public final class GeneticCode
extends java.lang.Object
Modifier and Type | Field and 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.
use
getGeneticCodes() instead |
static GeneticCode |
INVERTEBRATE_MT |
static GeneticCode |
MOLD_PROTOZOAN_MT |
static GeneticCode |
MYCOPLASMA |
static GeneticCode |
UNIVERSAL |
static GeneticCode |
VERTEBRATE_MT |
static GeneticCode |
YEAST |
Modifier and Type | Method and Description |
---|---|
java.lang.String |
getCodeTable()
Returns a length-64 string that for each nucleotide triplet contains the single-character
amino acid code (see
AminoAcids 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 code
|
static java.lang.Iterable<GeneticCode> |
getGeneticCodes()
Returns an iterable that allows you to iterate over all the standard genetic codes
|
static GeneticCode[] |
getGeneticCodesArray() |
java.lang.String |
getName()
Returns the name of the genetic code
|
int |
getNcbiTranslationTableNumber() |
java.util.Set<CodonState> |
getStartCodons() |
int |
getStopCodonCount()
Returns the number of terminator amino acids.
|
java.util.Set<CodonState> |
getStopCodons() |
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.
|
AminoAcidState |
getTranslation(java.lang.String nucleotides)
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) |
public static final GeneticCode UNIVERSAL
public static final GeneticCode VERTEBRATE_MT
public static final GeneticCode YEAST
public static final GeneticCode MOLD_PROTOZOAN_MT
public static final GeneticCode MYCOPLASMA
public static final GeneticCode INVERTEBRATE_MT
public static final GeneticCode CILIATE
public static final GeneticCode ECHINODERM_MT
public static final GeneticCode EUPLOTID_NUC
public static final GeneticCode BACTERIAL
public static final GeneticCode ALT_YEAST
public static final GeneticCode ASCIDIAN_MT
public static final GeneticCode FLATWORM_MT
public static final GeneticCode BLEPHARISMA_NUC
@Deprecated public static final GeneticCode[] GENETIC_CODES
getGeneticCodes()
insteadpublic static java.lang.Iterable<GeneticCode> getGeneticCodes()
public static GeneticCode[] getGeneticCodesArray()
public static GeneticCode valueOf(java.lang.String name)
name
- the name of the genetic codegetDescription()
equals namepublic static GeneticCode valueOf(int NCBITranslationTableNumber)
NCBITranslationTableNumber
- the name of the genetic codegetNcbiTranslationTableNumber()
equals NCBITranslationTableNumberpublic java.lang.String getName()
public java.lang.String getDescription()
public java.lang.String getCodeTable()
AminoAcids
to which that triplet is translated in this genetic code.codeTable
argument.public AminoAcidState getTranslation(CodonState codonState)
AminoAcids
,
Codons
public AminoAcidState getTranslation(NucleotideState nucleotide1, NucleotideState nucleotide2, NucleotideState nucleotide3)
AminoAcids
,
Codons
public AminoAcidState getTranslation(java.lang.String nucleotides)
nucleotides
- a string consisting of exactly 3 residues in any case.AminoAcids
,
Codons
public MaybeBoolean isStartCodonString(java.lang.String tripletString) throws java.lang.IllegalArgumentException
tripletString
- A string of length 3, with each character representing one nucleotide or ambiguity symboljava.lang.IllegalArgumentException
- if tripletString doesn't consist of 3 nucleotide or ambiguity symbolsjava.lang.NullPointerException
- if tripletString is null@Deprecated public boolean isStartCodon(CodonState codonState)
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.codonState
- @Deprecated public boolean isStopCodon(CodonState codonState)
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.codonState
- public MaybeBoolean isStopCodonString(java.lang.String tripletString) throws java.lang.IllegalArgumentException
tripletString
- A string of length 3, with each character representing one nucleotide or ambiguity symboljava.lang.IllegalArgumentException
- if tripletString doesn't consist of 3 nucleotide or ambiguity symbolsjava.lang.NullPointerException
- if tripletString is nullpublic java.util.Set<CodonState> getCodonsForAminoAcid(AminoAcidState aminoAcidState)
public java.util.Set<CodonState> getStartCodons()
public java.util.Set<CodonState> getStopCodons()
public int getStopCodonCount()
public int getNcbiTranslationTableNumber()
public java.lang.String toString()
toString
in class java.lang.Object
http://code.google.com/p/jebl2/