@jbrowse/app-core 5.0.0-beta.11 → 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,
@@ -123,11 +124,6 @@ export default function RootConfiguration({ pluginManager, extraConfigSlots, }:
         } & {
             defaultValue: boolean;
         };
-        readonly useWorkspaces: {
-            type: "boolean";
-        } & {
-            defaultValue: boolean;
-        };
         readonly developerMode: {
             type: "boolean";
         } & {
@@ -145,8 +141,6 @@ export default function RootConfiguration({ pluginManager, extraConfigSlots, }:
         defaultValue: unknown;
     };
     readonly logoPath: {
-        type: "fileLocation";
-    } & {
-        defaultValue: unknown;
+        type: "maybeFileLocation";
     };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;

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,
@@ -90,12 +91,8 @@ export default function RootConfiguration({ pluginManager, extraConfigSlots = {}
          * #slot configuration.logoPath
          */
         logoPath: {
-            type: 'fileLocation',
-            description: 'path to a custom logo image displayed in the app header',
-            defaultValue: {
-                uri: '',
-                locationType: 'UriLocation',
-            },
+            type: 'maybeFileLocation',
+            description: 'a custom logo image displayed in the app header; unset, the JBrowse logo',
             advanced: true,
         },
         /**

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
@@ -126,11 +125,6 @@ export declare function JBrowseConfigF({ pluginManager, assemblyConfigSchema, ex
             } & {
                 defaultValue: boolean;
             };
-            readonly useWorkspaces: {
-                type: "boolean";
-            } & {
-                defaultValue: boolean;
-            };
             readonly developerMode: {
                 type: "boolean";
             } & {
@@ -148,9 +142,7 @@ export declare function JBrowseConfigF({ pluginManager, assemblyConfigSchema, ex
             defaultValue: unknown;
         };
         readonly logoPath: {
-            type: "fileLocation";
-        } & {
-            defaultValue: unknown;
+            type: "maybeFileLocation";
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
     /**

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;
@@ -115,11 +123,6 @@ export declare function JBrowseModelF({ pluginManager, assemblyConfigSchema, ext
             } & {
                 defaultValue: boolean;
             };
-            readonly useWorkspaces: {
-                type: "boolean";
-            } & {
-                defaultValue: boolean;
-            };
             readonly developerMode: {
                 type: "boolean";
             } & {
@@ -137,9 +140,7 @@ export declare function JBrowseModelF({ pluginManager, assemblyConfigSchema, ext
             defaultValue: unknown;
         };
         readonly logoPath: {
-            type: "fileLocation";
-        } & {
-            defaultValue: unknown;
+            type: "maybeFileLocation";
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
     plugins: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<PluginDefinition, PluginDefinition, PluginDefinition>>;
@@ -172,7 +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.d.ts

@@ -1018,9 +1018,9 @@ export declare function createJbApi(pluginManager: PluginManager, options?: JbAp
         total: number;
         note?: string | undefined;
         tracks: {
-            trackId: string;
+            trackId: any;
             name: string;
-            type: string;
+            type: any;
             assemblyNames: string[];
         }[];
     };

package/esm/JbApi/jbApi.js

@@ -1,5 +1,5 @@
 import { getReExportRegistry, setReExportRegistry, } from '@jbrowse/core/ReExports/registry';
-import { getConf, getConfigurationSchemaDefinition, getConfigurationSchemaMetadata, isSlotDefinitionEntry, readConfObject, shorthandTargets, } from '@jbrowse/core/configuration';
+import { getConf, getConfigurationSchemaDefinition, getConfigurationSchemaMetadata, hydrateTrackConfig, isSlotDefinitionEntry, readConfObject, shorthandTargets, } from '@jbrowse/core/configuration';
 import { releaseAdapterSession, retainAdapterSession, } from '@jbrowse/core/data_adapters/adapterSessionRefcount';
 import { adapterByteLimit } from '@jbrowse/core/rpc/byteBudget';
 import { isElectron, isSessionWithAddSessionTrack, objectHash, parseLocString, sum, } from '@jbrowse/core/util';
@@ -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',
@@ -594,7 +597,7 @@ async function fitToWindow(session, settleMs, root = document) {
 function trackEntry(conf) {
     return {
         trackId: conf.trackId,
-        name: readConfObject(conf, 'name'),
+        name: conf.name ?? '',
         type: conf.type,
         // getConfAssemblyNamesOrNone, not the slot: an assembly's sequence track
         // has no assemblyNames slot and answers through its parent assembly
@@ -826,8 +829,13 @@ async function visibleRegionsOf(session, viewId, preferTrackId, trackAssemblies
 // file's own refNames during serialization (RpcMethodTypeWithRenameRegions),
 // and the features come back rebuilt as SimpleFeature. What crosses the worker
 // boundary is bounded by the byte gate that runs first.
-async function fetchFeatures(session, trackId, regions, requestedByteLimit) {
-    const conf = session.getTrackById(trackId);
+async function fetchFeatures(pluginManager, session, trackId, regions, requestedByteLimit) {
+    const entry = session.getTrackById(trackId);
+    // the node a shown track reads: its adapter is in the hydrated form, which is
+    // what the shown track's session id hashes
+    const conf = isStateTreeNode(entry)
+        ? entry
+        : entry && hydrateTrackConfig(pluginManager, entry);
     if (!conf) {
         throw new Error(`No track with trackId "${trackId}" — jb.listTracks() shows what is available`);
     }
@@ -1019,7 +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, 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.
 
@@ -1107,7 +1115,7 @@ export function createJbApi(pluginManager, options = {}) {
                         await locToRegion(session, conf, fetchArgs.loc, fetchArgs.assembly),
                     ]
                     : await visibleRegionsOf(session, fetchArgs.viewId, fetchArgs.trackId, getConfAssemblyNamesOrNone(conf));
-            return fetchFeatures(session, fetchArgs.trackId, regions, fetchArgs.byteLimit);
+            return fetchFeatures(pluginManager, session, fetchArgs.trackId, regions, fetchArgs.byteLimit);
         },
     };
     return jb;
@@ -1192,9 +1200,6 @@ async function addTrack(pluginManager, session, args) {
 }
 // A track already in the catalog, shown: the same view choice and the same
 // settle the file route ends in.
-// `conf` is whatever `session.getTrackById` answered, which is a track config
-// but not necessarily a `BaseTrackConfig` — an assembly's ReferenceSequenceTrack
-// declares a subset of those slots. The four reads below are all ones it has.
 async function showCatalogTrack(pluginManager, session, conf, args) {
     // index, assembly and name describe the file being added, and the catalog's
     // copy already has all three — taking them here would drop them in silence
@@ -1207,7 +1212,7 @@ async function showCatalogTrack(pluginManager, session, conf, args) {
         trackType: conf.type,
         assembly: getConfAssemblyNamesOrNone(conf)[0],
     };
-    const adapterType = readConfObject(conf, ['adapter', 'type']);
+    const adapterType = conf.adapter?.type;
     const summary = { ...track, ...(adapterType ? { adapterType } : {}) };
     // show:false over a catalog trackId asks for nothing — there is no file to
     // add — and showing it anyway would contradict the flag

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/loadSessionSpec.js

@@ -132,18 +132,8 @@ function unresolvedLayoutRefs(node, viewCount, knownIds) {
             : []),
     ];
 }
-// A `tabs` node shares one cell between its children rather than dividing the
-// space, so a `size` on one of them describes nothing. This is the ONLY case
-// left where a stated size is dropped.
-//
-// It used to be far wider — dockview forces its branches to alternate
-// orientation by depth, so a nested container had no branch to size against and
-// the whole sizing pass bailed, top-level numbers included. That is gone
-// (ADR-068): the spec's nesting is the tree's nesting, `size` applies wherever
-// it is written, and a bare sibling takes an equal share of the remainder. The
-// wider check outlived the limitation it reported and told an author their
-// nested or partial sizes had been ignored while the layout honoured them —
-// which is also what website/docs/urlparams.md promises.
+// A `tabs` node shares one cell between its children, so a `size` on one of
+// them describes nothing; it is the only stated size the layout drops.
 function unsizeableLayoutNodes(layout) {
     const children = Array.isArray(layout.children) ? layout.children : [];
     const sizedTabsChild = layout.direction === 'tabs' && children.some(c => c.size !== undefined);

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/LayoutRenderer.d.ts

@@ -2,16 +2,6 @@ import type { WorkspaceLayout } from './model.ts';
 import type { PanelChrome } from './panelChrome.ts';
 import type { LayoutTree } from './tree.ts';
 import type { DragState } from './useLayoutDrag.ts';
-/**
- * The layout, rendered. There is no imperative api and no event to listen to:
- * the tree is state, this is a function of it, and a gesture is an action.
- *
- * Sizes are `flex-grow`, which is why there is no resize handling anywhere in
- * here. A branch's children divide its space in proportion to their `size`
- * whatever that space becomes, so a window resize is the browser's problem —
- * this is the layout maths dockview does in pixels, and it is the part of a
- * grid engine most likely to be got subtly wrong.
- */
 interface Props {
     node: LayoutTree;
     layout: WorkspaceLayout;