@jbrowse/app-core 5.0.0-beta.13 → 5.0.0-beta.14

package/esm/Assemblies/AssembliesMixin.d.ts

@@ -29,6 +29,11 @@ export declare function AssembliesMixin(_pluginManager: PluginManager, assemblyC
         } & {
             defaultValue: unknown;
         };
+        readonly circularRefNames: {
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
+        };
         readonly geneticCodesLocation: {
             type: "maybeFileLocation";
         };
@@ -69,6 +74,11 @@ export declare function AssembliesMixin(_pluginManager: PluginManager, assemblyC
         } & {
             defaultValue: unknown;
         };
+        readonly circularRefNames: {
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
+        };
         readonly geneticCodesLocation: {
             type: "maybeFileLocation";
         };
@@ -128,6 +138,11 @@ export declare function AssembliesMixin(_pluginManager: PluginManager, assemblyC
         } & {
             defaultValue: unknown;
         };
+        readonly circularRefNames: {
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
+        };
         readonly geneticCodesLocation: {
             type: "maybeFileLocation";
         };
@@ -164,6 +179,11 @@ export declare function AssembliesMixin(_pluginManager: PluginManager, assemblyC
         } & {
             defaultValue: unknown;
         };
+        readonly circularRefNames: {
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
+        };
         readonly geneticCodesLocation: {
             type: "maybeFileLocation";
         };
@@ -217,6 +237,11 @@ export declare function AssembliesMixin(_pluginManager: PluginManager, assemblyC
         } & {
             defaultValue: unknown;
         };
+        readonly circularRefNames: {
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
+        };
         readonly geneticCodesLocation: {
             type: "maybeFileLocation";
         };
@@ -253,6 +278,11 @@ export declare function AssembliesMixin(_pluginManager: PluginManager, assemblyC
         } & {
             defaultValue: unknown;
         };
+        readonly circularRefNames: {
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
+        };
         readonly geneticCodesLocation: {
             type: "maybeFileLocation";
         };

package/esm/HistoryManagement/index.d.ts

@@ -3,6 +3,8 @@ export declare function historyShortcut(e: ShortcutKeys): "redo" | "undo" | unde
 /**
  * #stateModel HistoryManagementMixin
  * #category root
+ * Adds undo and redo of session changes to the root model, bound to Ctrl+Z
+ * and Ctrl+Y (Cmd on macOS).
  */
 export declare function HistoryManagementMixin(): import("@jbrowse/mobx-state-tree").IModelType<{
     /**

package/esm/HistoryManagement/index.js

@@ -28,6 +28,8 @@ export function historyShortcut(e) {
 /**
  * #stateModel HistoryManagementMixin
  * #category root
+ * Adds undo and redo of session changes to the root model, bound to Ctrl+Z
+ * and Ctrl+Y (Cmd on macOS).
  */
 export function HistoryManagementMixin() {
     return types

package/esm/JBrowseConfig/RootConfiguration.d.ts

@@ -3,8 +3,9 @@ import type { ConfigurationSchemaDefinition } from '@jbrowse/core/configuration'
 /**
  * #config JBrowseConfiguration
  * #category root
- * this is the entry under the `configuration` key
- * e.g.
+ * Holds the app-wide settings in the `configuration` key of a config file,
+ * beside `assemblies` and `tracks`.
+ *
  * ```json
  * {
  *   assemblies,

package/esm/JBrowseConfig/RootConfiguration.js

@@ -5,8 +5,9 @@ import { DEFAULT_SHARE_URL } from './defaultShareUrl.js';
 /**
  * #config JBrowseConfiguration
  * #category root
- * this is the entry under the `configuration` key
- * e.g.
+ * Holds the app-wide settings in the `configuration` key of a config file,
+ * beside `assemblies` and `tracks`.
+ *
  * ```json
  * {
  *   assemblies,

package/esm/JBrowseConfig/index.d.ts

@@ -6,9 +6,8 @@ export { DEFAULT_SHARE_URL } from './defaultShareUrl.ts';
  * #config JBrowseRootConfig
  * #category root
  *
- * this is a config model representing a config.json (for jbrowse-web) or
- * somefile.jbrowse (for jbrowse-desktop, where configs have the .jbrowse
- * extension)
+ * Holds a whole JBrowse config file: the `config.json` of jbrowse-web, or a
+ * file with the `.jbrowse` extension in jbrowse-desktop.
  *
  * also includes any pluginManager.pluginConfigurationSchemas(), so plugins
  * that have a configurationSchema field on their class are mixed into this

package/esm/JBrowseConfig/index.js

@@ -5,9 +5,8 @@ export { DEFAULT_SHARE_URL } from './defaultShareUrl.js';
  * #config JBrowseRootConfig
  * #category root
  *
- * this is a config model representing a config.json (for jbrowse-web) or
- * somefile.jbrowse (for jbrowse-desktop, where configs have the .jbrowse
- * extension)
+ * Holds a whole JBrowse config file: the `config.json` of jbrowse-web, or a
+ * file with the `.jbrowse` extension in jbrowse-desktop.
  *
  * also includes any pluginManager.pluginConfigurationSchemas(), so plugins
  * that have a configurationSchema field on their class are mixed into this

package/esm/JBrowseModel/index.d.ts

@@ -3,6 +3,14 @@ import type { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager';
 import type { AnyConfiguration, AnyConfigurationModel, ConfigurationSchemaDefinition } from '@jbrowse/core/configuration';
 import type { PluginDefinition } from '@jbrowse/core/pluginDefinitions';
 import type RpcManager from '@jbrowse/core/rpc/RpcManager';
+/**
+ * #stateModel AppCoreJBrowseModel
+ * #category root
+ * Holds the loaded config file, usually at `rootModel.jbrowse`, with actions
+ * that add and remove its assemblies and tracks. The model builds on the
+ * [JBrowseRootConfig](/docs/config/jbrowserootconfig) config model, which a
+ * state model can do because a config model is itself an MST tree.
+ */
 export declare function JBrowseModelF({ pluginManager, assemblyConfigSchema, extraConfigSlots, }: {
     pluginManager: PluginManager;
     assemblyConfigSchema: BaseAssemblyConfigSchema;
@@ -165,7 +173,7 @@ export declare function JBrowseModelF({ pluginManager, assemblyConfigSchema, ext
     /**
      * #action
      */
-    addAssemblyConf(conf: AnyConfigurationModel): (import("@jbrowse/core/configuration").ConfigNodeProps<any> & import("@jbrowse/core/configuration").ConfigNodeActions & import("@jbrowse/core/configuration").ConfigNodeBrand<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | undefined;
+    addAssemblyConf(conf: AnyConfiguration): (import("@jbrowse/core/configuration").ConfigNodeProps<any> & import("@jbrowse/core/configuration").ConfigNodeActions & import("@jbrowse/core/configuration").ConfigNodeBrand<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | undefined;
     /**
      * #action
      */

package/esm/JBrowseModel/index.js

@@ -6,13 +6,6 @@ import { expandLooseTrackConfig } from '@jbrowse/core/util/tracks';
 import { cast, getParent, getSnapshot, isStateTreeNode, types, } from '@jbrowse/mobx-state-tree';
 import { toJS } from 'mobx';
 import { JBrowseConfigF } from '../JBrowseConfig/index.js';
-/**
- * #stateModel AppCoreJBrowseModel
- * #category root
- * built on the [JBrowseRootConfig](/docs/config/jbrowserootconfig) config model —
- * config models are MST trees themselves, which is why this state model is
- * allowed to build on one. Generally found on a property named rootModel.jbrowse
- */
 // A config with exactly one assembly is what every loose track and search index
 // is on, so `assemblyNames` may be left off; with several, each has to say.
 function expandLooseTracks(snapshot, pluginManager) {
@@ -42,6 +35,14 @@ function expandLooseTracks(snapshot, pluginManager) {
                 : {}),
         };
 }
+/**
+ * #stateModel AppCoreJBrowseModel
+ * #category root
+ * Holds the loaded config file, usually at `rootModel.jbrowse`, with actions
+ * that add and remove its assemblies and tracks. The model builds on the
+ * [JBrowseRootConfig](/docs/config/jbrowserootconfig) config model, which a
+ * state model can do because a config model is itself an MST tree.
+ */
 export function JBrowseModelF({ pluginManager, assemblyConfigSchema, extraConfigSlots, }) {
     const model = JBrowseConfigF({
         pluginManager,

package/esm/JbApi/jbApi.js

@@ -72,6 +72,9 @@ function displayState(track) {
         return { display: display.type, error: String(e) };
     }
 }
+function raisesPicker(views) {
+    return !!views?.some(view => view.searchPicker || raisesPicker(view.ownViews));
+}
 /**
  * The drawer and any modal, for the same reason `offscreen` is reported: both
  * are on top of the views in a screenshot that otherwise looks right.
@@ -94,7 +97,7 @@ function sessionChrome(session) {
             },
         }
         : {};
-    const dialog = s.DialogComponent
+    const dialog = s.DialogComponent || raisesPicker(s.views)
         ? {
             dialog: {
                 note: 'a modal dialog is open over the app, so a screenshot is of the dialog',
@@ -1024,7 +1027,7 @@ const JB_HELP = `jb drives this JBrowse app programmatically (window.jb in a bro
 
 Orient first: jb.sessionSummary(). Introspect, never guess: jb.listTracks(search?, limit?) answers { total, tracks } with the trackIds; jb.describeSlots(jb.trackModel('someTrackId').activeDisplay.configuration) for the settings keys a display accepts — an unknown settings key is not an error, it lands in applyDisplaySettings' "unapplied" list as { key, reason }, so read the report; jb.inspect(node) — jb.view(), jb.trackModel('someTrackId'), session.views[0] — for its getters, actions and modelType.
 
-The model is mobx-state-tree: mutate only through actions (raw assignment throws), and write display settings with track.applyDisplaySettings(settings). A display's grammar settings are its plot, activeDisplay.plot, by slot name: facet ('strand' or { field, domain? }), color (a CSS color or { field: 'type', domain?, range? }), rows, unit (what a row stands for: 'read' | 'chain' on alignments, 'sample' | 'haplotype' on multi-sample variants), scales, filter (['jexl:feature.score > 10']), and on a mark display marks and transform. Edit structuredClone(activeDisplay.plot), check it with activeDisplay.plotProblems(draft), which throws what a config refuses, and write it with activeDisplay.applyPlot(draft): each setting replaced whole, null resetting one. An alignments track takes the same facet, its field a read dimension ('pairOrientation', 'mapq', ...) or a tag ('tags.HP'). LinearMarkDisplay plots a track's features as ggplot2 does, on a feature, alignments, variant or quantitative track, in seven settings: marks, a list drawn in order of { mark: 'bar' | 'point' | 'rule' | 'line' | 'span' | 'text' | 'link', encoding: { y: 'score', x?, x2?, row?, color?, shape?, text?, size? }, each a feature field or a jexl: expression, a constant written { value: 'red' }, transform?: steps such as { type: 'coverage' } or a bin then an aggregate, which fill the y they write, minBpPerPx?, maxBpPerPx? }, beside transform, facet, rows, rowColor, scales ({ y: { type, domainMin, domainMax, autoscaleGroup, title } }) and filter. await view.launchTrack(trackId, {}, { type: 'LinearMarkDisplay', marks: [...] }) draws a track with it, shown already or not (on a GWASTrack, type 'LinearManhattanDisplay'). activeDisplay.notices names a mark the config cannot draw, or one whose field no loaded feature holds. Build views declaratively with jb.loadSessionSpec({ views: [{ type: 'LinearGenomeView', assembly, loc, tracks: [...] }] }), which replaces the session; jb.addView(oneViewSpec) opens one more view beside what is open; jb.setSession(document) rewrites the session as a document — what jb.mst.getSnapshot(jb.session) answers, edited: a view keeps its id and is patched in place, loc on it navigates, a { trackId } entry in its tracks opens that track. Act on a view with await view.navToLocString('BRCA1' or 'chr1:1-1000'), which also SHOWS the track whose search index answered a gene name unless a 4th arg { showHitTrack: false } says not to; await view.launchTrack(trackId, {}, settings) shows a track with settings, view.hideTrack(trackId) hides it. Arrange open views into panels with session.layoutViews({ direction: 'horizontal', children: [{ views: [viewId] }, ...] }), a leaf naming view ids or session.views indexes; await jb.fitToWindow() shrinks what is open until the session fits the window; add data with jb.addTrack({ location }) (an absolute path or a URL), or show a track the catalog already holds with jb.addTrack({ trackId, settings? }); read data with await jb.getFeatures({ trackId, loc?, assembly?, viewId?, regions?, byteLimit? }), which renames refNames ("chr1" vs "1") so the file answers and reads on the worker the track's display uses. Anything lower level is jb.require('@jbrowse/core/util') and friends, the module registry plugins link against. After changing anything, await jb.waitReady(ms) and read its notifications and notReady lists before trusting the screen.
+The model is mobx-state-tree: mutate only through actions (raw assignment throws), and write display settings with track.applyDisplaySettings(settings). A display's grammar settings are its plot, activeDisplay.plot, by slot name: facet ('strand' or { field, domain? }), color (a CSS color or { field: 'type', domain?, range? }), rows, unit (what a row stands for: 'read' | 'chain' on alignments, 'sample' | 'haplotype' on multi-sample variants), sort (an alignments row order: 'split', or { type: 'strand', pos, refName }), scales, filter (['jexl:feature.score > 10']), and on a mark display marks and transform. Edit structuredClone(activeDisplay.plot), check it with activeDisplay.plotProblems(draft), which throws what a config refuses, and write it with activeDisplay.applyPlot(draft): each setting replaced whole, null resetting one. An alignments track takes the same facet, its field a read dimension ('pairOrientation', 'mapq', ...) or a tag ('tags.HP'). LinearMarkDisplay plots a track's features as ggplot2 does, on a feature, alignments, variant or quantitative track, in seven settings: marks, a list drawn in order of { mark: 'bar' | 'point' | 'rule' | 'line' | 'span' | 'text' | 'link', encoding: { y: 'score', x?, x2?, row?, color?, shape?, text?, size? }, each a feature field or a jexl: expression, a constant written { value: 'red' }, transform?: steps such as { type: 'coverage' } or a bin then an aggregate, which fill the y they write, minBpPerPx?, maxBpPerPx? }, beside transform, facet, rows, rowColor, scales ({ y: { type, domainMin, domainMax, autoscaleGroup, title } }) and filter. await view.launchTrack(trackId, {}, { type: 'LinearMarkDisplay', marks: [...] }) draws a track with it, shown already or not (on a GWASTrack, type 'LinearManhattanDisplay'). activeDisplay.notices names a mark the config cannot draw, or one whose field no loaded feature holds. Build views declaratively with jb.loadSessionSpec({ views: [{ type: 'LinearGenomeView', assembly, loc, tracks: [...] }] }), which replaces the session; jb.addView(oneViewSpec) opens one more view beside what is open; jb.setSession(document) rewrites the session as a document — what jb.mst.getSnapshot(jb.session) answers, edited: a view keeps its id and is patched in place, loc on it navigates, a { trackId } entry in its tracks opens that track. Act on a view with await view.navToLocString('BRCA1' or 'chr1:1-1000'), which also SHOWS the track whose search index answered a gene name unless a 4th arg { showHitTrack: false } says not to; await view.launchTrack(trackId, {}, settings) shows a track with settings, view.hideTrack(trackId) hides it. Arrange open views into panels with session.layoutViews({ direction: 'horizontal', children: [{ views: [viewId] }, ...] }), a leaf naming view ids or session.views indexes; await jb.fitToWindow() shrinks what is open until the session fits the window; add data with jb.addTrack({ location }) (an absolute path or a URL), or show a track the catalog already holds with jb.addTrack({ trackId, settings? }); read data with await jb.getFeatures({ trackId, loc?, assembly?, viewId?, regions?, byteLimit? }), which renames refNames ("chr1" vs "1") so the file answers and reads on the worker the track's display uses. Anything lower level is jb.require('@jbrowse/core/util') and friends, the module registry plugins link against. After changing anything, await jb.waitReady(ms) and read its notifications and notReady lists before trusting the screen.
 
 Views nest and several can be open. jb.view(viewId?) is the open view, and jb.view(), jb.trackModel(trackId), jb.visibleRegions(), jb.addTrack and jb.getFeatures over a visible region throw naming the candidates rather than picking one when more than one view could answer — pass viewId (from jb.sessionSummary()) to say which. A synteny or breakpoint view's viewId also covers its rows: the named view answers when it can, and otherwise its rows do.
 

package/esm/RootMenu/index.d.ts

@@ -2,6 +2,8 @@ import type { MenuAction } from '../menus.ts';
 import type { MenuItem } from '@jbrowse/core/ui/menuItems';
 /**
  * #stateModel RootAppMenuMixin
+ * Adds actions to the root model that let plugins add menus and menu items to
+ * the app bar.
  */
 export declare function RootAppMenuMixin(): import("@jbrowse/mobx-state-tree").IModelType<{}, {
     mutableMenuActions: MenuAction[];

package/esm/RootMenu/index.js

@@ -1,6 +1,8 @@
 import { types } from '@jbrowse/mobx-state-tree';
 /**
  * #stateModel RootAppMenuMixin
+ * Adds actions to the root model that let plugins add menus and menu items to
+ * the app bar.
  */
 export function RootAppMenuMixin() {
     return types

package/esm/SessionSpec/index.d.ts

@@ -1,6 +1,6 @@
 export { buildLgvInit, buildLgvInitFromParams, hubConnectionSpec, readHubUrlParam, readNavParam, readTracklistParam, shortHubLabel, splitHighlights, } from './lgvUrlInit.ts';
 export { addSessionTracks, launchSpecView, launchableSpecView, loadSessionSpec, viewTypeProblem, } from './loadSessionSpec.ts';
-export { parseSessionSpecUrl } from './parseSessionSpecUrl.ts';
+export { parseSessionSnapshotUrl, parseSessionSpecUrl, } from './parseSessionSpecUrl.ts';
 export type { LgvUrlInit } from './lgvUrlInit.ts';
-export type { ParsedSessionSpec } from './parseSessionSpecUrl.ts';
+export type { ParsedSessionSnapshotUrl, ParsedSessionSpec, } from './parseSessionSpecUrl.ts';
 export type { LayoutNode, ViewSpec } from './types.ts';

package/esm/SessionSpec/index.js

@@ -1,3 +1,3 @@
 export { buildLgvInit, buildLgvInitFromParams, hubConnectionSpec, readHubUrlParam, readNavParam, readTracklistParam, shortHubLabel, splitHighlights, } from './lgvUrlInit.js';
 export { addSessionTracks, launchSpecView, launchableSpecView, loadSessionSpec, viewTypeProblem, } from './loadSessionSpec.js';
-export { parseSessionSpecUrl } from './parseSessionSpecUrl.js';
+export { parseSessionSnapshotUrl, parseSessionSpecUrl, } from './parseSessionSpecUrl.js';

package/esm/SessionSpec/parseSessionSpecUrl.d.ts

@@ -4,4 +4,23 @@ export interface ParsedSessionSpec {
     spec: Omit<SessionSpec, 'sessionName'>;
     sessionName?: string;
 }
+export interface ParsedSessionSnapshotUrl {
+    configUrl: string;
+    /** the `session=` value as it is in the link, prefix included, undecoded */
+    session: string;
+    /** a `share-` link's key; the share service never sees it */
+    password?: string;
+    /** the JBrowse Web page the link points at, which a relative shareURL is relative to */
+    pageUrl: string;
+}
+/**
+ * The session snapshot a link hands over whole — carried in it (`encoded-…`,
+ * `json-…`) or stored by the share service under the id it names (`share-…`) —
+ * with the config it applies to. Undefined for any other link.
+ *
+ * A link with no `config=` means the instance's own `config.json`, as it does
+ * to the JBrowse Web page the link points at. A snapshot names assemblies and
+ * tracks by id and holds none of them, so there is always a config to fetch.
+ */
+export declare function parseSessionSnapshotUrl(input: string): ParsedSessionSnapshotUrl | undefined;
 export declare function parseSessionSpecUrl(input: string): ParsedSessionSpec;

package/esm/SessionSpec/parseSessionSpecUrl.js

@@ -134,6 +134,35 @@ function readSessionTracks(params) {
     }
     return parsed;
 }
+/**
+ * The session snapshot a link hands over whole — carried in it (`encoded-…`,
+ * `json-…`) or stored by the share service under the id it names (`share-…`) —
+ * with the config it applies to. Undefined for any other link.
+ *
+ * A link with no `config=` means the instance's own `config.json`, as it does
+ * to the JBrowse Web page the link points at. A snapshot names assemblies and
+ * tracks by id and holds none of them, so there is always a config to fetch.
+ */
+export function parseSessionSnapshotUrl(input) {
+    let url;
+    try {
+        url = unwrapProtocolUrl(new URL(input.trim()));
+    }
+    catch {
+        return undefined;
+    }
+    const params = readAllQueryParams(url);
+    const session = params.get('session');
+    return session && /^(share|encoded|json)-/.test(session)
+        ? {
+            configUrl: new URL(params.get('config') ?? 'config.json', url.href)
+                .href,
+            session,
+            password: params.get('password') ?? undefined,
+            pageUrl: url.href,
+        }
+        : undefined;
+}
 export function parseSessionSpecUrl(input) {
     let url;
     try {

package/esm/WorkspaceLayout/WorkspaceContainer.js

@@ -1,7 +1,6 @@
 import { jsx as _jsx } from "react/jsx-runtime";
-import { Suspense, useCallback, useEffect, useMemo } from 'react';
+import { Suspense, useCallback, useMemo } from 'react';
 import { makeStyles } from '@jbrowse/core/util/tss-react';
-import { autorun } from 'mobx';
 import { observer } from 'mobx-react';
 import ViewStack from '../ui/App/ViewStack.js';
 import { ViewLauncher } from '../ui/App/lazyParts.js';
@@ -27,13 +26,6 @@ const useStyles = makeStyles()(theme => ({
 export const WorkspaceContainer = observer(function WorkspaceContainer({ session, }) {
     const { classes } = useStyles();
     const { drag, handlers } = useLayoutDrag(session);
-    // #region autorunInEffect
-    useEffect(() => autorun(() => {
-        // homes newly launched views; reads session.views here because an
-        // action's reads are untracked
-        session.homeUnassignedViews(session.views.map(v => v.id));
-    }), [session]);
-    // #endregion
     // the layout does not own views, so every close gesture goes through here
     // or leaks them
     const closeViews = useCallback((viewIds) => {
@@ -65,7 +57,7 @@ export const WorkspaceContainer = observer(function WorkspaceContainer({ session
         renderPanelActions: panel => (_jsx(WorkspacePanelActions, { panel: panel, session: session, onClose: () => {
                 closePanel(panel.id);
             } })),
-        renderTabLabel: tab => (_jsx(WorkspaceTab, { tab: tab, views: viewsOf(session, tab.viewIds), session: session, layout: session, onClose: () => {
+        renderTabLabel: tab => (_jsx(WorkspaceTab, { tab: tab, views: viewsOf(session, tab.viewIds), session: session, onClose: () => {
                 closeTab(tab.id);
             } })),
         renderTabContent: tab => {

package/esm/WorkspaceLayout/WorkspacePanelActions.js

@@ -33,7 +33,7 @@ export const WorkspacePanelActions = observer(function WorkspacePanelActions({ p
     const canClose = session.panels.length > 1;
     const maximized = session.maximizedPanelId === panel.id;
     const tile = (mode) => {
-        session.tileViews(mode, session.views.map(v => v.id));
+        session.tileViews(mode);
     };
     return (_jsxs("div", { className: classes.actions, children: [_jsx(CascadingMenuButton, { menuItems: [
                     {

package/esm/WorkspaceLayout/WorkspaceTab.d.ts

@@ -2,11 +2,10 @@ import type { WorkspaceSessionType } from '../ui/App/types.ts';
 import type { WorkspaceLayout } from './model.ts';
 import type { TabNode } from './tree.ts';
 import type { AbstractViewModel } from '@jbrowse/core/util';
-export declare const WorkspaceTab: ({ tab, views, session, layout, onClose, }: {
+export declare const WorkspaceTab: ({ tab, views, session, onClose, }: {
     tab: TabNode;
     views: AbstractViewModel[];
-    session: WorkspaceSessionType;
-    layout: WorkspaceLayout;
+    session: WorkspaceSessionType & WorkspaceLayout;
     /** closes the tab and the views it holds */
     onClose: () => void;
 }) => import("react").JSX.Element;

package/esm/WorkspaceLayout/WorkspaceTab.js

@@ -31,7 +31,7 @@ const useStyles = makeStyles()(theme => ({
         flex: 1,
     },
 }));
-export const WorkspaceTab = observer(function WorkspaceTab({ tab, views, session, layout, onClose, }) {
+export const WorkspaceTab = observer(function WorkspaceTab({ tab, views, session, onClose, }) {
     const { classes } = useStyles();
     const [editing, setEditing] = useState(false);
     const [draft, setDraft] = useState('');
@@ -44,7 +44,7 @@ export const WorkspaceTab = observer(function WorkspaceTab({ tab, views, session
     const save = () => {
         const name = draft.trim();
         const automatic = tabDisplayName({ ...tab, title: undefined }, views, session);
-        layout.renameTab(tab.id, name && name !== automatic ? name : undefined);
+        session.renameTab(tab.id, name && name !== automatic ? name : undefined);
         setEditing(false);
     };
     return (_jsx("div", { className: classes.tab, children: editing ? (_jsx(InputBase, { autoFocus: true, className: classes.editInput, value: draft, onChange: e => {

package/esm/WorkspaceLayout/model.d.ts

@@ -97,10 +97,6 @@ export declare function WorkspaceLayoutMixin(): import("@jbrowse/mobx-state-tree
     findTab(tabId: string): TabHome | undefined;
     tabContainingView(viewId: string): TabHome | undefined;
     panelContainingView(viewId: string): PanelNode | undefined;
-    /** The views a tab renders: its members, in `session.views` order. */
-    viewIdsForTab(tabId: string, order: string[]): string[];
-    /** The tab a panel is showing, or its first. */
-    activeTabOf(panelId: string): TabNode | undefined;
     /**
      * The maximized cell alone, or the whole tree. The cell is resized to 1
      * because CSS hands out free space by grow factor only up to a total of
@@ -144,35 +140,32 @@ export declare function WorkspaceLayoutMixin(): import("@jbrowse/mobx-state-tree
     applyLayoutSpec(spec: LayoutSpecNode): string[];
     /**
      * ViewMenu's "move to new tab": the view leaves its tab for a new one.
-     * `allViewIds` is EVERY view in the session, defaulting to the host's
-     * own list, since homing drops any view the list omits.
      */
-    moveViewToNewTab(viewId: string, allViewIds?: string[]): string | undefined;
+    moveViewToNewTab(viewId: string): string | undefined;
     /**
      * ViewMenu's "move to split": the view leaves for a new cell to the
      * right (`row`) or below (`column`) of its own.
      */
-    moveViewToSplit(viewId: string, direction: 'row' | 'column', allViewIds?: string[]): string | undefined;
+    moveViewToSplit(viewId: string, direction: 'row' | 'column'): string | undefined;
     /**
      * ViewMenu's "move to tab": the view joins an existing tab, which
      * becomes the one shown.
      */
-    moveViewToTab(viewId: string, tabId: string, allViewIds?: string[]): void;
+    moveViewToTab(viewId: string, tabId: string): void;
     homeUnassignedViews(viewIds: string[]): void;
 } & {
     /**
      * Move one view to a new tab or a split beside its cell, keeping the
      * rest of the arrangement. PUBLIC API: protein3d and msaview call it
-     * with the move alone, so `allViewIds` stays optional; it is read only
-     * on a host with no view list.
+     * with the move alone. The second argument is an old plugin signature;
+     * the session's own views are read instead.
      */
-    setPendingMove(move: PendingMove | undefined, allViewIds?: string[]): void;
+    setPendingMove(move: PendingMove | undefined, _allViewIds?: string[]): void;
     /**
      * Re-arrange the whole workspace, one view per cell, in one of four
-     * shapes. Pass `allViewIds` in `session.views` order so there is
-     * nothing for `orderViews` to apply.
+     * shapes, in `session.views` order.
      */
-    tileViews(mode: TileMode, allViewIds: string[]): void;
+    tileViews(mode: TileMode): void;
     /**
      * #action
      * Arrange the session's views into panels: `applyLayoutSpec`, then
@@ -183,6 +176,8 @@ export declare function WorkspaceLayoutMixin(): import("@jbrowse/mobx-state-tree
      * re-layout both call it.
      */
     layoutViews(spec: LayoutSpecNode): string[];
+} & {
+    afterAttach(): void;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export type WorkspaceLayoutMixinType = ReturnType<typeof WorkspaceLayoutMixin>;
 export interface WorkspaceLayout extends Instance<WorkspaceLayoutMixinType> {