Class/Object

org.bdgenomics.adam.models

ReferencePosition

Related Docs: object ReferencePosition | package models

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class ReferencePosition extends ReferenceRegion

Linear Supertypes
ReferenceRegion, Serializable, Serializable, Product, Equals, Interval, Comparable[ReferenceRegion], AnyRef, Any
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Inherited
  1. ReferencePosition
  2. ReferenceRegion
  3. Serializable
  4. Serializable
  5. Product
  6. Equals
  7. Interval
  8. Comparable
  9. AnyRef
  10. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new ReferencePosition(referenceName: String, pos: Long, orientation: Strand = Strand.INDEPENDENT)

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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 compareTo(that: ReferenceRegion): Int

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    Definition Classes
    ReferenceRegion → Comparable
  7. def contains(other: ReferenceRegion): Boolean

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    Definition Classes
    ReferenceRegion
  8. def contains(other: ReferencePosition): Boolean

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    Definition Classes
    ReferenceRegion
  9. def disorient: ReferenceRegion

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    Definition Classes
    ReferenceRegion
  10. def distance(other: ReferenceRegion): Option[Long]

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    Returns the distance between this reference region and another region in the reference space.

    Returns the distance between this reference region and another region in the reference space.

    other

    Region to compare against.

    returns

    Returns an option containing the distance between two points. If the point is not in our reference space, we return an empty option (None).

    Definition Classes
    ReferenceRegion
    Note

    Distance here is defined as the minimum distance between any point within this region, and any point within the other region we are measuring against. If the two sets overlap, the distance will be 0. If the sets abut, the distance will be 1. Else, the distance will be greater.

  11. val end: Long

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    The 0-based residue-coordinate for the first residue after the start which is not in the region -- i.e.

    The 0-based residue-coordinate for the first residue after the start which is not in the region -- i.e. [start, end) define a 0-based half-open interval.

    Definition Classes
    ReferenceRegion → Interval
  12. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  13. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  14. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any
  15. def hashCode(): Int

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    Definition Classes
    ReferenceRegion → AnyRef → Any
  16. def hull(region: ReferenceRegion): ReferenceRegion

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    Creates a region corresponding to the convex hull of two regions.

    Creates a region corresponding to the convex hull of two regions. Has no preconditions about the adjacency or overlap of two regions. However, regions must be in the same reference space.

    region

    Other region to compute hull of with this region.

    returns

    The convex hull of both unions.

    Definition Classes
    ReferenceRegion
    Exceptions thrown

    AssertionError Thrown if regions are in different reference spaces.

    See also

    merge

  17. def intersection(region: ReferenceRegion): ReferenceRegion

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    Calculates the intersection of two reference regions.

    Calculates the intersection of two reference regions.

    region

    Region to intersect with.

    returns

    A smaller reference region.

    Definition Classes
    ReferenceRegion
  18. def isAdjacent(region: ReferenceRegion): Boolean

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    Returns whether two regions are adjacent.

    Returns whether two regions are adjacent. Adjacent regions do not overlap, but have no separation between start/end.

    region

    Region to compare against.

    returns

    True if regions are adjacent.

    Definition Classes
    ReferenceRegion
  19. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  20. def length(): Long

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    Definition Classes
    ReferenceRegion
  21. def merge(region: ReferenceRegion): ReferenceRegion

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    Merges two reference regions that are contiguous.

    Merges two reference regions that are contiguous.

    region

    Other region to merge with this region.

    returns

    The merger of both unions.

    Definition Classes
    ReferenceRegion
    Exceptions thrown

    AssertionError Thrown if regions are not overlapping or adjacent.

    See also

    hull

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

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

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

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    Definition Classes
    AnyRef
  25. val orientation: Strand

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    Definition Classes
    ReferencePositionReferenceRegion
  26. def overlaps(other: ReferenceRegion): Boolean

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    Definition Classes
    ReferenceRegion
  27. def pad(byStart: Long, byEnd: Long): ReferenceRegion

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    byStart

    The number of bases to move the start position forward by.

    byEnd

    The number of bases to move the end position back by.

    returns

    Returns a new reference region where the start and/or end have been moved.

    Definition Classes
    ReferenceRegion
  28. def pad(by: Long): ReferenceRegion

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    by

    The number of bases to extend the region by from both the start and the end.

    returns

    Returns a new reference region where the start and end have been moved.

    Definition Classes
    ReferenceRegion
  29. val pos: Long

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  30. val referenceName: String

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    Definition Classes
    ReferencePositionReferenceRegion
  31. val start: Long

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    The 0-based residue-coordinate for the start of the region

    The 0-based residue-coordinate for the start of the region

    Definition Classes
    ReferenceRegion → Interval
  32. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef
  33. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  34. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  35. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  36. def width: Long

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    Definition Classes
    Interval

Inherited from ReferenceRegion

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from Interval

Inherited from Comparable[ReferenceRegion]

Inherited from AnyRef

Inherited from Any

Ungrouped