Packages

final case class SampledFrequencies(table: MinTable, minimizerCounts: Array[Long]) 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. This table will be mutated and cannot be reused after passing into SampledFrequencies.

minimizerCounts

Maps encoded minimizer to count.

Linear Supertypes
Serializable, Serializable, Product, Equals, AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. SampledFrequencies
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. AnyRef
  7. Any
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

Instance Constructors

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

    table

    Template table, whose ordering of motifs will be refined based on counted frequencies. This table will be mutated and cannot be reused after passing into SampledFrequencies.

    minimizerCounts

    Maps encoded minimizer to count.

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. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  5. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @IntrinsicCandidate()
  6. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  7. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @IntrinsicCandidate()
  8. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  9. val minimizerCounts: Array[Long]
  10. def motifsAndCounts: Iterator[(Int, Long)]
  11. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  12. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @IntrinsicCandidate()
  13. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @IntrinsicCandidate()
  14. def print(): Unit

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

  15. lazy val sortedMotifs: Array[Int]

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

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

    returns

    Pairs of (motif, frequency)

  16. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  17. val table: MinTable
  18. def toTable(): MinTable

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

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

Deprecated Value Members

  1. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] ) @Deprecated
    Deprecated

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

Ungrouped