Object

org.bdgenomics.adam.rdd.read.realignment

TargetOrdering

Related Doc: package realignment

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object TargetOrdering extends Ordering[IndelRealignmentTarget]

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

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    Definition Classes
    Ordering

Value Members

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

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    Definition Classes
    AnyRef → Any
  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  4. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any
  5. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  6. def compare(a: IndelRealignmentTarget, b: IndelRealignmentTarget): Int

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

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    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.

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

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    Definition Classes
    AnyRef
  9. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  10. def equiv(x: IndelRealignmentTarget, y: IndelRealignmentTarget): Boolean

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    Definition Classes
    Ordering → PartialOrdering → Equiv
  11. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  12. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any
  13. def gt(x: IndelRealignmentTarget, y: IndelRealignmentTarget): Boolean

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    Definition Classes
    Ordering → PartialOrdering
  14. def gteq(x: IndelRealignmentTarget, y: IndelRealignmentTarget): Boolean

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    Definition Classes
    Ordering → PartialOrdering
  15. def hashCode(): Int

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    Definition Classes
    AnyRef → Any
  16. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  17. def lt(target: IndelRealignmentTarget, read: RichAlignmentRecord): Boolean

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    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.

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

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    Definition Classes
    Ordering → PartialOrdering
  19. def lteq(x: IndelRealignmentTarget, y: IndelRealignmentTarget): Boolean

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    Definition Classes
    Ordering → PartialOrdering
  20. def max(x: IndelRealignmentTarget, y: IndelRealignmentTarget): IndelRealignmentTarget

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    Definition Classes
    Ordering
  21. def min(x: IndelRealignmentTarget, y: IndelRealignmentTarget): IndelRealignmentTarget

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    Definition Classes
    Ordering
  22. implicit def mkOrderingOps(lhs: IndelRealignmentTarget): Ops

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    Definition Classes
    Ordering
  23. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  24. final def notify(): Unit

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    Definition Classes
    AnyRef
  25. final def notifyAll(): Unit

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    Definition Classes
    AnyRef
  26. def on[U](f: (U) ⇒ IndelRealignmentTarget): Ordering[U]

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    Definition Classes
    Ordering
  27. def overlap(a: IndelRealignmentTarget, b: IndelRealignmentTarget): Boolean

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    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.

  28. def reverse: Ordering[IndelRealignmentTarget]

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    Definition Classes
    Ordering → PartialOrdering
  29. def reversed(): Comparator[IndelRealignmentTarget]

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    Definition Classes
    Comparator
  30. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef
  31. def thenComparing[U <: Comparable[_ >: U]](arg0: Function[_ >: IndelRealignmentTarget, _ <: U]): Comparator[IndelRealignmentTarget]

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

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    Definition Classes
    Comparator
  33. def thenComparing(arg0: Comparator[_ >: IndelRealignmentTarget]): Comparator[IndelRealignmentTarget]

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    Definition Classes
    Comparator
  34. def thenComparingDouble(arg0: ToDoubleFunction[_ >: IndelRealignmentTarget]): Comparator[IndelRealignmentTarget]

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    Definition Classes
    Comparator
  35. def thenComparingInt(arg0: ToIntFunction[_ >: IndelRealignmentTarget]): Comparator[IndelRealignmentTarget]

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    Definition Classes
    Comparator
  36. def thenComparingLong(arg0: ToLongFunction[_ >: IndelRealignmentTarget]): Comparator[IndelRealignmentTarget]

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    Definition Classes
    Comparator
  37. def toString(): String

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    Definition Classes
    AnyRef → Any
  38. def tryCompare(x: IndelRealignmentTarget, y: IndelRealignmentTarget): Some[Int]

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    Definition Classes
    Ordering → PartialOrdering
  39. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  40. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
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    Annotations
    @throws( ... )
  41. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Ordering[IndelRealignmentTarget]

Inherited from PartialOrdering[IndelRealignmentTarget]

Inherited from Equiv[IndelRealignmentTarget]

Inherited from Serializable

Inherited from Serializable

Inherited from Comparator[IndelRealignmentTarget]

Inherited from AnyRef

Inherited from Any

Ungrouped