case class DuplexFamilySizeMetric(ab_size: Int, ba_size: Int, count: Count = 0, fraction: Proportion = 0, fraction_gt_or_eq_size: Proportion = 0) extends Metric with Ordered[DuplexFamilySizeMetric] with Product with Serializable
Metrics produced by CollectDuplexSeqMetrics
to describe the distribution of double-stranded (duplex)
tag families in terms of the number of reads observed on each strand.
We refer to the two strands as ab
and ba
because we identify the two strands by observing the same pair of
UMIs (A and B) in opposite order (A->B vs B->A). Which strand is ab
and which is ba
is largely arbitrary, so
to make interpretation of the metrics simpler we use a definition here that for a given tag family
ab
is the sub-family with more reads and ba
is the tag family with fewer reads.
- ab_size
The number of reads in the
ab
sub-family (the larger sub-family) for this double-strand tag family.- ba_size
The number of reads in the
ba
sub-family (the smaller sub-family) for this double-strand tag family.- count
The number of families with the
ab
andba
single-strand families of sizeab_size
andba_size
.- fraction
The fraction of all double-stranded tag families that have
ab_size
andba_size
.- fraction_gt_or_eq_size
The fraction of all double-stranded tag families that have
ab reads >= ab_size
andba reads >= ba_size
.
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- DuplexFamilySizeMetric
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Instance Constructors
-
new
DuplexFamilySizeMetric(ab_size: Int, ba_size: Int, count: Count = 0, fraction: Proportion = 0, fraction_gt_or_eq_size: Proportion = 0)
- ab_size
The number of reads in the
ab
sub-family (the larger sub-family) for this double-strand tag family.- ba_size
The number of reads in the
ba
sub-family (the smaller sub-family) for this double-strand tag family.- count
The number of families with the
ab
andba
single-strand families of sizeab_size
andba_size
.- fraction
The fraction of all double-stranded tag families that have
ab_size
andba_size
.- fraction_gt_or_eq_size
The fraction of all double-stranded tag families that have
ab reads >= ab_size
andba reads >= ba_size
.
Type Members
-
type
Self = Iterable[(String, String)]
- Attributes
- protected[this]
- Definition Classes
- TraversableLike
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class
WithFilter extends FilterMonadic[A, Repr]
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Value Members
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final
def
!=(arg0: Any): Boolean
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final
def
##(): Int
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-
def
+(other: String): String
- Implicit
- This member is added by an implicit conversion from DuplexFamilySizeMetric to any2stringadd[DuplexFamilySizeMetric] performed by method any2stringadd in scala.Predef.
- Definition Classes
- any2stringadd
-
def
++[B >: (String, String), That](that: GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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def
++:[B >: (String, String), That](that: Traversable[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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def
++:[B >: (String, String), That](that: TraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
- Definition Classes
- TraversableLike
-
def
->[B](y: B): (DuplexFamilySizeMetric, B)
- Implicit
- This member is added by an implicit conversion from DuplexFamilySizeMetric to ArrowAssoc[DuplexFamilySizeMetric] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc
- Annotations
- @inline()
-
def
<(that: DuplexFamilySizeMetric): Boolean
- Definition Classes
- Ordered
-
def
<=(that: DuplexFamilySizeMetric): Boolean
- Definition Classes
- Ordered
-
final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
def
>(that: DuplexFamilySizeMetric): Boolean
- Definition Classes
- Ordered
-
def
>=(that: DuplexFamilySizeMetric): Boolean
- Definition Classes
- Ordered
- val ab_size: Int
-
def
addString(b: StringBuilder): StringBuilder
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def
addString(b: StringBuilder, sep: String): StringBuilder
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def
addString(b: StringBuilder, start: String, sep: String, end: String): StringBuilder
- Definition Classes
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def
aggregate[B](z: ⇒ B)(seqop: (B, (String, String)) ⇒ B, combop: (B, B) ⇒ B): B
- Definition Classes
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-
def
apply(name: String): String
Gets the value of the field by name.
Gets the value of the field by name.
- Definition Classes
- Metric
-
final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
- val ba_size: Int
-
def
canEqual(that: Any): Boolean
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def
clone(): AnyRef
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def
collect[B, That](pf: PartialFunction[(String, String), B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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def
collectFirst[B](pf: PartialFunction[(String, String), B]): Option[B]
- Definition Classes
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def
companion: GenericCompanion[Iterable]
- Definition Classes
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-
def
compare(that: DuplexFamilySizeMetric): Int
Orders by ab_size, then ba_size.
Orders by ab_size, then ba_size.
- Definition Classes
- DuplexFamilySizeMetric → Ordered
-
def
compareTo(that: DuplexFamilySizeMetric): Int
- Definition Classes
- Ordered → Comparable
-
def
copyToArray[B >: (String, String)](xs: Array[B], start: Int, len: Int): Unit
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def
copyToArray[B >: (String, String)](xs: Array[B]): Unit
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def
copyToArray[B >: (String, String)](xs: Array[B], start: Int): Unit
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def
copyToBuffer[B >: (String, String)](dest: Buffer[B]): Unit
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def
count(p: ((String, String)) ⇒ Boolean): Int
- Definition Classes
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- val count: Count
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def
drop(n: Int): Iterable[(String, String)]
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def
dropRight(n: Int): Iterable[(String, String)]
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def
dropWhile(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]
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def
ensuring(cond: (DuplexFamilySizeMetric) ⇒ Boolean, msg: ⇒ Any): DuplexFamilySizeMetric
- Implicit
- This member is added by an implicit conversion from DuplexFamilySizeMetric to Ensuring[DuplexFamilySizeMetric] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: (DuplexFamilySizeMetric) ⇒ Boolean): DuplexFamilySizeMetric
- Implicit
- This member is added by an implicit conversion from DuplexFamilySizeMetric to Ensuring[DuplexFamilySizeMetric] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean, msg: ⇒ Any): DuplexFamilySizeMetric
- Implicit
- This member is added by an implicit conversion from DuplexFamilySizeMetric to Ensuring[DuplexFamilySizeMetric] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean): DuplexFamilySizeMetric
- Implicit
- This member is added by an implicit conversion from DuplexFamilySizeMetric to Ensuring[DuplexFamilySizeMetric] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
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def
exists(p: ((String, String)) ⇒ Boolean): Boolean
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def
filter(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]
- Definition Classes
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def
filterNot(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]
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def
finalize(): Unit
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def
find(p: ((String, String)) ⇒ Boolean): Option[(String, String)]
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fold[A1 >: (String, String)](z: A1)(op: (A1, A1) ⇒ A1): A1
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def
foldLeft[B](z: B)(op: (B, (String, String)) ⇒ B): B
- Definition Classes
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def
foldRight[B](z: B)(op: ((String, String), B) ⇒ B): B
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def
forall(p: ((String, String)) ⇒ Boolean): Boolean
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def
foreach[U](f: ((String, String)) ⇒ U): Unit
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def
formatValue(value: Any): String
Override this method to customize how values are formatted.
Override this method to customize how values are formatted.
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-
def
formatted(fmtstr: String): String
- Implicit
- This member is added by an implicit conversion from DuplexFamilySizeMetric to StringFormat[DuplexFamilySizeMetric] performed by method StringFormat in scala.Predef.
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- @inline()
- var fraction: Proportion
- var fraction_gt_or_eq_size: Proportion
-
def
genericBuilder[B]: Builder[B, Iterable[B]]
- Definition Classes
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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
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final
def
getClass(): Class[_]
- Definition Classes
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def
groupBy[K](f: ((String, String)) ⇒ K): Map[K, Iterable[(String, String)]]
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-
def
grouped(size: Int): Iterator[Iterable[(String, String)]]
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def
hasDefiniteSize: Boolean
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def
head: (String, String)
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def
headOption: Option[(String, String)]
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def
init: Iterable[(String, String)]
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def
inits: Iterator[Iterable[(String, String)]]
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def
isEmpty: Boolean
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final
def
isInstanceOf[T0]: Boolean
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final
def
isTraversableAgain: Boolean
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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
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def
last: (String, String)
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def
lastOption: Option[(String, String)]
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def
map[B, That](f: ((String, String)) ⇒ B)(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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def
max[B >: (String, String)](implicit cmp: Ordering[B]): (String, String)
- Definition Classes
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def
maxBy[B](f: ((String, String)) ⇒ B)(implicit cmp: Ordering[B]): (String, String)
- Definition Classes
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-
def
min[B >: (String, String)](implicit cmp: Ordering[B]): (String, String)
- Definition Classes
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def
minBy[B](f: ((String, String)) ⇒ B)(implicit cmp: Ordering[B]): (String, String)
- Definition Classes
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def
mkString: String
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def
mkString(sep: String): String
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-
def
mkString(start: String, sep: String, end: String): String
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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.
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final
def
ne(arg0: AnyRef): Boolean
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def
newBuilder: Builder[(String, String), Iterable[(String, String)]]
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def
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final
def
notify(): Unit
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final
def
notifyAll(): Unit
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def
par: ParIterable[(String, String)]
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-
def
parCombiner: Combiner[(String, String), ParIterable[(String, String)]]
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def
partition(p: ((String, String)) ⇒ Boolean): (Iterable[(String, String)], Iterable[(String, String)])
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-
def
product[B >: (String, String)](implicit num: Numeric[B]): B
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def
reduce[A1 >: (String, String)](op: (A1, A1) ⇒ A1): A1
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def
reduceLeft[B >: (String, String)](op: (B, (String, String)) ⇒ B): B
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def
reduceLeftOption[B >: (String, String)](op: (B, (String, String)) ⇒ B): Option[B]
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def
reduceOption[A1 >: (String, String)](op: (A1, A1) ⇒ A1): Option[A1]
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def
reduceRight[B >: (String, String)](op: ((String, String), B) ⇒ B): B
- Definition Classes
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def
reduceRightOption[B >: (String, String)](op: ((String, String), B) ⇒ B): Option[B]
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def
repr: Iterable[(String, String)]
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def
reversed: List[(String, String)]
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def
sameElements[B >: (String, String)](that: GenIterable[B]): Boolean
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def
scan[B >: (String, String), That](z: B)(op: (B, B) ⇒ B)(implicit cbf: CanBuildFrom[Iterable[(String, String)], B, That]): That
- Definition Classes
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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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def
scanRight[B, That](z: B)(op: ((String, String), B) ⇒ B)(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
- Definition Classes
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- Migration
(Changed in version 2.9.0) The behavior of
scanRight
has changed. The previous behavior can be reproduced with scanRight.reverse.
-
def
seq: Iterable[(String, String)]
- Definition Classes
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-
def
size: Int
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def
sizeHintIfCheap: Int
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def
slice(from: Int, until: Int): Iterable[(String, String)]
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-
def
sliding(size: Int, step: Int): Iterator[Iterable[(String, String)]]
- Definition Classes
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-
def
sliding(size: Int): Iterator[Iterable[(String, String)]]
- Definition Classes
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-
def
span(p: ((String, String)) ⇒ Boolean): (Iterable[(String, String)], Iterable[(String, String)])
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def
splitAt(n: Int): (Iterable[(String, String)], Iterable[(String, String)])
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def
stringPrefix: String
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def
sum[B >: (String, String)](implicit num: Numeric[B]): B
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final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
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-
def
tail: Iterable[(String, String)]
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def
tails: Iterator[Iterable[(String, String)]]
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-
def
take(n: Int): Iterable[(String, String)]
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def
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def
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def
thisCollection: Iterable[(String, String)]
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def
to[Col[_]](implicit cbf: CanBuildFrom[Nothing, (String, String), Col[(String, String)]]): Col[(String, String)]
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def
toArray[B >: (String, String)](implicit arg0: ClassTag[B]): Array[B]
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def
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def
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def
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def
toIterable: Iterable[(String, String)]
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def
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- Annotations
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-
def
toList: List[(String, String)]
- Definition Classes
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def
toMap[T, U](implicit ev: <:<[(String, String), (T, U)]): Map[T, U]
- Definition Classes
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-
def
toParArray: ParArray[T]
- Implicit
- This member is added by an implicit conversion from DuplexFamilySizeMetric to CollectionsHaveToParArray[DuplexFamilySizeMetric, T] performed by method CollectionsHaveToParArray in scala.collection.parallel. This conversion will take place only if an implicit value of type (DuplexFamilySizeMetric) ⇒ GenTraversableOnce[T] is in scope.
- Definition Classes
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-
def
toSeq: Seq[(String, String)]
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def
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def
toStream: Stream[(String, String)]
- Definition Classes
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def
toString(): String
- Definition Classes
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-
def
toTraversable: Traversable[(String, String)]
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-
def
toVector: Vector[(String, String)]
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def
transpose[B](implicit asTraversable: ((String, String)) ⇒ GenTraversableOnce[B]): Iterable[Iterable[B]]
- Definition Classes
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- Annotations
- @migration
- Migration
(Changed in version 2.9.0)
transpose
throws anIllegalArgumentException
if collections are not uniformly sized.
-
def
unzip[A1, A2](implicit asPair: ((String, String)) ⇒ (A1, A2)): (Iterable[A1], Iterable[A2])
- Definition Classes
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-
def
unzip3[A1, A2, A3](implicit asTriple: ((String, String)) ⇒ (A1, A2, A3)): (Iterable[A1], Iterable[A2], Iterable[A3])
- Definition Classes
- GenericTraversableTemplate
-
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
-
def
view(from: Int, until: Int): IterableView[(String, String), Iterable[(String, String)]]
- Definition Classes
- IterableLike → TraversableLike
-
def
view: IterableView[(String, String), Iterable[(String, String)]]
- Definition Classes
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-
final
def
wait(): Unit
- Definition Classes
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- @throws( ... )
-
final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
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- @throws( ... )
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final
def
wait(arg0: Long): Unit
- Definition Classes
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- @throws( ... ) @native()
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def
withFilter(p: ((String, String)) ⇒ Boolean): FilterMonadic[(String, String), Iterable[(String, String)]]
- Definition Classes
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-
def
zip[A1 >: (String, String), B, That](that: GenIterable[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, B), That]): That
- Definition Classes
- IterableLike → GenIterableLike
-
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
- IterableLike → GenIterableLike
-
def
zipWithIndex[A1 >: (String, String), That](implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, Int), That]): That
- Definition Classes
- IterableLike → GenIterableLike
-
def
→[B](y: B): (DuplexFamilySizeMetric, B)
- Implicit
- This member is added by an implicit conversion from DuplexFamilySizeMetric to ArrowAssoc[DuplexFamilySizeMetric] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc
Shadowed Implicit Value Members
-
def
<(that: DuplexFamilySizeMetric): Boolean
- Implicit
- This member is added by an implicit conversion from DuplexFamilySizeMetric to Ordered[DuplexFamilySizeMetric] performed by method orderingToOrdered in scala.math.Ordered. This conversion will take place only if an implicit value of type Ordering[DuplexFamilySizeMetric] is in scope.
- 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:(duplexFamilySizeMetric: Ordered[DuplexFamilySizeMetric]).<(that)
- Definition Classes
- Ordered
-
def
<=(that: DuplexFamilySizeMetric): Boolean
- Implicit
- This member is added by an implicit conversion from DuplexFamilySizeMetric to Ordered[DuplexFamilySizeMetric] performed by method orderingToOrdered in scala.math.Ordered. This conversion will take place only if an implicit value of type Ordering[DuplexFamilySizeMetric] is in scope.
- 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:(duplexFamilySizeMetric: Ordered[DuplexFamilySizeMetric]).<=(that)
- Definition Classes
- Ordered
-
def
>(that: DuplexFamilySizeMetric): Boolean
- Implicit
- This member is added by an implicit conversion from DuplexFamilySizeMetric to Ordered[DuplexFamilySizeMetric] performed by method orderingToOrdered in scala.math.Ordered. This conversion will take place only if an implicit value of type Ordering[DuplexFamilySizeMetric] is in scope.
- 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:(duplexFamilySizeMetric: Ordered[DuplexFamilySizeMetric]).>(that)
- Definition Classes
- Ordered
-
def
>=(that: DuplexFamilySizeMetric): Boolean
- Implicit
- This member is added by an implicit conversion from DuplexFamilySizeMetric to Ordered[DuplexFamilySizeMetric] performed by method orderingToOrdered in scala.math.Ordered. This conversion will take place only if an implicit value of type Ordering[DuplexFamilySizeMetric] is in scope.
- 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:(duplexFamilySizeMetric: Ordered[DuplexFamilySizeMetric]).>=(that)
- Definition Classes
- Ordered
-
def
compare(that: DuplexFamilySizeMetric): Int
- Implicit
- This member is added by an implicit conversion from DuplexFamilySizeMetric to Ordered[DuplexFamilySizeMetric] performed by method orderingToOrdered in scala.math.Ordered. This conversion will take place only if an implicit value of type Ordering[DuplexFamilySizeMetric] is in scope.
- 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:(duplexFamilySizeMetric: Ordered[DuplexFamilySizeMetric]).compare(that)
- Definition Classes
- Ordered
-
def
compareTo(that: DuplexFamilySizeMetric): Int
- Implicit
- This member is added by an implicit conversion from DuplexFamilySizeMetric to Ordered[DuplexFamilySizeMetric] performed by method orderingToOrdered in scala.math.Ordered. This conversion will take place only if an implicit value of type Ordering[DuplexFamilySizeMetric] is in scope.
- 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:(duplexFamilySizeMetric: Ordered[DuplexFamilySizeMetric]).compareTo(that)
- Definition Classes
- Ordered → Comparable
-
def
filter(p: ((String, String)) ⇒ Boolean): TraversableOnce[(String, String)]
- Implicit
- This member is added by an implicit conversion from DuplexFamilySizeMetric 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:(duplexFamilySizeMetric: MonadOps[(String, String)]).filter(p)
- Definition Classes
- MonadOps
-
def
flatMap[B](f: ((String, String)) ⇒ GenTraversableOnce[B]): TraversableOnce[B]
- Implicit
- This member is added by an implicit conversion from DuplexFamilySizeMetric 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:(duplexFamilySizeMetric: MonadOps[(String, String)]).flatMap(f)
- Definition Classes
- MonadOps
-
def
map[B](f: ((String, String)) ⇒ B): TraversableOnce[B]
- Implicit
- This member is added by an implicit conversion from DuplexFamilySizeMetric 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:(duplexFamilySizeMetric: MonadOps[(String, String)]).map(f)
- Definition Classes
- MonadOps
-
def
withFilter(p: ((String, String)) ⇒ Boolean): Iterator[(String, String)]
- Implicit
- This member is added by an implicit conversion from DuplexFamilySizeMetric 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:(duplexFamilySizeMetric: MonadOps[(String, String)]).withFilter(p)
- Definition Classes
- MonadOps
Deprecated Value Members
-
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 /:
-
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 :\
-
def
formatValues(value: Any): String
- Attributes
- protected
- Definition Classes
- Metric
- Annotations
- @deprecated
- Deprecated
(Since version 0.5.0) Use formatValue instead.