Packages

c

feature

FeatureBuilder

final class FeatureBuilder extends AnyRef

A builder for Features.

Feature properties such as Blocks, name, gene name, and CDS start and end can be added one by one. The appropriate type in the Feature hierarchy is determined automatically based on the properties that have been added.

The Feature is obtained by calling get.

The following are the valid combinations of provided properties and the types they give rise to.

One or more blocks, optional feature name, no gene name, no CDS start, no CDS end -> GenericFeature

One or more blocks, optional feature name, a gene name, no CDS start, no CDS end -> Transcript

One or more blocks, optional feature name, optional gene name, a CDS start, a CDS end -> MessengerRNA. If the CDS is invalid (length < 6 or length not divisible by 3) a Transcript is returned instead.

Any other combination of properties results in an IllegalArgumentException when calling get.

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Instance Constructors

  1. new FeatureBuilder(blocks: List[Block] = Nil, cdsStart: Option[Int] = None, cdsEnd: Option[Int] = None, featureId: Option[String] = None, geneId: Option[String] = None)

Value Members

  1. final def !=(arg0: Any): Boolean
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  2. final def ##(): Int
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  3. final def ==(arg0: Any): Boolean
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  4. def addBlock(b: Block): FeatureBuilder

    Returns a new FeatureBuilder with an additional Block added.

    Returns a new FeatureBuilder with an additional Block added.

    The new Block must be on the same chromosome as any existing Blocks in this FeatureBuilder, have the same Orientation, and not overlap any existing Blocks.

    b

    New Block to add

    returns

    New FeatureBuilder with the same properties as this plus the new Block added

  5. final def asInstanceOf[T0]: T0
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  6. val blocks: List[Block]
  7. val cdsEnd: Option[Int]
  8. val cdsStart: Option[Int]
  9. def clone(): AnyRef
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  10. final def eq(arg0: AnyRef): Boolean
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  11. def equals(arg0: Any): Boolean
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  12. val featureId: Option[String]
  13. def finalize(): Unit
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    @throws( classOf[java.lang.Throwable] )
  14. val geneId: Option[String]
  15. def get(): Feature

    Returns a Feature built from the provided properties.

    Returns a Feature built from the provided properties.

    The type of the returned object depends on which properties have been provided. Certain combinations of provided properties are invalid. See FeatureBuilder documentation for details.

    returns

    The specified Feature

  16. final def getClass(): Class[_]
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  17. def hashCode(): Int
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  18. final def isInstanceOf[T0]: Boolean
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  19. final def ne(arg0: AnyRef): Boolean
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  20. final def notify(): Unit
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  21. final def notifyAll(): Unit
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  22. def setCdsEnd(e: Int): FeatureBuilder

    Returns a new FeatureBuilder with the specified CDS end.

    Returns a new FeatureBuilder with the specified CDS end.

    If this FeatureBuilder already has a CDS end specified, the returned object will have the new CDS end and will have no memory of the previous CDS end.

    e

    New zero-based CDS end position as in MessengerRNA.cdsEnd

    returns

    New FeatureBuilder with the same properties as this but the new CDS end

  23. def setCdsStart(s: Int): FeatureBuilder

    Returns a new FeatureBuilder with the specified CDS start.

    Returns a new FeatureBuilder with the specified CDS start.

    If this FeatureBuilder already has a CDS start specified, the returned object will have the new CDS start and will have no memory of the previous CDS start.

    s

    New zero-based CDS start position as in MessengerRNA.cdsStart

    returns

    New FeatureBuilder with the same properties as this but the new CDS start

  24. def setFeatureId(t: String): FeatureBuilder

    Returns a new FeatureBuilder with the specified feature name.

    Returns a new FeatureBuilder with the specified feature name.

    If this FeatureBuilder already has a feature name specified, the returned object will have the new feature name and will have no memory of the previous feature name.

    t

    New feature name

    returns

    New FeatureBuilder with the same properties as this but the new feature name

  25. def setGeneId(g: String): FeatureBuilder

    Returns a new FeatureBuilder with the specified gene name.

    Returns a new FeatureBuilder with the specified gene name.

    If this FeatureBuilder already has a gene name specified, the returned object will have the new gene name and will have no memory of the previous gene name.

    g

    New gene name

    returns

    New FeatureBuilder with the same properties as this but the new gene name

  26. final def synchronized[T0](arg0: ⇒ T0): T0
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  27. def toString(): String
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  28. final def wait(): Unit
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  29. final def wait(arg0: Long, arg1: Int): Unit
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  30. final def wait(arg0: Long): Unit
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