org.bdgenomics.adam.models

Transcript

case class Transcript(id: String, names: Seq[String], geneId: String, strand: Boolean, exons: Iterable[Exon], cds: Iterable[CDS], utrs: Iterable[UTR]) extends Product with Serializable

A transcript model (here represented as a value of the Transcript class) is a simple, hierarchical model containing a collection of exon models as well as an associated gene identifier, transcript identifier, and a set of common names (synonyms).

id

the (unique) identifier of the Transcript

names

Common names for the transcript

geneId

The (unique) identifier of the gene to which the transcript belongs

exons

The set of exons in the transcript model; each of these contain a reference region whose coordinates are in genomic space.

cds

the set of CDS regions (the subset of the exons that are coding) for this transcript

utrs

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Instance Constructors

  1. new Transcript(id: String, names: Seq[String], geneId: String, strand: Boolean, exons: Iterable[Exon], cds: Iterable[CDS], utrs: Iterable[UTR])

    id

    the (unique) identifier of the Transcript

    names

    Common names for the transcript

    geneId

    The (unique) identifier of the gene to which the transcript belongs

    exons

    The set of exons in the transcript model; each of these contain a reference region whose coordinates are in genomic space.

    cds

    the set of CDS regions (the subset of the exons that are coding) for this transcript

    utrs

Value Members

  1. final def !=(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  2. final def !=(arg0: Any): Boolean

    Definition Classes
    Any
  3. final def ##(): Int

    Definition Classes
    AnyRef → Any
  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
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  5. final def ==(arg0: Any): Boolean

    Definition Classes
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  6. final def asInstanceOf[T0]: T0

    Definition Classes
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  7. val cds: Iterable[CDS]

    the set of CDS regions (the subset of the exons that are coding) for this transcript

  8. def clone(): AnyRef

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    protected[java.lang]
    Definition Classes
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    @throws( ... )
  9. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  10. val exons: Iterable[Exon]

    The set of exons in the transcript model; each of these contain a reference region whose coordinates are in genomic space.

  11. def extractCodingSequence(referenceSequence: String): String

    Returns the _coding sequence_ of the Transcript -- essentially, the subset of the exon(s) after the translation-start codon and before the translation-stop codon, as annotated in the Exon and CDS objects of the transcript.

    Returns the _coding sequence_ of the Transcript -- essentially, the subset of the exon(s) after the translation-start codon and before the translation-stop codon, as annotated in the Exon and CDS objects of the transcript.

    referenceSequence

    The reference sequence (e.g. chromosomal sequence) with respect to which the Transcript's coordinates or locators are given

    returns

    the String representation of this Transcript's spliced mRNA sequence

  12. def extractSplicedmRNASequence(referenceSequence: String): String

    Returns the _exonic_ sequence of the Transcript -- basically, the sequences of each exon concatenated together, with the intervening intronic sequences omitted.

    Returns the _exonic_ sequence of the Transcript -- basically, the sequences of each exon concatenated together, with the intervening intronic sequences omitted.

    referenceSequence

    The reference sequence (e.g. chromosomal sequence) with respect to which the Transcript's coordinates or locators are given

    returns

    the String representation of this Transcript's spliced mRNA sequence

  13. def extractTranscribedRNASequence(referenceSequence: String): String

    Returns the concatenated sequence of the exons of the Transcript.

    Returns the concatenated sequence of the exons of the Transcript.

    referenceSequence

    The reference sequence (e.g. chromosomal sequence) with respect to which the Transcript's coordinates or locators are given

    returns

    the String representation of this Transcript's spliced mRNA sequence

  14. def finalize(): Unit

    Attributes
    protected[java.lang]
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    @throws( classOf[java.lang.Throwable] )
  15. val geneId: String

    The (unique) identifier of the gene to which the transcript belongs

  16. final def getClass(): Class[_]

    Definition Classes
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  17. val id: String

    the (unique) identifier of the Transcript

  18. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any
  19. val names: Seq[String]

    Common names for the transcript

  20. final def ne(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  21. final def notify(): Unit

    Definition Classes
    AnyRef
  22. final def notifyAll(): Unit

    Definition Classes
    AnyRef
  23. lazy val region: ReferenceRegion

  24. val strand: Boolean

  25. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
    AnyRef
  26. val utrs: Iterable[UTR]

  27. final def wait(): Unit

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    @throws( ... )
  28. final def wait(arg0: Long, arg1: Int): Unit

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  29. final def wait(arg0: Long): Unit

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