Return array of all stop codons for the configured genetic code - stop codons as 3 letter nucleotide letters eg "TGA" - Java Data Structure

Java examples for Data Structure:DNA

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Description

Return array of all stop codons for the configured genetic code - stop codons as 3 letter nucleotide letters eg "TGA"

Demo Code

/*// w  w w  . j  a va  2 s . c  o m
 **  DNAUtils
 **  (c) Copyright 1997, Neomorphic Sofware, Inc.
 **  All Rights Reserved
 **
 **  CONFIDENTIAL
 **  DO NOT DISTRIBUTE
 **
 **  File: DNAUtils.java
 **
 */
import java.util.List;
import java.util.ArrayList;

public class Main{
    private static List stopCodonCharArrayList;
    /** Genetic Code in 1-character amino acid codes. by default set to default
     genetic code 1 */
    protected static String aa1[][][] = aa1Default;
    /** ascii character codes for each nucleotide (or set of nucleotides). */
    protected static char[] id_to_letter = new char[LETTERS];
    /** Return array of all stop codons for the configured genetic code - stop codons
        as 3 letter nucleotide  letters eg "TGA" */
    public static String[] get3NucleotideStopCodons() {
        //synchGeneticCodeWithConfig();

        if (threeNucleotideStopCodons == null) {
            createStopCodons();
        }
        return threeNucleotideStopCodons;
    }
    private static void createStopCodons() {
        List stopList = new ArrayList(5);
        stopCodonCharArrayList = new ArrayList(5);
        for (int i = 0; i < 4; i++) {
            for (int j = 0; j < 4; j++) {
                for (int k = 0; k < 4; k++) {
                    if (aa1[i][j][k].equals("*")) {
                        String codon = get3LetterCodeFromInts(i, j, k);
                        stopList.add(codon);
                        char[] charCodon = getCharArrayCodonFromInts(i, j,
                                k);
                        stopCodonCharArrayList.add(charCodon);
                    }
                }
            }
        }
        String[] threeNucleotideStopCodons = new String[stopList.size()];
        for (int i = 0; i < stopList.size(); i++)
            threeNucleotideStopCodons[i] = (String) stopList.get(i);

    }
    private static String get3LetterCodeFromInts(int i, int j, int k) {
        return "" + getResidueChar(i) + getResidueChar(j)
                + getResidueChar(k);
    }
    private static char[] getCharArrayCodonFromInts(int i, int j, int k) {
        return new char[] { getResidueChar(i), getResidueChar(j),
                getResidueChar(k) };
    }
    /**
     * gets a nucleotide code.
     * 
     * @param residue_id ordinal of nucleotide letter code.
     * @return letter representation of a nucleotide.
     * @see #getResidueChar
     */
    public static char getResidueChar(int residue_id) {
        return id_to_letter[residue_id];
    }
}

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