trait GenomicSpan extends Locatable

A simple trait that extends htsjdk.samtools.util.Locatable but provides a few easier to use methods for getting the location.

Linear Supertypes
Locatable, AnyRef, Any
Known Subclasses
PhaseBlock
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Inherited
  1. GenomicSpan
  2. Locatable
  3. AnyRef
  4. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Visibility
  1. Public
  2. All

Abstract Value Members

  1. abstract def contig: String
  2. abstract def end: Int
  3. abstract def start: Int

Concrete Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. def +(other: String): String
    Implicit
    This member is added by an implicit conversion from GenomicSpan to any2stringadd[GenomicSpan] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (GenomicSpan, B)
    Implicit
    This member is added by an implicit conversion from GenomicSpan to ArrowAssoc[GenomicSpan] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  5. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → 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 encloses(other: GenomicSpan): Boolean

    True if this genomic span encloses the other genomic span, false otherwise.

  9. def ensuring(cond: (GenomicSpan) ⇒ Boolean, msg: ⇒ Any): GenomicSpan
    Implicit
    This member is added by an implicit conversion from GenomicSpan to Ensuring[GenomicSpan] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  10. def ensuring(cond: (GenomicSpan) ⇒ Boolean): GenomicSpan
    Implicit
    This member is added by an implicit conversion from GenomicSpan to Ensuring[GenomicSpan] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  11. def ensuring(cond: Boolean, msg: ⇒ Any): GenomicSpan
    Implicit
    This member is added by an implicit conversion from GenomicSpan to Ensuring[GenomicSpan] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  12. def ensuring(cond: Boolean): GenomicSpan
    Implicit
    This member is added by an implicit conversion from GenomicSpan to Ensuring[GenomicSpan] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  13. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  14. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  15. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  16. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from GenomicSpan to StringFormat[GenomicSpan] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  17. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  18. def getContig(): String
    Definition Classes
    GenomicSpan → Locatable
  19. def getEnd(): Int
    Definition Classes
    GenomicSpan → Locatable
  20. def getStart(): Int
    Definition Classes
    GenomicSpan → Locatable
  21. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  22. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  23. def length: Int
  24. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  25. final def notify(): Unit
    Definition Classes
    AnyRef
  26. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  27. def overlaps(other: GenomicSpan): Boolean

    True if the two genomic spans overlap, false otherwise.

  28. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  29. def toString(): String
    Definition Classes
    AnyRef → Any
  30. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  31. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  32. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  33. def →[B](y: B): (GenomicSpan, B)
    Implicit
    This member is added by an implicit conversion from GenomicSpan to ArrowAssoc[GenomicSpan] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from Locatable

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion any2stringadd from GenomicSpan to any2stringadd[GenomicSpan]

Inherited by implicit conversion StringFormat from GenomicSpan to StringFormat[GenomicSpan]

Inherited by implicit conversion Ensuring from GenomicSpan to Ensuring[GenomicSpan]

Inherited by implicit conversion ArrowAssoc from GenomicSpan to ArrowAssoc[GenomicSpan]

Ungrouped