Package pal.datatype

Class CodonTableUtils

java.lang.Object
pal.datatype.CodonTableUtils
public class CodonTableUtils extends Object
Nucleotide Translating Utilities
Version:
$Id: CodonTableUtils.java,v 1.4 2003/11/13 04:05:38 matt Exp $
Author:
Matthew Goode

  • Constructor Details

    • CodonTableUtils

      public CodonTableUtils()

  • Method Details

    • convertNucleotideToAminoAcid

      public static final String convertNucleotideToAminoAcid(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.