Class

bio

PhylipReader

Related Doc: package bio

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class PhylipReader extends Iterator[(String, String)]

PhylipReader opens a file and parses the Phylip contents using an iterator. This implementation is not ready - it may use the BioJava PHYLIPFileListener as below, but one problem is that ID names are restricted to 9 characters.

Note: this is a hack. I am trying to get to grips with the BioJava way of doing this - and it does not map easily to an iterator.

Linear Supertypes
Iterator[(String, String)], TraversableOnce[(String, String)], GenTraversableOnce[(String, String)], AnyRef, Any
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Inherited
  1. PhylipReader
  2. Iterator
  3. TraversableOnce
  4. GenTraversableOnce
  5. AnyRef
  6. Any
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Visibility
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Instance Constructors

  1. new PhylipReader(filename: 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

  2. class PhylipReaderException extends Exception

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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 >: (String, String)](that: ⇒ GenTraversableOnce[B]): Iterator[B]

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    Definition Classes
    Iterator

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  5. def :\[B](z: B)(op: ((String, String), 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. object PhylipListener

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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, (String, String)) ⇒ 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[(String, String)]

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    Definition Classes
    Iterator

  14. def clone(): AnyRef

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

  15. def collect[B](pf: PartialFunction[(String, String), 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[(String, String), B]): Option[B]

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    Definition Classes
    TraversableOnce

  17. def contains(elem: Any): Boolean

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  19. def copyToArray[B >: (String, String)](xs: Array[B]): Unit

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  21. def copyToBuffer[B >: (String, String)](dest: Buffer[B]): Unit

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    Definition Classes
    TraversableOnce

  22. def corresponds[B](that: GenTraversableOnce[B])(p: ((String, String), B) ⇒ Boolean): Boolean

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    Definition Classes
    Iterator

  23. def count(p: ((String, String)) ⇒ Boolean): Int

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  24. def drop(n: Int): Iterator[(String, String)]

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    Definition Classes
    Iterator

  25. def dropWhile(p: ((String, String)) ⇒ Boolean): Iterator[(String, String)]

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    Definition Classes
    Iterator

  26. def duplicate: (Iterator[(String, String)], Iterator[(String, String)])

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    Definition Classes
    Iterator

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

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    Definition Classes
    AnyRef

  28. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  29. def exists(p: ((String, String)) ⇒ Boolean): Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  30. val filename: String

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

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

  33. def finalize(): Unit

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

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

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    Iterator

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  39. def forall(p: ((String, String)) ⇒ Boolean): Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  40. def foreach[U](f: ((String, String)) ⇒ 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 >: (String, String)](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
    PhylipReader → Iterator

  45. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  46. var id_list: List[String]

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  47. def indexOf[B >: (String, String)](elem: B): Int

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    Definition Classes
    Iterator

  48. def indexWhere(p: ((String, String)) ⇒ Boolean): Int

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    Definition Classes
    Iterator

  49. def isEmpty: Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  50. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  51. def isTraversableAgain: Boolean

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    Definition Classes
    Iterator → GenTraversableOnce

  52. def length: Int

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    Definition Classes
    Iterator

  53. val list: List[(String, String)]

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  54. lazy val listener: PhylipListener.type

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

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    Definition Classes
    Iterator

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  60. def mkString: String

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    TraversableOnce → GenTraversableOnce

  61. def mkString(sep: String): String

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    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(): (String, String)

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    Definition Classes
    PhylipReader → 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 >: (String, String)](len: Int, elem: A1): Iterator[A1]

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

  71. var pos: Int

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  72. def product[B >: (String, String)](implicit num: Numeric[B]): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  73. def reduce[A1 >: (String, String)](op: (A1, A1) ⇒ A1): A1

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  74. def reduceLeft[B >: (String, String)](op: (B, (String, String)) ⇒ B): B

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    Definition Classes
    TraversableOnce

  75. def reduceLeftOption[B >: (String, String)](op: (B, (String, String)) ⇒ B): Option[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  76. def reduceOption[A1 >: (String, String)](op: (A1, A1) ⇒ A1): Option[A1]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  77. def reduceRight[B >: (String, String)](op: ((String, String), B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  78. def reduceRightOption[B >: (String, String)](op: ((String, String), B) ⇒ B): Option[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  79. def reversed: List[(String, String)]

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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, (String, String)) ⇒ B): Iterator[B]

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    Definition Classes
    Iterator

  82. def scanRight[B](z: B)(op: ((String, String), B) ⇒ B): Iterator[B]

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    Definition Classes
    Iterator

  83. def seq: Iterator[(String, String)]

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    Iterator → TraversableOnce → GenTraversableOnce

  84. var seq_list: List[String]

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  85. def size: Int

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  86. def slice(from: Int, until: Int): Iterator[(String, String)]

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

  88. def span(p: ((String, String)) ⇒ Boolean): (Iterator[(String, String)], Iterator[(String, String)])

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    Definition Classes
    Iterator

  89. def sum[B >: (String, 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 take(n: Int): Iterator[(String, String)]

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  95. def toBuffer[B >: (String, String)]: Buffer[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  96. def toIndexedSeq: IndexedSeq[(String, String)]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  97. def toIterable: Iterable[(String, String)]

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    TraversableOnce → GenTraversableOnce

  98. def toIterator: Iterator[(String, String)]

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    Definition Classes
    Iterator → GenTraversableOnce

  99. def toList: List[(String, String)]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  101. def toSeq: Seq[(String, String)]

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    TraversableOnce → GenTraversableOnce

  102. def toSet[B >: (String, String)]: Set[B]

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    TraversableOnce → GenTraversableOnce

  103. def toStream: Stream[(String, String)]

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    Iterator → GenTraversableOnce

  104. def toString(): String

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    Definition Classes
    Iterator → AnyRef → Any

  105. def toTraversable: Traversable[(String, String)]

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce

  106. def toVector: Vector[(String, String)]

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    Definition Classes
    TraversableOnce → GenTraversableOnce

  107. final def wait(): Unit

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    Annotations
    @throws( ... )

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

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    @throws( ... )

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

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    Annotations
    @throws( ... )

  110. def withFilter(p: ((String, String)) ⇒ Boolean): Iterator[(String, String)]

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    Definition Classes
    Iterator

  111. def zip[B](that: Iterator[B]): Iterator[((String, String), B)]

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    Definition Classes
    Iterator

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

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    Definition Classes
    Iterator

  113. def zipWithIndex: Iterator[((String, String), Int)]

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    Definition Classes
    Iterator

Inherited from Iterator[(String, String)]

Inherited from TraversableOnce[(String, String)]

Inherited from GenTraversableOnce[(String, String)]

Inherited from AnyRef

Inherited from Any

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