org.bdgenomics.adam.models

ReferenceRegionWithOrientation

case class ReferenceRegionWithOrientation(region: ReferenceRegion, negativeStrand: Boolean) extends Ordered[ReferenceRegionWithOrientation] with Product with Serializable

Represents a contiguous region of the reference genome with strand information.

region

The genomic locus as a ReferenceRegion

negativeStrand

Boolean flag as to whether the region is on the forward or reverse strand of the reference region.

Linear Supertypes
Serializable, Serializable, Product, Equals, Ordered[ReferenceRegionWithOrientation], Comparable[ReferenceRegionWithOrientation], AnyRef, Any
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Inherited
  1. ReferenceRegionWithOrientation
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. Ordered
  7. Comparable
  8. AnyRef
  9. Any
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Instance Constructors

  1. new ReferenceRegionWithOrientation(region: ReferenceRegion, negativeStrand: Boolean)

    region

    The genomic locus as a ReferenceRegion

    negativeStrand

    Boolean flag as to whether the region is on the forward or reverse strand of the reference region.

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. def <(that: ReferenceRegionWithOrientation): Boolean

    Definition Classes
    Ordered

  5. def <=(that: ReferenceRegionWithOrientation): Boolean

    Definition Classes
    Ordered

  6. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  8. def >(that: ReferenceRegionWithOrientation): Boolean

    Definition Classes
    Ordered

  9. def >=(that: ReferenceRegionWithOrientation): Boolean

    Definition Classes
    Ordered

  10. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  11. def clone(): AnyRef

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

  12. def compare(that: ReferenceRegionWithOrientation): Int

    Definition Classes
    ReferenceRegionWithOrientation → Ordered

  13. def compareTo(that: ReferenceRegionWithOrientation): Int

    Definition Classes
    Ordered → Comparable

  14. def contains(other: ReferenceRegionWithOrientation): Boolean

  15. def contains(other: ReferencePositionWithOrientation): Boolean

  16. def end: Long

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

    Definition Classes
    AnyRef

  18. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  20. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

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

    Definition Classes
    AnyRef

  22. val negativeStrand: Boolean

    Boolean flag as to whether the region is on the forward or reverse strand of the reference region.

  23. final def notify(): Unit

    Definition Classes
    AnyRef

  24. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  25. def overlaps(other: ReferenceRegionWithOrientation): Boolean

  26. def referenceName: String

  27. val region: ReferenceRegion

    The genomic locus as a ReferenceRegion

  28. def start: Long

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

    Definition Classes
    AnyRef

  30. def toReferenceRegion: ReferenceRegion

  31. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  34. def width: Long

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from Ordered[ReferenceRegionWithOrientation]

Inherited from Comparable[ReferenceRegionWithOrientation]

Inherited from AnyRef

Inherited from Any

Ungrouped