javagene.seq
Class AminoAcid

java.lang.Object
  javagene.seq.AminoAcid

public class AminoAcid
extends java.lang.Object

An amino acid object with codon/residue utility methods. Implements the classic 20, plus STOP.

Field Summary

static AminoAcid	ALA
static AminoAcid	ARG
static AminoAcid	ASN
static AminoAcid	ASP
static AminoAcid	CYS
static AminoAcid	GLN
static AminoAcid	GLU
static AminoAcid	GLY
static AminoAcid	HIS
static AminoAcid	ILE
static AminoAcid	LEU
static AminoAcid	LYS
static AminoAcid	MET
static AminoAcid	PHE
static AminoAcid	PRO
static AminoAcid	SER
static AminoAcid	STOP
static AminoAcid	THR
static AminoAcid	TRP
static AminoAcid	TYR
static AminoAcid	UNDEFINED
static AminoAcid	VAL

Method Summary

static int	blosum62(AminoAcid a, AminoAcid b) Get BLOSUM62 distance between two AminoAcids.
boolean	isSynonym(java.lang.String str) Check if a three-letter Dna/Rna codon codes for this AminoAcid.
static AminoAcid	lookup(java.lang.String str) Find the AminoAcid object corresponding to a three-letter Dna/Rna codon.
java.lang.String	toString() Get the IUPAC single letter representation of this AminoAcid.
static java.lang.String	translate(java.lang.String str) Translate from IUPAC nucleotide string to IUPAC protein string.

Methods inherited from class java.lang.Object

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

Field Detail

ALA

public static final AminoAcid ALA

ARG

public static final AminoAcid ARG

ASN

public static final AminoAcid ASN

ASP

public static final AminoAcid ASP

CYS

public static final AminoAcid CYS

GLN

public static final AminoAcid GLN

GLU

public static final AminoAcid GLU

GLY

public static final AminoAcid GLY

HIS

public static final AminoAcid HIS

ILE

public static final AminoAcid ILE

LEU

public static final AminoAcid LEU

LYS

public static final AminoAcid LYS

MET

public static final AminoAcid MET

PHE

public static final AminoAcid PHE

PRO

public static final AminoAcid PRO

SER

public static final AminoAcid SER

STOP

public static final AminoAcid STOP

THR

public static final AminoAcid THR

TRP

public static final AminoAcid TRP

TYR

public static final AminoAcid TYR

UNDEFINED

public static final AminoAcid UNDEFINED

VAL

public static final AminoAcid VAL

Method Detail

blosum62

public static int blosum62(AminoAcid a,
                           AminoAcid b)

Get BLOSUM62 distance between two AminoAcids. Distances between AminoAcid.STOP, AminoAcid.UNDEFINED and other AminoAcids are not defined.

Parameters:

a - An AminoAcid.

b - Another AminoAcid.

Returns:

An integer distance based on the Blosum62 table.

Throws:

java.lang.IllegalArgumentException - A parameter specified either a STOP or UNDEFINED AminoAcid.

isSynonym

public boolean isSynonym(java.lang.String str)

Check if a three-letter Dna/Rna codon codes for this AminoAcid.

Parameters:

str - A string of exactly three letters representing a codon. Letters can be upper or lower case. Both U and T are accepted and considered equivalent.

Returns:

True if str codes for this AminoAcid.

lookup

public static AminoAcid lookup(java.lang.String str)

Find the AminoAcid object corresponding to a three-letter Dna/Rna codon.

Parameters:

str - A string of exactly three letters to look up. Letters can be upper or lower case. Both U and T are accepted.

Returns:

An AminoAcid object. Unknown codons return AminoAcid.UNDEFINED. Stop codons (TGA, TAG, TAA ) return AminoAcid.STOP.

Throws:

java.lang.IllegalArgumentException - The str parameter was not of length 3.

toString

public java.lang.String toString()

Get the IUPAC single letter representation of this AminoAcid.

Overrides:

toString in class java.lang.Object

Returns:

The uppercase single letter representation. "X" is returned for both STOP and UNDEFINED.

translate

public static java.lang.String translate(java.lang.String str)

Translate from IUPAC nucleotide string to IUPAC protein string. The nucleotides are considered in groups of three, starting at the beginning of the string, and translated using the lookup() and toString() methods. If the string length is not divisible by three, the final one or two letters are ignored (no error indication).

Parameters:

str - A Dna/Rna string.

Returns:

A string of the IUPAC amino acid single letter abbreviations for the translated codons.