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

package/esm/displayKitTests/perRegionTestEnv.js

@@ -28,44 +28,49 @@ function makeStateModel(control, gate, configSchema) {
         .volatile(() => ({
         /** every `fetchNeeded` call, as the region list it was handed */
         fetchLog: [],
-        loadedData: new Map(),
         /**
-         * What `regionFetchKey` answers. A volatile, not a `control` knob, and
-         * that is the point: a real display's key reads view state, so the
-         * autorun re-runs when it moves. A plain closure value would be memoized
-         * by the computed and never invalidate.
+         * What `zoomFetchArgs` answers. A volatile, not a `control` knob, and
+         * that is the point: a real display's args read view state, so the
+         * autorun re-runs when they move. A plain closure value would be
+         * memoized by the computed and never invalidate.
          */
         fetchKey: '',
     }))
+        .views(self => {
+        // chained, not replaced: `staleAnswers` forces a false answer for a
+        // bounded number of calls, and everything else is the foundation's own
+        // store-derived default
+        const superRegionHasData = self.regionHasData;
+        return {
+            regionHasData(displayedRegionIndex) {
+                control.cacheValidCalls += 1;
+                if (control.staleAnswers > 0) {
+                    control.staleAnswers -= 1;
+                    return false;
+                }
+                return superRegionHasData.call(self, displayedRegionIndex);
+            },
+        };
+    })
         .views(self => ({
+        /** the fetched payloads, off the foundation's store */
+        get loadedData() {
+            return self.regionPayloads;
+        },
         get gateEnabled() {
             return gate.gateEnabled ?? false;
         },
         get densityTooLarge() {
             return control.densityTooLarge;
         },
-        get regionFetchKey() {
-            return self.fetchKey;
-        },
-        regionHasData(_displayedRegionIndex) {
-            control.cacheValidCalls += 1;
-            if (control.staleAnswers > 0) {
-                control.staleAnswers -= 1;
-                return false;
-            }
-            return true;
+        zoomFetchArgs() {
+            return { key: self.fetchKey };
         },
     }))
         .actions(self => ({
         setFetchKey(key) {
             self.fetchKey = key;
         },
-        setLoaded(displayedRegionIndex, value) {
-            self.loadedData.set(displayedRegionIndex, value);
-        },
-        clearDisplaySpecificData() {
-            self.loadedData.clear();
-        },
     }))
         .actions(self => ({
         fetchNeeded(needed) {
@@ -90,17 +95,15 @@ function makeStateModel(control, gate, configSchema) {
                     // budget means no measurement at all, which is why `estimateCalls`
                     // stays at zero for an ungated display.
                     if (byteLimit === undefined) {
-                        return { value: 'data' };
+                        return { value: control.payloadTag };
                     }
                     control.estimateCalls += 1;
                     const bytes = control.estimateBytes;
                     return bytes > byteLimit
                         ? { regionTooLarge: true, bytes }
-                        : { value: 'data', bytes };
-                },
-                onResult: (idx, result) => {
-                    self.setLoaded(idx, result.value);
+                        : { value: control.payloadTag, bytes };
                 },
+                onResult: (_idx, result) => result.value,
             });
         },
     }));
@@ -118,6 +121,7 @@ export function createPerRegionTestEnvironment({ measuresBytes = false, gate, es
         estimateBytes,
         estimateCalls: 0,
         densityTooLarge: false,
+        payloadTag: 'data',
     };
     const optIns = gate ?? { gateEnabled: measuresBytes };
     const env = createDisplayTestEnvironment({

package/esm/index.d.ts

@@ -2,141 +2,63 @@ import Plugin from '@jbrowse/core/Plugin';
 import type PluginManager from '@jbrowse/core/PluginManager';
 export default class LinearGenomeViewPlugin extends Plugin {
     name: string;
-    exports: {
-        baseLinearDisplayConfigSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            readonly densityTier: {
-                readonly type: 'stringEnum';
-                readonly model: import("@jbrowse/mobx-state-tree").ISimpleType<"auto" | "density" | "features">;
-                readonly defaultValue: 'auto';
-                readonly description: 'when to draw the features-per-bin density band in place of features: "auto" swaps to it where the region is too large to fetch, "features" never does and keeps the banner, "density" always does. Needs a density source on the adapter (its densityAdapter slot)';
-                readonly advanced: true;
-            };
-            readonly densityTierBpPerPx: {
-                readonly type: 'number';
-                readonly defaultValue: 0;
-                readonly description: 'in "auto" mode, also draw the density band from this many bp per pixel outward, before the region is too large to fetch; 0 leaves the swap to the fetch-size gate alone';
-                readonly advanced: true;
-            };
-            readonly fetchSizeLimit: {
-                readonly type: 'number';
-                readonly defaultValue: 1000000;
-                readonly description: "maximum data to attempt to download for a given track, used if adapter doesn't specify one";
-                readonly advanced: true;
-            };
-            readonly forceLoad: {
-                readonly type: 'boolean';
-                readonly defaultValue: false;
-                readonly description: 'Declarative equivalent of the "Force load" button on the "too much data" banner: when true the display always renders, however large the region or dense the features. Off by default (the gate guards against huge downloads). Set it on a view no one can interact with — an embedded / notebook view, or a screenshot — where the region is known and you want it drawn without a click.';
-                readonly advanced: true;
-            };
-            readonly maxFeatureScreenDensity: {
-                readonly type: "number";
-                readonly description: "maximum features per pixel before showing a \"too many features\" message";
-                readonly defaultValue: 1;
-                readonly advanced: true;
-            };
-            readonly height: {
-                readonly type: "number";
-                readonly defaultValue: 100;
-                readonly description: "default height for the track";
-            };
-            readonly mouseover: {
-                readonly type: "string";
-                readonly description: "text to display when the cursor hovers over a feature";
-                readonly defaultValue: "jexl:get(feature,'_mouseOver')||get(feature,'name')||get(feature,'function')||get(feature,'id')";
-                readonly contextVariable: ["feature"];
-            };
-            readonly jexlFilters: {
-                readonly type: "stringArray";
-                readonly description: "default set of jexl filters to apply to a track. note: these do not use the jexl prefix because they have a deferred evaluation system";
-                readonly defaultValue: readonly [];
-            };
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
-        SearchBox: {
-            (props: {
-                model: import("./index.ts").LinearGenomeViewModel;
-                showHelp?: boolean;
-                minWidth?: number;
-                maxWidth?: number;
-                style?: React.CSSProperties;
-            }): import("react").JSX.Element;
-            displayName: string;
-        };
-        ZoomControls: {
-            (props: {
-                model: import("./index.ts").LinearGenomeViewModel;
-            }): import("react").JSX.Element;
-            displayName: string;
-        };
-        LinearGenomeView: {
-            (props: {
-                model: import("./index.ts").LinearGenomeViewModel;
-            }): import("react").JSX.Element;
-            displayName: string;
-        };
-    };
     /**
      * #config LinearGenomeViewConfigSchema
      * #category root
+     * Sets defaults for every linear genome view, on the root config under
+     * `configuration.LinearGenomeViewPlugin`.
      */
     configurationSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #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 "Show..." submenu sets the same
-         * thing per session, under its "Track labels" heading
-         */
         readonly trackLabels: {
-            readonly type: "string";
-            readonly defaultValue: "offset";
-            readonly model: import("@jbrowse/mobx-state-tree").ISimpleType<"hidden" | "offset" | "overlapping">;
+            type: "string";
+        } & {
+            model: import("@jbrowse/mobx-state-tree").ISimpleType<"hidden" | "offset" | "overlapping">;
+        } & {
+            defaultValue: string;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
     install(pluginManager: PluginManager): void;
     configure(pluginManager: PluginManager): void;
 }
 export { DisplayChromeOverlayProvider, DisplayUIProvider, FloatingLegend, TrackControlProvider, plainChromeOverlays, plainTrackControl, useTrackControlMenu, } from '@jbrowse/display-ui';
-export type { DisplayBackgroundProgressModel, DisplayChromeOverlays, DisplayErrorBarModel, DisplayLoadingOverlayModel, LegendItem, LegendSection, TooLargeMessageModel, TrackControlComponent, TrackControlIcon, TrackControlMenu, TrackControlOption, TrackControlProps, } from '@jbrowse/display-ui';
-export { HighlightBand, HighlightChip, type LinearGenomeViewModel, type LinearGenomeViewStateModel, OverviewHighlightBand, SVGHighlightBand, installLinkedViewSync, stateModelFactory as linearGenomeViewStateModelFactory, } from './LinearGenomeView/index.ts';
+export type { BackgroundProgressProps, DisplayChromeOverlays, ErrorBarProps, LegendItem, LegendSection, LoadingProps, RenderErrorProps, TooLargeProps, TrackControlComponent, TrackControlIcon, TrackControlMenu, TrackControlOption, TrackControlProps, } from '@jbrowse/display-ui';
+export { HighlightChip, type LinearGenomeViewModel, type LinearGenomeViewStateModel, installLinkedViewSync, stateModelFactory as linearGenomeViewStateModelFactory, } from './LinearGenomeView/index.ts';
 export { default as SearchBox } from './LinearGenomeView/components/SearchBox.tsx';
-export { default as HeaderSearchBoxes } from './LinearGenomeView/components/HeaderSearchBoxes.tsx';
 export { default as HeaderSearchBoxRow } from './LinearGenomeView/components/HeaderSearchBoxRow.tsx';
 export { searchBoxMenuItems, useSearchBoxPrefs, } from './LinearGenomeView/components/useSearchBoxPrefs.ts';
 export type { SearchBoxPrefs } from './LinearGenomeView/components/useSearchBoxPrefs.ts';
 export { normalizeTrackInit } from '@jbrowse/core/util/tracks';
-export { linearGenomeViewPropKeys, partitionLaunchKeys, } from './LinearGenomeView/initKeys.ts';
-export { applyInitHighlights } from './LinearGenomeView/afterAttach.ts';
-export { MultiLevelRubberband } from './MultiLevelRubberband/index.ts';
+export { applyInitHighlights, navToInitLoc, showInitTracks, } from './LinearGenomeView/afterAttach.ts';
+export { launchTrackInit, launchTrackWithModifiers, openedDisplayType, writeFilter, writeMembers, writeReadFilter, } from './TrackModifiers/index.ts';
+export type { ModifierView } from './TrackModifiers/index.ts';
+export { MultiLevelRubberband, multiLevelRowClickMenuItems, multiLevelRowMenuItems, rowLabels, } from './MultiLevelRubberband/index.ts';
 export { fetchResults, SearchResultsNotFoundError } from './searchUtils.ts';
 export type { LaunchLinearGenomeViewArgs } from './LaunchLinearGenomeView/index.ts';
-export type { BpOffset, ExportSvgOptions, HighlightType, InitState, LinearGenomeViewLaunchProps, NavLocation, TrackLabelMode, VolatileGuide, } from './LinearGenomeView/types.ts';
+export type { BpOffset, ExportSvgOptions, HighlightInput, HighlightType, InitState, LinearGenomeViewLaunchProps, LinearGenomeViewPanelInit, NavLocation, TrackLabelMode, ViewTrackLabelMode, VolatileGuide, } from './LinearGenomeView/types.ts';
 export type { ScalebarRefNameLabel } from './LinearGenomeView/util.ts';
+export type { HighlightRegion, SearchHits, SearchPickerRow, SearchPickerState, } from './LinearGenomeView/model.ts';
 export type { RegionsOrientation } from './LinearGenomeView/util.ts';
+export type { RegionEdit } from './LinearGenomeView/util.ts';
 export { makeTicks } from './LinearGenomeView/util.ts';
 export type { Tick } from './LinearGenomeView/util.ts';
+export { containingLgv } from './LinearGenomeView/containingLgv.ts';
 export { showRegionsWithUndo } from './LinearGenomeView/showRegionsWithUndo.ts';
 export type { SharedFit } from './LinearGenomeView/sharedScaleContainer.ts';
 export { fitAllRegionsWindow } from './LinearGenomeView/util.ts';
 export { renderToSvg } from './LinearGenomeView/svgcomponents/SVGLinearGenomeView.tsx';
 export { useViewSvgFigure } from './LinearGenomeView/svgcomponents/useViewSvgFigure.tsx';
 export type { ViewSvgFigureOptions, ViewSvgFigureResult, } from './LinearGenomeView/svgcomponents/useViewSvgFigure.tsx';
-export { default as SVGTracks } from './LinearGenomeView/svgcomponents/SVGTracks.tsx';
-export { default as SVGView } from './LinearGenomeView/svgcomponents/SVGView.tsx';
-export { default as SVGRowHeader } from './LinearGenomeView/svgcomponents/SVGRowHeader.tsx';
-export { default as SVGHighlights } from './LinearGenomeView/svgcomponents/SVGHighlights.tsx';
-export { default as SVGHighlightsOverlay } from './LinearGenomeView/svgcomponents/SVGHighlightsOverlay.tsx';
+export { default as SVGStackedRow } from './LinearGenomeView/svgcomponents/SVGStackedRow.tsx';
 export { default as ExportSvgDialog } from './LinearGenomeView/components/ExportSvgDialog.tsx';
 export { GetSequenceDialog } from './LinearGenomeView/lazyDialogs.ts';
 export { default as ConnectedHoverHighlight } from './LinearGenomeView/components/ConnectedHoverHighlight.tsx';
-export { default as HoverPositionHighlight } from './LinearGenomeView/components/HoverPositionHighlight.tsx';
-export { FloatingSvgOverlay, TrackOverlayContext, TrackOverlayPortal, TrackOverlaySlot, } from '@jbrowse/display-ui';
 export type { HoverHighlightPosition } from './LinearGenomeView/components/HoverPositionHighlight.tsx';
+export { FloatingSvgOverlay, TrackOverlayContext, TrackOverlayPortal, TrackOverlaySlot, } from '@jbrowse/display-ui';
 export { SvgChrome, SvgClipRect } from '@jbrowse/core/svg/SvgExport';
 export { svgSafeId } from '@jbrowse/core/svg/svgId';
 export { awaitSvgReady, awaitSvgRenders } from '@jbrowse/core/svg/svgReady';
 export type { SvgExportable } from '@jbrowse/core/svg/svgReady';
-export { defaultTextHeight, getRowHeaderLayout, labelBaselineFromTop, labelOffset, totalHeight, trackBoxHeight, trackBoxOffsets, trackLabelLeftOffset, } from './LinearGenomeView/svgcomponents/util.ts';
+export { defaultTextHeight, getRowHeaderLayout, labelOffset, totalHeight, trackBoxHeight, trackBoxOffsets, trackLabelLeftOffset, } from './LinearGenomeView/svgcomponents/util.ts';
 export { notifySkippedSvgTracks } from '@jbrowse/core/svg/trackNames';
 export { renderViewTracks } from './LinearGenomeView/svgcomponents/renderViewTracks.ts';
 export type { SvgExportTrack, ViewTracksSvg, } from './LinearGenomeView/svgcomponents/renderViewTracks.ts';

package/esm/index.js

@@ -1,48 +1,37 @@
 import Plugin from '@jbrowse/core/Plugin';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { isAbstractMenuManager } from '@jbrowse/core/util';
-import baseLinearDisplayConfigSchema from '@jbrowse/display-kit/configSchema';
+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 FeatureTrackF from './FeatureTrack/index.js';
 import LaunchLinearGenomeViewF from './LaunchLinearGenomeView/index.js';
 import SequenceFeatureHoverHighlightExtensionF from './LinearGenomeView/components/SequenceFeatureHoverHighlightExtension.js';
 import LinearGenomeViewF from './LinearGenomeView/index.js';
-import { LinearGenomeView, SearchBox, ZoomControls, } from './lazyPluginExports.js';
 export default class LinearGenomeViewPlugin extends Plugin {
     name = 'LinearGenomeViewPlugin';
-    // the three components here are lazy, see lazyPluginExports.tsx — naming a
-    // component in this object is enough to pin it into every host's first paint
-    exports = {
-        baseLinearDisplayConfigSchema,
-        SearchBox,
-        ZoomControls,
-        LinearGenomeView,
-    };
     /**
      * #config LinearGenomeViewConfigSchema
      * #category root
+     * Sets defaults for every linear genome view, on the root config under
+     * `configuration.LinearGenomeViewPlugin`.
      */
     configurationSchema = ConfigurationSchema('LinearGenomeViewConfigSchema', {
         /**
          * #slot configuration.LinearGenomeViewPlugin.trackLabels
-         * where a track's name is drawn: `offset` gives it its own line above the
+         * The placement of a track's name: `offset` puts it on a line above the
          * data, `overlapping` floats it over the top of the data to save vertical
-         * space, `hidden` omits it. The view menu's "Show..." submenu sets the same
-         * thing per session, under its "Track labels" heading
+         * space, `hidden` omits it. The view menu's "Track labels" submenu sets the
+         * same thing per session
          */
         trackLabels: {
             type: 'string',
             defaultValue: 'offset',
             model: types.enumeration('trackLabelOptions', [
-                'offset',
-                'overlapping',
-                'hidden',
+                ...VIEW_TRACK_LABEL_MODES,
             ]),
         },
     });
     install(pluginManager) {
-        FeatureTrackF(pluginManager);
         LinearGenomeViewF(pluginManager);
         LaunchLinearGenomeViewF(pluginManager);
         SequenceFeatureHoverHighlightExtensionF(pluginManager);
@@ -65,15 +54,10 @@ export default class LinearGenomeViewPlugin extends Plugin {
 // `@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 { HighlightBand, HighlightChip, OverviewHighlightBand, SVGHighlightBand, installLinkedViewSync, stateModelFactory as linearGenomeViewStateModelFactory, } from './LinearGenomeView/index.js';
-// Deliberately the component itself, and deliberately not the same `SearchBox`
-// the `exports` object above hands runtime plugins — that one is lazy. An
-// in-tree consumer (comparative view, breakpoint split view) imports this
-// barrel and gets shaken out of every build that doesn't, which is all the
-// laziness it needs; a runtime plugin resolves `exports` at module scope, where
-// only `lazy()` keeps the component out of the host's first paint. Imported
-// straight from the component rather than through `LinearGenomeView/index.ts`
-// so the view registration module holds no React component at all.
+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
@@ -81,13 +65,12 @@ export { default as SearchBox } from './LinearGenomeView/components/SearchBox.js
 // 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 HeaderSearchBoxes } from './LinearGenomeView/components/HeaderSearchBoxes.js';
 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 { linearGenomeViewPropKeys, partitionLaunchKeys, } from './LinearGenomeView/initKeys.js';
-export { applyInitHighlights } from './LinearGenomeView/afterAttach.js';
-export { MultiLevelRubberband } from './MultiLevelRubberband/index.js';
+export { applyInitHighlights, navToInitLoc, showInitTracks, } from './LinearGenomeView/afterAttach.js';
+export { launchTrackInit, launchTrackWithModifiers, openedDisplayType, writeFilter, writeMembers, writeReadFilter, } from './TrackModifiers/index.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
@@ -99,6 +82,7 @@ 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';
@@ -106,15 +90,10 @@ export { renderToSvg } from './LinearGenomeView/svgcomponents/SVGLinearGenomeVie
 // 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 SVGTracks } from './LinearGenomeView/svgcomponents/SVGTracks.js';
-export { default as SVGView } from './LinearGenomeView/svgcomponents/SVGView.js';
-export { default as SVGRowHeader } from './LinearGenomeView/svgcomponents/SVGRowHeader.js';
-export { default as SVGHighlights } from './LinearGenomeView/svgcomponents/SVGHighlights.js';
-export { default as SVGHighlightsOverlay } from './LinearGenomeView/svgcomponents/SVGHighlightsOverlay.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';
-export { default as HoverPositionHighlight } from './LinearGenomeView/components/HoverPositionHighlight.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
@@ -131,7 +110,7 @@ export { SvgChrome, SvgClipRect } from '@jbrowse/core/svg/SvgExport';
 // 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, labelBaselineFromTop, labelOffset, totalHeight, trackBoxHeight, trackBoxOffsets, trackLabelLeftOffset, } from './LinearGenomeView/svgcomponents/util.js';
+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

package/esm/searchUtils.d.ts

@@ -3,8 +3,7 @@ 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 { AssemblyHost, NotificationSink, TrackCatalog } from '@jbrowse/core/util';
-import type { StopToken } from '@jbrowse/core/util/stopToken';
+import type { AbstractSessionModel, AssemblyHost, NotificationSink, TrackCatalog } from '@jbrowse/core/util';
 declare module '@jbrowse/core/PluginManager' {
     interface ExtensionPointRegistry {
         'LinearGenomeView-searchResultSelected': {
@@ -24,14 +23,14 @@ export declare function navigateToSelectedOption({ option, model, assemblyName,
     option: BaseResult;
     model: LinearGenomeViewModel;
     assemblyName: string;
-}): Promise<void>;
+}): Promise<boolean>;
 export declare function isOpenInView(result: BaseResult, model: LinearGenomeViewModel): boolean;
-export declare function unanimousResult({ results, model, session, assembly, }: {
+export declare function distinctDestinations({ results, model, session, assembly, }: {
     results: BaseResult[];
     model: LinearGenomeViewModel;
     session: TrackCatalog;
     assembly?: Assembly;
-}): BaseResult | undefined;
+}): BaseResult[];
 export declare function showSearchResults({ results, query, model, assemblyName, grow, showHitTrack, }: {
     results: BaseResult[];
     query: string;
@@ -40,6 +39,7 @@ export declare function showSearchResults({ results, query, model, assemblyName,
     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;
@@ -58,13 +58,29 @@ export declare function handleSelectedRegion({ input, model, assemblyName, grow,
     grow?: number;
     showHitTrack?: boolean;
 }): Promise<boolean>;
-export declare function checkRef(str: string, isRef: (name: string) => boolean): boolean;
-export declare function fetchResults({ queryString, searchType, assemblyName, textSearchManager, assembly, stopToken, }: {
+interface SearchArgs {
     queryString: string;
     assemblyName: string;
     searchType?: SearchType;
     textSearchManager?: TextSearchManager;
     assembly?: Assembly;
-    stopToken?: StopToken;
-}): Promise<BaseResult[]>;
-export declare function splitLast(str: string, split: string): [string, string];
+    signal?: AbortSignal;
+}
+interface SessionSearchArgs {
+    session: Pick<AbstractSessionModel, 'assemblyManager' | 'textSearchManager'>;
+    queryString: string;
+    assemblyName: string;
+    searchType?: SearchType;
+    signal?: AbortSignal;
+}
+/**
+ * The search box's hits for a query: refNames and text-index results, merged.
+ * Pass the session and the function finds the index manager and the assembly
+ * itself; passing `textSearchManager` and `assembly` is the older form.
+ */
+export declare function fetchResults(args: SessionSearchArgs | SearchArgs): Promise<BaseResult[]>;
+export declare function nameNotFound(input: string, assemblyName: string, { indexCount, failures }: {
+    indexCount: number;
+    failures: unknown[];
+}): Error;
+export {};