Package pl.poznan.put.notation

Enum Saenger

java.lang.Object
java.lang.Enum<Saenger>
pl.poznan.put.notation.Saenger
All Implemented Interfaces:
Serializable, Comparable<Saenger>, java.lang.constant.Constable
public enum Saenger extends Enum<Saenger>
A classification of RNA base pairs described in Principles of Nucleic Acid Structure. W. Saenger.

  • Enum Constant Details

    • I

      public static final Saenger I

    • II

      public static final Saenger II

    • III

      public static final Saenger III

    • IV

      public static final Saenger IV

    • V

      public static final Saenger V

    • VI

      public static final Saenger VI

    • VII

      public static final Saenger VII

    • VIII

      public static final Saenger VIII

    • IX

      public static final Saenger IX

    • X

      public static final Saenger X

    • XI

      public static final Saenger XI

    • XII

      public static final Saenger XII

    • XIII

      public static final Saenger XIII

    • XIV

      public static final Saenger XIV

    • XV

      public static final Saenger XV

    • XVI

      public static final Saenger XVI

    • XVII

      public static final Saenger XVII

    • XVIII

      public static final Saenger XVIII

    • XIX

      public static final Saenger XIX

    • XX

      public static final Saenger XX

    • XXI

      public static final Saenger XXI

    • XXII

      public static final Saenger XXII

    • XXIII

      public static final Saenger XXIII

    • XXIV

      public static final Saenger XXIV

    • XXV

      public static final Saenger XXV

    • XXVI

      public static final Saenger XXVI

    • XXVII

      public static final Saenger XXVII

    • XXVIII

      public static final Saenger XXVIII

    • UNKNOWN

      public static final Saenger UNKNOWN

  • Method Details

    • values

      public static Saenger[] values()
      Returns an array containing the constants of this enum type, in the order they are declared.
      Returns:
      an array containing the constants of this enum type, in the order they are declared

    • valueOf

      public static Saenger valueOf(String name)
      Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)
      Parameters:
      name - the name of the enum constant to be returned.
      Returns:
      the enum constant with the specified name
      Throws:
      IllegalArgumentException - if this enum type has no constant with the specified name
      NullPointerException - if the argument is null

    • fromString

      public static Saenger fromString(String str)
      Finds an enum that matches the given name or return UNKNOWN otherwise.
      Parameters:
      str - A string representing Saenger notation.
      Returns:
      An instance of this enum that matches the given name or UNKNOWN if none does.

    • fromNumber

      public static Saenger fromNumber(int number)
      Matches a value in range 1-28 to an instance of this class with the same value written as a Roman numeral. The number is used in mmCIF files in hbond_28 field.
      Parameters:
      number - An integer in range [1; 28].
      Returns:
      An instance of this class that matches ordinal or UNKNOWN if none does.

    • assumeCanonical

      public static Saenger assumeCanonical(BasePair basePair)
      Checks which one of Saenger instances matches a canonical base pair of provided sequence. C-G canonical base pairs are XIX, A-U are XX and G-U are XXVIII. If base pair sequence is other than C-G, A-U or G-U, then this method returns UNKNOWN.
      Parameters:
      basePair - A base pair to be checked.
      Returns:
      XIX for C-G base pair, XX for A-U base pair, XXVIII for G-U base pair and UNKNOWN for all others.

    • isCanonical

      public static boolean isCanonical(Saenger saenger)
      Checks if instance of Saenger represents a canonical base pair (XIX, XX and XXVIII).
      Parameters:
      saenger - An instance to be checked.
      Returns:
      True if saenger is either XIX, XX or XXVIII.

    • toString

      public String toString()
      Overrides:
      toString in class Enum<Saenger>

    • isCanonical

      public boolean isCanonical()
      Returns:
      True if this instance is either XIX, XX or XXVIII.