Packages

case class Gene(contig: String, start: Int, end: Int, negativeStrand: Boolean, name: String, transcripts: Seq[Transcript]) extends Interval with Iterable[Transcript] with Product with Serializable

A gene with zero or more transcripts, that all are on the same transcription strand.

Linear Supertypes
Serializable, Serializable, Product, Iterable[Transcript], IterableLike[Transcript, Iterable[Transcript]], Equals, GenIterable[Transcript], GenIterableLike[Transcript, Iterable[Transcript]], Traversable[Transcript], GenTraversable[Transcript], GenericTraversableTemplate[Transcript, Iterable], TraversableLike[Transcript, Iterable[Transcript]], GenTraversableLike[Transcript, Iterable[Transcript]], Parallelizable[Transcript, ParIterable[Transcript]], TraversableOnce[Transcript], GenTraversableOnce[Transcript], FilterMonadic[Transcript, Iterable[Transcript]], HasNewBuilder[Transcript, Iterable[com.fulcrumgenomics.util.GeneAnnotations.Transcript] @scala.annotation.unchecked.uncheckedVariance], Interval, Locatable, Cloneable, Comparable[Interval], AnyRef, Any
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Inherited
  1. Gene
  2. Serializable
  3. Serializable
  4. Product
  5. Iterable
  6. IterableLike
  7. Equals
  8. GenIterable
  9. GenIterableLike
  10. Traversable
  11. GenTraversable
  12. GenericTraversableTemplate
  13. TraversableLike
  14. GenTraversableLike
  15. Parallelizable
  16. TraversableOnce
  17. GenTraversableOnce
  18. FilterMonadic
  19. HasNewBuilder
  20. Interval
  21. Locatable
  22. Cloneable
  23. Comparable
  24. AnyRef
  25. 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

Instance Constructors

  1. new Gene(contig: String, start: Int, end: Int, negativeStrand: Boolean, name: String, transcripts: Seq[Transcript])

Type Members

  1. type Self = Iterable[Transcript]
    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 Gene to any2stringadd[Gene] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ++[B >: Transcript, That](that: GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[Transcript], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  5. def ++:[B >: Transcript, That](that: Traversable[B])(implicit bf: CanBuildFrom[Iterable[Transcript], B, That]): That
    Definition Classes
    TraversableLike
  6. def ++:[B >: Transcript, That](that: TraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[Transcript], B, That]): That
    Definition Classes
    TraversableLike
  7. def ->[B](y: B): (Gene, B)
    Implicit
    This member is added by an implicit conversion from Gene to ArrowAssoc[Gene] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  8. def /:[B](z: B)(op: (B, Transcript) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  9. def :\[B](z: B)(op: (Transcript, B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  10. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  11. def abuts(arg0: Interval): Boolean
    Definition Classes
    Interval
  12. def addString(b: StringBuilder): StringBuilder
    Definition Classes
    TraversableOnce
  13. def addString(b: StringBuilder, sep: String): StringBuilder
    Definition Classes
    TraversableOnce
  14. def addString(b: StringBuilder, start: String, sep: String, end: String): StringBuilder
    Definition Classes
    TraversableOnce
  15. def aggregate[B](z: ⇒ B)(seqop: (B, Transcript) ⇒ B, combop: (B, B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  16. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  17. def canEqual(that: Any): Boolean
    Definition Classes
    IterableLike → Equals
  18. def clone(): Interval
    Definition Classes
    Interval → AnyRef
  19. def collect[B, That](pf: PartialFunction[Transcript, B])(implicit bf: CanBuildFrom[Iterable[Transcript], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  20. def collectFirst[B](pf: PartialFunction[Transcript, B]): Option[B]
    Definition Classes
    TraversableOnce
  21. def companion: GenericCompanion[Iterable]
    Definition Classes
    Iterable → GenIterable → Traversable → GenTraversable → GenericTraversableTemplate
  22. def compareTo(arg0: Interval): Int
    Definition Classes
    Interval → Comparable
  23. val contig: String
  24. def copyToArray[B >: Transcript](xs: Array[B], start: Int, len: Int): Unit
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  25. def copyToArray[B >: Transcript](xs: Array[B]): Unit
    Definition Classes
    TraversableOnce → GenTraversableOnce
  26. def copyToArray[B >: Transcript](xs: Array[B], start: Int): Unit
    Definition Classes
    TraversableOnce → GenTraversableOnce
  27. def copyToBuffer[B >: Transcript](dest: Buffer[B]): Unit
    Definition Classes
    TraversableOnce
  28. def count(p: (Transcript) ⇒ Boolean): Int
    Definition Classes
    TraversableOnce → GenTraversableOnce
  29. def drop(n: Int): Iterable[Transcript]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  30. def dropRight(n: Int): Iterable[Transcript]
    Definition Classes
    IterableLike
  31. def dropWhile(p: (Transcript) ⇒ Boolean): Iterable[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  32. val end: Int
  33. def ensuring(cond: (Gene) ⇒ Boolean, msg: ⇒ Any): Gene
    Implicit
    This member is added by an implicit conversion from Gene to Ensuring[Gene] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  34. def ensuring(cond: (Gene) ⇒ Boolean): Gene
    Implicit
    This member is added by an implicit conversion from Gene to Ensuring[Gene] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  35. def ensuring(cond: Boolean, msg: ⇒ Any): Gene
    Implicit
    This member is added by an implicit conversion from Gene to Ensuring[Gene] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  36. def ensuring(cond: Boolean): Gene
    Implicit
    This member is added by an implicit conversion from Gene to Ensuring[Gene] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  37. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  38. def equals(arg0: Any): Boolean
    Definition Classes
    Interval → AnyRef → Any
  39. def exists(p: (Transcript) ⇒ Boolean): Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  40. def filter(p: (Transcript) ⇒ Boolean): Iterable[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  41. def filterNot(p: (Transcript) ⇒ Boolean): Iterable[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  42. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  43. def find(p: (Transcript) ⇒ Boolean): Option[Transcript]
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  44. def flatMap[B, That](f: (Transcript) ⇒ GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[Transcript], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  45. def flatten[B](implicit asTraversable: (Transcript) ⇒ GenTraversableOnce[B]): Iterable[B]
    Definition Classes
    GenericTraversableTemplate
  46. def fold[A1 >: Transcript](z: A1)(op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  47. def foldLeft[B](z: B)(op: (B, Transcript) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  48. def foldRight[B](z: B)(op: (Transcript, B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  49. def forall(p: (Transcript) ⇒ Boolean): Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  50. def foreach[U](f: (Transcript) ⇒ U): Unit
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike → TraversableOnce → GenTraversableOnce → FilterMonadic
  51. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from Gene to StringFormat[Gene] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  52. def genericBuilder[B]: Builder[B, Iterable[B]]
    Definition Classes
    GenericTraversableTemplate
  53. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  54. def getContig(): String
    Definition Classes
    Interval → Locatable
  55. def getEnd(): Int
    Definition Classes
    Interval → Locatable
  56. def getIntersectionLength(arg0: Interval): Int
    Definition Classes
    Interval
  57. def getName(): String
    Definition Classes
    Interval
  58. def getStart(): Int
    Definition Classes
    Interval → Locatable
  59. def groupBy[K](f: (Transcript) ⇒ K): Map[K, Iterable[Transcript]]
    Definition Classes
    TraversableLike → GenTraversableLike
  60. def grouped(size: Int): Iterator[Iterable[Transcript]]
    Definition Classes
    IterableLike
  61. def hasDefiniteSize: Boolean
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  62. def hashCode(): Int
    Definition Classes
    Interval → AnyRef → Any
  63. def head: Transcript
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  64. def headOption: Option[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  65. def init: Iterable[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  66. def inits: Iterator[Iterable[Transcript]]
    Definition Classes
    TraversableLike
  67. def intersect(arg0: Interval): Interval
    Definition Classes
    Interval
  68. def intersects(arg0: Interval): Boolean
    Definition Classes
    Interval
  69. def isEmpty: Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  70. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  71. def isNegativeStrand(): Boolean
    Definition Classes
    Interval
  72. def isPositiveStrand(): Boolean
    Definition Classes
    Interval
  73. final def isTraversableAgain: Boolean
    Definition Classes
    TraversableLike → GenTraversableLike → GenTraversableOnce
  74. def iterator: Iterator[Transcript]
    Definition Classes
    Gene → IterableLike → GenIterableLike
  75. def last: Transcript
    Definition Classes
    TraversableLike → GenTraversableLike
  76. def lastOption: Option[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  77. def length(): Int
    Definition Classes
    Interval
  78. def map[B, That](f: (Transcript) ⇒ B)(implicit bf: CanBuildFrom[Iterable[Transcript], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  79. def max[B >: Transcript](implicit cmp: Ordering[B]): Transcript
    Definition Classes
    TraversableOnce → GenTraversableOnce
  80. def maxBy[B](f: (Transcript) ⇒ B)(implicit cmp: Ordering[B]): Transcript
    Definition Classes
    TraversableOnce → GenTraversableOnce
  81. def min[B >: Transcript](implicit cmp: Ordering[B]): Transcript
    Definition Classes
    TraversableOnce → GenTraversableOnce
  82. def minBy[B](f: (Transcript) ⇒ B)(implicit cmp: Ordering[B]): Transcript
    Definition Classes
    TraversableOnce → GenTraversableOnce
  83. def mkString: String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  84. def mkString(sep: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  85. def mkString(start: String, sep: String, end: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  86. val name: String
  87. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  88. val negativeStrand: Boolean
  89. def newBuilder: Builder[Transcript, Iterable[Transcript]]
    Attributes
    protected[this]
    Definition Classes
    GenericTraversableTemplate → HasNewBuilder
  90. def nonEmpty: Boolean
    Definition Classes
    TraversableOnce → GenTraversableOnce
  91. final def notify(): Unit
    Definition Classes
    AnyRef
  92. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  93. def pad(arg0: Int, arg1: Int): Interval
    Definition Classes
    Interval
  94. def par: ParIterable[Transcript]
    Definition Classes
    Parallelizable
  95. def parCombiner: Combiner[Transcript, ParIterable[Transcript]]
    Attributes
    protected[this]
    Definition Classes
    TraversableLike → Parallelizable
  96. def partition(p: (Transcript) ⇒ Boolean): (Iterable[Transcript], Iterable[Transcript])
    Definition Classes
    TraversableLike → GenTraversableLike
  97. def product[B >: Transcript](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  98. def reduce[A1 >: Transcript](op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  99. def reduceLeft[B >: Transcript](op: (B, Transcript) ⇒ B): B
    Definition Classes
    TraversableOnce
  100. def reduceLeftOption[B >: Transcript](op: (B, Transcript) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  101. def reduceOption[A1 >: Transcript](op: (A1, A1) ⇒ A1): Option[A1]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  102. def reduceRight[B >: Transcript](op: (Transcript, B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  103. def reduceRightOption[B >: Transcript](op: (Transcript, B) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  104. def repr: Iterable[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  105. def reversed: List[Transcript]
    Attributes
    protected[this]
    Definition Classes
    TraversableOnce
  106. def sameElements[B >: Transcript](that: GenIterable[B]): Boolean
    Definition Classes
    IterableLike → GenIterableLike
  107. def scan[B >: Transcript, That](z: B)(op: (B, B) ⇒ B)(implicit cbf: CanBuildFrom[Iterable[Transcript], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  108. def scanLeft[B, That](z: B)(op: (B, Transcript) ⇒ B)(implicit bf: CanBuildFrom[Iterable[Transcript], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  109. def scanRight[B, That](z: B)(op: (Transcript, B) ⇒ B)(implicit bf: CanBuildFrom[Iterable[Transcript], 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.

  110. def seq: Iterable[Transcript]
    Definition Classes
    Iterable → GenIterable → Traversable → GenTraversable → Parallelizable → TraversableOnce → GenTraversableOnce
  111. def size: Int
    Definition Classes
    TraversableOnce → GenTraversableOnce
  112. def sizeHintIfCheap: Int
    Attributes
    protected[scala.collection]
    Definition Classes
    GenTraversableOnce
  113. def slice(from: Int, until: Int): Iterable[Transcript]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  114. def sliding(size: Int, step: Int): Iterator[Iterable[Transcript]]
    Definition Classes
    IterableLike
  115. def sliding(size: Int): Iterator[Iterable[Transcript]]
    Definition Classes
    IterableLike
  116. def span(p: (Transcript) ⇒ Boolean): (Iterable[Transcript], Iterable[Transcript])
    Definition Classes
    TraversableLike → GenTraversableLike
  117. def splitAt(n: Int): (Iterable[Transcript], Iterable[Transcript])
    Definition Classes
    TraversableLike → GenTraversableLike
  118. val start: Int
  119. def stringPrefix: String
    Definition Classes
    TraversableLike → GenTraversableLike
  120. def sum[B >: Transcript](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  121. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  122. def tail: Iterable[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  123. def tails: Iterator[Iterable[Transcript]]
    Definition Classes
    TraversableLike
  124. def take(n: Int): Iterable[Transcript]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  125. def takeRight(n: Int): Iterable[Transcript]
    Definition Classes
    IterableLike
  126. def takeWhile(p: (Transcript) ⇒ Boolean): Iterable[Transcript]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  127. def thisCollection: Iterable[Transcript]
    Attributes
    protected[this]
    Definition Classes
    IterableLike → TraversableLike
  128. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, Transcript, Col[Transcript]]): Col[Transcript]
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  129. def toArray[B >: Transcript](implicit arg0: ClassTag[B]): Array[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  130. def toBuffer[B >: Transcript]: Buffer[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  131. def toCollection(repr: Iterable[Transcript]): Iterable[Transcript]
    Attributes
    protected[this]
    Definition Classes
    IterableLike → TraversableLike
  132. def toIndexedSeq: IndexedSeq[Transcript]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  133. def toIterable: Iterable[Transcript]
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  134. def toIterator: Iterator[Transcript]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  135. def toList: List[Transcript]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  136. def toMap[T, U](implicit ev: <:<[Transcript, (T, U)]): Map[T, U]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  137. def toParArray: ParArray[T]
    Implicit
    This member is added by an implicit conversion from Gene to CollectionsHaveToParArray[Gene, T] performed by method CollectionsHaveToParArray in scala.collection.parallel. This conversion will take place only if an implicit value of type (Gene) ⇒ GenTraversableOnce[T] is in scope.
    Definition Classes
    CollectionsHaveToParArray
  138. def toSeq: Seq[Transcript]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  139. def toSet[B >: Transcript]: Set[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  140. def toStream: Stream[Transcript]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
  141. def toString(): String
    Definition Classes
    TraversableLike → Any
  142. def toTraversable: Traversable[Transcript]
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  143. def toVector: Vector[Transcript]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  144. val transcripts: Seq[Transcript]
  145. def transpose[B](implicit asTraversable: (Transcript) ⇒ 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.

  146. def unzip[A1, A2](implicit asPair: (Transcript) ⇒ (A1, A2)): (Iterable[A1], Iterable[A2])
    Definition Classes
    GenericTraversableTemplate
  147. def unzip3[A1, A2, A3](implicit asTriple: (Transcript) ⇒ (A1, A2, A3)): (Iterable[A1], Iterable[A2], Iterable[A3])
    Definition Classes
    GenericTraversableTemplate
  148. def view(from: Int, until: Int): IterableView[Transcript, Iterable[Transcript]]
    Definition Classes
    IterableLike → TraversableLike
  149. def view: IterableView[Transcript, Iterable[Transcript]]
    Definition Classes
    IterableLike → TraversableLike
  150. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  151. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  152. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  153. def withFilter(p: (Transcript) ⇒ Boolean): FilterMonadic[Transcript, Iterable[Transcript]]
    Definition Classes
    TraversableLike → FilterMonadic
  154. def zip[A1 >: Transcript, B, That](that: GenIterable[B])(implicit bf: CanBuildFrom[Iterable[Transcript], (A1, B), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  155. def zipAll[B, A1 >: Transcript, That](that: GenIterable[B], thisElem: A1, thatElem: B)(implicit bf: CanBuildFrom[Iterable[Transcript], (A1, B), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  156. def zipWithIndex[A1 >: Transcript, That](implicit bf: CanBuildFrom[Iterable[Transcript], (A1, Int), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  157. def →[B](y: B): (Gene, B)
    Implicit
    This member is added by an implicit conversion from Gene to ArrowAssoc[Gene] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Shadowed Implicit Value Members

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

Deprecated Value Members

  1. def getSequence(): String
    Definition Classes
    Interval
    Annotations
    @Deprecated @deprecated
    Deprecated

    (Since version ) see corresponding Javadoc for more information.

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Iterable[Transcript]

Inherited from IterableLike[Transcript, Iterable[Transcript]]

Inherited from Equals

Inherited from GenIterable[Transcript]

Inherited from GenIterableLike[Transcript, Iterable[Transcript]]

Inherited from Traversable[Transcript]

Inherited from GenTraversable[Transcript]

Inherited from GenericTraversableTemplate[Transcript, Iterable]

Inherited from TraversableLike[Transcript, Iterable[Transcript]]

Inherited from GenTraversableLike[Transcript, Iterable[Transcript]]

Inherited from Parallelizable[Transcript, ParIterable[Transcript]]

Inherited from TraversableOnce[Transcript]

Inherited from GenTraversableOnce[Transcript]

Inherited from FilterMonadic[Transcript, Iterable[Transcript]]

Inherited from HasNewBuilder[Transcript, Iterable[com.fulcrumgenomics.util.GeneAnnotations.Transcript] @scala.annotation.unchecked.uncheckedVariance]

Inherited from Interval

Inherited from Locatable

Inherited from Cloneable

Inherited from Comparable[Interval]

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion MonadOps from Gene to MonadOps[Transcript]

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

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

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

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

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

Inherited by implicit conversion alternateImplicit from Gene to ForceImplicitAmbiguity

Ungrouped