trait Alphabet extends AnyRef

An alphabet of symbols and related operations

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Abstract Value Members

  1. abstract 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

  2. abstract val symbols: Seq[Symbol]

    the symbols in this alphabet

Concrete Value Members

  1. final def !=(arg0: Any): Boolean
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  2. final def ##(): Int
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  3. final def ==(arg0: Any): Boolean
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  4. def apply(c: Char): Symbol

    c

    char to lookup as a symbol in this alphabet

    returns

    the given symbol

  5. final def asInstanceOf[T0]: T0
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  6. def clone(): AnyRef
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  7. final def eq(arg0: AnyRef): Boolean
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  9. final def getClass(): Class[_]
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  10. def hashCode(): Int
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  11. final def isInstanceOf[T0]: Boolean
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  12. final def ne(arg0: AnyRef): Boolean
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  13. final def notify(): Unit
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  14. final def notifyAll(): Unit
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  15. 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.

    See also

    reverseComplementExact

  16. 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.

    Exceptions thrown

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

    See also

    reverseComplement

  17. def size: Int

    The number of symbols in the alphabet.

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

    map of the symbol char to the symbol

  19. final def synchronized[T0](arg0: ⇒ T0): T0
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  20. def toString(): String
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  21. final def wait(arg0: Long, arg1: Int): Unit
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  1. def finalize(): Unit
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    @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
    Deprecated

    (Since version ) see corresponding Javadoc for more information.

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