RNACodon

java.lang.Object
- java.lang.Enum<RNACodon>
- - org.mathIT.genes.RNACodon

All Implemented Interfaces:: Serializable, Comparable<RNACodon>

public enum RNACodon
extends Enum<RNACodon>

This enum provides the 4³ = 64 mRNA codons made of the alphabet U, C, A, G; associated to each cocon is the amino acid to which it is transformed by the genetic code during the process of genetic expression. The genetic code is adapted from Mortimer, Müller: Chemie. Thieme, Stuttgart 2007, S.627.

   UUU (Phe), UCU (Ser), UAU (Tyr), UGU (Cys),
   UUC (Phe), UCC (Ser), UAC (Tyr), UGC (Cys),
   UUA (Leu), UCA (Ser), UAA (Stop),UGA (Sec),
   UUG (Leu), UCG (Ser), UAG (Pyl), UGG (Trp),

   CUU (Leu), CCU (Pro), CAU (His), CGU (Arg),
   CUC (Leu), CCC (Pro), CAC (His), CGC (Arg),
   CUA (Leu), CCA (Pro), CAA (Gln), CGA (Arg),
   CUG (Leu), CCG (Pro), CAG (Gln), CGG (Arg),

   AUU (Ile), ACU (Thr), AAU (Asn), AGU (Ser),
   AUC (Ile), ACC (Thr), AAC (Asn), AGC (Ser),
   AUA (Ile), ACA (Thr), AAA (Lys), AGA (Arg),
   AUG (Met), ACG (Thr), AAG (Lys), AGG (Arg),

   GUU (Val), GCU (Ala), GAU (Asp), GGU (Gly),
   GUC (Val), GCC (Ala), GAC (Asp), GGC (Gly),
   GUA (Val), GCA (Ala), GAA (Glu), GGA (Gly),
   GUG (Val), GCG (Ala), GAG (Glu), GGG (Gly);

Version:: 1.0
Author:: Andreas de Vries

Enum Constant Summary

Enum Constants
Enum Constant and Description
`AAA`
`AAC`
`AAG`
`AAU`
`ACA`
`ACC`
`ACG`
`ACU`
`AGA`
`AGC`
`AGG`
`AGU`
`AUA`
`AUC`
`AUG`
`AUU`
`CAA`
`CAC`
`CAG`
`CAU`
`CCA`
`CCC`
`CCG`
`CCU`
`CGA`
`CGC`
`CGG`
`CGU`
`CUA`
`CUC`
`CUG`
`CUU`
`GAA`
`GAC`
`GAG`
`GAU`
`GCA`
`GCC`
`GCG`
`GCU`
`GGA`
`GGC`
`GGG`
`GGU`
`GUA`
`GUC`
`GUG`
`GUU`
`UAA`
`UAC`
`UAG`
`UAU`
`UCA`
`UCC`
`UCG`
`UCU`
`UGA`
`UGC`
`UGG`
`UGU`
`UUA`
`UUC`
`UUG`
`UUU` Genetic code according to Mortimer, Müller: Chemie.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static RNACodon`	`decode(AminoAcid aminoAcid)` Returns the amino acid which is related to this codon by the genetic code.
`AminoAcid`	`encode()` Returns the amino acid which is related to this codon by the genetic code.
`static RNACodon`	`fromString(String triplet)` Returns the DNA codon which is represented by the specified three-letter string, a triplet, consisting of the DNA letters T, C, A, G.
`AminoAcid`	`getAminoAcid()` Returns the amino acid which is related to this codon by the genetic code.
`static RNACodon`	`valueOf(String name)` Returns the enum constant of this type with the specified name.
`static RNACodon[]`	`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

UUU
```
public static final RNACodon UUU
```
Genetic code according to Mortimer, Müller: Chemie. Thieme, Stuttgart 2007, S.627.

UCU
```
public static final RNACodon UCU
```

UAU
```
public static final RNACodon UAU
```

UGU
```
public static final RNACodon UGU
```

UUC
```
public static final RNACodon UUC
```

UCC
```
public static final RNACodon UCC
```

UAC
```
public static final RNACodon UAC
```

UGC
```
public static final RNACodon UGC
```

UUA
```
public static final RNACodon UUA
```

UCA
```
public static final RNACodon UCA
```

UAA
```
public static final RNACodon UAA
```

UGA
```
public static final RNACodon UGA
```

UUG
```
public static final RNACodon UUG
```

UCG
```
public static final RNACodon UCG
```

UAG
```
public static final RNACodon UAG
```

UGG
```
public static final RNACodon UGG
```

CUU
```
public static final RNACodon CUU
```

CCU
```
public static final RNACodon CCU
```

CAU
```
public static final RNACodon CAU
```

CGU
```
public static final RNACodon CGU
```

CUC
```
public static final RNACodon CUC
```

CCC
```
public static final RNACodon CCC
```

CAC
```
public static final RNACodon CAC
```

CGC
```
public static final RNACodon CGC
```

CUA
```
public static final RNACodon CUA
```

CCA
```
public static final RNACodon CCA
```

CAA
```
public static final RNACodon CAA
```

CGA
```
public static final RNACodon CGA
```

CUG
```
public static final RNACodon CUG
```

CCG
```
public static final RNACodon CCG
```

CAG
```
public static final RNACodon CAG
```

CGG
```
public static final RNACodon CGG
```

AUU
```
public static final RNACodon AUU
```

ACU
```
public static final RNACodon ACU
```

AAU
```
public static final RNACodon AAU
```

AGU
```
public static final RNACodon AGU
```

AUC
```
public static final RNACodon AUC
```

ACC
```
public static final RNACodon ACC
```

AAC
```
public static final RNACodon AAC
```

AGC
```
public static final RNACodon AGC
```

AUA
```
public static final RNACodon AUA
```

ACA
```
public static final RNACodon ACA
```

AAA
```
public static final RNACodon AAA
```

AGA
```
public static final RNACodon AGA
```

AUG
```
public static final RNACodon AUG
```

ACG
```
public static final RNACodon ACG
```

AAG
```
public static final RNACodon AAG
```

AGG
```
public static final RNACodon AGG
```

GUU
```
public static final RNACodon GUU
```

GCU
```
public static final RNACodon GCU
```

GAU
```
public static final RNACodon GAU
```

GGU
```
public static final RNACodon GGU
```

GUC
```
public static final RNACodon GUC
```

GCC
```
public static final RNACodon GCC
```

GAC
```
public static final RNACodon GAC
```

GGC
```
public static final RNACodon GGC
```

GUA
```
public static final RNACodon GUA
```

GCA
```
public static final RNACodon GCA
```

GAA
```
public static final RNACodon GAA
```

GGA
```
public static final RNACodon GGA
```

GUG
```
public static final RNACodon GUG
```

GCG
```
public static final RNACodon GCG
```

GAG
```
public static final RNACodon GAG
```

GGG
```
public static final RNACodon GGG
```

Method Detail
- values
```
public static RNACodon[] 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 (RNACodon c : RNACodon.values())
    System.out.println(c);
```
  Returns:
  
  an array containing the constants of this enum type, in the order they are declared
- valueOf
```
public static RNACodon 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
- getAminoAcid
```
public AminoAcid getAminoAcid()
```
  Returns the amino acid which is related to this codon by the genetic code. Note that the stop codon TAA returns "Stop" instead of an amino acid.
  
  Returns:
  
  the amino acid coded by this codon
- encode
```
public AminoAcid encode()
```
  Returns the amino acid which is related to this codon by the genetic code. Note that the stop codon TAA returns "Stop" instead of an amino acid.
  
  Returns:
  
  the amino acid coded by this codon
- decode
```
public static RNACodon decode(AminoAcid aminoAcid)
```
  Returns the amino acid which is related to this codon by the genetic code. Note that the stop codon TAA returns "Stop" instead of an amino acid.
  
  Parameters:
  
  aminoAcid - amino acid
  
  Returns:
  
  the amino acid coded by this codon
- fromString
```
public static RNACodon fromString(String triplet)
```
  Returns the DNA codon which is represented by the specified three-letter string, a triplet, consisting of the DNA letters T, C, A, G.
  
  Parameters:
  
  triplet - three-letter string representing a codon.
  
  Returns:
  
  the codon represented by the specified triplet
  
  Throws:
  
  IllegalArgumentException - if the string is not a codon triplet

Enum RNACodon

Enum Constant Summary

Method Summary

Methods inherited from class java.lang.Enum

Methods inherited from class java.lang.Object

Enum Constant Detail

UUU

UCU

UAU

UGU

UUC

UCC

UAC

UGC

UUA

UCA

UAA

UGA

UUG

UCG

UAG

UGG

CUU

CCU

CAU

CGU

CUC

CCC

CAC

CGC

CUA

CCA

CAA

CGA

CUG

CCG

CAG

CGG

AUU

ACU

AAU

AGU

AUC

ACC

AAC

AGC

AUA

ACA

AAA

AGA

AUG

ACG

AAG

AGG

GUU

GCU

GAU

GGU

GUC

GCC

GAC

GGC

GUA

GCA

GAA

GGA

GUG

GCG

GAG

GGG

Method Detail

values

valueOf

getAminoAcid

encode

decode

fromString