BioKotlin/biokotlin.kmer/AbstractSparseKmerSet

AbstractSparseKmerSet

abstract class AbstractSparseKmerSet(val kmerSize: Int, val bothStrands: Boolean, val stepSize: Int, val keepMinOnly: Boolean) : AbstractKmerSet

Represents some AbstractKmerSet where most of the unique kmers of kmerSize are not represented. The maximum number of kmers cannot exceed MAX_VALUE of Int.

Inheritors

Constructors

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constructor(kmerSize: Int, bothStrands: Boolean, stepSize: Int, keepMinOnly: Boolean)

Properties

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val kmerSize: Int
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val stepSize: Int

Functions

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fun addKmersFromNewSeq(seq: NucSeq)

Generates kmers from a nucleotide sequence and adds those kmers to this set.

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fun ambiguousKmers(): Long

Returns the number of ambiguous kmers in the set.

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abstract fun contains(kmer: Kmer): Boolean

Returns true if kmer is in the set.

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abstract fun getCountOf(kmer: Kmer): Int

Returns the count of kmer in the set. If the set does not store counts, returns 1 if kmer is in the set.

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fun getEvenOddHashMap(): Long2ObjectOpenHashMap<LongOpenHashSet>

Hashes the longs in the set based on their even nucleotides and their odd nucleotides, placing each long into two bins. Returns this map of bins.

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abstract fun isEmpty(): Boolean

Returns true if set contains no kmers.

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abstract fun longSet(): LongSet

Returns the set of kmers in the set as Longs

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fun minHammingDistance(kmer: Kmer, bothStrands: Boolean = true): Int

Returns the minimum hamming distance between the query kmer and all kmers in this map

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fun sequenceLength(): Long

Returns the total length of sequence(s) used to generate this set.

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abstract fun set(): Set<Kmer>

Returns the set of kmers in this set

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abstract fun setSize(): Long

Returns the number of unique kmers in the set (not the count of total kmers).

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open override fun toString(): String

Summarizes set parameters and size in string format.