Packages

final case class CanonicalPriorities[+P <: MinimizerPriorities](inner: P) extends MinimizerPriorities with Product with Serializable

Canonicalise a minimizer ordering. This maps each potential minimizer to its forward orientation (which must also be a valid minimizer). This effectively cuts the size of the minimizer set by up to half.

Linear Supertypes
Product, Equals, MinimizerPriorities, Serializable, Serializable, AnyRef, Any
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Inherited
  1. CanonicalPriorities
  2. Product
  3. Equals
  4. MinimizerPriorities
  5. Serializable
  6. Serializable
  7. AnyRef
  8. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new CanonicalPriorities(inner: P)

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. lazy val decoder: ThreadLocal[NTBitDecoder]
    Attributes
    protected
    Definition Classes
    MinimizerPriorities
    Annotations
    @transient()
  7. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  8. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @IntrinsicCandidate()
  9. def humanReadable(priority: NTBitArray): NTSeq

    Human-readable string corresponding to a given minimizer.

    Human-readable string corresponding to a given minimizer. Not optimized for frequent use.

    Definition Classes
    MinimizerPriorities
  10. def humanReadable(priority: Long): NTSeq
    Definition Classes
    MinimizerPriorities
  11. val inner: P
  12. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  13. def motifFor(priority: NTBitArray): NTBitArray

    Get the minimizer for a given priority.

    Get the minimizer for a given priority. For canonical orderings, this is not a true inverse of priorityOf (reverse and forward minimizers would map to the same value).

    Definition Classes
    CanonicalPriorities → MinimizerPriorities
  14. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  15. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @IntrinsicCandidate()
  16. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @IntrinsicCandidate()
  17. def numLargeBuckets: Long

    Number of buckets (minimizers) expected to be very large (frequent), if any

    Number of buckets (minimizers) expected to be very large (frequent), if any

    Definition Classes
    CanonicalPriorities → MinimizerPriorities
  18. def numMinimizers: Option[BucketId]

    Total number of distinct minimizers in this ordering, if available.

    Total number of distinct minimizers in this ordering, if available. This may be an upper bound. The largest value returned by priorityOf will be smaller than this value.

    Definition Classes
    CanonicalPriorities → MinimizerPriorities
  19. def priorityOf(motif: NTBitArray): NTBitArray

    Get the priority of the given minimizer.

    Get the priority of the given minimizer. If not every m-mer is a minimizer, then util.NTBitArray.empty indicates an invalid minimizer.

    Definition Classes
    CanonicalPriorities → MinimizerPriorities
  20. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  21. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  22. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  23. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  24. def width: Int

    Minimizer width (m)

    Minimizer width (m)

    Definition Classes
    CanonicalPriorities → MinimizerPriorities
  25. def writePriorityOf(motif: NTBitArray, buffer: NTBitArray): NTBitArray

    Write the priority of the given minimizer to the provided buffer.

    Write the priority of the given minimizer to the provided buffer. If not every m-mer is a minimizer, then util.NTBitArray.empty indicates an invalid minimizer.

    motif

    The motif to get the priority of

    buffer

    The buffer to write the priority to

    returns

    The buffer for chaining

    Definition Classes
    CanonicalPriorities → MinimizerPriorities

Deprecated Value Members

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

Inherited from Product

Inherited from Equals

Inherited from MinimizerPriorities

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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