AminoAcid (MzJava 1.1.1-SNAPSHOT API)

java.lang.Object
- java.lang.Enum<AminoAcid>
- - org.expasy.mzjava.proteomics.mol.AminoAcid

All Implemented Interfaces:

Serializable, Comparable<AminoAcid>, Symbol
```
public enum AminoAcid
extends Enum<AminoAcid>
implements Symbol
```
Enum that represents the 21 Proteinogenic amino acids and 3 B, Z and X to represent amino acids for which there is ambiguity. The method isUnambiguous() can be used to check if a particular AA is unambigous or not. The molecular mass and composition can be retrieved for amino acids that are unambiguous. Both the mass and composition are for amino acids that are missing the n-term H and c-term OH

Version:

1.0

Author:

Oliver Horlacher

Enum Constant Summary

Enum Constants
Enum Constant and Description
`A`
`B`
`C`
`D`
`E`
`F`
`G`
`H`
`I`
`J`
`K`
`L`
`M`
`N`
`O`
`P`
`Q`
`R`
`S`
`T`
`U`
`V`
`W`
`X`
`Y`
`Z`

Method Summary

Methods
Modifier and Type	Method and Description
`Composition`	`getCompositionOfMonomer()` Returns the composition of this amino acid when it is part of a polymer.
`double`	`getMassOfMonomer()` Returns the mass of this amino acid when it is part of a polymer.
`String`	`getSymbol()`
`boolean`	`isUnambiguous()` Returns true if this amino acid symbol unambiguously refers to only one amino acid.
`static AminoAcid`	`valueOf(char aa)`
`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
  - A
```
public static final AminoAcid A
```
  - R
```
public static final AminoAcid R
```
  - N
```
public static final AminoAcid N
```
  - D
```
public static final AminoAcid D
```
  - C
```
public static final AminoAcid C
```
  - E
```
public static final AminoAcid E
```
  - Q
```
public static final AminoAcid Q
```
  - G
```
public static final AminoAcid G
```
  - H
```
public static final AminoAcid H
```
  - K
```
public static final AminoAcid K
```
  - M
```
public static final AminoAcid M
```
  - F
```
public static final AminoAcid F
```
  - P
```
public static final AminoAcid P
```
  - S
```
public static final AminoAcid S
```
  - T
```
public static final AminoAcid T
```
  - W
```
public static final AminoAcid W
```
  - Y
```
public static final AminoAcid Y
```
  - V
```
public static final AminoAcid V
```
  - J
```
public static final AminoAcid J
```
  - I
```
public static final AminoAcid I
```
  - L
```
public static final AminoAcid L
```
  - O
```
public static final AminoAcid O
```
  - U
```
public static final AminoAcid U
```
  - X
```
public static final AminoAcid X
```
  - B
```
public static final AminoAcid B
```
  - Z
```
public static final AminoAcid Z
```
- 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
  - getSymbol
```
public String getSymbol()
```
    Specified by:
    
    getSymbol in interface Symbol
  - valueOf
```
public static AminoAcid valueOf(char aa)
```
  - getMassOfMonomer
```
public double getMassOfMonomer()
```
    Returns the mass of this amino acid when it is part of a polymer. When an amino acid is part of a polymer the n-term H and c-term OH are removed.
    
    Returns:
    the mass of this amino acid when it is part of a polymer
  - getCompositionOfMonomer
```
public Composition getCompositionOfMonomer()
```
    Returns the composition of this amino acid when it is part of a polymer.
    
    Returns:
    the composition of this amino acid when it is part of a polymer
  - isUnambiguous
```
public boolean isUnambiguous()
```
    Returns true if this amino acid symbol unambiguously refers to only one amino acid.
    
    Returns:
    true if this amino acid symbol unambiguously refers to only one amino acid.

Enum AminoAcid

Enum Constant Summary

Method Summary

Methods inherited from class java.lang.Enum

Methods inherited from class java.lang.Object

Enum Constant Detail

A

R

N

D

C

E

Q

G

H

K

M

F

P

S

T

W

Y

V

J

I

L

O

U

X

B

Z

Method Detail

values

valueOf

getSymbol

valueOf

getMassOfMonomer

getCompositionOfMonomer

isUnambiguous