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PreferencesSessionMixin

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

loads and persists user-preference overrides (the BaseSession preferencesOverrides volatile) to localStorage. Compose into products that let users edit preferences (web, desktop); embedded sessions omit it and resolve preferences from configuration.preferences admin defaults only.

PreferencesSessionMixin declares no members of its own — it composes the models below, and everything here is theirs.

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

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 (getDisplayTypeDefault in a track's rpcProps). A single spread-replaced object made every setter wake every reader, so toggling scroll-to-zoom re-fetched every track. For the same reason each promoted per-display-type default is a flat composite key (see displayTypeDefaultKey), not a single nested displayTypeDefaults object — promoting one default can't wake readers of a different one.

deep: false is load-bearing, not a micro-optimization. The default enhancer wraps an object/array value in a MobX Proxy on set, and a promoted default is handed straight back out by getConf — so an object-valued promotable slot (alignments colorBy) put a Proxy into rpcProps(), and V8's structured-clone serializer rejects a Proxy: worker.postMessage threw DataCloneError on the next fetch of any track following that default (electron IPC and structuredClone in the share bake likewise). 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
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<…> & { setSubschema(slotName: string, data: Record<string, unknown>): any; setSlot(slotName: string, value: unknown): void; } & 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
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
getDisplayTypeDefault
(displayType: string, slot: string) => unknown		resolved value of a per-display-type slot default the user promoted (see setDisplayTypeDefault); undefined when nothing was promoted.BaseSessionModel
getDisplayTypeDefaults
() => { displayType: string; slot: string; value: unknown; }[]		every per-display-type default the user has promoted, as { displayType, slot, value } — the inventory the Preferences dialog lists and clears one at a time (setDisplayTypeDefault(…, undefined)).

Here rather than filtered out of getPreferenceChanges by the dialog, because the composite-key layout is this file's: a consumer that recognized these rows by matching the path head is exactly the coupling DISPLAY_TYPE_DEFAULTS_PATH_HEAD stopped being exported over, where a rename on one side alone silently no-ops the other.		BaseSessionModel
getPreferenceChanges
() => TrackConfigChange[]		every runtime preference-override that currently differs from its config/admin default, as { path, from, to } rows — the exact set clearPreferenceOverrides reverts. Backs the confirmation diff shown before "Reset to defaults" (mirrors the per-track changes dialog). A scalar pref (animationMode, scrollZoom) whose override equals the default is omitted (reverting it is a no-op); each promoted per-display-type default is always a difference from the un-promoted state, so from reads "(default)".BaseSessionModel

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 never silently swallowed by 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 — scrollZoom, animationMode, and every promoted per-display-type default (see setDisplayTypeDefault) — 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
resetPreferenceChange
(path: string[]) => void		revert one row emitted by getPreferenceChanges, addressed by its display path. Backs the per-entry reset in the Preferences dialog's "Reset to defaults" confirmation.

Lives here rather than in that dialog because this model owns both path shapes it has to undo: a promoted per-display-type default, whose row path is a readable label over a flat composite storage key, and every other override, whose path is its key. The dialog used to re-derive the first case from an exported path-head constant.		BaseSessionModel
setScrollZoom
(flag: boolean) => void		set the global scroll-to-zoom preference (see the scrollZoom getter)BaseSessionModel
setDisplayTypeDefault
(displayType: string, slot: string, value: unknown) => void		promote (or, with value undefined, clear) a per-display-type slot default. Just a preference override under one flat composite key (see displayTypeDefaultKey), so it persists and independently tracks like any other pref, and clearing deletes only that key.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