@jbrowse/plugin-linear-genome-view 5.0.0-beta.16 → 5.0.0-beta.18

package/esm/LinearGenomeView/model.d.ts

@@ -1,4 +1,4 @@
-import type { BpOffset, ExportSvgOptions, HighlightType, InitState, NavLocation, ViewTrackLabelMode, VolatileGuide } from './types.ts';
+import type { BpOffset, ExportSvgOptions, HighlightInput, HighlightType, InitState, NavLocation, ViewTrackLabelMode, VolatileGuide } from './types.ts';
 import type { RegionEdit } from './util.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type BaseResult from '@jbrowse/core/TextSearch/BaseResults';
@@ -20,18 +20,24 @@ export interface SearchPickerRow {
     trackName: string;
 }
 /**
- * The hits of a name search that point at more than one place, waiting for the
- * user to choose. A host draws them however it likes: the Material view shows
- * a dialog, and `SearchPicker` in `@jbrowse/display-ui/embed` a plain list.
+ * A name search's hits as a host lists them: what `view.search` returns, and
+ * what the picker holds.
  */
-export interface SearchPickerState {
+export interface SearchHits {
     query: string;
     assemblyName: string;
-    /** one row per place, hits in a track the view already shows first */
+    /** one row per hit, hits in a track the view already shows first */
     rows: SearchPickerRow[];
-    /** navigates to the row's place, reports a failure and closes the picker */
+    /** lands on the row's place and reports a failure */
     pick: (id: string) => Promise<unknown>;
 }
+/**
+ * The hits of a name search that point at more than one place, waiting for the
+ * user to choose; its `pick` also closes the picker. A host draws them however
+ * it likes: the Material view shows a dialog, and `SearchPicker` in
+ * `@jbrowse/display-ui/embed` a plain list.
+ */
+export type SearchPickerState = SearchHits;
 export type { PaddingSpan } from './util.ts';
 export interface HighlightRegion {
     assemblyName?: string;
@@ -55,7 +61,7 @@ export interface HighlightRegion {
  *   views: [
  *     {
  *       type: 'LinearGenomeView',
- *       colorByCDS: true,
+ *       colorByFrame: true,
  *       assembly: 'hg38',
  *       loc: 'chr1:1,000,000-1,100,000',
  *       tracks: ['genes', 'alignments'],
@@ -65,7 +71,7 @@ export interface HighlightRegion {
  * ```
  * `assembly`, `loc`, `tracks`, `tracklist`, `nav` and `highlight` need
  * on-attach resolution and are captured into the `launch` property below;
- * `colorByCDS`, `showAminoAcids`, `showCenterLine` and `trackLabels` are plain
+ * `colorByFrame`, `showAminoAcids`, `showCenterLine` and `trackLabels` are plain
  * view props MST restores natively. Both are written the same way.
  * At runtime the same model is driven imperatively — every property and action
  * below is reachable on `viewState.session.views[0]`:
@@ -80,7 +86,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-}, "colorByCDS" | "displayedRegions" | "hideHeader" | "hideHeaderOverview" | "hideNoTracksActive" | "id" | "launch" | "legacyBpPerPx" | "scalebarOnly" | "showAminoAcids" | "showCenterLine" | "showCytobands" | "showGridlines" | "showTrackOutlines" | "trackLabels" | "trackSelectorType" | "tracks" | "type" | "windowStartBp" | "windowWidthBp"> & {
+}, "axis" | "colorByFrame" | "displayedRegions" | "hideHeader" | "hideHeaderOverview" | "hideNoTracksActive" | "id" | "launch" | "legacyBpPerPx" | "scalebarOnly" | "showAminoAcids" | "showCenterLine" | "showCytobands" | "showTrackOutlines" | "trackLabels" | "trackSelectorType" | "tracks" | "type" | "windowStartBp" | "windowWidthBp"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
     windowStartBp: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -95,8 +101,14 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     showCenterLine: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showCytobands: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
-    showGridlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    axis: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        readonly grid: {
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>, [undefined]>;
+    colorByFrame: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showAminoAcids: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     scalebarOnly: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -166,6 +178,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #volatile
      */
     coarseBpPerPx: number;
+    /**
+     * #volatile
+     * the scroll offset the coarse blocks were laid out at, in px at
+     * `coarseBpPerPx`: the settled viewport's left edge, which the first
+     * coarse block is not while the view is scrolled before the first region
+     */
+    coarseOffsetPx: number;
     /**
      * #volatile
      */
@@ -184,6 +203,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      */
     volatileGuides: VolatileGuide[];
 } & {
+    /**
+     * #getter
+     * `axis.grid`: whether the ruler's ticks run down through the tracks.
+     */
+    readonly axisGrid: boolean;
     /**
      * #getter
      * the launch state that still has something to apply — the gate every
@@ -857,7 +881,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    setColorByCDS(flag: boolean): void;
+    setColorByFrame(flag: boolean): void;
     /**
      * #action
      */
@@ -916,7 +940,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    setShowGridlines(b: boolean): void;
+    setAxisGrid(grid: boolean): void;
     /**
      * #action
      * set temporary vertical guides (e.g., for LD display hover)
@@ -956,6 +980,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * there and shows the track its index came from
      */
     setSearchResults(searchResults: BaseResult[], searchQuery: string, assemblyName: string, onPick?: (result: BaseResult) => Promise<unknown>): void;
+    /**
+     * #action
+     * Search the view's assembly by name, for a host listing the hits
+     * itself. A row's `pick` lands as the search box does: it navigates
+     * there and shows the track the hit's index came from.
+     */
+    search(query: string, opts?: {
+        signal?: AbortSignal;
+    }): Promise<SearchHits>;
     /**
      * #action
      */
@@ -977,6 +1010,22 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * loaded: loads it, then shows
      */
     launchTrack(trackId: string, initialSnapshot?: any, displayInitialSnapshot?: any, inlineConf?: Record<string, unknown>): Promise<any>;
+    /**
+     * #action
+     * Replace the highlights `highlights` reads, each written as the launch
+     * spec's `highlight` writes one: a locstring, or an object whose
+     * `assemblyName` defaults to the view's. Throws on one that names no
+     * region, writing none.
+     */
+    setHighlights(highlights: readonly (string | HighlightInput)[]): void;
+    /**
+     * #action
+     * Show files from the user's disk as session tracks: one per data file,
+     * beside the index among them that names it, its type guessed from its
+     * name. Adds nothing when one file has no known type. Resolves the new
+     * tracks' ids.
+     */
+    showFiles(files: readonly File[]): Promise<string[]>;
 } & {
     /**
      * #method
@@ -1808,7 +1857,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-}, "colorByCDS" | "displayedRegions" | "hideHeader" | "hideHeaderOverview" | "hideNoTracksActive" | "id" | "launch" | "legacyBpPerPx" | "scalebarOnly" | "showAminoAcids" | "showCenterLine" | "showCytobands" | "showGridlines" | "showTrackOutlines" | "trackLabels" | "trackSelectorType" | "tracks" | "type" | "windowStartBp" | "windowWidthBp"> & {
+}, "axis" | "colorByFrame" | "displayedRegions" | "hideHeader" | "hideHeaderOverview" | "hideNoTracksActive" | "id" | "launch" | "legacyBpPerPx" | "scalebarOnly" | "showAminoAcids" | "showCenterLine" | "showCytobands" | "showTrackOutlines" | "trackLabels" | "trackSelectorType" | "tracks" | "type" | "windowStartBp" | "windowWidthBp"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
     windowStartBp: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -1823,8 +1872,14 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     showCenterLine: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showCytobands: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
-    showGridlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    colorByCDS: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    axis: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        readonly grid: {
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>, [undefined]>;
+    colorByFrame: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showAminoAcids: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showTrackOutlines: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     scalebarOnly: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -1894,6 +1949,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #volatile
      */
     coarseBpPerPx: number;
+    /**
+     * #volatile
+     * the scroll offset the coarse blocks were laid out at, in px at
+     * `coarseBpPerPx`: the settled viewport's left edge, which the first
+     * coarse block is not while the view is scrolled before the first region
+     */
+    coarseOffsetPx: number;
     /**
      * #volatile
      */
@@ -1912,6 +1974,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      */
     volatileGuides: VolatileGuide[];
 } & {
+    /**
+     * #getter
+     * `axis.grid`: whether the ruler's ticks run down through the tracks.
+     */
+    readonly axisGrid: boolean;
     /**
      * #getter
      * the launch state that still has something to apply — the gate every
@@ -2585,7 +2652,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    setColorByCDS(flag: boolean): void;
+    setColorByFrame(flag: boolean): void;
     /**
      * #action
      */
@@ -2644,7 +2711,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    setShowGridlines(b: boolean): void;
+    setAxisGrid(grid: boolean): void;
     /**
      * #action
      * set temporary vertical guides (e.g., for LD display hover)
@@ -2684,6 +2751,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * there and shows the track its index came from
      */
     setSearchResults(searchResults: BaseResult[], searchQuery: string, assemblyName: string, onPick?: (result: BaseResult) => Promise<unknown>): void;
+    /**
+     * #action
+     * Search the view's assembly by name, for a host listing the hits
+     * itself. A row's `pick` lands as the search box does: it navigates
+     * there and shows the track the hit's index came from.
+     */
+    search(query: string, opts?: {
+        signal?: AbortSignal;
+    }): Promise<SearchHits>;
     /**
      * #action
      */
@@ -2705,6 +2781,22 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * loaded: loads it, then shows
      */
     launchTrack(trackId: string, initialSnapshot?: any, displayInitialSnapshot?: any, inlineConf?: Record<string, unknown>): Promise<any>;
+    /**
+     * #action
+     * Replace the highlights `highlights` reads, each written as the launch
+     * spec's `highlight` writes one: a locstring, or an object whose
+     * `assemblyName` defaults to the view's. Throws on one that names no
+     * region, writing none.
+     */
+    setHighlights(highlights: readonly (string | HighlightInput)[]): void;
+    /**
+     * #action
+     * Show files from the user's disk as session tracks: one per data file,
+     * beside the index among them that names it, its type guessed from its
+     * name. Adds nothing when one file has no known type. Resolves the new
+     * tracks' ids.
+     */
+    showFiles(files: readonly File[]): Promise<string[]>;
 } & {
     /**
      * #method
@@ -3532,7 +3624,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
 } & {
     afterCreate(): void;
     afterAttach(): void;
-}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, InitState, "bpPerPx" | "offsetPx" | "showCytobandsSetting">, {
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, InitState, "bpPerPx" | "colorByCDS" | "offsetPx" | "showCytobandsSetting">, {
     displayName: string | undefined;
     minimized: boolean;
     id: string;
@@ -3548,8 +3640,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackSelectorType: "hierarchical";
     showCytobands: boolean;
     trackLabels: string;
-    showGridlines: boolean;
-    colorByCDS: boolean;
+    axis: import("@jbrowse/mobx-state-tree").ModelSnapshotType<Record<string, any>>;
+    colorByFrame: boolean;
     showAminoAcids: boolean;
     showTrackOutlines: boolean;
     scalebarOnly: boolean;

package/esm/LinearGenomeView/model.js

@@ -1,5 +1,5 @@
 import { canonicalLocString } from '@jbrowse/core/TextSearch/places';
-import { getConf } from '@jbrowse/core/configuration';
+import { getConf, readConfObject } from '@jbrowse/core/configuration';
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models';
 import { exportViewSvg } from '@jbrowse/core/svg/exportViewSvg';
 import { assembleLocString, clamp, getBpDisplayStr, getNotificationSink, getSession, isSessionModelWithWidgets, localStorageGetBoolean, localStorageGetItem, localStorageSetBoolean, localStorageSetItem, springAnimate, sum, } from '@jbrowse/core/util';
@@ -8,6 +8,7 @@ import { scaleBandHeights } from '@jbrowse/core/util/bandHeight';
 import { wholeBaseRegions } from '@jbrowse/core/util/blockTypes';
 import calculateDynamicBlocks from '@jbrowse/core/util/calculateDynamicBlocks';
 import calculateStaticBlocks from '@jbrowse/core/util/calculateStaticBlocks';
+import { coerceHighlight } from '@jbrowse/core/util/highlights';
 import { hideTrackGeneric, launchToggleTrackGeneric, launchTrackGeneric, showTrackGeneric, toggleTrackGeneric, } from '@jbrowse/core/util/tracks';
 import { ElementId } from '@jbrowse/core/util/types/mst';
 import { highlightsOnAssemblies } from '@jbrowse/core/util/viewHighlights';
@@ -15,10 +16,11 @@ import { assemblyErrorMessage, computeViewStatus, viewLoading, } from '@jbrowse/
 import { pendingLaunch, withLaunchInput, } from '@jbrowse/core/util/withLaunchInput';
 import { MIN_DISPLAY_HEIGHT } from '@jbrowse/display-kit/const';
 import { contentRightEdgePx } from '@jbrowse/display-kit/regionHost';
-import { cast, getParent, hasParent, isAlive, types, } from '@jbrowse/mobx-state-tree';
+import { cast, getParent, getSnapshot, hasParent, isAlive, types, } from '@jbrowse/mobx-state-tree';
 import { observable, when } from 'mobx';
-import { handleSelectedRegion, isOpenInView, navToOption, } from '../searchUtils.js';
+import { fetchResults, handleSelectedRegion, isOpenInView, navToOption, } from '../searchUtils.js';
 import { doAfterAttach } from './afterAttach.js';
+import { linearGenomeViewAxisConfigSchema } from './axisConfigSchema.js';
 import { getCytobands, shouldSwapTracks } from './components/util.js';
 import { HEADER_BAR_HEIGHT, HEADER_OVERVIEW_HEIGHT, MIN_BP_PER_PX, MINIMIZED_TRACK_HEIGHT, MINIMUM_BLOCK_WIDTH, RESIZE_ALL_HANDLE_HEIGHT, RESIZE_HANDLE_HEIGHT, SCALE_BAR_HEIGHT, SHOW_ALL_REGIONS_FILL, TRACK_OUTLINE_BORDER, TRACK_TOP_GAP, } from './consts.js';
 import { planFlight } from './flyTo.js';
@@ -26,7 +28,43 @@ import { setupKeyboardHandler } from './keyboardHandler.js';
 import { lgvLaunchKeys } from './launchKeys.js';
 import { buildHighlightsSubMenuItems, buildMenuItems, buildRubberBandMenuItems, buildRubberbandClickMenuItems, } from './menuItems.js';
 import { sharedScaleContainerOf } from './sharedScaleContainer.js';
+import { showFiles } from './showFiles.js';
 import { calculateVisibleLocStrings, cytobandLabelGutterWidth, expandRegion, fitAllRegionsWindow, generateLocations, getGridlineTicks, getPaddingSpans, getScalebarLabels, getScalebarRefNameLabels, regionsOrientation, setDisplayedRegionsKeepingCenter, } from './util.js';
+function searchHitsOf(model, results, query, assemblyName, land) {
+    const session = getSession(model);
+    const assembly = session.assemblyManager.get(assemblyName);
+    const ordered = [...results].sort((a, b) => Number(isOpenInView(b, model)) - Number(isOpenInView(a, model)));
+    return {
+        query,
+        assemblyName,
+        rows: ordered.map(result => {
+            const location = result.getLocation() ?? '';
+            const trackId = result.getTrackId();
+            return {
+                id: result.getId(),
+                label: result.getLabel(),
+                location: assembly && location
+                    ? canonicalLocString(location, assembly)
+                    : location,
+                trackName: trackId ? (session.getTrackById(trackId)?.name ?? '') : '',
+            };
+        }),
+        pick: async (id) => {
+            const picked = ordered.find(result => result.getId() === id);
+            try {
+                if (picked) {
+                    await land(picked);
+                }
+            }
+            catch (e) {
+                console.error(e);
+                if (isAlive(model)) {
+                    getNotificationSink(model).notifyError(`${e}`, e);
+                }
+            }
+        },
+    };
+}
 /**
  * Calculate the offsetPx needed to center content within a viewport.
  * Returns a negative offset when content is smaller than viewport (padding on left).
@@ -154,7 +192,7 @@ function isTrackSelectorVisible(self) {
  *   views: [
  *     {
  *       type: 'LinearGenomeView',
- *       colorByCDS: true,
+ *       colorByFrame: true,
  *       assembly: 'hg38',
  *       loc: 'chr1:1,000,000-1,100,000',
  *       tracks: ['genes', 'alignments'],
@@ -164,7 +202,7 @@ function isTrackSelectorVisible(self) {
  * ```
  * `assembly`, `loc`, `tracks`, `tracklist`, `nav` and `highlight` need
  * on-attach resolution and are captured into the `launch` property below;
- * `colorByCDS`, `showAminoAcids`, `showCenterLine` and `trackLabels` are plain
+ * `colorByFrame`, `showAminoAcids`, `showCenterLine` and `trackLabels` are plain
  * view props MST restores natively. Both are written the same way.
  * At runtime the same model is driven imperatively — every property and action
  * below is reachable on `viewState.session.views[0]`:
@@ -267,7 +305,7 @@ export function stateModelFactory(pluginManager) {
         /**
          * #property
          * show the "center line". A personal preference: never in a session
-         * snapshot. It, showCytobands, trackLabels, colorByCDS, showAminoAcids
+         * snapshot. It, showCytobands, trackLabels, colorByFrame, showAminoAcids
          * and showTrackOutlines start from this browser's last choice, which
          * their setters record.
          */
@@ -291,20 +329,21 @@ export function stateModelFactory(pluginManager) {
         trackLabels: types.optional(types.string, () => localStorageGetItem('lgv-trackLabels') ?? ''),
         /**
          * #property
-         * show the "gridlines" in the track area
+         * The ruler's guide, a [](/docs/config/lineargenomeviewaxis) object:
+         * `{ grid: false }` stops its ticks running down through the tracks.
          */
-        showGridlines: types.stripDefault(types.boolean, true),
+        axis: types.stripDefault(linearGenomeViewAxisConfigSchema, {}),
         /**
          * #property
          * color CDS segments by reading frame
          */
-        colorByCDS: types.optional(types.boolean, () => localStorageGetBoolean('lgv-colorByCDS', false)),
+        colorByFrame: types.optional(types.boolean, () => localStorageGetBoolean('lgv-colorByFrame', false)),
         /**
          * #property
          * draw translated codons on coding features once zoomed in far enough:
          * an alternating per-codon shading, and the amino acid letters on top of
-         * it at base-level zoom. Independent of `colorByCDS`, which only recolors
-         * the segments by frame.
+         * it at base-level zoom. Independent of `colorByFrame`, which only
+         * recolors the segments by frame.
          */
         showAminoAcids: types.optional(types.boolean, () => localStorageGetBoolean('lgv-showAminoAcids', true)),
         /**
@@ -386,6 +425,13 @@ export function stateModelFactory(pluginManager) {
             // displays that lay out against it; `setWidth` seeds the true one at
             // the first measure.
             coarseBpPerPx: 1,
+            /**
+             * #volatile
+             * the scroll offset the coarse blocks were laid out at, in px at
+             * `coarseBpPerPx`: the settled viewport's left edge, which the first
+             * coarse block is not while the view is scrolled before the first region
+             */
+            coarseOffsetPx: 0,
             /**
              * #volatile
              */
@@ -406,6 +452,13 @@ export function stateModelFactory(pluginManager) {
         };
     })
         .views(self => ({
+        /**
+         * #getter
+         * `axis.grid`: whether the ruler's ticks run down through the tracks.
+         */
+        get axisGrid() {
+            return readConfObject(self.axis, 'grid');
+        },
         // The viewport in pixels, derived from the window it frames — declared
         // ahead of every other getter so that the ~300 reads of `self.bpPerPx` /
         // `self.offsetPx` across the codebase go on resolving by name. Only the
@@ -1053,9 +1106,9 @@ export function stateModelFactory(pluginManager) {
         /**
          * #action
          */
-        setColorByCDS(flag) {
-            self.colorByCDS = flag;
-            localStorageSetBoolean('lgv-colorByCDS', flag);
+        setColorByFrame(flag) {
+            self.colorByFrame = flag;
+            localStorageSetBoolean('lgv-colorByFrame', flag);
         },
         /**
          * #action
@@ -1130,6 +1183,7 @@ export function stateModelFactory(pluginManager) {
                 // The debounced coarse autorun is 500ms out; a restored snapshot's
                 // consumers would lay out and fetch at 1 bp/px until then.
                 self.coarseBpPerPx = self.bpPerPx;
+                self.coarseOffsetPx = self.offsetPx;
             }
         },
         /**
@@ -1171,8 +1225,8 @@ export function stateModelFactory(pluginManager) {
         /**
          * #action
          */
-        setShowGridlines(b) {
-            self.showGridlines = b;
+        setAxisGrid(grid) {
+            self.axis = cast({ ...getSnapshot(self.axis), grid });
         },
         /**
          * #action
@@ -1255,40 +1309,11 @@ export function stateModelFactory(pluginManager) {
             model: self,
             assemblyName,
         })) {
-            const session = getSession(self);
-            const assembly = session.assemblyManager.get(assemblyName);
-            const ordered = [...searchResults].sort((a, b) => Number(isOpenInView(b, self)) -
-                Number(isOpenInView(a, self)));
+            const hits = searchHitsOf(self, searchResults, searchQuery, assemblyName, onPick);
             const picker = {
-                query: searchQuery,
-                assemblyName,
-                rows: ordered.map(result => {
-                    const location = result.getLocation() ?? '';
-                    const trackId = result.getTrackId();
-                    return {
-                        id: result.getId(),
-                        label: result.getLabel(),
-                        location: assembly && location
-                            ? canonicalLocString(location, assembly)
-                            : location,
-                        trackName: trackId
-                            ? (session.getTrackById(trackId)?.name ?? '')
-                            : '',
-                    };
-                }),
+                ...hits,
                 pick: async (id) => {
-                    const picked = ordered.find(result => result.getId() === id);
-                    try {
-                        if (picked) {
-                            await onPick(picked);
-                        }
-                    }
-                    catch (e) {
-                        console.error(e);
-                        if (isAlive(self)) {
-                            getNotificationSink(self).notifyError(`${e}`, e);
-                        }
-                    }
+                    await hits.pick(id);
                     if (isAlive(self) && self.searchPicker === picker) {
                         self.closeSearchPicker();
                     }
@@ -1296,6 +1321,31 @@ export function stateModelFactory(pluginManager) {
             };
             self.searchPicker = picker;
         },
+        /**
+         * #action
+         * Search the view's assembly by name, for a host listing the hits
+         * itself. A row's `pick` lands as the search box does: it navigates
+         * there and shows the track the hit's index came from.
+         */
+        async search(query, opts) {
+            const assemblyName = self.assemblyNames[0] ?? self.launchAssemblyName;
+            if (!assemblyName) {
+                throw new Error('the view has no assembly to search yet');
+            }
+            const { assemblyManager, textSearchManager } = getSession(self);
+            const results = await fetchResults({
+                queryString: query,
+                assemblyName,
+                textSearchManager,
+                assembly: await assemblyManager.waitForAssembly(assemblyName),
+                signal: opts?.signal,
+            });
+            return searchHitsOf(self, results, query, assemblyName, result => navToOption({
+                option: result,
+                model: self,
+                assemblyName,
+            }));
+        },
         /**
          * #action
          */
@@ -1328,6 +1378,34 @@ export function stateModelFactory(pluginManager) {
         async launchTrack(trackId, initialSnapshot = {}, displayInitialSnapshot = {}, inlineConf) {
             return launchTrackGeneric(self, trackId, initialSnapshot, displayInitialSnapshot, inlineConf);
         },
+        /**
+         * #action
+         * Replace the highlights `highlights` reads, each written as the launch
+         * spec's `highlight` writes one: a locstring, or an object whose
+         * `assemblyName` defaults to the view's. Throws on one that names no
+         * region, writing none.
+         */
+        setHighlights(highlights) {
+            const session = getSession(self);
+            const assemblyName = self.assemblyNames[0] ?? self.launchAssemblyName ?? '';
+            session.setHighlights(highlights.map(h => {
+                const highlight = coerceHighlight(h, assemblyName, (ref, asm) => session.assemblyManager.isValidRefName(ref, asm ?? assemblyName));
+                if (!highlight) {
+                    throw new Error(`not a region to highlight: ${JSON.stringify(h)}`);
+                }
+                return highlight;
+            }));
+        },
+        /**
+         * #action
+         * Show files from the user's disk as session tracks: one per data file,
+         * beside the index among them that names it, its type guessed from its
+         * name. Adds nothing when one file has no known type. Resolves the new
+         * tracks' ids.
+         */
+        async showFiles(files) {
+            return showFiles(self, files);
+        },
     }))
         .views(self => ({
         /**
@@ -2158,6 +2236,9 @@ export function stateModelFactory(pluginManager) {
                 self.coarseTotalBp = blocks.totalBp;
                 self.coarseBpPerPx = bpPerPx;
             }
+            // on every call, since a scroll through the padding before the first
+            // region moves the viewport and leaves the blocks the same
+            self.coarseOffsetPx = self.offsetPx;
         },
     }))
         .actions(self => ({
@@ -2891,12 +2972,14 @@ export function stateModelFactory(pluginManager) {
             return snap;
         }
         // v4's `showCytobandsSetting` persists as the bare `showCytobands` prop
-        // (the capability-gated getter is `effectiveShowCytobands`).
-        const { showCytobandsSetting, offsetPx, bpPerPx, ...rest } = snap;
+        // (the capability-gated getter is `effectiveShowCytobands`), and v4's
+        // `colorByCDS` as `colorByFrame`.
+        const { showCytobandsSetting, colorByCDS, offsetPx, bpPerPx, ...rest } = snap;
         return {
             ...(showCytobandsSetting !== undefined
                 ? { showCytobands: showCytobandsSetting }
                 : {}),
+            ...(colorByCDS !== undefined ? { colorByFrame: colorByCDS } : {}),
             // The viewport used to persist as pixels. Half of that converts
             // exactly and needs no width — the left edge in bp is offsetPx *
             // bpPerPx — and half of it cannot convert at all, because the width

package/esm/LinearGenomeView/rExport/rScript.d.ts

@@ -15,6 +15,18 @@ export interface RExportTrack {
     heightMode?: unknown;
     height?: unknown;
 }
+/**
+ * Each display ggjbrowse reads, by the reader that reads it, and the adapters
+ * it opens (the slot holding the file and the extension the reader knows it
+ * by).
+ */
+export declare const READERS: Record<string, {
+    call: string;
+    adapters: Record<string, {
+        slot?: string;
+        ext?: RegExp;
+    }>;
+}>;
 /** The ggjbrowse release whose readers and `jbrowse_stack` the script calls. */
 export declare const GGJBROWSE_VERSION = "0.10.0";
 /**
@@ -35,6 +47,15 @@ export declare function rValue(value: unknown): string;
  * `file://` URL as its path, or a `localPath`.
  */
 export declare function locationPath(location: unknown): string | undefined;
+/**
+ * Each sequence adapter `jbrowse_assembly()` builds from a path, by the
+ * extension ggjbrowse reads it off, and the index each takes beside it.
+ */
+export declare const SEQUENCE_ADAPTERS: Record<string, {
+    slot: string;
+    ext: RegExp;
+    beside: Record<string, string>;
+}>;
 /**
  * The view's assembly as the R value every reader takes: `jbrowse_assembly()`
  * of its sequence and alias files where ggjbrowse builds the same config from