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EmbeddedSessionMixin

Auto-generated @jbrowse/mobx-state-tree API for the current JBrowse release — see pluggable elements for concepts. Built into JBrowse core. View source.

Everything the two single-view embedded products' sessions (react-linear-genome-view, react-circular-genome-view) share: the mixin set they compose and the three getters that read the root model. The twin of createEmbeddedRootModel one level down.

Each product composes this mixin. A factory taking the product's view type and tracks mixin as parameters does not typecheck usefully: types.compose's overloads are declared over IModelType<P, O, FC, FS>, so a model passed as a naked type parameter gives nothing to infer those four from, and session.view becomes any at every embedder call site with no type error. Passing only concrete types to compose keeps the products' views typed.

Each product therefore declares its tracks mixin, view prop, and the views/addView/removeView members that read self.view, because those members need its concrete view type.

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

Properties

MemberDescriptionDefined by
id
id: ElementId		BaseSessionModel
name
name: types.string		BaseSessionModel
focusedViewId
focusedViewId: types.maybe(types.string)		used to keep track of which view is in focusBaseSessionModel
highlightsVisible
highlightsVisible: types.stripDefault(types.boolean, true)		one session-wide toggle for all region highlight bands (URL/view highlights and bookmark overlays)BaseSessionModel
heldForMissingPlugins
heldForMissingPlugins: types.stripDefault(
        types.frozen<HeldNode[] | undefined>(),
        undefined,
      )
views, tracks, displays and widgets pruneUnbuildableNodes took out of the tree because this build has no plugin for their type, each with the anchor that puts it back. Nothing in the session reads its contents, and pruneUnbuildableNodes defines their structure.

It is a declared property because MST drops undeclared snapshot keys without error. Without this declaration the held nodes survive the prune and are then discarded when setSession builds the tree, while every unit test of the prune still passes. heldNodesSurviveTheSession.test.ts tests that they survive.		BaseSessionModel
drawerPosition
drawerPosition: types.optional(
        types.enumeration<DrawerPosition>('DrawerPosition', [
          ...drawerPositions,
        ]),
        storedDrawerPosition,
      )
DrawerWidgetSessionMixin
drawerWidth
drawerWidth: types.stripDefault(
        types.refinement(types.integer, width => width >= minDrawerWidth),
        384,
      )
DrawerWidgetSessionMixin
widgets
widgets: types.stripDefault(types.map(widgetStateModelType), {})		DrawerWidgetSessionMixin
activeWidgets
activeWidgets: types.stripDefault(
        types.map(types.safeReference(widgetStateModelType)),
        {},
      )
DrawerWidgetSessionMixin
minimized
minimized: types.stripDefault(types.boolean, false)		DrawerWidgetSessionMixin
connectionInstances
connectionInstances: types.stripDefault(
        types.array(pluginManager.pluggableMstType('connection', 'stateModel')),
        [],
      )
ConnectionManagementSessionMixin
connectionTrackConfigs
connectionTrackConfigs: types.stripDefault(
        types.frozen<Record<string, ConnectionTrackConfigEntry>>(),
        {},
      )
Persisted configs of connection tracks the user has opened, keyed by trackId. Unlike connectionInstances (stripped from snapshots, holds the whole fetched hub), this holds only the tracks in use, so an open connection track resolves synchronously on session load without re-establishing the connection.ConnectionManagementSessionMixin

Volatiles

MemberDescriptionDefined by
selection
selection: undefined as unknown		this is the globally "selected" object. can be anything. code that wants to deal with this should examine it to see what kind of thing it is.BaseSessionModel
hovered
hovered: undefined as unknown		this is the globally "hovered" object. can be anything. code that wants to deal with this should examine it to see what kind of thing it is.BaseSessionModel
queueOfDialogs
queueOfDialogs: [] as [DialogComponentType, Record<string, unknown>][]
BaseSessionModel
preferencesOverrides
preferencesOverrides: observable.map<string, unknown>(undefined, {
        deep: false,
      })
runtime user-preference overrides keyed by preference id, resolved by getPreference against the configuration.preferences admin defaults. Empty here (config-only); products that let users edit preferences load and persist these via localStorage. A runtime override map layered over config defaults, kept off the snapshot since prefs are local UI.

An observable.map (not a plain object reassigned wholesale) so each preference is its own tracked key: writing one (setScrollZoom) can't invalidate a reader of another. A single spread-replaced object made every setter wake every reader, so toggling scroll-to-zoom re-fetched every track.

deep: false keeps an object-valued preference a plain object rather than a MobX Proxy, which V8's structured-clone serializer rejects. The map still notifies per key on set, so shallow values lose no reactivity — and nothing can mutate a preference in place, because setPreferenceOverride freezes what it stores.		BaseSessionModel
snackbarMessages
snackbarMessages: observable.array<SnackbarMessage>()		SnackbarModel
errorDialog
errorDialog: undefined as ErrorDialogState | undefined		the error currently shown in the stack-trace dialog. Kept off the dialog queue so it can stack on top of an already-open dialog (e.g. the one whose action raised the error) instead of waiting behind itSnackbarModel
poppedOut
poppedOut: false		true while the visible widget is shown in a modal dialog instead of the drawer. Volatile because a restored session that opened straight into a modal, with no drawer behind it, is disorientingDrawerWidgetSessionMixin

Getters

MemberDescriptionDefined by
viewTitleBars
boolean		An embedded view is drawn with no title bar above it, so its menu lives in the view's own controls.EmbeddedSessionMixin
version
string		EmbeddedSessionMixin
assemblyNames
string[]		EmbeddedSessionMixin
assemblyManager
ModelInstanceTypeProps<…> & {…} & {…} & {…} & {…} & {…} & {…} & IStateTreeNode<…>
EmbeddedSessionMixin
root
TypeOrStateTreeNodeToStateTreeNode<ROOT_MODEL_TYPE>		BaseSessionModel
jbrowse
any		BaseSessionModel
rpcManager
RpcManager		BaseSessionModel
configuration
Instance<JB_CONFIG_SCHEMA>		BaseSessionModel
adminMode
boolean		BaseSessionModel
textSearchManager
TextSearchManager		BaseSessionModel
assemblies
(ConfigNodeProps<…> & ConfigNodeActions & ConfigNodeBrand<...>)[]
BaseSessionModel
DialogComponent
DialogComponentType		BaseSessionModel
DialogProps
Record<string, unknown>		BaseSessionModel
animationMode
AnimationMode		resolved feature-layout animation mode (never undefined)BaseSessionModel
scrollZoom
boolean		resolved scroll-to-zoom preference. Global and personal (never shared in a session snapshot); every wheel-zoom view reads this single value.BaseSessionModel
numberGrouping
boolean		resolved thousand-separator preference. Read for display in the Preferences dialog; the formatter itself reads a plain module variable set at startup in each realm (see setNumberGrouping), because worker- built strings can't see a main-thread observable.BaseSessionModel
snackbarMessageSet
Map<string, SnackbarMessage>		SnackbarModel
visibleWidget
Widget | undefined		DrawerWidgetSessionMixin
drawerVisible
boolean		whether the drawer column is on screen: there is something to show, it is not minimized to the FAB, and it is not currently a modal instead.

A getter rather than each host's own &&, because the hosts drifted -- the app shell tested poppedOut and the embedded view did not, so the day a popout button reaches the embedded drawer header it would render the modal and the drawer at once.		DrawerWidgetSessionMixin
connections
(ConfigNodeProps<…> & ConfigNodeActions & ConfigNodeBrand<...>)[]
ConnectionManagementSessionMixin
themeOptions
SerializableThemeArgs		Serializable theme description (the canonical themeOptions contract shared with the app-core/web sessions). This is what crosses the RPC worker boundary — e.g. the canvas display reads getSession(self).themeOptions in its rpcProps so worker-baked colors (CDS frames, stroke fallback) honor the config theme slot.EmbeddedSessionThemeMixin
palette
JBrowsePalette		Every color JBrowse renders, resolved to plain strings and free of any UI toolkit. This is what rendering reads. See the canonical ThemeManagerSessionMixin getter of the same name.EmbeddedSessionThemeMixin
styleTheme
JBrowseStyleTheme		The palette plus the sizing tokens makeStyles reads. See the canonical ThemeManagerSessionMixin getter of the same name.EmbeddedSessionThemeMixin
theme
Theme		Resolved MUI theme, mirroring the product's ThemeProvider. Lets headless/RPC consumers derive theme-dependent state without a mounted component. Shares its colors with palette by construction.EmbeddedSessionThemeMixin

Methods

MemberDescriptionDefined by
getPreferenceDefault
(key: string) => unknown		the admin/embedder configuration.preferences value for a key, ignoring any runtime override — i.e. what a reset falls back to. Exposed rather than inlined because "differs from the default" is a question the Preferences reset diff asks about settings this map doesn't hold (see defaultUseWorkspaces).BaseSessionModel
getPreference
(key: string) => unknown		resolved value of a user preference: a runtime override if the user set one, otherwise the admin/embedder configuration.preferences default. The override map is empty unless the product loads it (web/desktop).BaseSessionModel
getPreferenceChanges
() => TrackConfigChange[]		every scalar preference override that currently differs from its config/admin default, as { path, from, to } rows whose path is the override's own key. A scalar pref (animationMode, scrollZoom) whose override equals the default is omitted, since reverting it is a no-op.BaseSessionModel
getReferringMultiple
(trackIds: string[]) => Map<string, ReferringNode[]>		Walk the tree once and map each requested trackId to the nodes holding a types.reference that resolves to it (a view's track entry, a config editor widget). Track configs are matched by trackId, not identity, so a frozen base and its hydrated MST node compare equal.ReferenceManagementSessionMixin
getReferring
(trackId: string) => ReferringNode[]		The nodes currently referring to trackId (see getReferringMultiple).ReferenceManagementSessionMixin
getTrackListMenuItems
(config: AnyConfigurationModel, view?: TrackActionView | undefined) => MenuItem[]
flattened menu items for use in hierarchical track selectorTrackMenuSessionMixin
getTrackActionMenuItems
({ config, view, }: { config: AnyConfigurationModel; view?: TrackActionView | undefined; }) => MenuItem[]
TrackMenuSessionMixin
getActiveThemeOptions
(_name?: string | undefined) => ThemeOptions | undefined		Raw ThemeOptions for the active theme, which every view's SVG export threads into each display's renderSvg as a configTheme and rebuilds outside React. The config slot is the whole answer here because it is the whole of an embedded product's theming: no picker, no allThemes, and it is what setThemeMode writes and palette resolves from. name is accepted and ignored — the app session's counterpart looks a named preset up in allThemes().EmbeddedSessionThemeMixin

Actions

MemberDescriptionDefined by
setSelection
(thing: unknown) => void		set the global selection, i.e. the globally-selected object. can be a feature, a view, just about anything

A feature is unwrapped on the way in, so app state never holds a jexlFeatureProxy. isFeature accepts a proxy, but on one id is a data field rather than the method the Feature type promises — every consumer doing isFeature(selection) ? selection.id() : … would throw.		BaseSessionModel
clearSelection
() => void		clears the global selectionBaseSessionModel
setHovered
(thing: unknown) => void		BaseSessionModel
setHighlightsVisible
(arg: boolean) => void		toggle all region highlight bands across every viewBaseSessionModel
revealHighlights
() => void		turn highlight bands back on, so a newly made highlight or bookmark is visible even after an earlier "highlights off"BaseSessionModel
setPreferenceOverride
(key: string, value: unknown) => void		set a runtime user-preference override (see getPreference). Mutates volatile state; products persist these to localStorage. An undefined value deletes the key (rather than leaving a phantom entry that getPreference reads as absent) so the store never holds dead keys.BaseSessionModel
clearPreferenceOverrides
() => void		clear every runtime preference override at once, so each falls back to its config/admin default. Backs the Preferences dialog "Reset to defaults" button.BaseSessionModel
clearPreferenceOverride
(key: string) => void		clear a single runtime preference override (see getPreference) so it falls back to its config/admin default. Backs the per-entry reset in the Preferences dialog "Reset to defaults" confirmation.BaseSessionModel
setScrollZoom
(flag: boolean) => void		set the global scroll-to-zoom preference (see the scrollZoom getter)BaseSessionModel
setName
(str: string) => void		BaseSessionModel
setFocusedViewId
(viewId: string | undefined) => void		undefined is "no view is focused", which the property has always been able to hold (types.maybe) and this had no way to spell. Nothing cleared it on teardown as a result: a view that was focused when it left the session left its id behind, and since every consumer compares focusedViewId === view.id, the id matched nothing, the focus ring vanished with nothing to say why, and the dead id persisted into a saved or shared session. takeOut clears it now.BaseSessionModel
removeActiveDialog
() => void		BaseSessionModel
queueDialog
(doneCallback: DoneCallback) => void		BaseSessionModel
notify
(message: string, level?: NotificationLevel | undefined, action?: SnackAction | SnackAction[] | undefined) => void
SnackbarModel
notifyError
(errorMessage: string, error?: unknown, extra?: unknown, action?: SnackAction | undefined) => void
SnackbarModel
setErrorDialog
(state: ErrorDialogState | undefined) => void		SnackbarModel
pushSnackbarMessage
(message: string, level?: NotificationLevel | undefined, actions?: SnackAction[] | undefined) => void
SnackbarModel
popSnackbarMessage
() => SnackbarMessage | undefined		SnackbarModel
removeSnackbarMessage
(message: string) => void		SnackbarModel
setDrawerPosition
(arg: DrawerPosition) => void		DrawerWidgetSessionMixin
updateDrawerWidth
(drawerWidth: number, availableWidth?: number) => number		DrawerWidgetSessionMixin
resizeDrawer
(distance: number, availableWidth?: number) => number		DrawerWidgetSessionMixin
addWidget
(typeName: string, id: string, initialState?: any, conf?: unknown) => any
DrawerWidgetSessionMixin
showWidget
(widget: any) => void		DrawerWidgetSessionMixin
hideWidget
(widget: any) => void		DrawerWidgetSessionMixin
minimizeWidgetDrawer
() => void		DrawerWidgetSessionMixin
showWidgetDrawer
() => void		DrawerWidgetSessionMixin
popoutWidget
() => void		show the visible widget in a modal dialog, freeing the drawer columnDrawerWidgetSessionMixin
returnWidgetToDrawer
() => void		DrawerWidgetSessionMixin
hideAllWidgets
() => void		DrawerWidgetSessionMixin
editConfiguration
(configuration: AnyConfigurationModel | { trackId: string; }, opts?: { expandedDisplayId?: string | undefined; } | undefined) => void
opens a configuration editor to configure the given thing, and sets the current task to be configuring itDrawerWidgetSessionMixin
makeConnection
(configuration: AnyConfigurationModel, initialSnapshot?: object) => any
ConnectionManagementSessionMixin
breakConnection
(configuration: AnyConfigurationModel) => void		Remove a live connection instance. Tolerant of an already-dormant connection (its instance is stripped from the session on reload). Leaves persisted open-track configs alone — the connect() error path calls this and the user's already-open tracks must survive a transient failure. Full removal goes through deleteConnection.ConnectionManagementSessionMixin
teardownConnection
(configuration: AnyConfigurationModel) => void		Close every track a connection contributed — the live instance's tracks plus any persisted open-track configs (a dormant connection, never expanded this session, still renders its opened tracks from connectionTrackConfigs) — from all views/widgets, drop the live instance, and drop the persisted configs. The session is left as if the connection had never loaded.ConnectionManagementSessionMixin
deleteConnection
(configuration: AnyConfigurationModel) => any		Fully remove a connection: tear down its tracks and live instance, then delete its config.ConnectionManagementSessionMixin
addConnectionConf
(connectionConf: AnyConfiguration) => any		Adds to the config, not the session: jbrowse.connections, which every visitor to this instance loads. jbrowse-web overrides this so a non-admin's connection lands in sessionConnections instead — see WebSessionConnectionsMixin, whose addSessionConnectionConf is what to call when you mean the session specifically rather than "wherever this user's edits go".

Applications without that override (Desktop, the embedded products) have only this one destination, and it is the right one there: their config and session are saved as a single document.		ConnectionManagementSessionMixin
clearConnections
() => void		ConnectionManagementSessionMixin
captureConnectionTrack
(trackId: string) => void		Snapshot a just-opened connection track's config into connectionTrackConfigs so it survives session reload. No-op if the track isn't connection-provided or is already captured (edits go through updateConnectionTrackConfig).ConnectionManagementSessionMixin
updateConnectionTrackConfig
(trackConf: Record<string, unknown> & { trackId: string; }) => void
Persist an edit to an opened connection track. The full config is stored (not a delta): the connection's fetched "base" isn't present at load, so only a complete config resolves synchronously.ConnectionManagementSessionMixin
setConnectionTrackConfig
(trackId: string, connectionId: string, config: Record<string, unknown>) => void
Upsert one opened connection track's persisted config.ConnectionManagementSessionMixin
pruneConnectionTrackConfig
(trackId: string) => void		Drop a connection track's persisted config once no open view still references it, so the session doesn't accumulate closed tracks.ConnectionManagementSessionMixin
hydrateConnection
(connectionId: string) => void		Lazily establish a single connection by id if it isn't already live; the track selector calls it when the connection's category is expanded. Fetches without launching a view or showing a success snackbar; already-open tracks keep rendering from connectionTrackConfigs meanwhile. Idempotent.ConnectionManagementSessionMixin
dereferenceTrack
(trackId: string, referring: ReferringNode[]) => void		Remove trackId from every view referring to it and close any config editor widget open on it. Runs immediately: the walk that produced referring has finished, so mutating those views here is safe.ReferenceManagementSessionMixin
setThemeMode
(mode: "dark" | "light") => void		Switch the session to light or dark. themeOptions sends the theme slot to the renderer, so labels drawn in the worker follow it, and palette is derived from the same slot, so React-drawn elements follow it too. An embedder who sets only a React-side palette leaves the worker-drawn labels in the old mode.

Merges into the existing theme at both levels. theme is a frozen slot, so setConf(session, 'theme', { palette: { mode } }) replaces every other key in it, discarding whatever the host passed as createViewState's configuration.theme (a brand primary, say) the first time their dark-mode toggle fires. resolvePalette spreads configTheme.palette over the preset shallowly, so mode and primary are siblings and both levels have to be kept.		EmbeddedSessionThemeMixin