org.concord.biologica.engine
Class Codon

java.lang.Object
  |
  +--org.concord.biologica.engine.Codon

public final class Codon

extends java.lang.Object

This class represents a Codon object, groups of 3 bases which code for particular amino acids.

This class contains mainly static methods now, but will have other methods in the future.

Version:

$Revision: 1.1.1.1 $ $Date: 2001/04/28 00:39:11 $

Author:

$Author: ed $

Field Summary

static byte	START Start codon.
static byte	STOP Stop codon.

Constructor Summary

Codon()

Method Summary

static byte

getAminoAcidForCodon(byte firstBase, byte secondBase, byte thirdBase) Get the amino acid, stop or start for a given codon.

Methods inherited from class java.lang.Object

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

Field Detail

START

public static final byte START

Start codon. This value MUST be different from any of the amino acid values in AminoAcid.java, as there's a reasonable chance they'll be used together and we must be able to distinguish them.

STOP

public static final byte STOP

Stop codon. This value MUST be different from any of the amino acid values in AminoAcid.java, as there's a reasonable chance they'll be used together and we must be able to distinguish them.

Constructor Detail

Codon

public Codon()

Method Detail

getAminoAcidForCodon

public static byte getAminoAcidForCodon(byte firstBase,
                                        byte secondBase,
                                        byte thirdBase)

Get the amino acid, stop or start for a given codon.

In other words, this function will return either one of the 20 amino acids defined in AminoAcid.java or Codon.START and Codon.STOP.

Parameters:

firstBase - byte - first base value in codon

secondBase - byte - second base value in codon

thirdBase - byte - third base value in codon

Returns:

byte - amino acid or start or stop value

Throws:

java.lang.IllegalArgumentException - - input arguments not valid