Class/Object

org.hammerlab.genomics.reference

Position

Related Docs: object Position | package reference

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case class Position(contigName: ContigName, locus: Locus) extends Region with HasLocus with Product with Serializable

Base trait for classes that logically exist at one genomic locus.

Linear Supertypes
Serializable, Serializable, Product, Equals, HasLocus, Region, Interval, HasContig, AnyRef, Any
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Inherited
  1. Position
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. HasLocus
  7. Region
  8. Interval
  9. HasContig
  10. AnyRef
  11. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new Position(contigName: ContigName, locus: Locus)

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Value Members

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

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any

  3. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  4. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  5. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  6. def contains(locus: Locus): Boolean

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    Definition Classes
    Interval

  7. val contigName: ContigName

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    Definition Classes
    Position → HasContig

  8. def end: Locus

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    0-based end position on a contig.

    0-based end position on a contig.

    Definition Classes
    Position → Interval

  9. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  10. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

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

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    Definition Classes
    AnyRef → Any

  12. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  13. def iterator(): Iterator[Locus]

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    Iterate through elements in the range.

    Iterate through elements in the range.

    Definition Classes
    Interval

  14. def length: NumLoci

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    Number of elements in the range.

    Number of elements in the range.

    Definition Classes
    Interval

  15. val locus: Locus

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    Definition Classes
    Position → HasLocus

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

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    Definition Classes
    AnyRef

  17. final def notify(): Unit

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    Definition Classes
    AnyRef

  18. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  19. def overlaps(other: Region): Boolean

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    Does the region overlap another reference region

    Does the region overlap another reference region

    other

    another region on the genome

    returns

    True if the the regions overlap

    Definition Classes
    Region

  20. def overlapsLocus(locus: Locus, halfWindowSize: WindowSize = 0): Boolean

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    Does the region overlap the given locus, with halfWindowSize padding?

    Does the region overlap the given locus, with halfWindowSize padding?

    Definition Classes
    Region

  21. def start: Locus

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    0-based start position on a contig.

    0-based start position on a contig.

    Definition Classes
    Position → Interval

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

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    Definition Classes
    AnyRef

  23. def toString(): String

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    Definition Classes
    Position → Region → Interval → AnyRef → Any

  24. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  25. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from HasLocus

Inherited from Region

Inherited from Interval

Inherited from HasContig

Inherited from AnyRef

Inherited from Any

Ungrouped