Package pal.datatype
Class CodonTableUtils
java.lang.Object
pal.datatype.CodonTableUtils
Nucleotide Translating Utilities
- Version:
- $Id: CodonTableUtils.java,v 1.4 2003/11/13 04:05:38 matt Exp $
- Author:
- Matthew Goode
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic final char[]
convertNucleotideToAminoAcid
(char[] nucleotideSequence, int startingPosition, int length, boolean reverse, CodonTable translator) Translates a Nucleotide sequence into a Amino Acid sequencestatic final String
convertNucleotideToAminoAcid
(String nucleotideSequence, int startingPosition, int length, boolean reverse, CodonTable translator) Translates a Nucleotide sequence into a Amino Acid sequence
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Constructor Details
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CodonTableUtils
public CodonTableUtils()
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Method Details
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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 arraylength
- - 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.starting
- position - the starting position to begin reading from
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