package jalview.analysis;

public interface GeneticCodeI
{
  /**
   * Answers the single letter amino acid code (e.g. "D") for the given codon
   * (e.g. "GAC"), or "*" for a stop codon, or null for an unknown input. The
   * codon is not case-sensitive, the return value is upper case.
   * <p>
   * If the codon includes any of the standard ambiguity codes
   * <ul>
   * <li>if all possible translations are the same, returns that value</li>
   * <li>else returns null</li>
   * </ul>
   * 
   * @param codon
   * @return
   */
  String translate(String codon);

  /**
   * Answers the single letter amino acid code (e.g. "D") for the given codon
   * (e.g. "GAC"), or "*" for a stop codon, or null for an unknown input. The
   * codon is not case-sensitive, the return value is upper case. If the codon
   * includes any of the standard ambiguity codes, this method returns null.
   * 
   * @param codon
   * @return
   */
  String translateCanonical(String codon);

  /**
   * Answers a unique identifier for the genetic code (using the numbering
   * system as on NCBI)
   * 
   * @return
   */
  String getId();

  /**
   * Answers a display name suitable for use in menus, reports etc
   * 
   * @return
   */
  String getName();
}