pal.datatype

Class CodonTableUtils

java.lang.Object

pal.datatype.CodonTableUtils

public class CodonTableUtils
extends java.lang.Object

Nucleotide Translating Utilities

Version:

$Id: CodonTableUtils.java,v 1.4 2003/11/13 04:05:38 matt Exp $

Author:

Matthew Goode

Constructor Summary

Constructors

Constructor and Description
CodonTableUtils()

Method Summary

Methods

Modifier and Type	Method and Description
static char[]	convertNucleotideToAminoAcid(char[] nucleotideSequence, int startingPosition, int length, boolean reverse, CodonTable translator) Translates a Nucleotide sequence into a Amino Acid sequence
static java.lang.String	convertNucleotideToAminoAcid(java.lang.String nucleotideSequence, int startingPosition, int length, boolean reverse, CodonTable translator) Translates a Nucleotide sequence into a Amino Acid sequence

Methods inherited from class java.lang.Object

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

Constructor Detail

CodonTableUtils

public CodonTableUtils()

Method Detail

convertNucleotideToAminoAcid

public static final java.lang.String convertNucleotideToAminoAcid(java.lang.String nucleotideSequence,
                                            int startingPosition,
                                            int length,
                                            boolean reverse,
                                            CodonTable translator)

Translates a Nucleotide sequence into a Amino Acid sequence

convertNucleotideToAminoAcid

public static final char[] convertNucleotideToAminoAcid(char[] nucleotideSequence,
                                  int startingPosition,
                                  int length,
                                  boolean reverse,
                                  CodonTable translator)

Translates a Nucleotide sequence into a Amino Acid sequence

Parameters:

nucleotideSequence - - the base nucleotide sequence as a char array

starting - position - the starting position to begin reading from

length - - the length of the reading frame (in nucleotide units - should be a multiple of 3, if not remainder is truncated!)

reverse - - if true works backwards with codon at starting position being last in translation (codon read in reverse as well). Else reads forwards.

translator - - the nucleotide translator to use for translation nucleotides into amino acids.