DNAAlphabet

Value Members

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

   

   Definition Classes

   AnyRef → Any

2. final def ##(): Int

   

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

   

   Definition Classes

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4. def apply(c: Char): Symbol

   
   c

   char to lookup as a symbol in this alphabet

   returns

   the given symbol

   Definition Classes

   Alphabet

5. final def asInstanceOf[T0]: T0

   

   Definition Classes

   Any

6. 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

7. def clone(): AnyRef

   

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

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   @throws( ... )

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

   

   Definition Classes

   AnyRef

9. def equals(arg0: Any): Boolean

   

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10. def finalize(): Unit

    

    Attributes

    protected[java.lang]

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

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

    

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12. def hashCode(): Int

    

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13. final def isInstanceOf[T0]: Boolean

    

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    Any

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

    

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15. final def notify(): Unit

    

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16. final def notifyAll(): Unit

    

    Definition Classes

    AnyRef

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

    
    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

18. def reverseComplementExact(s: String): String

    
    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

19. def size: Int

    

    number of symbols in the alphabet

    number of symbols in the alphabet

    Definition Classes

    Alphabet

20. 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

21. val symbols: Seq[Symbol]

    

    the symbols in this alphabet

    the symbols in this alphabet

    Definition Classes

    DNAAlphabet → Alphabet

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

    

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    AnyRef

23. def toString(): String

    

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24. final def wait(): Unit

    

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    @throws( ... )

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

    

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    @throws( ... )

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

    

    Definition Classes

    AnyRef

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    @throws( ... )