@jbrowse/plugin-linear-genome-view 2.5.0 → 2.6.1

package/src/LinearGenomeView/components/TrackRenderingContainer.tsx

@@ -0,0 +1,96 @@
+import React, { useEffect, useRef } from 'react'
+import { makeStyles } from 'tss-react/mui'
+import { observer } from 'mobx-react'
+
+// jbrowse core
+import { BaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models'
+import { getConf } from '@jbrowse/core/configuration'
+
+// locals
+import { LinearGenomeViewModel } from '..'
+
+const useStyles = makeStyles()({
+  // aligns with block boundaries. check for example the breakpoint split view
+  // demo to see if features align if wanting to change things
+  renderingComponentContainer: {
+    position: 'absolute',
+    // -1 offset because of the 1px border of the Paper
+    left: -1,
+    height: '100%',
+    width: '100%',
+  },
+
+  trackRenderingContainer: {
+    overflowY: 'auto',
+    overflowX: 'hidden',
+    whiteSpace: 'nowrap',
+    position: 'relative',
+    background: 'none',
+    zIndex: 2,
+  },
+})
+
+type LGV = LinearGenomeViewModel
+
+export default observer(function TrackRenderingContainer({
+  model,
+  track,
+  onDragEnter,
+}: {
+  model: LGV
+  track: BaseTrackModel
+  onDragEnter: () => void
+}) {
+  const { classes } = useStyles()
+  const display = track.displays[0]
+  const { height, RenderingComponent, DisplayBlurb } = display
+  const trackId = getConf(track, 'trackId')
+  const ref = useRef<HTMLDivElement>(null)
+  const minimized = track.minimized
+
+  useEffect(() => {
+    if (ref.current) {
+      model.trackRefs[trackId] = ref.current
+    }
+    return () => {
+      delete model.trackRefs[trackId]
+    }
+  }, [model.trackRefs, trackId])
+
+  return (
+    <div
+      className={classes.trackRenderingContainer}
+      style={{ height: minimized ? 20 : height }}
+      onScroll={evt => display.setScrollTop(evt.currentTarget.scrollTop)}
+      onDragEnter={onDragEnter}
+      data-testid={`trackRenderingContainer-${model.id}-${trackId}`}
+    >
+      {!minimized ? (
+        <>
+          <div
+            ref={ref}
+            className={classes.renderingComponentContainer}
+            style={{ transform: `scaleX(${model.scaleFactor})` }}
+          >
+            <RenderingComponent
+              model={display}
+              onHorizontalScroll={model.horizontalScroll}
+            />
+          </div>
+
+          {DisplayBlurb ? (
+            <div
+              style={{
+                position: 'absolute',
+                left: 0,
+                top: display.height - 20,
+              }}
+            >
+              <DisplayBlurb model={display} />
+            </div>
+          ) : null}
+        </>
+      ) : null}
+    </div>
+  )
+})

package/src/LinearGenomeView/components/TracksContainer.tsx

@@ -53,7 +53,7 @@ export default observer(function TracksContainer({
   } = useRangeSelect(ref, model, true)
   useWheelScroll(ref, model)
 
-  const additionals = pluginManager.evaluateExtensionPoint(
+  const additional = pluginManager.evaluateExtensionPoint(
     'LinearGenomeView-TracksContainerComponent',
     undefined,
     { model },
@@ -107,7 +107,7 @@ export default observer(function TracksContainer({
           />
         }
       />
-      {additionals}
+      {additional}
       {children}
     </div>
   )

package/src/LinearGenomeView/components/__snapshots__/LinearGenomeView.test.tsx.snap

@@ -484,7 +484,7 @@ exports[`renders one track, one region 1`] = `
           </span>
           <button
             aria-haspopup="true"
-            class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeMedium css-15mrns3-MuiButtonBase-root-MuiIconButton-root-iconButton"
+            class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeMedium css-78trlr-MuiButtonBase-root-MuiIconButton-root"
             data-testid="track_menu_icon"
             tabindex="0"
             type="button"
@@ -1303,7 +1303,7 @@ exports[`renders two tracks, two regions 1`] = `
           </span>
           <button
             aria-haspopup="true"
-            class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeMedium css-15mrns3-MuiButtonBase-root-MuiIconButton-root-iconButton"
+            class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeMedium css-78trlr-MuiButtonBase-root-MuiIconButton-root"
             data-testid="track_menu_icon"
             tabindex="0"
             type="button"
@@ -1435,7 +1435,7 @@ exports[`renders two tracks, two regions 1`] = `
           </span>
           <button
             aria-haspopup="true"
-            class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeMedium css-15mrns3-MuiButtonBase-root-MuiIconButton-root-iconButton"
+            class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeMedium css-78trlr-MuiButtonBase-root-MuiIconButton-root"
             data-testid="track_menu_icon"
             tabindex="0"
             type="button"

package/src/LinearGenomeView/model.ts

@@ -3,7 +3,7 @@ import { getConf, AnyConfigurationModel } from '@jbrowse/core/configuration'
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models'
 import { Region } from '@jbrowse/core/util/types'
 import { ElementId, Region as MUIRegion } from '@jbrowse/core/util/types/mst'
-import { MenuItem, ReturnToImportFormDialog } from '@jbrowse/core/ui'
+import { MenuItem } from '@jbrowse/core/ui'
 import {
   assembleLocString,
   clamp,
@@ -51,21 +51,19 @@ import PhotoCameraIcon from '@mui/icons-material/PhotoCamera'
 import ZoomInIcon from '@mui/icons-material/ZoomIn'
 import MenuOpenIcon from '@mui/icons-material/MenuOpen'
 
-// locals
-import { renderToSvg } from './svgcomponents/SVGLinearGenomeView'
-
-import ExportSvgDlg from './components/ExportSvgDialog'
 import MiniControls from './components/MiniControls'
 import Header from './components/Header'
 import { generateLocations, parseLocStrings } from './util'
 
 // lazies
+const ReturnToImportFormDialog = lazy(
+  () => import('@jbrowse/core/ui/ReturnToImportFormDialog'),
+)
 const SequenceSearchDialog = lazy(
   () => import('./components/SequenceSearchDialog'),
 )
-
+const ExportSvgDialog = lazy(() => import('./components/ExportSvgDialog'))
 const GetSequenceDialog = lazy(() => import('./components/GetSequenceDialog'))
-
 const SearchResultsDialog = lazy(
   () => import('./components/SearchResultsDialog'),
 )
@@ -131,6 +129,7 @@ export const WIDGET_HEIGHT = 32
 
 /**
  * #stateModel LinearGenomeView
+ * #category view
  */
 export function stateModelFactory(pluginManager: PluginManager) {
   return types
@@ -250,8 +249,7 @@ export function stateModelFactory(pluginManager: PluginManager) {
       // which is basically like an onLoad
       afterDisplayedRegionsSetCallbacks: [] as Function[],
       scaleFactor: 1,
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      trackRefs: {} as { [key: string]: any },
+      trackRefs: {} as { [key: string]: HTMLDivElement },
       coarseDynamicBlocks: [] as BaseBlock[],
       coarseTotalBp: 0,
       leftOffset: undefined as undefined | BpOffset,
@@ -622,10 +620,8 @@ export function stateModelFactory(pluginManager: PluginManager) {
       ) {
         getSession(self).queueDialog(handleClose => [
           SearchResultsDialog,
-
           {
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            model: self as any,
+            model: self as LinearGenomeViewModel,
             searchResults,
             searchQuery,
             handleClose,
@@ -926,8 +922,10 @@ export function stateModelFactory(pluginManager: PluginManager) {
        * creates an svg export and save using FileSaver
        */
       async exportSvg(opts: ExportSvgOptions = {}) {
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        const html = await renderToSvg(self as any, opts)
+        const { renderToSvg } = await import(
+          './svgcomponents/SVGLinearGenomeView'
+        )
+        const html = await renderToSvg(self as LinearGenomeViewModel, opts)
         const blob = new Blob([html], { type: 'image/svg+xml' })
         saveAs(blob, opts.filename || 'image.svg')
       },
@@ -1056,7 +1054,7 @@ export function stateModelFactory(pluginManager: PluginManager) {
             icon: PhotoCameraIcon,
             onClick: () => {
               getSession(self).queueDialog(handleClose => [
-                ExportSvgDlg,
+                ExportSvgDialog,
                 { model: self, handleClose },
               ])
             },
@@ -1172,10 +1170,10 @@ export function stateModelFactory(pluginManager: PluginManager) {
         /**
          * #getter
          * static blocks are an important concept jbrowse uses to avoid
-         * re-rendering when you scroll to the side. when you horizontally scroll to the
-         * right, old blocks to the left may be removed, and new blocks may be
-         * instantiated on the right. tracks may use the static blocks to render their
-         * data for the region represented by the block
+         * re-rendering when you scroll to the side. when you horizontally
+         * scroll to the right, old blocks to the left may be removed, and new
+         * blocks may be instantiated on the right. tracks may use the static
+         * blocks to render their data for the region represented by the block
          */
         get staticBlocks() {
           const ret = calculateStaticBlocks(self)
@@ -1189,9 +1187,9 @@ export function stateModelFactory(pluginManager: PluginManager) {
         /**
          * #getter
          * dynamic blocks represent the exact coordinates of the currently
-         * visible genome regions on the screen. they are similar to static blocks, but
-         * static blocks can go offscreen while dynamic blocks represent exactly what
-         * is on screen
+         * visible genome regions on the screen. they are similar to static
+         * blocks, but static blocks can go offscreen while dynamic blocks
+         * represent exactly what is on screen
          */
         get dynamicBlocks() {
           return calculateDynamicBlocks(self)
@@ -1213,8 +1211,8 @@ export function stateModelFactory(pluginManager: PluginManager) {
 
         /**
          * #getter
-         * a single "combo-locstring" representing all the regions visible
-         * on the screen
+         * a single "combo-locstring" representing all the regions visible on
+         * the screen
          */
         get visibleLocStrings() {
           return calculateVisibleLocStrings(this.dynamicBlocks.contentBlocks)
@@ -1346,8 +1344,8 @@ export function stateModelFactory(pluginManager: PluginManager) {
        * Navigate to a location based on its refName and optionally start, end,
        * and assemblyName. Will not try to change displayed regions, use
        * `navToLocations` instead. Only navigates to a location if it is
-       * entirely within a displayedRegion. Navigates to the first matching location
-       * encountered.
+       * entirely within a displayedRegion. Navigates to the first matching
+       * location encountered.
        *
        * Throws an error if navigation was unsuccessful
        *
@@ -1378,8 +1376,11 @@ export function stateModelFactory(pluginManager: PluginManager) {
         ) {
           throw new Error('found start greater than end')
         }
-        const f1 = locations[0]
-        const f2 = locations[locations.length - 1]
+        const f1 = locations.at(0)
+        const f2 = locations.at(-1)
+        if (!f1 || !f2) {
+          return
+        }
         const a = self.assemblyNames[0]
         const { assemblyManager } = getSession(self)
         const assembly1 = assemblyManager.get(f1.assemblyName || a)

package/src/LinearGenomeView/svgcomponents/SVGHeader.tsx

@@ -10,15 +10,13 @@ import { Polygon } from '../components/OverviewScalebar'
 import SVGRuler from './SVGRuler'
 import SVGScalebar from './SVGScalebar'
 
-type LGV = LinearGenomeViewModel
-
 export default function SVGHeader({
   model,
   fontSize,
   cytobandHeight,
   rulerHeight,
 }: {
-  model: LGV
+  model: LinearGenomeViewModel
   rulerHeight: number
   fontSize: number
   cytobandHeight: number
@@ -35,19 +33,23 @@ export default function SVGHeader({
     minimumBlockWidth: model.minimumBlockWidth,
   })
   const visibleRegions = model.dynamicBlocks.contentBlocks
+  if (!visibleRegions.length) {
+    return null
+  }
 
   overview.setVolatileWidth(width)
   overview.showAllRegions()
   const block = overview.dynamicBlocks.contentBlocks[0]
-
-  const first = visibleRegions[0]
+  // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+  const first = visibleRegions.at(0)!
+  // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+  const last = visibleRegions.at(-1)!
   const firstOverviewPx =
     overview.bpToPx({
       ...first,
       coord: first.reversed ? first.end : first.start,
     }) || 0
 
-  const last = visibleRegions[visibleRegions.length - 1]
   const lastOverviewPx =
     overview.bpToPx({
       ...last,

package/src/LinearGenomeView/svgcomponents/SVGLinearGenomeView.tsx

@@ -59,7 +59,7 @@ export async function renderToSvg(model: LGV, opts: ExportSvgOptions) {
   const displayResults = await Promise.all(
     tracks.map(async track => {
       const display = track.displays[0]
-      await when(() => (display.ready !== undefined ? display.ready : true))
+      await when(() => !display.renderProps().notReady)
       return { track, result: await display.renderSvg({ ...opts, theme }) }
     }),
   )

package/src/index.ts

@@ -19,7 +19,6 @@ import LinearGenomeViewF, {
 } from './LinearGenomeView'
 
 import LinearBasicDisplayF from './LinearBasicDisplay'
-
 import FeatureTrackF from './FeatureTrack'
 import BasicTrackF from './BasicTrack'
 import LaunchLinearGenomeViewF from './LaunchLinearGenomeView'
@@ -58,19 +57,26 @@ export default class LinearGenomeViewPlugin extends Plugin {
   }
 }
 
-export type { BaseLinearDisplayModel, BlockModel } from './BaseLinearDisplay'
+export type {
+  ExportSvgDisplayOptions,
+  BaseLinearDisplayModel,
+  BlockModel,
+} from './BaseLinearDisplay'
 
 export { configSchemaFactory as linearBareDisplayConfigSchemaFactory } from './LinearBareDisplay'
 export {
-  BlockMsg,
   baseLinearDisplayConfigSchema,
-  BaseLinearDisplayComponent,
   BaseLinearDisplay,
+  BlockMsg,
+  BaseLinearDisplayComponent,
+  TrackHeightMixin,
+  FeatureDensityMixin,
+  TooLargeMessage,
 } from './BaseLinearDisplay'
 export {
   type LinearGenomeViewModel,
-  RefNameAutocomplete,
   type LinearGenomeViewStateModel,
+  RefNameAutocomplete,
   SearchBox,
 } from './LinearGenomeView'
 export {

package/dist/LinearGenomeView/components/HelpDialog.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"HelpDialog.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/HelpDialog.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,4CAA6E;AAC7E,yCAAyC;AAEzC,SAAwB,UAAU,CAAC,EACjC,WAAW,GAGZ;IACC,OAAO,CACL,8BAAC,WAAM,IACL,IAAI,QACJ,QAAQ,EAAC,IAAI,EACb,OAAO,EAAE,WAAW,EACpB,KAAK,EAAC,sBAAsB;QAE5B,8BAAC,wBAAa;YACZ,sDAAkB;YAClB;gBACE,+IAGK;gBACL;;oBAEM,6DAA2B;;oBAAI,4DAA0B;wKAI1D,CACF;YACL,6DAAyB;YACzB;gBACE;oBACE,mDAAiB;6DACd;gBACL;oBACE,mDAAiB;+CACd;gBACL;oBACE,0EAAwC;mFAErC;gBACL;oBACE,oEAAkC;0EAE/B;gBACL;oBACE,6DAA2B;8DACxB;gBACL;oBACE,yEAAuC;0FAEpC;gBACL;oBACE,2DAAyB;sEAEtB,CACF,CACS;QAChB,8BAAC,kBAAO,OAAG;QACX,8BAAC,wBAAa;YACZ,8BAAC,iBAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAAE,KAAK,EAAC,SAAS,YAE5C,CACK,CACT,CACV,CAAA;AACH,CAAC;AAhED,6BAgEC"}

package/dist/LinearGenomeView/components/RefNameAutocomplete.d.ts

@@ -1,23 +0,0 @@
-import React from 'react';
-import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
-import { TextFieldProps as TFP } from '@mui/material';
-import { LinearGenomeViewModel } from '..';
-export interface Option {
-    group?: string;
-    result: BaseResult;
-}
-declare function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResults, onChange, value, showHelp, minWidth, maxWidth, TextFieldProps, }: {
-    model: LinearGenomeViewModel;
-    onSelect?: (region: BaseResult) => void;
-    onChange?: (val: string) => void;
-    assemblyName?: string;
-    value?: string;
-    fetchResults: (query: string) => Promise<BaseResult[]>;
-    style?: React.CSSProperties;
-    minWidth?: number;
-    maxWidth?: number;
-    showHelp?: boolean;
-    TextFieldProps?: TFP;
-}): JSX.Element;
-declare const _default: typeof RefNameAutocomplete;
-export default _default;

package/dist/LinearGenomeView/components/RefNameAutocomplete.js

@@ -1,189 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const util_1 = require("@jbrowse/core/util");
-const BaseResults_1 = __importStar(require("@jbrowse/core/TextSearch/BaseResults"));
-const material_1 = require("@mui/material");
-// icons
-const Search_1 = __importDefault(require("@mui/icons-material/Search"));
-const Help_1 = __importDefault(require("@mui/icons-material/Help"));
-// lazy
-const HelpDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./HelpDialog'))));
-function aggregateResults(results) {
-    const m = {};
-    for (const result of results) {
-        const displayString = result.getDisplayString();
-        if (!m[displayString]) {
-            m[displayString] = [];
-        }
-        m[displayString].push(result);
-    }
-    return m;
-}
-function getDeduplicatedResult(results) {
-    return Object.entries(aggregateResults(results)).map(([displayString, results]) => results.length === 1
-        ? {
-            result: results[0],
-        }
-        : {
-            // deduplicate a "multi-result"
-            result: new BaseResults_1.default({
-                displayString,
-                results,
-                label: displayString,
-            }),
-        });
-}
-// the logic of this method is to only apply a filter to RefSequenceResults
-// because they do not have a matchedObject. the trix search results already
-// filter so don't need re-filtering
-function filterOptions(options, searchQuery) {
-    return options.filter(({ result }) => result.getLabel().toLowerCase().includes(searchQuery) ||
-        result.matchedObject);
-}
-function getFiltered(opts, inputValue) {
-    const filtered = filterOptions(opts, inputValue.toLocaleLowerCase());
-    return [
-        ...filtered.slice(0, 100),
-        ...(filtered.length > 100
-            ? [
-                {
-                    group: 'limitOption',
-                    result: new BaseResults_1.default({
-                        label: 'keep typing for more results',
-                    }),
-                },
-            ]
-            : []),
-    ];
-}
-function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResults, onChange, value, showHelp = true, minWidth = 200, maxWidth = 550, TextFieldProps = {}, }) {
-    const session = (0, util_1.getSession)(model);
-    const { assemblyManager } = session;
-    const [open, setOpen] = (0, react_1.useState)(false);
-    const [loaded, setLoaded] = (0, react_1.useState)(true);
-    const [currentSearch, setCurrentSearch] = (0, react_1.useState)('');
-    const [inputValue, setInputValue] = (0, react_1.useState)('');
-    const [searchOptions, setSearchOptions] = (0, react_1.useState)();
-    const debouncedSearch = (0, util_1.useDebounce)(currentSearch, 300);
-    const assembly = assemblyName ? assemblyManager.get(assemblyName) : undefined;
-    const { coarseVisibleLocStrings, hasDisplayedRegions } = model;
-    const regions = assembly === null || assembly === void 0 ? void 0 : assembly.regions;
-    const options = (0, react_1.useMemo)(() => (regions === null || regions === void 0 ? void 0 : regions.map(option => ({
-        result: new BaseResults_1.RefSequenceResult({
-            refName: option.refName,
-            label: option.refName,
-            matchedAttribute: 'refName',
-        }),
-    }))) || [], [regions]);
-    (0, react_1.useEffect)(() => {
-        let active = true;
-        (async () => {
-            try {
-                if (debouncedSearch === '' || !assemblyName) {
-                    return;
-                }
-                setLoaded(false);
-                const results = await fetchResults(debouncedSearch);
-                if (active) {
-                    setLoaded(true);
-                    setSearchOptions(getDeduplicatedResult(results));
-                }
-            }
-            catch (e) {
-                console.error(e);
-                if (active) {
-                    session.notify(`${e}`, 'error');
-                }
-            }
-        })();
-        return () => {
-            active = false;
-        };
-    }, [assemblyName, fetchResults, debouncedSearch, session, model]);
-    const inputBoxVal = coarseVisibleLocStrings || value || '';
-    // heuristic, text width + 60 accommodates help icon and search
-    // icon
-    const width = Math.min(Math.max((0, util_1.measureText)(inputBoxVal, 14) + 100, minWidth), maxWidth);
-    // notes on implementation:
-    // The selectOnFocus setting helps highlight the field when clicked
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(material_1.Autocomplete, { "data-testid": "autocomplete", disableListWrap: true, disableClearable: true, disabled: !assemblyName, freeSolo: true, includeInputInList: true, selectOnFocus: true, style: { ...style, width }, value: inputBoxVal, loading: !loaded, inputValue: inputValue, onInputChange: (_event, newInputValue) => {
-                setInputValue(newInputValue);
-                onChange === null || onChange === void 0 ? void 0 : onChange(newInputValue);
-            }, loadingText: "loading results", open: open, onOpen: () => setOpen(true), onClose: () => {
-                setOpen(false);
-                setLoaded(true);
-                if (hasDisplayedRegions) {
-                    setCurrentSearch('');
-                    setSearchOptions(undefined);
-                }
-            }, onChange: (_event, selectedOption) => {
-                if (!selectedOption || !assemblyName) {
-                    return;
-                }
-                if (typeof selectedOption === 'string') {
-                    // handles string inputs on keyPress enter
-                    onSelect === null || onSelect === void 0 ? void 0 : onSelect(new BaseResults_1.default({ label: selectedOption }));
-                }
-                else {
-                    onSelect === null || onSelect === void 0 ? void 0 : onSelect(selectedOption.result);
-                }
-                setInputValue(inputBoxVal);
-            }, options: !(searchOptions === null || searchOptions === void 0 ? void 0 : searchOptions.length) ? options : searchOptions, getOptionDisabled: option => option.group === 'limitOption', filterOptions: (opts, { inputValue }) => getFiltered(opts, inputValue), renderInput: params => (react_1.default.createElement(AutocompleteTextField, { showHelp: showHelp, params: params, inputBoxVal: inputBoxVal, TextFieldProps: TextFieldProps, setCurrentSearch: setCurrentSearch, setInputValue: setInputValue })), getOptionLabel: opt => typeof opt === 'string' ? opt : opt.result.getDisplayString() })));
-}
-function AutocompleteTextField({ TextFieldProps, inputBoxVal, params, showHelp, setInputValue, setCurrentSearch, }) {
-    const { helperText, InputProps = {} } = TextFieldProps;
-    return (react_1.default.createElement(material_1.TextField, { onBlur: () => 
-        // this is used to restore a refName or the non-user-typed input
-        // to the box on blurring
-        setInputValue(inputBoxVal), ...params, ...TextFieldProps, size: "small", helperText: helperText, InputProps: {
-            ...params.InputProps,
-            ...InputProps,
-            endAdornment: (react_1.default.createElement(EndAdornment, { showHelp: showHelp, endAdornment: params.InputProps.endAdornment })),
-        }, placeholder: "Search for location", onChange: e => setCurrentSearch(e.target.value) }));
-}
-function HelpAdornment() {
-    const [isHelpDialogDisplayed, setHelpDialogDisplayed] = (0, react_1.useState)(false);
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(material_1.IconButton, { onClick: () => setHelpDialogDisplayed(true), size: "small" },
-            react_1.default.createElement(Help_1.default, { fontSize: "small" })),
-        isHelpDialogDisplayed ? (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
-            react_1.default.createElement(HelpDialog, { handleClose: () => setHelpDialogDisplayed(false) }))) : null));
-}
-function EndAdornment({ showHelp, endAdornment, }) {
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(material_1.InputAdornment, { position: "end", style: { marginRight: 7 } },
-            react_1.default.createElement(Search_1.default, { fontSize: "small" }),
-            showHelp ? react_1.default.createElement(HelpAdornment, null) : null),
-        endAdornment));
-}
-exports.default = (0, mobx_react_1.observer)(RefNameAutocomplete);
-//# sourceMappingURL=RefNameAutocomplete.js.map

package/dist/LinearGenomeView/components/RefNameAutocomplete.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"RefNameAutocomplete.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/RefNameAutocomplete.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAA2E;AAC3E,2CAAqC;AACrC,6CAAyE;AACzE,oFAE6C;AAC7C,4CAOsB;AAEtB,QAAQ;AACR,wEAAmD;AACnD,oEAA+C;AAK/C,OAAO;AACP,MAAM,UAAU,GAAG,IAAA,YAAI,EAAC,GAAG,EAAE,mDAAQ,cAAc,GAAC,CAAC,CAAA;AAOrD,SAAS,gBAAgB,CAAC,OAAqB;IAC7C,MAAM,CAAC,GAAoC,EAAE,CAAA;IAE7C,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;QAC5B,MAAM,aAAa,GAAG,MAAM,CAAC,gBAAgB,EAAE,CAAA;QAC/C,IAAI,CAAC,CAAC,CAAC,aAAa,CAAC,EAAE;YACrB,CAAC,CAAC,aAAa,CAAC,GAAG,EAAE,CAAA;SACtB;QACD,CAAC,CAAC,aAAa,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;KAC9B;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AAED,SAAS,qBAAqB,CAAC,OAAqB;IAClD,OAAO,MAAM,CAAC,OAAO,CAAC,gBAAgB,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAClD,CAAC,CAAC,aAAa,EAAE,OAAO,CAAC,EAAE,EAAE,CAC3B,OAAO,CAAC,MAAM,KAAK,CAAC;QAClB,CAAC,CAAC;YACE,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC;SACnB;QACH,CAAC,CAAC;YACE,+BAA+B;YAC/B,MAAM,EAAE,IAAI,qBAAU,CAAC;gBACrB,aAAa;gBACb,OAAO;gBACP,KAAK,EAAE,aAAa;aACrB,CAAC;SACH,CACR,CAAA;AACH,CAAC;AAED,2EAA2E;AAC3E,4EAA4E;AAC5E,oCAAoC;AACpC,SAAS,aAAa,CAAC,OAAiB,EAAE,WAAmB;IAC3D,OAAO,OAAO,CAAC,MAAM,CACnB,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE,CACb,MAAM,CAAC,QAAQ,EAAE,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;QACrD,MAAM,CAAC,aAAa,CACvB,CAAA;AACH,CAAC;AAED,SAAS,WAAW,CAAC,IAAc,EAAE,UAAkB;IACrD,MAAM,QAAQ,GAAG,aAAa,CAAC,IAAI,EAAE,UAAU,CAAC,iBAAiB,EAAE,CAAC,CAAA;IACpE,OAAO;QACL,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC;QACzB,GAAG,CAAC,QAAQ,CAAC,MAAM,GAAG,GAAG;YACvB,CAAC,CAAC;gBACE;oBACE,KAAK,EAAE,aAAa;oBACpB,MAAM,EAAE,IAAI,qBAAU,CAAC;wBACrB,KAAK,EAAE,8BAA8B;qBACtC,CAAC;iBACH;aACF;YACH,CAAC,CAAC,EAAE,CAAC;KACR,CAAA;AACH,CAAC;AAED,SAAS,mBAAmB,CAAC,EAC3B,KAAK,EACL,QAAQ,EACR,YAAY,EACZ,KAAK,EACL,YAAY,EACZ,QAAQ,EACR,KAAK,EACL,QAAQ,GAAG,IAAI,EACf,QAAQ,GAAG,GAAG,EACd,QAAQ,GAAG,GAAG,EACd,cAAc,GAAG,EAAE,GAapB;IACC,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IACjC,MAAM,EAAE,eAAe,EAAE,GAAG,OAAO,CAAA;IACnC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IACvC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAQ,EAAC,IAAI,CAAC,CAAA;IAC1C,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,IAAA,gBAAQ,EAAC,EAAE,CAAC,CAAA;IACtD,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,IAAA,gBAAQ,EAAC,EAAE,CAAC,CAAA;IAChD,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,IAAA,gBAAQ,GAAY,CAAA;IAC9D,MAAM,eAAe,GAAG,IAAA,kBAAW,EAAC,aAAa,EAAE,GAAG,CAAC,CAAA;IACvD,MAAM,QAAQ,GAAG,YAAY,CAAC,CAAC,CAAC,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IAC7E,MAAM,EAAE,uBAAuB,EAAE,mBAAmB,EAAE,GAAG,KAAK,CAAA;IAE9D,MAAM,OAAO,GAAG,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,OAAO,CAAA;IAEjC,MAAM,OAAO,GAAG,IAAA,eAAO,EACrB,GAAG,EAAE,CACH,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;QACtB,MAAM,EAAE,IAAI,+BAAiB,CAAC;YAC5B,OAAO,EAAE,MAAM,CAAC,OAAO;YACvB,KAAK,EAAE,MAAM,CAAC,OAAO;YACrB,gBAAgB,EAAE,SAAS;SAC5B,CAAC;KACH,CAAC,CAAC,KAAI,EAAE,EACX,CAAC,OAAO,CAAC,CACV,CAAA;IAED,IAAA,iBAAS,EAAC,GAAG,EAAE;QACb,IAAI,MAAM,GAAG,IAAI,CAGhB;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI;gBACF,IAAI,eAAe,KAAK,EAAE,IAAI,CAAC,YAAY,EAAE;oBAC3C,OAAM;iBACP;gBAED,SAAS,CAAC,KAAK,CAAC,CAAA;gBAChB,MAAM,OAAO,GAAG,MAAM,YAAY,CAAC,eAAe,CAAC,CAAA;gBACnD,IAAI,MAAM,EAAE;oBACV,SAAS,CAAC,IAAI,CAAC,CAAA;oBACf,gBAAgB,CAAC,qBAAqB,CAAC,OAAO,CAAC,CAAC,CAAA;iBACjD;aACF;YAAC,OAAO,CAAC,EAAE;gBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBAChB,IAAI,MAAM,EAAE;oBACV,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,EAAE,OAAO,CAAC,CAAA;iBAChC;aACF;QACH,CAAC,CAAC,EAAE,CAAA;QAEJ,OAAO,GAAG,EAAE;YACV,MAAM,GAAG,KAAK,CAAA;QAChB,CAAC,CAAA;IACH,CAAC,EAAE,CAAC,YAAY,EAAE,YAAY,EAAE,eAAe,EAAE,OAAO,EAAE,KAAK,CAAC,CAAC,CAAA;IAEjE,MAAM,WAAW,GAAG,uBAAuB,IAAI,KAAK,IAAI,EAAE,CAAA;IAE1D,+DAA+D;IAC/D,OAAO;IACP,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CACpB,IAAI,CAAC,GAAG,CAAC,IAAA,kBAAW,EAAC,WAAW,EAAE,EAAE,CAAC,GAAG,GAAG,EAAE,QAAQ,CAAC,EACtD,QAAQ,CACT,CAAA;IAED,2BAA2B;IAC3B,mEAAmE;IACnE,OAAO,CACL;QACE,8BAAC,uBAAY,mBACC,cAAc,EAC1B,eAAe,QACf,gBAAgB,QAChB,QAAQ,EAAE,CAAC,YAAY,EACvB,QAAQ,QACR,kBAAkB,QAClB,aAAa,QACb,KAAK,EAAE,EAAE,GAAG,KAAK,EAAE,KAAK,EAAE,EAC1B,KAAK,EAAE,WAAW,EAClB,OAAO,EAAE,CAAC,MAAM,EAChB,UAAU,EAAE,UAAU,EACtB,aAAa,EAAE,CAAC,MAAM,EAAE,aAAa,EAAE,EAAE;gBACvC,aAAa,CAAC,aAAa,CAAC,CAAA;gBAC5B,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAG,aAAa,CAAC,CAAA;YAC3B,CAAC,EACD,WAAW,EAAC,iBAAiB,EAC7B,IAAI,EAAE,IAAI,EACV,MAAM,EAAE,GAAG,EAAE,CAAC,OAAO,CAAC,IAAI,CAAC,EAC3B,OAAO,EAAE,GAAG,EAAE;gBACZ,OAAO,CAAC,KAAK,CAAC,CAAA;gBACd,SAAS,CAAC,IAAI,CAAC,CAAA;gBACf,IAAI,mBAAmB,EAAE;oBACvB,gBAAgB,CAAC,EAAE,CAAC,CAAA;oBACpB,gBAAgB,CAAC,SAAS,CAAC,CAAA;iBAC5B;YACH,CAAC,EACD,QAAQ,EAAE,CAAC,MAAM,EAAE,cAAc,EAAE,EAAE;gBACnC,IAAI,CAAC,cAAc,IAAI,CAAC,YAAY,EAAE;oBACpC,OAAM;iBACP;gBAED,IAAI,OAAO,cAAc,KAAK,QAAQ,EAAE;oBACtC,0CAA0C;oBAC1C,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAG,IAAI,qBAAU,CAAC,EAAE,KAAK,EAAE,cAAc,EAAE,CAAC,CAAC,CAAA;iBACtD;qBAAM;oBACL,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAG,cAAc,CAAC,MAAM,CAAC,CAAA;iBAClC;gBACD,aAAa,CAAC,WAAW,CAAC,CAAA;YAC5B,CAAC,EACD,OAAO,EAAE,CAAC,CAAA,aAAa,aAAb,aAAa,uBAAb,aAAa,CAAE,MAAM,CAAA,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,aAAa,EACzD,iBAAiB,EAAE,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,KAAK,aAAa,EAC3D,aAAa,EAAE,CAAC,IAAI,EAAE,EAAE,UAAU,EAAE,EAAE,EAAE,CAAC,WAAW,CAAC,IAAI,EAAE,UAAU,CAAC,EACtE,WAAW,EAAE,MAAM,CAAC,EAAE,CAAC,CACrB,8BAAC,qBAAqB,IACpB,QAAQ,EAAE,QAAQ,EAClB,MAAM,EAAE,MAAM,EACd,WAAW,EAAE,WAAW,EACxB,cAAc,EAAE,cAAc,EAC9B,gBAAgB,EAAE,gBAAgB,EAClC,aAAa,EAAE,aAAa,GAC5B,CACH,EACD,cAAc,EAAE,GAAG,CAAC,EAAE,CACpB,OAAO,GAAG,KAAK,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,gBAAgB,EAAE,GAE/D,CACD,CACJ,CAAA;AACH,CAAC;AAED,SAAS,qBAAqB,CAAC,EAC7B,cAAc,EACd,WAAW,EACX,MAAM,EACN,QAAQ,EACR,aAAa,EACb,gBAAgB,GAQjB;IACC,MAAM,EAAE,UAAU,EAAE,UAAU,GAAG,EAAE,EAAE,GAAG,cAAc,CAAA;IACtD,OAAO,CACL,8BAAC,oBAAS,IACR,MAAM,EAAE,GAAG,EAAE;QACX,gEAAgE;QAChE,yBAAyB;QACzB,aAAa,CAAC,WAAW,CAAC,KAExB,MAAM,KACN,cAAc,EAClB,IAAI,EAAC,OAAO,EACZ,UAAU,EAAE,UAAU,EACtB,UAAU,EAAE;YACV,GAAG,MAAM,CAAC,UAAU;YACpB,GAAG,UAAU;YAEb,YAAY,EAAE,CACZ,8BAAC,YAAY,IACX,QAAQ,EAAE,QAAQ,EAClB,YAAY,EAAE,MAAM,CAAC,UAAU,CAAC,YAAY,GAC5C,CACH;SACF,EACD,WAAW,EAAC,qBAAqB,EACjC,QAAQ,EAAE,CAAC,CAAC,EAAE,CAAC,gBAAgB,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,GAC/C,CACH,CAAA;AACH,CAAC;AAED,SAAS,aAAa;IACpB,MAAM,CAAC,qBAAqB,EAAE,sBAAsB,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IACvE,OAAO,CACL;QACE,8BAAC,qBAAU,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,sBAAsB,CAAC,IAAI,CAAC,EAAE,IAAI,EAAC,OAAO;YACnE,8BAAC,cAAQ,IAAC,QAAQ,EAAC,OAAO,GAAG,CAClB;QACZ,qBAAqB,CAAC,CAAC,CAAC,CACvB,8BAAC,gBAAQ,IAAC,QAAQ,EAAE,0CAAO;YACzB,8BAAC,UAAU,IAAC,WAAW,EAAE,GAAG,EAAE,CAAC,sBAAsB,CAAC,KAAK,CAAC,GAAI,CACvD,CACZ,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC;AAED,SAAS,YAAY,CAAC,EACpB,QAAQ,EACR,YAAY,GAIb;IACC,OAAO,CACL;QACE,8BAAC,yBAAc,IAAC,QAAQ,EAAC,KAAK,EAAC,KAAK,EAAE,EAAE,WAAW,EAAE,CAAC,EAAE;YACtD,8BAAC,gBAAU,IAAC,QAAQ,EAAC,OAAO,GAAG;YAC9B,QAAQ,CAAC,CAAC,CAAC,8BAAC,aAAa,OAAG,CAAC,CAAC,CAAC,IAAI,CACrB;QAChB,YAAY,CACZ,CACJ,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,mBAAmB,CAAC,CAAA"}

package/esm/LinearGenomeView/components/HelpDialog.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"HelpDialog.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/HelpDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;AAC7E,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AAEzC,MAAM,CAAC,OAAO,UAAU,UAAU,CAAC,EACjC,WAAW,GAGZ;IACC,OAAO,CACL,oBAAC,MAAM,IACL,IAAI,QACJ,QAAQ,EAAC,IAAI,EACb,OAAO,EAAE,WAAW,EACpB,KAAK,EAAC,sBAAsB;QAE5B,oBAAC,aAAa;YACZ,4CAAkB;YAClB;gBACE,qIAGK;gBACL;;oBAEM,mDAA2B;;oBAAI,kDAA0B;wKAI1D,CACF;YACL,mDAAyB;YACzB;gBACE;oBACE,yCAAiB;6DACd;gBACL;oBACE,yCAAiB;+CACd;gBACL;oBACE,gEAAwC;mFAErC;gBACL;oBACE,0DAAkC;0EAE/B;gBACL;oBACE,mDAA2B;8DACxB;gBACL;oBACE,+DAAuC;0FAEpC;gBACL;oBACE,iDAAyB;sEAEtB,CACF,CACS;QAChB,oBAAC,OAAO,OAAG;QACX,oBAAC,aAAa;YACZ,oBAAC,MAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAAE,KAAK,EAAC,SAAS,YAE5C,CACK,CACT,CACV,CAAA;AACH,CAAC"}

package/esm/LinearGenomeView/components/RefNameAutocomplete.d.ts

@@ -1,23 +0,0 @@
-import React from 'react';
-import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
-import { TextFieldProps as TFP } from '@mui/material';
-import { LinearGenomeViewModel } from '..';
-export interface Option {
-    group?: string;
-    result: BaseResult;
-}
-declare function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResults, onChange, value, showHelp, minWidth, maxWidth, TextFieldProps, }: {
-    model: LinearGenomeViewModel;
-    onSelect?: (region: BaseResult) => void;
-    onChange?: (val: string) => void;
-    assemblyName?: string;
-    value?: string;
-    fetchResults: (query: string) => Promise<BaseResult[]>;
-    style?: React.CSSProperties;
-    minWidth?: number;
-    maxWidth?: number;
-    showHelp?: boolean;
-    TextFieldProps?: TFP;
-}): JSX.Element;
-declare const _default: typeof RefNameAutocomplete;
-export default _default;