DNAAlphabet

Value Members

1. final def !=(arg0: AnyRef): Boolean

   Definition Classes

   AnyRef

2. final def !=(arg0: Any): Boolean

   Definition Classes

   Any

3. final def ##(): Int

   Definition Classes

   AnyRef → Any

4. final def ==(arg0: AnyRef): Boolean

   Definition Classes

   AnyRef

5. final def ==(arg0: Any): Boolean

   Definition Classes

   Any

6. def apply(c: Char): Symbol

   c

   char to lookup as a symbol in this alphabet

   returns

   the given symbol

   Definition Classes

   Alphabet

7. final def asInstanceOf[T0]: T0

   Definition Classes

   Any

8. val caseSensitive: Boolean

   flag if symbols are case-sensitive.

   flag if symbols are case-sensitive. if true, this alphabet will treat symbols representing upper and lower case symbols as distinct if false, this alphabet will treat upper or lower case chars as the same for its symbols

   Definition Classes

   DNAAlphabet → Alphabet

9. def clone(): AnyRef

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

10. final def eq(arg0: AnyRef): Boolean

    Definition Classes

    AnyRef

11. def equals(arg0: Any): Boolean

    Definition Classes

    AnyRef → Any

12. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( classOf[java.lang.Throwable] )

13. final def getClass(): Class[_]

    Definition Classes

    AnyRef → Any

14. def hashCode(): Int

    Definition Classes

    AnyRef → Any

15. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

16. final def ne(arg0: AnyRef): Boolean

    Definition Classes

    AnyRef

17. final def notify(): Unit

    Definition Classes

    AnyRef

18. final def notifyAll(): Unit

    Definition Classes

    AnyRef

19. def reverseComplement(s: String, notFound: (Char) ⇒ Symbol = (c: Char) => Symbol(c, c)): String

    Reverses the string and compliments each residue.

    Reverses the string and compliments each residue.

    If a residue has no known complement, that residue is replaced with a placeholder "not-found" value.

    s

    Each char in this string represents a symbol on the alphabet.

    notFound

    If the char is not in the alphabet then this function is called. default behavior is to return a new Symbol representing the unknown character, so that the unknown char is treated as the complement

    returns

    the reversed complement of the given string.

    Definition Classes

    Alphabet

    See also

    reverseComplementExact

20. def reverseComplementExact(s: String): String

    Reverses the string and compliments each residue.

    Reverses the string and compliments each residue.

    Fails if a residue has no complement.

    s

    Each char in this string represents a symbol on the alphabet. If the char is not in the alphabet then a NoSuchElementException is thrown

    returns

    the reversed complement of the given string.

    Definition Classes

    Alphabet

    Exceptions thrown

    IllegalArgumentException

    if the string contains a symbol which is not in the alphabet

    See also

    reverseComplement

21. def size: Int

    The number of symbols in the alphabet.

    The number of symbols in the alphabet.

    Definition Classes

    Alphabet

22. lazy val symbolMap: Map[Char, Symbol]

    map of the symbol char to the symbol

    map of the symbol char to the symbol

    Definition Classes

    Alphabet

23. val symbols: Seq[Symbol]

    the symbols in this alphabet

    the symbols in this alphabet

    Definition Classes

    DNAAlphabet → Alphabet

24. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes

    AnyRef

25. def toString(): String

    Definition Classes

    AnyRef → Any

26. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

27. final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

28. final def wait(arg0: Long): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )