Gff3Annotation

class Gff3Annotation

An Annotation class for storing GFF3 records. For more information see http://gmod.org/wiki/GFF3/

Constructors

(config: Gff3AnnotationConfig): Gff3Annotation

Parameters

  • config: Gff3AnnotationConfig

Properties

attributes

attributes: undefined | Map <string, string>

A horrifying GFF3 field that is essentially an anything goes set of key value pairs describing anything anybody every wants to add to a GFF3 record.

end

end: number

The end position of the annotation in semantic coordinates (generally a position on a chromosome in base pairs).

id

id: string

A unique identifier for an Annotation object. If an ID is not provided, one will be automatically generated by SODA when the Annotation is instantiated.

phase

phase: undefined | None | None | None

A GFF3 field that describes the phase for CDS (coding sequence) annotations.

row

row: number

This describes which horizontal row the Annotation will be rendered in a Chart, assuming that the y-positioning is not overwritten during a call to the glyph rendering API.

score

score: undefined | number

A GFF3 field that should describe the score of the annotation.

seqid

seqid: undefined | string

A GFF3 field: “The ID of the landmark used to establish the coordinate system for the current feature…”

source

source: undefined | string

A GFF3 field: “The source is a free text qualifier intended to describe the algorithm or operating procedure that generated this feature…”

start

start: number

The start position of the annotation in semantic coordinates (generally a position on a chromosome in base pairs).

strand

strand: undefined | Forward | Reverse | Unknown | Unoriented

A GFF3 field that describes the strand of the annotation.

tag

tag: undefined | string

An optional tag for the annotation. This can be thought of as a something of a secondary ID.

type

type: undefined | string

A GFF3 field that is supposed to be “constrained to be either: (a) a term from the “lite” sequence ontology, SOFA; or (b) a SOFA accession number.” However, this is currently not enforced by SODA.

width

width: number

The width of the annotation in semantic coordinates.

Accessors

w

get w(): number

A convenience getter that returns the width property.

set w(w: number): void

A convenience setter that sets the width property.

x

get x(): number

A convenience getter that returns the start property.

set x(x: number): void

A convenience setter that sets the start property.

x2

get x2(): number

A convenience getter that returns the end property.

set x2(x: number): void

A convenience setter that sets the end property.

y

get y(): number

A convenience getter that returns the row property.

set y(y: number): void

A convenience setter that sets the row property.