Trait/Object

org.bdgenomics.utils.interval.array

IntervalArray

Related Docs: object IntervalArray | package array

Permalink

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

Linear Supertypes
Serializable, Serializable, AnyRef, Any
Known Subclasses
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. IntervalArray
  2. Serializable
  3. Serializable
  4. AnyRef
  5. Any
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

Abstract Value Members

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

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

    Permalink

    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

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

    Permalink
    Attributes
    protected

Concrete Value Members

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

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

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

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

    Permalink
    Definition Classes
    Any
  5. def clone(): AnyRef

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

    Permalink

    Collects and returns all elements in this array.

    Collects and returns all elements in this array.

    returns

    An array containing all elements.

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

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

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

    Permalink

    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.

  10. def finalize(): Unit

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

    Permalink

    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.

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

    Permalink

    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.

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

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

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

    Permalink

    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.

  16. final def isInstanceOf[T0]: Boolean

    Permalink
    Definition Classes
    Any
  17. def length: Int

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

    Permalink

    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.

  19. def midpoint: Int

    Permalink
  20. final def ne(arg0: AnyRef): Boolean

    Permalink
    Definition Classes
    AnyRef
  21. final def notify(): Unit

    Permalink
    Definition Classes
    AnyRef
  22. final def notifyAll(): Unit

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

    Permalink
    Definition Classes
    AnyRef
  24. def toString(): String

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

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

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

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped