org.bdgenomics.utils.intervalarray

IntervalArray

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

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

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Instance Constructors

  1. new IntervalArray(arr: Array[(K, T)], maxIntervalWidth: Long, sorted: Boolean = false)(implicit arg0: ClassTag[T])

    arr

    An array of values for the left side of the join.

    maxIntervalWidth

    The maximum width across all intervals in this array.

    sorted

    True if arr is sorted. If false, we sort arr.

Value Members

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

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

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

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

    Definition Classes
    Any
  5. def clone(): AnyRef

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

    Collects and returns all elements in this array.

    Collects and returns all elements in this array.

    returns

    array containing all elements

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

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

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

    Filters items in IntervalArray based on predicate on (K,V) tuples.

    Filters items in IntervalArray based on predicate on (K,V) tuples.

    pred

    predicate to filter elements by

    returns

    new IntervalArray with filtered elements

  10. def finalize(): Unit

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

    Filters elements in this array by an overlapping Interval.

    Filters elements in this array by an overlapping Interval.

    rr

    Interval to filter by

    returns

    Iterable of elements filtered by Interval rr

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

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

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

    Insert an Iterator of (K,V) items into existing IntervalArray.

    Insert an Iterator of (K,V) items into existing IntervalArray.

    kvs

    (K,V) tuples to insert into IntervalArray

    returns

    new IntervalArray with inserted values

  15. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any
  16. def length: Int

  17. 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

    new type to map values to

    f

    Function mapping T to T2

    returns

    new IntervalArray with mapped values

  18. def midpoint: Int

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

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

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

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

    Definition Classes
    AnyRef
  23. def toString(): String

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

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

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

    Definition Classes
    AnyRef
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    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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