LociMap

Instance Constructors

new LociMap(map: SortedMap[ContigName, Contig[T]])

map
Map from contig names to Contig instances giving the regions and values on that contig.

Value Members

final def !=(arg0: Any): Boolean

Definition Classes
AnyRef → Any
final def ##(): Int

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

Definition Classes
AnyRef → Any
def apply(contig: ContigName): Contig[T]

Returns the loci map on the specified contig.
Returns the loci map on the specified contig.
contig
The contig name
returns
A Contig instance giving the loci mapping on the specified contig.
final def asInstanceOf[T0]: T0

Definition Classes
Any
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
lazy val contigs: Seq[Contig[T]]

The contigs included in this LociMap with a nonempty set of loci.
lazy val count: NumLoci

The number of loci in this LociMap.
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] )
def getAll(r: Region, halfWindowSize: Int = 0): Set[T]

Return values corresponding to any ranges that overlap the given Region, with a halfWindowSize margin of error.
final def getClass(): Class[_]

Definition Classes
AnyRef → Any
lazy val inverse: Map[T, LociSet]

The "inverse map", i.e.
The "inverse map", i.e. a T → LociSet map that gives the loci that map to each value.
final def isInstanceOf[T0]: Boolean

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

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
def prettyPrint(os: OutputStream): Unit
def stringPieces: Iterator[String]

Build a truncate-able toString() out of underlying contig pieces.
Build a truncate-able toString() out of underlying contig pieces.

Definition Classes
LociMap → TruncatedToString
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def toString(maxLength: Int, separator: String, ellipses: String): String

Definition Classes
TruncatedToString
def toString(): String

Definition Classes
TruncatedToString → AnyRef → Any
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( ... )

Related Docs: object LociMap | package map

case class LociMap[T](map: SortedMap[ContigName, Contig[T]]) extends TruncatedToString with Product with Serializable

Instance Constructors

new LociMap(map: SortedMap[ContigName, Contig[T]])

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

def apply(contig: ContigName): Contig[T]

final def asInstanceOf[T0]: T0

def clone(): AnyRef

lazy val contigs: Seq[Contig[T]]

lazy val count: NumLoci

final def eq(arg0: AnyRef): Boolean

def finalize(): Unit

def getAll(r: Region, halfWindowSize: Int = 0): Set[T]

final def getClass(): Class[_]

lazy val inverse: Map[T, LociSet]

final def isInstanceOf[T0]: Boolean

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

def prettyPrint(os: OutputStream): Unit

def stringPieces: Iterator[String]

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

def toString(maxLength: Int, separator: String, ellipses: String): String

def toString(): String

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 TruncatedToString

Inherited from AnyRef

Inherited from Any

Ungrouped