Codon

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

All Implemented Interfaces:: Serializable, Comparable<Codon>

public enum Codon
extends Enum<Codon>

This enum provides the 4³ = 64 DNA codons made of the alphabet T, 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.

   TTT (Phe), TCT (Ser), TAT (Tyr), TGT (Cys),
   TTC (Phe), TCC (Ser), TAC (Tyr), TGC (Cys),
   TTA (Leu), TCA (Ser), TAA (Stop),TGA (Sec),
   TTG (Leu), TCG (Ser), TAG (Pyl), TGG (Trp),

   CTT (Leu), CCT (Pro), CAT (His), CGT (Arg),
   CTC (Leu), CCC (Pro), CAC (His), CGC (Arg),
   CTA (Leu), CCA (Pro), CAA (Gln), CGA (Arg),
   CTG (Leu), CCG (Pro), CAG (Gln), CGG (Arg),

   ATT (Ile), ACT (Thr), AAT (Asn), AGT (Ser),
   ATC (Ile), ACC (Thr), AAC (Asn), AGC (Ser),
   ATA (Ile), ACA (Thr), AAA (Lys), AGA (Arg),
   ATG (Met), ACG (Thr), AAG (Lys), AGG (Arg),

   GTT (Val), GCT (Ala), GAT (Asp), GGT (Gly),
   GTC (Val), GCC (Ala), GAC (Asp), GGC (Gly),
   GTA (Val), GCA (Ala), GAA (Glu), GGA (Gly),
   GTG (Val, 61), GCG (Ala, 62), GAG (Glu, 63), GGG (Gly, 64),
   NNN (null, 65);

Version:: 1.1
Author:: Andreas de Vries

Enum Constant Summary

Enum Constants
Enum Constant and Description
`AAA`
`AAC`
`AAG`
`AAT`
`ACA`
`ACC`
`ACG`
`ACT`
`AGA`
`AGC`
`AGG`
`AGT`
`ATA`
`ATC`
`ATG`
`ATT`
`CAA`
`CAC`
`CAG`
`CAT`
`CCA`
`CCC`
`CCG`
`CCT`
`CGA`
`CGC`
`CGG`
`CGT`
`CTA`
`CTC`
`CTG`
`CTT`
`GAA`
`GAC`
`GAG`
`GAT`
`GCA`
`GCC`
`GCG`
`GCT`
`GGA`
`GGC`
`GGG`
`GGT`
`GTA`
`GTC`
`GTG`
`GTT`
`NNN`
`TAA`
`TAC`
`TAG`
`TAT`
`TCA`
`TCC`
`TCG`
`TCT`
`TGA`
`TGC`
`TGG`
`TGT`
`TTA`
`TTC`
`TTG`
`TTT` Genetic code according to Mortimer, Müller: Chemie.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static Codon`	`decode(AminoAcid aminoAcid)` Returns the codon which is related to the specified amino acid by the genetic code.
`AminoAcid`	`encode()` Returns the amino acid which is related to this codon by the genetic code.
`static Codon`	`fromBitmaskCode(byte bitmaskCode)` Returns the DNA codon which is represented by the specified bitmask code, an integer x satisfying 0 ≤ x < 64.
`static Codon`	`fromString(CharSequence 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.
`static Codon`	`fromTriplet(char x, char y, char z)` Returns the DNA codon which is represented by the specified three nucleobases, 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.
`byte`	`getBitmaskCode()` Returns the bitmask code referring to this codon.
`static void`	`main(String... args)`
`static Codon`	`valueOf(String name)` Returns the enum constant of this type with the specified name.
`static Codon[]`	`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

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

TCT
```
public static final Codon TCT
```

TAT
```
public static final Codon TAT
```

TGT
```
public static final Codon TGT
```

TTC
```
public static final Codon TTC
```

TCC
```
public static final Codon TCC
```

TAC
```
public static final Codon TAC
```

TGC
```
public static final Codon TGC
```

TTA
```
public static final Codon TTA
```

TCA
```
public static final Codon TCA
```

TAA
```
public static final Codon TAA
```

TGA
```
public static final Codon TGA
```

TTG
```
public static final Codon TTG
```

TCG
```
public static final Codon TCG
```

TAG
```
public static final Codon TAG
```

TGG
```
public static final Codon TGG
```

CTT
```
public static final Codon CTT
```

CCT
```
public static final Codon CCT
```

CAT
```
public static final Codon CAT
```

CGT
```
public static final Codon CGT
```

CTC
```
public static final Codon CTC
```

CCC
```
public static final Codon CCC
```

CAC
```
public static final Codon CAC
```

CGC
```
public static final Codon CGC
```

CTA
```
public static final Codon CTA
```

CCA
```
public static final Codon CCA
```

CAA
```
public static final Codon CAA
```

CGA
```
public static final Codon CGA
```

CTG
```
public static final Codon CTG
```

CCG
```
public static final Codon CCG
```

CAG
```
public static final Codon CAG
```

CGG
```
public static final Codon CGG
```

ATT
```
public static final Codon ATT
```

ACT
```
public static final Codon ACT
```

AAT
```
public static final Codon AAT
```

AGT
```
public static final Codon AGT
```

ATC
```
public static final Codon ATC
```

ACC
```
public static final Codon ACC
```

AAC
```
public static final Codon AAC
```

AGC
```
public static final Codon AGC
```

ATA
```
public static final Codon ATA
```

ACA
```
public static final Codon ACA
```

AAA
```
public static final Codon AAA
```

AGA
```
public static final Codon AGA
```

ATG
```
public static final Codon ATG
```

ACG
```
public static final Codon ACG
```

AAG
```
public static final Codon AAG
```

AGG
```
public static final Codon AGG
```

GTT
```
public static final Codon GTT
```

GCT
```
public static final Codon GCT
```

GAT
```
public static final Codon GAT
```

GGT
```
public static final Codon GGT
```

GTC
```
public static final Codon GTC
```

GCC
```
public static final Codon GCC
```

GAC
```
public static final Codon GAC
```

GGC
```
public static final Codon GGC
```

GTA
```
public static final Codon GTA
```

GCA
```
public static final Codon GCA
```

GAA
```
public static final Codon GAA
```

GGA
```
public static final Codon GGA
```

GTG
```
public static final Codon GTG
```

GCG
```
public static final Codon GCG
```

GAG
```
public static final Codon GAG
```

GGG
```
public static final Codon GGG
```

NNN
```
public static final Codon NNN
```

Method Detail
- values
```
public static Codon[] 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 (Codon c : Codon.values())
    System.out.println(c);
```
  Returns:
  
  an array containing the constants of this enum type, in the order they are declared
- valueOf
```
public static Codon 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
- getBitmaskCode
```
public byte getBitmaskCode()
```
  Returns the bitmask code referring to this codon. It is (arbitrarily chosen to be) as follows.
```
       1 → TTT,  2 → TCT,  3 → TAT,  4 → TGT,
       5 → TTC,  6 → TCC,  7 → TAC,  8 → TGC,
       9 → TTA, 10 → TCA, 11 → TAA, 12 → TGA,
      13 → TTG, 14 → TCG, 15 → TAG, 16 → TGG,
   
      17 → CTT, 18 → CCT, 19 → CAT, 20 → CGT,
      21 → CTC, 22 → CCC, 23 → CAC, 24 → CGC,
      25 → CTA, 26 → CCA, 27 → CAA, 28 → CGA,
      29 → CTG, 30 → CCG, 31 → CAG, 32 → CGG,
   
      33 → ATT, 34 → ACT, 35 → AAT, 36 → AGT,
      37 → ATC, 38 → ACC, 39 → AAC, 40 → AGC,
      41 → ATA, 42 → ACA, 43 → AAA, 44 → AGA,
      45 → ATG, 46 → ACG, 47 → AAG, 48 → AGG,
   
      49 → GTT, 50 → GCT, 51 → GAT, 52 → GGT,
      53 → GTC, 54 → GCC, 55 → GAC, 56 → GGC,
      57 → GTA, 58 → GCA, 59 → GAA, 60 → GGA,
      61 → GTG, 62 → GCG, 63 → GAG, 64 → GGG
      
      65 → NNN (unknown codon)
  
```
  Returns:
  
  the bitmask code of this codon
- 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 Codon decode(AminoAcid aminoAcid)
```
  Returns the codon which is related to the specified amino acid by the genetic code. If the amino acid cannot be decoded the unknown Codon NNN is returned.
  
  Parameters:
  
  aminoAcid - an amino acid
  
  Returns:
  
  the amino acid coded by this codon
- fromBitmaskCode
```
public static Codon fromBitmaskCode(byte bitmaskCode)
```
  Returns the DNA codon which is represented by the specified bitmask code, an integer x satisfying 0 ≤ x < 64. It is (arbitrarily) chosen to be as follows.
```
       1 → TTT,  2 → TCT,  3 → TAT,  4 → TGT,
       5 → TTC,  6 → TCC,  7 → TAC,  8 → TGC,
       9 → TTA, 10 → TCA, 11 → TAA, 12 → TGA,
      13 → TTG, 14 → TCG, 15 → TAG, 16 → TGG,
   
      17 → CTT, 18 → CCT, 19 → CAT, 20 → CGT,
      21 → CTC, 22 → CCC, 23 → CAC, 24 → CGC,
      25 → CTA, 26 → CCA, 27 → CAA, 28 → CGA,
      29 → CTG, 30 → CCG, 31 → CAG, 32 → CGG,
   
      33 → ATT, 34 → ACT, 35 → AAT, 36 → AGT,
      37 → ATC, 38 → ACC, 39 → AAC, 40 → AGC,
      41 → ATA, 42 → ACA, 43 → AAA, 44 → AGA,
      45 → ATG, 46 → ACG, 47 → AAG, 48 → AGG,
   
      49 → GTT, 50 → GCT, 51 → GAT, 52 → GGT,
      53 → GTC, 54 → GCC, 55 → GAC, 56 → GGC,
      57 → GTA, 58 → GCA, 59 → GAA, 60 → GGA,
      61 → GTG, 62 → GCG, 63 → GAG, 64 → GGG
      
      65 → NNN (unknown codon)
  
```
  Parameters:
  
  bitmaskCode - the bitmask code representing a codon.
  
  Returns:
  
  the codon represented by the specified bitmask code
  
  Throws:
  
  IllegalArgumentException - if the string is not a codon triplet
- fromTriplet
```
public static Codon fromTriplet(char x,
                                char y,
                                char z)
```
  Returns the DNA codon which is represented by the specified three nucleobases, a triplet, consisting of the DNA letters T, C, A, G.
  
  Parameters:
  
  x - the first of the three-letter string representing a codon.
  
  y - the second of the three-letter string representing a codon.
  
  z - the third of the three-letter string representing a codon.
  
  Returns:
  
  the codon represented by the specified triplet
  
  Throws:
  
  IllegalArgumentException - if the string is not a codon triplet
- fromString
```
public static Codon fromString(CharSequence 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
- main
```
public static void main(String... args)
```

Enum Codon

Enum Constant Summary

Method Summary

Methods inherited from class java.lang.Enum

Methods inherited from class java.lang.Object

Enum Constant Detail

TTT

TCT

TAT

TGT

TTC

TCC

TAC

TGC

TTA

TCA

TAA

TGA

TTG

TCG

TAG

TGG

CTT

CCT

CAT

CGT

CTC

CCC

CAC

CGC

CTA

CCA

CAA

CGA

CTG

CCG

CAG

CGG

ATT

ACT

AAT

AGT

ATC

ACC

AAC

AGC

ATA

ACA

AAA

AGA

ATG

ACG

AAG

AGG

GTT

GCT

GAT

GGT

GTC

GCC

GAC

GGC

GTA

GCA

GAA

GGA

GTG

GCG

GAG

GGG

NNN

Method Detail

values

valueOf

getBitmaskCode

getAminoAcid

encode

decode

fromBitmaskCode

fromTriplet