TargetOrdering

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 compare(a: IndelRealignmentTarget, b: IndelRealignmentTarget): Int

   Order two indel realignment targets by earlier starting position.

   Order two indel realignment targets by earlier starting position.

   a

   Indel realignment target to compare.

   b

   Indel realignment target to compare.

   returns

   Comparison done by starting position.

   Definition Classes

   TargetOrdering → Ordering → Comparator

9. def contains(target: IndelRealignmentTarget, read: AlignmentRecord): Boolean

   Check to see if an indel realignment target contains the given read.

   Check to see if an indel realignment target contains the given read.

   target

   Realignment target to compare.

   read

   Read to compare.

   returns

   True if read alignment is contained in target span.

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

    Definition Classes

    AnyRef

11. def equals(arg0: Any): Boolean

    Definition Classes

    AnyRef → Any

12. def equiv(x: IndelRealignmentTarget, y: IndelRealignmentTarget): Boolean

    Definition Classes

    Ordering → PartialOrdering → Equiv

13. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( classOf[java.lang.Throwable] )

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

    Definition Classes

    AnyRef → Any

15. def gt(x: IndelRealignmentTarget, y: IndelRealignmentTarget): Boolean

    Definition Classes

    Ordering → PartialOrdering

16. def gteq(x: IndelRealignmentTarget, y: IndelRealignmentTarget): Boolean

    Definition Classes

    Ordering → PartialOrdering

17. def hashCode(): Int

    Definition Classes

    AnyRef → Any

18. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

19. def lt(target: IndelRealignmentTarget, read: RichAlignmentRecord): Boolean

    Compares a read to an indel realignment target to see if it starts before the start of the indel realignment target.

    Compares a read to an indel realignment target to see if it starts before the start of the indel realignment target.

    target

    Realignment target to compare.

    read

    Read to compare.

    returns

    True if start of read is before the start of the indel alignment target.

20. def lt(x: IndelRealignmentTarget, y: IndelRealignmentTarget): Boolean

    Definition Classes

    Ordering → PartialOrdering

21. def lteq(x: IndelRealignmentTarget, y: IndelRealignmentTarget): Boolean

    Definition Classes

    Ordering → PartialOrdering

22. def max(x: IndelRealignmentTarget, y: IndelRealignmentTarget): IndelRealignmentTarget

    Definition Classes

    Ordering

23. def min(x: IndelRealignmentTarget, y: IndelRealignmentTarget): IndelRealignmentTarget

    Definition Classes

    Ordering

24. implicit def mkOrderingOps(lhs: IndelRealignmentTarget): Ops

    Definition Classes

    Ordering

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

    Definition Classes

    AnyRef

26. final def notify(): Unit

    Definition Classes

    AnyRef

27. final def notifyAll(): Unit

    Definition Classes

    AnyRef

28. def on[U](f: (U) ⇒ IndelRealignmentTarget): Ordering[U]

    Definition Classes

    Ordering

29. def overlap(a: IndelRealignmentTarget, b: IndelRealignmentTarget): Boolean

    Compares two indel realignment targets to see if they overlap.

    Compares two indel realignment targets to see if they overlap.

    a

    Indel realignment target to compare.

    b

    Indel realignment target to compare.

    returns

    True if two targets overlap.

30. def reverse: Ordering[IndelRealignmentTarget]

    Definition Classes

    Ordering → PartialOrdering

31. def reversed(): Comparator[IndelRealignmentTarget]

    Definition Classes

    Comparator

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

    Definition Classes

    AnyRef

33. def thenComparing[U <: Comparable[_ >: U]](arg0: Function[_ >: IndelRealignmentTarget, _ <: U]): Comparator[IndelRealignmentTarget]

    Definition Classes

    Comparator

34. def thenComparing[U](arg0: Function[_ >: IndelRealignmentTarget, _ <: U], arg1: Comparator[_ >: U]): Comparator[IndelRealignmentTarget]

    Definition Classes

    Comparator

35. def thenComparing(arg0: Comparator[_ >: IndelRealignmentTarget]): Comparator[IndelRealignmentTarget]

    Definition Classes

    Comparator

36. def thenComparingDouble(arg0: ToDoubleFunction[_ >: IndelRealignmentTarget]): Comparator[IndelRealignmentTarget]

    Definition Classes

    Comparator

37. def thenComparingInt(arg0: ToIntFunction[_ >: IndelRealignmentTarget]): Comparator[IndelRealignmentTarget]

    Definition Classes

    Comparator

38. def thenComparingLong(arg0: ToLongFunction[_ >: IndelRealignmentTarget]): Comparator[IndelRealignmentTarget]

    Definition Classes

    Comparator

39. def toString(): String

    Definition Classes

    AnyRef → Any

40. def tryCompare(x: IndelRealignmentTarget, y: IndelRealignmentTarget): Some[Int]

    Definition Classes

    Ordering → PartialOrdering

41. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )