Packages

case class UmiMetric(umi: String, raw_observations: Count = 0, raw_observations_with_errors: Count = 0, unique_observations: Count = 0, fraction_raw_observations: Proportion = 0, fraction_unique_observations: Proportion = 0) extends Metric with Product with Serializable

Metrics produced by CollectDuplexSeqMetrics describing the set of observed UMI sequences and the frequency of their observations. The UMI sequences reported may have been corrected using information within a double-stranded tag family. For example if a tag family is comprised of three read pairs with UMIs ACGT-TGGT, ACGT-TGGT, and ACGT-TGGG then a consensus UMI of ACGT-TGGT will be generated, and three raw observations counted for each of ACGT and TGGT, and no observations counted for TGGG.

umi

The UMI sequence, possibly-corrected.

raw_observations

The number of read pairs in the input BAM that observe the UMI (after correction).

raw_observations_with_errors

The subset of raw-observations that underwent any correction.

unique_observations

The number of double-stranded tag families (i.e unique double-stranded molecules) that observed the UMI.

fraction_raw_observations

The fraction of all raw observations that the UMI accounts for.

fraction_unique_observations

The fraction of all unique observations that the UMI accounts for.

Linear Supertypes
Serializable, Serializable, Metric, Iterable[(String, String)], IterableLike[(String, String), Iterable[(String, String)]], GenIterable[(String, String)], GenIterableLike[(String, String), Iterable[(String, String)]], Traversable[(String, String)], GenTraversable[(String, String)], GenericTraversableTemplate[(String, String), Iterable], TraversableLike[(String, String), Iterable[(String, String)]], GenTraversableLike[(String, String), Iterable[(String, String)]], Parallelizable[(String, String), ParIterable[(String, String)]], TraversableOnce[(String, String)], GenTraversableOnce[(String, String)], FilterMonadic[(String, String), Iterable[(String, String)]], HasNewBuilder[(String, String), Iterable[(String, String)] @scala.annotation.unchecked.uncheckedVariance], Product, Equals, AnyRef, Any
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  1. UmiMetric
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Implicitly
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  3. by any2stringadd
  4. by StringFormat
  5. by Ensuring
  6. by ArrowAssoc
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Instance Constructors

  1. new UmiMetric(umi: String, raw_observations: Count = 0, raw_observations_with_errors: Count = 0, unique_observations: Count = 0, fraction_raw_observations: Proportion = 0, fraction_unique_observations: Proportion = 0)

    umi

    The UMI sequence, possibly-corrected.

    raw_observations

    The number of read pairs in the input BAM that observe the UMI (after correction).

    raw_observations_with_errors

    The subset of raw-observations that underwent any correction.

    unique_observations

    The number of double-stranded tag families (i.e unique double-stranded molecules) that observed the UMI.

    fraction_raw_observations

    The fraction of all raw observations that the UMI accounts for.

    fraction_unique_observations

    The fraction of all unique observations that the UMI accounts for.

Type Members

  1. type Self = Iterable[(String, String)]
    Attributes
    protected[this]
    Definition Classes
    TraversableLike
  2. class WithFilter extends FilterMonadic[A, Repr]
    Definition Classes
    TraversableLike

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
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  3. def +(other: String): String
    Implicit
    This member is added by an implicit conversion from UmiMetric to any2stringadd[UmiMetric] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ++[B >: (String, String), That](that: GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  5. def ++:[B >: (String, String), That](that: Traversable[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
    Definition Classes
    TraversableLike
  6. def ++:[B >: (String, String), That](that: TraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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    TraversableLike
  7. def ->[B](y: B): (UmiMetric, B)
    Implicit
    This member is added by an implicit conversion from UmiMetric to ArrowAssoc[UmiMetric] performed by method ArrowAssoc in scala.Predef.
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    @inline()
  8. final def ==(arg0: Any): Boolean
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  9. def addString(b: StringBuilder): StringBuilder
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  10. def addString(b: StringBuilder, sep: String): StringBuilder
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  11. def addString(b: StringBuilder, start: String, sep: String, end: String): StringBuilder
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  12. def aggregate[B](z: ⇒ B)(seqop: (B, (String, String)) ⇒ B, combop: (B, B) ⇒ B): B
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    TraversableOnce → GenTraversableOnce
  13. def apply(name: String): String

    Gets the value of the field by name.

    Gets the value of the field by name.

    Definition Classes
    Metric
  14. final def asInstanceOf[T0]: T0
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  15. def canEqual(that: Any): Boolean
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  16. def clone(): AnyRef
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  17. def collect[B, That](pf: PartialFunction[(String, String), B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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  18. def collectFirst[B](pf: PartialFunction[(String, String), B]): Option[B]
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  19. def companion: GenericCompanion[Iterable]
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  20. def copyToArray[B >: (String, String)](xs: Array[B], start: Int, len: Int): Unit
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  21. def copyToArray[B >: (String, String)](xs: Array[B]): Unit
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  22. def copyToArray[B >: (String, String)](xs: Array[B], start: Int): Unit
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  23. def copyToBuffer[B >: (String, String)](dest: Buffer[B]): Unit
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  24. def count(p: ((String, String)) ⇒ Boolean): Int
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  25. def drop(n: Int): Iterable[(String, String)]
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  26. def dropRight(n: Int): Iterable[(String, String)]
    Definition Classes
    IterableLike
  27. def dropWhile(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]
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    TraversableLike → GenTraversableLike
  28. def ensuring(cond: (UmiMetric) ⇒ Boolean, msg: ⇒ Any): UmiMetric
    Implicit
    This member is added by an implicit conversion from UmiMetric to Ensuring[UmiMetric] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  29. def ensuring(cond: (UmiMetric) ⇒ Boolean): UmiMetric
    Implicit
    This member is added by an implicit conversion from UmiMetric to Ensuring[UmiMetric] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  30. def ensuring(cond: Boolean, msg: ⇒ Any): UmiMetric
    Implicit
    This member is added by an implicit conversion from UmiMetric to Ensuring[UmiMetric] performed by method Ensuring in scala.Predef.
    Definition Classes
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  31. def ensuring(cond: Boolean): UmiMetric
    Implicit
    This member is added by an implicit conversion from UmiMetric to Ensuring[UmiMetric] performed by method Ensuring in scala.Predef.
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    Ensuring
  32. final def eq(arg0: AnyRef): Boolean
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  33. def exists(p: ((String, String)) ⇒ Boolean): Boolean
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  34. def filter(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]
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  35. def filterNot(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]
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  36. def finalize(): Unit
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    @throws( classOf[java.lang.Throwable] )
  37. def find(p: ((String, String)) ⇒ Boolean): Option[(String, String)]
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  38. def flatMap[B, That](f: ((String, String)) ⇒ GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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  39. def flatten[B](implicit asTraversable: ((String, String)) ⇒ GenTraversableOnce[B]): Iterable[B]
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  40. def fold[A1 >: (String, String)](z: A1)(op: (A1, A1) ⇒ A1): A1
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  41. def foldLeft[B](z: B)(op: (B, (String, String)) ⇒ B): B
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  42. def foldRight[B](z: B)(op: ((String, String), B) ⇒ B): B
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  43. def forall(p: ((String, String)) ⇒ Boolean): Boolean
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  44. def foreach[U](f: ((String, String)) ⇒ U): Unit
    Definition Classes
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  45. def formatValue(value: Any): String

    Override this method to customize how values are formatted.

    Override this method to customize how values are formatted.

    Attributes
    protected
    Definition Classes
    Metric
  46. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from UmiMetric to StringFormat[UmiMetric] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  47. var fraction_raw_observations: Proportion
  48. var fraction_unique_observations: Proportion
  49. def genericBuilder[B]: Builder[B, Iterable[B]]
    Definition Classes
    GenericTraversableTemplate
  50. def get(name: String): Option[String]

    Gets the value of the field by name, returns None if it does not exist.

    Gets the value of the field by name, returns None if it does not exist.

    Definition Classes
    Metric
  51. final def getClass(): Class[_]
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  52. def groupBy[K](f: ((String, String)) ⇒ K): Map[K, Iterable[(String, String)]]
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  53. def grouped(size: Int): Iterator[Iterable[(String, String)]]
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  54. def hasDefiniteSize: Boolean
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  55. def head: (String, String)
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  56. def headOption: Option[(String, String)]
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  57. def init: Iterable[(String, String)]
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  58. def inits: Iterator[Iterable[(String, String)]]
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  59. def isEmpty: Boolean
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  60. final def isInstanceOf[T0]: Boolean
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  61. final def isTraversableAgain: Boolean
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  62. def iterator: Iterator[(String, String)]

    Gets an iterator over the fields of this metric in the order they were defined.

    Gets an iterator over the fields of this metric in the order they were defined. Returns tuples of names and values

    Definition Classes
    Metric → IterableLike → GenIterableLike
  63. def last: (String, String)
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  64. def lastOption: Option[(String, String)]
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  65. def map[B, That](f: ((String, String)) ⇒ B)(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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  66. def max[B >: (String, String)](implicit cmp: Ordering[B]): (String, String)
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  67. def maxBy[B](f: ((String, String)) ⇒ B)(implicit cmp: Ordering[B]): (String, String)
    Definition Classes
    TraversableOnce → GenTraversableOnce
  68. def min[B >: (String, String)](implicit cmp: Ordering[B]): (String, String)
    Definition Classes
    TraversableOnce → GenTraversableOnce
  69. def minBy[B](f: ((String, String)) ⇒ B)(implicit cmp: Ordering[B]): (String, String)
    Definition Classes
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  70. def mkString: String
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  71. def mkString(sep: String): String
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  72. def mkString(start: String, sep: String, end: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  73. def names: Seq[String]

    Get the names of the arguments in the order they were defined.

    Get the names of the arguments in the order they were defined.

    Definition Classes
    Metric
  74. final def ne(arg0: AnyRef): Boolean
    Definition Classes
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  75. def newBuilder: Builder[(String, String), Iterable[(String, String)]]
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  76. def nonEmpty: Boolean
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  77. final def notify(): Unit
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    @native()
  78. final def notifyAll(): Unit
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  79. def par: ParIterable[(String, String)]
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  80. def parCombiner: Combiner[(String, String), ParIterable[(String, String)]]
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    protected[this]
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  81. def partition(p: ((String, String)) ⇒ Boolean): (Iterable[(String, String)], Iterable[(String, String)])
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  82. def product[B >: (String, String)](implicit num: Numeric[B]): B
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    TraversableOnce → GenTraversableOnce
  83. var raw_observations: Count
  84. var raw_observations_with_errors: Count
  85. def reduce[A1 >: (String, String)](op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  86. def reduceLeft[B >: (String, String)](op: (B, (String, String)) ⇒ B): B
    Definition Classes
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  87. def reduceLeftOption[B >: (String, String)](op: (B, (String, String)) ⇒ B): Option[B]
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    TraversableOnce → GenTraversableOnce
  88. def reduceOption[A1 >: (String, String)](op: (A1, A1) ⇒ A1): Option[A1]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  89. def reduceRight[B >: (String, String)](op: ((String, String), B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  90. def reduceRightOption[B >: (String, String)](op: ((String, String), B) ⇒ B): Option[B]
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  91. def repr: Iterable[(String, String)]
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  92. def reversed: List[(String, String)]
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  93. def sameElements[B >: (String, String)](that: GenIterable[B]): Boolean
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  94. def scan[B >: (String, String), That](z: B)(op: (B, B) ⇒ B)(implicit cbf: CanBuildFrom[Iterable[(String, String)], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  95. def scanLeft[B, That](z: B)(op: (B, (String, String)) ⇒ B)(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
    Definition Classes
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  96. def scanRight[B, That](z: B)(op: ((String, String), B) ⇒ B)(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
    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.

  97. def seq: Iterable[(String, String)]
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    Iterable → GenIterable → Traversable → GenTraversable → Parallelizable → TraversableOnce → GenTraversableOnce
  98. def size: Int
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  99. def sizeHintIfCheap: Int
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  100. def slice(from: Int, until: Int): Iterable[(String, String)]
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  101. def sliding(size: Int, step: Int): Iterator[Iterable[(String, String)]]
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  102. def sliding(size: Int): Iterator[Iterable[(String, String)]]
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  103. def span(p: ((String, String)) ⇒ Boolean): (Iterable[(String, String)], Iterable[(String, String)])
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  104. def splitAt(n: Int): (Iterable[(String, String)], Iterable[(String, String)])
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  105. def stringPrefix: String
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  106. def sum[B >: (String, String)](implicit num: Numeric[B]): B
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  107. final def synchronized[T0](arg0: ⇒ T0): T0
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  108. def tail: Iterable[(String, String)]
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  109. def tails: Iterator[Iterable[(String, String)]]
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  110. def take(n: Int): Iterable[(String, String)]
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  111. def takeRight(n: Int): Iterable[(String, String)]
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  112. def takeWhile(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]
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  113. def thisCollection: Iterable[(String, String)]
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    protected[this]
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    IterableLike → TraversableLike
  114. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, (String, String), Col[(String, String)]]): Col[(String, String)]
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    TraversableLike → TraversableOnce → GenTraversableOnce
  115. def toArray[B >: (String, String)](implicit arg0: ClassTag[B]): Array[B]
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  116. def toBuffer[B >: (String, String)]: Buffer[B]
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  117. def toCollection(repr: Iterable[(String, String)]): Iterable[(String, String)]
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    protected[this]
    Definition Classes
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  118. def toIndexedSeq: IndexedSeq[(String, String)]
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  119. def toIterable: Iterable[(String, String)]
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  120. def toIterator: Iterator[(String, String)]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  121. def toList: List[(String, String)]
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  122. def toMap[T, U](implicit ev: <:<[(String, String), (T, U)]): Map[T, U]
    Definition Classes
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  123. def toParArray: ParArray[T]
    Implicit
    This member is added by an implicit conversion from UmiMetric to CollectionsHaveToParArray[UmiMetric, T] performed by method CollectionsHaveToParArray in scala.collection.parallel. This conversion will take place only if an implicit value of type (UmiMetric) ⇒ GenTraversableOnce[T] is in scope.
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  124. def toSeq: Seq[(String, String)]
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  125. def toSet[B >: (String, String)]: Set[B]
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  126. def toStream: Stream[(String, String)]
    Definition Classes
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  127. def toString(): String
    Definition Classes
    Metric → TraversableLike → AnyRef → Any
  128. def toTraversable: Traversable[(String, String)]
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  129. def toVector: Vector[(String, String)]
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  130. def transpose[B](implicit asTraversable: ((String, String)) ⇒ GenTraversableOnce[B]): Iterable[Iterable[B]]
    Definition Classes
    GenericTraversableTemplate
    Annotations
    @migration
    Migration

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

  131. val umi: String
  132. var unique_observations: Count
  133. def unzip[A1, A2](implicit asPair: ((String, String)) ⇒ (A1, A2)): (Iterable[A1], Iterable[A2])
    Definition Classes
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  134. def unzip3[A1, A2, A3](implicit asTriple: ((String, String)) ⇒ (A1, A2, A3)): (Iterable[A1], Iterable[A2], Iterable[A3])
    Definition Classes
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  135. def values: Seq[String]

    Get the values of the arguments in the order they were defined.

    Get the values of the arguments in the order they were defined.

    Definition Classes
    Metric
  136. def view(from: Int, until: Int): IterableView[(String, String), Iterable[(String, String)]]
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  137. def view: IterableView[(String, String), Iterable[(String, String)]]
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  138. final def wait(): Unit
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  139. final def wait(arg0: Long, arg1: Int): Unit
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  140. final def wait(arg0: Long): Unit
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  141. def withFilter(p: ((String, String)) ⇒ Boolean): FilterMonadic[(String, String), Iterable[(String, String)]]
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  142. def zip[A1 >: (String, String), B, That](that: GenIterable[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, B), That]): That
    Definition Classes
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  143. def zipAll[B, A1 >: (String, String), That](that: GenIterable[B], thisElem: A1, thatElem: B)(implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, B), That]): That
    Definition Classes
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  144. def zipWithIndex[A1 >: (String, String), That](implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, Int), That]): That
    Definition Classes
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  145. def →[B](y: B): (UmiMetric, B)
    Implicit
    This member is added by an implicit conversion from UmiMetric to ArrowAssoc[UmiMetric] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
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Shadowed Implicit Value Members

  1. def filter(p: ((String, String)) ⇒ Boolean): TraversableOnce[(String, String)]
    Implicit
    This member is added by an implicit conversion from UmiMetric to MonadOps[(String, String)] 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:
    (umiMetric: MonadOps[(String, String)]).filter(p)
    Definition Classes
    MonadOps
  2. def flatMap[B](f: ((String, String)) ⇒ GenTraversableOnce[B]): TraversableOnce[B]
    Implicit
    This member is added by an implicit conversion from UmiMetric to MonadOps[(String, String)] 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:
    (umiMetric: MonadOps[(String, String)]).flatMap(f)
    Definition Classes
    MonadOps
  3. def map[B](f: ((String, String)) ⇒ B): TraversableOnce[B]
    Implicit
    This member is added by an implicit conversion from UmiMetric to MonadOps[(String, String)] 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:
    (umiMetric: MonadOps[(String, String)]).map(f)
    Definition Classes
    MonadOps
  4. def withFilter(p: ((String, String)) ⇒ Boolean): Iterator[(String, String)]
    Implicit
    This member is added by an implicit conversion from UmiMetric to MonadOps[(String, String)] 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:
    (umiMetric: MonadOps[(String, String)]).withFilter(p)
    Definition Classes
    MonadOps

Deprecated Value Members

  1. def /:[B](z: B)(op: (B, (String, String)) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
    Annotations
    @deprecated
    Deprecated

    (Since version 2.12.10) Use foldLeft instead of /:

  2. def :\[B](z: B)(op: ((String, String), B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
    Annotations
    @deprecated
    Deprecated

    (Since version 2.12.10) Use foldRight instead of :\

  3. def formatValues(value: Any): String

    Attributes
    protected
    Definition Classes
    Metric
    Annotations
    @deprecated
    Deprecated

    (Since version 0.5.0) Use formatValue instead.

Inherited from Serializable

Inherited from Serializable

Inherited from Metric

Inherited from Iterable[(String, String)]

Inherited from IterableLike[(String, String), Iterable[(String, String)]]

Inherited from GenIterable[(String, String)]

Inherited from GenIterableLike[(String, String), Iterable[(String, String)]]

Inherited from Traversable[(String, String)]

Inherited from GenTraversable[(String, String)]

Inherited from GenericTraversableTemplate[(String, String), Iterable]

Inherited from TraversableLike[(String, String), Iterable[(String, String)]]

Inherited from GenTraversableLike[(String, String), Iterable[(String, String)]]

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

Inherited from TraversableOnce[(String, String)]

Inherited from GenTraversableOnce[(String, String)]

Inherited from FilterMonadic[(String, String), Iterable[(String, String)]]

Inherited from HasNewBuilder[(String, String), Iterable[(String, String)] @scala.annotation.unchecked.uncheckedVariance]

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion CollectionsHaveToParArray from UmiMetric to CollectionsHaveToParArray[UmiMetric, T]

Inherited by implicit conversion MonadOps from UmiMetric to MonadOps[(String, String)]

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

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

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

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

Inherited by implicit conversion alternateImplicit from UmiMetric to ForceImplicitAmbiguity

Ungrouped