case class ClippingMetrics(read_type: ReadType, reads: Long = 0, reads_unmapped: Long = 0, reads_clipped_pre: Long = 0, reads_clipped_post: Long = 0, reads_clipped_five_prime: Long = 0, reads_clipped_three_prime: Long = 0, reads_clipped_overlapping: Long = 0, bases: Long = 0, bases_clipped_pre: Long = 0, bases_clipped_post: Long = 0, bases_clipped_five_prime: Long = 0, bases_clipped_three_prime: Long = 0, bases_clipped_overlapping: Long = 0) extends Metric with Product with Serializable
Metrics produced by ClipBam that detail how many reads and bases are clipped respectively.
- read_type
The type of read (i.e. Fragment, ReadOne, ReadTwo).
- reads
The number of reads examined.
- reads_unmapped
The number of reads that became unmapped due to clipping.
- reads_clipped_pre
The number of reads with any type of clipping prior to clipping with ClipBam.
- reads_clipped_post
The number of reads with any type of clipping after clipping with ClipBam, including reads that became unmapped.
- reads_clipped_five_prime
The number of reads with the 5' end clipped.
- reads_clipped_three_prime
The number of reads with the 3' end clipped.
- reads_clipped_overlapping
The number of reads clipped due to overlapping reads.
- bases
The number of aligned bases after clipping.
- bases_clipped_pre
The number of bases clipped prior to clipping with ClipBam.
- bases_clipped_post
The number of bases clipped after clipping with ClipBam, including bases from reads that became unmapped.
- bases_clipped_five_prime
The number of bases clipped on the 5' end of the read.
- bases_clipped_three_prime
The number of bases clipped on the 3 end of the read.
- bases_clipped_overlapping
The number of bases clipped due to overlapping reads.
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Instance Constructors
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new
ClippingMetrics(read_type: ReadType, reads: Long = 0, reads_unmapped: Long = 0, reads_clipped_pre: Long = 0, reads_clipped_post: Long = 0, reads_clipped_five_prime: Long = 0, reads_clipped_three_prime: Long = 0, reads_clipped_overlapping: Long = 0, bases: Long = 0, bases_clipped_pre: Long = 0, bases_clipped_post: Long = 0, bases_clipped_five_prime: Long = 0, bases_clipped_three_prime: Long = 0, bases_clipped_overlapping: Long = 0)
- read_type
The type of read (i.e. Fragment, ReadOne, ReadTwo).
- reads
The number of reads examined.
- reads_unmapped
The number of reads that became unmapped due to clipping.
- reads_clipped_pre
The number of reads with any type of clipping prior to clipping with ClipBam.
- reads_clipped_post
The number of reads with any type of clipping after clipping with ClipBam, including reads that became unmapped.
- reads_clipped_five_prime
The number of reads with the 5' end clipped.
- reads_clipped_three_prime
The number of reads with the 3' end clipped.
- reads_clipped_overlapping
The number of reads clipped due to overlapping reads.
- bases
The number of aligned bases after clipping.
- bases_clipped_pre
The number of bases clipped prior to clipping with ClipBam.
- bases_clipped_post
The number of bases clipped after clipping with ClipBam, including bases from reads that became unmapped.
- bases_clipped_five_prime
The number of bases clipped on the 5' end of the read.
- bases_clipped_three_prime
The number of bases clipped on the 3 end of the read.
- bases_clipped_overlapping
The number of bases clipped due to overlapping reads.
Type Members
-
type
Self = Iterable[(String, String)]
- Attributes
- protected[this]
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- TraversableLike
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class
WithFilter extends FilterMonadic[A, Repr]
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final
def
!=(arg0: Any): Boolean
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final
def
##(): Int
- Definition Classes
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-
def
+(other: String): String
- Implicit
- This member is added by an implicit conversion from ClippingMetrics to any2stringadd[ClippingMetrics] performed by method any2stringadd in scala.Predef.
- Definition Classes
- any2stringadd
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def
++[B >: (String, String), That](that: GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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-
def
->[B](y: B): (ClippingMetrics, B)
- Implicit
- This member is added by an implicit conversion from ClippingMetrics to ArrowAssoc[ClippingMetrics] performed by method ArrowAssoc in scala.Predef.
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final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
- def add(metric: ClippingMetrics*): Unit
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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
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def
aggregate[B](z: ⇒ B)(seqop: (B, (String, String)) ⇒ B, combop: (B, B) ⇒ B): B
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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
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-
final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
- var bases: Long
- var bases_clipped_five_prime: Long
- var bases_clipped_overlapping: Long
- var bases_clipped_post: Long
- var bases_clipped_pre: Long
- var bases_clipped_three_prime: Long
-
def
canEqual(that: Any): Boolean
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clone(): AnyRef
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def
dropWhile(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]
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def
ensuring(cond: (ClippingMetrics) ⇒ Boolean, msg: ⇒ Any): ClippingMetrics
- Implicit
- This member is added by an implicit conversion from ClippingMetrics to Ensuring[ClippingMetrics] performed by method Ensuring in scala.Predef.
- Definition Classes
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-
def
ensuring(cond: (ClippingMetrics) ⇒ Boolean): ClippingMetrics
- Implicit
- This member is added by an implicit conversion from ClippingMetrics to Ensuring[ClippingMetrics] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean, msg: ⇒ Any): ClippingMetrics
- Implicit
- This member is added by an implicit conversion from ClippingMetrics to Ensuring[ClippingMetrics] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean): ClippingMetrics
- Implicit
- This member is added by an implicit conversion from ClippingMetrics to Ensuring[ClippingMetrics] performed by method Ensuring in scala.Predef.
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final
def
eq(arg0: AnyRef): Boolean
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filterNot(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]
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finalize(): Unit
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foldLeft[B](z: B)(op: (B, (String, String)) ⇒ B): B
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foldRight[B](z: B)(op: ((String, String), B) ⇒ B): B
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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 ClippingMetrics to StringFormat[ClippingMetrics] performed by method StringFormat in scala.Predef.
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def
genericBuilder[B]: Builder[B, Iterable[B]]
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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.
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final
def
getClass(): Class[_]
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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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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)
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def
maxBy[B](f: ((String, String)) ⇒ B)(implicit cmp: Ordering[B]): (String, String)
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def
min[B >: (String, String)](implicit cmp: Ordering[B]): (String, String)
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def
minBy[B](f: ((String, String)) ⇒ B)(implicit cmp: Ordering[B]): (String, String)
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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
- Definition Classes
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newBuilder: Builder[(String, String), Iterable[(String, String)]]
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notify(): Unit
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par: 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
- Definition Classes
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- val read_type: ReadType
- var reads: Long
- var reads_clipped_five_prime: Long
- var reads_clipped_overlapping: Long
- var reads_clipped_post: Long
- var reads_clipped_pre: Long
- var reads_clipped_three_prime: Long
- var reads_unmapped: Long
-
def
reduce[A1 >: (String, String)](op: (A1, A1) ⇒ A1): A1
- Definition Classes
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-
def
reduceLeft[B >: (String, String)](op: (B, (String, String)) ⇒ B): B
- Definition Classes
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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
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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
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def
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def
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(Changed in version 2.9.0) The behavior of
scanRight
has changed. The previous behavior can be reproduced with scanRight.reverse.
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def
seq: Iterable[(String, String)]
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def
size: Int
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def
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def
slice(from: Int, until: Int): Iterable[(String, String)]
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def
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def
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def
span(p: ((String, String)) ⇒ Boolean): (Iterable[(String, String)], Iterable[(String, String)])
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def
stringPrefix: String
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def
synchronized[T0](arg0: ⇒ T0): T0
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def
tail: Iterable[(String, String)]
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def
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def
toArray[B >: (String, String)](implicit arg0: ClassTag[B]): Array[B]
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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 ClippingMetrics to CollectionsHaveToParArray[ClippingMetrics, T] performed by method CollectionsHaveToParArray in scala.collection.parallel. This conversion will take place only if an implicit value of type (ClippingMetrics) ⇒ GenTraversableOnce[T] is in scope.
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def
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- Definition Classes
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- 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 update(rec: SamRecord, priorBasesClipped: Int, numFivePrime: Int, numThreePrime: Int, numOverlappingBases: Int): Unit
-
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)]]
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def
view: IterableView[(String, String), Iterable[(String, String)]]
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final
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final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... ) @native()
-
def
withFilter(p: ((String, String)) ⇒ Boolean): FilterMonadic[(String, String), Iterable[(String, String)]]
- Definition Classes
- TraversableLike → FilterMonadic
-
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): (ClippingMetrics, B)
- Implicit
- This member is added by an implicit conversion from ClippingMetrics to ArrowAssoc[ClippingMetrics] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc
Shadowed Implicit Value Members
-
def
filter(p: ((String, String)) ⇒ Boolean): TraversableOnce[(String, String)]
- Implicit
- This member is added by an implicit conversion from ClippingMetrics 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:(clippingMetrics: 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 ClippingMetrics 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:(clippingMetrics: 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 ClippingMetrics 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:(clippingMetrics: 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 ClippingMetrics 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:(clippingMetrics: 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.