Value Members

1.  final def !=(arg0: Any): Boolean

   Definition Classes

   AnyRef → Any

2.  final def ##(): Int

   Definition Classes

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3.  final def ==(arg0: Any): Boolean

   Definition Classes

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4.  val A: Byte
5.  val C: Byte
6.  val G: Byte
7.  val INVALID: Byte
8.  val T: Byte
9.  val U: Byte
10.  val WHITESPACE: Byte
11.  final def asInstanceOf[T0]: T0

    Definition Classes

    Any

12.  def byteToQuad(byte: Byte): NTSeq

    Unpack a byte to a 4-character string (quad).

13.  val byteToQuadLookup: Array[NTSeq]

    Map a single byte to a quad-string for unpacking.

    Map a single byte to a quad-string for unpacking. Precomputed lookup array.

14.  def bytesToString(bytes: Array[Byte], builder: StringBuilder, offset: Int, size: Int): NTSeq

    Convert a byte array of quads to a string.

    Convert a byte array of quads to a string. The length of the resulting string must be supplied.

15.  def charToTwobit(char: Char): Byte

    Convert a single nucleotide from string (char) representation to "twobit" representation.

    Convert a single nucleotide from string (char) representation to "twobit" representation. Returns one of the twobit codes, or WHITESPACE for skippable whitespace.

16.  def charToTwobitWithInvalid(char: Char): Byte

    Convert a single nucleotide from string (char) representation to "twobit" representation.

    Convert a single nucleotide from string (char) representation to "twobit" representation. Does not throw an exception, but returns INVALID on invalid characters.

17.  def clone(): AnyRef

    Attributes

    protected[lang]

    Definition Classes

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    Annotations

    @throws( ... ) @native()

18.  def complement(byte: Byte): Byte

    Complement of a number of BPs packed in a byte.

19.  def complementOne(byte: Byte): Int

    Complement of a single BP.

20.  final def eq(arg0: AnyRef): Boolean

    Definition Classes

    AnyRef

21.  def equals(arg0: Any): Boolean

    Definition Classes

    AnyRef → Any

22.  def finalize(): Unit

    Attributes

    protected[lang]

    Definition Classes

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    Annotations

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

23.  final def getClass(): Class[_]

    Definition Classes

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    Annotations

    @native()

24.  def hashCode(): Int

    Definition Classes

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    Annotations

    @native()

25.  final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

26.  final def ne(arg0: AnyRef): Boolean

    Definition Classes

    AnyRef

27.  final def notify(): Unit

    Definition Classes

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    Annotations

    @native()

28.  final def notifyAll(): Unit

    Definition Classes

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    Annotations

    @native()

29.  def quadToByte(quad: String, offset: Int): Byte

    Convert an NT quad (string of length 4) to encoded byte form.

    Convert an NT quad (string of length 4) to encoded byte form. The string will be padded on the right with 'A' if it's too short.

30.  def quadToByte(quad: NTSeq): Byte

    Map a quad-string (four letters) to an encoded byte

31.  def reverseComplement(encodedNTs: Long, width: Int, complementMask: Long): Long
32.  def stringToBytes(bps: NTSeq): Array[Byte]
33.  final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes

    AnyRef

34.  def toString(): String

    Definition Classes

    AnyRef → Any

35.  def twobitToChar(byte: Byte): Char

    Convert a single BP from twobit representation to string representation.

36.  val twobits: List[Byte]
37.  final def wait(): Unit

    Definition Classes

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    @throws( ... )

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

    Definition Classes

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    @throws( ... )

39.  final def wait(arg0: Long): Unit

    Definition Classes

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    Annotations

    @throws( ... ) @native()