Exon

An exon model (here represented as a value of the Exon class) is a representation of a single exon from a transcript in genomic coordinates.

NOTE: we're not handling shared exons here

transcriptId: the (unique) identifier of the transcript to which the exon belongs
region: The region (in genomic coordinates) to which the exon maps

Linear Supertypes

Serializable, Serializable, Product, Equals, BlockExtractable, Extractable, AnyRef, Any

Instance Constructors

new Exon(exonId: String, transcriptId: String, strand: Boolean, region: ReferenceRegion)

transcriptId
the (unique) identifier of the transcript to which the exon belongs
region
The region (in genomic coordinates) to which the exon maps

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
val exonId: String
def extractSequence(referenceSequence: String): String

Returns the subset of the given referenceSequence that corresponds to this Extractable (not necessarily a contiguous substring, and possibly reverse- complemented or transformed in other ways).
Returns the subset of the given referenceSequence that corresponds to this Extractable (not necessarily a contiguous substring, and possibly reverse- complemented or transformed in other ways).
referenceSequence
The reference sequence (e.g. chromosomal sequence) with respect to which the Extractable's coordinates or locators are given
returns
the String representation of this Extractable

Definition Classes
BlockExtractable → Extractable
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
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
val region: ReferenceRegion

The region (in genomic coordinates) to which the exon maps
val strand: Boolean
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
val transcriptId: String

the (unique) identifier of the transcript to which the exon belongs
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( ... )

case class Exon(exonId: String, transcriptId: String, strand: Boolean, region: ReferenceRegion) extends BlockExtractable with Product with Serializable

Instance Constructors

new Exon(exonId: String, transcriptId: String, strand: Boolean, region: ReferenceRegion)

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

val exonId: String

def extractSequence(referenceSequence: String): String

def finalize(): Unit

final def getClass(): Class[_]

final def isInstanceOf[T0]: Boolean

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

val region: ReferenceRegion

val strand: Boolean

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

val transcriptId: 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 BlockExtractable

Inherited from Extractable

Inherited from AnyRef

Inherited from Any

Ungrouped