@jbrowse/core 2.17.0 → 2.18.0

package/BaseFeatureWidget/SequenceFeatureDetails/hooks.js

@@ -2,8 +2,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.useFeatureSequence = useFeatureSequence;
 const react_1 = require("react");
-const util_1 = require("../../util");
 const configuration_1 = require("../../configuration");
+const util_1 = require("../../util");
 const BPLIMIT = 500000;
 function useFeatureSequence(model, feature, upDownBp, forceLoad) {
     const [sequence, setSequence] = (0, react_1.useState)();
@@ -36,7 +36,6 @@ function useFeatureSequence(model, feature, upDownBp, forceLoad) {
             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 {

package/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts

@@ -1,79 +1,25 @@
-import { Instance } from 'mobx-state-tree';
-import { SimpleFeatureSerialized } from '../../util';
+import type { SimpleFeatureSerialized } from '../../util';
+import type { Instance } from 'mobx-state-tree';
 export declare function SequenceFeatureDetailsF(): import("mobx-state-tree").IModelType<{}, {
-    /**
-     * #volatile
-     */
     showCoordinatesSetting: string;
-    /**
-     * #volatile
-     */
     intronBp: number;
-    /**
-     * #volatile
-     */
     upDownBp: number;
-    /**
-     * #volatile
-     */
     upperCaseCDS: boolean;
-    /**
-     * #volatile
-     */
     charactersPerRow: number;
-    /**
-     * #volatile
-     */
     feature: SimpleFeatureSerialized | undefined;
-    /**
-     * #volatile
-     */
     mode: string;
 } & {
-    /**
-     * #action
-     */
     setFeature(f: SimpleFeatureSerialized): void;
-    /**
-     * #action
-     */
     setUpDownBp(f: number): void;
-    /**
-     * #action
-     */
     setIntronBp(f: number): void;
-    /**
-     * #action
-     */
     setUpperCaseCDS(f: boolean): void;
-    /**
-     * #action
-     */
     setShowCoordinates(f: "none" | "relative" | "genomic"): void;
-    /**
-     * #action
-     */
     setMode(mode: string): void;
 } & {
-    /**
-     * #getter
-     */
     readonly showCoordinates: boolean;
-    /**
-     * #getter
-     */
     readonly showGenomicCoordsOption: boolean;
-    /**
-     * #getter
-     */
     readonly hasCDS: boolean | undefined;
-    /**
-     * #getter
-     */
     readonly hasExon: boolean | undefined;
-    /**
-     * #getter
-     */
     readonly hasExonOrCDS: boolean | undefined;
 } & {
     afterAttach(): void;

package/BaseFeatureWidget/SequenceFeatureDetails/model.js

@@ -1,9 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.SequenceFeatureDetailsF = SequenceFeatureDetailsF;
-const mobx_state_tree_1 = require("mobx-state-tree");
 const mobx_1 = require("mobx");
-// locals
+const mobx_state_tree_1 = require("mobx-state-tree");
 const util_1 = require("../../util");
 function localStorageGetNumber(key, defaultVal) {
     var _a;
@@ -23,106 +22,52 @@ function SequenceFeatureDetailsF() {
     return mobx_state_tree_1.types
         .model('SequenceFeatureDetails')
         .volatile(() => ({
-        /**
-         * #volatile
-         */
         showCoordinatesSetting: (0, util_1.localStorageGetItem)(`${p}-showCoordinatesSetting`) || 'none',
-        /**
-         * #volatile
-         */
         intronBp: localStorageGetNumber(`${p}-intronBp`, 10),
-        /**
-         * #volatile
-         */
         upDownBp: localStorageGetNumber(`${p}-upDownBp`, 100),
-        /**
-         * #volatile
-         */
         upperCaseCDS: localStorageGetBoolean(`${p}-upperCaseCDS`, true),
-        /**
-         * #volatile
-         */
         charactersPerRow: 100,
-        /**
-         * #volatile
-         */
         feature: undefined,
-        /**
-         * #volatile
-         */
         mode: '',
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setFeature(f) {
             self.feature = f;
         },
-        /**
-         * #action
-         */
         setUpDownBp(f) {
             self.upDownBp = f;
         },
-        /**
-         * #action
-         */
         setIntronBp(f) {
             self.intronBp = f;
         },
-        /**
-         * #action
-         */
         setUpperCaseCDS(f) {
             self.upperCaseCDS = f;
         },
-        /**
-         * #action
-         */
         setShowCoordinates(f) {
             self.showCoordinatesSetting = f;
         },
-        /**
-         * #action
-         */
         setMode(mode) {
             self.mode = mode;
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get showCoordinates() {
             return self.showCoordinatesSetting !== 'none';
         },
-        /**
-         * #getter
-         */
         get showGenomicCoordsOption() {
             return (self.mode === 'gene' ||
                 self.mode === 'gene_updownstream' ||
                 self.mode === 'genomic' ||
                 self.mode === 'genomic_sequence_updownstream');
         },
-        /**
-         * #getter
-         */
         get hasCDS() {
             var _a, _b;
             return (_b = (_a = self.feature) === null || _a === void 0 ? void 0 : _a.subfeatures) === null || _b === void 0 ? void 0 : _b.some(sub => sub.type === 'CDS');
         },
-        /**
-         * #getter
-         */
         get hasExon() {
             var _a, _b;
             return (_b = (_a = self.feature) === null || _a === void 0 ? void 0 : _a.subfeatures) === null || _b === void 0 ? void 0 : _b.some(sub => sub.type === 'exon');
         },
-        /**
-         * #getter
-         */
         get hasExonOrCDS() {
             return this.hasExon || this.hasCDS;
         },

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts

@@ -1,7 +1,7 @@
 import React from 'react';
-import { Feat } from '../../util';
-import { SequenceFeatureDetailsModel } from '../model';
-import { SimpleFeatureSerialized } from '../../../util';
+import type { SimpleFeatureSerialized } from '../../../util';
+import type { Feat } from '../../util';
+import type { SequenceFeatureDetailsModel } from '../model';
 declare const CDNASequence: ({ utr, cds, exons, sequence, upstream, downstream, feature, includeIntrons, collapseIntron, model, }: {
     utr: Feat[];
     cds: Feat[];

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
-import { Feat } from '../../util';
-import { SequenceFeatureDetailsModel } from '../model';
+import type { Feat } from '../../util';
+import type { SequenceFeatureDetailsModel } from '../model';
 declare const CDSSequence: ({ cds, sequence, model, }: {
     cds: Feat[];
     sequence: string;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js

@@ -5,17 +5,16 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 const mobx_react_1 = require("mobx-react");
-// locals
-const util_1 = require("../util");
-const util_2 = require("../../util");
+const util_1 = require("../../util");
+const util_2 = require("../util");
 const SequenceDisplay_1 = __importDefault(require("./SequenceDisplay"));
 const CDSSequence = (0, mobx_react_1.observer)(function ({ cds, sequence, model, }) {
     const { charactersPerRow, showCoordinates } = model;
-    const { segments } = (0, util_1.splitString)({
-        str: (0, util_2.stitch)(cds, sequence),
+    const { segments } = (0, util_2.splitString)({
+        str: (0, util_1.stitch)(cds, sequence),
         charactersPerRow,
         showCoordinates,
     });
-    return (react_1.default.createElement(SequenceDisplay_1.default, { model: model, color: util_1.cdsColor, chunks: segments, start: 0 }));
+    return (react_1.default.createElement(SequenceDisplay_1.default, { model: model, color: util_2.cdsColor, chunks: segments, start: 0 }));
 });
 exports.default = CDSSequence;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
-import { SequenceFeatureDetailsModel } from '../model';
-import { SimpleFeatureSerialized } from '../../../util';
+import type { SimpleFeatureSerialized } from '../../../util';
+import type { SequenceFeatureDetailsModel } from '../model';
 declare const GenomicSequence: ({ sequence, upstream, feature, downstream, model, }: {
     sequence: string;
     feature: SimpleFeatureSerialized;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js

@@ -5,7 +5,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 const mobx_react_1 = require("mobx-react");
-// locals
 const util_1 = require("../util");
 const SequenceDisplay_1 = __importDefault(require("./SequenceDisplay"));
 const GenomicSequence = (0, mobx_react_1.observer)(function ({ sequence, upstream, feature, downstream, model, }) {

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
-import { Feat } from '../../util';
-import { SequenceFeatureDetailsModel } from '../model';
+import type { Feat } from '../../util';
+import type { SequenceFeatureDetailsModel } from '../model';
 declare const ProteinSequence: ({ cds, sequence, codonTable, model, }: {
     cds: Feat[];
     sequence: string;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js

@@ -5,7 +5,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 const mobx_react_1 = require("mobx-react");
-// locals
 const util_1 = require("../../util");
 const util_2 = require("../util");
 const SequenceDisplay_1 = __importDefault(require("./SequenceDisplay"));
@@ -14,7 +13,6 @@ const ProteinSequence = (0, mobx_react_1.observer)(function ({ cds, sequence, co
     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)] || '&';
     }
     const { segments } = (0, util_2.splitString)({

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { SequenceFeatureDetailsModel } from '../model';
+import type { SequenceFeatureDetailsModel } from '../model';
 declare const SequenceDisplay: ({ chunks, start, color, strand, coordStart, model, }: {
     chunks: string[];
     start: number;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js

@@ -21,9 +21,7 @@ const SequenceDisplay = (0, mobx_react_1.observer)(function ({ chunks, start, co
             : showCoordinates
                 ? ' \n'
                 : '';
-        return (
-        /* biome-ignore lint/suspicious/noArrayIndexKey: */
-        react_1.default.createElement(react_1.default.Fragment, { key: `${chunk}-${idx}` },
+        return (react_1.default.createElement(react_1.default.Fragment, { key: `${chunk}-${idx}` },
             showCoordinates ? prefix : null,
             react_1.default.createElement("span", { style: { background: color } }, chunk),
             postfix));

package/BaseFeatureWidget/SequenceFeatureDetails/util.js

@@ -2,8 +2,6 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.genomeColor = exports.updownstreamColor = exports.cdsColor = exports.proteinColor = exports.utrColor = exports.intronColor = void 0;
 exports.splitString = splitString;
-// 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
 exports.intronColor = undefined;
 exports.utrColor = 'rgb(200,240,240)';
 exports.proteinColor = 'rgb(220,160,220)';
@@ -26,8 +24,6 @@ function splitString({ str, charactersPerRow, showCoordinates, currRemainder = 0
         if (showCoordinates) {
             let res = '';
             for (let i = 0, j = splitStart; i < r.length; i++, j++) {
-                // note: this adds a space at the start but it causes trouble to try to
-                // say e.g. j%splitSize==0 && j to try to only add non-zero spaces
                 if (j % splitSize === 0) {
                     res += ' ';
                     j = 0;
@@ -41,7 +37,7 @@ function splitString({ str, charactersPerRow, showCoordinates, currRemainder = 0
         else {
             chunks[iter] = r;
         }
-        splitStart = 0; // after newline, reset
+        splitStart = 0;
         offset += inc;
     }
     return {

package/BaseFeatureWidget/stateModelFactory.d.ts

@@ -1,56 +1,16 @@
-import { Instance } from 'mobx-state-tree';
-import PluginManager from '../PluginManager';
-/**
- * #stateModel BaseFeatureWidget
- * displays data about features, allowing configuration callbacks to modify the
- * contents of what is displayed
- *
- * see: formatDetails-\>feature,formatDetails-\>subfeatures
- */
+import type PluginManager from '../PluginManager';
+import type { Instance } from 'mobx-state-tree';
 export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    /**
-     * #property
-     */
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    /**
-     * #property
-     */
     type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
-    /**
-     * #property
-     */
     featureData: import("mobx-state-tree").IType<any, any, any>;
-    /**
-     * #property
-     */
     formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    /**
-     * #property
-     */
     unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
-    /**
-     * #property
-     */
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    /**
-     * #property
-     */
     track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    /**
-     * #property
-     */
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    /**
-     * #property
-     */
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    /**
-     * #property
-     */
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    /**
-     * #property
-     */
     sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
         showCoordinatesSetting: string;
         intronBp: number;
@@ -76,77 +36,26 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }, {
-    /**
-     * #volatile
-     */
     error: unknown;
 } & {
-    /**
-     * #action
-     */
     setFeatureData(featureData: Record<string, unknown>): void;
-    /**
-     * #action
-     */
     clearFeatureData(): void;
-    /**
-     * #action
-     */
     setFormattedData(feat: Record<string, unknown>): void;
-    /**
-     * #action
-     */
     setExtra(type?: string, trackId?: string, maxDepth?: number): void;
-    /**
-     * #action
-     */
     setError(e: unknown): void;
 } & {
     afterCreate(): void;
 }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-    /**
-     * #property
-     */
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    /**
-     * #property
-     */
     type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
-    /**
-     * #property
-     */
     featureData: import("mobx-state-tree").IType<any, any, any>;
-    /**
-     * #property
-     */
     formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    /**
-     * #property
-     */
     unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
-    /**
-     * #property
-     */
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    /**
-     * #property
-     */
     track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    /**
-     * #property
-     */
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    /**
-     * #property
-     */
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    /**
-     * #property
-     */
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    /**
-     * #property
-     */
     sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
         showCoordinatesSetting: string;
         intronBp: number;

package/BaseFeatureWidget/stateModelFactory.js

@@ -1,17 +1,13 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.stateModelFactory = stateModelFactory;
-const mobx_state_tree_1 = require("mobx-state-tree");
 const mobx_1 = require("mobx");
-const clone_1 = __importDefault(require("clone"));
+const mobx_state_tree_1 = require("mobx-state-tree");
 const configuration_1 = require("../configuration");
 const util_1 = require("../util");
-const mst_1 = require("../util/types/mst");
 const model_1 = require("./SequenceFeatureDetails/model");
 const util_2 = require("./util");
+const mst_1 = require("../util/types/mst");
 function formatSubfeatures(obj, depth, parse, currentDepth = 0, returnObj = {}) {
     var _a;
     if (depth <= currentDepth) {
@@ -22,97 +18,39 @@ function formatSubfeatures(obj, depth, parse, currentDepth = 0, returnObj = {})
         parse(sub);
     });
 }
-/**
- * #stateModel BaseFeatureWidget
- * displays data about features, allowing configuration callbacks to modify the
- * contents of what is displayed
- *
- * see: formatDetails-\>feature,formatDetails-\>subfeatures
- */
 function stateModelFactory(pluginManager) {
     return mobx_state_tree_1.types
         .model('BaseFeatureWidget', {
-        /**
-         * #property
-         */
         id: mst_1.ElementId,
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.literal('BaseFeatureWidget'),
-        /**
-         * #property
-         */
         featureData: mobx_state_tree_1.types.frozen(),
-        /**
-         * #property
-         */
         formattedFields: mobx_state_tree_1.types.frozen(),
-        /**
-         * #property
-         */
         unformattedFeatureData: mobx_state_tree_1.types.frozen(),
-        /**
-         * #property
-         */
         view: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
-        /**
-         * #property
-         */
         track: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('track', 'stateModel')),
-        /**
-         * #property
-         */
         trackId: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        /**
-         * #property
-         */
         trackType: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        /**
-         * #property
-         */
         maxDepth: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-        /**
-         * #property
-         */
         sequenceFeatureDetails: mobx_state_tree_1.types.optional((0, model_1.SequenceFeatureDetailsF)(), {}),
     })
         .volatile(() => ({
-        /**
-         * #volatile
-         */
         error: undefined,
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setFeatureData(featureData) {
             self.unformattedFeatureData = featureData;
         },
-        /**
-         * #action
-         */
         clearFeatureData() {
             self.featureData = undefined;
         },
-        /**
-         * #action
-         */
         setFormattedData(feat) {
             self.featureData = feat;
         },
-        /**
-         * #action
-         */
         setExtra(type, trackId, maxDepth) {
             self.trackId = trackId;
             self.trackType = type;
             self.maxDepth = maxDepth;
         },
-        /**
-         * #action
-         */
         setError(e) {
             self.error = e;
         },
@@ -127,7 +65,7 @@ function stateModelFactory(pluginManager) {
                         self.setExtra(track.type, track.configuration.trackId, (0, configuration_1.getConf)(track, ['formatDetails', 'maxDepth']));
                     }
                     if (unformattedFeatureData) {
-                        const feature = (0, clone_1.default)(unformattedFeatureData);
+                        const feature = structuredClone(unformattedFeatureData);
                         const combine = (arg2, feature) => ({
                             ...(0, configuration_1.getConf)(session, ['formatDetails', arg2], { feature }),
                             ...(0, configuration_1.getConf)(track, ['formatDetails', arg2], { feature }),
@@ -149,7 +87,6 @@ function stateModelFactory(pluginManager) {
         },
     }))
         .preProcessSnapshot(snap => {
-        // @ts-expect-error
         const { featureData, finalizedFeatureData, ...rest } = snap;
         return {
             unformattedFeatureData: featureData,
@@ -158,15 +95,8 @@ function stateModelFactory(pluginManager) {
         };
     })
         .postProcessSnapshot(snap => {
-        // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
         const { unformattedFeatureData, featureData, ...rest } = snap;
-        // finalizedFeatureData avoids running formatter twice if loading from
-        // snapshot
         return {
-            // replacing undefined with null helps with allowing fields to be
-            // hidden, setting null is not allowed by jexl so we set it to
-            // undefined to hide. see config guide. this replacement happens both
-            // here and when displaying the featureData in base feature widget
             finalizedFeatureData: (0, util_2.replaceUndefinedWithNull)(featureData),
             ...rest,
         };

package/BaseFeatureWidget/types.d.ts

@@ -1,6 +1,6 @@
-import React from 'react';
-import { SimpleFeatureSerialized } from '../util/simpleFeature';
-import { BaseFeatureWidgetModel } from './stateModelFactory';
+import type React from 'react';
+import type { BaseFeatureWidgetModel } from './stateModelFactory';
+import type { SimpleFeatureSerialized } from '../util/simpleFeature';
 export interface BaseProps extends BaseCardProps {
     feature: SimpleFeatureSerialized;
     formatter?: (val: unknown, key: string) => React.ReactNode;