Trait

org.bdgenomics.utils.interval.array

Interval

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trait Interval[T <: Interval[T]] extends Comparable[T]

An interval is a 2-dimensional 0-based coordinate consisting of a closed start value and open end value. Each 2-dimensional coordinate has a defined width. This can be used to express a region of a genome, a transcript, a gene, etc.

T

Recursive type extending Interval. Used for return type of functions overlap() and compareTo()

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Comparable[T], AnyRef, Any
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Abstract Value Members

  1. abstract def compareTo(interval: T): Int

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    Compares the distance between this interval and the specified interval.

    Compares the distance between this interval and the specified interval.

    interval

    Another interval to compare against.

    returns

    Greater than/equal to/less than comparison.

    Definition Classes
    Interval → Comparable
  2. abstract def covers(interval: T): Boolean

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    Return true if the range of positions covered by this interval intersects the range of positions the specified interval covers.

    Return true if the range of positions covered by this interval intersects the range of positions the specified interval covers.

    In many cases, this function is identical to the overlaps function. However, some coordinate spaces may allow two intervals to cover the same start/end interval, while not truly overlapping. E.g., in a genomic coordinate space, two objects may cover the same range on a chromosome, but may have opposite strandedness.

    Essentially, this is a relaxed variant of overlaps where we have projected a complex coordinate space down to a set of 1D ranges. Two intervals cover each other if they are on the same 1D range out of the sets, and if their start/end coordinates overlap.

    interval

    Another interval to compare against.

    returns

    True if two intervals cover intersecting indices in a coordinate space.

    See also

    overlaps

  3. abstract def distance(interval: T): Option[Long]

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    Provides an absolute distance, if defined, between this interval and the specified interval.

    Provides an absolute distance, if defined, between this interval and the specified interval.

    interval

    Another interval to compare against.

    returns

    Absolute distance between this interval and the specified interval, or None if not defined

  4. abstract def end: Long

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    returns

    The end of this interval.

  5. abstract def overlaps(interval: T): Boolean

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    Determines whether Interval intersects with another Interval T.

    Determines whether Interval intersects with another Interval T.

    interval

    Another interval to compare against.

    returns

    True if this interval overlaps with the specified interval.

    See also

    covers

  6. abstract def start: Long

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    returns

    The start of this interval.

Concrete Value Members

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

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  2. final def ##(): Int

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  3. final def ==(arg0: Any): Boolean

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  4. final def asInstanceOf[T0]: T0

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  5. def clone(): AnyRef

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

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  7. def equals(arg0: Any): Boolean

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  8. def finalize(): Unit

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

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  10. def hashCode(): Int

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  11. final def isInstanceOf[T0]: Boolean

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

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  13. final def notify(): Unit

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  14. final def notifyAll(): Unit

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  15. final def synchronized[T0](arg0: ⇒ T0): T0

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  17. final def wait(): Unit

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  18. final def wait(arg0: Long, arg1: Int): Unit

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  19. final def wait(arg0: Long): Unit

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  20. def width: Long

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    A width is the key property of an interval, which can represent a genomic region, a transcript, a gene, etc.

    A width is the key property of an interval, which can represent a genomic region, a transcript, a gene, etc.

    returns

    The width of this interval.

Inherited from Comparable[T]

Inherited from AnyRef

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