class ReadStructure extends Seq[ReadSegment]

Describes the structure of a give read. A read contains one or more read segments. A read segment describes a contiguous stretch of bases of the same type (ex. template bases) of some length and some offset from the start of the read.

Linear Supertypes
Seq[ReadSegment], Seq[ReadSegment], SeqLike[ReadSegment, Seq[ReadSegment]], GenSeq[ReadSegment], GenSeqLike[ReadSegment, Seq[ReadSegment]], PartialFunction[Int, ReadSegment], (Int) ⇒ ReadSegment, Iterable[ReadSegment], Iterable[ReadSegment], IterableLike[ReadSegment, Seq[ReadSegment]], Equals, GenIterable[ReadSegment], GenIterableLike[ReadSegment, Seq[ReadSegment]], Traversable[ReadSegment], Immutable, Traversable[ReadSegment], GenTraversable[ReadSegment], GenericTraversableTemplate[ReadSegment, Seq], TraversableLike[ReadSegment, Seq[ReadSegment]], GenTraversableLike[ReadSegment, Seq[ReadSegment]], Parallelizable[ReadSegment, ParSeq[ReadSegment]], TraversableOnce[ReadSegment], GenTraversableOnce[ReadSegment], FilterMonadic[ReadSegment, Seq[ReadSegment]], HasNewBuilder[ReadSegment, scala.collection.immutable.Seq[com.fulcrumgenomics.util.ReadSegment] @scala.annotation.unchecked.uncheckedVariance], AnyRef, Any
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Inherited
  1. ReadStructure
  2. Seq
  3. Seq
  4. SeqLike
  5. GenSeq
  6. GenSeqLike
  7. PartialFunction
  8. Function1
  9. Iterable
  10. Iterable
  11. IterableLike
  12. Equals
  13. GenIterable
  14. GenIterableLike
  15. Traversable
  16. Immutable
  17. Traversable
  18. GenTraversable
  19. GenericTraversableTemplate
  20. TraversableLike
  21. GenTraversableLike
  22. Parallelizable
  23. TraversableOnce
  24. GenTraversableOnce
  25. FilterMonadic
  26. HasNewBuilder
  27. AnyRef
  28. Any
Implicitly
  1. by MonadOps
  2. by CollectionsHaveToParArray
  3. by any2stringadd
  4. by StringFormat
  5. by Ensuring
  6. by ArrowAssoc
  7. by alternateImplicit
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Visibility
  1. Public
  2. All

Type Members

  1. type Self = Seq[ReadSegment]
    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
    AnyRef → Any
  3. def +(other: String): String
    Implicit
    This member is added by an implicit conversion from ReadStructure to any2stringadd[ReadStructure] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ++[B >: ReadSegment, That](that: GenTraversableOnce[B])(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  5. def ++:[B >: ReadSegment, That](that: Traversable[B])(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    TraversableLike
  6. def ++:[B >: ReadSegment, That](that: TraversableOnce[B])(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    TraversableLike
  7. def +:[B >: ReadSegment, That](elem: B)(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  8. def ->[B](y: B): (ReadStructure, B)
    Implicit
    This member is added by an implicit conversion from ReadStructure to ArrowAssoc[ReadStructure] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  9. def /:[B](z: B)(op: (B, ReadSegment) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  10. def :+[B >: ReadSegment, That](elem: B)(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  11. def :\[B](z: B)(op: (ReadSegment, B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  12. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  13. def addString(b: StringBuilder): StringBuilder
    Definition Classes
    TraversableOnce
  14. def addString(b: StringBuilder, sep: String): StringBuilder
    Definition Classes
    TraversableOnce
  15. def addString(b: StringBuilder, start: String, sep: String, end: String): StringBuilder
    Definition Classes
    TraversableOnce
  16. def aggregate[B](z: ⇒ B)(seqop: (B, ReadSegment) ⇒ B, combop: (B, B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  17. def andThen[C](k: (ReadSegment) ⇒ C): PartialFunction[Int, C]
    Definition Classes
    PartialFunction → Function1
  18. def apply(idx: Int): ReadSegment

    Fetches the segment at the given index.

    Fetches the segment at the given index.

    Definition Classes
    ReadStructure → SeqLike → GenSeqLike → Function1
  19. def applyOrElse[A1 <: Int, B1 >: ReadSegment](x: A1, default: (A1) ⇒ B1): B1
    Definition Classes
    PartialFunction
  20. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  21. def canEqual(that: Any): Boolean
    Definition Classes
    IterableLike → Equals
  22. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  23. def collect[B, That](pf: PartialFunction[ReadSegment, B])(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  24. def collectFirst[B](pf: PartialFunction[ReadSegment, B]): Option[B]
    Definition Classes
    TraversableOnce
  25. def combinations(n: Int): Iterator[Seq[ReadSegment]]
    Definition Classes
    SeqLike
  26. def companion: GenericCompanion[Seq]
    Definition Classes
    Seq → Seq → GenSeq → Iterable → Iterable → GenIterable → Traversable → Traversable → GenTraversable → GenericTraversableTemplate
  27. def compose[A](g: (A) ⇒ Int): (A) ⇒ ReadSegment
    Definition Classes
    Function1
    Annotations
    @unspecialized()
  28. def contains[A1 >: ReadSegment](elem: A1): Boolean
    Definition Classes
    SeqLike
  29. def containsSlice[B](that: GenSeq[B]): Boolean
    Definition Classes
    SeqLike
  30. def copyToArray[B >: ReadSegment](xs: Array[B], start: Int, len: Int): Unit
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  31. def copyToArray[B >: ReadSegment](xs: Array[B]): Unit
    Definition Classes
    TraversableOnce → GenTraversableOnce
  32. def copyToArray[B >: ReadSegment](xs: Array[B], start: Int): Unit
    Definition Classes
    TraversableOnce → GenTraversableOnce
  33. def copyToBuffer[B >: ReadSegment](dest: Buffer[B]): Unit
    Definition Classes
    TraversableOnce
  34. def corresponds[B](that: GenSeq[B])(p: (ReadSegment, B) ⇒ Boolean): Boolean
    Definition Classes
    SeqLike → GenSeqLike
  35. def count(p: (ReadSegment) ⇒ Boolean): Int
    Definition Classes
    TraversableOnce → GenTraversableOnce
  36. def diff[B >: ReadSegment](that: GenSeq[B]): Seq[ReadSegment]
    Definition Classes
    SeqLike → GenSeqLike
  37. def distinct: Seq[ReadSegment]
    Definition Classes
    SeqLike → GenSeqLike
  38. def drop(n: Int): Seq[ReadSegment]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  39. def dropRight(n: Int): Seq[ReadSegment]
    Definition Classes
    IterableLike
  40. def dropWhile(p: (ReadSegment) ⇒ Boolean): Seq[ReadSegment]
    Definition Classes
    TraversableLike → GenTraversableLike
  41. def endsWith[B](that: GenSeq[B]): Boolean
    Definition Classes
    SeqLike → GenSeqLike
  42. def ensuring(cond: (ReadStructure) ⇒ Boolean, msg: ⇒ Any): ReadStructure
    Implicit
    This member is added by an implicit conversion from ReadStructure to Ensuring[ReadStructure] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  43. def ensuring(cond: (ReadStructure) ⇒ Boolean): ReadStructure
    Implicit
    This member is added by an implicit conversion from ReadStructure to Ensuring[ReadStructure] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  44. def ensuring(cond: Boolean, msg: ⇒ Any): ReadStructure
    Implicit
    This member is added by an implicit conversion from ReadStructure to Ensuring[ReadStructure] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  45. def ensuring(cond: Boolean): ReadStructure
    Implicit
    This member is added by an implicit conversion from ReadStructure to Ensuring[ReadStructure] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  46. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  47. def equals(that: Any): Boolean
    Definition Classes
    GenSeqLike → Equals → Any
  48. def exists(p: (ReadSegment) ⇒ Boolean): Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  49. def extract(bases: String, quals: String): Seq[SubReadWithQuals]

    Splits the given bases and qualities into triples with its associated read segment.

    Splits the given bases and qualities into triples with its associated read segment. If strict is false then only return tuples for which we have bases in bases, otherwise throw an exception.

  50. def extract(bases: String): Seq[SubReadWithoutQuals]

    Splits the given bases into tuples with its associated read segment.

    Splits the given bases into tuples with its associated read segment. If strict is false then only return tuples for which we have bases in bases, otherwise throw an exception.

  51. def filter(p: (ReadSegment) ⇒ Boolean): Seq[ReadSegment]
    Definition Classes
    TraversableLike → GenTraversableLike
  52. def filterNot(p: (ReadSegment) ⇒ Boolean): Seq[ReadSegment]
    Definition Classes
    TraversableLike → GenTraversableLike
  53. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  54. def find(p: (ReadSegment) ⇒ Boolean): Option[ReadSegment]
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  55. def fixedLength: Int

    Returns the fixed length if there is one.

    Returns the fixed length if there is one. Throws an exception on segments without fixed lengths!

  56. def flatMap[B, That](f: (ReadSegment) ⇒ GenTraversableOnce[B])(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  57. def flatten[B](implicit asTraversable: (ReadSegment) ⇒ GenTraversableOnce[B]): Seq[B]
    Definition Classes
    GenericTraversableTemplate
  58. def fold[A1 >: ReadSegment](z: A1)(op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  59. def foldLeft[B](z: B)(op: (B, ReadSegment) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  60. def foldRight[B](z: B)(op: (ReadSegment, B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  61. def forall(p: (ReadSegment) ⇒ Boolean): Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  62. def foreach[U](f: (ReadSegment) ⇒ U): Unit
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike → TraversableOnce → GenTraversableOnce → FilterMonadic
  63. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from ReadStructure to StringFormat[ReadStructure] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  64. def genericBuilder[B]: Builder[B, Seq[B]]
    Definition Classes
    GenericTraversableTemplate
  65. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  66. def groupBy[K](f: (ReadSegment) ⇒ K): Map[K, Seq[ReadSegment]]
    Definition Classes
    TraversableLike → GenTraversableLike
  67. def grouped(size: Int): Iterator[Seq[ReadSegment]]
    Definition Classes
    IterableLike
  68. def hasDefiniteSize: Boolean
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  69. def hasFixedLength: Boolean

    Returns true if the ReadStructure has a fixed (i.e.

    Returns true if the ReadStructure has a fixed (i.e. non-variable) length.

  70. def hashCode(): Int
    Definition Classes
    GenSeqLike → Any
  71. def head: ReadSegment
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  72. def headOption: Option[ReadSegment]
    Definition Classes
    TraversableLike → GenTraversableLike
  73. def indexOf[B >: ReadSegment](elem: B, from: Int): Int
    Definition Classes
    GenSeqLike
  74. def indexOf[B >: ReadSegment](elem: B): Int
    Definition Classes
    GenSeqLike
  75. def indexOfSlice[B >: ReadSegment](that: GenSeq[B], from: Int): Int
    Definition Classes
    SeqLike
  76. def indexOfSlice[B >: ReadSegment](that: GenSeq[B]): Int
    Definition Classes
    SeqLike
  77. def indexWhere(p: (ReadSegment) ⇒ Boolean, from: Int): Int
    Definition Classes
    SeqLike → GenSeqLike
  78. def indexWhere(p: (ReadSegment) ⇒ Boolean): Int
    Definition Classes
    GenSeqLike
  79. def indices: Range
    Definition Classes
    SeqLike
  80. def init: Seq[ReadSegment]
    Definition Classes
    TraversableLike → GenTraversableLike
  81. def inits: Iterator[Seq[ReadSegment]]
    Definition Classes
    TraversableLike
  82. def intersect[B >: ReadSegment](that: GenSeq[B]): Seq[ReadSegment]
    Definition Classes
    SeqLike → GenSeqLike
  83. def isDefinedAt(idx: Int): Boolean
    Definition Classes
    GenSeqLike
  84. def isEmpty: Boolean
    Definition Classes
    SeqLike → IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  85. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  86. final def isTraversableAgain: Boolean
    Definition Classes
    TraversableLike → GenTraversableLike → GenTraversableOnce
  87. def iterator: Iterator[ReadSegment]

    Provides an iterator over the segments.

    Provides an iterator over the segments.

    Definition Classes
    ReadStructure → IterableLike → GenIterableLike
  88. def last: ReadSegment
    Definition Classes
    TraversableLike → GenTraversableLike
  89. def lastIndexOf[B >: ReadSegment](elem: B, end: Int): Int
    Definition Classes
    GenSeqLike
  90. def lastIndexOf[B >: ReadSegment](elem: B): Int
    Definition Classes
    GenSeqLike
  91. def lastIndexOfSlice[B >: ReadSegment](that: GenSeq[B], end: Int): Int
    Definition Classes
    SeqLike
  92. def lastIndexOfSlice[B >: ReadSegment](that: GenSeq[B]): Int
    Definition Classes
    SeqLike
  93. def lastIndexWhere(p: (ReadSegment) ⇒ Boolean, end: Int): Int
    Definition Classes
    SeqLike → GenSeqLike
  94. def lastIndexWhere(p: (ReadSegment) ⇒ Boolean): Int
    Definition Classes
    GenSeqLike
  95. def lastOption: Option[ReadSegment]
    Definition Classes
    TraversableLike → GenTraversableLike
  96. def length: Int

    Length is defined as the number of segments (not bases!) in the read structure.

    Length is defined as the number of segments (not bases!) in the read structure.

    Definition Classes
    ReadStructure → SeqLike → GenSeqLike
  97. def lengthCompare(len: Int): Int
    Definition Classes
    SeqLike
  98. def lift: (Int) ⇒ Option[ReadSegment]
    Definition Classes
    PartialFunction
  99. def map[B, That](f: (ReadSegment) ⇒ B)(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  100. def max[B >: ReadSegment](implicit cmp: Ordering[B]): ReadSegment
    Definition Classes
    TraversableOnce → GenTraversableOnce
  101. def maxBy[B](f: (ReadSegment) ⇒ B)(implicit cmp: Ordering[B]): ReadSegment
    Definition Classes
    TraversableOnce → GenTraversableOnce
  102. def min[B >: ReadSegment](implicit cmp: Ordering[B]): ReadSegment
    Definition Classes
    TraversableOnce → GenTraversableOnce
  103. def minBy[B](f: (ReadSegment) ⇒ B)(implicit cmp: Ordering[B]): ReadSegment
    Definition Classes
    TraversableOnce → GenTraversableOnce
  104. def mkString: String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  105. def mkString(sep: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  106. def mkString(start: String, sep: String, end: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  107. def molecularBarcodeSegments: Seq[ReadSegment]
  108. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  109. def newBuilder: Builder[ReadSegment, Seq[ReadSegment]]
    Attributes
    protected[this]
    Definition Classes
    GenericTraversableTemplate → HasNewBuilder
  110. def nonEmpty: Boolean
    Definition Classes
    TraversableOnce → GenTraversableOnce
  111. final def notify(): Unit
    Definition Classes
    AnyRef
  112. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  113. def orElse[A1 <: Int, B1 >: ReadSegment](that: PartialFunction[A1, B1]): PartialFunction[A1, B1]
    Definition Classes
    PartialFunction
  114. def padTo[B >: ReadSegment, That](len: Int, elem: B)(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  115. def par: ParSeq[ReadSegment]
    Definition Classes
    Parallelizable
  116. def parCombiner: Combiner[ReadSegment, ParSeq[ReadSegment]]
    Attributes
    protected[this]
    Definition Classes
    Seq → SeqLike → Iterable → TraversableLike → Parallelizable
  117. def partition(p: (ReadSegment) ⇒ Boolean): (Seq[ReadSegment], Seq[ReadSegment])
    Definition Classes
    TraversableLike → GenTraversableLike
  118. def patch[B >: ReadSegment, That](from: Int, patch: GenSeq[B], replaced: Int)(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  119. def permutations: Iterator[Seq[ReadSegment]]
    Definition Classes
    SeqLike
  120. def prefixLength(p: (ReadSegment) ⇒ Boolean): Int
    Definition Classes
    GenSeqLike
  121. def product[B >: ReadSegment](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  122. def reduce[A1 >: ReadSegment](op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  123. def reduceLeft[B >: ReadSegment](op: (B, ReadSegment) ⇒ B): B
    Definition Classes
    TraversableOnce
  124. def reduceLeftOption[B >: ReadSegment](op: (B, ReadSegment) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  125. def reduceOption[A1 >: ReadSegment](op: (A1, A1) ⇒ A1): Option[A1]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  126. def reduceRight[B >: ReadSegment](op: (ReadSegment, B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  127. def reduceRightOption[B >: ReadSegment](op: (ReadSegment, B) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  128. def repr: Seq[ReadSegment]
    Definition Classes
    TraversableLike → GenTraversableLike
  129. def reverse: Seq[ReadSegment]
    Definition Classes
    SeqLike → GenSeqLike
  130. def reverseIterator: Iterator[ReadSegment]
    Definition Classes
    SeqLike
  131. def reverseMap[B, That](f: (ReadSegment) ⇒ B)(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  132. def reversed: List[ReadSegment]
    Attributes
    protected[this]
    Definition Classes
    TraversableOnce
  133. def runWith[U](action: (ReadSegment) ⇒ U): (Int) ⇒ Boolean
    Definition Classes
    PartialFunction
  134. def sameElements[B >: ReadSegment](that: GenIterable[B]): Boolean
    Definition Classes
    IterableLike → GenIterableLike
  135. def sampleBarcodeSegments: Seq[ReadSegment]
  136. def scan[B >: ReadSegment, That](z: B)(op: (B, B) ⇒ B)(implicit cbf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  137. def scanLeft[B, That](z: B)(op: (B, ReadSegment) ⇒ B)(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  138. def scanRight[B, That](z: B)(op: (ReadSegment, B) ⇒ B)(implicit bf: CanBuildFrom[Seq[ReadSegment], 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.

  139. def segmentLength(p: (ReadSegment) ⇒ Boolean, from: Int): Int
    Definition Classes
    SeqLike → GenSeqLike
  140. def segments(kind: SegmentType): Seq[ReadSegment]

    Returns just the segments of a given kind.

  141. val segments: Seq[ReadSegment]
  142. def seq: Seq[ReadSegment]
    Definition Classes
    Seq → Seq → GenSeq → GenSeqLike → Iterable → Iterable → GenIterable → Traversable → Traversable → GenTraversable → Parallelizable → TraversableOnce → GenTraversableOnce
  143. def size: Int
    Definition Classes
    SeqLike → GenTraversableLike → TraversableOnce → GenTraversableOnce
  144. def sizeHintIfCheap: Int
    Attributes
    protected[scala.collection]
    Definition Classes
    GenTraversableOnce
  145. def skipSegments: Seq[ReadSegment]
  146. def slice(from: Int, until: Int): Seq[ReadSegment]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  147. def sliding(size: Int, step: Int): Iterator[Seq[ReadSegment]]
    Definition Classes
    IterableLike
  148. def sliding(size: Int): Iterator[Seq[ReadSegment]]
    Definition Classes
    IterableLike
  149. def sortBy[B](f: (ReadSegment) ⇒ B)(implicit ord: Ordering[B]): Seq[ReadSegment]
    Definition Classes
    SeqLike
  150. def sortWith(lt: (ReadSegment, ReadSegment) ⇒ Boolean): Seq[ReadSegment]
    Definition Classes
    SeqLike
  151. def sorted[B >: ReadSegment](implicit ord: Ordering[B]): Seq[ReadSegment]
    Definition Classes
    SeqLike
  152. def span(p: (ReadSegment) ⇒ Boolean): (Seq[ReadSegment], Seq[ReadSegment])
    Definition Classes
    TraversableLike → GenTraversableLike
  153. def splitAt(n: Int): (Seq[ReadSegment], Seq[ReadSegment])
    Definition Classes
    TraversableLike → GenTraversableLike
  154. def startsWith[B](that: GenSeq[B], offset: Int): Boolean
    Definition Classes
    SeqLike → GenSeqLike
  155. def startsWith[B](that: GenSeq[B]): Boolean
    Definition Classes
    GenSeqLike
  156. def stringPrefix: String
    Definition Classes
    TraversableLike → GenTraversableLike
  157. def sum[B >: ReadSegment](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  158. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  159. def tail: Seq[ReadSegment]
    Definition Classes
    TraversableLike → GenTraversableLike
  160. def tails: Iterator[Seq[ReadSegment]]
    Definition Classes
    TraversableLike
  161. def take(n: Int): Seq[ReadSegment]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  162. def takeRight(n: Int): Seq[ReadSegment]
    Definition Classes
    IterableLike
  163. def takeWhile(p: (ReadSegment) ⇒ Boolean): Seq[ReadSegment]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  164. def templateSegments: Seq[ReadSegment]
  165. def thisCollection: Seq[ReadSegment]
    Attributes
    protected[this]
    Definition Classes
    SeqLike → IterableLike → TraversableLike
  166. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, ReadSegment, Col[ReadSegment]]): Col[ReadSegment]
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  167. def toArray[B >: ReadSegment](implicit arg0: ClassTag[B]): Array[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  168. def toBuffer[B >: ReadSegment]: Buffer[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  169. def toCollection(repr: Seq[ReadSegment]): Seq[ReadSegment]
    Attributes
    protected[this]
    Definition Classes
    SeqLike → IterableLike → TraversableLike
  170. def toIndexedSeq: IndexedSeq[ReadSegment]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  171. def toIterable: Iterable[ReadSegment]
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  172. def toIterator: Iterator[ReadSegment]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  173. def toList: List[ReadSegment]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  174. def toMap[T, U](implicit ev: <:<[ReadSegment, (T, U)]): Map[T, U]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  175. def toParArray: ParArray[T]
    Implicit
    This member is added by an implicit conversion from ReadStructure to CollectionsHaveToParArray[ReadStructure, T] performed by method CollectionsHaveToParArray in scala.collection.parallel. This conversion will take place only if an implicit value of type (ReadStructure) ⇒ GenTraversableOnce[T] is in scope.
    Definition Classes
    CollectionsHaveToParArray
  176. def toSeq: Seq[ReadSegment]
    Definition Classes
    Seq → SeqLike → GenSeqLike → TraversableOnce → GenTraversableOnce
  177. def toSet[B >: ReadSegment]: Set[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  178. def toStream: Stream[ReadSegment]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
  179. def toString(): String

    Generates the String format of the ReadStructure that can be re-parsed.

    Generates the String format of the ReadStructure that can be re-parsed.

    Definition Classes
    ReadStructure → SeqLike → Function1 → TraversableLike → AnyRef → Any
  180. def toTraversable: Traversable[ReadSegment]
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  181. def toVector: Vector[ReadSegment]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  182. def transpose[B](implicit asTraversable: (ReadSegment) ⇒ GenTraversableOnce[B]): Seq[Seq[B]]
    Definition Classes
    GenericTraversableTemplate
    Annotations
    @migration
    Migration

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

  183. def union[B >: ReadSegment, That](that: GenSeq[B])(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  184. def unzip[A1, A2](implicit asPair: (ReadSegment) ⇒ (A1, A2)): (Seq[A1], Seq[A2])
    Definition Classes
    GenericTraversableTemplate
  185. def unzip3[A1, A2, A3](implicit asTriple: (ReadSegment) ⇒ (A1, A2, A3)): (Seq[A1], Seq[A2], Seq[A3])
    Definition Classes
    GenericTraversableTemplate
  186. def updated[B >: ReadSegment, That](index: Int, elem: B)(implicit bf: CanBuildFrom[Seq[ReadSegment], B, That]): That
    Definition Classes
    SeqLike → GenSeqLike
  187. def view(from: Int, until: Int): SeqView[ReadSegment, Seq[ReadSegment]]
    Definition Classes
    SeqLike → IterableLike → TraversableLike
  188. def view: SeqView[ReadSegment, Seq[ReadSegment]]
    Definition Classes
    SeqLike → IterableLike → TraversableLike
  189. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  190. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  191. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  192. def withFilter(p: (ReadSegment) ⇒ Boolean): FilterMonadic[ReadSegment, Seq[ReadSegment]]
    Definition Classes
    TraversableLike → FilterMonadic
  193. def withVariableLastSegment: ReadStructure

    Generates a new ReadStucture that is the same as this one except that the last segment has undefined length.

  194. def zip[A1 >: ReadSegment, B, That](that: GenIterable[B])(implicit bf: CanBuildFrom[Seq[ReadSegment], (A1, B), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  195. def zipAll[B, A1 >: ReadSegment, That](that: GenIterable[B], thisElem: A1, thatElem: B)(implicit bf: CanBuildFrom[Seq[ReadSegment], (A1, B), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  196. def zipWithIndex[A1 >: ReadSegment, That](implicit bf: CanBuildFrom[Seq[ReadSegment], (A1, Int), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  197. def →[B](y: B): (ReadStructure, B)
    Implicit
    This member is added by an implicit conversion from ReadStructure to ArrowAssoc[ReadStructure] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Shadowed Implicit Value Members

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

Inherited from Seq[ReadSegment]

Inherited from Seq[ReadSegment]

Inherited from SeqLike[ReadSegment, Seq[ReadSegment]]

Inherited from GenSeq[ReadSegment]

Inherited from GenSeqLike[ReadSegment, Seq[ReadSegment]]

Inherited from PartialFunction[Int, ReadSegment]

Inherited from (Int) ⇒ ReadSegment

Inherited from Iterable[ReadSegment]

Inherited from Iterable[ReadSegment]

Inherited from IterableLike[ReadSegment, Seq[ReadSegment]]

Inherited from Equals

Inherited from GenIterable[ReadSegment]

Inherited from GenIterableLike[ReadSegment, Seq[ReadSegment]]

Inherited from Traversable[ReadSegment]

Inherited from Immutable

Inherited from Traversable[ReadSegment]

Inherited from GenTraversable[ReadSegment]

Inherited from GenericTraversableTemplate[ReadSegment, Seq]

Inherited from TraversableLike[ReadSegment, Seq[ReadSegment]]

Inherited from GenTraversableLike[ReadSegment, Seq[ReadSegment]]

Inherited from Parallelizable[ReadSegment, ParSeq[ReadSegment]]

Inherited from TraversableOnce[ReadSegment]

Inherited from GenTraversableOnce[ReadSegment]

Inherited from FilterMonadic[ReadSegment, Seq[ReadSegment]]

Inherited from HasNewBuilder[ReadSegment, scala.collection.immutable.Seq[com.fulcrumgenomics.util.ReadSegment] @scala.annotation.unchecked.uncheckedVariance]

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion MonadOps from ReadStructure to MonadOps[ReadSegment]

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

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

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

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

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

Inherited by implicit conversion alternateImplicit from ReadStructure to ForceImplicitAmbiguity

Ungrouped