package jalview.analysis;

import java.util.Random;

/**
 * Generates a random Fasta format DNA alignment for given sequence length and
 * count.
 * 
 * @author gmcarstairs
 *
 */
public class DnaAlignmentGenerator
{
  private static final char GAP = '-';
  
  private static final char[] BASES = new char[]
    { 'G', 'T', 'C', 'A', GAP };

  private Random random;
  
  /**
   * Given args for sequence length and count, output a DNA 'alignment' where
   * each position is a random choice from 'GTCA-'.
   * 
   * @param args
   *          the width (base count) and height (sequence count) to generate
   *          plus an integer random seed value
   */
  public static void main(String[] args)
  {
    int width = Integer.parseInt(args[0]);
    int height = Integer.parseInt(args[1]);
    long randomSeed = Long.valueOf(args[2]);
    new DnaAlignmentGenerator().generate(width, height, randomSeed);
  }

  /**
   * Outputs a DNA 'alignment' of given width and height, where each position is
   * a random choice from 'GTCA-'.
   * 
   * @param width
   * @param height
   * @param randomSeed
   */
  private void generate(int width, int height, long randomSeed)
  {
    random = new Random(randomSeed);
    for (int seqno = 0; seqno < height; seqno++)
    {
      generateSequence(seqno + 1, width);
    }
  }

  /**
   * Outputs a DNA 'sequence' of given length, with some random gaps included.
   * 
   * @param seqno
   * @param length
   */
  private void generateSequence(int seqno, int length)
  {
    System.out.println(">SEQ" + seqno);
    StringBuilder seq = new StringBuilder(length);

    /*
     * Loop till we've output 'length' real bases (excluding gaps)
     */
    for (int count = 0 ; count < length ; ) {
      char c = BASES[random.nextInt(Integer.MAX_VALUE) % 5];
      seq.append(c);
      if (c != GAP)
      {
        count++;
      }
    }
    System.out.println(seq.toString());
  }
}