Return the reverse complement version of a DNA string in upper case. - Java Data Structure

Java examples for Data Structure:DNA

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

Description

Return the reverse complement version of a DNA string in upper case.

Demo Code


//package com.java2s;

public class Main {
    /**/*from w  w  w.  j a v  a2 s  . co  m*/
     * Return the reverse complement version of a DNA string in upper case. Note that no checking is done in this code
     * since the parse code checks for valid DNA and upper-cases the input. This code will break if these assumptions
     * are not valid.
     *
     * @param sq
     *            original, upper-case cDNA string
     * @return reverse complement version of the input string sq.
     */
    public static String reverseComplement(String sq) {
        if (sq.equals("-"))
            return sq; // deletion, insertion do not need rc

        StringBuffer sb = new StringBuffer();
        for (int i = sq.length() - 1; i >= 0; i--) {
            char c = sq.charAt(i);
            char match = 0;
            switch (c) {
            case 'A':
                match = 'T';
                break;
            case 'C':
                match = 'G';
                break;
            case 'G':
                match = 'C';
                break;
            case 'T':
                match = 'A';
                break;
            case 'N':
                match = 'N';
                break;
            }
            if (match > 0)
                sb.append(match);
        }
        return sb.toString();
    }
}

Related Tutorials