Contig

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. def difference(other: Contig): Contig

    Remove the loci of another contig

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

    Definition Classes

    AnyRef

12. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( classOf[java.lang.Throwable] )

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

    Definition Classes

    AnyRef → Any

14. def intersect(other: Contig): Contig

    Intersect this Contig with another

15. def intersects(start: Long, end: Long): Boolean

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

16. def isEmpty: Boolean

    Is this contig empty?

17. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

18. def iterator: LociIterator

    Iterator through loci on this contig, sorted.

19. var name: ContigName

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

    Definition Classes

    AnyRef

21. def nonEmpty: Boolean

22. final def notify(): Unit

    Definition Classes

    AnyRef

23. final def notifyAll(): Unit

    Definition Classes

    AnyRef

24. lazy val ranges: Vector[Interval]

    This set as a regular scala array of ranges.

25. 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

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

    Definition Classes

    AnyRef

27. def toString(): String

    Definition Classes

    TruncatedToString → AnyRef → Any

28. def truncatedString(maxLength: Int = 500): String

    String representation, truncated to maxLength characters.

    String representation, truncated to maxLength characters.

    Definition Classes

    TruncatedToString

29. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )