Convert a number into a string of nucleotide codes. - Java Data Structure

Java examples for Data Structure:DNA

  1. HOME
  2. Java
  3. Data Structure
  4. DNA

Description

Convert a number into a string of nucleotide codes.

Demo Code

/*/*ww  w  .jav  a  2  s .co m*/
 * Copyright (c) 2014. Real Time Genomics Limited.
 *
 * Use of this source code is bound by the Real Time Genomics Limited Software Licence Agreement
 * for Academic Non-commercial Research Purposes only.
 *
 * If you did not receive a license accompanying this file, a copy must first be obtained by email
 * from support@realtimegenomics.com.  On downloading, using and/or continuing to use this source
 * code you accept the terms of that license agreement and any amendments to those terms that may
 * be made from time to time by Real Time Genomics Limited.
 */
//package com.java2s;

public class Main {
    /**
     * Convert a number into a string of nucleotide codes.
     * This is handy for displaying hash function bits.
     * @param x number to be displayed
     * @param len number of bits and codes to display.
     * @return string giving bit decomposition of x.
     */
    public static String toCodes(final long x, final int len) {
        if (len <= 0 || len > 32) {
            throw new IllegalArgumentException("length out of range=" + len);
        }
        final StringBuilder sb = new StringBuilder();
        final int left = 64 - 2 * len;
        long t = x << left;
        long u = x << (left + len);
        for (int i = 0; i < len; i++) {
            final int code = (t < 0 ? 2 : 0) + (u < 0 ? 1 : 0);
            sb.append(new String[] { "A", "C", "G", "T" }[code]);
            t = t << 1;
            u = u << 1;
        }
        assert u == 0;
        return sb.toString();
    }

    /**
     * Convert a number into a string of nucleotide codes.
     * This is handy for displaying hash function bits.
     * @param v0 first set of bits.
     * @param v1 second set of bits.
     * @param len number of bits and codes to display.
     * @return string giving bit decomposition of x.
     */
    public static String toCodes(final long v0, final long v1, final int len) {
        if (len <= 0 || len > 64) {
            throw new IllegalArgumentException("length out of range=" + len);
        }
        final StringBuilder sb = new StringBuilder();
        final int left = 64 - len;
        long t = v0 << left;
        long u = v1 << left;
        for (int i = 0; i < len; i++) {
            final int code = (t < 0 ? 2 : 0) + (u < 0 ? 1 : 0);
            sb.append(new String[] { "A", "C", "G", "T" }[code]);
            t = t << 1;
            u = u << 1;
        }
        assert u == 0;
        return sb.toString();
    }
}

Related Tutorials