org.bdgenomics.utils.interval.array

IntervalArray

trait IntervalArray[K <: Interval[K], T] extends Serializable

Originally, an IntervalArray was a collection of trees. Alas, we have no trees anymore. I blame global warming.

WARNING: CONTAINS A VARIABLE THAT IS NOT THREAD SAFE TO SAFELY USE THIS VARIABLE IN A SPARK CONTEXT, CREATE A SHALLOW COPY OF THE INTERVAL ARRAY.

See also

optLastIndex

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Abstract Value Members

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

  2. abstract def duplicate(): IntervalArray[K, T]

    returns

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

  3. abstract val maxIntervalWidth: Long

  4. abstract def replace(arr: Array[(K, T)], maxWidth: Long): IntervalArray[K, T]

    Attributes
    protected

Concrete Value Members

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

    Definition Classes
    AnyRef
  2. final def !=(arg0: Any): Boolean

    Definition Classes
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  3. final def ##(): Int

    Definition Classes
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  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
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  5. final def ==(arg0: Any): Boolean

    Definition Classes
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  6. final def asInstanceOf[T0]: T0

    Definition Classes
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  7. def clone(): AnyRef

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

    Collects and returns all elements in this array.

    Collects and returns all elements in this array.

    returns

    An array containing all elements.

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

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

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

    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.

  12. def finalize(): Unit

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

    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.

  14. def get(rr: K): Iterable[(K, T)]

    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.

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

    Definition Classes
    AnyRef → Any
  16. def hashCode(): Int

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

    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.

  18. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any
  19. def length: Int

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

    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.

  21. def midpoint: Int

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

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

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

    Definition Classes
    AnyRef
  25. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
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  26. def toString(): String

    Definition Classes
    AnyRef → Any
  27. final def wait(): Unit

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

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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