Packages

case class Transcript(name: String, chrom: String, start: Int, end: Int, cdsStart: Option[Int] = None, cdsEnd: Option[Int] = None, negativeStrand: Boolean, exons: Seq[Exon]) extends Locatable with Product with Serializable

A transcript [mapping] associated with a given gene locus. Contains zero or more exons. The exons should be given in the order of transcription.

Linear Supertypes
Serializable, Serializable, Product, Equals, Locatable, AnyRef, Any
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Inherited
  1. Transcript
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. Locatable
  7. AnyRef
  8. 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, chrom: String, start: Int, end: Int, cdsStart: Option[Int] = None, cdsEnd: Option[Int] = None, negativeStrand: Boolean, 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: Option[Int]
  8. val cdsStart: Option[Int]
  9. val chrom: String
  10. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  11. def contains(arg0: Locatable): Boolean
    Definition Classes
    Locatable
  12. def contigsMatch(arg0: Locatable): Boolean
    Definition Classes
    Locatable
  13. val end: Int
  14. 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
  15. 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
  16. 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
  17. 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
  18. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  19. val exons: Seq[Exon]
  20. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  21. 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()
  22. def genomicOrder: Iterator[Exon]

    The order in which exons appear in the genome

  23. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  24. def getContig(): String
    Definition Classes
    Transcript → Locatable
  25. def getEnd(): Int
    Definition Classes
    Transcript → Locatable
  26. def getLengthOnReference(): Int
    Definition Classes
    Locatable
  27. def getStart(): Int
    Definition Classes
    Transcript → Locatable
  28. def isCoding: Boolean

    True if the transcript is coding, false otherwise.

  29. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  30. def lengthOnGenome: Int

    The length of the transcript mapping on the genome (including introns).

  31. val name: String
  32. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  33. val negativeStrand: Boolean
  34. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  35. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  36. def overlaps(arg0: Locatable): Boolean
    Definition Classes
    Locatable
  37. def positiveStrand: Boolean
  38. val start: Int
  39. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  40. def transcribedLength: Int

    The length of the transcribed product after introns are removed.

  41. def transcriptOrder: Iterator[Exon]

    The order in which exons appear in the transcripts

  42. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  43. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  44. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  45. def withinDistanceOf(arg0: Locatable, arg1: Int): Boolean
    Definition Classes
    Locatable
  46. 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 Locatable

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