OrderedTrackedLayout

An implementation of TrackedLayout which takes a sequence of ReferenceMappable values, and lays them out in order (i.e. from first-to-last) in the naive way: for each value, it looks for the track with the lowest index that doesn't already have an overlapping value, and it doesn't use any special data structures (it just does a linear search for each track.)

T: the type of value which is to be tracked.

Linear Supertypes

TrackedLayout[T], AnyRef, Any

Instance Constructors

new OrderedTrackedLayout(reads: Traversable[T])(implicit mapping: ReferenceMapping[T])

reads
The set of values (i.e. "reads", but anything that is mappable to the reference genome ultimately) to lay out in tracks
mapping
The (implicit) reference mapping which converts values to ReferenceRegions

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
final def ==(arg0: AnyRef): Boolean

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

Definition Classes
Any
final def asInstanceOf[T0]: T0

Definition Classes
Any
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def equals(arg0: Any): Boolean

Definition Classes
AnyRef → Any
def finalize(): Unit

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

Definition Classes
AnyRef → Any
def hashCode(): Int

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

Definition Classes
Any
implicit val mapping: ReferenceMapping[T]

The (implicit) reference mapping which converts values to ReferenceRegions
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
val numTracks: Int

Definition Classes
OrderedTrackedLayout → TrackedLayout
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def toString(): String

Definition Classes
AnyRef → Any
val trackAssignments: Map[T, Int]

Definition Classes
OrderedTrackedLayout → TrackedLayout
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( ... )

class OrderedTrackedLayout[T] extends TrackedLayout[T]

Instance Constructors

new OrderedTrackedLayout(reads: Traversable[T])(implicit mapping: ReferenceMapping[T])

Value Members

final def !=(arg0: AnyRef): Boolean

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: AnyRef): Boolean

final def ==(arg0: Any): Boolean

final def asInstanceOf[T0]: T0

def clone(): AnyRef

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def finalize(): Unit

final def getClass(): Class[_]

def hashCode(): Int

final def isInstanceOf[T0]: Boolean

implicit val mapping: ReferenceMapping[T]

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

val numTracks: Int

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

def toString(): String

val trackAssignments: Map[T, Int]

final def wait(): Unit

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

final def wait(arg0: Long): Unit

Inherited from TrackedLayout[T]

Inherited from AnyRef

Inherited from Any

Ungrouped