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TracksManagerSessionMixin

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
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
highlights
highlights: types.stripDefault(
        types.array(types.frozen<HighlightType>()),
        [],
      )
translucent bands over genomic regions; every view draws the ones on its own assembliesBaseSessionModel
highlightsVisible
highlightsVisible: types.stripDefault(types.boolean, true)		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
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
AnyConfigurationModel[]		TracksManagerSessionMixin
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

Methods

MemberDescriptionDefined by
getTrackById
(id: string) => AnyConfigurationModel | 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<string, AnyConfigurationModel>		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.

This mixin's session has no separate session-track store, so the destination is the jbrowse config — which in the products that compose it (desktop) is the single user's own file rather than something a server hands other visitors, so the two scopes are the same place. Defined here anyway so that every session has it: a feature standing a track up on the user's behalf can then call one action everywhere instead of asking which mixin it landed on. SessionTracksManagerSessionMixin overrides it with the real session-scoped store.		TracksManagerSessionMixin
publishTrackConf
(trackConf: AnyConfiguration) => any		Add a track config wherever this user's catalog edits belong — the "Add track" workflows, where an admin adding a track means to add it for the whole site. SessionTracksManagerSessionMixin overrides it to send a non-admin's to the session instead; here there is only the one destination.

Anything that is not an Add-track workflow wants addSessionTrackConf: a track a feature stands up on the user's behalf — a search result, a computed consensus, a reconstruction's labels — is not a catalog entry, and publishing one writes it into the config.json every visitor is served, once per click.		TracksManagerSessionMixin
addTrackConf
(trackConf: AnyConfiguration) => any		Deprecated alias of addSessionTrackConf. Call that, or publishTrackConf, which say which destination they mean.TracksManagerSessionMixin
updateTrackConfiguration
(trackConf: { [key: string]: unknown; trackId: string; }) => void
Persist edited track config back to the in-memory jbrowse config. The session-tracks mixin overrides this so a non-admin's edits become a shareable session-track override instead.TracksManagerSessionMixin
deleteTrackConf
(trackConf: AnyConfigurationModel) => any		TracksManagerSessionMixin
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		BaseSessionModel
addHighlight
(highlight: HighlightType) => void		an identical entry is not added twice, so a spec launched again does not stack its bands. Adding shows the bands again, since a highlight made while they are off would otherwise read as nothing happeningBaseSessionModel
removeHighlight
(highlight: HighlightType) => void		BaseSessionModel
updateHighlight
(old: HighlightType, updates: Partial<HighlightType>) => void		BaseSessionModel
setHighlights
(highlights: HighlightType[]) => void		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