org.bdgenomics.adam.rdd.read.realignment

# TargetOrdering

#### object TargetOrdering extends Ordering[IndelRealignmentTarget]

Linear Supertypes
Ordering[IndelRealignmentTarget], PartialOrdering[IndelRealignmentTarget], Equiv[IndelRealignmentTarget], Serializable, Serializable, Comparator[IndelRealignmentTarget], AnyRef, Any
Ordering

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2. By inheritance

Inherited

1. TargetOrdering
2. Ordering
3. PartialOrdering
4. Equiv
5. Serializable
6. Serializable
7. Comparator
8. AnyRef
9. Any

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### Type Members

1. #### class Ops extends AnyRef

   Definition Classes
     Ordering

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

    Definition Classes
      AnyRef

32. #### def toString(): String

    Definition Classes
      AnyRef → Any

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

    Definition Classes
      Ordering → PartialOrdering

34. #### final def wait(): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

36. #### final def wait(arg0: Long): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

### Inherited from Ordering[IndelRealignmentTarget]

### Inherited from PartialOrdering[IndelRealignmentTarget]

### Inherited from Equiv[IndelRealignmentTarget]

### Inherited from Serializable

### Inherited from Comparator[IndelRealignmentTarget]

### Inherited from AnyRef

### Inherited from Any

### Ungrouped