Trait

org.hammerlab.bam.iterator

PosStreamI

Related Doc: package iterator

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trait PosStreamI[Stream <: UncompressedBytesI[_]] extends RecordIterator[Pos, Stream]

Interface for iterating over record-start Poss in a BAM file

Linear Supertypes
RecordIterator[Pos, Stream], Closeable, AutoCloseable, SimpleIterator[Pos], BufferedIterator[Pos], Iterator[Pos], TraversableOnce[Pos], GenTraversableOnce[Pos], AnyRef, Any
Known Subclasses
PosStream, SeekablePosStream
Ordering
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Inherited
  1. PosStreamI
  2. RecordIterator
  3. Closeable
  4. AutoCloseable
  5. SimpleIterator
  6. BufferedIterator
  7. Iterator
  8. TraversableOnce
  9. GenTraversableOnce
  10. AnyRef
  11. Any
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Visibility
  1. Public
  2. All

Type Members

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

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    Definition Classes
    Iterator

Abstract Value Members

  1. abstract def header: Header

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    Definition Classes
    RecordIterator

  2. abstract val uncompressedBytes: Stream

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    Definition Classes
    RecordIterator

Concrete 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 >: Pos](that: ⇒ GenTraversableOnce[B]): Iterator[B]

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    Definition Classes
    Iterator

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  5. def :\[B](z: B)(op: (Pos, 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 _advance: Option[Pos]

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    Attributes
    protected
    Definition Classes
    PosStreamI → SimpleIterator

  8. def addString(b: StringBuilder): StringBuilder

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    Definition Classes
    TraversableOnce

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

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    Definition Classes
    TraversableOnce

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

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    Definition Classes
    TraversableOnce

  11. def aggregate[B](z: ⇒ B)(seqop: (B, Pos) ⇒ B, combop: (B, B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  12. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  13. def buffered: PosStreamI.this.type

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    Definition Classes
    BufferedIterator → Iterator

  14. def clear(): Unit

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    Definition Classes
    SimpleIterator

  15. def clone(): AnyRef

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

  16. def close(): Unit

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    Definition Classes
    RecordIterator → Closeable → AutoCloseable

  17. def collect[B](pf: PartialFunction[Pos, 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.

  18. def collectFirst[B](pf: PartialFunction[Pos, B]): Option[B]

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    Definition Classes
    TraversableOnce

  19. def contains(elem: Any): Boolean

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  21. def copyToArray[B >: Pos](xs: Array[B]): Unit

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  23. def copyToBuffer[B >: Pos](dest: Buffer[B]): Unit

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    Definition Classes
    TraversableOnce

  24. def corresponds[B](that: GenTraversableOnce[B])(p: (Pos, B) ⇒ Boolean): Boolean

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    Definition Classes
    Iterator

  25. def count(p: (Pos) ⇒ Boolean): Int

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  26. def curBlock: Option[Block]

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    Definition Classes
    RecordIterator

  27. def curPos: Option[Pos]

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    Definition Classes
    RecordIterator

  28. def done(): Unit

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    Attributes
    protected
    Definition Classes
    SimpleIterator

  29. def drop(n: Int): Iterator[Pos]

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    Definition Classes
    Iterator

  30. def dropWhile(p: (Pos) ⇒ Boolean): Iterator[Pos]

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    Definition Classes
    Iterator

  31. def duplicate: (Iterator[Pos], Iterator[Pos])

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    Definition Classes
    Iterator

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

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    Definition Classes
    AnyRef

  33. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  34. def exists(p: (Pos) ⇒ Boolean): Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  35. def filter(p: (Pos) ⇒ Boolean): Iterator[Pos]

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    Definition Classes
    Iterator

  36. def filterNot(p: (Pos) ⇒ Boolean): Iterator[Pos]

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    Definition Classes
    Iterator

  37. def finalize(): Unit

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

  38. def find(p: (Pos) ⇒ Boolean): Option[Pos]

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  39. def flatMap[B](f: (Pos) ⇒ GenTraversableOnce[B]): Iterator[B]

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    Definition Classes
    Iterator

  40. def fold[A1 >: Pos](z: A1)(op: (A1, A1) ⇒ A1): A1

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  41. def foldLeft[B](z: B)(op: (B, Pos) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  42. def foldRight[B](z: B)(op: (Pos, B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  43. def forall(p: (Pos) ⇒ Boolean): Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  44. def foreach[U](f: (Pos) ⇒ U): Unit

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    AnyRef → Any

  46. def grouped[B >: Pos](size: Int): GroupedIterator[B]

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    Definition Classes
    Iterator

  47. def hasDefiniteSize: Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  48. final def hasNext: Boolean

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    Definition Classes
    SimpleIterator → Iterator

  49. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  50. final def head: Pos

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    Definition Classes
    SimpleIterator → BufferedIterator

  51. def indexOf[B >: Pos](elem: B): Int

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    Definition Classes
    Iterator

  52. def indexWhere(p: (Pos) ⇒ Boolean): Int

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    Definition Classes
    Iterator

  53. def isEmpty: Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  54. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  55. def isTraversableAgain: Boolean

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    Definition Classes
    Iterator → GenTraversableOnce

  56. def length: Int

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    Definition Classes
    Iterator

  57. def map[B](f: (Pos) ⇒ B): Iterator[B]

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    Definition Classes
    Iterator

  58. def max[B >: Pos](implicit cmp: Ordering[B]): Pos

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  59. def maxBy[B](f: (Pos) ⇒ B)(implicit cmp: Ordering[B]): Pos

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  60. def min[B >: Pos](implicit cmp: Ordering[B]): Pos

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  61. def minBy[B](f: (Pos) ⇒ B)(implicit cmp: Ordering[B]): Pos

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  62. def mkString: String

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  63. def mkString(sep: String): String

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    AnyRef

  66. final def next(): Pos

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    Definition Classes
    SimpleIterator → Iterator

  67. def nonEmpty: Boolean

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  68. final def notify(): Unit

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    Definition Classes
    AnyRef

  69. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  70. def padTo[A1 >: Pos](len: Int, elem: A1): Iterator[A1]

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    Definition Classes
    Iterator

  71. def partition(p: (Pos) ⇒ Boolean): (Iterator[Pos], Iterator[Pos])

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

  73. def postNext(): Unit

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    Attributes
    protected
    Definition Classes
    SimpleIterator

  74. def product[B >: Pos](implicit num: Numeric[B]): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  75. def reduce[A1 >: Pos](op: (A1, A1) ⇒ A1): A1

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  76. def reduceLeft[B >: Pos](op: (B, Pos) ⇒ B): B

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    Definition Classes
    TraversableOnce

  77. def reduceLeftOption[B >: Pos](op: (B, Pos) ⇒ B): Option[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  78. def reduceOption[A1 >: Pos](op: (A1, A1) ⇒ A1): Option[A1]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  79. def reduceRight[B >: Pos](op: (Pos, B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  80. def reduceRightOption[B >: Pos](op: (Pos, B) ⇒ B): Option[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  81. def reversed: List[Pos]

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    Attributes
    protected[this]
    Definition Classes
    TraversableOnce

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

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    Definition Classes
    Iterator

  83. def scanLeft[B](z: B)(op: (B, Pos) ⇒ B): Iterator[B]

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    Definition Classes
    Iterator

  84. def scanRight[B](z: B)(op: (Pos, B) ⇒ B): Iterator[B]

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    Definition Classes
    Iterator

  85. def seq: Iterator[Pos]

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  86. def size: Int

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  87. def slice(from: Int, until: Int): Iterator[Pos]

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    Definition Classes
    Iterator

  88. def sliding[B >: Pos](size: Int, step: Int): GroupedIterator[B]

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    Definition Classes
    Iterator

  89. def span(p: (Pos) ⇒ Boolean): (Iterator[Pos], Iterator[Pos])

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    Definition Classes
    Iterator

  90. def sum[B >: Pos](implicit num: Numeric[B]): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    AnyRef

  92. def take(n: Int): Iterator[Pos]

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    Definition Classes
    Iterator

  93. def takeWhile(p: (Pos) ⇒ Boolean): Iterator[Pos]

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    Definition Classes
    Iterator

  94. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, Pos, Col[Pos]]): Col[Pos]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  95. def toArray[B >: Pos](implicit arg0: ClassTag[B]): Array[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  96. def toBuffer[B >: Pos]: Buffer[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  97. def toIndexedSeq: IndexedSeq[Pos]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  98. def toIterable: Iterable[Pos]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  99. def toIterator: Iterator[Pos]

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    Definition Classes
    Iterator → GenTraversableOnce

  100. def toList: List[Pos]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  101. def toMap[T, U](implicit ev: <:<[Pos, (T, U)]): Map[T, U]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  102. def toSeq: Seq[Pos]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  103. def toSet[B >: Pos]: Set[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  104. def toStream: Stream[Pos]

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    Definition Classes
    Iterator → GenTraversableOnce

  105. def toString(): String

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    Definition Classes
    SimpleIterator → Iterator → AnyRef → Any

  106. def toTraversable: Traversable[Pos]

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  107. def toVector: Vector[Pos]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  108. val uncompressedByteChannel: ByteChannel

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    Definition Classes
    RecordIterator

  109. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  112. def withFilter(p: (Pos) ⇒ Boolean): Iterator[Pos]

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    Definition Classes
    Iterator

  113. def zip[B](that: Iterator[B]): Iterator[(Pos, B)]

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

  115. def zipWithIndex: Iterator[(Pos, Int)]

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    Definition Classes
    Iterator

Inherited from RecordIterator[Pos, Stream]

Inherited from Closeable

Inherited from AutoCloseable

Inherited from SimpleIterator[Pos]

Inherited from BufferedIterator[Pos]

Inherited from Iterator[Pos]

Inherited from TraversableOnce[Pos]

Inherited from GenTraversableOnce[Pos]

Inherited from AnyRef

Inherited from Any

Ungrouped