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Packages

package root

Definition Classes
root
package feature
Provides classes to represent genomic features, i.e., annotations with block coordinates, an orientation, and other associated information.
Provides classes to represent genomic features, i.e., annotations with block coordinates, an orientation, and other associated information.
The main classes to use are feature.GenericFeature, feature.Transcript, and feature.MessengerRNA. These can be instantiated directly or by using a feature.FeatureBuilder.
In addition, genomic annotations with no associated information can be represented with feature.Block, a single contiguous block, and feature.BlockSet, an annotation consisting of multiple blocks.

Definition Classes
root
package format

Definition Classes
feature
Block
BlockSet
Empty
Exceptions
Feature
FeatureBuilder
FeatureBuilderModifier
Gene
GenericFeature
MessengerRNA
Minus
Orientation
Plus
Region
Transcript
Unstranded

c

feature

Gene

final case class Gene(transcripts: Set[Transcript], name: String) extends Product with Serializable

A gene giving rise to one or more Transcripts.

transcripts: Non-empty Set of Transcripts
name: Gene name

Linear Supertypes

Serializable, Serializable, Product, Equals, AnyRef, Any

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Gene
Serializable
Serializable
Product
Equals
AnyRef
Any

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Instance Constructors

new Gene(transcripts: Set[Transcript], name: String)
transcripts
Non-empty Set of Transcripts
name
Gene name

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
final def asInstanceOf[T0]: T0

Definition Classes
Any
val chr: String
def clone(): AnyRef

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

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
lazy val span: Block
The gene span from minimum start position of transcripts to maximum end position of transcripts Orientation is the common orientation if all transcripts have same orientation, or Unstranded otherwise
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
val transcripts: Set[Transcript]
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( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

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