Package jebl.evolution.sequences
Class GeneticCode
- java.lang.Object
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- jebl.evolution.sequences.GeneticCode
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public final class GeneticCode extends java.lang.Object
A set of standard genetic codes.- Version:
- $Id: GeneticCode.java 1044 2009-12-09 03:33:54Z stevensh $
- Author:
- Andrew Rambaut, Alexei Drummond
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Field Summary
Fields Modifier and Type Field Description static GeneticCode
ALT_YEAST
static GeneticCode
ASCIDIAN_MT
static GeneticCode
BACTERIAL
static GeneticCode
BLEPHARISMA_NUC
static GeneticCode
CILIATE
static GeneticCode
ECHINODERM_MT
static GeneticCode
EUPLOTID_NUC
static GeneticCode
FLATWORM_MT
static GeneticCode[]
GENETIC_CODES
Deprecated.usegetGeneticCodes()
insteadstatic GeneticCode
INVERTEBRATE_MT
static GeneticCode
MOLD_PROTOZOAN_MT
static GeneticCode
MYCOPLASMA
static GeneticCode
UNIVERSAL
static GeneticCode
VERTEBRATE_MT
static GeneticCode
YEAST
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description java.lang.String
getCodeTable()
Returns a length-64 string that for each nucleotide triplet contains the single-character amino acid code (seeAminoAcids
to which that triplet is translated in this genetic code.java.util.Set<CodonState>
getCodonsForAminoAcid(AminoAcidState aminoAcidState)
java.lang.String
getDescription()
Returns the description of the genetic codestatic java.lang.Iterable<GeneticCode>
getGeneticCodes()
Returns an iterable that allows you to iterate over all the standard genetic codesstatic GeneticCode[]
getGeneticCodesArray()
java.lang.String
getName()
Returns the name of the genetic codeint
getNcbiTranslationTableNumber()
java.util.Set<CodonState>
getStartCodons()
int
getStopCodonCount()
Returns the number of terminator amino acids.java.util.Set<CodonState>
getStopCodons()
AminoAcidState
getTranslation(java.lang.String nucleotides)
Returns the state associated with AminoAcid represented by the three nucleotides.AminoAcidState
getTranslation(CodonState codonState)
Returns the state associated with AminoAcid represented by codonState.AminoAcidState
getTranslation(NucleotideState nucleotide1, NucleotideState nucleotide2, NucleotideState nucleotide3)
Returns the state associated with AminoAcid represented by the three nucleotides.boolean
isStartCodon(CodonState codonState)
Deprecated.MaybeBoolean
isStartCodonString(java.lang.String tripletString)
Checks whether all possible disambiguations of a given nucleotide triplet string represents a start codon.boolean
isStopCodon(CodonState codonState)
Deprecated.MaybeBoolean
isStopCodonString(java.lang.String tripletString)
Checks whether a given String represents a stop codon.java.lang.String
toString()
Same as getDescription() (so that GeneticCode objects can be used e.g.static GeneticCode
valueOf(int NCBITranslationTableNumber)
static GeneticCode
valueOf(java.lang.String name)
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Field Detail
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UNIVERSAL
public static final GeneticCode UNIVERSAL
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VERTEBRATE_MT
public static final GeneticCode VERTEBRATE_MT
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YEAST
public static final GeneticCode YEAST
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MOLD_PROTOZOAN_MT
public static final GeneticCode MOLD_PROTOZOAN_MT
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MYCOPLASMA
public static final GeneticCode MYCOPLASMA
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INVERTEBRATE_MT
public static final GeneticCode INVERTEBRATE_MT
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CILIATE
public static final GeneticCode CILIATE
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ECHINODERM_MT
public static final GeneticCode ECHINODERM_MT
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EUPLOTID_NUC
public static final GeneticCode EUPLOTID_NUC
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BACTERIAL
public static final GeneticCode BACTERIAL
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ALT_YEAST
public static final GeneticCode ALT_YEAST
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ASCIDIAN_MT
public static final GeneticCode ASCIDIAN_MT
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FLATWORM_MT
public static final GeneticCode FLATWORM_MT
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BLEPHARISMA_NUC
public static final GeneticCode BLEPHARISMA_NUC
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GENETIC_CODES
@Deprecated public static final GeneticCode[] GENETIC_CODES
Deprecated.usegetGeneticCodes()
insteadUse of this field is deprecated because being an array it is mutable, i.e. an attacker could potentially replace values in this array.
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Method Detail
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getGeneticCodes
public static java.lang.Iterable<GeneticCode> getGeneticCodes()
Returns an iterable that allows you to iterate over all the standard genetic codes- Returns:
- An iterable over the genetic codes
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getGeneticCodesArray
public static GeneticCode[] getGeneticCodesArray()
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valueOf
public static GeneticCode valueOf(java.lang.String name)
- Parameters:
name
- the name of the genetic code- Returns:
- the genetic code such that
getDescription()
equals name
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valueOf
public static GeneticCode valueOf(int NCBITranslationTableNumber)
- Parameters:
NCBITranslationTableNumber
- the name of the genetic code- Returns:
- the genetic code such that
getNcbiTranslationTableNumber()
equals NCBITranslationTableNumber
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getName
public java.lang.String getName()
Returns the name of the genetic code- Returns:
- the name of this genetic code
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getDescription
public java.lang.String getDescription()
Returns the description of the genetic code- Returns:
- the description of this genetic code
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getCodeTable
public java.lang.String getCodeTable()
Returns a length-64 string that for each nucleotide triplet contains the single-character amino acid code (seeAminoAcids
to which that triplet is translated in this genetic code.- Returns:
- the string passed to the constructor as the
codeTable
argument.
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getTranslation
public AminoAcidState getTranslation(CodonState codonState)
Returns the state associated with AminoAcid represented by codonState. Note that the state is the canonical state (generated combinatorially)- Returns:
- '?' if codon unknown
- See Also:
AminoAcids
,Codons
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getTranslation
public AminoAcidState getTranslation(NucleotideState nucleotide1, NucleotideState nucleotide2, NucleotideState nucleotide3)
Returns the state associated with AminoAcid represented by the three nucleotides. If one or more of the nucleotides are ambiguous, and all combinations translate to the same protein, then this method will return that protein- Returns:
- '?' if codon unknown
- See Also:
AminoAcids
,Codons
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getTranslation
public AminoAcidState getTranslation(java.lang.String nucleotides)
Returns the state associated with AminoAcid represented by the three nucleotides. If one or more of the nucleotides are ambiguous, and all combinations translate to the same protein, then this method will return that protein- Parameters:
nucleotides
- a string consisting of exactly 3 residues in any case.- Returns:
- '?' if codon unknown
- See Also:
AminoAcids
,Codons
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isStartCodonString
public MaybeBoolean isStartCodonString(java.lang.String tripletString) throws java.lang.IllegalArgumentException
Checks whether all possible disambiguations of a given nucleotide triplet string represents a start codon.- Parameters:
tripletString
- A string of length 3, with each character representing one nucleotide or ambiguity symbol- Returns:
- Whether all possible disambiguations of tripletString represent a start codon.
- Throws:
java.lang.IllegalArgumentException
- if tripletString doesn't consist of 3 nucleotide or ambiguity symbolsjava.lang.NullPointerException
- if tripletString is null
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isStartCodon
@Deprecated public boolean isStartCodon(CodonState codonState)
Deprecated.As of 2007-07-30,CodonState
s exist only for nonambiguous nucleotide triplets. Therefore, this method cannot be used to check if an ambiguous triplet of nucleotides codes for a transcription, start and therefore this method is deprecated.- Parameters:
codonState
-- Returns:
- True if the specified codonState codes for a transcription start under this genetic code.
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isStopCodon
@Deprecated public boolean isStopCodon(CodonState codonState)
Deprecated.As of 2007-07-30,CodonState
s exist only for nonambiguous nucleotide triplets. Therefore, this method cannot be used to check if an ambiguous triplet of nucleotides codes for a stop, and therefore this method is deprecated.- Parameters:
codonState
-- Returns:
- True if the specified codonState codes for a stop under this genetic code.
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isStopCodonString
public MaybeBoolean isStopCodonString(java.lang.String tripletString) throws java.lang.IllegalArgumentException
Checks whether a given String represents a stop codon.- Parameters:
tripletString
- A string of length 3, with each character representing one nucleotide or ambiguity symbol- Returns:
- true if tripletString represents a stop codon.
- Throws:
java.lang.IllegalArgumentException
- if tripletString doesn't consist of 3 nucleotide or ambiguity symbolsjava.lang.NullPointerException
- if tripletString is null
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getCodonsForAminoAcid
public java.util.Set<CodonState> getCodonsForAminoAcid(AminoAcidState aminoAcidState)
- Returns:
- all the possible codons for a given amino acid
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getStartCodons
public java.util.Set<CodonState> getStartCodons()
- Returns:
- the codon states of starts
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getStopCodons
public java.util.Set<CodonState> getStopCodons()
- Returns:
- the codon states of stops.
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getStopCodonCount
public int getStopCodonCount()
Returns the number of terminator amino acids.
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getNcbiTranslationTableNumber
public int getNcbiTranslationTableNumber()
- Returns:
- the number used by NCBI to represent this genetic code or -1 if none. Eg. 1 = Standard...
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toString
public java.lang.String toString()
Same as getDescription() (so that GeneticCode objects can be used e.g. in a JComboBox).- Overrides:
toString
in classjava.lang.Object
- Returns:
- the description of this genetic code
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