org.hammerlab.genomics.loci.set

Contig

case class Contig(name: ContigName, rangeSet: RangeSet[Locus]) extends TruncatedToString with Product with Serializable

A set of loci on a contig, stored/manipulated as loci ranges.

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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Instance Constructors

  1. new Contig(name: ContigName, rangeSet: RangeSet[Locus])

Value Members

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  6. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  7. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  8. def contains(locus: Locus): Boolean

    Is the given locus contained in this set?

  9. def count: NumLoci

    Number of loci on this contig.

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

    Definition Classes
    AnyRef

  11. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

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

    Definition Classes
    AnyRef → Any

  13. def intersects(start: Locus, end: Locus): Boolean

    Returns whether a given genomic region overlaps with any loci on this contig.

  14. def isEmpty: Boolean

    Is this contig empty?

  15. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  16. def iterator: LociIterator

    Iterator through loci on this contig, sorted.

  17. var name: ContigName

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

    Definition Classes
    AnyRef

  19. def nonEmpty: Boolean

  20. final def notify(): Unit

    Definition Classes
    AnyRef

  21. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  22. lazy val ranges: Vector[Interval]

    This set as a regular scala array of ranges.

  23. def regions: Iterator[Region]

  24. def stringPieces: Iterator[String]

    Iterator over string representations of each range in the map, used to assemble (possibly truncated) .

    Iterator over string representations of each range in the map, used to assemble (possibly truncated) .toString() output.

    Definition Classes
    Contig → TruncatedToString

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

    Definition Classes
    AnyRef

  26. def toString(maxLength: Int, separator: String, ellipses: String): String

    Definition Classes
    TruncatedToString

  27. def toString(): String

    Definition Classes
    TruncatedToString → AnyRef → Any

  28. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    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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