SlidingWindow

Suppose we have a set of loci on a given contig and some objects that are mapped to that contig, and at each locus we want to look at the regions that overlap a window of a certain number of bases surrounding that locus. This class implements this "sliding window" functionality.

After instantiating this class, call setCurrentLocus repeatedly for each locus being considered. After calling this method, the currentRegions property will contain the objects that overlap the current locus. s To enable an efficient implementation, we require that both the sequence of loci to be considered and the iterator of objects are sorted.

halfWindowSize: Number of nucleotide bases to either side of the specified locus to provide regions for. For example, if halfWindowSize=5, and our currentLocus=100, then currentRegions will include regions that map to anywhere between 95 and 105, inclusive. Set to 0 to consider only regions that overlap the exact locus being considered, with no surrounding window.
rawSortedRegions: Iterator of regions, sorted by the aligned start locus.

Linear Supertypes

Serializable, Serializable, Product, Equals, AnyRef, Any

Instance Constructors

new SlidingWindow(contigName: ContigName, halfWindowSize: Int, rawSortedRegions: Iterator[R])

halfWindowSize
Number of nucleotide bases to either side of the specified locus to provide regions for. For example, if halfWindowSize=5, and our currentLocus=100, then currentRegions will include regions that map to anywhere between 95 and 105, inclusive. Set to 0 to consider only regions that overlap the exact locus being considered, with no surrounding window.
rawSortedRegions
Iterator of regions, sorted by the aligned start locus.

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( ... )
val contigName: ContigName
var currentLocus: Long

The locus currently under consideration.
def currentRegions(): Vector[R]

The regions that overlap the window surrounding currentLocus.
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
val halfWindowSize: Int

Number of nucleotide bases to either side of the specified locus to provide regions for.
Number of nucleotide bases to either side of the specified locus to provide regions for. For example, if halfWindowSize=5, and our currentLocus=100, then currentRegions will include regions that map to anywhere between 95 and 105, inclusive. Set to 0 to consider only regions that overlap the exact locus being considered, with no surrounding window.
final def isInstanceOf[T0]: Boolean

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

Definition Classes
AnyRef
var newRegions: Seq[R]

The new regions that were added to currentRegions as a result of the most recent call to setCurrentLocus.
def nextLocusWithRegions(): Option[Long]

Find the next locus for which calling setCurrentLocus(locus) would result in a non-empty set of regions in currentRegions.
Find the next locus for which calling setCurrentLocus(locus) would result in a non-empty set of regions in currentRegions.
returns
Some(locus) if such a locus exists, otherwise None
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
val rawSortedRegions: Iterator[R]

Iterator of regions, sorted by the aligned start locus.
def setCurrentLocus(locus: Locus): Vector[R]

Advance to the specified locus, which must be greater than the current locus.
Advance to the specified locus, which must be greater than the current locus. After calling this, the currentRegions method will give the overlapping regions at the new locus.
locus
Locus to advance to.
returns
The *new regions* that were added as a result of this call. Note that this is not the full set of regions in the window: you must examine currentRegions for that.
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
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
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Annotations
@throws( ... )

case class SlidingWindow[R <: ReferenceRegion](contigName: ContigName, halfWindowSize: Int, rawSortedRegions: Iterator[R]) extends Product with Serializable

Instance Constructors

new SlidingWindow(contigName: ContigName, halfWindowSize: Int, rawSortedRegions: Iterator[R])

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

val contigName: ContigName

var currentLocus: Long

def currentRegions(): Vector[R]

final def eq(arg0: AnyRef): Boolean

def finalize(): Unit

final def getClass(): Class[_]

val halfWindowSize: Int

final def isInstanceOf[T0]: Boolean

final def ne(arg0: AnyRef): Boolean

var newRegions: Seq[R]

def nextLocusWithRegions(): Option[Long]

final def notify(): Unit

final def notifyAll(): Unit

val rawSortedRegions: Iterator[R]

def setCurrentLocus(locus: Locus): Vector[R]

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

final def wait(): Unit

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

final def wait(arg0: Long): Unit

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

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