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com.jnpersson.kmers.util

BitRepresentation

object BitRepresentation

Helper functions for working with a low level bit representation of nucleotide sequences.

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  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. final val A: Int(0)
  5. final val C: Int(1)
  6. final val G: Int(2)
  7. final val INVALID: Int(5)
  8. final val T: Int(3)
  9. final val U: Int(3)
  10. final val WHITESPACE: Int(4)
  11. final def asInstanceOf[T0]: T0
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  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.

    bytes

    encoded data to convert

    builder

    reusable StringBuilder instance

    offset

    offset (expressed in letters, 4 per quad) to start conversion from

    size

    length (expressed in letters, 4 per quad) to convert

  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
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    @throws( ... ) @native() @IntrinsicCandidate()
  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
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  21. def equals(arg0: Any): Boolean
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  22. final def getClass(): Class[_]
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  23. def hashCode(): Int
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  24. final def isInstanceOf[T0]: Boolean
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  25. def isValid(char: Char): Boolean

    Test whether a single character is encodable.

  26. final def ne(arg0: AnyRef): Boolean
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  27. final def notify(): Unit
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    @native() @IntrinsicCandidate()
  28. final def notifyAll(): Unit
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  29. def reverseComplement(encodedNTs: Long, width: Int, complementMask: Long): Long

    Reverse complement an encoded NT sequence that is right-aligned in a long

  30. def reverseComplementLeftAligned(encodedNTs: Long, complementMask: Long): Long

    Reverse complement an encoded NT sequence that is left-aligned in a long

  31. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
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  32. def toString(): String
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  33. def twobitToChar(byte: Byte): Char

    Convert a single BP from twobit representation to string representation.

  34. val twobits: List[Byte]
  35. final def wait(arg0: Long, arg1: Int): Unit
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  36. final def wait(arg0: Long): Unit
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  37. final def wait(): Unit
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  1. def finalize(): Unit
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