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
Method Summary |
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 |
CodonTableUtils
public CodonTableUtils()
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 arraystarting
- position - the starting position to begin reading fromlength
- - 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.