Packages

final class KmerTable2 extends KmerTable

Specialized KmerTable for n = 2 (k <= 64)

Linear Supertypes
KmerTable, IndexedSeq[Array[Long]], IndexedSeqLike[Array[Long], IndexedSeq[Array[Long]]], Seq[Array[Long]], SeqLike[Array[Long], IndexedSeq[Array[Long]]], GenSeq[Array[Long]], GenSeqLike[Array[Long], IndexedSeq[Array[Long]]], Iterable[Array[Long]], IterableLike[Array[Long], IndexedSeq[Array[Long]]], Equals, GenIterable[Array[Long]], GenIterableLike[Array[Long], IndexedSeq[Array[Long]]], Traversable[Array[Long]], GenTraversable[Array[Long]], GenericTraversableTemplate[Array[Long], IndexedSeq], TraversableLike[Array[Long], IndexedSeq[Array[Long]]], GenTraversableLike[Array[Long], IndexedSeq[Array[Long]]], Parallelizable[Array[Long], ParSeq[Array[Long]]], TraversableOnce[Array[Long]], GenTraversableOnce[Array[Long]], FilterMonadic[Array[Long], IndexedSeq[Array[Long]]], HasNewBuilder[Array[Long], IndexedSeq[Array[Long]] @scala.annotation.unchecked.uncheckedVariance], PartialFunction[Int, Array[Long]], (Int) ⇒ Array[Long], AnyRef, Any
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Inherited
  1. KmerTable2
  2. KmerTable
  3. IndexedSeq
  4. IndexedSeqLike
  5. Seq
  6. SeqLike
  7. GenSeq
  8. GenSeqLike
  9. Iterable
  10. IterableLike
  11. Equals
  12. GenIterable
  13. GenIterableLike
  14. Traversable
  15. GenTraversable
  16. GenericTraversableTemplate
  17. TraversableLike
  18. GenTraversableLike
  19. Parallelizable
  20. TraversableOnce
  21. GenTraversableOnce
  22. FilterMonadic
  23. HasNewBuilder
  24. PartialFunction
  25. Function1
  26. AnyRef
  27. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new KmerTable2(kmers: Array[Array[Long]], width: Int, tagWidth: Int, k: Int, length: Int)

    kmers

    k-mer data, column-major

    width

    number of columns (longs per row) in the table, including k-mer and tag data

    tagWidth

    number of additional columns on the right used for tag data

    k

    length of k-mers

    length

    number of items in the table

Type Members

  1. class Elements extends AbstractIterator[A] with BufferedIterator[A] with Serializable
    Attributes
    protected
    Definition Classes
    IndexedSeqLike
    Annotations
    @SerialVersionUID()
  2. type Self = IndexedSeq[Array[Long]]
    Attributes
    protected[this]
    Definition Classes
    TraversableLike
  3. class WithFilter extends FilterMonadic[A, Repr]
    Definition Classes
    TraversableLike

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. def ++[B >: Array[Long], That](that: GenTraversableOnce[B])(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  4. def ++:[B >: Array[Long], That](that: Traversable[B])(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    TraversableLike
  5. def ++:[B >: Array[Long], That](that: TraversableOnce[B])(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    TraversableLike
  6. def +:[B >: Array[Long], That](elem: B)(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  7. def :+[B >: Array[Long], That](elem: B)(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  8. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  9. def addString(b: StringBuilder): StringBuilder
    Definition Classes
    TraversableOnce
  10. def addString(b: StringBuilder, sep: String): StringBuilder
    Definition Classes
    TraversableOnce
  11. def addString(b: StringBuilder, start: String, sep: String, end: String): StringBuilder
    Definition Classes
    TraversableOnce
  12. def aggregate[B](z: ⇒ B)(seqop: (B, Array[Long]) ⇒ B, combop: (B, B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  13. def andThen[C](k: (Array[Long]) ⇒ C): PartialFunction[Int, C]
    Definition Classes
    PartialFunction → Function1
  14. def apply(i: Int): Array[Long]

    K-mer only at position i.

    K-mer only at position i. Allocates a new object.

    Definition Classes
    KmerTable2 → KmerTable → SeqLike → GenSeqLike → Function1
  15. def applyOrElse[A1 <: Int, B1 >: Array[Long]](x: A1, default: (A1) ⇒ B1): B1
    Definition Classes
    PartialFunction
  16. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  17. def canEqual(that: Any): Boolean
    Definition Classes
    IterableLike → Equals
  18. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @IntrinsicCandidate()
  19. def collect[B, That](pf: PartialFunction[Array[Long], B])(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  20. def collectFirst[B](pf: PartialFunction[Array[Long], B]): Option[B]
    Definition Classes
    TraversableOnce
  21. def combinations(n: Int): Iterator[IndexedSeq[Array[Long]]]
    Definition Classes
    SeqLike
  22. def companion: GenericCompanion[IndexedSeq]
    Definition Classes
    IndexedSeq → Seq → GenSeq → Iterable → GenIterable → Traversable → GenTraversable → GenericTraversableTemplate
  23. def compareKmers(idx: Int, other: KmerTable, otherIdx: Int): Int

    Compare k-mer at position idx in this table with an equal length k-mer at position otherIdx in the other table.

    Compare k-mer at position idx in this table with an equal length k-mer at position otherIdx in the other table.

    idx

    Index in this table

    other

    Other table

    otherIdx

    Index in other table

    returns

    -1, 0, or 1 according to the Comparable contract (prior to, equal, or after)

    Definition Classes
    KmerTable2 → KmerTable
  24. def compose[A](g: (A) ⇒ Int): (A) ⇒ Array[Long]
    Definition Classes
    Function1
    Annotations
    @unspecialized()
  25. def contains[A1 >: Array[Long]](elem: A1): Boolean
    Definition Classes
    SeqLike
  26. def containsSlice[B](that: GenSeq[B]): Boolean
    Definition Classes
    SeqLike
  27. def copyKmerAndTagsToBuilder(destination: KmerTableBuilder, i: Int): Unit

    Copy k-mer and tag data from position i to a builder.

    Copy k-mer and tag data from position i to a builder.

    Definition Classes
    KmerTable
  28. def copyKmerOnlyToBuilder(destination: KmerTableBuilder, i: Int): Unit

    Copy k-mer data only from position i to a builder.

    Copy k-mer data only from position i to a builder.

    Definition Classes
    KmerTable
  29. def copyTagsOnlyToBuilder(destination: KmerTableBuilder, i: Int): Unit

    Copy tag data only from position i to a builder.

    Copy tag data only from position i to a builder.

    Definition Classes
    KmerTable
  30. def copyToArray[B >: Array[Long]](xs: Array[B], start: Int, len: Int): Unit
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  31. def copyToArray[B >: Array[Long]](xs: Array[B]): Unit
    Definition Classes
    TraversableOnce → GenTraversableOnce
  32. def copyToArray[B >: Array[Long]](xs: Array[B], start: Int): Unit
    Definition Classes
    TraversableOnce → GenTraversableOnce
  33. def copyToBuffer[B >: Array[Long]](dest: Buffer[B]): Unit
    Definition Classes
    TraversableOnce
  34. def corresponds[B](that: GenSeq[B])(p: (Array[Long], B) ⇒ Boolean): Boolean
    Definition Classes
    SeqLike → GenSeqLike
  35. def count(p: (Array[Long]) ⇒ Boolean): Int
    Definition Classes
    TraversableOnce → GenTraversableOnce
  36. def countedKmers: Iterator[(Array[Long], Abundance)]

    An iterator of distinct k-mers and their counts.

    An iterator of distinct k-mers and their counts. Requires that the KmerTable was sorted at construction time. Counts are expected in the first tag column.

    Definition Classes
    KmerTable
  37. def diff[B >: Array[Long]](that: GenSeq[B]): IndexedSeq[Array[Long]]
    Definition Classes
    SeqLike → GenSeqLike
  38. def distinct: IndexedSeq[Array[Long]]
    Definition Classes
    SeqLike → GenSeqLike
  39. def distinctKmers: Iterator[Array[Long]]

    An iterator of distinct k-mers.

    An iterator of distinct k-mers. Requires that the KmerTable was sorted at construction time.

    Definition Classes
    KmerTable
  40. def drop(n: Int): IndexedSeq[Array[Long]]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  41. def dropRight(n: Int): IndexedSeq[Array[Long]]
    Definition Classes
    IterableLike
  42. def dropWhile(p: (Array[Long]) ⇒ Boolean): IndexedSeq[Array[Long]]
    Definition Classes
    TraversableLike → GenTraversableLike
  43. def endsWith[B](that: GenSeq[B]): Boolean
    Definition Classes
    SeqLike → GenSeqLike
  44. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  45. def equalKmers(i: Int, kmer: Array[Long]): Boolean

    Test whether the k-mer at position i is equal to the given one.

    Test whether the k-mer at position i is equal to the given one.

    Definition Classes
    KmerTable2 → KmerTable
  46. def equals(that: Any): Boolean
    Definition Classes
    GenSeqLike → Equals → Any
  47. def exists(p: (Array[Long]) ⇒ Boolean): Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  48. def filter(p: (Array[Long]) ⇒ Boolean): IndexedSeq[Array[Long]]
    Definition Classes
    TraversableLike → GenTraversableLike
  49. def filterNot(p: (Array[Long]) ⇒ Boolean): IndexedSeq[Array[Long]]
    Definition Classes
    TraversableLike → GenTraversableLike
  50. def find(p: (Array[Long]) ⇒ Boolean): Option[Array[Long]]
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  51. def flatMap[B, That](f: (Array[Long]) ⇒ GenTraversableOnce[B])(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  52. def flatten[B](implicit asTraversable: (Array[Long]) ⇒ GenTraversableOnce[B]): IndexedSeq[B]
    Definition Classes
    GenericTraversableTemplate
  53. def fold[A1 >: Array[Long]](z: A1)(op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  54. def foldLeft[B](z: B)(op: (B, Array[Long]) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  55. def foldRight[B](z: B)(op: (Array[Long], B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  56. def forall(p: (Array[Long]) ⇒ Boolean): Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  57. def foreach[U](f: (Array[Long]) ⇒ U): Unit
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike → TraversableOnce → GenTraversableOnce → FilterMonadic
  58. def genericBuilder[B]: Builder[B, IndexedSeq[B]]
    Definition Classes
    GenericTraversableTemplate
  59. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @IntrinsicCandidate()
  60. def groupBy[K](f: (Array[Long]) ⇒ K): Map[K, IndexedSeq[Array[Long]]]
    Definition Classes
    TraversableLike → GenTraversableLike
  61. def grouped(size: Int): Iterator[IndexedSeq[Array[Long]]]
    Definition Classes
    IterableLike
  62. def hasDefiniteSize: Boolean
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  63. def hashCode(): Int
    Definition Classes
    IndexedSeqLike → GenSeqLike → Any
  64. def head: Array[Long]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  65. def headOption: Option[Array[Long]]
    Definition Classes
    TraversableLike → GenTraversableLike
  66. def indexIterator: Iterator[Int]
    Definition Classes
    KmerTable
  67. def indexOf[B >: Array[Long]](elem: B, from: Int): Int
    Definition Classes
    GenSeqLike
  68. def indexOf[B >: Array[Long]](elem: B): Int
    Definition Classes
    GenSeqLike
  69. def indexOfSlice[B >: Array[Long]](that: GenSeq[B], from: Int): Int
    Definition Classes
    SeqLike
  70. def indexOfSlice[B >: Array[Long]](that: GenSeq[B]): Int
    Definition Classes
    SeqLike
  71. def indexWhere(p: (Array[Long]) ⇒ Boolean, from: Int): Int
    Definition Classes
    SeqLike → GenSeqLike
  72. def indexWhere(p: (Array[Long]) ⇒ Boolean): Int
    Definition Classes
    GenSeqLike
  73. def indices: Range
    Definition Classes
    SeqLike
  74. def init: IndexedSeq[Array[Long]]
    Definition Classes
    TraversableLike → GenTraversableLike
  75. def inits: Iterator[IndexedSeq[Array[Long]]]
    Definition Classes
    TraversableLike
  76. def intersect[B >: Array[Long]](that: GenSeq[B]): IndexedSeq[Array[Long]]
    Definition Classes
    SeqLike → GenSeqLike
  77. def isDefinedAt(idx: Int): Boolean
    Definition Classes
    GenSeqLike
  78. def isEmpty: Boolean
    Definition Classes
    SeqLike → IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  79. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  80. final def isTraversableAgain: Boolean
    Definition Classes
    TraversableLike → GenTraversableLike → GenTraversableOnce
  81. def iterator: Iterator[Array[Long]]

    Iterator with k-mer data only

    Iterator with k-mer data only

    Definition Classes
    KmerTable → IndexedSeqLike → IterableLike → GenIterableLike
  82. def iteratorWithTags: Iterator[Array[Long]]

    Iterator including both k-mer data and tag data

    Iterator including both k-mer data and tag data

    Definition Classes
    KmerTable
  83. val k: Int
    Definition Classes
    KmerTable
  84. val kmerWidth: Int
    Definition Classes
    KmerTable
  85. def kmerWithTags(i: Int): Array[Long]

    K-mer and tags at position i.

    K-mer and tags at position i. Allocates a new object.

    Definition Classes
    KmerTable
  86. val kmers: Array[Array[Long]]
    Definition Classes
    KmerTable
  87. def last: Array[Long]
    Definition Classes
    TraversableLike → GenTraversableLike
  88. def lastIndexOf[B >: Array[Long]](elem: B, end: Int): Int
    Definition Classes
    GenSeqLike
  89. def lastIndexOf[B >: Array[Long]](elem: B): Int
    Definition Classes
    GenSeqLike
  90. def lastIndexOfSlice[B >: Array[Long]](that: GenSeq[B], end: Int): Int
    Definition Classes
    SeqLike
  91. def lastIndexOfSlice[B >: Array[Long]](that: GenSeq[B]): Int
    Definition Classes
    SeqLike
  92. def lastIndexWhere(p: (Array[Long]) ⇒ Boolean, end: Int): Int
    Definition Classes
    SeqLike → GenSeqLike
  93. def lastIndexWhere(p: (Array[Long]) ⇒ Boolean): Int
    Definition Classes
    GenSeqLike
  94. def lastOption: Option[Array[Long]]
    Definition Classes
    TraversableLike → GenTraversableLike
  95. val length: Int
    Definition Classes
    KmerTable → SeqLike → GenSeqLike
  96. def lengthCompare(len: Int): Int
    Definition Classes
    SeqLike
  97. def lift: (Int) ⇒ Option[Array[Long]]
    Definition Classes
    PartialFunction
  98. def map[B, That](f: (Array[Long]) ⇒ B)(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  99. def max[B >: Array[Long]](implicit cmp: Ordering[B]): Array[Long]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  100. def maxBy[B](f: (Array[Long]) ⇒ B)(implicit cmp: Ordering[B]): Array[Long]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  101. def min[B >: Array[Long]](implicit cmp: Ordering[B]): Array[Long]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  102. def minBy[B](f: (Array[Long]) ⇒ B)(implicit cmp: Ordering[B]): Array[Long]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  103. def mkString: String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  104. def mkString(sep: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  105. def mkString(start: String, sep: String, end: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  106. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  107. def newBuilder: Builder[Array[Long], IndexedSeq[Array[Long]]]
    Attributes
    protected[this]
    Definition Classes
    GenericTraversableTemplate → HasNewBuilder
  108. def nonEmpty: Boolean
    Definition Classes
    TraversableOnce → GenTraversableOnce
  109. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @IntrinsicCandidate()
  110. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @IntrinsicCandidate()
  111. def orElse[A1 <: Int, B1 >: Array[Long]](that: PartialFunction[A1, B1]): PartialFunction[A1, B1]
    Definition Classes
    PartialFunction
  112. def padTo[B >: Array[Long], That](len: Int, elem: B)(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  113. def par: ParSeq[Array[Long]]
    Definition Classes
    Parallelizable
  114. def parCombiner: Combiner[Array[Long], ParSeq[Array[Long]]]
    Attributes
    protected[this]
    Definition Classes
    SeqLike → TraversableLike → Parallelizable
  115. def partition(p: (Array[Long]) ⇒ Boolean): (IndexedSeq[Array[Long]], IndexedSeq[Array[Long]])
    Definition Classes
    TraversableLike → GenTraversableLike
  116. def patch[B >: Array[Long], That](from: Int, patch: GenSeq[B], replaced: Int)(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  117. def permutations: Iterator[IndexedSeq[Array[Long]]]
    Definition Classes
    SeqLike
  118. def prefixLength(p: (Array[Long]) ⇒ Boolean): Int
    Definition Classes
    GenSeqLike
  119. def product[B >: Array[Long]](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  120. def reduce[A1 >: Array[Long]](op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  121. def reduceLeft[B >: Array[Long]](op: (B, Array[Long]) ⇒ B): B
    Definition Classes
    TraversableOnce
  122. def reduceLeftOption[B >: Array[Long]](op: (B, Array[Long]) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  123. def reduceOption[A1 >: Array[Long]](op: (A1, A1) ⇒ A1): Option[A1]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  124. def reduceRight[B >: Array[Long]](op: (Array[Long], B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  125. def reduceRightOption[B >: Array[Long]](op: (Array[Long], B) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  126. def repr: IndexedSeq[Array[Long]]
    Definition Classes
    TraversableLike → GenTraversableLike
  127. def reverse: IndexedSeq[Array[Long]]
    Definition Classes
    SeqLike → GenSeqLike
  128. def reverseIterator: Iterator[Array[Long]]
    Definition Classes
    SeqLike
  129. def reverseMap[B, That](f: (Array[Long]) ⇒ B)(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  130. def reversed: List[Array[Long]]
    Attributes
    protected[this]
    Definition Classes
    TraversableOnce
  131. def runWith[U](action: (Array[Long]) ⇒ U): (Int) ⇒ Boolean
    Definition Classes
    PartialFunction
  132. def sameElements[B >: Array[Long]](that: GenIterable[B]): Boolean
    Definition Classes
    IterableLike → GenIterableLike
  133. def scan[B >: Array[Long], That](z: B)(op: (B, B) ⇒ B)(implicit cbf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  134. def scanLeft[B, That](z: B)(op: (B, Array[Long]) ⇒ B)(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  135. def scanRight[B, That](z: B)(op: (Array[Long], B) ⇒ B)(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
    Annotations
    @migration
    Migration

    (Changed in version 2.9.0) The behavior of scanRight has changed. The previous behavior can be reproduced with scanRight.reverse.

  136. def segmentLength(p: (Array[Long]) ⇒ Boolean, from: Int): Int
    Definition Classes
    SeqLike → GenSeqLike
  137. def seq: IndexedSeq[Array[Long]]
    Definition Classes
    IndexedSeq → IndexedSeqLike → Seq → GenSeq → GenSeqLike → Iterable → GenIterable → Traversable → GenTraversable → Parallelizable → TraversableOnce → GenTraversableOnce
  138. def size: Int
    Definition Classes
    SeqLike → GenTraversableLike → TraversableOnce → GenTraversableOnce
  139. def sizeHintIfCheap: Int
    Attributes
    protected[collection]
    Definition Classes
    IndexedSeqLike → GenTraversableOnce
  140. def slice(from: Int, until: Int): IndexedSeq[Array[Long]]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  141. def sliding(size: Int, step: Int): Iterator[IndexedSeq[Array[Long]]]
    Definition Classes
    IterableLike
  142. def sliding(size: Int): Iterator[IndexedSeq[Array[Long]]]
    Definition Classes
    IterableLike
  143. def sortBy[B](f: (Array[Long]) ⇒ B)(implicit ord: Ordering[B]): IndexedSeq[Array[Long]]
    Definition Classes
    SeqLike
  144. def sortWith(lt: (Array[Long], Array[Long]) ⇒ Boolean): IndexedSeq[Array[Long]]
    Definition Classes
    SeqLike
  145. def sorted[B >: Array[Long]](implicit ord: Ordering[B]): IndexedSeq[Array[Long]]
    Definition Classes
    SeqLike
  146. def span(p: (Array[Long]) ⇒ Boolean): (IndexedSeq[Array[Long]], IndexedSeq[Array[Long]])
    Definition Classes
    TraversableLike → GenTraversableLike
  147. def splitAt(n: Int): (IndexedSeq[Array[Long]], IndexedSeq[Array[Long]])
    Definition Classes
    TraversableLike → GenTraversableLike
  148. def startsWith[B](that: GenSeq[B], offset: Int): Boolean
    Definition Classes
    SeqLike → GenSeqLike
  149. def startsWith[B](that: GenSeq[B]): Boolean
    Definition Classes
    GenSeqLike
  150. def stringPrefix: String
    Definition Classes
    TraversableLike → GenTraversableLike
  151. def sum[B >: Array[Long]](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  152. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  153. val tagWidth: Int
    Definition Classes
    KmerTable
  154. def tagsIterator: Iterator[Array[Long]]

    Iterator including only tags data

    Iterator including only tags data

    Definition Classes
    KmerTable
  155. def tagsOnly(i: Int): Array[Long]

    Tags only at position i.

    Tags only at position i. Allocates a new object.

    Definition Classes
    KmerTable
  156. def tail: IndexedSeq[Array[Long]]
    Definition Classes
    TraversableLike → GenTraversableLike
  157. def tails: Iterator[IndexedSeq[Array[Long]]]
    Definition Classes
    TraversableLike
  158. def take(n: Int): IndexedSeq[Array[Long]]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  159. def takeRight(n: Int): IndexedSeq[Array[Long]]
    Definition Classes
    IterableLike
  160. def takeWhile(p: (Array[Long]) ⇒ Boolean): IndexedSeq[Array[Long]]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  161. def thisCollection: IndexedSeq[Array[Long]]
    Attributes
    protected[this]
    Definition Classes
    IndexedSeqLike → SeqLike → IterableLike → TraversableLike
  162. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, Array[Long], Col[Array[Long]]]): Col[Array[Long]]
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  163. def toArray[B >: Array[Long]](implicit arg0: ClassTag[B]): Array[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  164. def toBuffer[A1 >: Array[Long]]: Buffer[A1]
    Definition Classes
    IndexedSeqLike → TraversableOnce → GenTraversableOnce
  165. def toCollection(repr: IndexedSeq[Array[Long]]): IndexedSeq[Array[Long]]
    Attributes
    protected[this]
    Definition Classes
    IndexedSeqLike → SeqLike → IterableLike → TraversableLike
  166. def toIndexedSeq: IndexedSeq[Array[Long]]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  167. def toIterable: Iterable[Array[Long]]
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  168. def toIterator: Iterator[Array[Long]]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  169. def toList: List[Array[Long]]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  170. def toMap[T, U](implicit ev: <:<[Array[Long], (T, U)]): Map[T, U]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  171. def toSeq: Seq[Array[Long]]
    Definition Classes
    SeqLike → GenSeqLike → TraversableOnce → GenTraversableOnce
  172. def toSet[B >: Array[Long]]: Set[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  173. def toStream: Stream[Array[Long]]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
  174. def toString(): String
    Definition Classes
    KmerTable → SeqLike → TraversableLike → Function1 → AnyRef → Any
  175. def toTraversable: Traversable[Array[Long]]
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  176. def toVector: Vector[Array[Long]]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  177. def transpose[B](implicit asTraversable: (Array[Long]) ⇒ GenTraversableOnce[B]): IndexedSeq[IndexedSeq[B]]
    Definition Classes
    GenericTraversableTemplate
    Annotations
    @migration
    Migration

    (Changed in version 2.9.0) transpose throws an IllegalArgumentException if collections are not uniformly sized.

  178. def union[B >: Array[Long], That](that: GenSeq[B])(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  179. def unzip[A1, A2](implicit asPair: (Array[Long]) ⇒ (A1, A2)): (IndexedSeq[A1], IndexedSeq[A2])
    Definition Classes
    GenericTraversableTemplate
  180. def unzip3[A1, A2, A3](implicit asTriple: (Array[Long]) ⇒ (A1, A2, A3)): (IndexedSeq[A1], IndexedSeq[A2], IndexedSeq[A3])
    Definition Classes
    GenericTraversableTemplate
  181. def updated[B >: Array[Long], That](index: Int, elem: B)(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  182. def view(from: Int, until: Int): SeqView[Array[Long], IndexedSeq[Array[Long]]]
    Definition Classes
    SeqLike → IterableLike → TraversableLike
  183. def view: SeqView[Array[Long], IndexedSeq[Array[Long]]]
    Definition Classes
    SeqLike → IterableLike → TraversableLike
  184. def visitCountedKmers(v: KmerVisitor): Unit

    Visit counted k-mers.

    Visit counted k-mers. Requires that the KmerTable was sorted at construction time. Counts are expected in the first tag column.

    Definition Classes
    KmerTable
  185. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  186. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  187. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  188. val width: Int
    Definition Classes
    KmerTable
  189. def withFilter(p: (Array[Long]) ⇒ Boolean): FilterMonadic[Array[Long], IndexedSeq[Array[Long]]]
    Definition Classes
    TraversableLike → FilterMonadic
  190. def zip[A1 >: Array[Long], B, That](that: GenIterable[B])(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], (A1, B), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  191. def zipAll[B, A1 >: Array[Long], That](that: GenIterable[B], thisElem: A1, thatElem: B)(implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], (A1, B), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  192. def zipWithIndex[A1 >: Array[Long], That](implicit bf: CanBuildFrom[IndexedSeq[Array[Long]], (A1, Int), That]): That
    Definition Classes
    IterableLike → GenIterableLike

Deprecated Value Members

  1. def /:[B](z: B)(op: (B, Array[Long]) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
    Annotations
    @deprecated
    Deprecated

    (Since version 2.12.10) Use foldLeft instead of /:

  2. def :\[B](z: B)(op: (Array[Long], B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
    Annotations
    @deprecated
    Deprecated

    (Since version 2.12.10) Use foldRight instead of :\

  3. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] ) @Deprecated
    Deprecated

Inherited from KmerTable

Inherited from IndexedSeq[Array[Long]]

Inherited from IndexedSeqLike[Array[Long], IndexedSeq[Array[Long]]]

Inherited from Seq[Array[Long]]

Inherited from SeqLike[Array[Long], IndexedSeq[Array[Long]]]

Inherited from GenSeq[Array[Long]]

Inherited from GenSeqLike[Array[Long], IndexedSeq[Array[Long]]]

Inherited from Iterable[Array[Long]]

Inherited from IterableLike[Array[Long], IndexedSeq[Array[Long]]]

Inherited from Equals

Inherited from GenIterable[Array[Long]]

Inherited from GenIterableLike[Array[Long], IndexedSeq[Array[Long]]]

Inherited from Traversable[Array[Long]]

Inherited from GenTraversable[Array[Long]]

Inherited from GenericTraversableTemplate[Array[Long], IndexedSeq]

Inherited from TraversableLike[Array[Long], IndexedSeq[Array[Long]]]

Inherited from GenTraversableLike[Array[Long], IndexedSeq[Array[Long]]]

Inherited from Parallelizable[Array[Long], ParSeq[Array[Long]]]

Inherited from TraversableOnce[Array[Long]]

Inherited from GenTraversableOnce[Array[Long]]

Inherited from FilterMonadic[Array[Long], IndexedSeq[Array[Long]]]

Inherited from HasNewBuilder[Array[Long], IndexedSeq[Array[Long]] @scala.annotation.unchecked.uncheckedVariance]

Inherited from PartialFunction[Int, Array[Long]]

Inherited from (Int) ⇒ Array[Long]

Inherited from AnyRef

Inherited from Any

Ungrouped