Class

nl.biopet.tools.mergesv

MultiReader

Related Doc: package mergesv

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class MultiReader extends Iterator[SvCall] with AutoCloseable

Linear Supertypes
AutoCloseable, Iterator[SvCall], TraversableOnce[SvCall], GenTraversableOnce[SvCall], AnyRef, Any
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Inherited
  1. MultiReader
  2. AutoCloseable
  3. Iterator
  4. TraversableOnce
  5. GenTraversableOnce
  6. AnyRef
  7. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new MultiReader(init: Init, contig: SAMSequenceRecord, defaultCi: Int, keepNonVariants: Boolean, callerFields: Map[String, Set[String]])

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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 >: SvCall](that: ⇒ GenTraversableOnce[B]): Iterator[B]

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    Definition Classes
    Iterator

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  5. def :\[B](z: B)(op: (SvCall, 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. var _total: Long

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  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, SvCall) ⇒ 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: BufferedIterator[SvCall]

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    Definition Classes
    Iterator

  14. val buffers: Map[String, Array[BufferedIterator[VariantContext]]]

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    Attributes
    protected

  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
    MultiReader → AutoCloseable

  17. def collect[B](pf: PartialFunction[SvCall, 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[SvCall, 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 >: SvCall](xs: Array[B], start: Int, len: Int): Unit

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce

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

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    Definition Classes
    Iterator

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  26. def drop(n: Int): Iterator[SvCall]

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    Definition Classes
    Iterator

  27. def dropWhile(p: (SvCall) ⇒ Boolean): Iterator[SvCall]

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    Definition Classes
    Iterator

  28. def duplicate: (Iterator[SvCall], Iterator[SvCall])

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    Definition Classes
    Iterator

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

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    Definition Classes
    AnyRef

  30. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  31. def exists(p: (SvCall) ⇒ Boolean): Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  32. def filter(p: (SvCall) ⇒ Boolean): Iterator[SvCall]

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    Definition Classes
    Iterator

  33. def filterNot(p: (SvCall) ⇒ Boolean): Iterator[SvCall]

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    Definition Classes
    Iterator

  34. def finalize(): Unit

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

  35. def find(p: (SvCall) ⇒ Boolean): Option[SvCall]

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  36. def flatMap[B](f: (SvCall) ⇒ GenTraversableOnce[B]): Iterator[B]

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    Definition Classes
    Iterator

  37. def fold[A1 >: SvCall](z: A1)(op: (A1, A1) ⇒ A1): A1

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  38. def foldLeft[B](z: B)(op: (B, SvCall) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  39. def foldRight[B](z: B)(op: (SvCall, B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  40. def forall(p: (SvCall) ⇒ Boolean): Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  41. def foreach[U](f: (SvCall) ⇒ U): Unit

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    AnyRef → Any

  43. def grouped[B >: SvCall](size: Int): GroupedIterator[B]

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    Definition Classes
    Iterator

  44. def hasDefiniteSize: Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  45. def hasNext: Boolean

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    Definition Classes
    MultiReader → Iterator

  46. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  47. def headOption: Option[SvCall]

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  48. def indexOf[B >: SvCall](elem: B): Int

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    Definition Classes
    Iterator

  49. def indexWhere(p: (SvCall) ⇒ Boolean): Int

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    Definition Classes
    Iterator

  50. def isEmpty: Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  51. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  52. def isTraversableAgain: Boolean

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    Definition Classes
    Iterator → GenTraversableOnce

  53. val its: Map[String, List[CloseableIterator[VariantContext]]]

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    Attributes
    protected

  54. def length: Int

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    Definition Classes
    Iterator

  55. def map[B](f: (SvCall) ⇒ B): Iterator[B]

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    Definition Classes
    Iterator

  56. def max[B >: SvCall](implicit cmp: Ordering[B]): SvCall

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  57. def maxBy[B](f: (SvCall) ⇒ B)(implicit cmp: Ordering[B]): SvCall

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  58. def min[B >: SvCall](implicit cmp: Ordering[B]): SvCall

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  59. def minBy[B](f: (SvCall) ⇒ B)(implicit cmp: Ordering[B]): SvCall

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  60. def mkString: String

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  61. def mkString(sep: String): String

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    AnyRef

  64. def next(): SvCall

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    Definition Classes
    MultiReader → Iterator

  65. def nonEmpty: Boolean

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  66. final def notify(): Unit

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    Definition Classes
    AnyRef

  67. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  68. def padTo[A1 >: SvCall](len: Int, elem: A1): Iterator[A1]

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    Definition Classes
    Iterator

  69. def partition(p: (SvCall) ⇒ Boolean): (Iterator[SvCall], Iterator[SvCall])

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  78. def reversed: List[SvCall]

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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, SvCall) ⇒ B): Iterator[B]

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

  82. def seq: Iterator[SvCall]

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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[SvCall]

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

  87. def sum[B >: SvCall](implicit num: Numeric[B]): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    AnyRef

  89. def take(n: Int): Iterator[SvCall]

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    Definition Classes
    Iterator

  90. def takeWhile(p: (SvCall) ⇒ Boolean): Iterator[SvCall]

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    Definition Classes
    Iterator

  91. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, SvCall, Col[SvCall]]): Col[SvCall]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  92. def toArray[B >: SvCall](implicit arg0: ClassTag[B]): Array[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  93. def toBuffer[B >: SvCall]: Buffer[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  94. def toIndexedSeq: IndexedSeq[SvCall]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  95. def toIterable: Iterable[SvCall]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  96. def toIterator: Iterator[SvCall]

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    Definition Classes
    Iterator → GenTraversableOnce

  97. def toList: List[SvCall]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  98. def toMap[T, U](implicit ev: <:<[SvCall, (T, U)]): Map[T, U]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  99. def toSeq: Seq[SvCall]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  100. def toSet[B >: SvCall]: Set[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  101. def toStream: Stream[SvCall]

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    Definition Classes
    Iterator → GenTraversableOnce

  102. def toString(): String

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    Definition Classes
    Iterator → AnyRef → Any

  103. def toTraversable: Traversable[SvCall]

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  104. def toVector: Vector[SvCall]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  105. def total: Long

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  106. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  109. def withFilter(p: (SvCall) ⇒ Boolean): Iterator[SvCall]

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    Definition Classes
    Iterator

  110. def zip[B](that: Iterator[B]): Iterator[(SvCall, B)]

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

  112. def zipWithIndex: Iterator[(SvCall, Int)]

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    Definition Classes
    Iterator

Inherited from AutoCloseable

Inherited from Iterator[SvCall]

Inherited from TraversableOnce[SvCall]

Inherited from GenTraversableOnce[SvCall]

Inherited from AnyRef

Inherited from Any

Ungrouped