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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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).
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- def advanceWindow(): Unit
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def
hasNext: Boolean
Does this object have more motifs?
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hashCode(): Int
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def
head: Int
Peek at the position of the next top-ranked motif without advancing
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def
isInstanceOf[T0]: Boolean
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- val motifRanks: Array[Long]
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def
ne(arg0: AnyRef): Boolean
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def
next: Int
Obtain the position of the next top-ranked motif and advance
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