org.hammerlab.genomics.reference

Region

trait Region extends HasContig with Interval

Trait for objects that are associated with an interval on a genomic contig.

Linear Supertypes
Interval, HasContig, Any
Known Subclasses
Position, Slice
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Inherited
  1. Region
  2. Interval
  3. HasContig
  4. Any
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Abstract Value Members

  1. abstract def contigName: ContigName

    Definition Classes
    HasContig

  2. abstract def end: Locus

    0-based end position on a contig.

    0-based end position on a contig.

    Definition Classes
    Interval

  3. abstract def getClass(): Class[_]

    Definition Classes
    Any

  4. abstract def start: Locus

    0-based start position on a contig.

    0-based start position on a contig.

    Definition Classes
    Interval

Concrete Value Members

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

    Definition Classes
    Any

  2. final def ##(): Int

    Definition Classes
    Any

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

    Definition Classes
    Any

  4. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  5. def contains(locus: Locus): Boolean

    Definition Classes
    Interval

  6. def equals(arg0: Any): Boolean

    Definition Classes
    Any

  7. def hashCode(): Int

    Definition Classes
    Any

  8. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  9. def iterator(): Iterator[Locus]

    Iterate through elements in the range.

    Iterate through elements in the range.

    Definition Classes
    Interval

  10. def length: NumLoci

    Number of elements in the range.

    Number of elements in the range.

    Definition Classes
    Interval

  11. def overlaps(other: Region): Boolean

    Does the region overlap another reference region

    Does the region overlap another reference region

    other

    another region on the genome

    returns

    True if the the regions overlap

  12. def overlapsLocus(locus: Locus, halfWindowSize: WindowSize = 0): Boolean

    Does the region overlap the given locus, with halfWindowSize padding?

  13. def toString(): String

    Definition Classes
    Region → Interval → Any

Inherited from Interval

Inherited from HasContig

Inherited from Any

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