package jalview.datamodel;

/**
 * Holds the aligned column positions (base 0) for one codon in a nucleotide
 * sequence. The object is immutable once created.
 * 
 * Example: in "G-AT-C-GA" the aligned codons are (0, 2, 3) and (5, 7, 8).
 * 
 * @author gmcarstairs
 *
 */
public final class AlignedCodon
{
  public final int pos1;

  public final int pos2;

  public final int pos3;

  public AlignedCodon(int i, int j, int k)
  {
    pos1 = i;
    pos2 = j;
    pos3 = k;
  }

  /**
   * Returns the column position for the given base (1, 2, 3).
   * 
   * @param base
   * @return
   * @throws IllegalArgumentException
   *           if an argument value other than 1, 2 or 3 is supplied
   */
  public int getBaseColumn(int base)
  {
    if (base < 1 || base > 3)
    {
      throw new IllegalArgumentException(Integer.toString(base));
    }
    return base == 1 ? pos1 : (base == 2 ? pos2 : pos3);
  }

  /**
   * Two aligned codons are equal if all their base positions are the same.
   */
  @Override
  public boolean equals(Object o)
  {
    /*
     * Equality with null value required for consistency with
     * Dna.compareCodonPos
     */
    if (o == null)
    {
      return true;
    }
    if (!(o instanceof AlignedCodon))
    {
      return false;
    }
    AlignedCodon ac = (AlignedCodon) o;
    return (pos1 == ac.pos1 && pos2 == ac.pos2 && pos3 == ac.pos3);
  }

  @Override
  public String toString()
  {
    return "[" + pos1 + ", " + pos2 + ", " + pos3 + "]";
  }
}