Packages

final case class MinTable(byPriority: Array[Int], width: Int, numLargeBuckets: Long = 0) extends MinimizerPriorities with Product with Serializable

A lookup table of minimizers with relative priorities (minimizer ordering). This can represent any ordering. The downside is that the entire table must be stored in memory, so there is a natural limit to how wide m can be.

byPriority

Encoded minimizers ordered from high priority to low. The position in the array is the rank of the corresponding minimizer. All minimizers must be of equal length.

numLargeBuckets

Number of buckets expected to be "very large", if any. Intended as a heuristic for algorithms that may need to know this.

Linear Supertypes
Product, Equals, MinimizerPriorities, Serializable, Serializable, AnyRef, Any
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  1. MinTable
  2. Product
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Instance Constructors

  1. new MinTable(byPriority: Array[Int], width: Int, numLargeBuckets: Long = 0)

    byPriority

    Encoded minimizers ordered from high priority to low. The position in the array is the rank of the corresponding minimizer. All minimizers must be of equal length.

    numLargeBuckets

    Number of buckets expected to be "very large", if any. Intended as a heuristic for algorithms that may need to know this.

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: Array[Int]
  6. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @IntrinsicCandidate()
  7. lazy val decoder: ThreadLocal[NTBitDecoder]
    Attributes
    protected
    Definition Classes
    MinimizerPriorities
    Annotations
    @transient()
  8. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  9. def equals(other: Any): Boolean
    Definition Classes
    MinTable → Equals → AnyRef → Any
  10. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @IntrinsicCandidate()
  11. def hashCode(): Int
    Definition Classes
    MinTable → AnyRef → Any
  12. 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
    MinTable → MinimizerPriorities
  13. def humanReadable(priority: Long): NTSeq
    Definition Classes
    MinimizerPriorities
  14. def humanReadableIterator: Iterator[NTSeq]

    Motifs as human-readable strings in priority order

  15. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  16. def motifArray(priority: Int): NTBitArray

    Encoded motif as a NTBitArray (a new object will be allocated)

  17. def motifArrays: Array[NTBitArray]

    Encoded motifs as NTBitArray objects (new objects allocated on the fly) in priority order

  18. def motifArraysIterator: Iterator[NTBitArray]

    Encoded motifs as NTBitArray objects (new objects allocated on the fly) in priority order

  19. def motifFor(priority: NTBitArray): NTBitArray

    Get the minimizer for a given priority.

    Get the minimizer for a given priority. Inverse of the function above. Only defined for values originally computed by the priorityOf function.

    Definition Classes
    MinTable → MinimizerPriorities
  20. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  21. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @IntrinsicCandidate()
  22. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @IntrinsicCandidate()
  23. val 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
  24. def numMinimizers: Option[Long]

    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
    MinTable → MinimizerPriorities
  25. lazy val priorityLookup: 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. (This is the inverse of byPriority above). priorityLookup always has size 4 ^ width. Positions in the array correspond to the encoded form (see above), values correspond to the rank we use (as used in the byPriority array). Invalid entries will be set to -1.

    Annotations
    @transient()
  26. 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
    MinTable → MinimizerPriorities
  27. 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()
  28. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  29. def toString(): String
    Definition Classes
    MinTable → AnyRef → Any
  30. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  31. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  32. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  33. val width: Int

    Minimizer width (m)

    Minimizer width (m)

    Definition Classes
    MinTable → MinimizerPriorities
  34. 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
    MinTable → 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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