Package pal.datatype

Class 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 Description
      CodonTableUtils()  
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method 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.