Class DNA

src/main/java/com/rtg/mode/DNA.java:37–291

Individual nucleotides including an unknown value.

 * Individual nucleotides including an unknown value.
 */
public abstract class DNA implements Residue, PseudoEnum {
  //It is important that the ordinal of the unknown value be 0 (it is used in the hashing code).
  //Do not modify unless you have really thought about it
  /** Unknown. */
  public static final DNA N = new DNA(0, DNASimple.N) {
    @Override
    public boolean ignore() {
      return true;
    }
    @Override
    public DNA complement() {
      return N;
    }
  };

  /** adenine. */
  public static final DNA A = new DNA(1, DNASimple.A)  {
    @Override
    public DNA complement() {
      return T;
    }
  };

  /** cytosine */
  public static final DNA C  = new DNA(2, DNASimple.C) {
    @Override
    public DNA complement() {
      return G;
    }
  };

  /** guanine */
  public static final DNA G  = new DNA(3, DNASimple.G) {
    @Override
    public DNA complement() {
      return C;
    }
  };

  /** thymine or in RNA uracil (no distinction is drawn here). */
  public static final DNA T  = new DNA(4, DNASimple.T) {
    @Override
    public DNA complement() {
      return A;
    }
  };


  private static final DNA[] VALUES = {N, A, C, G, T};

  /**
   * Record fast way of getting complements directly from codes.
   */
  static final byte[] COMPLEMENT = new byte[DNA.values().length];
  static {
    populateComplementArray(COMPLEMENT, DNA.values());
  }