Class/Object

org.hammerlab.genomics.bases

Bases

Related Docs: object Bases | package bases

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final class Bases extends AnyVal with BasesBuffer with IndexedSeqLike[Base, Bases]

Bases wraps a Vector[Byte] where each Byte holds the ASCII value of one of 5 values: A, C, G, T, N.

Linear Supertypes
IndexedSeqLike[Base, Bases], SeqLike[Base, Bases], GenSeqLike[Base, Bases], IterableLike[Base, Bases], GenIterableLike[Base, Bases], TraversableLike[Base, Bases], GenTraversableLike[Base, Bases], Parallelizable[Base, ParSeq[Base]], TraversableOnce[Base], GenTraversableOnce[Base], FilterMonadic[Base, Bases], HasNewBuilder[Base, Bases], Equals, BasesBuffer, AnyVal, Any
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Inherited
  1. Bases
  2. IndexedSeqLike
  3. SeqLike
  4. GenSeqLike
  5. IterableLike
  6. GenIterableLike
  7. TraversableLike
  8. GenTraversableLike
  9. Parallelizable
  10. TraversableOnce
  11. GenTraversableOnce
  12. FilterMonadic
  13. HasNewBuilder
  14. Equals
  15. BasesBuffer
  16. AnyVal
  17. Any
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Type Members

  1. class Elements extends AbstractIterator[A] with BufferedIterator[A] with Serializable

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    Attributes
    protected
    Definition Classes
    IndexedSeqLike
    Annotations
    @SerialVersionUID()

  2. type LengthT = Int

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    Definition Classes
    Bases → BasesBuffer

  3. type Self = Bases

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    Attributes
    protected[this]
    Definition Classes
    TraversableLike

  4. class WithFilter extends FilterMonadic[A, Repr]

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    Definition Classes
    TraversableLike

Value Members

  1. final def !=(arg0: Any): Boolean

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    Definition Classes
    Any

  2. final def ##(): Int

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    Definition Classes
    Any

  3. def +(right: Bases): Bases

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  4. def ++[B >: Base, That](that: GenTraversableOnce[B])(implicit bf: CanBuildFrom[Bases, B, That]): That

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    Definition Classes
    TraversableLike → GenTraversableLike

  5. def ++:[B >: Base, That](that: Traversable[B])(implicit bf: CanBuildFrom[Bases, B, That]): That

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    Definition Classes
    TraversableLike

  6. def ++:[B >: Base, That](that: TraversableOnce[B])(implicit bf: CanBuildFrom[Bases, B, That]): That

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    Definition Classes
    TraversableLike

  7. def +:[B >: Base, That](elem: B)(implicit bf: CanBuildFrom[Bases, B, That]): That

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    Definition Classes
    SeqLike → GenSeqLike

  8. def /:[B](z: B)(op: (B, Base) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  9. def :+[B >: Base, That](elem: B)(implicit bf: CanBuildFrom[Bases, B, That]): That

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    Definition Classes
    SeqLike → GenSeqLike

  10. def :\[B](z: B)(op: (Base, B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  11. final def ==(arg0: Any): Boolean

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    Definition Classes
    Any

  12. def addString(b: StringBuilder): StringBuilder

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    Definition Classes
    TraversableOnce

  13. def addString(b: StringBuilder, sep: String): StringBuilder

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    Definition Classes
    TraversableOnce

  14. def addString(b: StringBuilder, start: String, sep: String, end: String): StringBuilder

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    Definition Classes
    TraversableOnce

  15. def aggregate[B](z: ⇒ B)(seqop: (B, Base) ⇒ B, combop: (B, B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  16. def allStandardBases: Boolean

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    Are all the given bases standard?

  17. def apply(idx: LengthT): Base

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    Definition Classes
    Bases → SeqLike → GenSeqLike → BasesBuffer

  18. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  19. val bytes: Bytes

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  20. def canEqual(that: Any): Boolean

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    Definition Classes
    IterableLike → Equals

  21. def collect[B, That](pf: PartialFunction[Base, B])(implicit bf: CanBuildFrom[Bases, B, That]): That

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    Definition Classes
    TraversableLike → GenTraversableLike

  22. def collectFirst[B](pf: PartialFunction[Base, B]): Option[B]

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    Definition Classes
    TraversableOnce

  23. def combinations(n: Int): Iterator[Bases]

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    Definition Classes
    SeqLike

  24. def complement: Bases

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    Watson-Crick complement of a sequence of bases.

  25. def contains[A1 >: Base](elem: A1): Boolean

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    Definition Classes
    SeqLike

  26. def containsSlice[B](that: GenSeq[B]): Boolean

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    Definition Classes
    SeqLike

  27. def copyToArray[B >: Base](xs: Array[B], start: Int, len: Int): Unit

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    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce

  28. def copyToArray[B >: Base](xs: Array[B]): Unit

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  29. def copyToArray[B >: Base](xs: Array[B], start: Int): Unit

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  30. def copyToBuffer[B >: Base](dest: Buffer[B]): Unit

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    Definition Classes
    TraversableOnce

  31. def corresponds[B](that: GenSeq[B])(p: (Base, B) ⇒ Boolean): Boolean

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    Definition Classes
    SeqLike → GenSeqLike

  32. def count(p: (Base) ⇒ Boolean): Int

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  33. def diff[B >: Base](that: GenSeq[B]): Bases

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    Definition Classes
    SeqLike → GenSeqLike

  34. def distinct: Bases

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    Definition Classes
    SeqLike → GenSeqLike

  35. def drop(n: Int): Bases

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    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike

  36. def dropRight(n: Int): Bases

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    Definition Classes
    IterableLike

  37. def dropWhile(p: (Base) ⇒ Boolean): Bases

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    Definition Classes
    TraversableLike → GenTraversableLike

  38. def endsWith[B](that: GenSeq[B]): Boolean

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    Definition Classes
    SeqLike → GenSeqLike

  39. def exists(p: (Base) ⇒ Boolean): Boolean

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    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce

  40. def filter(p: (Base) ⇒ Boolean): Bases

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    Definition Classes
    TraversableLike → GenTraversableLike

  41. def filterNot(p: (Base) ⇒ Boolean): Bases

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    Definition Classes
    TraversableLike → GenTraversableLike

  42. def find(p: (Base) ⇒ Boolean): Option[Base]

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    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce

  43. def flatMap[B, That](f: (Base) ⇒ GenTraversableOnce[B])(implicit bf: CanBuildFrom[Bases, B, That]): That

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    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic

  44. def fold[A1 >: Base](z: A1)(op: (A1, A1) ⇒ A1): A1

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  45. def foldLeft[B](z: B)(op: (B, Base) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  46. def foldRight[B](z: B)(op: (Base, B) ⇒ B): B

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    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce

  47. def forall(p: (Base) ⇒ Boolean): Boolean

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    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce

  48. def foreach[U](f: (Base) ⇒ U): Unit

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    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike → TraversableOnce → GenTraversableOnce → FilterMonadic

  49. def getClass(): Class[_ <: AnyVal]

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    Definition Classes
    AnyVal → Any

  50. def groupBy[K](f: (Base) ⇒ K): Map[K, Bases]

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    Definition Classes
    TraversableLike → GenTraversableLike

  51. def grouped(size: Int): Iterator[Bases]

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    Definition Classes
    IterableLike

  52. def hasDefiniteSize: Boolean

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    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce

  53. def head: Base

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    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike

  54. def headOption: Option[Base]

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    Definition Classes
    TraversableLike → GenTraversableLike

  55. def indexOf[B >: Base](elem: B, from: Int): Int

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    Definition Classes
    GenSeqLike

  56. def indexOf[B >: Base](elem: B): Int

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    Definition Classes
    GenSeqLike

  57. def indexOfSlice[B >: Base](that: GenSeq[B], from: Int): Int

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    Definition Classes
    SeqLike

  58. def indexOfSlice[B >: Base](that: GenSeq[B]): Int

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    Definition Classes
    SeqLike

  59. def indexWhere(p: (Base) ⇒ Boolean, from: Int): Int

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    Definition Classes
    SeqLike → GenSeqLike

  60. def indexWhere(p: (Base) ⇒ Boolean): Int

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    Definition Classes
    GenSeqLike

  61. def indices: Range

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    Definition Classes
    SeqLike

  62. def init: Bases

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    Definition Classes
    TraversableLike → GenTraversableLike

  63. def inits: Iterator[Bases]

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    Definition Classes
    TraversableLike

  64. def intersect[B >: Base](that: GenSeq[B]): Bases

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    Definition Classes
    SeqLike → GenSeqLike

  65. def isDefinedAt(idx: Int): Boolean

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    Definition Classes
    GenSeqLike

  66. def isEmpty: Boolean

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    Definition Classes
    SeqLike → IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce

  67. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  68. final def isTraversableAgain: Boolean

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    Definition Classes
    TraversableLike → GenTraversableLike → GenTraversableOnce

  69. def iterator: Iterator[Base]

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    Definition Classes
    IndexedSeqLike → IterableLike → GenIterableLike

  70. def last: Base

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    Definition Classes
    TraversableLike → GenTraversableLike

  71. def lastIndexOf[B >: Base](elem: B, end: Int): Int

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    Definition Classes
    GenSeqLike

  72. def lastIndexOf[B >: Base](elem: B): Int

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    Definition Classes
    GenSeqLike

  73. def lastIndexOfSlice[B >: Base](that: GenSeq[B], end: Int): Int

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    Definition Classes
    SeqLike

  74. def lastIndexOfSlice[B >: Base](that: GenSeq[B]): Int

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    Definition Classes
    SeqLike

  75. def lastIndexWhere(p: (Base) ⇒ Boolean, end: Int): Int

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    Definition Classes
    SeqLike → GenSeqLike

  76. def lastIndexWhere(p: (Base) ⇒ Boolean): Int

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    Definition Classes
    GenSeqLike

  77. def lastOption: Option[Base]

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    Definition Classes
    TraversableLike → GenTraversableLike

  78. def length: LengthT

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    Definition Classes
    Bases → SeqLike → GenSeqLike → BasesBuffer

  79. def lengthCompare(len: Int): Int

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    Definition Classes
    SeqLike

  80. def map[B, That](f: (Base) ⇒ B)(implicit bf: CanBuildFrom[Bases, B, That]): That

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    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic

  81. def max[B >: Base](implicit cmp: Ordering[B]): Base

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  82. def maxBy[B](f: (Base) ⇒ B)(implicit cmp: Ordering[B]): Base

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  83. def min[B >: Base](implicit cmp: Ordering[B]): Base

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  84. def minBy[B](f: (Base) ⇒ B)(implicit cmp: Ordering[B]): Base

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  85. def mkString: String

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  86. def mkString(sep: String): String

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  87. def mkString(start: String, sep: String, end: String): String

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  88. def newBuilder: Builder[Base, Bases]

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    Attributes
    protected[this]
    Definition Classes
    Bases → TraversableLike → HasNewBuilder

  89. def nonEmpty: Boolean

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  90. def padTo[B >: Base, That](len: Int, elem: B)(implicit bf: CanBuildFrom[Bases, B, That]): That

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    Definition Classes
    SeqLike → GenSeqLike

  91. def par: ParSeq[Base]

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    Definition Classes
    Parallelizable

  92. def parCombiner: Combiner[Base, ParSeq[Base]]

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    Attributes
    protected[this]
    Definition Classes
    SeqLike → TraversableLike → Parallelizable

  93. def partition(p: (Base) ⇒ Boolean): (Bases, Bases)

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    Definition Classes
    TraversableLike → GenTraversableLike

  94. def patch[B >: Base, That](from: Int, patch: GenSeq[B], replaced: Int)(implicit bf: CanBuildFrom[Bases, B, That]): That

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    Definition Classes
    SeqLike → GenSeqLike

  95. def permutations: Iterator[Bases]

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    Definition Classes
    SeqLike

  96. def prefixLength(p: (Base) ⇒ Boolean): Int

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    Definition Classes
    GenSeqLike

  97. def product[B >: Base](implicit num: Numeric[B]): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  98. def reduce[A1 >: Base](op: (A1, A1) ⇒ A1): A1

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  99. def reduceLeft[B >: Base](op: (B, Base) ⇒ B): B

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    Definition Classes
    TraversableOnce

  100. def reduceLeftOption[B >: Base](op: (B, Base) ⇒ B): Option[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  101. def reduceOption[A1 >: Base](op: (A1, A1) ⇒ A1): Option[A1]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  102. def reduceRight[B >: Base](op: (Base, B) ⇒ B): B

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    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce

  103. def reduceRightOption[B >: Base](op: (Base, B) ⇒ B): Option[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  104. def repr: Bases

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    Definition Classes
    TraversableLike → GenTraversableLike

  105. def reverse: Bases

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    Definition Classes
    SeqLike → GenSeqLike

  106. def reverseComplement: Bases

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    Watson-Crick complement of a sequence of bases, with the sequence reversed.

  107. def reverseIterator: Iterator[Base]

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    Definition Classes
    SeqLike

  108. def reverseMap[B, That](f: (Base) ⇒ B)(implicit bf: CanBuildFrom[Bases, B, That]): That

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    Definition Classes
    SeqLike → GenSeqLike

  109. def reversed: List[Base]

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    Attributes
    protected[this]
    Definition Classes
    TraversableOnce

  110. def sameElements[B >: Base](that: GenIterable[B]): Boolean

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    Definition Classes
    IterableLike → GenIterableLike

  111. def scan[B >: Base, That](z: B)(op: (B, B) ⇒ B)(implicit cbf: CanBuildFrom[Bases, B, That]): That

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    Definition Classes
    TraversableLike → GenTraversableLike

  112. def scanLeft[B, That](z: B)(op: (B, Base) ⇒ B)(implicit bf: CanBuildFrom[Bases, B, That]): That

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    Definition Classes
    TraversableLike → GenTraversableLike

  113. def scanRight[B, That](z: B)(op: (Base, B) ⇒ B)(implicit bf: CanBuildFrom[Bases, B, That]): That

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    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.

  114. def segmentLength(p: (Base) ⇒ Boolean, from: Int): Int

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    Definition Classes
    SeqLike → GenSeqLike

  115. def seq: IndexedSeq[Base]

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    Definition Classes
    Bases → IndexedSeqLike → GenSeqLike → Parallelizable → TraversableOnce → GenTraversableOnce

  116. def size: Int

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    Definition Classes
    SeqLike → GenTraversableLike → TraversableOnce → GenTraversableOnce

  117. def slice(from: Int, until: Int): Bases

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    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike

  118. def sliding(size: Int, step: Int): Iterator[Bases]

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    Definition Classes
    IterableLike

  119. def sliding(size: Int): Iterator[Bases]

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    Definition Classes
    IterableLike

  120. def sortBy[B](f: (Base) ⇒ B)(implicit ord: Ordering[B]): Bases

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    Definition Classes
    SeqLike

  121. def sortWith(lt: (Base, Base) ⇒ Boolean): Bases

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    Definition Classes
    SeqLike

  122. def sorted[B >: Base](implicit ord: Ordering[B]): Bases

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    Definition Classes
    SeqLike

  123. def span(p: (Base) ⇒ Boolean): (Bases, Bases)

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    Definition Classes
    TraversableLike → GenTraversableLike

  124. def splitAt(n: Int): (Bases, Bases)

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    Definition Classes
    TraversableLike → GenTraversableLike

  125. def startsWith[B](that: GenSeq[B], offset: Int): Boolean

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    Definition Classes
    SeqLike → GenSeqLike

  126. def startsWith[B](that: GenSeq[B]): Boolean

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    Definition Classes
    GenSeqLike

  127. def stringPrefix: String

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    Definition Classes
    TraversableLike → GenTraversableLike

  128. def sum[B >: Base](implicit num: Numeric[B]): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  129. def tail: Bases

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    Definition Classes
    TraversableLike → GenTraversableLike

  130. def tails: Iterator[Bases]

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    Definition Classes
    TraversableLike

  131. def take(n: Int): Bases

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    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike

  132. def takeRight(n: Int): Bases

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    Definition Classes
    IterableLike

  133. def takeWhile(p: (Base) ⇒ Boolean): Bases

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    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike

  134. def thisCollection: IndexedSeq[Base]

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    Attributes
    protected[this]
    Definition Classes
    Bases → IndexedSeqLike → SeqLike → IterableLike → TraversableLike

  135. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, Base, Col[Base]]): Col[Base]

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    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce

  136. def toArray[B >: Base](implicit arg0: ClassTag[B]): Array[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  137. def toBuffer[A1 >: Base]: Buffer[A1]

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    Definition Classes
    IndexedSeqLike → TraversableOnce → GenTraversableOnce

  138. def toCollection(repr: Bases): IndexedSeq[Base]

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    Attributes
    protected[this]
    Definition Classes
    Bases → IndexedSeqLike → SeqLike → IterableLike → TraversableLike

  139. def toIndexedSeq: IndexedSeq[Base]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  140. def toIterable: Iterable[Base]

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    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce

  141. def toIterator: Iterator[Base]

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    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )

  142. def toList: List[Base]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  143. def toMap[T, U](implicit ev: <:<[Base, (T, U)]): Map[T, U]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  144. def toSeq: Seq[Base]

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    Definition Classes
    SeqLike → GenSeqLike → TraversableOnce → GenTraversableOnce

  145. def toSet[B >: Base]: Set[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  146. def toStream: Stream[Base]

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    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce

  147. def toString(): String

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    Definition Classes
    Bases → SeqLike → TraversableLike → Any

  148. def toTraversable: Traversable[Base]

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    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )

  149. def toVector: Vector[Base]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  150. def union[B >: Base, That](that: GenSeq[B])(implicit bf: CanBuildFrom[Bases, B, That]): That

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    Definition Classes
    SeqLike → GenSeqLike

  151. def updated[B >: Base, That](index: Int, elem: B)(implicit bf: CanBuildFrom[Bases, B, That]): That

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    Definition Classes
    SeqLike → GenSeqLike

  152. def view(from: Int, until: Int): SeqView[Base, Bases]

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    Definition Classes
    SeqLike → IterableLike → TraversableLike

  153. def view: SeqView[Base, Bases]

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    Definition Classes
    SeqLike → IterableLike → TraversableLike

  154. def withFilter(p: (Base) ⇒ Boolean): FilterMonadic[Base, Bases]

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    Definition Classes
    TraversableLike → FilterMonadic

  155. def zip[A1 >: Base, B, That](that: GenIterable[B])(implicit bf: CanBuildFrom[Bases, (A1, B), That]): That

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    Definition Classes
    IterableLike → GenIterableLike

  156. def zipAll[B, A1 >: Base, That](that: GenIterable[B], thisElem: A1, thatElem: B)(implicit bf: CanBuildFrom[Bases, (A1, B), That]): That

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    Definition Classes
    IterableLike → GenIterableLike

  157. def zipWithIndex[A1 >: Base, That](implicit bf: CanBuildFrom[Bases, (A1, Int), That]): That

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    Definition Classes
    IterableLike → GenIterableLike

Inherited from IndexedSeqLike[Base, Bases]

Inherited from SeqLike[Base, Bases]

Inherited from GenSeqLike[Base, Bases]

Inherited from IterableLike[Base, Bases]

Inherited from GenIterableLike[Base, Bases]

Inherited from TraversableLike[Base, Bases]

Inherited from GenTraversableLike[Base, Bases]

Inherited from Parallelizable[Base, ParSeq[Base]]

Inherited from TraversableOnce[Base]

Inherited from GenTraversableOnce[Base]

Inherited from FilterMonadic[Base, Bases]

Inherited from HasNewBuilder[Base, Bases]

Inherited from Equals

Inherited from BasesBuffer

Inherited from AnyVal

Inherited from Any

Ungrouped