Class

org.bdgenomics.utils.interval.array

ConcreteIntervalArray

Related Doc: package array

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case class ConcreteIntervalArray[K <: Interval[K], T](array: Array[(K, T)], maxIntervalWidth: Long)(implicit evidence$10: ClassTag[T]) extends IntervalArray[K, T] with Product with Serializable

Linear Supertypes
Product, Equals, IntervalArray[K, T], Serializable, Serializable, AnyRef, Any
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Inherited
  1. ConcreteIntervalArray
  2. Product
  3. Equals
  4. IntervalArray
  5. Serializable
  6. Serializable
  7. AnyRef
  8. Any
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Visibility
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Instance Constructors

  1. new ConcreteIntervalArray(array: Array[(K, T)], maxIntervalWidth: Long)(implicit arg0: ClassTag[T])

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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. val array: Array[(K, T)]

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    Definition Classes
    ConcreteIntervalArrayIntervalArray
  5. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any
  6. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  7. def collect(): Array[(K, T)]

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    Collects and returns all elements in this array.

    Collects and returns all elements in this array.

    returns

    An array containing all elements.

    Definition Classes
    IntervalArray
  8. def duplicate(): IntervalArray[K, T]

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    returns

    Makes a copy of the interval array. The underlying array is shallow copied, but the thread unsafe optLastIndex variable is not shared.

    Definition Classes
    ConcreteIntervalArrayIntervalArray
  9. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  10. def filter(pred: ((K, T)) ⇒ Boolean): IntervalArray[K, T]

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    Filters items in an IntervalArray based on a given predicate.

    Filters items in an IntervalArray based on a given predicate.

    pred

    The predicate to filter elements by.

    returns

    A new IntervalArray with filtered elements.

    Definition Classes
    IntervalArray
  11. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  12. def get(rr: K, requireOverlap: Boolean = true): Iterable[(K, T)]

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    Gets all overlapping intervals in array for a given K, however if no overlapping intervals are found, uses the element that is the closest to the query.

    Gets all overlapping intervals in array for a given K, however if no overlapping intervals are found, uses the element that is the closest to the query.

    rr

    The interval to filter by.

    returns

    An Iterable of elements filtered by the query interval containing overlapping or the closest element in array.

    Definition Classes
    IntervalArray
  13. def get(rr: K): Iterable[(K, T)]

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    Gets all overlapping intervals in array for a given query interval.

    Gets all overlapping intervals in array for a given query interval.

    rr

    The interval to filter by.

    returns

    Iterable of elements filtered by the query interval containing overlapping elements in array. If none exist, returns an empty Iterable.

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

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    Definition Classes
    AnyRef → Any
  15. def insert(kvs: Iterator[(K, T)], sorted: Boolean = false): IntervalArray[K, T]

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    Insert an Iterator of items into existing IntervalArray.

    Insert an Iterator of items into existing IntervalArray.

    kvs

    The tuples to insert into IntervalArray.

    returns

    new IntervalArray with inserted values.

    Definition Classes
    IntervalArray
  16. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  17. def length: Int

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    Definition Classes
    IntervalArray
  18. def mapValues[T2](f: (T) ⇒ T2)(implicit arg0: ClassTag[T2]): IntervalArray[K, T2]

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    Maps values from T to T2.

    Maps values from T to T2.

    T2

    The new type to map values to.

    f

    Function mapping T to T2.

    returns

    new IntervalArray with mapped values.

    Definition Classes
    IntervalArray
  19. val maxIntervalWidth: Long

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    Definition Classes
    ConcreteIntervalArrayIntervalArray
  20. def midpoint: Int

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    Definition Classes
    IntervalArray
  21. final def ne(arg0: AnyRef): Boolean

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

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

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    Definition Classes
    AnyRef
  24. def replace(arr: Array[(K, T)], maxWidth: Long): IntervalArray[K, T]

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    Attributes
    protected
    Definition Classes
    ConcreteIntervalArrayIntervalArray
  25. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef
  26. final def wait(): Unit

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

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Product

Inherited from Equals

Inherited from IntervalArray[K, T]

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped