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SessionTracksManagerSessionMixin

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

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

Properties

MemberDescriptionDefined by
sessionTracks
sessionTracks: types.stripDefault(
        types.array(pluginManager.pluggableConfigSchemaType('track')),
        [],
      )
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
trackConfigDeltas: types.stripDefault(
        types.frozen<Record<string, PlainTrackConfig>>(),
        {},
      )
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
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

Volatiles

MemberDescriptionDefined by
editableTrackConfigs
editableTrackConfigs: 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
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

Getters

MemberDescriptionDefined by
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
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
(ModelInstanceTypeProps<…> & {…} & IStateTreeNode<…>)[]		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

Methods

MemberDescriptionDefined by
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
(trackId: string, frozenConfig: unknown, schemaType: IAnyType) => IAnyStateTreeNode | undefined
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
(id: string) => (ModelInstanceTypeProps<…> & {…} & IStateTreeNode<…>) | undefined
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
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

Actions

MemberDescriptionDefined by
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
(trackConf: ModelInstanceTypeProps<…> & {…} & IStateTreeNode<…>) => any[] | undefined
SessionTracksManagerSessionMixin
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
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