org.hammerlab.genomics.reference

Position

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
Ordering
  1. Alphabetic
  2. By inheritance
Inherited
  1. Position
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. HasLocus
  7. Region
  8. Interval
  9. HasContig
  10. AnyRef
  11. Any
  1. Hide All
  2. Show all
Learn more about member selection
Visibility
  1. Public
  2. All

Instance Constructors

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

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 contains(locus: Locus): Boolean

    Definition Classes
    Interval

  9. val contigName: ContigName

    Definition Classes
    Position → HasContig

  10. def end: Locus

    0-based end position on a contig.

    0-based end position on a contig.

    Definition Classes
    Position → Interval

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

    Definition Classes
    AnyRef

  12. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  14. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  15. def iterator(): Iterator[Locus]

    Iterate through elements in the range.

    Iterate through elements in the range.

    Definition Classes
    Interval

  16. def length: NumLoci

    Number of elements in the range.

    Number of elements in the range.

    Definition Classes
    Interval

  17. val locus: Locus

    Definition Classes
    Position → HasLocus

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

    Definition Classes
    AnyRef

  19. final def notify(): Unit

    Definition Classes
    AnyRef

  20. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  21. def overlaps(other: Region): Boolean

    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

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

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

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

    Definition Classes
    Region

  23. def start: Locus

    0-based start position on a contig.

    0-based start position on a contig.

    Definition Classes
    Position → Interval

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

    Definition Classes
    AnyRef

  25. def toString(): String

    Definition Classes
    Position → Region → Interval → AnyRef → Any

  26. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    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