JBrowseReactCircularGenomeViewSessionModel
Auto-generated @jbrowse/mobx-state-tree API for the current JBrowse release — see pluggable elements for concepts. View source.
The shared EmbeddedSessionMixin plus this product's tracks mixin and
its single CircularView. Both are spelled out here rather than passed to a
shared factory because types.compose cannot infer through a generic — see
EmbeddedSessionMixin.
The tracks mixin is the session-tracks one, the same the linear embed uses.
The plainer TracksManagerSessionMixin sends addTrackConf on to
jbrowse.addTrackConf, which the embedded root config model does not have —
so a host adding a track after mount got a TypeError, and there was no other
door: this product's whole track set had to be decided at build time.
Members a composed model contributes are listed here too, so these tables are the whole surface.
Properties
| Member | Description | Defined by |
|---|---|---|
viewview: pluginManager.getViewType('CircularView').stateModel | JBrowseReactCircularGenomeViewSessionModel | |
idid: ElementId | BaseSessionModel | |
namename: types.string | BaseSessionModel | |
focusedViewIdfocusedViewId: types.maybe(types.string) | used to keep track of which view is in focus | BaseSessionModel |
highlightsVisiblehighlightsVisible: types.stripDefault(types.boolean, true) | one session-wide toggle for all region highlight bands (URL/view highlights and bookmark overlays) | BaseSessionModel |
| heldForMissingPlugins | 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 | DrawerWidgetSessionMixin | |
| drawerWidth | DrawerWidgetSessionMixin | |
widgetswidgets: types.stripDefault(types.map(widgetStateModelType), {}) | DrawerWidgetSessionMixin | |
| activeWidgets | DrawerWidgetSessionMixin | |
minimizedminimized: types.stripDefault(types.boolean, false) | DrawerWidgetSessionMixin | |
| connectionInstances | ConnectionManagementSessionMixin | |
| connectionTrackConfigs | 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 |
| sessionTracks | User-added session tracks (no matching admin config track). A non-admin's edits to an existing config track are stored as deltas (trackConfigDeltas), not here. | SessionTracksManagerSessionMixin |
| trackConfigDeltas | Per-track config overrides for a non-admin, keyed by trackId, stored as a delta against the admin-owned base config (jbrowse.tracks entry) rather than a full copy — so a later admin change to an untouched field still flows through (see trackConfigDelta.ts). Frozen (not a typed track array) on purpose: a typed create() would fill defaults, erasing the "unset vs default" distinction the delta merge relies on.stripDefault for the reason every other persisted prop beside it has it: without it the empty map is written into every snapshot and every share link, so a session that never overrode a track still ships "trackConfigDeltas":{}. It was the one prop added since that convention without it. | SessionTracksManagerSessionMixin |
Volatiles
| Member | Description | Defined by |
|---|---|---|
selectionselection: 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 |
hoveredhovered: 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 | BaseSessionModel | |
| preferencesOverrides | 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 |
snackbarMessagessnackbarMessages: observable.array<SnackbarMessage>() | SnackbarModel | |
errorDialogerrorDialog: 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 it | SnackbarModel |
poppedOutpoppedOut: 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 disorienting | DrawerWidgetSessionMixin |
editableTrackConfigseditableTrackConfigs: new Map<string, EditableTrackConfig>() | Per-track private working copies (non-admin), keyed by trackId. A plain Map — not observable, not persisted — mirroring the pluginManager hydration cache: it holds the live MST config node a shown track's in-place quick-edits mutate, so the shared frozen base is never touched. See ADR-032. Not evicted: it's a pure memoization cache, bounded by the count of distinct tracks shown this session (each entry a lazily-hydrated config node), holding no authoritative state — the persisted delta is the source of truth, and reset/programmatic edits keep a retained copy in sync. Retention is volatile RAM only (never serialized), so it's not worth a reference-counted prune at every track-removal path. Each entry carries the delta it mirrors, so a delta replaced from outside this mixin invalidates it — see getEditableTrackConfig. | SessionTracksManagerSessionMixin |
Getters
| Member | Description | Defined by |
|---|---|---|
| views | JBrowseReactCircularGenomeViewSessionModel | |
viewTitleBarsboolean | An embedded view is drawn with no title bar above it, so its menu lives in the view's own controls. | EmbeddedSessionMixin |
versionstring | EmbeddedSessionMixin | |
assemblyNamesstring[] | EmbeddedSessionMixin | |
| assemblyManager | EmbeddedSessionMixin | |
rootTypeOrStateTreeNodeToStateTreeNode<ROOT_MODEL_TYPE> | BaseSessionModel | |
jbrowseany | BaseSessionModel | |
rpcManagerRpcManager | BaseSessionModel | |
configurationInstance<JB_CONFIG_SCHEMA> | BaseSessionModel | |
adminModeboolean | BaseSessionModel | |
textSearchManagerTextSearchManager | BaseSessionModel | |
assemblies(ModelInstanceTypeProps<…> & {…} & IStateTreeNode<…>)[] | BaseSessionModel | |
DialogComponentDialogComponentType | BaseSessionModel | |
DialogPropsRecord<string, unknown> | BaseSessionModel | |
animationModeAnimationMode | resolved feature-layout animation mode (never undefined) | BaseSessionModel |
scrollZoomboolean | resolved scroll-to-zoom preference. Global and personal (never shared in a session snapshot); every wheel-zoom view reads this single value. | BaseSessionModel |
numberGroupingboolean | 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 |
snackbarMessageSetMap<string, SnackbarMessage> | SnackbarModel | |
visibleWidgetWidget | undefined | DrawerWidgetSessionMixin | |
drawerVisibleboolean | 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(ModelInstanceTypeProps<…> & {…} & IStateTreeNode<…>)[] | ConnectionManagementSessionMixin | |
themeOptionsSerializableThemeArgs | 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 |
paletteJBrowsePalette | 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 |
styleThemeJBrowseStyleTheme | The palette plus the sizing tokens makeStyles reads. See the canonical ThemeManagerSessionMixin getter of the same name. | EmbeddedSessionThemeMixin |
themeTheme | 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 |
tracks(ModelInstanceTypeProps<…> & {…} & IStateTreeNode<…>)[] | User-added session tracks first, then each admin config track with its delta (trackConfigDeltas) merged over it. A base track without a delta is returned unchanged by identity to keep the hydration cache warm. | SessionTracksManagerSessionMixin |
Methods
| Member | Description | Defined 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 |
| flattened menu items for use in hierarchical track selector | TrackMenuSessionMixin | |
| 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 |
getTrackConfigChanges(trackId: string) => TrackConfigChange[] | The overridden slots for trackId (empty when it has no delta): each changed setting's path, its base/default value and the edited value. Drives the "view changes" dialog opened from the edited badge. | SessionTracksManagerSessionMixin |
| getEditableTrackConfig | A non-admin's private working copy of a track config, created on first access from the current frozen (base+delta) value and cached by trackId, so a shown track's in-place quick-edits (setSlot) mutate this copy and never the shared frozen base node (see ADR-032). Undefined in admin mode — there the base jbrowse.tracks entry is edited in place. Called by TrackConfigurationReference during lazy hydration. Cached against the delta it was built from, not by trackId alone. A delta this mixin wrote re-stamps the entry, so the copy an edit is still being typed into is never swapped out mid-keystroke; a delta replaced from outside — an undo's applySnapshot on the session, a session restore — cannot, so the next read rebuilds the copy from the delta that now exists. Reading trackConfigDeltas here is also what makes an undo re-resolve the reference at all: the resolver's caller is already subscribed to it through getTrackById. | SessionTracksManagerSessionMixin |
| getTrackById | Config for one trackId — a track, assembly sequence, or connection track — or undefined. Per-id reactive: every display resolves its config through this (via TrackConfigurationReference) and subscribes only to its own id, so one track's settings edit doesn't re-render the others. | TracksManagerSessionMixin |
getTracksById() => Record<…> | Every track config the session can resolve, keyed by trackId. Prefer the per-id reactive getTrackById(id): reading this whole map subscribes the caller to every track, so an edit to any one of them wakes it — the reason internal display config resolution moved off it. Kept for plugins that look up ids in a non-reactive context. | TracksManagerSessionMixin |
Actions
| Member | Description | Defined by |
|---|---|---|
| addView | replaces view in this case | JBrowseReactCircularGenomeViewSessionModel |
removeView() => void | does nothing | JBrowseReactCircularGenomeViewSessionModel |
| launchView | addView, async to satisfy the AbstractViewContainer contract | JBrowseReactCircularGenomeViewSessionModel |
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 selection | BaseSessionModel |
setHovered(thing: unknown) => void | BaseSessionModel | |
setHighlightsVisible(arg: boolean) => void | toggle all region highlight bands across every view | BaseSessionModel |
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 | SnackbarModel | |
| notifyError | SnackbarModel | |
setErrorDialog(state: ErrorDialogState | undefined) => void | SnackbarModel | |
| pushSnackbarMessage | 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 | 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 column | DrawerWidgetSessionMixin |
returnWidgetToDrawer() => void | DrawerWidgetSessionMixin | |
hideAllWidgets() => void | DrawerWidgetSessionMixin | |
| editConfiguration | opens a configuration editor to configure the given thing, and sets the current task to be configuring it | DrawerWidgetSessionMixin |
| makeConnection | ConnectionManagementSessionMixin | |
| breakConnection | 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 | 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 | 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 | 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 | 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 |
addSessionTrackConf(trackConf: AnyConfiguration) => any | Add a track config to this session: it lands in sessionTracks, travels with the session when it is saved or shared, and never reaches the config.json the server hands every visitor.The default destination. Everything that is not an Add-track workflow wants this one, whoever is looking — a session spec's sessionTracks, a URL's &sessionTracks=, and every track a feature stands up on the user's behalf. Mirrors addSessionConnectionConf in the connections mixins. | SessionTracksManagerSessionMixin |
publishTrackConf(trackConf: AnyConfiguration) => any | Publish a track config to the shared catalog if this user can, and fall back to their session if they cannot: an admin's goes to jbrowse.tracks, which the admin server writes back into the config.json every visitor is served; everyone else's goes to sessionTracks.Call it only from the "Add track" workflows, where an admin adding a track means to add it for the whole site. For a track a feature creates on the user's behalf (a search result, a computed consensus, a reconstruction's segment labels), one admin click on this publishes it to every visitor, and each later click publishes another copy, because the per-launch trackId prevents deduplication. Use addSessionTrackConf above for those.An admin's track still goes to the session when it names an assembly the config.json does not carry: a session spec's assembly, a MAF sample's genome, or a comparative view's synthesized pair. The Add-track widget takes its assembly from the containing view, so an admin adding a track in such a view passes a name no visitor can resolve. Publishing it would write an entry the server sends to every visitor and no visitor can draw. Adding it to the session keeps the track usable and writes no dangling entry; a snackbar names the assembly that caused the fallback. The snackbar names the assembly and not the track, so a batch produces one message: pushSnackbarMessage dedupes on the exact text, and BulkAddTracksWorkflow publishes in a loop. Including the track name would show one snackbar per file to an admin adding thirty. The assembly is all the admin needs to act on. | SessionTracksManagerSessionMixin |
addTrackConf(trackConf: AnyConfiguration) => any | Deprecated alias of addSessionTrackConf. Call that, or publishTrackConf. | SessionTracksManagerSessionMixin |
updateTrackConfiguration(trackConf: PlainTrackConfig) => void | Persist a non-admin's edited track config as a delta (trackConfigDeltas) against the admin-owned base — only the changed slots — so the edits persist and are shared while admin changes to untouched fields still flow through. A user-added session track (no base) is edited in place. Everything else (admin edits, opened connection tracks) defers to the base mixin, which routes connection tracks to connectionTrackConfigs and the rest to the jbrowse config. | SessionTracksManagerSessionMixin |
resetTrackConfiguration(trackId: string) => void | Drop a non-admin's delta (trackConfigDeltas) so the track reverts to its admin config (jbrowse.tracks) default. Unlike deleteTrackConf this does not dereference the track from open views — the base config re-resolves in place, so an open track stays open and simply reverts. | SessionTracksManagerSessionMixin |
| deleteTrackConf | SessionTracksManagerSessionMixin |