@jbrowse/plugin-linear-genome-view 4.3.0 → 5.0.0-beta.10

package/esm/index.js

@@ -1,48 +1,44 @@
 import Plugin from '@jbrowse/core/Plugin';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { isAbstractMenuManager } from '@jbrowse/core/util';
+import { VIEW_TRACK_LABEL_MODES } from '@jbrowse/display-kit/types';
 import { types } from '@jbrowse/mobx-state-tree';
 import LineStyleIcon from '@mui/icons-material/LineStyle';
-import { BaseLinearDisplay, BaseLinearDisplayComponent, baseLinearDisplayConfigSchema, } from "./BaseLinearDisplay/index.js";
-import BasicTrackF from "./BasicTrack/index.js";
-import FeatureTrackF from "./FeatureTrack/index.js";
-import LaunchLinearGenomeViewF from "./LaunchLinearGenomeView/index.js";
-import LinearBareDisplayF from "./LinearBareDisplay/index.js";
-import LinearBasicDisplayF from "./LinearBasicDisplay/index.js";
-import ZoomControls from "./LinearGenomeView/components/HeaderZoomControls.js";
-import LinearGenomeViewF, { LinearGenomeView, SearchBox, } from "./LinearGenomeView/index.js";
+import FeatureTrackF from './FeatureTrack/index.js';
+import LaunchLinearGenomeViewF from './LaunchLinearGenomeView/index.js';
+import SequenceFeatureHoverHighlightExtensionF from './LinearGenomeView/components/SequenceFeatureHoverHighlightExtension.js';
+import LinearGenomeViewF from './LinearGenomeView/index.js';
 export default class LinearGenomeViewPlugin extends Plugin {
     name = 'LinearGenomeViewPlugin';
-    exports = {
-        BaseLinearDisplayComponent,
-        BaseLinearDisplay,
-        baseLinearDisplayConfigSchema,
-        SearchBox,
-        ZoomControls,
-        LinearGenomeView,
-    };
+    /**
+     * #config LinearGenomeViewConfigSchema
+     * #category root
+     */
     configurationSchema = ConfigurationSchema('LinearGenomeViewConfigSchema', {
+        /**
+         * #slot configuration.LinearGenomeViewPlugin.trackLabels
+         * where a track's name is drawn: `offset` gives it its own line above the
+         * data, `overlapping` floats it over the top of the data to save vertical
+         * space, `hidden` omits it. The view menu's "Track labels" submenu sets the
+         * same thing per session
+         */
         trackLabels: {
             type: 'string',
-            defaultValue: 'overlapping',
+            defaultValue: 'offset',
             model: types.enumeration('trackLabelOptions', [
-                'offset',
-                'overlapping',
-                'hidden',
+                ...VIEW_TRACK_LABEL_MODES,
             ]),
         },
     });
     install(pluginManager) {
         FeatureTrackF(pluginManager);
-        BasicTrackF(pluginManager);
-        LinearBasicDisplayF(pluginManager);
         LinearGenomeViewF(pluginManager);
-        LinearBareDisplayF(pluginManager);
         LaunchLinearGenomeViewF(pluginManager);
+        SequenceFeatureHoverHighlightExtensionF(pluginManager);
     }
     configure(pluginManager) {
         if (isAbstractMenuManager(pluginManager.rootModel)) {
-            pluginManager.rootModel.appendToSubMenu(['Add'], {
+            pluginManager.rootModel.appendToMenu('Add', {
                 label: 'Linear genome view',
                 icon: LineStyleIcon,
                 onClick: (session) => {
@@ -52,12 +48,71 @@ export default class LinearGenomeViewPlugin extends Plugin {
         }
     }
 }
-export { configSchemaFactory as linearBareDisplayConfigSchemaFactory, stateModelFactory as linearBareDisplayStateModelFactory, } from "./LinearBareDisplay/index.js";
-export { BaseLinearDisplay, BaseLinearDisplayComponent, BlockMsg, FeatureDensityMixin, FloatingLegend, NonBlockCanvasDisplayComponent, NonBlockCanvasDisplayMixin, SVGLegend, TooLargeMessage, TrackHeightMixin, baseLinearDisplayConfigSchema, calculateSvgLegendWidth, createSubfeatureLabelMetadata, drawCanvasImageData, } from "./BaseLinearDisplay/index.js";
-export { HighlightBand, RefNameAutocomplete, SearchBox, } from "./LinearGenomeView/index.js";
-export { fetchResults } from "./searchUtils.js";
-export { SVGGridlines, SVGRuler, SVGTracks, renderToSvg, } from "./LinearGenomeView/svgcomponents/SVGLinearGenomeView.js";
-export { totalHeight } from "./LinearGenomeView/svgcomponents/util.js";
-export { configSchema as linearBasicDisplayConfigSchemaFactory, modelFactory as linearBasicDisplayModelFactory, } from "./LinearBasicDisplay/index.js";
-export { configSchema as linearFeatureDisplayConfigSchemaFactory, modelFactory as linearFeatureDisplayModelFactory, } from "./LinearFeatureDisplay/index.js";
-export { default as LinearBasicDisplayComponent } from "./LinearBasicDisplay/components/LinearBasicDisplayComponent.js";
+// The toolkit-free chrome contract, re-exported for code already reaching
+// this plugin; its home is `@jbrowse/display-ui`. The display layer itself
+// (the fetch foundations, the chrome, SVG export, the byte gate) is
+// `@jbrowse/display-kit`, and is imported from there by subpath, never from
+// here.
+export { DisplayChromeOverlayProvider, DisplayUIProvider, FloatingLegend, TrackControlProvider, plainChromeOverlays, plainTrackControl, useTrackControlMenu, } from '@jbrowse/display-ui';
+export { HighlightChip, installLinkedViewSync, stateModelFactory as linearGenomeViewStateModelFactory, } from './LinearGenomeView/index.js';
+// Imported straight from the component rather than through
+// `LinearGenomeView/index.ts` so the view registration module holds no React
+// component at all; a consumer that never renders it shakes it out.
+export { default as SearchBox } from './LinearGenomeView/components/SearchBox.js';
+// The same two consumers, one composition further on: a header stacking several
+// views draws one search box per row beside the span it is showing, and
+// `HeaderSearchBoxRow` is the whole strip of them. `useSearchBoxPrefs` holds the
+// visibility/orientation choice and `searchBoxMenuItems` the rows that set it —
+// shared rather than copied, since the copies had already drifted on what to
+// call `sideBySide: false`. Only the storage prefix stays with each container.
+export { default as HeaderSearchBoxRow } from './LinearGenomeView/components/HeaderSearchBoxRow.js';
+export { searchBoxMenuItems, useSearchBoxPrefs, } from './LinearGenomeView/components/useSearchBoxPrefs.js';
+export { normalizeTrackInit } from '@jbrowse/core/util/tracks';
+export { applyInitHighlights } from './LinearGenomeView/afterAttach.js';
+export { MultiLevelRubberband, multiLevelRowClickMenuItems, multiLevelRowMenuItems, rowLabels, } from './MultiLevelRubberband/index.js';
+export { fetchResults, SearchResultsNotFoundError } from './searchUtils.js';
+// The scalebar's grid, published because it is a contract other views draw
+// against rather than an internal of this one: the synteny view's location
+// markers continue this ruler down through the ribbons, and pin their pitch AND
+// PHASE against this function rather than re-deriving them (which is how they
+// came to sit one base off it). `Tick` comes with it so the declaration doesn't
+// leak the source path — see the note above.
+export { makeTicks } from './LinearGenomeView/util.js';
+// The two halves of "show these regions instead": navigate the view you are
+// looking at, or seed a snapshot for a new one. A caller deriving either itself
+// lands on a viewport property the model no longer reads — see each for how.
+export { containingLgv } from './LinearGenomeView/containingLgv.js';
+export { showRegionsWithUndo } from './LinearGenomeView/showRegionsWithUndo.js';
+export { fitAllRegionsWindow } from './LinearGenomeView/util.js';
+export { renderToSvg } from './LinearGenomeView/svgcomponents/SVGLinearGenomeView.js';
+// The third form of the same export: not a file, not a markup string, but the
+// components mounted in a host's own page. See the file for the three pieces
+// between `renderToSvg` and inline JSX that each fail quietly.
+export { useViewSvgFigure } from './LinearGenomeView/svgcomponents/useViewSvgFigure.js';
+export { default as SVGStackedRow } from './LinearGenomeView/svgcomponents/SVGStackedRow.js';
+export { default as ExportSvgDialog } from './LinearGenomeView/components/ExportSvgDialog.js';
+export { GetSequenceDialog } from './LinearGenomeView/lazyDialogs.js';
+export { default as ConnectedHoverHighlight } from './LinearGenomeView/components/ConnectedHoverHighlight.js';
+// The overlay layer lives in `@jbrowse/display-ui` — a package rather than this
+// plugin, because `packages/tree-sidebar` needed it and had to depend on a
+// *plugin* to get it. Re-exported here, since every display already names it
+// from this one.
+//
+// The host-side half of the portal is `TrackOverlaySlot`: the display's box, the
+// overlay node beside it and the paint order between them. `TrackContainer`
+// mounts it, and so does an embedder mounting `RenderingComponent` directly —
+// who otherwise supplies no node at all and gets display chrome buried under
+// their own region masks.
+export { FloatingSvgOverlay, TrackOverlayContext, TrackOverlayPortal, TrackOverlaySlot, } from '@jbrowse/display-ui';
+export { SvgChrome, SvgClipRect } from '@jbrowse/core/svg/SvgExport';
+// for a display that hand-rolls a <clipPath> instead of using SvgClipRect (an
+// inset or non-rect clip); ids built from a trackId/refName need it
+export { svgSafeId } from '@jbrowse/core/svg/svgId';
+export { awaitSvgReady, awaitSvgRenders } from '@jbrowse/core/svg/svgReady';
+export { defaultTextHeight, getRowHeaderLayout, labelOffset, totalHeight, trackBoxHeight, trackBoxOffsets, trackLabelLeftOffset, } from './LinearGenomeView/svgcomponents/util.js';
+// Re-exported from core, where it moved so the circular view — which depends
+// on neither this plugin nor the LGV geometry around it — can send the same
+// notification. Kept on this plugin's surface because published plugins
+// resolve it here.
+export { notifySkippedSvgTracks } from '@jbrowse/core/svg/trackNames';
+export { renderViewTracks } from './LinearGenomeView/svgcomponents/renderViewTracks.js';

package/esm/searchUtils.d.ts

@@ -1,26 +1,76 @@
-import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
 import type { LinearGenomeViewModel } from './LinearGenomeView/index.ts';
-import type { SearchScope } from '@jbrowse/core/TextSearch/TextSearchManager';
+import type BaseResult from '@jbrowse/core/TextSearch/BaseResults';
+import type TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
 import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
 import type { SearchType } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { TextSearchManager } from '@jbrowse/core/util';
-export declare function navToOption({ option, model, assemblyName, }: {
+import type { AssemblyHost, NotificationSink, TrackCatalog } from '@jbrowse/core/util';
+declare module '@jbrowse/core/PluginManager' {
+    interface ExtensionPointRegistry {
+        'LinearGenomeView-searchResultSelected': {
+            args: undefined;
+            result: undefined | Promise<void>;
+            props: {
+                session: AssemblyHost & NotificationSink & TrackCatalog;
+                /** the search result that was selected */
+                result: BaseResult;
+                model: LinearGenomeViewModel;
+                assemblyName: string;
+            };
+        };
+    }
+}
+export declare function navigateToSelectedOption({ option, model, assemblyName, }: {
+    option: BaseResult;
+    model: LinearGenomeViewModel;
+    assemblyName: string;
+}): Promise<void>;
+export declare function isOpenInView(result: BaseResult, model: LinearGenomeViewModel): boolean;
+export declare function distinctDestinations({ results, model, session, assembly, }: {
+    results: BaseResult[];
+    model: LinearGenomeViewModel;
+    session: TrackCatalog;
+    assembly?: Assembly;
+}): BaseResult[];
+export declare function showSearchResults({ results, query, model, assemblyName, grow, showHitTrack, }: {
+    results: BaseResult[];
+    query: string;
+    model: LinearGenomeViewModel;
+    assemblyName: string;
+    grow?: number;
+    showHitTrack?: boolean;
+}): Promise<boolean>;
+export declare function hitTrackToShow(result: BaseResult, session: TrackCatalog): string | undefined;
+export declare function navToOption({ option, model, assemblyName, grow, showHitTrack, }: {
     model: LinearGenomeViewModel;
     option: BaseResult;
     assemblyName: string;
+    grow?: number;
+    showHitTrack?: boolean;
 }): Promise<void>;
-export declare function handleSelectedRegion({ input, model, assembly, }: {
+export declare class SearchResultsNotFoundError extends Error {
+    name: string;
+}
+export declare function notifySearchFailure(session: NotificationSink, e: unknown): void;
+export declare function handleSelectedRegion({ input, model, assemblyName, grow, showHitTrack, }: {
     input: string;
     model: LinearGenomeViewModel;
-    assembly: Assembly;
-}): Promise<void>;
-export declare function checkRef(str: string, allRefs: string[]): boolean;
-export declare function fetchResults({ queryString, searchType, searchScope, rankSearchResults, textSearchManager, assembly, }: {
+    assemblyName: string;
+    grow?: number;
+    showHitTrack?: boolean;
+}): Promise<boolean>;
+export declare function checkRef(str: string, isRef: (name: string) => boolean): boolean;
+interface SearchArgs {
     queryString: string;
-    searchScope: SearchScope;
-    rankSearchResults: (results: BaseResult[]) => BaseResult[];
+    assemblyName: string;
     searchType?: SearchType;
     textSearchManager?: TextSearchManager;
     assembly?: Assembly;
-}): Promise<BaseResult[]>;
+    signal?: AbortSignal;
+}
+export declare function fetchResults(args: SearchArgs): Promise<BaseResult[]>;
+export declare function nameNotFound(input: string, assemblyName: string, { indexCount, failures }: {
+    indexCount: number;
+    failures: unknown[];
+}): Error;
 export declare function splitLast(str: string, split: string): [string, string];
+export {};