@jbrowse/core 2.4.1 → 2.5.0

package/util/io/index.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.RemoteFileWithRangeCache = exports.getFetcher = exports.openLocation = void 0;
+exports.RemoteFileWithRangeCache = exports.getFetcher = exports.openLocation = exports.resolveUriLocation = void 0;
 const generic_filehandle_1 = require("generic-filehandle");
 const detect_node_1 = __importDefault(require("detect-node"));
 // locals
@@ -17,6 +17,13 @@ function isLocalPathLocation(location) {
 function isBlobLocation(location) {
     return 'blobId' in location;
 }
+/** if a UriLocation has a baseUri, resolves its uri with respect to that base */
+function resolveUriLocation(location) {
+    return location.baseUri
+        ? { ...location, uri: new URL(location.uri, location.baseUri).href }
+        : location;
+}
+exports.resolveUriLocation = resolveUriLocation;
 function openLocation(location, pluginManager) {
     if (!location) {
         throw new Error('must provide a location to openLocation');
@@ -46,9 +53,7 @@ function openLocation(location, pluginManager) {
             throw new Error('No URI provided');
         }
         // Resolve any relative URLs to absolute URLs
-        const absoluteLocation = location.baseUri
-            ? { ...location, uri: new URL(location.uri, location.baseUri).href }
-            : location;
+        const absoluteLocation = resolveUriLocation(location);
         // If there is a plugin manager, we can try internet accounts
         if (pluginManager) {
             const internetAccount = getInternetAccount(location, pluginManager);

package/util/layouts/PrecomputedMultiLayout.d.ts

@@ -1,4 +1,4 @@
 export default class PrecomputedMultiLayout extends MultiLayout<any, any> {
     constructor(json: any);
 }
-import MultiLayout from "./MultiLayout";
+import MultiLayout from './MultiLayout';

package/util/mst-reflection.d.ts

@@ -1,29 +1,24 @@
+import { IAnyType, IModelReflectionPropertiesData, IAnyComplexType, ISimpleType, UnionStringArray } from 'mobx-state-tree';
+export interface ILiteralType<T> extends ISimpleType<T> {
+    value: T;
+}
 /**
  * get the inner type of an MST optional, array, or late type object
- *
- * @param {IModelType} type
- * @returns {IModelType}
  */
-export function getSubType(type: IModelType): IModelType;
+export declare function getSubType(type: IAnyType): IAnyType;
 /**
- * get the array of
- * @param {MST Union Type obj} unionType
- * @returns {Array<IModelType>}
+ * get the array of the subtypes in a union
  */
-export function getUnionSubTypes(unionType: any): Array<IModelType>;
+export declare function getUnionSubTypes(unionType: IAnyType): IAnyType[];
 /**
  * get the type of one of the properties of the given MST model type
- *
- * @param {IModelType} type
- * @param {string} propertyName
- * @returns {IModelType}
  */
-export function getPropertyType(type: IModelType, propertyName: string): IModelType;
+export declare function getPropertyType(type: IModelReflectionPropertiesData, propertyName: string): IAnyType;
 /**
  * get the base type from inside an MST optional type
- * @param {*} type
  */
-export function getDefaultValue(type: any): any;
+export declare function getDefaultValue(type: IAnyType): any;
+export type IEnumerationType<T extends string> = ISimpleType<UnionStringArray<T[]>>;
 /** get the string values of an MST enumeration type */
-export function getEnumerationValues(type: any): any[];
-export function resolveLateType(maybeLate: any): any;
+export declare function getEnumerationValues(type: IAnyComplexType): string[];
+export declare function resolveLateType(maybeLate: IAnyType): any;

package/util/mst-reflection.js

@@ -5,19 +5,20 @@ exports.resolveLateType = exports.getEnumerationValues = exports.getDefaultValue
 const mobx_state_tree_1 = require("mobx-state-tree");
 /**
  * get the inner type of an MST optional, array, or late type object
- *
- * @param {IModelType} type
- * @returns {IModelType}
  */
 function getSubType(type) {
     let t;
     if ((0, mobx_state_tree_1.isOptionalType)(type)) {
+        // @ts-expect-error
         t = type._subtype || type.type;
     }
     else if ((0, mobx_state_tree_1.isArrayType)(type) || (0, mobx_state_tree_1.isMapType)(type)) {
+        // @ts-expect-error
         t = type._subtype || type._subType || type.subType;
+        // @ts-expect-error
     }
     else if (typeof type.getSubType === 'function') {
+        // @ts-expect-error
         return type.getSubType();
     }
     else {
@@ -31,17 +32,20 @@ function getSubType(type) {
 }
 exports.getSubType = getSubType;
 /**
- * get the array of
- * @param {MST Union Type obj} unionType
- * @returns {Array<IModelType>}
+ * get the array of the subtypes in a union
  */
 function getUnionSubTypes(unionType) {
     if (!(0, mobx_state_tree_1.isUnionType)(unionType)) {
         throw new TypeError('not an MST union type');
     }
-    const t = unionType._types ||
+    const t = 
+    // @ts-expect-error
+    unionType._types ||
+        // @ts-expect-error
         unionType.types ||
+        // @ts-expect-error
         getSubType(unionType)._types ||
+        // @ts-expect-error
         getSubType(unionType).types;
     if (!t) {
         // debugger
@@ -52,10 +56,6 @@ function getUnionSubTypes(unionType) {
 exports.getUnionSubTypes = getUnionSubTypes;
 /**
  * get the type of one of the properties of the given MST model type
- *
- * @param {IModelType} type
- * @param {string} propertyName
- * @returns {IModelType}
  */
 function getPropertyType(type, propertyName) {
     const propertyType = type.properties[propertyName];
@@ -64,12 +64,12 @@ function getPropertyType(type, propertyName) {
 exports.getPropertyType = getPropertyType;
 /**
  * get the base type from inside an MST optional type
- * @param {*} type
  */
 function getDefaultValue(type) {
     if (!(0, mobx_state_tree_1.isOptionalType)(type)) {
         throw new TypeError('type must be an optional type');
     }
+    // @ts-expect-error
     return type._defaultValue || type.defaultValue;
 }
 exports.getDefaultValue = getDefaultValue;
@@ -84,6 +84,7 @@ function resolveLateType(maybeLate) {
     if (!(0, mobx_state_tree_1.isUnionType)(maybeLate) &&
         !(0, mobx_state_tree_1.isArrayType)(maybeLate) &&
         (0, mobx_state_tree_1.isLateType)(maybeLate)) {
+        // @ts-expect-error
         return maybeLate.getSubType();
     }
     return maybeLate;

package/util/stats.d.ts

@@ -1,7 +1,7 @@
 import { Observable } from 'rxjs';
 import { NoAssemblyRegion } from './types';
 import { Feature } from './simpleFeature';
-export interface UnrectifiedFeatureStats {
+export interface UnrectifiedQuantitativeStats {
     scoreMin: number;
     scoreMax: number;
     scoreSum: number;
@@ -9,7 +9,7 @@ export interface UnrectifiedFeatureStats {
     featureCount: number;
     basesCovered: number;
 }
-export interface FeatureStats extends UnrectifiedFeatureStats {
+export interface QuantitativeStats extends UnrectifiedQuantitativeStats {
     featureDensity: number;
     scoreMean: number;
     scoreStdDev: number;
@@ -31,7 +31,7 @@ export declare function calcStdFromSums(sum: number, sumSquares: number, n: numb
  * @returns - a summary stats object with
  * scoreMean, scoreStdDev, and featureDensity added
  */
-export declare function rectifyStats(s: UnrectifiedFeatureStats): FeatureStats;
+export declare function rectifyStats(s: UnrectifiedQuantitativeStats): QuantitativeStats;
 /**
  * calculates per-base scores for variable width features over a region
  *
@@ -47,5 +47,5 @@ export declare function calcPerBaseStats(region: NoAssemblyRegion, features: Fea
  * @param features - array of features which are possibly summary features
  * @returns - object with scoreMax, scoreMin, scoreSum, scoreSumSquares, etc
  */
-export declare function scoresToStats(region: NoAssemblyRegion, feats: Observable<Feature>): Promise<FeatureStats>;
-export declare function blankStats(): FeatureStats;
+export declare function scoresToStats(region: NoAssemblyRegion, feats: Observable<Feature>): Promise<QuantitativeStats>;
+export declare function blankStats(): QuantitativeStats;

package/util/types/index.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
 import { Instance, SnapshotIn, IAnyStateTreeNode, IStateTreeNode, IType } from 'mobx-state-tree';
-import { AnyConfigurationModel } from '../../configuration/configurationSchema';
+import { AnyConfigurationModel } from '../../configuration';
 import assemblyManager from '../../assemblyManager';
 import TextSearchManager from '../../TextSearch/TextSearchManager';
 import { MenuItem } from '../../ui';
@@ -65,6 +65,7 @@ export interface AbstractSessionModel extends AbstractViewContainer {
         name: string;
         connectionId: string;
         tracks: AnyConfigurationModel[];
+        configuration: AnyConfigurationModel;
     }[];
     makeConnection?: Function;
     adminMode?: boolean;
@@ -144,6 +145,7 @@ export interface AbstractViewModel {
 export declare function isViewModel(thing: unknown): thing is AbstractViewModel;
 export interface AbstractTrackModel {
     displays: AbstractDisplayModel[];
+    configuration: AnyConfigurationModel;
 }
 export declare function isTrackModel(thing: unknown): thing is AbstractTrackModel;
 export interface AbstractDisplayModel {
@@ -194,6 +196,7 @@ export interface AbstractMenuManager {
 export declare function isAbstractMenuManager(thing: unknown): thing is AbstractMenuManager;
 export interface NoAssemblyRegion extends SnapshotIn<typeof MUNoAssemblyRegion> {
 }
+/** a description of a specific genomic region. assemblyName, refName, start, end, and reversed */
 export interface Region extends SnapshotIn<typeof MUIRegion> {
 }
 export interface AugmentedRegion extends Region {

package/util/types/mst.d.ts

@@ -99,7 +99,17 @@ export declare const FileLocation: import("mobx-state-tree").ISnapshotProcessor<
 }> | import("mobx-state-tree").ModelSnapshotType<{
     locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
     localPath: import("mobx-state-tree").ISimpleType<string>;
-}>, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+}>, import("mobx-state-tree").ModelInstanceType<{
+    locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+    name: import("mobx-state-tree").ISimpleType<string>;
+    blobId: import("mobx-state-tree").ISimpleType<string>;
+}, {}> | import("mobx-state-tree").ModelInstanceType<{
+    locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+    localPath: import("mobx-state-tree").ISimpleType<string>;
+}, {}> | ({
+    locationType: "UriLocation";
+    uri: string;
+} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
     locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
     uri: import("mobx-state-tree").ISimpleType<string>;
     baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -108,11 +118,4 @@ export declare const FileLocation: import("mobx-state-tree").ISnapshotProcessor<
         internetAccountType: import("mobx-state-tree").ISimpleType<string>;
         authInfo: import("mobx-state-tree").IType<any, any, any>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-}>> | import("mobx-state-tree").ModelInstanceType<{
-    locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
-    name: import("mobx-state-tree").ISimpleType<string>;
-    blobId: import("mobx-state-tree").ISimpleType<string>;
-}, {}> | import("mobx-state-tree").ModelInstanceType<{
-    locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-    localPath: import("mobx-state-tree").ISimpleType<string>;
-}, {}>>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/util/useMeasure.d.ts

@@ -0,0 +1,5 @@
+/// <reference types="react" />
+export default function useMeasure(): readonly [import("react").RefObject<HTMLDivElement>, {
+    width?: number | undefined;
+    height?: number | undefined;
+}];

package/util/useMeasure.js

@@ -0,0 +1,34 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = require("react");
+function useMeasure() {
+    const ref = (0, react_1.useRef)(null);
+    const [dims, setDims] = (0, react_1.useState)({
+        width: undefined,
+        height: undefined,
+    });
+    (0, react_1.useEffect)(() => {
+        if (!ref.current) {
+            return;
+        }
+        const RS = typeof window !== 'undefined' && 'ResizeObserver' in window
+            ? window.ResizeObserver
+            : undefined;
+        if (!RS) {
+            return;
+        }
+        const observer = new RS(entries => {
+            setDims({
+                width: entries[0].contentRect.width,
+                height: entries[0].contentRect.height,
+            });
+        });
+        observer.observe(ref.current);
+        // Callback fired when component is unmounted
+        return () => {
+            observer.disconnect();
+        };
+    }, []);
+    return [ref, dims];
+}
+exports.default = useMeasure;

package/BaseFeatureWidget/SequenceBox.d.ts

@@ -1,29 +0,0 @@
-/// <reference types="react" />
-import { Feat } from './util';
-export declare function GeneCDS({ cds, sequence }: {
-    cds: Feat[];
-    sequence: string;
-}): JSX.Element;
-export declare function GeneProtein({ cds, sequence, codonTable, }: {
-    cds: Feat[];
-    sequence: string;
-    codonTable: {
-        [key: string]: string;
-    };
-}): JSX.Element;
-export declare function GenecDNA({ utr, cds, exons, sequence, upstream, downstream, includeIntrons, collapseIntron, intronBp, }: {
-    utr: Feat[];
-    cds: Feat[];
-    exons: Feat[];
-    sequence: string;
-    upstream?: string;
-    downstream?: string;
-    includeIntrons?: boolean;
-    collapseIntron?: boolean;
-    intronBp: number;
-}): JSX.Element;
-export declare function Genomic({ sequence, upstream, downstream, }: {
-    sequence: string;
-    upstream?: string;
-    downstream?: string;
-}): JSX.Element;

package/BaseFeatureWidget/SequenceBox.js

@@ -1,63 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.Genomic = exports.GenecDNA = exports.GeneProtein = exports.GeneCDS = void 0;
-const react_1 = __importDefault(require("react"));
-const util_1 = require("./util");
-// note that these are currently put into the style section instead of being
-// defined in classes to aid copy and paste to an external document e.g. word
-const proteinColor = 'rgb(220,160,220)';
-const intronColor = undefined;
-const cdsColor = 'rgb(220,220,180)';
-const updownstreamColor = 'rgba(250,200,200)';
-const utrColor = 'rgb(200,240,240)';
-const genomeColor = 'rgb(200,280,200)';
-function GeneCDS({ cds, sequence }) {
-    return react_1.default.createElement("span", { style: { background: cdsColor } }, (0, util_1.stitch)(cds, sequence));
-}
-exports.GeneCDS = GeneCDS;
-function GeneProtein({ cds, sequence, codonTable, }) {
-    const str = (0, util_1.stitch)(cds, sequence);
-    let protein = '';
-    for (let i = 0; i < str.length; i += 3) {
-        // use & symbol for undefined codon, or partial slice
-        protein += codonTable[str.slice(i, i + 3)] || '&';
-    }
-    return react_1.default.createElement("span", { style: { background: proteinColor } }, protein);
-}
-exports.GeneProtein = GeneProtein;
-function GenecDNA({ utr, cds, exons, sequence, upstream, downstream, includeIntrons, collapseIntron, intronBp, }) {
-    const chunks = (cds.length ? [...cds, ...utr].sort((a, b) => a.start - b.start) : exons).filter(f => f.start !== f.end);
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        upstream ? (react_1.default.createElement("span", { style: {
-                background: updownstreamColor,
-            } }, upstream)) : null,
-        chunks.map((chunk, idx) => {
-            var _a;
-            const intron = sequence.slice(chunk.end, (_a = chunks[idx + 1]) === null || _a === void 0 ? void 0 : _a.start);
-            return (react_1.default.createElement(react_1.default.Fragment, { key: JSON.stringify(chunk) },
-                react_1.default.createElement("span", { style: {
-                        background: chunk.type === 'CDS' ? cdsColor : utrColor,
-                    } }, sequence.slice(chunk.start, chunk.end)),
-                includeIntrons && idx < chunks.length - 1 ? (react_1.default.createElement("span", { style: { background: intronColor } }, collapseIntron && intron.length > intronBp * 2
-                    ? `${intron.slice(0, intronBp)}...${intron.slice(-intronBp)}`
-                    : intron)) : null));
-        }),
-        downstream ? (react_1.default.createElement("span", { style: { background: updownstreamColor } }, downstream)) : null));
-}
-exports.GenecDNA = GenecDNA;
-function Genomic({ sequence, upstream, downstream, }) {
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        upstream ? (react_1.default.createElement("span", { style: {
-                background: updownstreamColor,
-            } }, upstream)) : null,
-        react_1.default.createElement("span", { style: {
-                background: genomeColor,
-            } }, sequence),
-        downstream ? (react_1.default.createElement("span", { style: {
-                background: updownstreamColor,
-            } }, downstream)) : null));
-}
-exports.Genomic = Genomic;

package/BaseFeatureWidget/SequenceFeatureDetails.d.ts

@@ -1,3 +0,0 @@
-/// <reference types="react" />
-import { BaseProps } from './types';
-export default function SequenceFeatureDetails({ model, feature }: BaseProps): JSX.Element | null;

package/BaseFeatureWidget/SequenceFeatureDetails.js

@@ -1,237 +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 material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
-// locals
-const util_1 = require("../util");
-const configuration_1 = require("../configuration");
-const ui_1 = require("../ui");
-// icons
-const Settings_1 = __importDefault(require("@mui/icons-material/Settings"));
-const Help_1 = __importDefault(require("@mui/icons-material/Help"));
-// lazies
-const SettingsDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SequenceFeatureSettingsDialog'))));
-const HelpDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SequenceHelpDialog'))));
-const SequencePanel = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SequencePanel'))));
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    button: {
-        margin: theme.spacing(1),
-    },
-    formControl: {
-        margin: 0,
-    },
-    container: {
-        margin: theme.spacing(1),
-    },
-    container2: {
-        marginTop: theme.spacing(1),
-    },
-}));
-const BPLIMIT = 500000;
-// display the stitched-together sequence of a gene's CDS, cDNA, or protein
-// sequence. this is a best effort and weird genomic phenomena could lead these
-// to not be 100% accurate
-function SequenceFeatureDetails({ model, feature }) {
-    var _a;
-    const { classes } = useStyles();
-    const parentFeature = feature;
-    const hasCDS = !!((_a = parentFeature.subfeatures) === null || _a === void 0 ? void 0 : _a.find(sub => sub.type === 'CDS'));
-    const isGene = feature.type === 'gene';
-    const [shown, setShown] = (0, react_1.useState)(false);
-    const [helpShown, setHelpShown] = (0, react_1.useState)(false);
-    return (isGene && !hasCDS) || !model ? null : (react_1.default.createElement("div", { className: classes.container2 },
-        react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => setShown(!shown) }, shown ? 'Hide feature sequence' : 'Show feature sequence'),
-        react_1.default.createElement(material_1.FormControl, { className: classes.formControl },
-            react_1.default.createElement(material_1.IconButton, { onClick: () => setHelpShown(true) },
-                react_1.default.createElement(Help_1.default, null))),
-        react_1.default.createElement("br", null),
-        shown ? react_1.default.createElement(FeatureSequence, { model: model, feature: feature }) : null,
-        helpShown ? (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
-            react_1.default.createElement(HelpDlg, { handleClose: () => setHelpShown(false) }))) : null));
-}
-exports.default = SequenceFeatureDetails;
-function FeatureSequence({ model, feature }) {
-    var _a;
-    const { classes } = useStyles();
-    const parentFeature = feature;
-    const hasCDS = !!((_a = parentFeature.subfeatures) === null || _a === void 0 ? void 0 : _a.find(sub => sub.type === 'CDS'));
-    const seqPanelRef = (0, react_1.useRef)(null);
-    const [settingsDlgOpen, setSettingsDlgOpen] = (0, react_1.useState)(false);
-    const [intronBp, setIntronBp] = (0, util_1.useLocalStorage)('intronBp', 10);
-    const [upDownBp, setUpDownBp] = (0, util_1.useLocalStorage)('upDownBp', 500);
-    const [sequence, setSequence] = (0, react_1.useState)();
-    const [error, setError] = (0, react_1.useState)();
-    const [copied, setCopied] = (0, react_1.useState)(false);
-    const [copiedHtml, setCopiedHtml] = (0, react_1.useState)(false);
-    const [forceLoad, setForceLoad] = (0, react_1.useState)({
-        id: feature.uniqueId,
-        force: false,
-    });
-    (0, react_1.useEffect)(() => {
-        setForceLoad({
-            id: feature.uniqueId,
-            force: false,
-        });
-    }, [feature]);
-    (0, react_1.useEffect)(() => {
-        var _a;
-        let finished = false;
-        if (!model) {
-            return () => { };
-        }
-        const { assemblyManager, rpcManager } = (0, util_1.getSession)(model);
-        const [assemblyName] = ((_a = model.view) === null || _a === void 0 ? void 0 : _a.assemblyNames) || [];
-        async function fetchSeq(start, end, refName) {
-            const assembly = await assemblyManager.waitForAssembly(assemblyName);
-            if (!assembly) {
-                throw new Error('assembly not found');
-            }
-            const sessionId = 'getSequence';
-            const feats = await rpcManager.call(sessionId, 'CoreGetFeatures', {
-                adapterConfig: (0, configuration_1.getConf)(assembly, ['sequence', 'adapter']),
-                sessionId,
-                regions: [
-                    {
-                        start,
-                        end,
-                        refName: assembly.getCanonicalRefName(refName),
-                        assemblyName,
-                    },
-                ],
-            });
-            const [feat] = feats;
-            return (feat === null || feat === void 0 ? void 0 : feat.get('seq')) || '';
-        }
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
-        ;
-        (async () => {
-            try {
-                setError(undefined);
-                const { start, end, refName } = feature;
-                if (!forceLoad.force && end - start > BPLIMIT) {
-                    setSequence({
-                        error: `Genomic sequence larger than ${BPLIMIT}bp, use "force load" button to display`,
-                    });
-                }
-                else {
-                    const seq = await fetchSeq(start, end, refName);
-                    const up = await fetchSeq(Math.max(0, start - upDownBp), start, refName);
-                    const down = await fetchSeq(end, end + upDownBp, refName);
-                    if (!finished) {
-                        setSequence({ seq, upstream: up, downstream: down });
-                    }
-                }
-            }
-            catch (e) {
-                console.error(e);
-                setError(e);
-            }
-        })();
-        return () => {
-            finished = true;
-        };
-    }, [feature, model, upDownBp, forceLoad]);
-    const loading = !sequence;
-    const session = (0, util_1.getSession)(model);
-    const defaultSeqTypes = ['mRNA', 'transcript', 'gene'];
-    const sequenceTypes = (0, configuration_1.getConf)(session, ['featureDetails', 'sequenceTypes']) || defaultSeqTypes;
-    // only attempt fetching gene type sequence on a bare CDS if it has no parent
-    const attemptGeneType = feature.type === 'CDS'
-        ? sequenceTypes.includes('CDS') && !feature.parentId
-        : sequenceTypes.includes(feature.type);
-    const val = attemptGeneType ? (hasCDS ? 'cds' : 'cdna') : 'genomic';
-    // this useEffect is needed to reset the mode/setMode useState because the
-    // contents of the select box can completely change depending on whether we
-    // click on a gene feature or non-gene feature, so the current value in the
-    // select box must change accordingly
-    (0, react_1.useEffect)(() => {
-        setMode(val);
-    }, [attemptGeneType, val]);
-    const [mode, setMode] = (0, react_1.useState)(attemptGeneType ? (hasCDS ? 'cds' : 'cdna') : 'genomic');
-    const rest = {
-        gene: 'Gene w/ introns',
-        gene_collapsed_intron: `Gene w/ ${intronBp}bp of intron`,
-        gene_updownstream: `Gene w/ ${upDownBp}bp up+down stream`,
-        gene_updownstream_collapsed_intron: `Gene w/ ${upDownBp}bp up+down stream w/ ${intronBp}bp intron`,
-        cdna: 'cDNA',
-    };
-    const arg = attemptGeneType
-        ? hasCDS
-            ? {
-                cds: 'CDS',
-                protein: 'Protein',
-                ...rest,
-            }
-            : rest
-        : {
-            genomic: 'Genomic seq',
-            genomic_sequence_updown: `Genomic seq w/ ${upDownBp}bp up+down stream`,
-        };
-    return (react_1.default.createElement("div", { className: classes.container2 },
-        react_1.default.createElement(material_1.FormControl, { className: classes.formControl },
-            react_1.default.createElement(material_1.Select, { value: mode, onChange: event => setMode(event.target.value) }, Object.entries(arg).map(([key, val]) => (react_1.default.createElement(material_1.MenuItem, { key: key, value: key }, val))))),
-        react_1.default.createElement(material_1.FormControl, { className: classes.formControl },
-            react_1.default.createElement(material_1.Button, { className: classes.button, variant: "contained", onClick: () => {
-                    const ref = seqPanelRef.current;
-                    if (ref) {
-                        (0, copy_to_clipboard_1.default)(ref.textContent || '', { format: 'text/plain' });
-                        setCopied(true);
-                        setTimeout(() => setCopied(false), 1000);
-                    }
-                } }, copied ? 'Copied to clipboard!' : 'Copy plaintext')),
-        react_1.default.createElement(material_1.FormControl, { className: classes.formControl },
-            react_1.default.createElement(material_1.Tooltip, { title: "The 'Copy HTML' function retains the colors from the sequence panel but cannot be pasted into some programs like notepad that only expect plain text" },
-                react_1.default.createElement(material_1.Button, { className: classes.button, variant: "contained", onClick: () => {
-                        const ref = seqPanelRef.current;
-                        if (ref) {
-                            (0, copy_to_clipboard_1.default)(ref.innerHTML, { format: 'text/html' });
-                            setCopiedHtml(true);
-                            setTimeout(() => setCopiedHtml(false), 1000);
-                        }
-                    } }, copiedHtml ? 'Copied to clipboard!' : 'Copy HTML'))),
-        react_1.default.createElement(material_1.FormControl, { className: classes.formControl },
-            react_1.default.createElement(material_1.IconButton, { onClick: () => setSettingsDlgOpen(true) },
-                react_1.default.createElement(Settings_1.default, null))),
-        react_1.default.createElement("br", null),
-        error ? (react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`)) : loading ? (react_1.default.createElement(ui_1.LoadingEllipses, null)) : sequence ? ('error' in sequence ? (react_1.default.createElement(react_1.default.Fragment, null,
-            react_1.default.createElement(material_1.Typography, { color: "error" }, sequence.error),
-            react_1.default.createElement(material_1.Button, { variant: "contained", color: "inherit", onClick: () => setForceLoad({ ...forceLoad, force: true }) }, "Force load"))) : (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null, "Loading") },
-            react_1.default.createElement(SequencePanel, { ref: seqPanelRef, feature: parentFeature, mode: mode, sequence: sequence, intronBp: intronBp })))) : (react_1.default.createElement(material_1.Typography, null, "No sequence found")),
-        settingsDlgOpen ? (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
-            react_1.default.createElement(SettingsDlg, { handleClose: arg => {
-                    if (arg) {
-                        const { upDownBp, intronBp } = arg;
-                        setIntronBp(intronBp);
-                        setUpDownBp(upDownBp);
-                    }
-                    setSettingsDlgOpen(false);
-                }, upDownBp: upDownBp, intronBp: intronBp }))) : null));
-}