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. def contains(arg0: Locatable): Boolean
    Definition Classes
    Locatable
  24. val contig: String
  25. def contigsMatch(arg0: Locatable): Boolean
    Definition Classes
    Locatable
  26. def copyToArray[B >: Transcript](xs: Array[B], start: Int, len: Int): Unit
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  27. def copyToArray[B >: Transcript](xs: Array[B]): Unit
    Definition Classes
    TraversableOnce → GenTraversableOnce
  28. def copyToArray[B >: Transcript](xs: Array[B], start: Int): Unit
    Definition Classes
    TraversableOnce → GenTraversableOnce
  29. def copyToBuffer[B >: Transcript](dest: Buffer[B]): Unit
    Definition Classes
    TraversableOnce
  30. def count(p: (Transcript) ⇒ Boolean): Int
    Definition Classes
    TraversableOnce → GenTraversableOnce
  31. def drop(n: Int): Iterable[Transcript]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  32. def dropRight(n: Int): Iterable[Transcript]
    Definition Classes
    IterableLike
  33. def dropWhile(p: (Transcript) ⇒ Boolean): Iterable[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  34. val end: Int
  35. 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
  36. 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
  37. 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
  38. 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
  39. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  40. def equals(arg0: Any): Boolean
    Definition Classes
    Interval → AnyRef → Any
  41. def exists(p: (Transcript) ⇒ Boolean): Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  42. def filter(p: (Transcript) ⇒ Boolean): Iterable[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  43. def filterNot(p: (Transcript) ⇒ Boolean): Iterable[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  44. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  45. def find(p: (Transcript) ⇒ Boolean): Option[Transcript]
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  46. def flatMap[B, That](f: (Transcript) ⇒ GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[Transcript], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  47. def flatten[B](implicit asTraversable: (Transcript) ⇒ GenTraversableOnce[B]): Iterable[B]
    Definition Classes
    GenericTraversableTemplate
  48. def fold[A1 >: Transcript](z: A1)(op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  49. def foldLeft[B](z: B)(op: (B, Transcript) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  50. def foldRight[B](z: B)(op: (Transcript, B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  51. def forall(p: (Transcript) ⇒ Boolean): Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  52. def foreach[U](f: (Transcript) ⇒ U): Unit
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike → TraversableOnce → GenTraversableOnce → FilterMonadic
  53. 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()
  54. def genericBuilder[B]: Builder[B, Iterable[B]]
    Definition Classes
    GenericTraversableTemplate
  55. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  56. def getContig(): String
    Definition Classes
    Interval → Locatable
  57. def getEnd(): Int
    Definition Classes
    Interval → Locatable
  58. def getIntersectionLength(arg0: Interval): Int
    Definition Classes
    Interval
  59. def getLengthOnReference(): Int
    Definition Classes
    Locatable
  60. def getName(): String
    Definition Classes
    Interval
  61. def getStart(): Int
    Definition Classes
    Interval → Locatable
  62. def groupBy[K](f: (Transcript) ⇒ K): Map[K, Iterable[Transcript]]
    Definition Classes
    TraversableLike → GenTraversableLike
  63. def grouped(size: Int): Iterator[Iterable[Transcript]]
    Definition Classes
    IterableLike
  64. def hasDefiniteSize: Boolean
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  65. def hashCode(): Int
    Definition Classes
    Interval → AnyRef → Any
  66. def head: Transcript
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  67. def headOption: Option[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  68. def init: Iterable[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  69. def inits: Iterator[Iterable[Transcript]]
    Definition Classes
    TraversableLike
  70. def intersect(arg0: Interval): Interval
    Definition Classes
    Interval
  71. def intersects(arg0: Interval): Boolean
    Definition Classes
    Interval
  72. def isEmpty: Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  73. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  74. def isNegativeStrand(): Boolean
    Definition Classes
    Interval
  75. def isPositiveStrand(): Boolean
    Definition Classes
    Interval
  76. final def isTraversableAgain: Boolean
    Definition Classes
    TraversableLike → GenTraversableLike → GenTraversableOnce
  77. def iterator: Iterator[Transcript]
    Definition Classes
    Gene → IterableLike → GenIterableLike
  78. def last: Transcript
    Definition Classes
    TraversableLike → GenTraversableLike
  79. def lastOption: Option[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  80. def length(): Int
    Definition Classes
    Interval
  81. def map[B, That](f: (Transcript) ⇒ B)(implicit bf: CanBuildFrom[Iterable[Transcript], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  82. def max[B >: Transcript](implicit cmp: Ordering[B]): Transcript
    Definition Classes
    TraversableOnce → GenTraversableOnce
  83. def maxBy[B](f: (Transcript) ⇒ B)(implicit cmp: Ordering[B]): Transcript
    Definition Classes
    TraversableOnce → GenTraversableOnce
  84. def min[B >: Transcript](implicit cmp: Ordering[B]): Transcript
    Definition Classes
    TraversableOnce → GenTraversableOnce
  85. def minBy[B](f: (Transcript) ⇒ B)(implicit cmp: Ordering[B]): Transcript
    Definition Classes
    TraversableOnce → GenTraversableOnce
  86. def mkString: String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  87. def mkString(sep: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  88. def mkString(start: String, sep: String, end: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  89. val name: String
  90. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  91. val negativeStrand: Boolean
  92. def newBuilder: Builder[Transcript, Iterable[Transcript]]
    Attributes
    protected[this]
    Definition Classes
    GenericTraversableTemplate → HasNewBuilder
  93. def nonEmpty: Boolean
    Definition Classes
    TraversableOnce → GenTraversableOnce
  94. final def notify(): Unit
    Definition Classes
    AnyRef
  95. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  96. def overlaps(arg0: Locatable): Boolean
    Definition Classes
    Locatable
  97. def pad(arg0: Int, arg1: Int): Interval
    Definition Classes
    Interval
  98. def par: ParIterable[Transcript]
    Definition Classes
    Parallelizable
  99. def parCombiner: Combiner[Transcript, ParIterable[Transcript]]
    Attributes
    protected[this]
    Definition Classes
    TraversableLike → Parallelizable
  100. def partition(p: (Transcript) ⇒ Boolean): (Iterable[Transcript], Iterable[Transcript])
    Definition Classes
    TraversableLike → GenTraversableLike
  101. def product[B >: Transcript](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  102. def reduce[A1 >: Transcript](op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  103. def reduceLeft[B >: Transcript](op: (B, Transcript) ⇒ B): B
    Definition Classes
    TraversableOnce
  104. def reduceLeftOption[B >: Transcript](op: (B, Transcript) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  105. def reduceOption[A1 >: Transcript](op: (A1, A1) ⇒ A1): Option[A1]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  106. def reduceRight[B >: Transcript](op: (Transcript, B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  107. def reduceRightOption[B >: Transcript](op: (Transcript, B) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  108. def repr: Iterable[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  109. def reversed: List[Transcript]
    Attributes
    protected[this]
    Definition Classes
    TraversableOnce
  110. def sameElements[B >: Transcript](that: GenIterable[B]): Boolean
    Definition Classes
    IterableLike → GenIterableLike
  111. def scan[B >: Transcript, That](z: B)(op: (B, B) ⇒ B)(implicit cbf: CanBuildFrom[Iterable[Transcript], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  112. def scanLeft[B, That](z: B)(op: (B, Transcript) ⇒ B)(implicit bf: CanBuildFrom[Iterable[Transcript], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  113. 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.

  114. def seq: Iterable[Transcript]
    Definition Classes
    Iterable → GenIterable → Traversable → GenTraversable → Parallelizable → TraversableOnce → GenTraversableOnce
  115. def size: Int
    Definition Classes
    TraversableOnce → GenTraversableOnce
  116. def sizeHintIfCheap: Int
    Attributes
    protected[scala.collection]
    Definition Classes
    GenTraversableOnce
  117. def slice(from: Int, until: Int): Iterable[Transcript]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  118. def sliding(size: Int, step: Int): Iterator[Iterable[Transcript]]
    Definition Classes
    IterableLike
  119. def sliding(size: Int): Iterator[Iterable[Transcript]]
    Definition Classes
    IterableLike
  120. def span(p: (Transcript) ⇒ Boolean): (Iterable[Transcript], Iterable[Transcript])
    Definition Classes
    TraversableLike → GenTraversableLike
  121. def splitAt(n: Int): (Iterable[Transcript], Iterable[Transcript])
    Definition Classes
    TraversableLike → GenTraversableLike
  122. val start: Int
  123. def stringPrefix: String
    Definition Classes
    TraversableLike → GenTraversableLike
  124. def sum[B >: Transcript](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  125. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  126. def tail: Iterable[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  127. def tails: Iterator[Iterable[Transcript]]
    Definition Classes
    TraversableLike
  128. def take(n: Int): Iterable[Transcript]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  129. def takeRight(n: Int): Iterable[Transcript]
    Definition Classes
    IterableLike
  130. def takeWhile(p: (Transcript) ⇒ Boolean): Iterable[Transcript]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  131. def thisCollection: Iterable[Transcript]
    Attributes
    protected[this]
    Definition Classes
    IterableLike → TraversableLike
  132. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, Transcript, Col[Transcript]]): Col[Transcript]
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  133. def toArray[B >: Transcript](implicit arg0: ClassTag[B]): Array[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  134. def toBuffer[B >: Transcript]: Buffer[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  135. def toCollection(repr: Iterable[Transcript]): Iterable[Transcript]
    Attributes
    protected[this]
    Definition Classes
    IterableLike → TraversableLike
  136. def toIndexedSeq: IndexedSeq[Transcript]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  137. def toIterable: Iterable[Transcript]
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  138. def toIterator: Iterator[Transcript]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  139. def toList: List[Transcript]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  140. def toMap[T, U](implicit ev: <:<[Transcript, (T, U)]): Map[T, U]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  141. 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
  142. def toSeq: Seq[Transcript]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  143. def toSet[B >: Transcript]: Set[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  144. def toStream: Stream[Transcript]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
  145. def toString(): String
    Definition Classes
    TraversableLike → Any
  146. def toTraversable: Traversable[Transcript]
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  147. def toVector: Vector[Transcript]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  148. val transcripts: Seq[Transcript]
  149. 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.

  150. def unzip[A1, A2](implicit asPair: (Transcript) ⇒ (A1, A2)): (Iterable[A1], Iterable[A2])
    Definition Classes
    GenericTraversableTemplate
  151. def unzip3[A1, A2, A3](implicit asTriple: (Transcript) ⇒ (A1, A2, A3)): (Iterable[A1], Iterable[A2], Iterable[A3])
    Definition Classes
    GenericTraversableTemplate
  152. def view(from: Int, until: Int): IterableView[Transcript, Iterable[Transcript]]
    Definition Classes
    IterableLike → TraversableLike
  153. def view: IterableView[Transcript, Iterable[Transcript]]
    Definition Classes
    IterableLike → TraversableLike
  154. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  155. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  156. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  157. def withFilter(p: (Transcript) ⇒ Boolean): FilterMonadic[Transcript, Iterable[Transcript]]
    Definition Classes
    TraversableLike → FilterMonadic
  158. def withinDistanceOf(arg0: Locatable, arg1: Int): Boolean
    Definition Classes
    Locatable
  159. def zip[A1 >: Transcript, B, That](that: GenIterable[B])(implicit bf: CanBuildFrom[Iterable[Transcript], (A1, B), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  160. 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
  161. def zipWithIndex[A1 >: Transcript, That](implicit bf: CanBuildFrom[Iterable[Transcript], (A1, Int), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  162. 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