey

Standard key for the latitude the taxon was sampled

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Constant Field Values

LongitudeKey

public static java.lang.String LongitudeKey

Standard key for the longitude the taxon was sampled

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Constant Field Values

AltitudeKey

public static java.lang.String AltitudeKey

Standard key for altitude the taxon was sampled

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Constant Field Values

GenusKey

public static java.lang.String GenusKey

Standard key for a genus of the taxon

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Constant Field Values

SpeciesKey

public static java.lang.String SpeciesKey

Standard key for a species of the taxon

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Constant Field Values

Constructor Detail

Taxon

public Taxon(java.lang.String name)

Taxon

public Taxon(java.lang.String name,
             GeneralAnnotation anno)

Method Detail

toString

public java.lang.String toString()

toStringWithVCFAnnotation

public java.lang.String toStringWithVCFAnnotation()

compareTo

public int compareTo(Taxon c)

equals

public boolean equals(java.lang.Object c)

getName

public java.lang.String getName()

hashCode

public int hashCode()

getAnnotation

public GeneralAnnotation getAnnotation()