org.jscience.biology
Class Alphabet

java.lang.Object
  org.jscience.biology.Alphabet

All Implemented Interfaces:

Named

public class Alphabet
extends java.lang.Object
implements Named

An class used to define the process by which mRNA is transformed (:translation) into a protein according to a given code.

Constructor Summary

Alphabet(java.lang.String name, java.lang.String aminoAcids, java.lang.String startCodons)
Creates a new Alphabet object.

Method Summary

boolean	equals(java.lang.Object o) DOCUMENT ME!
AminoAcid	getAminoAcid(Base base1, Base base2, Base base3) DOCUMENT ME!
java.lang.String	getAminoAcids() DOCUMENT ME!
java.util.Set	getInitiationCodons() DOCUMENT ME!
java.lang.String	getName() DOCUMENT ME!
java.lang.String	getStartCodons() DOCUMENT ME!
java.util.Set	getTerminationCodons() DOCUMENT ME!
boolean	isStartCodon(Base base1, Base base2, Base base3) DOCUMENT ME!
boolean	isStopCodon(Base base1, Base base2, Base base3) DOCUMENT ME!

Methods inherited from class java.lang.Object

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

Constructor Detail

Alphabet

public Alphabet(java.lang.String name,
                java.lang.String aminoAcids,
                java.lang.String startCodons)

Creates a new Alphabet object.

Parameters:

name - DOCUMENT ME!

aminoAcids - DOCUMENT ME!

startCodons - DOCUMENT ME!

Throws:

java.lang.IllegalArgumentException - DOCUMENT ME!

Method Detail

getName

public java.lang.String getName()

DOCUMENT ME!

Specified by:

getName in interface Named

Returns:

DOCUMENT ME!

getAminoAcids

public java.lang.String getAminoAcids()

DOCUMENT ME!

Returns:

DOCUMENT ME!

getStartCodons

public java.lang.String getStartCodons()

DOCUMENT ME!

Returns:

DOCUMENT ME!

isStartCodon

public boolean isStartCodon(Base base1,
                            Base base2,
                            Base base3)

DOCUMENT ME!

Parameters:

base1 - DOCUMENT ME!

base2 - DOCUMENT ME!

base3 - DOCUMENT ME!

Returns:

DOCUMENT ME!

Throws:

java.lang.IllegalArgumentException - DOCUMENT ME!

getInitiationCodons

public java.util.Set getInitiationCodons()

DOCUMENT ME!

Returns:

DOCUMENT ME!

getAminoAcid

public AminoAcid getAminoAcid(Base base1,
                              Base base2,
                              Base base3)

DOCUMENT ME!

Parameters:

base1 - DOCUMENT ME!

base2 - DOCUMENT ME!

base3 - DOCUMENT ME!

Returns:

DOCUMENT ME!

isStopCodon

public boolean isStopCodon(Base base1,
                           Base base2,
                           Base base3)

DOCUMENT ME!

Parameters:

base1 - DOCUMENT ME!

base2 - DOCUMENT ME!

base3 - DOCUMENT ME!

Returns:

DOCUMENT ME!

Throws:

java.lang.IllegalArgumentException - DOCUMENT ME!

getTerminationCodons

public java.util.Set getTerminationCodons()

DOCUMENT ME!

Returns:

DOCUMENT ME!

equals

public boolean equals(java.lang.Object o)

DOCUMENT ME!

Overrides:

equals in class java.lang.Object

Parameters:

o - DOCUMENT ME!

Returns:

DOCUMENT ME!