SvInspectorView

Auto-generated @jbrowse/mobx-state-tree API for the current JBrowse release — see pluggable elements for concepts. Provided by the sv-inspector plugin. View source.

Example usage

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

does not extend, but is a combination of a

Members a composed model contributes are listed here too, so these tables are the whole surface.

Properties

Member	Description	Defined by
id `id: ElementId`		SvInspectorView
type `type: types.literal('SvInspectorView')`		SvInspectorView
height `height: types.stripDefault(types.number, defaultHeight)`	height of the whole view in pixels	SvInspectorView
onlyDisplayRelevantRegionsInCircularView `onlyDisplayRelevantRegionsInCircularView: types.stripDefault( types.boolean, false, )`	draw only the chromosomes the visible rows touch	SvInspectorView
spreadsheetWidthFraction `spreadsheetWidthFraction: types.stripDefault(types.number, 0.66)`	share of the view's width given to the spreadsheet	SvInspectorView
spreadsheetView `spreadsheetView: types.optional(SpreadsheetModel, () => SpreadsheetModel.create({ type: 'SpreadsheetView', hideVerticalResizeHandle: true, }), )`		SvInspectorView
circularView `circularView: types.optional(CircularModel, () => CircularModel.create({ type: 'CircularView', hideVerticalResizeHandle: true, disableImportForm: true, }), )`		SvInspectorView
launch `launch: types.frozen< LaunchInput<SvInspectorViewCommands> \| undefined >()`	transient launch keys, forwarded to the sheet on attach and cleared; author them directly on the view	SvInspectorView
displayName `displayName: types.maybe(types.string)`	displayName is displayed in the header of the view, or assembly names being used if none is specified	BaseViewModel
minimized `minimized: types.stripDefault(types.boolean, false)`	collapse the view to its header bar, keeping it in the session rather than closing it	BaseViewModel

Volatiles

Member	Description	Defined by
SpreadsheetViewReactComponent `SpreadsheetViewReactComponent: SpreadsheetViewType.ReactComponent`		SvInspectorView
CircularViewReactComponent `CircularViewReactComponent: CircularViewType.ReactComponent`		SvInspectorView
width `width: 800`		BaseViewModel
bodyMounted `bodyMounted: true`	Whether the container has this view's body in the DOM. `ViewContainer` mounts a view's body only while an IntersectionObserver says it is on screen, to hold the app under the WebGL2 context ceiling (`reference/GPU_PORTABILITY.md`). A view below the fold therefore has no canvas, so nothing ever calls `markCanvasDrawn` and the pre-first-paint term of `displayPhase` pins every display in it at `loading` with nothing left to resolve it — which parks `[data-app-phase="ready"]` for the whole app on a view the user cannot see. Defaults true so the containers that always mount a body — embedded views, workspace panels, and any test rendering a display directly — are unaffected and need not set it. The raw flag, written by this view's own container. A display asks `effectiveBodyMounted` instead, because a nested view has no container of its own.	BaseViewModel

Getters

Member	Description	Defined by
pendingLaunch `LaunchInput<SvInspectorViewCommands & { unknown?: Record<…> \| undefined; malformed?: Record<…> \| undefined; legacyInit?: boolean \| undefined; } & IStateTreeNode<...>> \| undefined`		SvInspectorView
currentAssembly `(ModelInstanceTypeProps<…> & { error: unknown; loadingP: Promise<…> \| undefined; ... 10 more ...; refNameMismatches: Map<…>; } & ... 13 more ... & IStateTreeNode<...>) \| undefined`		SvInspectorView
assemblyName `string \| undefined`		SvInspectorView
showCircularView `boolean`	false while the sheet shows its import form	SvInspectorView
showLoading `boolean`	both halves' loading state; the circle counts only while shown	SvInspectorView
ownViews `((ModelInstanceTypeProps<…> & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & IStateTreeNode<…>) \| (ModelInstanceTypeProps<…> & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & IStateTreeNode<…>))[]`	an unshown circle never initializes, so it would read as loading forever	SvInspectorView
features `SimpleFeatureSerialized[]`	the records of the rows the sheet's filters leave	SvInspectorView
allFeatures `SimpleFeatureSerialized[]`	every record of the sheet, which the chord track holds; filters narrow it through visibleChordIds rather than rebuilding the track	SvInspectorView
visibleChordIds `string[] \| undefined`	undefined while no filter narrows the sheet	SvInspectorView
canonicalFeatureRefNameSet `Set<string>`	every canonical refName the visible features' chords land on, both ends included	SvInspectorView
circularDisplayedRegions `BasicRegion[] \| undefined`	never narrowed to nothing, which would draw an empty circle	SvInspectorView
effectiveSpreadsheetWidthFraction `number`		SvInspectorView
subviewWidths `{ spreadsheet: number; circular: number; }`		SvInspectorView
highlightedChordIds `string[] \| undefined`	the records of the selected record's event, which the circle keeps at full strength while it dims the rest	SvInspectorView
variantTrackId `string`		SvInspectorView
featuresCircularTrackConfiguration `{ type: string; trackId: string; name: string; adapter: {…}; assemblyNames: string[]; displays: {…}[]; } \| undefined`		SvInspectorView
rendersDisplays `boolean`	Overridable hook (default true): whether this view's mounted body renders its own displays. A linear genome view collapsed to its ruler mounts the scalebar and none of its tracks, so a display in it can no more paint than one in a view scrolled off screen. Views nested in this one are unaffected: they paint wherever their own body is.	BaseViewModel
effectiveBodyMounted `boolean`	Whether this view's displays have a canvas to paint into: its body is in the DOM, counting the views it is nested inside, and the body renders them (`rendersDisplays`). This is the question a display's phase asks. `bodyMounted` alone answers the DOM half only for a view a container renders directly. A view nested in another view (a synteny row, a breakpoint panel) has no container writing its flag, so it reads `true` forever while its whole subtree is out of the DOM, and every display in it waits for a first paint that nothing will make — the hang this flag exists to prevent, one level down. An ancestor that does not carry the flag at all leaves the answer alone rather than excusing the paint: only an explicit `false` unmounts, so a duck-typed stand-in that forgot it keeps waiting, which is the failure that shows up as a slow test rather than as a picture of an empty view.	BaseViewModel
ownTracks `AbstractTrackModel[]`	The tracks this view puts in the census — its own, not a nested view's. Empty here, and overridden by the views that have any: the base cannot read `self.tracks` for them, because what a view keeps under that name is the view's business. react-msaview's holds its MSA annotation rows — `{ReactComponent, model}` objects with no configuration and no displays — and a base that helped itself to them handed them to the readiness marker as tracks, which error-paged every session holding an MSA view.	BaseViewModel

Methods

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

Actions

Member	Description	Defined by
setHeight `(newHeight: number) => number`		SvInspectorView
setOnlyDisplayRelevantRegionsInCircularView `(val: boolean) => void`		SvInspectorView
resizeSpreadsheetWidth `(distance: number) => void`	accumulates onto the fraction, not the rounded spreadsheetView.width, so the divider doesn't creep a pixel per drag frame	SvInspectorView
setLaunch `(launch?: LaunchInput<SvInspectorViewCommands> \| undefined) => void`		SvInspectorView
resizeHeight `(distance: number) => number`		SvInspectorView
setDisplayName `(name: string) => void`		BaseViewModel
setWidth `(newWidth: number) => void`	width is an important attribute of the view model, when it becomes set, it often indicates when the app can start drawing to it. certain views like lgv are strict about this because if it tries to draw before it knows the width it should draw to, it may start fetching data for regions it doesn't need to setWidth is updated by a ResizeObserver generally, the views often need to know how wide they are to properly draw genomic regions	BaseViewModel
setBodyMounted `(flag: boolean) => void`	See `bodyMounted`. Written by the view's container, which is the only thing that knows whether it rendered the body.	BaseViewModel
setMinimized `(flag: boolean) => void`		BaseViewModel

Guide: URL query parameter API

SvInspectorView

Example usage#

Properties#

Volatiles#

Getters#

Methods#

Actions#

Related links#