Class/Object

org.hammerlab.genomics.reference

ContigsIterator

Related Docs: object ContigsIterator | package reference

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class ContigsIterator[T] extends hammerlab.iterator.SimpleIterator[(ContigName, ContigIterator[T])]

Divide an iterator into a series of contig-restricted iterators.

Takes an iterator of arbitrary elements and a function for extracting a ContigName from them.

Emits ContigIterator) tuples.

See companion object for public constructors.

Linear Supertypes
SimpleIterator[(ContigName, ContigIterator[T])], BufferedIterator[(ContigName, ContigIterator[T])], Iterator[(ContigName, ContigIterator[T])], TraversableOnce[(ContigName, ContigIterator[T])], GenTraversableOnce[(ContigName, ContigIterator[T])], AnyRef, Any
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Inherited
  1. ContigsIterator
  2. SimpleIterator
  3. BufferedIterator
  4. Iterator
  5. TraversableOnce
  6. GenTraversableOnce
  7. AnyRef
  8. Any
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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 >: (ContigName, ContigIterator[T])](that: ⇒ GenTraversableOnce[B]): Iterator[B]

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    Definition Classes
    Iterator

  4. def /:[B](z: B)(op: (B, (ContigName, ContigIterator[T])) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  5. def :\[B](z: B)(op: ((ContigName, ContigIterator[T]), 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[(ContigName, ContigIterator[T])]

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    Definition Classes
    ContigsIterator → 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, (ContigName, ContigIterator[T])) ⇒ 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: ContigsIterator.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 collect[B](pf: PartialFunction[(ContigName, ContigIterator[T]), 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.

  17. def collectFirst[B](pf: PartialFunction[(ContigName, ContigIterator[T]), B]): Option[B]

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    Definition Classes
    TraversableOnce

  18. def contains(elem: Any): Boolean

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    Definition Classes
    Iterator

  19. var contigRegions: ContigIterator[T]

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

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  21. def copyToArray[B >: (ContigName, ContigIterator[T])](xs: Array[B]): Unit

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  23. def copyToBuffer[B >: (ContigName, ContigIterator[T])](dest: Buffer[B]): Unit

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    Definition Classes
    TraversableOnce

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

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    Definition Classes
    Iterator

  25. def count(p: ((ContigName, ContigIterator[T])) ⇒ Boolean): Int

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  26. def done(): Unit

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    Attributes
    protected
    Definition Classes
    SimpleIterator

  27. def drop(n: Int): Iterator[(ContigName, ContigIterator[T])]

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    Definition Classes
    Iterator

  28. def dropWhile(p: ((ContigName, ContigIterator[T])) ⇒ Boolean): Iterator[(ContigName, ContigIterator[T])]

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    Definition Classes
    Iterator

  29. def duplicate: (Iterator[(ContigName, ContigIterator[T])], Iterator[(ContigName, ContigIterator[T])])

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    Definition Classes
    Iterator

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

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    Definition Classes
    AnyRef

  31. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  32. def exists(p: ((ContigName, ContigIterator[T])) ⇒ Boolean): Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  33. def filter(p: ((ContigName, ContigIterator[T])) ⇒ Boolean): Iterator[(ContigName, ContigIterator[T])]

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    Definition Classes
    Iterator

  34. def filterNot(p: ((ContigName, ContigIterator[T])) ⇒ Boolean): Iterator[(ContigName, ContigIterator[T])]

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    Definition Classes
    Iterator

  35. def finalize(): Unit

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

  36. def find(p: ((ContigName, ContigIterator[T])) ⇒ Boolean): Option[(ContigName, ContigIterator[T])]

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  37. def flatMap[B](f: ((ContigName, ContigIterator[T])) ⇒ GenTraversableOnce[B]): Iterator[B]

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    Definition Classes
    Iterator

  38. def fold[A1 >: (ContigName, ContigIterator[T])](z: A1)(op: (A1, A1) ⇒ A1): A1

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  39. def foldLeft[B](z: B)(op: (B, (ContigName, ContigIterator[T])) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  40. def foldRight[B](z: B)(op: ((ContigName, ContigIterator[T]), B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  41. def forall(p: ((ContigName, ContigIterator[T])) ⇒ Boolean): Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  42. def foreach[U](f: ((ContigName, ContigIterator[T])) ⇒ U): Unit

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    AnyRef → Any

  44. def grouped[B >: (ContigName, ContigIterator[T])](size: Int): GroupedIterator[B]

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    Definition Classes
    Iterator

  45. def hasDefiniteSize: Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  46. final def hasNext: Boolean

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    Definition Classes
    SimpleIterator → Iterator

  47. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  48. final def head: (ContigName, ContigIterator[T])

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    Definition Classes
    SimpleIterator → BufferedIterator

  49. def indexOf[B >: (ContigName, ContigIterator[T])](elem: B): Int

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    Definition Classes
    Iterator

  50. def indexWhere(p: ((ContigName, ContigIterator[T])) ⇒ Boolean): Int

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    Definition Classes
    Iterator

  51. def isEmpty: Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  52. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  53. def isTraversableAgain: Boolean

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    Definition Classes
    Iterator → GenTraversableOnce

  54. def length: Int

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    Definition Classes
    Iterator

  55. def map[B](f: ((ContigName, ContigIterator[T])) ⇒ B): Iterator[B]

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    Definition Classes
    Iterator

  56. def max[B >: (ContigName, ContigIterator[T])](implicit cmp: Ordering[B]): (ContigName, ContigIterator[T])

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  57. def maxBy[B](f: ((ContigName, ContigIterator[T])) ⇒ B)(implicit cmp: Ordering[B]): (ContigName, ContigIterator[T])

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  58. def min[B >: (ContigName, ContigIterator[T])](implicit cmp: Ordering[B]): (ContigName, ContigIterator[T])

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  59. def minBy[B](f: ((ContigName, ContigIterator[T])) ⇒ B)(implicit cmp: Ordering[B]): (ContigName, ContigIterator[T])

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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. final def next(): (ContigName, ContigIterator[T])

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    Definition Classes
    SimpleIterator → 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 >: (ContigName, ContigIterator[T])](len: Int, elem: A1): Iterator[A1]

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    Definition Classes
    Iterator

  69. def partition(p: ((ContigName, ContigIterator[T])) ⇒ Boolean): (Iterator[(ContigName, ContigIterator[T])], Iterator[(ContigName, ContigIterator[T])])

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

  71. def postNext(): Unit

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    Attributes
    protected
    Definition Classes
    SimpleIterator

  72. def product[B >: (ContigName, ContigIterator[T])](implicit num: Numeric[B]): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  73. def reduce[A1 >: (ContigName, ContigIterator[T])](op: (A1, A1) ⇒ A1): A1

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  74. def reduceLeft[B >: (ContigName, ContigIterator[T])](op: (B, (ContigName, ContigIterator[T])) ⇒ B): B

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    Definition Classes
    TraversableOnce

  75. def reduceLeftOption[B >: (ContigName, ContigIterator[T])](op: (B, (ContigName, ContigIterator[T])) ⇒ B): Option[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  76. def reduceOption[A1 >: (ContigName, ContigIterator[T])](op: (A1, A1) ⇒ A1): Option[A1]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  77. def reduceRight[B >: (ContigName, ContigIterator[T])](op: ((ContigName, ContigIterator[T]), B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  78. def reduceRightOption[B >: (ContigName, ContigIterator[T])](op: ((ContigName, ContigIterator[T]), B) ⇒ B): Option[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  79. def reversed: List[(ContigName, ContigIterator[T])]

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    Attributes
    protected[this]
    Definition Classes
    TraversableOnce

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

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    Definition Classes
    Iterator

  81. def scanLeft[B](z: B)(op: (B, (ContigName, ContigIterator[T])) ⇒ B): Iterator[B]

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    Definition Classes
    Iterator

  82. def scanRight[B](z: B)(op: ((ContigName, ContigIterator[T]), B) ⇒ B): Iterator[B]

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    Definition Classes
    Iterator

  83. val seenContigs: Set[ContigName]

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  84. def seq: Iterator[(ContigName, ContigIterator[T])]

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  85. def size: Int

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  86. def slice(from: Int, until: Int): Iterator[(ContigName, ContigIterator[T])]

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    Definition Classes
    Iterator

  87. def sliding[B >: (ContigName, ContigIterator[T])](size: Int, step: Int): GroupedIterator[B]

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    Definition Classes
    Iterator

  88. def span(p: ((ContigName, ContigIterator[T])) ⇒ Boolean): (Iterator[(ContigName, ContigIterator[T])], Iterator[(ContigName, ContigIterator[T])])

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    Definition Classes
    Iterator

  89. def sum[B >: (ContigName, ContigIterator[T])](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[(ContigName, ContigIterator[T])]

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    Definition Classes
    Iterator

  92. def takeWhile(p: ((ContigName, ContigIterator[T])) ⇒ Boolean): Iterator[(ContigName, ContigIterator[T])]

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    Definition Classes
    Iterator

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  94. def toArray[B >: (ContigName, ContigIterator[T])](implicit arg0: ClassTag[B]): Array[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  95. def toBuffer[B >: (ContigName, ContigIterator[T])]: Buffer[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  96. def toIndexedSeq: IndexedSeq[(ContigName, ContigIterator[T])]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  97. def toIterable: Iterable[(ContigName, ContigIterator[T])]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  98. def toIterator: Iterator[(ContigName, ContigIterator[T])]

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    Definition Classes
    Iterator → GenTraversableOnce

  99. def toList: List[(ContigName, ContigIterator[T])]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  101. def toSeq: Seq[(ContigName, ContigIterator[T])]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  102. def toSet[B >: (ContigName, ContigIterator[T])]: Set[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  103. def toStream: Stream[(ContigName, ContigIterator[T])]

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    Definition Classes
    Iterator → GenTraversableOnce

  104. def toString(): String

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    Definition Classes
    SimpleIterator → Iterator → AnyRef → Any

  105. def toTraversable: Traversable[(ContigName, ContigIterator[T])]

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  106. def toVector: Vector[(ContigName, ContigIterator[T])]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  107. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  110. def withFilter(p: ((ContigName, ContigIterator[T])) ⇒ Boolean): Iterator[(ContigName, ContigIterator[T])]

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    Definition Classes
    Iterator

  111. def zip[B](that: Iterator[B]): Iterator[((ContigName, ContigIterator[T]), B)]

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    Definition Classes
    Iterator

  112. def zipAll[B, A1 >: (ContigName, ContigIterator[T]), B1 >: B](that: Iterator[B], thisElem: A1, thatElem: B1): Iterator[(A1, B1)]

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    Definition Classes
    Iterator

  113. def zipWithIndex: Iterator[((ContigName, ContigIterator[T]), Int)]

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    Definition Classes
    Iterator

Inherited from SimpleIterator[(ContigName, ContigIterator[T])]

Inherited from BufferedIterator[(ContigName, ContigIterator[T])]

Inherited from Iterator[(ContigName, ContigIterator[T])]

Inherited from TraversableOnce[(ContigName, ContigIterator[T])]

Inherited from GenTraversableOnce[(ContigName, ContigIterator[T])]

Inherited from AnyRef

Inherited from Any

Ungrouped