Class TranslatedFrame

src/main/java/com/rtg/mode/TranslatedFrame.java:44–536

The possible ways a nucleotide sequence can be translated to a protein. (Forward and reverse and 3 different phases).

 *
 */
public abstract class TranslatedFrame implements Frame, PseudoEnum {

  /** The number of nucleotides per codon */
  public static final int NUCLEOTIDES_PER_CODON = 3;

  /**
   * Normal forward direction - phase 1.
   */
  public static final TranslatedFrame FORWARD1 = new TranslatedFrame(0, "FORWARD1", "+1", 0) {
    @Override
    public byte code(final byte[] codes, final int length, final int index) {
      return code(codes, length, index, 0, length);
    }

    @Override
    public byte code(byte[] codes, int length, int index, int firstValid, int lastValid) {
      final int x = firstValid + index + 2;
      if (x >= length) {
        throw new ArrayIndexOutOfBoundsException(index);
      }
      return codonToAmino(codes[firstValid + index], codes[firstValid + index + 1], codes[x]);
    }

    @Override
    public int calculateFirstValid(int offset, int length, int fullLength) {
      return f(offset);
    }

    @Override
    public int calculateLastValid(int offset, int length, int fullLength) {
      return length;
    }

    @Override
    public boolean isForward() {
      return true;
    }

    @Override
    public Frame getReverse() {
      return REVERSE1;
    }
  };

  /**
   * Normal forward direction - phase 2.
   */
  public static final TranslatedFrame FORWARD2 = new TranslatedFrame(1, "FORWARD2", "+2", 1) {
    @Override
    public byte code(final byte[] codes, final int length, final int index) {
      return code(codes, length, index, 0, length);
    }

    @Override
    public byte code(byte[] codes, int length, int index, int firstValid, int lastValid) {
      final int x = firstValid + index + 3;
      if (x >= length) {
        throw new ArrayIndexOutOfBoundsException(index);