Class

org.bdgenomics.adam.models

DNAAlphabet

Related Doc: package models

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class DNAAlphabet extends Alphabet

The standard DNA alphabet with A,T,C, and G

Linear Supertypes
Alphabet, AnyRef, Any
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Inherited
  1. DNAAlphabet
  2. Alphabet
  3. AnyRef
  4. Any
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Visibility
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Instance Constructors

  1. new DNAAlphabet()

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Value Members

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

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    Definition Classes
    AnyRef → Any
  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  4. def apply(c: Char): Symbol

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    c

    char to lookup as a symbol in this alphabet

    returns

    the given symbol

    Definition Classes
    Alphabet
  5. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any
  6. val caseSensitive: Boolean

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    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
    DNAAlphabetAlphabet
  7. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  8. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  9. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  10. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  11. final def getClass(): Class[_]

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    Definition Classes
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  12. def hashCode(): Int

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    Definition Classes
    AnyRef → Any
  13. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  14. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  15. final def notify(): Unit

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    Definition Classes
    AnyRef
  16. final def notifyAll(): Unit

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

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    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

  18. def reverseComplementExact(s: String): String

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    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

  19. def size: Int

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    The number of symbols in the alphabet.

    The number of symbols in the alphabet.

    Definition Classes
    Alphabet
  20. lazy val symbolMap: Map[Char, Symbol]

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    map of the symbol char to the symbol

    map of the symbol char to the symbol

    Definition Classes
    Alphabet
  21. val symbols: Seq[Symbol]

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    the symbols in this alphabet

    the symbols in this alphabet

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

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    Definition Classes
    AnyRef
  23. def toString(): String

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    Definition Classes
    AnyRef → Any
  24. final def wait(): Unit

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    AnyRef
    Annotations
    @throws( ... )
  25. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
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    @throws( ... )
  26. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Alphabet

Inherited from AnyRef

Inherited from Any

Ungrouped