Class

org.bdgenomics.adam.util

IntervalListReader

Related Doc: package util

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class IntervalListReader extends Traversable[(ReferenceRegion, String)]

Reads GATK-style interval list files e.g. example file taken from this page: http://www.broadinstitute.org/gatk/guide/article?id=1204

Linear Supertypes
Traversable[(ReferenceRegion, String)], GenTraversable[(ReferenceRegion, String)], GenericTraversableTemplate[(ReferenceRegion, String), Traversable], TraversableLike[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]], GenTraversableLike[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]], Parallelizable[(ReferenceRegion, String), ParIterable[(ReferenceRegion, String)]], TraversableOnce[(ReferenceRegion, String)], GenTraversableOnce[(ReferenceRegion, String)], FilterMonadic[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]], HasNewBuilder[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]], AnyRef, Any
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Inherited
  1. IntervalListReader
  2. Traversable
  3. GenTraversable
  4. GenericTraversableTemplate
  5. TraversableLike
  6. GenTraversableLike
  7. Parallelizable
  8. TraversableOnce
  9. GenTraversableOnce
  10. FilterMonadic
  11. HasNewBuilder
  12. AnyRef
  13. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new IntervalListReader(file: File)

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    file

    a File whose contents are a (line-based tab-separated) interval file in UTF-8 encoding

Type Members

  1. type Self = Traversable[(ReferenceRegion, String)]

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    Attributes
    protected[this]
    Definition Classes
    TraversableLike
  2. 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
    AnyRef → Any
  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any
  3. def ++[B >: (ReferenceRegion, String), That](that: GenTraversableOnce[B])(implicit bf: CanBuildFrom[Traversable[(ReferenceRegion, String)], B, That]): That

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    Definition Classes
    TraversableLike → GenTraversableLike
  4. def ++:[B >: (ReferenceRegion, String), That](that: Traversable[B])(implicit bf: CanBuildFrom[Traversable[(ReferenceRegion, String)], B, That]): That

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    Definition Classes
    TraversableLike
  5. def ++:[B >: (ReferenceRegion, String), That](that: TraversableOnce[B])(implicit bf: CanBuildFrom[Traversable[(ReferenceRegion, String)], B, That]): That

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    Definition Classes
    TraversableLike
  6. def /:[B](z: B)(op: (B, (ReferenceRegion, String)) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  7. def :\[B](z: B)(op: ((ReferenceRegion, String), B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  8. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  9. def addString(b: StringBuilder): StringBuilder

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    Definition Classes
    TraversableOnce
  10. def addString(b: StringBuilder, sep: String): StringBuilder

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    Definition Classes
    TraversableOnce
  11. def addString(b: StringBuilder, start: String, sep: String, end: String): StringBuilder

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    Definition Classes
    TraversableOnce
  12. def aggregate[B](z: ⇒ B)(seqop: (B, (ReferenceRegion, String)) ⇒ B, combop: (B, B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  13. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any
  14. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  15. def collect[B, That](pf: PartialFunction[(ReferenceRegion, String), B])(implicit bf: CanBuildFrom[Traversable[(ReferenceRegion, String)], B, That]): That

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    Definition Classes
    TraversableLike → GenTraversableLike
  16. def collectFirst[B](pf: PartialFunction[(ReferenceRegion, String), B]): Option[B]

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    Definition Classes
    TraversableOnce
  17. def companion: GenericCompanion[Traversable]

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    Definition Classes
    Traversable → GenTraversable → GenericTraversableTemplate
  18. def copyToArray[B >: (ReferenceRegion, String)](xs: Array[B], start: Int, len: Int): Unit

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    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  19. def copyToArray[B >: (ReferenceRegion, String)](xs: Array[B]): Unit

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  20. def copyToArray[B >: (ReferenceRegion, String)](xs: Array[B], start: Int): Unit

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  21. def copyToBuffer[B >: (ReferenceRegion, String)](dest: Buffer[B]): Unit

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    Definition Classes
    TraversableOnce
  22. def count(p: ((ReferenceRegion, String)) ⇒ Boolean): Int

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  23. def drop(n: Int): Traversable[(ReferenceRegion, String)]

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    Definition Classes
    TraversableLike → GenTraversableLike
  24. def dropWhile(p: ((ReferenceRegion, String)) ⇒ Boolean): Traversable[(ReferenceRegion, String)]

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    Definition Classes
    TraversableLike → GenTraversableLike
  25. val encoding: String

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

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    Definition Classes
    AnyRef
  27. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  28. def exists(p: ((ReferenceRegion, String)) ⇒ Boolean): Boolean

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    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  29. def filter(p: ((ReferenceRegion, String)) ⇒ Boolean): Traversable[(ReferenceRegion, String)]

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    Definition Classes
    TraversableLike → GenTraversableLike
  30. def filterNot(p: ((ReferenceRegion, String)) ⇒ Boolean): Traversable[(ReferenceRegion, String)]

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    Definition Classes
    TraversableLike → GenTraversableLike
  31. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  32. def find(p: ((ReferenceRegion, String)) ⇒ Boolean): Option[(ReferenceRegion, String)]

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    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  33. def flatMap[B, That](f: ((ReferenceRegion, String)) ⇒ GenTraversableOnce[B])(implicit bf: CanBuildFrom[Traversable[(ReferenceRegion, String)], B, That]): That

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    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  34. def flatten[B](implicit asTraversable: ((ReferenceRegion, String)) ⇒ GenTraversableOnce[B]): Traversable[B]

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    Definition Classes
    GenericTraversableTemplate
  35. def fold[A1 >: (ReferenceRegion, String)](z: A1)(op: (A1, A1) ⇒ A1): A1

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  36. def foldLeft[B](z: B)(op: (B, (ReferenceRegion, String)) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  37. def foldRight[B](z: B)(op: ((ReferenceRegion, String), B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  38. def forall(p: ((ReferenceRegion, String)) ⇒ Boolean): Boolean

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    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  39. def foreach[U](f: ((ReferenceRegion, String)) ⇒ U): Unit

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    Definition Classes
    IntervalListReader → GenericTraversableTemplate → TraversableLike → GenTraversableLike → TraversableOnce → GenTraversableOnce → FilterMonadic
  40. def genericBuilder[B]: Builder[B, Traversable[B]]

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

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    Definition Classes
    AnyRef → Any
  42. def groupBy[K](f: ((ReferenceRegion, String)) ⇒ K): Map[K, Traversable[(ReferenceRegion, String)]]

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    Definition Classes
    TraversableLike → GenTraversableLike
  43. def hasDefiniteSize: Boolean

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    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  44. def hashCode(): Int

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    Definition Classes
    AnyRef → Any
  45. def head: (ReferenceRegion, String)

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    Definition Classes
    TraversableLike → GenTraversableLike
  46. def headOption: Option[(ReferenceRegion, String)]

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    Definition Classes
    TraversableLike → GenTraversableLike
  47. def init: Traversable[(ReferenceRegion, String)]

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    Definition Classes
    TraversableLike → GenTraversableLike
  48. def inits: Iterator[Traversable[(ReferenceRegion, String)]]

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    Definition Classes
    TraversableLike
  49. def isEmpty: Boolean

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    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  50. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  51. final def isTraversableAgain: Boolean

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    Definition Classes
    TraversableLike → GenTraversableLike → GenTraversableOnce
  52. def last: (ReferenceRegion, String)

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    Definition Classes
    TraversableLike → GenTraversableLike
  53. def lastOption: Option[(ReferenceRegion, String)]

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    Definition Classes
    TraversableLike → GenTraversableLike
  54. def map[B, That](f: ((ReferenceRegion, String)) ⇒ B)(implicit bf: CanBuildFrom[Traversable[(ReferenceRegion, String)], B, That]): That

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    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  55. def max[B >: (ReferenceRegion, String)](implicit cmp: Ordering[B]): (ReferenceRegion, String)

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  56. def maxBy[B](f: ((ReferenceRegion, String)) ⇒ B)(implicit cmp: Ordering[B]): (ReferenceRegion, String)

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  57. def min[B >: (ReferenceRegion, String)](implicit cmp: Ordering[B]): (ReferenceRegion, String)

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  58. def minBy[B](f: ((ReferenceRegion, String)) ⇒ B)(implicit cmp: Ordering[B]): (ReferenceRegion, String)

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  59. def mkString: String

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  60. def mkString(sep: String): String

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  61. def mkString(start: String, sep: String, end: String): String

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  62. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  63. def newBuilder: Builder[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]]

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    Attributes
    protected[this]
    Definition Classes
    GenericTraversableTemplate → HasNewBuilder
  64. def nonEmpty: Boolean

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  65. final def notify(): Unit

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    Definition Classes
    AnyRef
  66. final def notifyAll(): Unit

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    Definition Classes
    AnyRef
  67. def par: ParIterable[(ReferenceRegion, String)]

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    Definition Classes
    Parallelizable
  68. def parCombiner: Combiner[(ReferenceRegion, String), ParIterable[(ReferenceRegion, String)]]

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    Attributes
    protected[this]
    Definition Classes
    TraversableLike → Parallelizable
  69. def partition(p: ((ReferenceRegion, String)) ⇒ Boolean): (Traversable[(ReferenceRegion, String)], Traversable[(ReferenceRegion, String)])

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    Definition Classes
    TraversableLike → GenTraversableLike
  70. def product[B >: (ReferenceRegion, String)](implicit num: Numeric[B]): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  71. def reduce[A1 >: (ReferenceRegion, String)](op: (A1, A1) ⇒ A1): A1

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  72. def reduceLeft[B >: (ReferenceRegion, String)](op: (B, (ReferenceRegion, String)) ⇒ B): B

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    Definition Classes
    TraversableOnce
  73. def reduceLeftOption[B >: (ReferenceRegion, String)](op: (B, (ReferenceRegion, String)) ⇒ B): Option[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  74. def reduceOption[A1 >: (ReferenceRegion, String)](op: (A1, A1) ⇒ A1): Option[A1]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  75. def reduceRight[B >: (ReferenceRegion, String)](op: ((ReferenceRegion, String), B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  76. def reduceRightOption[B >: (ReferenceRegion, String)](op: ((ReferenceRegion, String), B) ⇒ B): Option[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  77. def repr: Traversable[(ReferenceRegion, String)]

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    Definition Classes
    TraversableLike → GenTraversableLike
  78. def reversed: List[(ReferenceRegion, String)]

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    Attributes
    protected[this]
    Definition Classes
    TraversableOnce
  79. def scan[B >: (ReferenceRegion, String), That](z: B)(op: (B, B) ⇒ B)(implicit cbf: CanBuildFrom[Traversable[(ReferenceRegion, String)], B, That]): That

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    Definition Classes
    TraversableLike → GenTraversableLike
  80. def scanLeft[B, That](z: B)(op: (B, (ReferenceRegion, String)) ⇒ B)(implicit bf: CanBuildFrom[Traversable[(ReferenceRegion, String)], B, That]): That

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    Definition Classes
    TraversableLike → GenTraversableLike
  81. def scanRight[B, That](z: B)(op: ((ReferenceRegion, String), B) ⇒ B)(implicit bf: CanBuildFrom[Traversable[(ReferenceRegion, String)], 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.

  82. def seq: Traversable[(ReferenceRegion, String)]

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    Definition Classes
    Traversable → GenTraversable → Parallelizable → TraversableOnce → GenTraversableOnce
  83. lazy val sequenceDictionary: SequenceDictionary

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    The interval list file contains a SAM-style sequence dictionary as a header -- this value holds that dictionary, reading it if necessary (if the file hasn't been opened before).

  84. def size: Int

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  85. def slice(from: Int, until: Int): Traversable[(ReferenceRegion, String)]

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    Definition Classes
    TraversableLike → GenTraversableLike
  86. def span(p: ((ReferenceRegion, String)) ⇒ Boolean): (Traversable[(ReferenceRegion, String)], Traversable[(ReferenceRegion, String)])

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    Definition Classes
    TraversableLike → GenTraversableLike
  87. def splitAt(n: Int): (Traversable[(ReferenceRegion, String)], Traversable[(ReferenceRegion, String)])

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    Definition Classes
    TraversableLike → GenTraversableLike
  88. def stringPrefix: String

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    Definition Classes
    TraversableLike → GenTraversableLike
  89. def sum[B >: (ReferenceRegion, String)](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 tail: Traversable[(ReferenceRegion, String)]

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    Definition Classes
    TraversableLike → GenTraversableLike
  92. def tails: Iterator[Traversable[(ReferenceRegion, String)]]

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    Definition Classes
    TraversableLike
  93. def take(n: Int): Traversable[(ReferenceRegion, String)]

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    Definition Classes
    TraversableLike → GenTraversableLike
  94. def takeWhile(p: ((ReferenceRegion, String)) ⇒ Boolean): Traversable[(ReferenceRegion, String)]

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    Definition Classes
    TraversableLike → GenTraversableLike
  95. def thisCollection: Traversable[(ReferenceRegion, String)]

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    Attributes
    protected[this]
    Definition Classes
    TraversableLike
  96. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, (ReferenceRegion, String), Col[(ReferenceRegion, String)]]): Col[(ReferenceRegion, String)]

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    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  97. def toArray[B >: (ReferenceRegion, String)](implicit arg0: ClassTag[B]): Array[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  98. def toBuffer[B >: (ReferenceRegion, String)]: Buffer[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  99. def toCollection(repr: Traversable[(ReferenceRegion, String)]): Traversable[(ReferenceRegion, String)]

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    Attributes
    protected[this]
    Definition Classes
    TraversableLike
  100. def toIndexedSeq: IndexedSeq[(ReferenceRegion, String)]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  101. def toIterable: Iterable[(ReferenceRegion, String)]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  102. def toIterator: Iterator[(ReferenceRegion, String)]

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    Definition Classes
    TraversableLike → GenTraversableOnce
  103. def toList: List[(ReferenceRegion, String)]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  104. def toMap[T, U](implicit ev: <:<[(ReferenceRegion, String), (T, U)]): Map[T, U]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  105. def toSeq: Seq[(ReferenceRegion, String)]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  106. def toSet[B >: (ReferenceRegion, String)]: Set[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  107. def toStream: Stream[(ReferenceRegion, String)]

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    Definition Classes
    TraversableLike → GenTraversableOnce
  108. def toString(): String

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    Definition Classes
    TraversableLike → Any
  109. def toTraversable: Traversable[(ReferenceRegion, String)]

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    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  110. def toVector: Vector[(ReferenceRegion, String)]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  111. def transpose[B](implicit asTraversable: ((ReferenceRegion, String)) ⇒ GenTraversableOnce[B]): Traversable[Traversable[B]]

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    Definition Classes
    GenericTraversableTemplate
    Annotations
    @migration
    Migration

    (Changed in version 2.9.0) transpose throws an IllegalArgumentException if collections are not uniformly sized.

  112. def unzip[A1, A2](implicit asPair: ((ReferenceRegion, String)) ⇒ (A1, A2)): (Traversable[A1], Traversable[A2])

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    Definition Classes
    GenericTraversableTemplate
  113. def unzip3[A1, A2, A3](implicit asTriple: ((ReferenceRegion, String)) ⇒ (A1, A2, A3)): (Traversable[A1], Traversable[A2], Traversable[A3])

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    Definition Classes
    GenericTraversableTemplate
  114. def view(from: Int, until: Int): TraversableView[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]]

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    Definition Classes
    TraversableLike
  115. def view: TraversableView[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]]

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    Definition Classes
    TraversableLike
  116. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  117. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  118. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  119. def withFilter(p: ((ReferenceRegion, String)) ⇒ Boolean): FilterMonadic[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]]

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    Definition Classes
    TraversableLike → FilterMonadic

Inherited from Traversable[(ReferenceRegion, String)]

Inherited from GenTraversable[(ReferenceRegion, String)]

Inherited from GenericTraversableTemplate[(ReferenceRegion, String), Traversable]

Inherited from TraversableLike[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]]

Inherited from GenTraversableLike[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]]

Inherited from Parallelizable[(ReferenceRegion, String), ParIterable[(ReferenceRegion, String)]]

Inherited from TraversableOnce[(ReferenceRegion, String)]

Inherited from GenTraversableOnce[(ReferenceRegion, String)]

Inherited from FilterMonadic[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]]

Inherited from HasNewBuilder[(ReferenceRegion, String), Traversable[(ReferenceRegion, String)]]

Inherited from AnyRef

Inherited from Any

Ungrouped