Class/Object

org.hammerlab.genomics.loci.map

Contig

Related Docs: object Contig | package map

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case class Contig[T](name: ContigName, rangeMap: RangeMap[Locus, T]) extends TruncatedToString with Product with Serializable

A map from loci to instances of an arbitrary type where the loci are all on the same contig.

name

The contig name

rangeMap

The range map of loci intervals -> values.

Linear Supertypes
Serializable, Serializable, Product, Equals, TruncatedToString, AnyRef, Any
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Inherited
  1. Contig
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. TruncatedToString
  7. AnyRef
  8. Any
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Visibility
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Instance Constructors

  1. new Contig(name: ContigName, rangeMap: RangeMap[Locus, T])

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    name

    The contig name

    rangeMap

    The range map of loci intervals -> values.

Value Members

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

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

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

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

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    Definition Classes
    Any
  5. lazy val asMap: SortedMap[Interval, T]

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    This map as a regular scala immutable map from exclusive numeric ranges to values.

  6. def asRegionsMap: Iterator[(Region, T)]

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  7. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  8. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  9. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  10. def get(locus: Locus): Option[T]

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    Get the value associated with the given locus.

    Get the value associated with the given locus. Returns Some(value) if the given locus is in this map, None otherwise.

  11. def getAll(start: Locus, end: Locus, halfWindowSize: Int): Set[T]

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  12. def getAll(start: Locus, end: Locus): Set[T]

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  13. def getAll(interval: Interval, halfWindowSize: Int = 0): Set[T]

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    Given a loci interval, return the set of all values mapped to by any loci in the interval.

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

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    Definition Classes
    AnyRef → Any
  15. lazy val inverse: Map[T, set.Contig]

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    Map from each value found in this Contig to a LociSet Contig representing the loci that map to that value.

  16. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  17. val name: ContigName

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    The contig name

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

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

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

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    Definition Classes
    AnyRef
  21. def stringPieces: Iterator[String]

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    Iterator over string representations of each range in the map.

    Iterator over string representations of each range in the map.

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

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    Definition Classes
    AnyRef
  23. def toString(maxLength: Int, separator: String, ellipses: String): String

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    Definition Classes
    TruncatedToString
  24. def toString(): String

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

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

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from TruncatedToString

Inherited from AnyRef

Inherited from Any

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