com.hfg.bio.seq.translation

Class CodonTable

java.lang.Object

com.hfg.bio.seq.translation.CodonTable

All Implemented Interfaces:

TranslationTable

public class CodonTable
extends Object
implements TranslationTable

Table that maps codons to their respective amino acids.

Field Summary

Fields

Modifier and Type	Field and Description
static CodonTable	HUMAN
static CodonTable	MOUSE
static XMLName	XML_CODON_TABLE
static XMLName	XML_NAME_ATT
static XMLName	XML_SPECIES_ATT

Constructor Summary

Constructors

Modifier	Constructor and Description
	CodonTable(NCBITaxon inSpecies)
protected	CodonTable(String inRsrcPath)
	CodonTable(XMLTag inXMLTag)

Method Summary

Modifier and Type	Method and Description
CodonTable	addCodon(Codon inValue)
boolean	containsCodonUsageData()
Codon	getCodon(String inCodon) Can be used to retrieve the internal Codon object which can contain the AA mapping and codon usage data.
Codon	getCodonForAA_viaWeightedSelection(char inAA) Returns a weighted randomly selected codon for the specified amino acid.
Codon	getCodonForAA_viaWeightedSelection(char inAA, float inMinBias) Returns a weighted randomly selected codon meeting a specified minimum usage bias for the specified amino acid.
Set<Codon>	getCodons()
Set<Codon>	getCodonsForAA(char inAA)
String	name()
void	retrieveDataFromKazusa() Dynamically retrieves codon usage data from the Codon Usage Database (http://www.kazusa.or.jp/codon/)
XMLTag	toXMLTag()
char	translateCodon(Codon inCodon)
char	translateCodon(String inCodon) Converts the specified codon (3 nucleotides) into a character representing the corresponding amino acid.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface com.hfg.bio.seq.translation.TranslationTable

isStopCodon

Field Detail

XML_CODON_TABLE

public static final XMLName XML_CODON_TABLE

XML_NAME_ATT

public static final XMLName XML_NAME_ATT

XML_SPECIES_ATT

public static final XMLName XML_SPECIES_ATT

HUMAN

public static final CodonTable HUMAN

MOUSE

public static final CodonTable MOUSE

Constructor Detail

CodonTable

public CodonTable(NCBITaxon inSpecies)

CodonTable

public CodonTable(XMLTag inXMLTag)

CodonTable

protected CodonTable(String inRsrcPath)

Method Detail

name

public String name()

retrieveDataFromKazusa

public void retrieveDataFromKazusa()
                            throws Exception

Dynamically retrieves codon usage data from the Codon Usage Database (http://www.kazusa.or.jp/codon/)

Throws:

Exception - if the data cannot be retrieved

toXMLTag

public XMLTag toXMLTag()

addCodon

public CodonTable addCodon(Codon inValue)

getCodon

public Codon getCodon(String inCodon)

Can be used to retrieve the internal Codon object which can contain the AA mapping and codon usage data.

Parameters:

inCodon - the string representation of the Codon object to retrieve

Returns:

the Codon object corresponding to the specified nucleotide triplet

getCodons

public Set<Codon> getCodons()

getCodonsForAA

public Set<Codon> getCodonsForAA(char inAA)

getCodonForAA_viaWeightedSelection

public Codon getCodonForAA_viaWeightedSelection(char inAA)

Returns a weighted randomly selected codon for the specified amino acid.

Parameters:

inAA - the amino acid character for which codons should be selected

Returns:

the randomly selected Codon

getCodonForAA_viaWeightedSelection

public Codon getCodonForAA_viaWeightedSelection(char inAA,
                                                float inMinBias)

Returns a weighted randomly selected codon meeting a specified minimum usage bias for the specified amino acid.

Parameters:

inAA - the amino acid character for which codons should be selected

inMinBias - the minimum usage bias (frequency) for codons to be considered

Returns:

the randomly selected Codon

translateCodon

public char translateCodon(String inCodon)

Description copied from interface: TranslationTable

Converts the specified codon (3 nucleotides) into a character representing the corresponding amino acid.

Specified by:

translateCodon in interface TranslationTable

Parameters:

inCodon - 3-letter nucleotide (DNA or RNA) string to be translated

Returns:

single letter amino acid

translateCodon

public char translateCodon(Codon inCodon)

containsCodonUsageData

public boolean containsCodonUsageData()