Feature

sealed interface Feature : Parent

Represents a single annotation (feature) in a GFF (general feature format) file. Generally, these features correspond to a row in a gff file and have all the same properties.

Inheritors

MutableFeature

Properties

children

open val children: List<Feature>

All children of this parent

discontinuous

open val discontinuous: Boolean

end

open val end: Int

Positive, always greater than or equal to start. For discontinuous features, equivalent to maximum ending position among all ranges.

genome

abstract val genome: Genome

abstract val id: String?

The ID attribute of this feature, or null if no such attribute

length

open val length: Int

The length of the feature, equivalent to end - start + 1

lengths

open val lengths: List<Int>

multiplicity

open val multiplicity: Int

Discontinuous annotations are represented in featureTree as a single Feature object with a multiplicity equal to the number of discontinuous segments of the annotation. ranges represents all the start-end ranges of this discontinuous feature while phases represents all the phases.

name

abstract val name: String?

A name associated with this feature, as defined by the Name attribute. Null if no names are associated.

names

abstract val names: List<String>

All names associated with this feature, as defined by the Name attribute. Empty list if no names are associated.

parent

open val parent: Parent

Alias for parent[0]

parents

abstract val parents: List<Parent>

phase

open val phase: Phase

Alias for phases[0]

phases

abstract val phases: List<Phase>

All phases for this feature. Continuous features will only have one, while discontinuous features will have several. Size is equal to ranges.size. A feature of type "CDS" (or synonym) may not have any Phase.UNSPECIFIED in its phases property.

range

open val range: IntRange

Alias for ranges[0]

ranges

abstract val ranges: List<IntRange>

All start-end IntRanges that define this feature. Continuous features will only have one, while discontinuous features will have several. Size is equal to phases.size. All ranges are positive.

score

abstract val score: Double?

seqid

abstract val seqid: String

source

abstract val source: String

start

open val start: Int

Positive, always less than or equal to end. For discontinuous features, equivalent to the minimum starting position among all ranges.

strand

abstract val strand: Strand

type

abstract val type: String

Functions

allAttributes

abstract fun allAttributes(): Map<String, List<String>>

All attributes as tag-values pairs.

ancestors

abstract fun ancestors(): List<Parent>

Return all ancestors of this feature in a depth-first order. Multiple parentage will result in duplicate values.

asRow

abstract fun asRow(): String

The String representation of this Feature as it appears as a row in a GFF file.

attribute

abstract fun attribute(tag: String): List<String>

All attribute values for tag.

byID

abstract fun byID(id: String): Feature?

byName

abstract fun byName(name: String): List<Feature>

children

abstract fun children(type: String? = null): List<Feature>

All children of this parent of type type (including its synonyms), or all children if type is null.

descendants

abstract fun descendants(type: String? = null): Sequence<Feature>

All descendants of this parent of type type (including its synonyms) in depth-first order, or all descendants if type is null. Iterating over the descendants while modifying the topology of the tree will produce a ConcurrentModificationException (non-topological modifications are permissible). Multiple parentage will result in duplicate values

iterator

open operator fun iterator(): Iterator<Feature>

Iterates over children

parentString

abstract fun parentString(): String

subtree

abstract fun subtree(): Sequence<Feature>

Prepends this feature to Parent.descendants.