org.biojava.nbio.core.sequence.transcription

Class Table.Codon

java.lang.Object

org.biojava.nbio.core.sequence.transcription.Table.Codon

All Implemented Interfaces:

Compound

Enclosing interface:

Table

public static class Table.Codon
extends Object
implements Compound

Instance of a Codon which is 3 NucleotideCompounds, its corresponding AminoAcidCompound and if it is a start or stop codon. The object implements hashCode & equals but according to the nucleotide compounds & not to the designation of it being a start, stop & amino acid compound

Author:

ayates

Constructor Summary

Constructors

Constructor and Description
Codon(Table.CaseInsensitiveTriplet triplet)
Codon(Table.CaseInsensitiveTriplet triplet, AminoAcidCompound aminoAcid, boolean start, boolean stop)

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object obj)
boolean	equalsIgnoreCase(Compound compound)
AminoAcidCompound	getAminoAcid()
String	getDescription()
String	getLongName()
Float	getMolecularWeight()
NucleotideCompound	getOne()
String	getShortName()
NucleotideCompound	getThree()
Table.CaseInsensitiveTriplet	getTriplet()
NucleotideCompound	getTwo()
int	hashCode()
boolean	isStart()
boolean	isStop()
void	setDescription(String description)
void	setLongName(String longName)
void	setMolecularWeight(Float molecularWeight)
void	setShortName(String shortName)
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Codon

public Codon(Table.CaseInsensitiveTriplet triplet,
             AminoAcidCompound aminoAcid,
             boolean start,
             boolean stop)

Codon

public Codon(Table.CaseInsensitiveTriplet triplet)

Method Detail

getOne

public NucleotideCompound getOne()

getTwo

public NucleotideCompound getTwo()

getThree

public NucleotideCompound getThree()

isStart

public boolean isStart()

isStop

public boolean isStop()

getAminoAcid

public AminoAcidCompound getAminoAcid()

getTriplet

public Table.CaseInsensitiveTriplet getTriplet()

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object

equalsIgnoreCase

public boolean equalsIgnoreCase(Compound compound)

Specified by:

equalsIgnoreCase in interface Compound

getDescription

public String getDescription()

Specified by:

getDescription in interface Compound

getLongName

public String getLongName()

Specified by:

getLongName in interface Compound

getMolecularWeight

public Float getMolecularWeight()

Specified by:

getMolecularWeight in interface Compound

getShortName

public String getShortName()

Specified by:

getShortName in interface Compound

setDescription

public void setDescription(String description)

Specified by:

setDescription in interface Compound

setLongName

public void setLongName(String longName)

Specified by:

setLongName in interface Compound

setMolecularWeight

public void setMolecularWeight(Float molecularWeight)

Specified by:

setMolecularWeight in interface Compound

setShortName

public void setShortName(String shortName)

Specified by:

setShortName in interface Compound