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JBrowseReactLinearGenomeViewSessionModel

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, its single LinearGenomeView, and disableAddTracks, which is a root prop rather than a session one. The mixin and the view are spelled out here rather than passed to a shared factory because types.compose cannot infer through a generic — see EmbeddedSessionMixin.

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

Properties

MemberDescriptionDefined by
view
view: pluginManager.getViewType('LinearGenomeView')!
        .stateModel as LinearGenomeViewStateModel
JBrowseReactLinearGenomeViewSessionModel
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
drawerPosition
drawerPosition: types.optional(
        types.string,
        () => localStorageGetItem('drawerPosition') ?? 'right',
      )
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
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

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
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
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

Getters

MemberDescriptionDefined by
disableAddTracks
boolean		JBrowseReactLinearGenomeViewSessionModel
views
(ModelInstanceTypeProps<_OverrideProps<_OverrideProps<…>, { ...; }>> & ... 25 more ... & IStateTreeNode<...>)[]
JBrowseReactLinearGenomeViewSessionModel
stickyViewHeaders
boolean		Pin the header, and scroll the tracks under it, whenever the view is bounded -- which is the only time it means anything, since an unbounded view scrolls with the host's page and has nothing of its own to pin against. The LGV model reads this off the session (stickyViewHeaders === true) and so does the embedded view title above it, the same two readers the web app has.JBrowseReactLinearGenomeViewSessionModel
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
(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
visibleWidget
Widget | undefined		DrawerWidgetSessionMixin
connections
(ModelInstanceTypeProps<…> & { setSubschema(slotName: string, data: Record<string, unknown>): any; setSlot(slotName: string, value: unknown): void; } & IStateTreeNode<...>)[]
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
tracks
(ModelInstanceTypeProps<…> & { setSubschema(slotName: string, data: Record<string, unknown>): any; setSlot(slotName: string, value: unknown): void; } & 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

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
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: ModelInstanceTypeProps<…> & {…} & IStateTreeNode<…>, view?: TrackActionView | undefined) => MenuItem[]
flattened menu items for use in hierarchical track selectorTrackMenuSessionMixin
getTrackActionMenuItems
({…}: { config: ModelInstanceTypeProps<…> & {…} & IStateTreeNode<…>; 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
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<string, ModelInstanceTypeProps<…> & { setSubschema(slotName: string, data: Record<…>): any; setSlot(slotName: string, value: unknown): void; } & IStateTreeNode<...>>
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

MemberDescriptionDefined by
addView
(typeName: string, initialState?: any) => ModelInstanceTypeProps<_OverrideProps<_OverrideProps<…>, { ...; }>> & ... 25 more ... & IStateTreeNode<...>
JBrowseReactLinearGenomeViewSessionModel
removeView
() => void		JBrowseReactLinearGenomeViewSessionModel
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
setDrawerPosition
(arg: string) => void		DrawerWidgetSessionMixin
updateDrawerWidth
(drawerWidth: number) => number		DrawerWidgetSessionMixin
resizeDrawer
(distance: 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: (ModelInstanceTypeProps<…> & {…} & IStateTreeNode<…>) | { ...; }, opts?: { ...; } | undefined) => void
opens a configuration editor to configure the given thing, and sets the current task to be configuring itDrawerWidgetSessionMixin
makeConnection
(configuration: ModelInstanceTypeProps<…> & {…} & IStateTreeNode<…>, initialSnapshot?: object) => any
ConnectionManagementSessionMixin
breakConnection
(configuration: ModelInstanceTypeProps<…> & { setSubschema(slotName: string, data: Record<…>): any; setSlot(slotName: string, value: unknown): void; } & IStateTreeNode<…>) => 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: ModelInstanceTypeProps<…> & { setSubschema(slotName: string, data: Record<…>): any; setSlot(slotName: string, value: unknown): void; } & IStateTreeNode<…>) => 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: ModelInstanceTypeProps<…> & { setSubschema(slotName: string, data: Record<…>): any; setSlot(slotName: string, value: unknown): void; } & IStateTreeNode<...>) => 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 — used when its category is expanded in the track selector. Fetches silently (no view launch / 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		Point the session at light or dark. One write, not two: the theme slot is what themeOptions ships to the renderer, so the labels baked in the worker follow it, and palette is derived from the same slot, so what React draws follows it too. An embedder who sets only a React-side palette leaves the baked labels behind.

Merges rather than replaces, at both levels. theme is a frozen slot, so a bare setConf(session, 'theme', { palette: { mode } }) — the obvious form, and what the build-your-own examples each wrote — drops every other key in it. That silently discards 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 survive.		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.

Only the "Add track" workflows. Those are where an admin adding a track means to add it for the whole site. A track a feature stands up on the user's behalf — a search result, a computed consensus, a reconstruction's segment labels — is not a catalog entry, and one admin click on this publishes it to every visitor, again on the next click, with a per-launch trackId that defeats the dedupe. addSessionTrackConf above is the destination 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, a MAF sample's own genome, a comparative view's synthesized pair. The Add-track widget takes its assembly from the containing view, so an admin adding a track while looking at one of those arrives here with a name no visitor can resolve, and publishing it writes an entry the server hands everyone and nobody can draw. The session is the one destination where that track works, so the click keeps working and the dangling entry is never written; a snackbar says which assembly moved it.

The snackbar names the assembly and not the track, which is what lets a batch collapse to one message: pushSnackbarMessage dedupes on the exact text, and BulkAddTracksWorkflow publishes in a loop, so interpolating the track name stacked one identical-but-for-a-name toast per file over an admin adding thirty. The assembly is the whole of what an admin has to act on anyway.		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