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SvInspectorView

Auto-generated from the @jbrowse/mobx-state-tree model in the source — see the developer guide 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',
}

Shows a file of structural variants as a table beside a circular view that draws them as chords. The model holds a SpreadsheetView and a CircularView side by side, without extending either.

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

Properties

MemberDescription
id
id: ElementId
type
type: types.literal('SvInspectorView')
height
height: types.stripDefault(types.number, defaultHeight)		height of the whole view in pixels
onlyDisplayRelevantRegionsInCircularView
onlyDisplayRelevantRegionsInCircularView: types.stripDefault(
          types.boolean,
          false,
        )
draw only the chromosomes the visible rows touch
spreadsheetWidthFraction
spreadsheetWidthFraction: types.stripDefault(types.number, 0.66)		share of the view's width given to the spreadsheet
spreadsheetView
spreadsheetView: types.optional(SpreadsheetModel, () =>
          SpreadsheetModel.create({
            type: 'SpreadsheetView',
            hideVerticalResizeHandle: true,
          }),
        )
circularView
circularView: types.optional(CircularModel, () =>
          CircularModel.create({
            type: 'CircularView',
            hideVerticalResizeHandle: true,
            disableImportForm: true,
          }),
        )
launch
launch: types.frozen<
          LaunchInput<SvInspectorViewCommands> | undefined
        >()
transient launch keys, forwarded to the sheet on attach and cleared; author them directly on the view
2 inherited properties from one model

From BaseViewModel: displayName, minimized

Volatiles

MemberDescription
SpreadsheetViewReactComponent
ViewComponentType
CircularViewReactComponent
ViewComponentType
2 inherited volatiles from one model

From BaseViewModel: width, bodyMounted

Getters

MemberDescription
pendingLaunch
LaunchInput<SvInspectorViewCommands & { unknown?: Record<string, unknown> | undefined; malformed?: Record<string, unknown> | undefined; legacyInit?: boolean | undefined; } & IStateTreeNode<IType<LaunchInput<SvInspectorViewCommands> | undefined, LaunchInput<SvInspectorViewCommands> | undefined, LaunchInput<SvInspectorViewCommands> | undefined>>> | undefined
currentAssembly
(ModelInstanceTypeProps<…> & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & { getCanonicalRefName2(refName: string): string; isValidRefName(refName: string): boolean; } & { isCircularRefName(refName: string): boolean; getRefNamePosition(refName: string): number | undefined; getAliasesForRefName(refName: string): string[]; getRefNameMapForAdapter(adapterConf: AdapterConf, options: BaseOptions): Promise<…>; getRefNameMismatch(adapterCacheKey: string): RefNameMismatch | undefined; } & IStateTreeNode<…>) | undefined
assemblyName
string | undefined
showCircularView
boolean		false while the sheet shows its import form
showLoading
boolean		both halves' loading state; the circle counts only while shown
ownViews
((ModelInstanceTypeProps<…> & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & IStateTreeNode<…>) | (ModelInstanceTypeProps<…> & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & { afterCreate(): void; beforeDestroy(): void; afterAttach(): void; } & { tracksMenuItem(): MenuItem; } & { readonly legendSpec: LegendSpec; legendSpecIn(palette?: JBrowsePalette | undefined): LegendSpec; menuItems(): MenuItem[]; } & IStateTreeNode<…>))[]
an unshown circle never initializes, so it would read as loading forever
features
SimpleFeatureSerialized[]		the records of the rows the sheet's filters leave
allFeatures
SimpleFeatureSerialized[]		every record of the sheet, which the chord track holds; filters narrow it through visibleChordIds rather than rebuilding the track
visibleChordIds
string[] | undefined		undefined while no filter narrows the sheet
canonicalFeatureRefNameSet
Set<string>		every canonical refName the visible features' chords land on, both ends included
circularDisplayedRegions
BasicRegion[] | undefined		never narrowed to nothing, which would draw an empty circle
effectiveSpreadsheetWidthFraction
number
subviewWidths
{ spreadsheet: number; circular: number; }
highlightedChordIds
string[] | undefined		the records of the selected record's event, which the circle keeps at full strength while it dims the rest
variantTrackId
string
featuresCircularTrackConfiguration
{ type: string; trackId: string; name: string; adapter: { type: string; features: SimpleFeatureSerialized[]; }; assemblyNames: string[]; displays: { type: string; displayId: string; onChordClick: string; color: { field: string; }; opacity: number; }[]; } | undefined
3 inherited getters from one model

From BaseViewModel: rendersDisplays, effectiveBodyMounted, ownTracks

Methods

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

Actions

MemberDescription
setHeight
(newHeight: number) => number
setOnlyDisplayRelevantRegionsInCircularView
(val: boolean) => void
resizeSpreadsheetWidth
(distance: number) => void		accumulates onto the fraction, not the rounded spreadsheetView.width, so the divider doesn't creep a pixel per drag frame
setLaunch
(launch?: LaunchInput<SvInspectorViewCommands> | undefined) => void
resizeHeight
(distance: number) => number
4 inherited actions from one model

From BaseViewModel: setDisplayName, setWidth, setBodyMounted, setMinimized