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 allMatches(data: (Int) ⇒ Int, size: Int): (ZeroNTBitArray, Array[Long])

   Find all matches in a nucleotide string.

   Find all matches in a nucleotide string. Returns a pair of 1) the encoded nucleotide string, 2) an array with the IDs (rank values) of matches (potential minimizers) in order, or Motif.INVALID for positions where no valid matches were found. The first (m-1) items are always Motif.INVALID, so that the position in the array corresponds to a position in the string.

   The data() function is Int->Int rather than Int->Byte, since scala.Function1 is not specialized on Byte return values, causing boxing

   data

   Function to get the two-bit encoded nucleotide at the given position [0, size)

   size

   Length of input

   returns

   a pair of (encoded nucleotide string, minimizer IDs)

5.  def allMatches(data: ZeroNTBitArray, reverseComplement: Boolean = false): (ZeroNTBitArray, Array[Long])

   Find all matches in an encoded nucleotide string, or of its reverse complement.

   Find all matches in an encoded nucleotide string, or of its reverse complement.

   data

   the encoded nucleotide string to find minimizers in

   reverseComplement

   whether to traverse the RC of the string rather than the forward orientation

   returns

   a pair of (encoded nucleotide string, minimizer IDs)

6.  def allMatches(data: NTSeq): (ZeroNTBitArray, Array[Long])

   Find all matches in a nucleotide string.

   Find all matches in a nucleotide string.

   data

   input data (NT sequence)

   returns

   a pair of (encoded nucleotide string, minimizer IDs)

7.  final def asInstanceOf[T0]: T0

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   Any

8.  def clone(): AnyRef

   Attributes

   protected[lang]

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   @throws( ... ) @native()

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

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10.  def finalize(): Unit

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    protected[lang]

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

11.  final def getClass(): Class[_]

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    @native()

12.  final def isInstanceOf[T0]: Boolean

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13.  def matchesOnly(data: (Int) ⇒ Int, len: Int): Iterator[Long]

    Find all valid matches in a nucleotide string.

    Find all valid matches in a nucleotide string. Returns valid potential minimizers in order, but their positions will not be identifiable.

    The data() function is Int->Int rather than Int->Byte, since scala.Function1 is not specialized on Byte return values, causing boxing

    data

    Function to get the two-bit encoded nucleotide at the given position [0, size)

    len

    Length of input

    returns

    valid minimizer IDs

14.  def matchesOnly(data: NTSeq): Iterator[Long]

    Efficiently find valid matches only in a nucleotide string.

    Efficiently find valid matches only in a nucleotide string. Invalid bases will be skipped correctly as if the string was split.

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

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16.  final def notify(): Unit

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    @native()

17.  final def notifyAll(): Unit

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    @native()

18.  val priorities: MinimizerPriorities
19.  final def synchronized[T0](arg0: ⇒ T0): T0

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20.  final def wait(): Unit

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    @throws( ... )

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

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    @throws( ... )

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

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    @throws( ... ) @native()