ReferenceRegionWithOrientation

Represents a contiguous region of the reference genome with strand information.

referenceName: The name of the sequence (chromosome) in the reference genome
start: The 0-based residue-coordinate for the start of the region
end: The 0-based residue-coordinate for the first residue after the start which is not in the region -- i.e. [start, end) define a 0-based half-open interval.
negativeStrand: Boolean flag as to whether the region is on the forward or reverse strand of the reference region.

Linear Supertypes

Serializable, Serializable, Product, Equals, Ordered[ReferenceRegionWithOrientation], Comparable[ReferenceRegionWithOrientation], AnyRef, Any

Instance Constructors

new ReferenceRegionWithOrientation(referenceName: String, start: Long, end: Long, negativeStrand: Boolean)

referenceName
The name of the sequence (chromosome) in the reference genome
start
The 0-based residue-coordinate for the start of the region
end
The 0-based residue-coordinate for the first residue after the start which is not in the region -- i.e. [start, end) define a 0-based half-open interval.
negativeStrand
Boolean flag as to whether the region is on the forward or reverse strand of the reference region.

Value Members

final def !=(arg0: AnyRef): Boolean

Definition Classes
AnyRef
final def !=(arg0: Any): Boolean

Definition Classes
Any
final def ##(): Int

Definition Classes
AnyRef → Any
def <(that: ReferenceRegionWithOrientation): Boolean

Definition Classes
Ordered
def <=(that: ReferenceRegionWithOrientation): Boolean

Definition Classes
Ordered
final def ==(arg0: AnyRef): Boolean

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

Definition Classes
Any
def >(that: ReferenceRegionWithOrientation): Boolean

Definition Classes
Ordered
def >=(that: ReferenceRegionWithOrientation): Boolean

Definition Classes
Ordered
final def asInstanceOf[T0]: T0

Definition Classes
Any
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
def compare(that: ReferenceRegionWithOrientation): Int

Definition Classes
ReferenceRegionWithOrientation → Ordered
def compareTo(that: ReferenceRegionWithOrientation): Int

Definition Classes
Ordered → Comparable
def contains(other: ReferenceRegionWithOrientation): Boolean
def contains(other: ReferencePositionWithOrientation): Boolean
val end: Long

The 0-based residue-coordinate for the first residue after the start which is not in the region -- i.
The 0-based residue-coordinate for the first residue after the start which is not in the region -- i.e. [start, end) define a 0-based half-open interval.
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def finalize(): Unit

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( classOf[java.lang.Throwable] )
final def getClass(): Class[_]

Definition Classes
AnyRef → Any
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
val negativeStrand: Boolean

Boolean flag as to whether the region is on the forward or reverse strand of the reference region.
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
def overlaps(other: ReferenceRegionWithOrientation): Boolean
val referenceName: String

The name of the sequence (chromosome) in the reference genome
val start: Long

The 0-based residue-coordinate for the start of the region
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def toReferenceRegion: ReferenceRegion
final def wait(): Unit

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

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

Definition Classes
AnyRef
Annotations
@throws( ... )
def width: Long

case class ReferenceRegionWithOrientation(referenceName: String, start: Long, end: Long, negativeStrand: Boolean) extends Ordered[ReferenceRegionWithOrientation] with Product with Serializable

Instance Constructors

new ReferenceRegionWithOrientation(referenceName: String, start: Long, end: Long, negativeStrand: Boolean)

Value Members

final def !=(arg0: AnyRef): Boolean

final def !=(arg0: Any): Boolean

final def ##(): Int

def <(that: ReferenceRegionWithOrientation): Boolean

def <=(that: ReferenceRegionWithOrientation): Boolean

final def ==(arg0: AnyRef): Boolean

final def ==(arg0: Any): Boolean

def >(that: ReferenceRegionWithOrientation): Boolean

def >=(that: ReferenceRegionWithOrientation): Boolean

final def asInstanceOf[T0]: T0

def clone(): AnyRef

def compare(that: ReferenceRegionWithOrientation): Int

def compareTo(that: ReferenceRegionWithOrientation): Int

def contains(other: ReferenceRegionWithOrientation): Boolean

def contains(other: ReferencePositionWithOrientation): Boolean

val end: Long

final def eq(arg0: AnyRef): Boolean

def finalize(): Unit

final def getClass(): Class[_]

final def isInstanceOf[T0]: Boolean

final def ne(arg0: AnyRef): Boolean

val negativeStrand: Boolean

final def notify(): Unit

final def notifyAll(): Unit

def overlaps(other: ReferenceRegionWithOrientation): Boolean

val referenceName: String

val start: Long

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

def toReferenceRegion: ReferenceRegion

final def wait(): Unit

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

final def wait(arg0: Long): Unit

def width: Long

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from Ordered[ReferenceRegionWithOrientation]

Inherited from Comparable[ReferenceRegionWithOrientation]

Inherited from AnyRef

Inherited from Any

Ungrouped