Packages

case class Transcript(name: String, start: Int, end: Int, cdsStart: Int, cdsEnd: Int, exons: Seq[Exon]) extends Product with Serializable

A transcript associated with a given gene (which stores the transcription strand). Contains zero or more exons. The exons should be given in transcript order.

Linear Supertypes
Serializable, Serializable, Product, Equals, AnyRef, Any
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Inherited
  1. Transcript
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. AnyRef
  7. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new Transcript(name: String, start: Int, end: Int, cdsStart: Int, cdsEnd: Int, exons: Seq[Exon])

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 Transcript to any2stringadd[Transcript] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (Transcript, B)
    Implicit
    This member is added by an implicit conversion from Transcript to ArrowAssoc[Transcript] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  5. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  6. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  7. val cdsEnd: Int
  8. val cdsStart: Int
  9. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  10. val end: Int
  11. def ensuring(cond: (Transcript) ⇒ Boolean, msg: ⇒ Any): Transcript
    Implicit
    This member is added by an implicit conversion from Transcript to Ensuring[Transcript] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  12. def ensuring(cond: (Transcript) ⇒ Boolean): Transcript
    Implicit
    This member is added by an implicit conversion from Transcript to Ensuring[Transcript] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  13. def ensuring(cond: Boolean, msg: ⇒ Any): Transcript
    Implicit
    This member is added by an implicit conversion from Transcript to Ensuring[Transcript] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  14. def ensuring(cond: Boolean): Transcript
    Implicit
    This member is added by an implicit conversion from Transcript to Ensuring[Transcript] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  15. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  16. val exons: Seq[Exon]
  17. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  18. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from Transcript to StringFormat[Transcript] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  19. def genomicOrder: Iterator[Exon]

    The order in which exons appear in the genome

  20. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  21. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  22. val name: String
  23. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  24. final def notify(): Unit
    Definition Classes
    AnyRef
  25. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  26. val start: Int
  27. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  28. def transcriptOrder: Iterator[Exon]

    The order in which exons appear in the transcripts

  29. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  30. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  31. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  32. def →[B](y: B): (Transcript, B)
    Implicit
    This member is added by an implicit conversion from Transcript to ArrowAssoc[Transcript] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

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

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

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

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

Ungrouped