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MafTrack

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the maf plugin. View source.

Example usage

A tabix-indexed MAF, with the aligned species supplied by a Newick tree that also orders and labels the rows as a dendrogram (pass a samples array instead to list them explicitly, in track order):

{
  type: 'MafTrack',
  trackId: 'ce11.26way',
  name: 'UCSC 26-way multiple alignment',
  assemblyNames: ['ce11'],
  adapter: {
    type: 'MafTabixAdapter',
    uri: 'https://jbrowse.org/demos/ce/ce11.26way.bed.gz',
    nhLocation: {
      uri: 'https://hgdownload.soe.ucsc.edu/goldenPath/ce11/multiz26way/ce11.26way.nh',
    },
  },
}

See the Config slots section below for all available configuration fields.

Overview

used for multiple alignment (MAF/TAF) tracks, rendered as one row per aligned species with a conservation summary above them

MafTrack - Identifier

Every MafTrack has a unique trackId, a required top-level field that identifies it (not one of the config slots below).

Config slots

These slots are top-level fields of the track config, alongside trackId and name. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.

SlotDescription
Inherited from BaseTrack12 slots
name
string = ''		descriptive name of the track, falls back to the trackId when unset
assemblyNames
stringArray = ['assemblyName']		name of the assembly (or assemblies) track belongs to
description
string = ''		a description of the track
category
stringArray = []		the category and sub-categories of a track
metadata
frozen = {}		anything to add about this track
adapter
pluginManager.pluggableConfigSchemaType('adapter')		where this track's data comes from. Its type names the adapter for the file format (BamAdapter, Gff3TabixAdapter, ...) and the rest of the object is that adapter's own slots — see the adapter pages for each. Most adapters also accept a uri shorthand in place of writing their location slots out.
textSearching.indexingAttributes
stringArray = ['Name', 'ID', 'symbol']		list of which feature attributes to index for text searching
textSearching.indexingFeatureTypesToExclude
stringArray = ['CDS', 'exon']		list of feature types to exclude in text search index
textSearching.textSearchAdapter
pluginManager.pluggableConfigSchemaType(
  'text search adapter',
)
a per-track name search index, normally a TrixTextSearchAdapter over what jbrowse text-index --tracks built. Without one, this track's features are only findable through an assembly-wide search adapter.
displays
types.array(pluginManager.pluggableConfigSchemaType('display'))		An array of full display configs, e.g. displays: [{ type: 'LinearBasicDisplay', color: 'green' }]. Each entry names a display type; use this when you need exact control — your own displayId, different settings for two displays, or choosing which display is the default.

For the common case, prefer the displayDefaults shorthand instead — an object of appearance settings (e.g. displayDefaults: { color: 'green' }) that JBrowse routes to whichever display uses each setting, so you don't have to name the display or write the array.

See the track config guide.
formatDetails
FormatDetailsConfigSchemaFactory()		jexl callbacks that add, rewrite or hide fields in this track's feature-details panel. Four slots, listed at FormatDetails, and the same schema exists session-wide as configuration.formatDetails.
formatAbout
FormatAboutConfigSchemaFactory()		jexl callbacks that add, rewrite or hide fields in this track's About dialog. Two slots, listed at FormatAbout, and the same schema exists session-wide as configuration.formatAbout.