Packages

final case class MinTable(byPriority: ArrayBuffer[NTSeq], largeBuckets: ArrayBuffer[NTSeq] = ArrayBuffer.empty) extends MinimizerPriorities with Product with Serializable

A table of minimizers with relative priorities (minimizer ordering).

byPriority

Minimizers ordered from high priority to low. The position in the array is the rank, and also the unique ID in this table, of the corresponding minimizer. All minimizers must be of equal length.

largeBuckets

A subset of byPriority, indicating the motifs that have been found to correspond to large buckets, if any.

Linear Supertypes
Product, Equals, MinimizerPriorities, Serializable, Serializable, AnyRef, Any
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Inherited
  1. MinTable
  2. Product
  3. Equals
  4. MinimizerPriorities
  5. Serializable
  6. Serializable
  7. AnyRef
  8. Any
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Visibility
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Instance Constructors

  1. new MinTable(byPriority: ArrayBuffer[NTSeq], largeBuckets: ArrayBuffer[NTSeq] = ArrayBuffer.empty)

    byPriority

    Minimizers ordered from high priority to low. The position in the array is the rank, and also the unique ID in this table, of the corresponding minimizer. All minimizers must be of equal length.

    largeBuckets

    A subset of byPriority, indicating the motifs that have been found to correspond to large buckets, if any.

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. val byPriority: ArrayBuffer[NTSeq]
  6. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  7. def encodedMotif(motif: NTSeq): Int

    Compute the encoded form of a motif.

    Compute the encoded form of a motif. Inefficient, not for frequent use. Only works for widths up to 15 (30 bits). Reversibly represents the motif as a 32-bit integer. This encoding is different from the position in the byPriority array and independent of minimizer ordering. It depends only on the letters in the motif.

  8. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  9. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  10. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  11. def humanReadable(priority: BucketId): NTSeq

    Human-readable nucleotide sequence corresponding to a given minimizer

    Human-readable nucleotide sequence corresponding to a given minimizer

    Definition Classes
    MinTable → MinimizerPriorities
  12. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  13. val largeBuckets: ArrayBuffer[NTSeq]
  14. def motifForPriority(priority: BucketId): Long

    Get the minimizer for a given priority.

    Get the minimizer for a given priority. Inverse of the function above.

    Definition Classes
    MinTable → MinimizerPriorities
  15. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  16. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  17. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  18. 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
    MinTable → MinimizerPriorities
  19. def numMinimizers: Long

    Total number of distinct minimizers in this ordering

    Total number of distinct minimizers in this ordering

    Definition Classes
    MinTable → MinimizerPriorities
  20. def priorityLookup(motif: Long): BucketId

    Get the priority of the given minimizer.

    Get the priority of the given minimizer. If not every m-mer is a minimizer, then -1 indicates an invalid minimizer.

    Definition Classes
    MinTable → MinimizerPriorities
  21. val priorityLookupArray: Array[Int]

    Maps the bit-encoded integer form of each motif to its priority/rank.

    Maps the bit-encoded integer form of each motif to its priority/rank. priorityLookup always has size 4 ^ width. Invalid entries will have priority -1. Positions in the array correspond to the encoded form (see above), values correspond to the rank we use (as used in the byPriority array), except for those set to -1.

  22. lazy val scanner: ShiftScanner

    A ShiftScanner associated with this MinTable (using its minimizer ordering)

    A ShiftScanner associated with this MinTable (using its minimizer ordering)

    Annotations
    @transient()
  23. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  24. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  25. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  26. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  27. val width: Int

    Minimizer width

    Minimizer width

    Definition Classes
    MinTable → MinimizerPriorities

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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