org.mathIT.genes

Enum AminoAcid

java.lang.Object

java.lang.Enum<AminoAcid>

org.mathIT.genes.AminoAcid

All Implemented Interfaces:

Serializable, Comparable<AminoAcid>

public enum AminoAcid
extends Enum<AminoAcid>

This enum represents the 22 natural amino acids forming proteins.

 
   Gly - glycine,        'G'
   Ala - alanine,        'A'
   Val - valine,         'V'
   Leu - leucine,        'L'
   Ile - isoleucine,     'I'
   Phe - phenylalanine,  'F'
   Ser - serine,         'S'
   Thr - threonine,      'T'
   Tyr - tyrosine,       'Y'
   Cys - cysteine,       'C'
   Sec - selenocysteine, 'U' // 21st amino acid
   Met - methionine,     'M'
   Pro - proline,        'P'
   Lys - lysine,         'K'
   His - histidine,      'H'
   Trp - tryptophan,     'W'
   Arg - arginine,       'R'
   Asn - asparagine,     'N'
   Gln - glutamine,      'Q'
   Pyl - pyrrolysine,    'O' // 22nd amino acid
   Asp - aspartic acid,  'D'
   Glu - glutamic acid,  'E'
   Stop- -,              '*'
   

The order of the amino acids is taken from C.E. Mortimer & U. Müller: Chemie. 10th edition, Thieme, Stuttgart 2007.

Version:

1.1

Author:

Andreas de Vries

Enum Constant Summary

Enum Constants

Enum Constant and Description
Ala Alanine
Arg Arginine
Asn Asparagine
Asp Aspartic acid
Cys Cyteine
Gln Glutamine
Glu Glutamic acid
Gly Glycine
His Histidine
Ile Isoleucine
Leu Leucine
Lys Lysine
Met Methionine
Phe Phenylalanine
Pro Proline
Pyl Pyrrolysine. (22nd amino acid)
Sec Selenocysteine. (21st amino acid)
Ser Serine
Stop Stop symbol
Thr Threonine
Trp Tryptophan
Tyr Tyrosine
Val Valine

Method Summary

Modifier and Type	Method and Description
static AminoAcid	decode(char symbol) Returns the amino acid represented by the specified one-letter symbol.
static AminoAcid	decode(String name) Returns the amino acid represented by the specified name.
String	getName() Returns the name of this amino acid.
char	getSymbol() Returns the one-letter symbol of this amino acid.
static AminoAcid	valueOf(String name) Returns the enum constant of this type with the specified name.
static AminoAcid[]	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

Gly

public static final AminoAcid Gly

Glycine

Ala

public static final AminoAcid Ala

Alanine

Val

public static final AminoAcid Val

Valine

Leu

public static final AminoAcid Leu

Leucine

Ile

public static final AminoAcid Ile

Isoleucine

Phe

public static final AminoAcid Phe

Phenylalanine

Ser

public static final AminoAcid Ser

Serine

Thr

public static final AminoAcid Thr

Threonine

Tyr

public static final AminoAcid Tyr

Tyrosine

Cys

public static final AminoAcid Cys

Cyteine

Sec

public static final AminoAcid Sec

Selenocysteine. (21st amino acid)

Met

public static final AminoAcid Met

Methionine

Pro

public static final AminoAcid Pro

Proline

Lys

public static final AminoAcid Lys

Lysine

His

public static final AminoAcid His

Histidine

Trp

public static final AminoAcid Trp

Tryptophan

Arg

public static final AminoAcid Arg

Arginine

Asn

public static final AminoAcid Asn

Asparagine

Gln

public static final AminoAcid Gln

Glutamine

Pyl

public static final AminoAcid Pyl

Pyrrolysine. (22nd amino acid)

Asp

public static final AminoAcid Asp

Aspartic acid

Glu

public static final AminoAcid Glu

Glutamic acid

Stop

public static final AminoAcid Stop

Stop symbol

Method Detail

values

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

Returns:

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

valueOf

public static AminoAcid 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

getName

public String getName()

Returns the name of this amino acid.

Returns:

the name of this amino acid

getSymbol

public char getSymbol()

Returns the one-letter symbol of this amino acid.

Returns:

the one-letter symbol of this amino acid

decode

public static AminoAcid decode(String name)

Returns the amino acid represented by the specified name.

Parameters:

name - three-symbol string representing an amino acid

Returns:

the amino acid represented by the specified name

Throws:

IllegalArgumentException - if the string is not an amino acid name

decode

public static AminoAcid decode(char symbol)

Returns the amino acid represented by the specified one-letter symbol.

Parameters:

symbol - one-letter symbol representing an amino acid.

Returns:

the amino acid represented by symbol

Throws:

IllegalArgumentException - if the string does not represent an amino acid