Class: Feature

Feature

A Feature is a region on the map with a start and stop position.

Action and Events

Action Viewer Method Feature Method Event
Add addFeatures() - features-add
Update updateFeatures() update() features-update
Remove removeFeatures() remove() features-remove
Read features() - -

Attributes

Attribute Type Description
name String Name of feature
type String Feature type (e.g. CDS, rRNA, etc)
legend String|LegendItem Name of legendItem or the legendItem itself
source String Source of the feature
tags String|Array A single string or an array of strings associated with the feature as tags
contig String|Contig Name of contig or the contig itself
startrc Number Start base pair on the contig. Ignored if locations are present.
stoprc Number Stop base pair on the contig. Ignored if locations are present.
locations Array Array of locations (start, stop) on the contig (e.g. [[1, 100], [200, 300]]).
mapStartic Number Start base pair on the map (converted to contig position). Ignored if locations are present.
mapStopic Number Stop base pair on the map (converted to contig position). Ignored if locations are present.
strand String Strand the features is on [Default: 1]
score Number Score associated with the feature
favorite Boolean Feature is a favorite [Default: false]
visible Boolean Feature is visible [Default: true]
meta Object Meta data for Feature
qualifiers Object Qualifiers associated with the feature (from GenBank/EMBL) [Default: {}]
translation String Static translation of the feature. If set, this will be used instead of translating the sequence.

rc Required on Feature creation ic Ignored on Record creation

Implementation notes:

  • The feature range is the range on the contig
  • Feature.mapRange is the range on the Sequence.mapContig
  • If there is only one contig in the map, then Feature.mapRange === Feature.range
  • Feature.start/stop are positions on the contig
  • Feature mapStart/mapStop are position on Sequence.mapContig
  • If no contig is provided, the default contig will be Sequence.mapContig
    • Whenever mapContig is updated/regenerated the feature will be moved to the new mapContig
    • Features on the mapContig are able to span contigs
    • If contigs are rearranged, a mapContig feature will stay at the same position (start/stop)

new Feature(viewer, options, meta)

Feature.js, line 81

Create a new feature.

Name Type Description
viewer Viewer

The viewer
options Object

Attributes used to create the feature
meta Object optional

User-defined Meta data to add to the feature.

Extends

Members

canvasCanvas

Get the canvas.

codonStartString

Get or set the Codon start (Default: 1)

colorString

Get or set the color. TODO: reference COLOR class

contigContig

Get or set the Contig. The Contig can be set with a Contig object or with the name of a Contig.

decorationString

Get the decoration.

extractedFromSequenceBoolean

Get or set the extractedFromSequence. If true, this feature was generated directly from the sequence and will not be saved when exporting to JSON.

favoriteString

Get or set the feature as a favorite.

fullLengthNumber

Get the length of the feature in basepair (bp) using only the start and stop positions. This is the same as the range length. To get the length of the feature based on sub locations, use length.

fullSeqNumber

Get the sequence of the feature using only the start and stop positions (ignores locations). To get sequence of the feature based on sub locations, use seq.

geneticCodeString

Get or set the Genetic code used for translation. If no genetic code is set, the default for the map will be used.

hasLocationsNumber

Return true if the feature has multiple locations (i.e more than one).

labelString

Get or set the feature label.

layoutLayout

Get the layout.

legendLegendItem

Alias for legendItem.

legendItemLegendItem

Get or set the LegendItem. The LegendItem can be set with a LegendItem object or with the name of a legenedItem.

lengthNumber

Get the length of the feature in basepair (bp). If the feature has locations, the length is calculated as the sum of the length of each location. Otherwise, the length is the same as the range (i.e. stop - start + 1). To get the full length of the feature on the map, use fullLength.

locationsNumber

Get or set the locations of the feature in basepair (bp). An array of arrays where each sub-array contains the start and stop positions (e.g. [[1, 100], [200, 300]]). All start and stop positions are assumed to be going in a clockwise direction. Locations shouldn't overlap the origin but can overlap each other (e.g. due to ribosomal slippage). Locations are ignored unless there is more than one location. Validations:

  • that each array has 2 numbers
  • start must be less than stop TODO:
  • order of locations should be checked?

mapRangeRange

Get or set the range of the feature with respect to its contig. All ranges are assumed to be going in a clockwise direction.

mapStartNumber

Get or set the start position of the feature in basepair (bp). All start and stop positions are assumed to be going in a clockwise direction. Setting the mapStart position does not work if the feature has multiple locations.

mapStopNumber

Get or set the stop position of the feature in basepair (bp). All start and stop positions are assumed to be going in a clockwise direction. Setting the mapStop position does not work if the feature has multiple locations.

metaBoolean

Get or Set the meta data of this object. See the meta data tutorial for details.

nameString

Get or set the name via the Label.

qualifiersqualifiers

Get or set the qualifiers

rangeRange

Get or set the range of the feature. All ranges are assumed to be going in a clockwise direction.

scoreNumber

Get the Score

seq

Returns the DNA sequence for the feature. If the feature has multiple locations, the sequence will be concatenated. In some cases (e.g. ribosomal slippage) the locations may overlap. Example: [[1, 100], [100, 200]] will return a sequence of 201 bp. To get the sequence of the feature's fullLenth ignoring sub locations, use fullSeq.

sequenceSequence

Get the sequence.

startNumber

Get or set the start position of the feature in basepair (bp). All start and stop positions are assumed to be going in a clockwise direction. This position is relative to the contig the feature is on. If there is only one contig, this value will be the same as mapStart. Setting the start position does not work if the feature has multiple locations (use locations instead).

stopNumber

Get or set the stop position of the feature in basepair (bp). All start and stop positions are assumed to be going in a clockwise direction. This position is relative to the contig the feature is on. If there is only one contig, this value will be the same as mapStop. Setting the stop position does not work if the feature has multiple locations (use locations instead).

tagstag

Get or set the tags

translationqualifiers

Get or set the translation. If set, this translation will be used by translate() instead of translating the sequence

typetype

Get or set the type

viewerViewer

Get the Viewer

visibleBoolean

Get or Set the visibility of this object.

Methods

inherited addPluginOptions(id, options)

CGObject.js, line 150

Add a plugin to the object.

Name Type Description
id String

The id of the plugin
options Object

The plugin options

inherited deleteFromObjects()

CGObject.js, line 137

Remove the object from Viewer.objects

inherited hasPlugin(pluginID){Boolean}

CGObject.js, line 191

Does this object have a particular plugin?

Name Type Description
pluginID String

The ID of the plugin
Returns:
Type Description
Boolean
  • Whether the object has the plugin

highlight(slot)

Feature.js, line 742

Highlights the feature on every slot it is visible. An optional slot can be provided, in which case the feature will only be highlighted on the slot.

Name Type Description
slot Slot

Only highlight the feature on this slot.

moveTo(duration, ease)

Feature.js, line 839

Zoom and pan map to show the feature

Name Type Description
duration Number

Length of animation
ease Object

The d3 animation ease [Default: d3.easeCubic]

inherited optionsForPlugin(pluginName){Object}

CGObject.js, line 205

Get the options for a particular plugin.

Name Type Description
pluginName String

The name of the plugin
Returns:
Type Description
Object
  • The options for the plugin or undefined if the plugin is not found

remove()

Feature.js, line 829

Remove the feature from the viewer, tracks and slots

slots()

Feature.js, line 814

Return an array of the slots that contain this feature

toString(){String}

Feature.js, line 128

Return the class name as a string.

Returns:
Type Description
String
  • 'Feature'

tracks()

Feature.js, line 796

Return an array of the tracks that contain this feature FIXME: this will not return the tracks for features on tracks with 'from' = 'sequence' - is this a problem??

translate(geneticCode){String}

Feature.js, line 875

Translate the sequence of this feature.

The source of the genetic code used for translation uses the following precedence: geneticCode (provided to translate method) > geneticCode (of Feature) > geneticCode (of Viewer)

Note: if the feature has a translation property, it will be used instead of translating the sequence.

  • This can be overriden by providing a genetic code to the translate method. This forces the sequence to be translated.
Name Type Description
geneticCode Number

Number indicating the genetic code to use for the translation. This will override the any genetic code set for the feature or Viewer.
Returns:
Type Description
String
  • Amino acid sequence

update(attributes)

Feature.js, line 598

Update feature attributes. See updating records for details.

Name Type Description
attributes Object

Object describing the properties to change

inherited updatePluginOptions(id, options)

CGObject.js, line 170

Update plugin options. Merge the new options with the old options.

Name Type Description
id String

The id of the plugin
options Object

The plugin options