Contig

Value Members

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

   

   Definition Classes

   AnyRef → Any

2. final def ##(): Int

   

   Definition Classes

   AnyRef → Any

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

   

   Definition Classes

   AnyRef → Any

4. final def asInstanceOf[T0]: T0

   

   Definition Classes

   Any

5. def clone(): AnyRef

   

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

6. def contains(locus: Locus): Boolean

   

   Is the given locus contained in this set?

7. lazy val count: NumLoci

   

   Number of loci on this contig.

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

   

   Definition Classes

   AnyRef

9. def finalize(): Unit

   

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

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

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

    

    Definition Classes

    AnyRef → Any

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

    

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

12. def isEmpty: Boolean

    

    Is this contig empty?

13. final def isInstanceOf[T0]: Boolean

    

    Definition Classes

    Any

14. def iterator: LociIterator

    

    Iterator through loci on this contig, sorted.

15. val name: ContigName

    

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

    

    Definition Classes

    AnyRef

17. def nonEmpty: Boolean

    

18. final def notify(): Unit

    

    Definition Classes

    AnyRef

19. final def notifyAll(): Unit

    

    Definition Classes

    AnyRef

20. lazy val numRanges: Int

    

21. val rangeSet: RangeSet[Locus]

    

22. def ranges: Iterator[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) .toString() output.

    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( ... )

31. def writeReplace: AnyRef

    

    RangeSet is not Serializable, and we delegate work-around serialization logic to SerializableContig to avoid the requirement for a 0-arg constructor here.

    RangeSet is not Serializable, and we delegate work-around serialization logic to SerializableContig to avoid the requirement for a 0-arg constructor here.

    Attributes

    protected