@jbrowse/core 2.4.2 → 2.5.0

package/BaseFeatureWidget/SequenceFeatureDetails.js

@@ -1,230 +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,
-    },
-    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 }) {
-    const { classes } = useStyles();
-    const [shown, setShown] = (0, react_1.useState)(false);
-    const [helpShown, setHelpShown] = (0, react_1.useState)(false);
-    return !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, _b;
-    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) && ((_b = feature.subfeatures) === null || _b === void 0 ? void 0 : _b.length);
-    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));
-}

package/data_adapters/BaseAdapter.d.ts

@@ -1,138 +0,0 @@
-import { Observable } from 'rxjs';
-import { Feature } from '../util/simpleFeature';
-import { AnyConfigurationModel } from '../configuration';
-import { getSubAdapterType } from './dataAdapterCache';
-import { AugmentedRegion as Region, NoAssemblyRegion } from '../util/types';
-import BaseResult from '../TextSearch/BaseResults';
-import PluginManager from '../PluginManager';
-export interface BaseOptions {
-    signal?: AbortSignal;
-    bpPerPx?: number;
-    sessionId?: string;
-    statusCallback?: (message: string) => void;
-    headers?: Record<string, string>;
-    [key: string]: unknown;
-}
-export type SearchType = 'full' | 'prefix' | 'exact';
-export interface BaseArgs {
-    searchType?: SearchType;
-    queryString: string;
-    signal?: AbortSignal;
-    limit?: number;
-    pageNumber?: number;
-}
-export interface AnyAdapter {
-    new (config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager | undefined): AnyDataAdapter;
-}
-export type AnyDataAdapter = BaseAdapter | BaseFeatureDataAdapter | BaseRefNameAliasAdapter | BaseTextSearchAdapter | RegionsAdapter | BaseSequenceAdapter;
-export interface SequenceAdapter extends BaseFeatureDataAdapter, RegionsAdapter {
-}
-export declare abstract class BaseAdapter {
-    config: AnyConfigurationModel;
-    getSubAdapter?: getSubAdapterType | undefined;
-    pluginManager?: PluginManager | undefined;
-    id: string;
-    static capabilities: string[];
-    constructor(config?: AnyConfigurationModel, getSubAdapter?: getSubAdapterType | undefined, pluginManager?: PluginManager | undefined);
-    getConf(arg: string | string[]): any;
-    /**
-     * Called to provide a hint that data tied to a certain region will not be
-     * needed for the foreseeable future and can be purged from caches, etc
-     * @param region - Region
-     */
-    abstract freeResources(region: Region): void;
-}
-export interface Stats {
-    featureDensity?: number;
-    fetchSizeLimit?: number;
-    bytes?: number;
-}
-/**
- * Base class for feature adapters to extend. Defines some methods that
- * subclasses must implement.
- */
-export declare abstract class BaseFeatureDataAdapter extends BaseAdapter {
-    /**
-     * Get all reference sequence names used in the data source
-     *
-     * NOTE: If an adapter is unable to determine the reference sequence names,
-     * the array will be empty
-     * @param opts - Feature adapter options
-     */
-    abstract getRefNames(opts?: BaseOptions): Promise<string[]>;
-    /**
-     * Get features from the data source that overlap a region
-     * @param region - Region
-     * @param opts - Feature adapter options
-     * @returns Observable of Feature objects in the region
-     */
-    abstract getFeatures(region: Region, opts?: BaseOptions): Observable<Feature>;
-    /**
-     * Return "header info" that is fetched from the data file, or other info
-     * that would not simply be in the config of the file. The return value can
-     * be `{tag:string, data: any}[]` e.g. list of tags with their values which
-     * is how VCF,BAM,CRAM return values for getInfo or it can be a nested JSON
-     * object
-     */
-    getHeader(_opts?: BaseOptions): Promise<unknown>;
-    /**
-     * Return info that is primarily used for interpreting the data that is there,
-     * primarily in reference to being used for augmenting feature details panels
-     */
-    getMetadata(_opts?: BaseOptions): Promise<unknown>;
-    /**
-     * Checks if the store has data for the given assembly and reference
-     * sequence, and then gets the features in the region if it does.
-     */
-    getFeaturesInRegion(region: Region, opts?: BaseOptions): Observable<Feature>;
-    /**
-     * Checks if the store has data for the given assembly and reference
-     * sequence, and then gets the features in the region if it does.
-     *
-     * Currently this just calls getFeatureInRegion for each region. Adapters
-     * that are frequently called on multiple regions simultaneously may
-     * want to implement a more efficient custom version of this method.
-     *
-     * Currently this just calls getFeatureInRegion for each region. Adapters that
-     * are frequently called on multiple regions simultaneously may want to
-     * implement a more efficient custom version of this method.
-     *
-     * @param regions - Regions
-     * @param opts - Feature adapter options
-     * @returns Observable of Feature objects in the regions
-     */
-    getFeaturesInMultipleRegions(regions: Region[], opts?: BaseOptions): Observable<Feature>;
-    /**
-     * Check if the store has data for the given reference name.
-     * @param refName - Name of the reference sequence
-     * @returns Whether data source has data for the given reference name
-     */
-    hasDataForRefName(refName: string, opts?: BaseOptions): Promise<boolean>;
-    getRegionStats(region: Region, opts?: BaseOptions): Promise<import("../util/stats").FeatureStats>;
-    getMultiRegionStats(regions?: Region[], opts?: BaseOptions): Promise<import("../util/stats").FeatureStats>;
-    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<Stats>;
-}
-export interface RegionsAdapter extends BaseAdapter {
-    getRegions(opts: BaseOptions): Promise<NoAssemblyRegion[]>;
-}
-export declare abstract class BaseSequenceAdapter extends BaseFeatureDataAdapter implements RegionsAdapter {
-    estimateRegionsStats(): Promise<{
-        featureDensity: number;
-    }>;
-    abstract getRegions(opts: BaseOptions): Promise<NoAssemblyRegion[]>;
-}
-export declare function isSequenceAdapter(thing: AnyDataAdapter): thing is BaseSequenceAdapter;
-export declare function isRegionsAdapter(thing: AnyDataAdapter): thing is RegionsAdapter;
-export declare function isFeatureAdapter(thing: AnyDataAdapter): thing is BaseFeatureDataAdapter;
-export interface Alias {
-    refName: string;
-    aliases: string[];
-}
-export interface BaseRefNameAliasAdapter extends BaseAdapter {
-    getRefNameAliases(opts: BaseOptions): Promise<Alias[]>;
-}
-export declare function isRefNameAliasAdapter(thing: object): thing is BaseRefNameAliasAdapter;
-export interface BaseTextSearchAdapter extends BaseAdapter {
-    searchIndex(args: BaseArgs): Promise<BaseResult[]>;
-}
-export declare function isTextSearchAdapter(thing: AnyDataAdapter): thing is BaseTextSearchAdapter;