Taxon (net.maizegenetics:tassel 5.2.46 API)

java.lang.Object
- net.maizegenetics.taxa.Taxon

All Implemented Interfaces:

Comparable<Taxon>
```
public class Taxon
extends Object
implements Comparable<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.

Author:

Terry Casstevens, Ed Buckler

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class Taxon.Builder
A builder for creating immutable Taxon instances.

Nested Classes
Modifier and Type	Class and Description
`static class`	`Taxon.Builder` A builder for creating immutable Taxon instances.

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`AltitudeKey` Standard key for altitude the taxon was sampled
`static Taxon`	`ANONYMOUS`
`static String`	`DELIMITER`
`static String`	`FatherKey` Standard key for the father of the taxon
`static String`	`GenusKey` Standard key for a genus of the taxon
`static String`	`InbreedFKey` Standard key for inbreeding coefficient of the taxon
`static String`	`LatitudeKey` Standard key for the latitude the taxon was sampled
`static String`	`LongitudeKey` Standard key for the longitude the taxon was sampled
`static String`	`MotherKey` Standard key for the mother of the taxon
`static String`	`PedigreeKey` Standard key for the pedigree of the taxon
`static String`	`SexKey` Standard key for the sex of the taxon
`static String`	`SpeciesKey` Standard key for a species of the taxon
`static String`	`SynonymKey` Standard key for a synonym of the taxon

Constructor Summary

Constructors
Constructor and Description

Taxon(String name)

Taxon(String name, GeneralAnnotation anno)

Constructors
Constructor and Description
`Taxon(String name)`
`Taxon(String name, GeneralAnnotation anno)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`compareTo(Taxon c)`
`boolean`	`equals(Object c)`
`GeneralAnnotation`	`getAnnotation()`
`String`	`getName()`
`int`	`hashCode()`
`String`	`toString()`
`String`	`toStringWithVCFAnnotation()`

Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - DELIMITER
```
public static final String DELIMITER
```
    See Also:
    
    Constant Field Values
  - ANONYMOUS
```
public static Taxon ANONYMOUS
```
  - FatherKey
```
public static final String FatherKey
```
    Standard key for the father of the taxon
    
    See Also:
    
    Constant Field Values
  - MotherKey
```
public static final String MotherKey
```
    Standard key for the mother of the taxon
    
    See Also:
    
    Constant Field Values
  - PedigreeKey
```
public static final String PedigreeKey
```
    Standard key for the pedigree of the taxon
    
    See Also:
    
    Constant Field Values
  - SexKey
```
public static final String SexKey
```
    Standard key for the sex of the taxon
    
    See Also:
    
    Constant Field Values
  - InbreedFKey
```
public static final String InbreedFKey
```
    Standard key for inbreeding coefficient of the taxon
    
    See Also:
    
    Constant Field Values
  - SynonymKey
```
public static final String SynonymKey
```
    Standard key for a synonym of the taxon
    
    See Also:
    
    Constant Field Values
  - LatitudeKey
```
public static final String LatitudeKey
```
    Standard key for the latitude the taxon was sampled
    
    See Also:
    
    Constant Field Values
  - LongitudeKey
```
public static final String LongitudeKey
```
    Standard key for the longitude the taxon was sampled
    
    See Also:
    
    Constant Field Values
  - AltitudeKey
```
public static final String AltitudeKey
```
    Standard key for altitude the taxon was sampled
    
    See Also:
    
    Constant Field Values
  - GenusKey
```
public static final String GenusKey
```
    Standard key for a genus of the taxon
    
    See Also:
    
    Constant Field Values
  - SpeciesKey
```
public static final String SpeciesKey
```
    Standard key for a species of the taxon
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - Taxon
```
public Taxon(String name)
```
  - Taxon
```
public Taxon(String name,
             GeneralAnnotation anno)
```
- Method Detail
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - toStringWithVCFAnnotation
```
public String toStringWithVCFAnnotation()
```
  - compareTo
```
public int compareTo(Taxon c)
```
    Specified by:
    
    compareTo in interface Comparable<Taxon>
  - equals
```
public boolean equals(Object c)
```
    Overrides:
    
    equals in class Object
  - getName
```
public String getName()
```
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - getAnnotation
```
public GeneralAnnotation getAnnotation()
```

Class Taxon

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DELIMITER

ANONYMOUS

FatherKey

MotherKey

PedigreeKey

SexKey

InbreedFKey

SynonymKey

LatitudeKey

LongitudeKey

AltitudeKey

GenusKey

SpeciesKey

Constructor Detail

Taxon

Taxon

Method Detail

toString

toStringWithVCFAnnotation

compareTo

equals

getName

hashCode

getAnnotation