Gff3AnnotationConfig

interface Gff3AnnotationConfig

An interface that defines the initialization parameters for a Gff3Annotation.

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: undefined | number

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

id

id: undefined | 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: undefined | 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: undefined | 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: undefined | number

The width of the annotation in semantic coordinates.