org.bdgenomics.adam.models

Alphabet

trait Alphabet extends AnyRef

Created by bryan on 4/17/15.

An alphabet of symbols and related operations

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DNAAlphabet
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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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    protected[java.lang]
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  7. final def eq(arg0: AnyRef): Boolean

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  8. def equals(arg0: Any): Boolean

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  9. def finalize(): Unit

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

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

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  11. def hashCode(): Int

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  12. final def isInstanceOf[T0]: Boolean

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

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  14. final def notify(): Unit

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  15. final def notifyAll(): Unit

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  16. 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.

  17. 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.

    Exceptions thrown
    IllegalArgumentException

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

  18. def size: Int

    number of symbols in the alphabet

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

    map of the symbol char to the symbol

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

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  21. def toString(): String

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  22. final def wait(): Unit

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

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

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