Slice

Value Members

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

   

   Definition Classes

   AnyRef → Any

2. final def ##(): Int

   

   Definition Classes

   AnyRef → Any

3. def <(that: Interval): Boolean

   

   Definition Classes

   Ordered

4. def <=(that: Interval): Boolean

   

   Definition Classes

   Ordered

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

   

   Definition Classes

   AnyRef → Any

6. def >(that: Interval): Boolean

   

   Definition Classes

   Ordered

7. def >=(that: Interval): Boolean

   

   Definition Classes

   Ordered

8. def apply(locus: Locus): Byte

   

9. final def asInstanceOf[T0]: T0

   

   Definition Classes

   Any

10. val bases: Seq[Byte]

    

11. def clone(): AnyRef

    

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

12. def compare(other: Interval): Int

    

    Comparisons between ranges.

    Comparisons between ranges. Order is DESCENDING (i.e. reversed) from by start.

    Definition Classes

    Interval → Ordered

13. def compareTo(that: Interval): Int

    

    Definition Classes

    Ordered → Comparable

14. def contains(locus: Locus): Boolean

    

    Definition Classes

    Interval

15. val contigName: ContigName

    

    Definition Classes

    Slice → HasContig

16. val end: Locus

    

    The end position on the genome, *exclusive*.

    The end position on the genome, *exclusive*. Must be non-negative.

    Definition Classes

    Slice → Interval

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. def iterator(): Iterator[Long]

    

    Iterate through elements in the range.

    Iterate through elements in the range.

    Definition Classes

    Interval

22. def length: NumLoci

    

    Number of elements in the range.

    Number of elements in the range.

    Definition Classes

    Interval

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

    

    Definition Classes

    AnyRef

24. final def notify(): Unit

    

    Definition Classes

    AnyRef

25. final def notifyAll(): Unit

    

    Definition Classes

    AnyRef

26. 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

27. def overlapsLocus(locus: Locus, halfWindowSize: Int = 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

28. def regionStr: String

    

    Definition Classes

    Region

29. def slice(sliceStart: Locus, sliceEnd: Locus = end): Seq[Byte]

    

30. val start: Locus

    

    Start position on the genome, inclusive.

    Start position on the genome, inclusive. Must be non-negative.

    Definition Classes

    Slice → Interval

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

    

    Definition Classes

    AnyRef

32. final def wait(): Unit

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )