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final case class SampledFrequencies(table: MinTable, counts: Array[(Long, Int)]) extends Product with Serializable

Sampled motif frequencies that may be used to construct a new minimizer ordering.

table

Template table, whose ordering of motifs will be refined based on counted frequencies.

counts

Pairs of (minimizer rank, frequency). The minimizers should be a subset of those from the given template MinTable.

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Instance Constructors

  1. new SampledFrequencies(table: MinTable, counts: Array[(Long, Int)])

    table

    Template table, whose ordering of motifs will be refined based on counted frequencies.

    counts

    Pairs of (minimizer rank, frequency). The minimizers should be a subset of those from the given template MinTable.

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. def add(other: SampledFrequencies): SampledFrequencies

    Add frequencies from the other object to this one

  5. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  6. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  7. val counts: Array[(Long, Int)]
  8. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  9. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
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    Annotations
    @throws( classOf[java.lang.Throwable] )
  10. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  11. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  12. val lookup: Array[Int]
  13. lazy val motifsWithCounts: Array[(NTSeq, Int)]

    A sorted array of all motifs in the template space, refined based on the observed frequencies.

    A sorted array of all motifs in the template space, refined based on the observed frequencies. Defines a minimizer ordering.

    returns

    Pairs of (motif, frequency)

  14. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  15. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  16. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  17. def print(): Unit

    Print a summary of what has been counted, including the most and least frequent motifs

  18. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  19. val table: MinTable
  20. def toTable(sampledFraction: Double): MinTable

    Construct a new MinTable (minimizer ordering) where the least common motifs in this counter have the highest priority.

  21. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  22. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
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    @throws( ... )
  23. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
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    @throws( ... ) @native()

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