AbstractKmerSet

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

Represents some collection of kmers generated from nucleic acid sequence(s).

Constructors

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

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

Returns the number of ambiguous kmers in the set.

abstract fun contains(kmer: Kmer): Boolean

Returns true if kmer is in the set.

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.

abstract fun isEmpty(): Boolean

Returns true if set contains no kmers.

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

abstract fun setSize(): Long

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

open override fun toString(): String

Summarizes set parameters and size in string format.