Packages

c

com.jnpersson.discount.hash

PosRankWindow

final class PosRankWindow extends AnyRef

Tracks Motifs in a moving window, such that the top priority item can always be obtained efficiently. Mutates the array. Can only be used once. This class looks like an Iterator[Int], but to avoid boxing of integers, does not extend that trait.

Invariants: the leftmost position has the highest priority (minimal rank). Priority decreases (i.e. rank increases) monotonically going left to right. Motifs are sorted by position. The minimizer of the current k-length window is always the first motif in the list.

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Instance Constructors

  1. new PosRankWindow(m: Int, k: Int, motifRanks: Array[Long])

    motifRanks

    Array of motif priorities at the positions in the underlying read where the full motif can first be read (e.g. position 4 for a 5-length motif occupying positions 0-4).

Value Members

  1. final def !=(arg0: Any): Boolean
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  2. final def ##(): Int
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  3. final def ==(arg0: Any): Boolean
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  4. def advanceWindow(): Unit
  5. final def asInstanceOf[T0]: T0
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  6. def clone(): AnyRef
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  9. def finalize(): Unit
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  10. final def getClass(): Class[_]
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  11. def hasNext: Boolean

    Does this object have more motifs?

  12. def hashCode(): Int
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  13. def head: Int

    Peek at the position of the next top-ranked motif without advancing

  14. final def isInstanceOf[T0]: Boolean
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  15. val motifRanks: Array[Long]
  16. final def ne(arg0: AnyRef): Boolean
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  17. def next: Int

    Obtain the position of the next top-ranked motif and advance

  18. final def notify(): Unit
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  19. final def notifyAll(): Unit
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  23. final def wait(arg0: Long, arg1: Int): Unit
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  24. final def wait(arg0: Long): Unit
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