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

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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. Feature
  22. Locatable
  23. Cloneable
  24. Comparable
  25. AnyRef
  26. Any
Implicitly
  1. by CollectionsHaveToParArray
  2. by MonadOps
  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 equalsWithStrandAndName(arg0: Any): Boolean
    Definition Classes
    Interval
  42. def exists(p: (Transcript) ⇒ Boolean): Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  43. def filter(p: (Transcript) ⇒ Boolean): Iterable[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  44. def filterNot(p: (Transcript) ⇒ Boolean): Iterable[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  45. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  46. def find(p: (Transcript) ⇒ Boolean): Option[Transcript]
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  47. def flatMap[B, That](f: (Transcript) ⇒ GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[Transcript], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  48. def flatten[B](implicit asTraversable: (Transcript) ⇒ GenTraversableOnce[B]): Iterable[B]
    Definition Classes
    GenericTraversableTemplate
  49. def fold[A1 >: Transcript](z: A1)(op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  50. def foldLeft[B](z: B)(op: (B, Transcript) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  51. def foldRight[B](z: B)(op: (Transcript, B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  52. def forall(p: (Transcript) ⇒ Boolean): Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  53. def foreach[U](f: (Transcript) ⇒ U): Unit
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike → TraversableOnce → GenTraversableOnce → FilterMonadic
  54. 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()
  55. def genericBuilder[B]: Builder[B, Iterable[B]]
    Definition Classes
    GenericTraversableTemplate
  56. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  57. def getContig(): String
    Definition Classes
    Interval → Locatable
  58. def getEnd(): Int
    Definition Classes
    Interval → Locatable
  59. def getIntersectionLength(arg0: Interval): Int
    Definition Classes
    Interval
  60. def getLengthOnReference(): Int
    Definition Classes
    Locatable
  61. def getName(): String
    Definition Classes
    Interval
  62. def getStart(): Int
    Definition Classes
    Interval → Locatable
  63. def getStrand(): Strand
    Definition Classes
    Interval
  64. def groupBy[K](f: (Transcript) ⇒ K): Map[K, Iterable[Transcript]]
    Definition Classes
    TraversableLike → GenTraversableLike
  65. def grouped(size: Int): Iterator[Iterable[Transcript]]
    Definition Classes
    IterableLike
  66. def hasDefiniteSize: Boolean
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  67. def hashCode(): Int
    Definition Classes
    Interval → AnyRef → Any
  68. def head: Transcript
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  69. def headOption: Option[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  70. def init: Iterable[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  71. def inits: Iterator[Iterable[Transcript]]
    Definition Classes
    TraversableLike
  72. def intersect(arg0: Interval): Interval
    Definition Classes
    Interval
  73. def intersects(arg0: Interval): Boolean
    Definition Classes
    Interval
  74. def isEmpty: Boolean
    Definition Classes
    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  75. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  76. def isNegativeStrand(): Boolean
    Definition Classes
    Interval
  77. def isPositiveStrand(): Boolean
    Definition Classes
    Interval
  78. final def isTraversableAgain: Boolean
    Definition Classes
    TraversableLike → GenTraversableLike → GenTraversableOnce
  79. def iterator: Iterator[Transcript]
    Definition Classes
    Gene → IterableLike → GenIterableLike
  80. def last: Transcript
    Definition Classes
    TraversableLike → GenTraversableLike
  81. def lastOption: Option[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  82. def length(): Int
    Definition Classes
    Interval
  83. def map[B, That](f: (Transcript) ⇒ B)(implicit bf: CanBuildFrom[Iterable[Transcript], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike → FilterMonadic
  84. def max[B >: Transcript](implicit cmp: Ordering[B]): Transcript
    Definition Classes
    TraversableOnce → GenTraversableOnce
  85. def maxBy[B](f: (Transcript) ⇒ B)(implicit cmp: Ordering[B]): Transcript
    Definition Classes
    TraversableOnce → GenTraversableOnce
  86. def min[B >: Transcript](implicit cmp: Ordering[B]): Transcript
    Definition Classes
    TraversableOnce → GenTraversableOnce
  87. def minBy[B](f: (Transcript) ⇒ B)(implicit cmp: Ordering[B]): Transcript
    Definition Classes
    TraversableOnce → GenTraversableOnce
  88. def mkString: String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  89. def mkString(sep: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  90. def mkString(start: String, sep: String, end: String): String
    Definition Classes
    TraversableOnce → GenTraversableOnce
  91. val name: String
  92. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  93. val negativeStrand: Boolean
  94. def newBuilder: Builder[Transcript, Iterable[Transcript]]
    Attributes
    protected[this]
    Definition Classes
    GenericTraversableTemplate → HasNewBuilder
  95. def nonEmpty: Boolean
    Definition Classes
    TraversableOnce → GenTraversableOnce
  96. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  97. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  98. def overlaps(arg0: Locatable): Boolean
    Definition Classes
    Locatable
  99. def pad(arg0: Int, arg1: Int): Interval
    Definition Classes
    Interval
  100. def par: ParIterable[Transcript]
    Definition Classes
    Parallelizable
  101. def parCombiner: Combiner[Transcript, ParIterable[Transcript]]
    Attributes
    protected[this]
    Definition Classes
    TraversableLike → Parallelizable
  102. def partition(p: (Transcript) ⇒ Boolean): (Iterable[Transcript], Iterable[Transcript])
    Definition Classes
    TraversableLike → GenTraversableLike
  103. def product[B >: Transcript](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  104. def reduce[A1 >: Transcript](op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  105. def reduceLeft[B >: Transcript](op: (B, Transcript) ⇒ B): B
    Definition Classes
    TraversableOnce
  106. def reduceLeftOption[B >: Transcript](op: (B, Transcript) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  107. def reduceOption[A1 >: Transcript](op: (A1, A1) ⇒ A1): Option[A1]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  108. def reduceRight[B >: Transcript](op: (Transcript, B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  109. def reduceRightOption[B >: Transcript](op: (Transcript, B) ⇒ B): Option[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  110. def repr: Iterable[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  111. def reversed: List[Transcript]
    Attributes
    protected[this]
    Definition Classes
    TraversableOnce
  112. def sameElements[B >: Transcript](that: GenIterable[B]): Boolean
    Definition Classes
    IterableLike → GenIterableLike
  113. def scan[B >: Transcript, That](z: B)(op: (B, B) ⇒ B)(implicit cbf: CanBuildFrom[Iterable[Transcript], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  114. def scanLeft[B, That](z: B)(op: (B, Transcript) ⇒ B)(implicit bf: CanBuildFrom[Iterable[Transcript], B, That]): That
    Definition Classes
    TraversableLike → GenTraversableLike
  115. 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.

  116. def seq: Iterable[Transcript]
    Definition Classes
    Iterable → GenIterable → Traversable → GenTraversable → Parallelizable → TraversableOnce → GenTraversableOnce
  117. def size: Int
    Definition Classes
    TraversableOnce → GenTraversableOnce
  118. def sizeHintIfCheap: Int
    Attributes
    protected[scala.collection]
    Definition Classes
    GenTraversableOnce
  119. def slice(from: Int, until: Int): Iterable[Transcript]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  120. def sliding(size: Int, step: Int): Iterator[Iterable[Transcript]]
    Definition Classes
    IterableLike
  121. def sliding(size: Int): Iterator[Iterable[Transcript]]
    Definition Classes
    IterableLike
  122. def span(p: (Transcript) ⇒ Boolean): (Iterable[Transcript], Iterable[Transcript])
    Definition Classes
    TraversableLike → GenTraversableLike
  123. def splitAt(n: Int): (Iterable[Transcript], Iterable[Transcript])
    Definition Classes
    TraversableLike → GenTraversableLike
  124. val start: Int
  125. def stringPrefix: String
    Definition Classes
    TraversableLike → GenTraversableLike
  126. def sum[B >: Transcript](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  127. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  128. def tail: Iterable[Transcript]
    Definition Classes
    TraversableLike → GenTraversableLike
  129. def tails: Iterator[Iterable[Transcript]]
    Definition Classes
    TraversableLike
  130. def take(n: Int): Iterable[Transcript]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  131. def takeRight(n: Int): Iterable[Transcript]
    Definition Classes
    IterableLike
  132. def takeWhile(p: (Transcript) ⇒ Boolean): Iterable[Transcript]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableLike
  133. def thisCollection: Iterable[Transcript]
    Attributes
    protected[this]
    Definition Classes
    IterableLike → TraversableLike
  134. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, Transcript, Col[Transcript]]): Col[Transcript]
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
  135. def toArray[B >: Transcript](implicit arg0: ClassTag[B]): Array[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  136. def toBuffer[B >: Transcript]: Buffer[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  137. def toCollection(repr: Iterable[Transcript]): Iterable[Transcript]
    Attributes
    protected[this]
    Definition Classes
    IterableLike → TraversableLike
  138. def toIndexedSeq: IndexedSeq[Transcript]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  139. def toIterable: Iterable[Transcript]
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  140. def toIterator: Iterator[Transcript]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  141. def toList: List[Transcript]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  142. def toMap[T, U](implicit ev: <:<[Transcript, (T, U)]): Map[T, U]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  143. 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
  144. def toSeq: Seq[Transcript]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  145. def toSet[B >: Transcript]: Set[B]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  146. def toStream: Stream[Transcript]
    Definition Classes
    IterableLike → TraversableLike → GenTraversableOnce
  147. def toString(): String
    Definition Classes
    TraversableLike → Any
  148. def toTraversable: Traversable[Transcript]
    Definition Classes
    TraversableLike → TraversableOnce → GenTraversableOnce
    Annotations
    @deprecatedOverriding( ... , "2.11.0" )
  149. def toVector: Vector[Transcript]
    Definition Classes
    TraversableOnce → GenTraversableOnce
  150. val transcripts: Seq[Transcript]
  151. 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.

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

    (Since version ) see corresponding Javadoc for more information.

  2. 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 Feature

Inherited from Locatable

Inherited from Cloneable

Inherited from Comparable[Interval]

Inherited from AnyRef

Inherited from Any

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

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

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