org.bdgenomics.adam.models

ReferencePosition

class ReferencePosition extends ReferenceRegion

Linear Supertypes
ReferenceRegion, Serializable, Serializable, Product, Equals, Interval, Comparable[ReferenceRegion], AnyRef, Any
Ordering
  1. Alphabetic
  2. By inheritance
Inherited
  1. ReferencePosition
  2. ReferenceRegion
  3. Serializable
  4. Serializable
  5. Product
  6. Equals
  7. Interval
  8. Comparable
  9. AnyRef
  10. Any
  1. Hide All
  2. Show all
Learn more about member selection
Visibility
  1. Public
  2. All

Instance Constructors

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

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
    AnyRef
  5. final def ==(arg0: Any): Boolean

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

    Definition Classes
    Any
  7. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  8. def compareTo(that: ReferenceRegion): Int

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

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

    Definition Classes
    ReferenceRegion
  11. def disorient: ReferenceRegion

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

    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.

  13. val end: Long

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

    Definition Classes
    AnyRef
  15. def finalize(): Unit

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

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

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

    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

  19. def intersection(region: ReferenceRegion): ReferenceRegion

    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
  20. def isAdjacent(region: ReferenceRegion): Boolean

    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
  21. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any
  22. def length(): Long

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

    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

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

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

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

    Definition Classes
    AnyRef
  27. val orientation: Strand

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

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

    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
  30. def pad(by: Long): ReferenceRegion

    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
  31. val pos: Long

  32. val referenceName: String

    Definition Classes
    ReferencePositionReferenceRegion
  33. val start: Long

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

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

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

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

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

    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