ReferencePositionWithOrientation

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: ReferencePositionWithOrientation): Boolean

   Definition Classes

   Ordered

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

   Definition Classes

   Ordered

9. def >=(that: ReferencePositionWithOrientation): 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: ReferencePositionWithOrientation): Int

    Definition Classes

    ReferencePositionWithOrientation → Ordered

13. def compareTo(that: ReferencePositionWithOrientation): Int

    Definition Classes

    Ordered → Comparable

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. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

18. def liftOverFromReference(mapping: Seq[ReferenceRegionWithOrientation]): Long

    Given a sequence of regions that map from a reference genome to a sequence, returns an index into a sequence.

    Given a sequence of regions that map from a reference genome to a sequence, returns an index into a sequence.

    mapping

    Sequence of reference regions that maps the sequence to a reference genome.

    returns

    Returns an index into a sequence.

    Exceptions thrown

    AssertionError

    Throws an assertion error if the strandedness does not match between the reference position and the mapping regions.

    IllegalArgumentException

    Throws an exception if the index given is out of the range of the mappings given.

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

    Definition Classes

    AnyRef

20. val negativeStrand: Boolean

21. final def notify(): Unit

    Definition Classes

    AnyRef

22. final def notifyAll(): Unit

    Definition Classes

    AnyRef

23. val refPos: ReferencePosition

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

    Definition Classes

    AnyRef

25. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )