determines the reverse of a part of a sequence of nucleotides. - Java Data Structure

Java examples for Data Structure:DNA

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

Description

determines the reverse of a part of a sequence of nucleotides.

Demo Code

/*/*from  ww  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
 **
 */
//package com.java2s;

public class Main {
    /**
     * determines the reverse of a part of a sequence of nucleotides.
     *
     * @param s a string of nucleotide codes.
     * @param offset the number of characters to skip
     *               at the beginning of s.
     * @param chunk_size the number of characters in the portion
     *                   to be reversed
     * @return the codes of the specified chunk, in reverse order.
     */
    public static String chunkReverse(String s, int offset, int chunk_size) {
        if (s == null) {
            return null;
        }
        int reverse_offset = (s.length() - offset) % chunk_size;
        //    System.out.println(reverse_offset);
        StringBuffer buf = new StringBuffer(s.length());
        for (int i = 0; i < reverse_offset; i++) {
            buf.append(' ');
        }
        int max = s.length() - reverse_offset - chunk_size;
        //    System.out.println("Max: " + max);
        String chunk;
        for (int i = max; i >= 0; i -= chunk_size) {
            //      System.out.println(i + ", " + chunk_size);
            //      chunk = s.substring(i-chunk_size+1, i+1);
            chunk = s.substring(i, i + chunk_size);
            buf.append(chunk);
        }
        int end_spaces = s.length() - buf.length();
        for (int i = 0; i < end_spaces; i++) {
            buf.append(' ');
        }
        return buf.toString();
    }
}

Related Tutorials