Class/Object

org.hammerlab.bgzf.block

Block

Related Docs: object Block | package block

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case class Block(bytes: Array[Byte], start: Long, compressedSize: Int) extends Iterator[Byte] with Product with Serializable

Representation of an uncompressed BGZF block

bytes

uncompressed bytes

start

(compressed) start-position in the file

compressedSize

size of compressed block

Linear Supertypes
Serializable, Serializable, Product, Equals, Iterator[Byte], TraversableOnce[Byte], GenTraversableOnce[Byte], AnyRef, Any
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Inherited
  1. Block
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. Iterator
  7. TraversableOnce
  8. GenTraversableOnce
  9. AnyRef
  10. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new Block(bytes: Array[Byte], start: Long, compressedSize: Int)

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    bytes

    uncompressed bytes

    start

    (compressed) start-position in the file

    compressedSize

    size of compressed block

Type Members

  1. class GroupedIterator[B >: A] extends AbstractIterator[Seq[B]] with Iterator[Seq[B]]

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    Definition Classes
    Iterator

Value Members

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

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any

  3. def ++[B >: Byte](that: ⇒ GenTraversableOnce[B]): Iterator[B]

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    Definition Classes
    Iterator

  4. def /:[B](z: B)(op: (B, Byte) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  5. def :\[B](z: B)(op: (Byte, B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    AnyRef → Any

  7. def addString(b: StringBuilder): StringBuilder

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    Definition Classes
    TraversableOnce

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

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    Definition Classes
    TraversableOnce

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

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    Definition Classes
    TraversableOnce

  10. def aggregate[B](z: ⇒ B)(seqop: (B, Byte) ⇒ B, combop: (B, B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  11. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  12. def buffered: BufferedIterator[Byte]

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    Definition Classes
    Iterator

  13. val bytes: Array[Byte]

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    uncompressed bytes

  14. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  15. def collect[B](pf: PartialFunction[Byte, B]): Iterator[B]

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    Definition Classes
    Iterator
    Annotations
    @migration
    Migration

    (Changed in version 2.8.0) collect has changed. The previous behavior can be reproduced with toSeq.

  16. def collectFirst[B](pf: PartialFunction[Byte, B]): Option[B]

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    Definition Classes
    TraversableOnce

  17. val compressedSize: Int

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    size of compressed block

  18. def contains(elem: Any): Boolean

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  20. def copyToArray[B >: Byte](xs: Array[B]): Unit

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  22. def copyToBuffer[B >: Byte](dest: Buffer[B]): Unit

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    Definition Classes
    TraversableOnce

  23. def corresponds[B](that: GenTraversableOnce[B])(p: (Byte, B) ⇒ Boolean): Boolean

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    Definition Classes
    Iterator

  24. def count(p: (Byte) ⇒ Boolean): Int

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  25. def drop(n: Int): Iterator[Byte]

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    Definition Classes
    Iterator

  26. def dropWhile(p: (Byte) ⇒ Boolean): Iterator[Byte]

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    Definition Classes
    Iterator

  27. def duplicate: (Iterator[Byte], Iterator[Byte])

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    Definition Classes
    Iterator

  28. def endPos: Pos

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  29. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  30. def exists(p: (Byte) ⇒ Boolean): Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  31. def filter(p: (Byte) ⇒ Boolean): Iterator[Byte]

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    Definition Classes
    Iterator

  32. def filterNot(p: (Byte) ⇒ Boolean): Iterator[Byte]

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    Definition Classes
    Iterator

  33. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  34. def find(p: (Byte) ⇒ Boolean): Option[Byte]

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  35. def flatMap[B](f: (Byte) ⇒ GenTraversableOnce[B]): Iterator[B]

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    Definition Classes
    Iterator

  36. def fold[A1 >: Byte](z: A1)(op: (A1, A1) ⇒ A1): A1

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  37. def foldLeft[B](z: B)(op: (B, Byte) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  38. def foldRight[B](z: B)(op: (Byte, B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  39. def forall(p: (Byte) ⇒ Boolean): Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  40. def foreach[U](f: (Byte) ⇒ U): Unit

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  41. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any

  42. def grouped[B >: Byte](size: Int): GroupedIterator[B]

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    Definition Classes
    Iterator

  43. def hasDefiniteSize: Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  44. def hasNext: Boolean

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    Definition Classes
    Block → Iterator

  45. var idx: Int

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  46. def indexOf[B >: Byte](elem: B): Int

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    Definition Classes
    Iterator

  47. def indexWhere(p: (Byte) ⇒ Boolean): Int

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    Definition Classes
    Iterator

  48. def isEmpty: Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  49. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  50. def isTraversableAgain: Boolean

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    Definition Classes
    Iterator → GenTraversableOnce

  51. def length: Int

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    Definition Classes
    Iterator

  52. def map[B](f: (Byte) ⇒ B): Iterator[B]

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    Definition Classes
    Iterator

  53. def max[B >: Byte](implicit cmp: Ordering[B]): Byte

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  54. def maxBy[B](f: (Byte) ⇒ B)(implicit cmp: Ordering[B]): Byte

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  55. def min[B >: Byte](implicit cmp: Ordering[B]): Byte

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  56. def minBy[B](f: (Byte) ⇒ B)(implicit cmp: Ordering[B]): Byte

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  57. def mkString: String

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  58. def mkString(sep: String): String

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  60. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  61. def next(): Byte

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    Definition Classes
    Block → Iterator

  62. def nextStartPos: Pos

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  63. def nonEmpty: Boolean

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  64. final def notify(): Unit

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    Definition Classes
    AnyRef

  65. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  66. def padTo[A1 >: Byte](len: Int, elem: A1): Iterator[A1]

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    Definition Classes
    Iterator

  67. def partition(p: (Byte) ⇒ Boolean): (Iterator[Byte], Iterator[Byte])

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    Definition Classes
    Iterator

  68. def patch[B >: Byte](from: Int, patchElems: Iterator[B], replaced: Int): Iterator[B]

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    Definition Classes
    Iterator

  69. def pos: Pos

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  70. def positions: Iterator[Pos]

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  71. def product[B >: Byte](implicit num: Numeric[B]): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  72. def reduce[A1 >: Byte](op: (A1, A1) ⇒ A1): A1

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  73. def reduceLeft[B >: Byte](op: (B, Byte) ⇒ B): B

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    Definition Classes
    TraversableOnce

  74. def reduceLeftOption[B >: Byte](op: (B, Byte) ⇒ B): Option[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  75. def reduceOption[A1 >: Byte](op: (A1, A1) ⇒ A1): Option[A1]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  76. def reduceRight[B >: Byte](op: (Byte, B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  77. def reduceRightOption[B >: Byte](op: (Byte, B) ⇒ B): Option[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  78. def reversed: List[Byte]

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    Attributes
    protected[this]
    Definition Classes
    TraversableOnce

  79. def sameElements(that: Iterator[_]): Boolean

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    Definition Classes
    Iterator

  80. def scanLeft[B](z: B)(op: (B, Byte) ⇒ B): Iterator[B]

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    Definition Classes
    Iterator

  81. def scanRight[B](z: B)(op: (Byte, B) ⇒ B): Iterator[B]

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    Definition Classes
    Iterator

  82. def seq: Iterator[Byte]

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  83. def size: Int

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  84. def slice(from: Int, until: Int): Iterator[Byte]

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    Definition Classes
    Iterator

  85. def sliding[B >: Byte](size: Int, step: Int): GroupedIterator[B]

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    Definition Classes
    Iterator

  86. def span(p: (Byte) ⇒ Boolean): (Iterator[Byte], Iterator[Byte])

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    Definition Classes
    Iterator

  87. val start: Long

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    (compressed) start-position in the file

  88. def startPos: Pos

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  89. def sum[B >: Byte](implicit num: Numeric[B]): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  90. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef

  91. def take(n: Int): Iterator[Byte]

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    Definition Classes
    Iterator

  92. def takeWhile(p: (Byte) ⇒ Boolean): Iterator[Byte]

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    Definition Classes
    Iterator

  93. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, Byte, Col[Byte]]): Col[Byte]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  94. def toArray[B >: Byte](implicit arg0: ClassTag[B]): Array[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  95. def toBuffer[B >: Byte]: Buffer[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  96. def toIndexedSeq: IndexedSeq[Byte]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  97. def toIterable: Iterable[Byte]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  98. def toIterator: Iterator[Byte]

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    Definition Classes
    Iterator → GenTraversableOnce

  99. def toList: List[Byte]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  100. def toMap[T, U](implicit ev: <:<[Byte, (T, U)]): Map[T, U]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  101. def toSeq: Seq[Byte]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  102. def toSet[B >: Byte]: Set[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  103. def toStream: scala.collection.immutable.Stream[Byte]

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    Definition Classes
    Iterator → GenTraversableOnce

  104. def toString(): String

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    Definition Classes
    Block → Iterator → AnyRef → Any

  105. def toTraversable: Traversable[Byte]

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  106. def toVector: Vector[Byte]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  107. def uncompressedSize: Int

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  108. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  109. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  110. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  111. def withFilter(p: (Byte) ⇒ Boolean): Iterator[Byte]

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    Definition Classes
    Iterator

  112. def zip[B](that: Iterator[B]): Iterator[(Byte, B)]

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    Definition Classes
    Iterator

  113. def zipAll[B, A1 >: Byte, B1 >: B](that: Iterator[B], thisElem: A1, thatElem: B1): Iterator[(A1, B1)]

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    Definition Classes
    Iterator

  114. def zipWithIndex: Iterator[(Byte, Int)]

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    Definition Classes
    Iterator

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from Iterator[Byte]

Inherited from TraversableOnce[Byte]

Inherited from GenTraversableOnce[Byte]

Inherited from AnyRef

Inherited from Any

Ungrouped