org.bridgedb.bio
Enum Organism

java.lang.Object
  java.lang.Enum<Organism>
      org.bridgedb.bio.Organism

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<Organism>

public enum Organism
extends java.lang.Enum<Organism>

enum representing organisms understood by PathVisio. Handles conversion from full bionominal name to common name and short code. Still work in progress, currently not used everywhere it could be used.

TODO: make extensible TODO: use static initializer - static {...} - instead of multiple initMappings calls... TODO: link to taxonomy, e.g., using int constructor arg.; and new method: public Xref getTaxonomy(){...}

Enum Constant Summary

AnophelesGambiae

ArabidopsisThaliana

BacillusSubtilis

BosTaurus

CaenorhabditisElegans

CanisFamiliaris

CionaIntestinalis

DanioRerio

DasypusNovemcinctus

DrosophilaMelanogaster

EchinposTelfairi

EquusCaballus

EscherichiaColi

GallusGallus

HomoSapiens

LoxodontaAfricana

MacacaMulatta

MonodelphisDomestica

MusMusculus

MycobacteriumTuberculosis

OrnithorhynchusAnatinus

OryctolagusCuniculus

OryzaJaponica

OryzaSativa

OryziasLatipes

PanTroglodytes

PopulusTrichocarpa

RattusNorvegicus

SaccharomycesCerevisiae

SorexAraneus

SorghumBicolor

TetraodonNigroviridis

TriticumAestivum

VitisVinifera

XenopusTropicalis

ZeaMays

Method Summary

java.lang.String	code()
static java.lang.String[]	codes()
static Organism	fromCode(java.lang.String code)
static Organism	fromLatinName(java.lang.String latinName)
static Organism	fromShortName(java.lang.String shortName)
java.lang.String	latinName()
static java.util.List<java.lang.String>	latinNames()
static java.lang.String[]	latinNamesArray()
java.lang.String	shortName()
static Organism	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static Organism[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

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

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

AnophelesGambiae

public static final Organism AnophelesGambiae

ArabidopsisThaliana

public static final Organism ArabidopsisThaliana

BacillusSubtilis

public static final Organism BacillusSubtilis

BosTaurus

public static final Organism BosTaurus

CaenorhabditisElegans

public static final Organism CaenorhabditisElegans

CanisFamiliaris

public static final Organism CanisFamiliaris

CionaIntestinalis

public static final Organism CionaIntestinalis

DanioRerio

public static final Organism DanioRerio

DasypusNovemcinctus

public static final Organism DasypusNovemcinctus

DrosophilaMelanogaster

public static final Organism DrosophilaMelanogaster

EscherichiaColi

public static final Organism EscherichiaColi

EchinposTelfairi

public static final Organism EchinposTelfairi

EquusCaballus

public static final Organism EquusCaballus

GallusGallus

public static final Organism GallusGallus

HomoSapiens

public static final Organism HomoSapiens

LoxodontaAfricana

public static final Organism LoxodontaAfricana

MacacaMulatta

public static final Organism MacacaMulatta

MusMusculus

public static final Organism MusMusculus

MonodelphisDomestica

public static final Organism MonodelphisDomestica

MycobacteriumTuberculosis

public static final Organism MycobacteriumTuberculosis

OrnithorhynchusAnatinus

public static final Organism OrnithorhynchusAnatinus

OryzaSativa

public static final Organism OryzaSativa

OryzaJaponica

public static final Organism OryzaJaponica

OryziasLatipes

public static final Organism OryziasLatipes

OryctolagusCuniculus

public static final Organism OryctolagusCuniculus

PanTroglodytes

public static final Organism PanTroglodytes

PopulusTrichocarpa

public static final Organism PopulusTrichocarpa

RattusNorvegicus

public static final Organism RattusNorvegicus

SaccharomycesCerevisiae

public static final Organism SaccharomycesCerevisiae

SorexAraneus

public static final Organism SorexAraneus

SorghumBicolor

public static final Organism SorghumBicolor

TetraodonNigroviridis

public static final Organism TetraodonNigroviridis

TriticumAestivum

public static final Organism TriticumAestivum

XenopusTropicalis

public static final Organism XenopusTropicalis

VitisVinifera

public static final Organism VitisVinifera

ZeaMays

public static final Organism ZeaMays

Method Detail

values

public static Organism[] 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 (Organism c : Organism.values())
    System.out.println(c);

Returns:

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

valueOf

public static Organism valueOf(java.lang.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:

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

java.lang.NullPointerException - if the argument is null

code

public java.lang.String code()

latinName

public java.lang.String latinName()

shortName

public java.lang.String shortName()

fromCode

public static Organism fromCode(java.lang.String code)

fromShortName

public static Organism fromShortName(java.lang.String shortName)

latinNames

public static java.util.List<java.lang.String> latinNames()

codes

public static java.lang.String[] codes()

latinNamesArray

public static java.lang.String[] latinNamesArray()

fromLatinName

public static Organism fromLatinName(java.lang.String latinName)