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SpreadsheetView

Auto-generated from the @jbrowse/mobx-state-tree model in the source — see the developer guide for concepts. Provided by the spreadsheet-view plugin. View source.

Shows a VCF, BED, BEDPE or STAR-Fusion file as a filterable table whose rows open their genomic location in a new view.

Example usage

Hand-authored under defaultSession.views, with every setting written directly on the view object. uri loads a VCF, BED, BEDPE or STAR-Fusion file straight into the grid, skipping the import form; assembly names the assembly that resolves genomic coordinates in the rows:

{
  type: 'SpreadsheetView',
  assembly: 'hg38',
  uri: 'https://example.com/variants.vcf.gz',
  fileType: 'VCF',
}

Each section ends with the members a composed model contributes, linked to the page that documents them.

Properties

MemberDescription
type
type: types.literal('SpreadsheetView')
height
height: types.stripDefault(types.number, defaultHeight)		the height of the sheet in pixels
hideVerticalResizeHandle
hideVerticalResizeHandle: types.stripDefault(types.boolean, false)
chrome switch, for an embed that sizes the view itself
drilldownTracks
drilldownTracks: types.stripDefault(types.array(types.string), [])
trackIds the views a row opens start with, beside the loaded file's own track: the tumor and normal alignments, a coverage track, an assembly's synteny track
importWizard
importWizard: types.optional(ImportWizardModel, () =>
            ImportWizardModel.create(),
          )
spreadsheet
spreadsheet: types.maybe(Spreadsheet())
launch
launch: types.frozen<
            LaunchInput<SpreadsheetViewCommands> | undefined
          >()
transient launch keys lifted off the view object, applied on attach and then cleared; author them directly on the view
3 inherited properties from one model

From BaseViewModel: id, displayName, minimized

Volatiles

MemberDescription
width
number
1 inherited volatile from one model

From BaseViewModel: bodyMounted

Getters

MemberDescription
pendingLaunch
LaunchInput<SpreadsheetViewCommands & { unknown?: Record<string, unknown> | undefined; malformed?: Record<string, unknown> | undefined; legacyInit?: boolean | undefined; }> | undefined
the launch keys still waiting to be applied
showLoading
boolean		true while the file loads, which ViewContainer publishes as data-view-phase; the import form stays on screen under a spinner
drilldownTrackIds
string[]		every track a row's drill-down opens with, the loaded file's own first
4 inherited getters from one model

From BaseViewModel: rendersDisplays, effectiveBodyMounted, ownTracks, ownViews

Methods

MemberDescription
menuItems
() => { label: string; icon: OverridableComponent<SvgIconTypeMap<{}, "svg">> & { muiName: string; }; onClick: () => void; }[]

Actions

MemberDescription
setHeight
(newHeight: number) => number
resizeHeight
(distance: number) => number		returns the distance applied, which minHeight can cut short
displaySpreadsheet
(spreadsheet?: SpreadsheetSnapshot) => void		show a parsed sheet. One with the same columns as the sheet it replaces, as a reloaded session's re-fetch is, keeps that sheet's column visibility, filters and search
setLaunch
(launch?: LaunchInput<SpreadsheetViewCommands> | undefined) => void
setError
(error: unknown) => void		a failed launch's error, shown in the import form's banner
setDrilldownTracks
(trackIds: string[]) => void
registerImportedTrack
(assemblyName: string) => void		Put the loaded file in the session as a track, so the views a row opens show the records it came from. Idempotent: a session that already has a track for the file reuses it.

Nothing removes the track, since the views that opened it outlive the sheet; the reader closes it like any session track.
loadSpreadsheet
(assemblyName: string, superseded?: (() => boolean) | undefined) => Promise<void>
fetch, parse and show the wizard's file: the one path a launch, a session reload and the Open button all take
returnToImportForm
() => void		drop the sheet and its cached location, so a session reload does not fetch the dismissed file again
applyInit
(init: LaunchInput<SpreadsheetViewCommands>, superseded?: (() => boolean) | undefined) => Promise<void>
point the import wizard at a launch's file and load it; without a uri or an assembly, only seed the import form with what it names
4 inherited actions from one model

From BaseViewModel: setDisplayName, setWidth, setBodyMounted, setMinimized