@jbrowse/plugin-linear-genome-view 5.0.0-beta.2 → 5.0.0-beta.20

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "5.0.0-beta.2",
+  "version": "5.0.0-beta.20",
   "type": "module",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
@@ -21,15 +21,16 @@
     "esm"
   ],
   "dependencies": {
-    "@jbrowse/mobx-state-tree": "^6.5.1",
-    "@mui/icons-material": "^9.4.0",
-    "@mui/material": "^9.4.0",
-    "mobx": "^7.0.3",
-    "mobx-react": "^10.0.2",
-    "@jbrowse/core": "^5.0.0-beta.2",
-    "@jbrowse/render-core": "^5.0.0-beta.2",
-    "@jbrowse/display-ui": "^5.0.0-beta.2",
-    "@jbrowse/display-kit": "^5.0.0-beta.2"
+    "@jbrowse/mobx-state-tree": "^6.10.0",
+    "@mui/icons-material": "^9.5.0",
+    "@mui/material": "^9.5.0",
+    "mobx": "^7.1.3",
+    "mobx-react": "^10.0.3",
+    "@jbrowse/core": "^5.0.0-beta.20",
+    "@jbrowse/display-ui": "^5.0.0-beta.20",
+    "@jbrowse/display-kit": "^5.0.0-beta.20",
+    "@jbrowse/render-core": "^5.0.0-beta.20",
+    "@jbrowse/launch-args": "^5.0.0-beta.20"
   },
   "peerDependencies": {
     "react": ">=19.0.0",
@@ -40,7 +41,7 @@
   },
   "sideEffects": false,
   "devDependencies": {
-    "@jbrowse/display-test-utils": "^5.0.0-beta.2"
+    "@jbrowse/display-test-utils": "^5.0.0-beta.20"
   },
   "scripts": {
     "prebuild": "pnpm clean",

package/esm/FeatureTrack/configSchema.d.ts

@@ -1,124 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #config FeatureTrack
- * #category track
- * used for basic gene and feature tracks, generally used with LinearBasicDisplay
- *
- * #example
- * A minimal hand-authored entry in the top-level `tracks` array — `adapter`
- * points at the data file, and the track opens with a `LinearBasicDisplay`:
- * ```js
- * {
- *   type: 'FeatureTrack',
- *   trackId: 'genes',
- *   name: 'Genes',
- *   assemblyNames: ['hg38'],
- *   adapter: {
- *     type: 'Gff3TabixAdapter',
- *     uri: 'https://example.com/genes.sorted.gff.gz',
- *   },
- * }
- * ```
- *
- * #example
- * The same track, colored. Rather than writing out the full `displays` array,
- * you can put appearance settings in a `displayDefaults` object — JBrowse works
- * out which display they belong to and applies them for you (here, the track's
- * `LinearBasicDisplay`), so you don't have to know display names. A `jexl:`
- * value gives per-feature coloring:
- * ```js
- * {
- *   type: 'FeatureTrack',
- *   trackId: 'genes',
- *   name: 'Genes',
- *   assemblyNames: ['hg38'],
- *   adapter: {
- *     type: 'Gff3TabixAdapter',
- *     uri: 'https://example.com/genes.sorted.gff.gz',
- *   },
- *   displayDefaults: { color: "jexl:feature.type=='CDS'?'red':'blue'" },
- * }
- * ```
- */
-declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    readonly name: {
-        readonly description: "descriptive name of the track, falls back to the trackId when unset";
-        readonly type: "string";
-        readonly defaultValue: "";
-    };
-    readonly assemblyNames: {
-        readonly description: "name of the assembly (or assemblies) track belongs to";
-        readonly type: "stringArray";
-        readonly defaultValue: readonly ["assemblyName"];
-    };
-    readonly description: {
-        readonly description: "a description of the track";
-        readonly type: "string";
-        readonly defaultValue: "";
-    };
-    readonly category: {
-        readonly description: "the category and sub-categories of a track";
-        readonly type: "stringArray";
-        readonly defaultValue: readonly [];
-    };
-    readonly metadata: {
-        readonly type: "frozen";
-        readonly description: "anything to add about this track";
-        readonly defaultValue: {};
-    };
-    readonly adapter: import("@jbrowse/mobx-state-tree").IAnyType;
-    readonly textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        readonly indexingAttributes: {
-            readonly type: "stringArray";
-            readonly description: "list of which feature attributes to index for text searching";
-            readonly defaultValue: readonly ["Name", "ID", "symbol"];
-        };
-        readonly indexingFeatureTypesToExclude: {
-            readonly type: "stringArray";
-            readonly description: "list of feature types to exclude in text search index";
-            readonly defaultValue: readonly ["CDS", "exon"];
-        };
-        readonly indexingFeatureTypesToInclude: {
-            readonly type: "stringArray";
-            readonly description: "the only feature types to index; empty means index every type not excluded";
-            readonly defaultValue: readonly [];
-        };
-        readonly textSearchAdapter: import("@jbrowse/mobx-state-tree").IAnyType;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    readonly displays: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
-    readonly formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        readonly feature: {
-            readonly type: "frozen";
-            readonly description: "adds extra fields to the feature details";
-            readonly defaultValue: {};
-            readonly contextVariable: ["feature"];
-        };
-        readonly subfeatures: {
-            readonly type: "frozen";
-            readonly description: "adds extra fields to the subfeatures of a feature";
-            readonly defaultValue: {};
-            readonly contextVariable: ["feature"];
-        };
-        readonly depth: {
-            readonly type: "maybeNumber";
-            readonly description: "levels of subfeature the formatDetails.subfeatures callback runs on, default 2";
-        };
-        readonly maxDepth: {
-            readonly type: "maybeNumber";
-            readonly description: "hide subfeatures nested deeper than this, default no limit";
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    readonly formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        readonly config: {
-            readonly type: "frozen";
-            readonly description: "formats configuration object in about dialog";
-            readonly defaultValue: {};
-            readonly contextVariable: ["config"];
-        };
-        readonly hideUris: {
-            readonly type: "boolean";
-            readonly defaultValue: false;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, "trackId">>;
-export default configSchema;

package/esm/FeatureTrack/configSchema.js

@@ -1,54 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes';
-/**
- * #config FeatureTrack
- * #category track
- * used for basic gene and feature tracks, generally used with LinearBasicDisplay
- *
- * #example
- * A minimal hand-authored entry in the top-level `tracks` array — `adapter`
- * points at the data file, and the track opens with a `LinearBasicDisplay`:
- * ```js
- * {
- *   type: 'FeatureTrack',
- *   trackId: 'genes',
- *   name: 'Genes',
- *   assemblyNames: ['hg38'],
- *   adapter: {
- *     type: 'Gff3TabixAdapter',
- *     uri: 'https://example.com/genes.sorted.gff.gz',
- *   },
- * }
- * ```
- *
- * #example
- * The same track, colored. Rather than writing out the full `displays` array,
- * you can put appearance settings in a `displayDefaults` object — JBrowse works
- * out which display they belong to and applies them for you (here, the track's
- * `LinearBasicDisplay`), so you don't have to know display names. A `jexl:`
- * value gives per-feature coloring:
- * ```js
- * {
- *   type: 'FeatureTrack',
- *   trackId: 'genes',
- *   name: 'Genes',
- *   assemblyNames: ['hg38'],
- *   adapter: {
- *     type: 'Gff3TabixAdapter',
- *     uri: 'https://example.com/genes.sorted.gff.gz',
- *   },
- *   displayDefaults: { color: "jexl:feature.type=='CDS'?'red':'blue'" },
- * }
- * ```
- */
-const configSchema = (pluginManager) => ConfigurationSchema('FeatureTrack', {}, {
-    /**
-     * #baseConfiguration
-     */
-    baseConfiguration: createBaseTrackConfig(pluginManager),
-    /**
-     * #identifier
-     */
-    explicitIdentifier: 'trackId',
-});
-export default configSchema;

package/esm/FeatureTrack/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function FeatureTrackF(pm: PluginManager): void;

package/esm/FeatureTrack/index.js

@@ -1,13 +0,0 @@
-import { TrackType, createBaseTrackModel, } from '@jbrowse/core/pluggableElementTypes';
-import configSchemaF from './configSchema.js';
-export default function FeatureTrackF(pm) {
-    pm.addTrackType(() => {
-        const configSchema = configSchemaF(pm);
-        return new TrackType({
-            name: 'FeatureTrack',
-            displayName: 'Feature track',
-            configSchema,
-            stateModel: createBaseTrackModel(pm, 'FeatureTrack', configSchema),
-        });
-    });
-}

package/esm/LinearGenomeView/initKeys.d.ts

@@ -1,12 +0,0 @@
-export declare function partitionLaunchKeys(spec: object, viewPropKeys: ReadonlySet<string>): {
-    init: Record<string, unknown>;
-    viewProps: Record<string, unknown>;
-    unknown: Record<string, unknown>;
-};
-export declare function linearGenomeViewPropKeys(pluginManager: {
-    getViewType: (name: string) => {
-        stateModel: {
-            properties: object;
-        };
-    };
-}): ReadonlySet<string>;

package/esm/LinearGenomeView/initKeys.js

@@ -1,68 +0,0 @@
-import { lgvLaunchKeys } from './launchKeys.js';
-// The remaining v4 partition, still used by the synteny view to build its LGV
-// rows. `lgvLaunchKeys` is the one declaration of what a launch key is, so the
-// two cannot disagree while both exist.
-const knownInitKeys = new Set(Object.keys(lgvLaunchKeys.keys));
-// Never settable from a spec, whatever the model declares: `type` picks the
-// view, `id` is passed top-level so MST's optional identifier honors it, and
-// `launch` is the blob the partition fills rather than something anyone writes.
-const RESERVED = new Set(['id', 'type', 'launch']);
-const LEGACY_VIEWPORT_PROPS = new Set(lgvLaunchKeys.passThrough);
-// Partition launch keys three ways, once, for every caller that needs to know
-// which is which:
-//
-// - `init`: resolution keys (loc, tracks, highlight, …) with no direct MST
-//   representation, which afterAttach applies on attach and then discards
-// - `viewProps`: plain persisted props MST restores natively, so they belong on
-//   the view snapshot rather than in the blob
-// - `unknown`: neither, i.e. a typo. MST silently drops unknown snapshot keys and
-//   `init` is a frozen blob, so nothing else would notice
-//
-// The two callers differ only in what they do with each bucket: the launcher
-// spreads a flat spec across the new view's snapshot and warns about the typos,
-// while afterAttach — which only ever sees an already-built blob — warns about
-// both a typo and a view prop that ended up inside it.
-export function partitionLaunchKeys(spec, 
-// The view's declared property names. Callers with a live node read it off
-// `getPropertyMembers(self).properties`; callers building a snapshot read it
-// off the registered view type's `stateModel.properties` — see
-// `linearGenomeViewPropKeys`.
-viewPropKeys) {
-    const init = {};
-    const viewProps = {};
-    const unknown = {};
-    for (const [key, value] of Object.entries(spec)) {
-        const bucket = knownInitKeys.has(key)
-            ? init
-            : (viewPropKeys.has(key) || LEGACY_VIEWPORT_PROPS.has(key)) &&
-                !RESERVED.has(key)
-                ? viewProps
-                : unknown;
-        bucket[key] = value;
-    }
-    return { init, viewProps, unknown };
-}
-// The registered LinearGenomeView's declared property names, for a caller that
-// has a PluginManager but no view yet (a launcher, or a synteny row being built).
-// A caller holding a live node reads the same thing off
-// `getPropertyMembers(self).properties` instead.
-//
-// `getViewType` THROWS on an unregistered name, and that is left alone: this is
-// only ever called from code that is about to add a LinearGenomeView, so an
-// absent view type is a broken plugin manager rather than a case to degrade
-// through — and degrading would mean silently dropping every property the
-// caller asked for, which is the failure this whole mechanism exists to end.
-//
-// Cached: the set is fixed for the life of the manager, and a launch that opens
-// a stack of rows would otherwise rebuild it per row.
-const propKeyCache = new WeakMap();
-export function linearGenomeViewPropKeys(pluginManager) {
-    const cached = propKeyCache.get(pluginManager);
-    if (cached) {
-        return cached;
-    }
-    const { stateModel } = pluginManager.getViewType('LinearGenomeView');
-    const keys = new Set(Object.keys(stateModel.properties));
-    propKeyCache.set(pluginManager, keys);
-    return keys;
-}

package/esm/MultiLevelRubberband/VerticalGuide.d.ts

@@ -1,6 +0,0 @@
-import type { MultiLevelRubberbandModel } from './types.ts';
-declare const VerticalGuide: ({ model, coordX, }: {
-    model: MultiLevelRubberbandModel;
-    coordX: number;
-}) => import("react").JSX.Element;
-export default VerticalGuide;

package/esm/MultiLevelRubberband/VerticalGuide.js

@@ -1,21 +0,0 @@
-import { Fragment as _Fragment, jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { stringify } from '@jbrowse/core/util';
-import { makeStyles } from '@jbrowse/core/util/tss-react';
-import { observer } from 'mobx-react';
-import { GuideLabel } from '../shared/coordLabels.js';
-const useStyles = makeStyles()({
-    guide: {
-        pointerEvents: 'none',
-        height: '100%',
-        width: 1,
-        position: 'absolute',
-        background: 'red',
-        zIndex: 1001,
-    },
-});
-const VerticalGuide = observer(function VerticalGuide({ model, coordX, }) {
-    const { classes } = useStyles();
-    const { views } = model;
-    return (_jsxs(_Fragment, { children: [_jsx(GuideLabel, { coordX: coordX, viewWidth: Math.min(...views.map(view => view.width)), stickyTop: undefined, children: views.map(view => (_jsx("div", { children: stringify(view.pxToBp(coordX), true) }, view.id))) }), _jsx("div", { className: classes.guide, style: { left: coordX } })] }));
-});
-export default VerticalGuide;

package/esm/lazyPluginExports.d.ts

@@ -1,23 +0,0 @@
-import type { LinearGenomeViewModel } from './LinearGenomeView/index.ts';
-export declare const LinearGenomeView: {
-    (props: {
-        model: LinearGenomeViewModel;
-    }): import("react").JSX.Element;
-    displayName: string;
-};
-export declare const SearchBox: {
-    (props: {
-        model: LinearGenomeViewModel;
-        showHelp?: boolean;
-        minWidth?: number;
-        maxWidth?: number;
-        style?: React.CSSProperties;
-    }): import("react").JSX.Element;
-    displayName: string;
-};
-export declare const ZoomControls: {
-    (props: {
-        model: LinearGenomeViewModel;
-    }): import("react").JSX.Element;
-    displayName: string;
-};

package/esm/lazyPluginExports.js

@@ -1,36 +0,0 @@
-import { jsx as _jsx } from "react/jsx-runtime";
-import { Suspense, lazy } from 'react';
-/**
- * The three React components `LinearGenomeViewPlugin.exports` publishes to
- * external plugins, each behind its own chunk.
- *
- * They used to be plain static imports in the plugin's `index.ts`, and that one
- * object was enough to undo the `lazy()` the view type is registered with:
- * `exports` is evaluated when the plugin class body is, so **every** host that
- * installs this plugin pulled in the whole stock LGV component tree — and
- * through it `@jbrowse/core/ui` and most of Material UI — before first paint,
- * including a host that renders none of JBrowse's own chrome. Measured on
- * `products/jbrowse-build-your-own`'s examples site, where no page renders a
- * single one of these: 63 chunks, 239 KB raw / 89 KB gzipped.
- *
- * That is the shape to watch for. A `lazy()` at the registration site only
- * holds if nothing else in an eagerly-evaluated module names the same component,
- * and a plugin's `exports` object is the easiest place to name one by accident.
- *
- * The `Suspense` wrapper is what keeps the change invisible to a consumer: a
- * bare `lazy()` component handed to a plugin that renders it outside a boundary
- * would throw where a static one worked, and external plugins are exactly the
- * consumers we cannot check (`reference/PLUGIN_ABI_STABILITY.md`). Same
- * treatment, and the same reason, as core's `ReExports/lazify.tsx` — which is
- * not reused here only because it is not on core's exports map.
- */
-function suspend(displayName, Component) {
-    function Suspended(props) {
-        return (_jsx(Suspense, { fallback: null, children: _jsx(Component, { ...props }) }));
-    }
-    Suspended.displayName = displayName;
-    return Suspended;
-}
-export const LinearGenomeView = suspend('LinearGenomeView', lazy(() => import('./LinearGenomeView/components/LinearGenomeView.js')));
-export const SearchBox = suspend('SearchBox', lazy(() => import('./LinearGenomeView/components/SearchBox.js')));
-export const ZoomControls = suspend('ZoomControls', lazy(() => import('./LinearGenomeView/components/HeaderZoomControls.js')));