Class/Object

com.fulcrumgenomics.commons.util

DelimitedDataParser

Related Docs: object DelimitedDataParser | package util

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class DelimitedDataParser extends Iterator[Row] with LazyLogging

A parser for files of text columns delimited by some character (e.g. tab-delimited or csv).

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Inherited
  1. DelimitedDataParser
  2. LazyLogging
  3. Iterator
  4. TraversableOnce
  5. GenTraversableOnce
  6. AnyRef
  7. Any
Implicitly
  1. by MonadOps
  2. by any2stringadd
  3. by StringFormat
  4. by Ensuring
  5. by ArrowAssoc
  6. by alternateImplicit
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new DelimitedDataParser(lines: TraversableOnce[String], delimiter: Char, ignoreBlankLines: Boolean = ..., trimFields: Boolean = DelimitedDataParser.DefaultTrim)

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    lines

    the lines from the file

    delimiter

    the delimiter between columns

    ignoreBlankLines

    whether blank lines should be ignored

    trimFields

    whether individual fields should have their String values trimmed

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 +(other: String): String

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    Implicit information
    This member is added by an implicit conversion from DelimitedDataParser to any2stringadd[DelimitedDataParser] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ++[B >: Row](that: ⇒ GenTraversableOnce[B]): Iterator[B]

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    Definition Classes
    Iterator
  5. def ->[B](y: B): (DelimitedDataParser, B)

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    Implicit information
    This member is added by an implicit conversion from DelimitedDataParser to ArrowAssoc[DelimitedDataParser] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  6. def /:[B](z: B)(op: (B, Row) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  7. def :\[B](z: B)(op: (Row, 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, Row) ⇒ 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 buffered: BufferedIterator[Row]

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    Definition Classes
    Iterator
  15. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  16. def collect[B](pf: PartialFunction[Row, 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[Row, B]): Option[B]

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    Definition Classes
    TraversableOnce
  18. def contains(elem: Any): Boolean

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    Definition Classes
    Iterator
  19. def copyToArray[B >: Row](xs: Array[B], start: Int, len: Int): Unit

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  20. def copyToArray[B >: Row](xs: Array[B]): Unit

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  22. def copyToBuffer[B >: Row](dest: Buffer[B]): Unit

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    Definition Classes
    TraversableOnce
  23. def corresponds[B](that: GenTraversableOnce[B])(p: (Row, B) ⇒ Boolean): Boolean

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    Definition Classes
    Iterator
  24. def count(p: (Row) ⇒ Boolean): Int

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  25. val delimiter: Char

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    the delimiter between columns

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

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    Definition Classes
    Iterator
  27. def dropWhile(p: (Row) ⇒ Boolean): Iterator[Row]

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    Definition Classes
    Iterator
  28. def duplicate: (Iterator[Row], Iterator[Row])

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    Definition Classes
    Iterator
  29. def ensuring(cond: (DelimitedDataParser) ⇒ Boolean, msg: ⇒ Any): DelimitedDataParser

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    Implicit information
    This member is added by an implicit conversion from DelimitedDataParser to Ensuring[DelimitedDataParser] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  30. def ensuring(cond: (DelimitedDataParser) ⇒ Boolean): DelimitedDataParser

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    Implicit information
    This member is added by an implicit conversion from DelimitedDataParser to Ensuring[DelimitedDataParser] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  31. def ensuring(cond: Boolean, msg: ⇒ Any): DelimitedDataParser

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    Implicit information
    This member is added by an implicit conversion from DelimitedDataParser to Ensuring[DelimitedDataParser] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  32. def ensuring(cond: Boolean): DelimitedDataParser

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    Implicit information
    This member is added by an implicit conversion from DelimitedDataParser to Ensuring[DelimitedDataParser] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  33. final def eq(arg0: AnyRef): Boolean

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

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    Definition Classes
    AnyRef → Any
  35. def exists(p: (Row) ⇒ Boolean): Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  36. def filter(p: (Row) ⇒ Boolean): Iterator[Row]

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    Definition Classes
    Iterator
  37. def filterNot(p: (Row) ⇒ Boolean): Iterator[Row]

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    Definition Classes
    Iterator
  38. def finalize(): Unit

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

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  40. def flatMap[B](f: (Row) ⇒ GenTraversableOnce[B]): Iterator[B]

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    Definition Classes
    Iterator
  41. def fold[A1 >: Row](z: A1)(op: (A1, A1) ⇒ A1): A1

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  42. def foldLeft[B](z: B)(op: (B, Row) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  43. def foldRight[B](z: B)(op: (Row, B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  44. def forall(p: (Row) ⇒ Boolean): Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  45. def foreach[U](f: (Row) ⇒ U): Unit

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  46. def formatted(fmtstr: String): String

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    Implicit information
    This member is added by an implicit conversion from DelimitedDataParser to StringFormat[DelimitedDataParser] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  47. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any
  48. def grouped[B >: Row](size: Int): GroupedIterator[B]

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    Definition Classes
    Iterator
  49. def hasDefiniteSize: Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  50. def hasNext: Boolean

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    True if there is another line available for parsing.

    True if there is another line available for parsing.

    Definition Classes
    DelimitedDataParser → Iterator
  51. def hashCode(): Int

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    Definition Classes
    AnyRef → Any
  52. def headers: Seq[String]

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    Returns the headers encountered in the file, in order.

  53. val ignoreBlankLines: Boolean

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    whether blank lines should be ignored

  54. def indexOf[B >: Row](elem: B): Int

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    Definition Classes
    Iterator
  55. def indexWhere(p: (Row) ⇒ Boolean): Int

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    Definition Classes
    Iterator
  56. def isEmpty: Boolean

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  57. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  58. def isTraversableAgain: Boolean

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    Definition Classes
    Iterator → GenTraversableOnce
  59. def length: Int

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    Definition Classes
    Iterator
  60. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging
  61. def map[B](f: (Row) ⇒ B): Iterator[B]

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    Definition Classes
    Iterator
  62. def max[B >: Row](implicit cmp: Ordering[B]): Row

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  63. def maxBy[B](f: (Row) ⇒ B)(implicit cmp: Ordering[B]): Row

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  64. def min[B >: Row](implicit cmp: Ordering[B]): Row

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  65. def minBy[B](f: (Row) ⇒ B)(implicit cmp: Ordering[B]): Row

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  66. def mkString: String

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

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

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

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    Definition Classes
    AnyRef
  70. def next(): Row

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    Retrieves the next row.

    Retrieves the next row.

    Definition Classes
    DelimitedDataParser → Iterator
  71. def nonEmpty: Boolean

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

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

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    Definition Classes
    AnyRef
  74. def padTo[A1 >: Row](len: Int, elem: A1): Iterator[A1]

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    Definition Classes
    Iterator
  75. def partition(p: (Row) ⇒ Boolean): (Iterator[Row], Iterator[Row])

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    Definition Classes
    Iterator
  76. def patch[B >: Row](from: Int, patchElems: Iterator[B], replaced: Int): Iterator[B]

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    Definition Classes
    Iterator
  77. def product[B >: Row](implicit num: Numeric[B]): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  78. def reduce[A1 >: Row](op: (A1, A1) ⇒ A1): A1

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  79. def reduceLeft[B >: Row](op: (B, Row) ⇒ B): B

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    Definition Classes
    TraversableOnce
  80. def reduceLeftOption[B >: Row](op: (B, Row) ⇒ B): Option[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  81. def reduceOption[A1 >: Row](op: (A1, A1) ⇒ A1): Option[A1]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  82. def reduceRight[B >: Row](op: (Row, B) ⇒ B): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  83. def reduceRightOption[B >: Row](op: (Row, B) ⇒ B): Option[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  84. def reversed: List[Row]

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    Attributes
    protected[this]
    Definition Classes
    TraversableOnce
  85. def sameElements(that: Iterator[_]): Boolean

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    Definition Classes
    Iterator
  86. def scanLeft[B](z: B)(op: (B, Row) ⇒ B): Iterator[B]

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    Definition Classes
    Iterator
  87. def scanRight[B](z: B)(op: (Row, B) ⇒ B): Iterator[B]

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    Definition Classes
    Iterator
  88. def seq: Iterator[Row]

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  89. def size: Int

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  90. def slice(from: Int, until: Int): Iterator[Row]

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    Definition Classes
    Iterator
  91. def sliding[B >: Row](size: Int, step: Int): GroupedIterator[B]

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    Definition Classes
    Iterator
  92. def span(p: (Row) ⇒ Boolean): (Iterator[Row], Iterator[Row])

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    Definition Classes
    Iterator
  93. def split(line: String): Array[String]

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    Splits the line into it's constituent fields.

    Splits the line into it's constituent fields.

    Attributes
    protected[com.fulcrumgenomics.commons.util]
  94. def sum[B >: Row](implicit num: Numeric[B]): B

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  95. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef
  96. def take(n: Int): Iterator[Row]

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    Definition Classes
    Iterator
  97. def takeWhile(p: (Row) ⇒ Boolean): Iterator[Row]

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    Definition Classes
    Iterator
  98. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, Row, Col[Row]]): Col[Row]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  99. def toArray[B >: Row](implicit arg0: ClassTag[B]): Array[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  100. def toBuffer[B >: Row]: Buffer[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  101. def toIndexedSeq: IndexedSeq[Row]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  102. def toIterable: Iterable[Row]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  103. def toIterator: Iterator[Row]

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    Definition Classes
    Iterator → GenTraversableOnce
  104. def toList: List[Row]

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

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  106. def toSeq: Seq[Row]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  107. def toSet[B >: Row]: Set[B]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  108. def toStream: Stream[Row]

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    Definition Classes
    Iterator → GenTraversableOnce
  109. def toString(): String

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    Definition Classes
    Iterator → AnyRef → Any
  110. def toTraversable: Traversable[Row]

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    Definition Classes
    Iterator → TraversableOnce → GenTraversableOnce
  111. def toVector: Vector[Row]

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    Definition Classes
    TraversableOnce → GenTraversableOnce
  112. val trimFields: Boolean

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    whether individual fields should have their String values trimmed

  113. final def wait(): Unit

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

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  116. def withFilter(p: (Row) ⇒ Boolean): Iterator[Row]

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    Definition Classes
    Iterator
  117. def zip[B](that: Iterator[B]): Iterator[(Row, B)]

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    Definition Classes
    Iterator
  118. def zipAll[B, A1 >: Row, B1 >: B](that: Iterator[B], thisElem: A1, thatElem: B1): Iterator[(A1, B1)]

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    Definition Classes
    Iterator
  119. def zipWithIndex: Iterator[(Row, Int)]

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    Definition Classes
    Iterator
  120. def [B](y: B): (DelimitedDataParser, B)

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    Implicit information
    This member is added by an implicit conversion from DelimitedDataParser to ArrowAssoc[DelimitedDataParser] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Shadowed Implicit Value Members

  1. def filter(p: (Row) ⇒ Boolean): TraversableOnce[Row]

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    Implicit information
    This member is added by an implicit conversion from DelimitedDataParser to MonadOps[Row] performed by method MonadOps in scala.collection.TraversableOnce.
    Shadowing
    This implicitly inherited member is shadowed by one or more members in this class.
    To access this member you can use a type ascription:
    (delimitedDataParser: MonadOps[Row]).filter(p)
    Definition Classes
    MonadOps
  2. def flatMap[B](f: (Row) ⇒ GenTraversableOnce[B]): TraversableOnce[B]

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    Implicit information
    This member is added by an implicit conversion from DelimitedDataParser to MonadOps[Row] performed by method MonadOps in scala.collection.TraversableOnce.
    Shadowing
    This implicitly inherited member is shadowed by one or more members in this class.
    To access this member you can use a type ascription:
    (delimitedDataParser: MonadOps[Row]).flatMap(f)
    Definition Classes
    MonadOps
  3. def map[B](f: (Row) ⇒ B): TraversableOnce[B]

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    Implicit information
    This member is added by an implicit conversion from DelimitedDataParser to MonadOps[Row] performed by method MonadOps in scala.collection.TraversableOnce.
    Shadowing
    This implicitly inherited member is shadowed by one or more members in this class.
    To access this member you can use a type ascription:
    (delimitedDataParser: MonadOps[Row]).map(f)
    Definition Classes
    MonadOps
  4. def withFilter(p: (Row) ⇒ Boolean): Iterator[Row]

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    Implicit information
    This member is added by an implicit conversion from DelimitedDataParser to MonadOps[Row] performed by method MonadOps in scala.collection.TraversableOnce.
    Shadowing
    This implicitly inherited member is shadowed by one or more members in this class.
    To access this member you can use a type ascription:
    (delimitedDataParser: MonadOps[Row]).withFilter(p)
    Definition Classes
    MonadOps

Inherited from LazyLogging

Inherited from Iterator[Row]

Inherited from TraversableOnce[Row]

Inherited from GenTraversableOnce[Row]

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion MonadOps from DelimitedDataParser to MonadOps[Row]

Inherited by implicit conversion any2stringadd from DelimitedDataParser to any2stringadd[DelimitedDataParser]

Inherited by implicit conversion StringFormat from DelimitedDataParser to StringFormat[DelimitedDataParser]

Inherited by implicit conversion Ensuring from DelimitedDataParser to Ensuring[DelimitedDataParser]

Inherited by implicit conversion ArrowAssoc from DelimitedDataParser to ArrowAssoc[DelimitedDataParser]

Inherited by implicit conversion alternateImplicit from DelimitedDataParser to ForceImplicitAmbiguity

Ungrouped