Trait/Object

org.hammerlab.genomics.reference

Region

Related Docs: object Region | package reference

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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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Visibility
  1. Public
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Abstract Value Members

  1. abstract def contigName: ContigName

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    Definition Classes
    HasContig

  2. abstract def end: Locus

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    0-based end position on a contig.

    0-based end position on a contig.

    Definition Classes
    Interval

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

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    Definition Classes
    Any

  4. abstract def start: Locus

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    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

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    Definition Classes
    Any

  2. final def ##(): Int

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    Definition Classes
    Any

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

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    Definition Classes
    Any

  4. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  5. def contains(locus: Locus): Boolean

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    Definition Classes
    Interval

  6. def equals(arg0: Any): Boolean

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    Definition Classes
    Any

  7. def hashCode(): Int

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    Definition Classes
    Any

  8. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  9. def iterator(): Iterator[Locus]

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    Iterate through elements in the range.

    Iterate through elements in the range.

    Definition Classes
    Interval

  10. def length: NumLoci

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    Number of elements in the range.

    Number of elements in the range.

    Definition Classes
    Interval

  11. def overlaps(other: Region): Boolean

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    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

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

  13. def toString(): String

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    Definition Classes
    Region → Interval → Any

Inherited from Interval

Inherited from HasContig

Inherited from Any

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