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.