< Back

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

t

FeatureBuilderModifier

trait FeatureBuilderModifier extends AnyRef

A way to encapsulate arbitrary operations on a FeatureBuilder.

The op function performs the operations on a specified FeatureBuilder and returns a new modified FeatureBuilder.

Classes that mix in this trait include format.GTF22Record.

Linear Supertypes

AnyRef, Any

Known Subclasses

Ordering

Alphabetic
By Inheritance

Inherited

FeatureBuilderModifier
AnyRef
Any

Hide All
Show All

Visibility

Public
All

Abstract Value Members

abstract def op(fb: FeatureBuilder): FeatureBuilder
Returns a new, possibly modified FeatureBuilder.
Returns a new, possibly modified FeatureBuilder.
fb
Original FeatureBuilder
returns
New FeatureBuilder resulting from applying the function to the original

Concrete 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
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
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def toString(): String

Definition Classes
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( ... )

Inherited from AnyRef

Inherited from Any

Ungrouped