@jbrowse/core 3.7.0 → 4.0.0

package/util/analytics.js

@@ -1,86 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.writeAWSAnalytics = writeAWSAnalytics;
-exports.writeGAAnalytics = writeGAAnalytics;
-exports.doAnalytics = doAnalytics;
-const configuration_1 = require("../configuration");
-const util_1 = require("../util");
-async function writeAWSAnalytics(rootModel, initialTimeStamp, sessionQuery) {
-    try {
-        const url = 'https://analytics.jbrowse.org/api/v1';
-        const multiAssemblyTracks = rootModel.jbrowse.tracks.filter((track) => ((0, configuration_1.readConfObject)(track, 'assemblyNames') || []).length > 1).length;
-        const savedSessionCount = Object.keys(localStorage).filter(name => name.includes('localSaved-')).length;
-        const { jbrowse: config, session, version: ver } = rootModel;
-        const { tracks, assemblies, plugins } = config;
-        const stats = {
-            ver,
-            'plugins-count': (plugins === null || plugins === void 0 ? void 0 : plugins.length) || 0,
-            'plugin-names': plugins === null || plugins === void 0 ? void 0 : plugins.map((p) => p.name).join(','),
-            'assemblies-count': assemblies.length,
-            'tracks-count': tracks.length,
-            'session-tracks-count': (session === null || session === void 0 ? void 0 : session.sessionTracks.length) || 0,
-            'open-views': (session === null || session === void 0 ? void 0 : session.views.length) || 0,
-            'synteny-tracks-count': multiAssemblyTracks,
-            'saved-sessions-count': savedSessionCount,
-            'existing-session-param-type': (sessionQuery === null || sessionQuery === void 0 ? void 0 : sessionQuery.split('-')[0]) || 'none',
-            'scn-h': window.screen.height,
-            'scn-w': window.screen.width,
-            'win-h': window.innerHeight,
-            'win-w': window.innerWidth,
-            electron: util_1.isElectron,
-            loadTime: (Date.now() - initialTimeStamp) / 1000,
-            jb2: true,
-        };
-        tracks.forEach((track) => {
-            const key = `track-types-${track.type}`;
-            stats[key] = stats[key] + 1 || 1;
-        });
-        session === null || session === void 0 ? void 0 : session.sessionTracks.forEach((track) => {
-            const key = `sessionTrack-types-${track.type}`;
-            stats[key] = stats[key] + 1 || 1;
-        });
-        const qs = Object.keys(stats)
-            .map(key => `${key}=${stats[key]}`)
-            .join('&');
-        await fetch(`${url}?${qs}`);
-    }
-    catch (e) {
-        console.error('Failed to write analytics to AWS.', e);
-    }
-}
-async function writeGAAnalytics(rootModel, initialTimestamp) {
-    var _a;
-    const jbrowseUser = 'UA-7115575-5';
-    const stats = {
-        'tracks-count': rootModel.jbrowse.tracks.length,
-        ver: rootModel.version,
-        electron: util_1.isElectron,
-        loadTime: Date.now() - initialTimestamp,
-        pluginNames: ((_a = rootModel.jbrowse.plugins) === null || _a === void 0 ? void 0 : _a.map((plugin) => plugin.name)) || '',
-    };
-    let analyticsScript = "(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){";
-    analyticsScript +=
-        '(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),';
-    analyticsScript +=
-        'm=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)';
-    analyticsScript +=
-        "})(window,document,'script','https://www.google-analytics.com/analytics.js','ga');";
-    analyticsScript += `ga('create', '${jbrowseUser}', 'auto', 'jbrowseTracker');`;
-    const gaData = {};
-    const googleDimensions = 'tracks-count ver electron loadTime pluginNames';
-    for (const [index, key] of googleDimensions.split(/\s+/).entries()) {
-        gaData[`dimension${index + 1}`] = stats[key];
-    }
-    gaData.metric1 = Math.round(stats.loadTime);
-    analyticsScript += `ga('jbrowseTracker.send', 'pageview',${JSON.stringify(gaData)});`;
-    const analyticsScriptNode = document.createElement('script');
-    analyticsScriptNode.innerHTML = analyticsScript;
-    document.getElementsByTagName('head')[0].append(analyticsScriptNode);
-}
-function doAnalytics(rootModel, initialTimestamp, initialSessionQuery) {
-    if (rootModel &&
-        !(0, configuration_1.readConfObject)(rootModel.jbrowse.configuration, 'disableAnalytics')) {
-        writeAWSAnalytics(rootModel, initialTimestamp, initialSessionQuery);
-        writeGAAnalytics(rootModel, initialTimestamp);
-    }
-}

package/util/blobToDataURL.js

@@ -1,17 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.blobToDataURL = blobToDataURL;
-function blobToDataURL(blob) {
-    const a = new FileReader();
-    return new Promise((resolve, reject) => {
-        a.onload = e => {
-            if (e.target) {
-                resolve(e.target.result);
-            }
-            else {
-                reject(new Error('unknown result reading blob from canvas'));
-            }
-        };
-        a.readAsDataURL(blob);
-    });
-}

package/util/blockTypes.d.ts

@@ -1,58 +0,0 @@
-type Func<T> = (value: BaseBlock, index: number, array: BaseBlock[]) => T;
-export declare class BlockSet {
-    blocks: BaseBlock[];
-    constructor(blocks?: BaseBlock[]);
-    push(block: BaseBlock): void;
-    getBlocks(): BaseBlock[];
-    getRegions(): {
-        refName: string;
-        start: number;
-        end: number;
-        assemblyName: string;
-        reversed: boolean | undefined;
-    }[];
-    map<T, U = this>(func: Func<T>, thisarg?: U): T[];
-    forEach<T, U = this>(func: Func<T>, thisarg?: U): void;
-    get length(): number;
-    get totalWidthPx(): number;
-    get totalWidthPxWithoutBorders(): number;
-    get offsetPx(): number;
-    get contentBlocks(): BaseBlock[];
-    get totalBp(): number;
-}
-export declare class BaseBlock {
-    type: string;
-    regionNumber?: number;
-    reversed?: boolean;
-    refName: string;
-    start: number;
-    end: number;
-    assemblyName: string;
-    key: string;
-    offsetPx: number;
-    widthPx: number;
-    variant?: string;
-    isLeftEndOfDisplayedRegion?: boolean;
-    constructor(data: Record<string, any>);
-    toRegion(): {
-        refName: string;
-        start: number;
-        end: number;
-        assemblyName: string;
-        reversed: boolean | undefined;
-    };
-}
-export declare class ContentBlock extends BaseBlock {
-    type: string;
-}
-export declare class ElidedBlock extends BaseBlock {
-    type: string;
-    widthPx: number;
-    elidedBlockCount: number;
-    constructor(data: Record<string, any>);
-    push(otherBlock: ElidedBlock): void;
-}
-export declare class InterRegionPaddingBlock extends BaseBlock {
-    type: string;
-}
-export {};

package/util/blockTypes.js

@@ -1,110 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.InterRegionPaddingBlock = exports.ElidedBlock = exports.ContentBlock = exports.BaseBlock = exports.BlockSet = void 0;
-const _1 = require(".");
-class BlockSet {
-    constructor(blocks = []) {
-        this.blocks = blocks;
-    }
-    push(block) {
-        if (block.type === 'ElidedBlock' && this.blocks.length > 0) {
-            const lastBlock = this.blocks.at(-1);
-            if ((lastBlock === null || lastBlock === void 0 ? void 0 : lastBlock.type) === 'ElidedBlock') {
-                ;
-                lastBlock.push(block);
-                return;
-            }
-        }
-        this.blocks.push(block);
-    }
-    getBlocks() {
-        return this.blocks;
-    }
-    getRegions() {
-        return this.blocks.map(block => block.toRegion());
-    }
-    map(func, thisarg) {
-        return this.blocks.map(func, thisarg);
-    }
-    forEach(func, thisarg) {
-        this.blocks.forEach(func, thisarg);
-    }
-    get length() {
-        return this.blocks.length;
-    }
-    get totalWidthPx() {
-        return this.blocks.length > 0
-            ? (0, _1.sum)(this.blocks.map(blocks => blocks.widthPx))
-            : 0;
-    }
-    get totalWidthPxWithoutBorders() {
-        return this.blocks.length > 0
-            ? (0, _1.sum)(this.blocks
-                .filter(block => block.variant !== 'boundary')
-                .map(blocks => blocks.widthPx))
-            : 0;
-    }
-    get offsetPx() {
-        return this.blocks.length > 0 ? this.blocks[0].offsetPx : 0;
-    }
-    get contentBlocks() {
-        return this.blocks.filter(block => block.type === 'ContentBlock');
-    }
-    get totalBp() {
-        return (0, _1.sum)(this.contentBlocks.map(block => block.end - block.start));
-    }
-}
-exports.BlockSet = BlockSet;
-class BaseBlock {
-    constructor(data) {
-        this.type = 'BaseBlock';
-        this.widthPx = 0;
-        Object.assign(this, data);
-        this.assemblyName = data.assemblyName;
-        this.refName = data.refName;
-        this.start = data.start;
-        this.end = data.end;
-        this.key = data.key;
-        this.offsetPx = data.offsetPx;
-    }
-    toRegion() {
-        return {
-            refName: this.refName,
-            start: this.start,
-            end: this.end,
-            assemblyName: this.assemblyName,
-            reversed: this.reversed,
-        };
-    }
-}
-exports.BaseBlock = BaseBlock;
-class ContentBlock extends BaseBlock {
-    constructor() {
-        super(...arguments);
-        this.type = 'ContentBlock';
-    }
-}
-exports.ContentBlock = ContentBlock;
-class ElidedBlock extends BaseBlock {
-    constructor(data) {
-        super(data);
-        this.type = 'ElidedBlock';
-        this.elidedBlockCount = 0;
-        this.widthPx = data.widthPx;
-    }
-    push(otherBlock) {
-        this.elidedBlockCount += 1;
-        this.refName = '';
-        this.start = 0;
-        this.end = 0;
-        this.widthPx += otherBlock.widthPx;
-    }
-}
-exports.ElidedBlock = ElidedBlock;
-class InterRegionPaddingBlock extends BaseBlock {
-    constructor() {
-        super(...arguments);
-        this.type = 'InterRegionPaddingBlock';
-    }
-}
-exports.InterRegionPaddingBlock = InterRegionPaddingBlock;

package/util/calculateDynamicBlocks.d.ts

@@ -1,3 +0,0 @@
-import { BlockSet } from './blockTypes';
-import type { Base1DViewModel } from './calculateStaticBlocks';
-export default function calculateDynamicBlocks(model: Base1DViewModel, padding?: boolean, elision?: boolean): BlockSet;

package/util/calculateDynamicBlocks.js

@@ -1,100 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = calculateDynamicBlocks;
-const mobx_state_tree_1 = require("mobx-state-tree");
-const _1 = require(".");
-const blockTypes_1 = require("./blockTypes");
-const range_1 = require("./range");
-function calculateDynamicBlocks(model, padding = true, elision = true) {
-    const { offsetPx, displayedRegions, bpPerPx, width, minimumBlockWidth, interRegionPaddingWidth, } = model;
-    if (!width) {
-        throw new Error('view has no width, cannot calculate displayed blocks');
-    }
-    const blocks = new blockTypes_1.BlockSet();
-    let displayedRegionLeftPx = 0;
-    const windowLeftPx = offsetPx;
-    const windowRightPx = windowLeftPx + width;
-    for (let regionNumber = 0; regionNumber < displayedRegions.length; regionNumber++) {
-        const region = displayedRegions[regionNumber];
-        const { assemblyName, refName, start: regionStart, end: regionEnd, reversed, } = region;
-        const displayedRegionRightPx = displayedRegionLeftPx + (regionEnd - regionStart) / bpPerPx;
-        const regionWidthPx = (regionEnd - regionStart) / bpPerPx;
-        const parentRegion = (0, mobx_state_tree_1.isStateTreeNode)(region) ? (0, mobx_state_tree_1.getSnapshot)(region) : region;
-        const [leftPx, rightPx] = (0, range_1.intersection2)(windowLeftPx, windowRightPx, displayedRegionLeftPx, displayedRegionRightPx);
-        if (leftPx !== undefined && rightPx !== undefined) {
-            let start;
-            let end;
-            let isLeftEndOfDisplayedRegion;
-            let isRightEndOfDisplayedRegion;
-            let blockOffsetPx;
-            if (reversed) {
-                start = Math.max(regionStart, regionEnd - (rightPx - displayedRegionLeftPx) * bpPerPx);
-                end = regionEnd - (leftPx - displayedRegionLeftPx) * bpPerPx;
-                isLeftEndOfDisplayedRegion = end === regionEnd;
-                isRightEndOfDisplayedRegion = start === regionStart;
-                blockOffsetPx = displayedRegionLeftPx + (regionEnd - end) / bpPerPx;
-            }
-            else {
-                start = (leftPx - displayedRegionLeftPx) * bpPerPx + regionStart;
-                end = Math.min(regionEnd, (rightPx - displayedRegionLeftPx) * bpPerPx + regionStart);
-                isLeftEndOfDisplayedRegion = start === regionStart;
-                isRightEndOfDisplayedRegion = end === regionEnd;
-                blockOffsetPx = displayedRegionLeftPx + (start - regionStart) / bpPerPx;
-            }
-            const widthPx = (end - start) / bpPerPx;
-            const blockData = {
-                assemblyName,
-                refName,
-                start,
-                end,
-                reversed,
-                offsetPx: blockOffsetPx,
-                parentRegion,
-                regionNumber,
-                widthPx,
-                isLeftEndOfDisplayedRegion,
-                isRightEndOfDisplayedRegion,
-                key: '',
-            };
-            blockData.key = `${(0, _1.assembleLocStringFast)(blockData)}-${regionNumber}${reversed ? '-reversed' : ''}`;
-            if (padding && blocks.length === 0 && isLeftEndOfDisplayedRegion) {
-                blocks.push(new blockTypes_1.InterRegionPaddingBlock({
-                    key: `${blockData.key}-beforeFirstRegion`,
-                    widthPx: -offsetPx,
-                    offsetPx: blockData.offsetPx + offsetPx,
-                    variant: 'boundary',
-                }));
-            }
-            if (elision && regionWidthPx < minimumBlockWidth) {
-                blocks.push(new blockTypes_1.ElidedBlock(blockData));
-            }
-            else {
-                blocks.push(new blockTypes_1.ContentBlock(blockData));
-            }
-            if (padding) {
-                if (regionWidthPx >= minimumBlockWidth &&
-                    blockData.isRightEndOfDisplayedRegion &&
-                    regionNumber < displayedRegions.length - 1) {
-                    blocks.push(new blockTypes_1.InterRegionPaddingBlock({
-                        key: `${blockData.key}-rightpad`,
-                        widthPx: interRegionPaddingWidth,
-                        offsetPx: blockData.offsetPx + blockData.widthPx,
-                    }));
-                    displayedRegionLeftPx += interRegionPaddingWidth;
-                }
-                if (regionNumber === displayedRegions.length - 1 &&
-                    blockData.isRightEndOfDisplayedRegion) {
-                    blockOffsetPx = blockData.offsetPx + blockData.widthPx;
-                    blocks.push(new blockTypes_1.InterRegionPaddingBlock({
-                        key: `${blockData.key}-afterLastRegion`,
-                        widthPx: width - blockOffsetPx + offsetPx,
-                        offsetPx: blockOffsetPx,
-                        variant: 'boundary',
-                    }));
-                }
-            }
-        }
-        displayedRegionLeftPx += (regionEnd - regionStart) / bpPerPx;
-    }
-    return blocks;
-}

package/util/calculateStaticBlocks.d.ts

@@ -1,13 +0,0 @@
-import { BlockSet } from './blockTypes';
-import type { Region } from './types';
-import type { Region as RegionModel } from './types/mst';
-import type { Instance } from 'mobx-state-tree';
-export interface Base1DViewModel {
-    offsetPx: number;
-    width: number;
-    displayedRegions: (Region | Instance<typeof RegionModel>)[];
-    bpPerPx: number;
-    minimumBlockWidth: number;
-    interRegionPaddingWidth: number;
-}
-export default function calculateStaticBlocks(model: Base1DViewModel, padding?: boolean, elision?: boolean, extra?: number, width?: number): BlockSet;

package/util/calculateStaticBlocks.js

@@ -1,102 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = calculateStaticBlocks;
-const mobx_state_tree_1 = require("mobx-state-tree");
-const _1 = require(".");
-const blockTypes_1 = require("./blockTypes");
-function calculateStaticBlocks(model, padding = true, elision = true, extra = 0, width = 800) {
-    const { offsetPx, displayedRegions, bpPerPx, minimumBlockWidth, interRegionPaddingWidth, width: modelWidth, } = model;
-    const windowLeftBp = offsetPx * bpPerPx;
-    const windowRightBp = (offsetPx + modelWidth) * bpPerPx;
-    const blockSizePx = width;
-    const blockSizeBp = Math.ceil(blockSizePx * bpPerPx);
-    let regionBpOffset = 0;
-    const blocks = new blockTypes_1.BlockSet();
-    for (let regionNumber = 0; regionNumber < displayedRegions.length; regionNumber++) {
-        const region = displayedRegions[regionNumber];
-        const { assemblyName, refName, start: regionStart, end: regionEnd, reversed, } = region;
-        const regionBlockCount = Math.ceil((regionEnd - regionStart) / blockSizeBp);
-        const parentRegion = (0, mobx_state_tree_1.isStateTreeNode)(region) ? (0, mobx_state_tree_1.getSnapshot)(region) : region;
-        let windowRightBlockNum = Math.floor((windowRightBp - regionBpOffset) / blockSizeBp) + extra;
-        if (windowRightBlockNum >= regionBlockCount) {
-            windowRightBlockNum = regionBlockCount - 1;
-        }
-        let windowLeftBlockNum = Math.floor((windowLeftBp - regionBpOffset) / blockSizeBp) - extra;
-        if (windowLeftBlockNum < 0) {
-            windowLeftBlockNum = 0;
-        }
-        const regionWidthPx = (regionEnd - regionStart) / bpPerPx;
-        for (let blockNum = windowLeftBlockNum; blockNum <= windowRightBlockNum; blockNum += 1) {
-            let start;
-            let end;
-            let isLeftEndOfDisplayedRegion;
-            let isRightEndOfDisplayedRegion;
-            if (reversed) {
-                start = Math.max(regionStart, regionEnd - (blockNum + 1) * blockSizeBp);
-                end = regionEnd - blockNum * blockSizeBp;
-                isLeftEndOfDisplayedRegion = end === regionEnd;
-                isRightEndOfDisplayedRegion = start === regionStart;
-            }
-            else {
-                start = regionStart + blockNum * blockSizeBp;
-                end = Math.min(regionEnd, regionStart + (blockNum + 1) * blockSizeBp);
-                isLeftEndOfDisplayedRegion = start === regionStart;
-                isRightEndOfDisplayedRegion = end === regionEnd;
-            }
-            const widthPx = (end - start) / bpPerPx;
-            const blockData = {
-                assemblyName,
-                refName,
-                start,
-                end,
-                reversed,
-                offsetPx: (regionBpOffset + blockNum * blockSizeBp) / bpPerPx,
-                parentRegion,
-                regionNumber,
-                widthPx,
-                isLeftEndOfDisplayedRegion,
-                isRightEndOfDisplayedRegion,
-                key: '',
-            };
-            blockData.key = `${(0, _1.assembleLocStringFast)(blockData)}-${regionNumber}${reversed ? '-reversed' : ''}`;
-            if (padding && regionNumber === 0 && blockNum === 0) {
-                blocks.push(new blockTypes_1.InterRegionPaddingBlock({
-                    key: `${blockData.key}-beforeFirstRegion`,
-                    widthPx: width,
-                    offsetPx: blockData.offsetPx - width,
-                    variant: 'boundary',
-                }));
-            }
-            if (elision && regionWidthPx < minimumBlockWidth) {
-                blocks.push(new blockTypes_1.ElidedBlock(blockData));
-            }
-            else {
-                blocks.push(new blockTypes_1.ContentBlock(blockData));
-            }
-            if (padding) {
-                if (regionWidthPx >= minimumBlockWidth &&
-                    blockData.isRightEndOfDisplayedRegion &&
-                    regionNumber < displayedRegions.length - 1) {
-                    regionBpOffset += interRegionPaddingWidth * bpPerPx;
-                    blocks.push(new blockTypes_1.InterRegionPaddingBlock({
-                        key: `${blockData.key}-rightpad`,
-                        widthPx: interRegionPaddingWidth,
-                        offsetPx: blockData.offsetPx + blockData.widthPx,
-                    }));
-                }
-                if (regionNumber === displayedRegions.length - 1 &&
-                    blockData.isRightEndOfDisplayedRegion) {
-                    regionBpOffset += interRegionPaddingWidth * bpPerPx;
-                    blocks.push(new blockTypes_1.InterRegionPaddingBlock({
-                        key: `${blockData.key}-afterLastRegion`,
-                        widthPx: width,
-                        offsetPx: blockData.offsetPx + blockData.widthPx,
-                        variant: 'boundary',
-                    }));
-                }
-            }
-        }
-        regionBpOffset += regionEnd - regionStart;
-    }
-    return blocks;
-}

package/util/cluster.d.ts

@@ -1,17 +0,0 @@
-export declare function euclideanDistance(a: number[], b: number[]): number;
-export declare function averageDistance(setA: number[], setB: number[], distances: number[][]): number;
-export declare function clusterData({ data, distance, linkage, onProgress, stopToken, }: {
-    data: number[][];
-    distance?: (a: number[], b: number[]) => number;
-    linkage?: (a: number[], b: number[], distances: number[][]) => number;
-    onProgress?: (a: string) => void;
-    stopToken?: string;
-}): {
-    clusters: {
-        height: number;
-        indexes: number[];
-    } | undefined;
-    distances: number[][];
-    order: number[];
-    clustersGivenK: number[][][];
-};

package/util/cluster.js

@@ -1,102 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.euclideanDistance = euclideanDistance;
-exports.averageDistance = averageDistance;
-exports.clusterData = clusterData;
-const stopToken_1 = require("@jbrowse/core/util/stopToken");
-function toP(n) {
-    return Number.parseFloat((n * 100).toFixed(1));
-}
-function euclideanDistance(a, b) {
-    const size = Math.min(a.length, b.length);
-    let sum = 0;
-    for (let index = 0; index < size; index++) {
-        sum += (a[index] - b[index]) * (a[index] - b[index]);
-    }
-    return Math.sqrt(sum);
-}
-function averageDistance(setA, setB, distances) {
-    let distance = 0;
-    const lenA = setA.length;
-    const lenB = setB.length;
-    for (let i = 0; i < lenA; i++) {
-        for (let j = 0; j < lenB; j++) {
-            distance += distances[setA[i]][setB[j]];
-        }
-    }
-    return distance / setA.length / setB.length;
-}
-function clusterData({ data, distance = euclideanDistance, linkage = averageDistance, onProgress, stopToken, }) {
-    let stopTokenCheckerStart = performance.now();
-    let progressStart = performance.now();
-    const distances = [];
-    for (let i = 0; i < data.length; i++) {
-        const r = performance.now();
-        if (r - stopTokenCheckerStart > 400) {
-            (0, stopToken_1.checkStopToken)(stopToken);
-            stopTokenCheckerStart = performance.now();
-        }
-        if (r - progressStart > 50) {
-            onProgress === null || onProgress === void 0 ? void 0 : onProgress(`Making distance matrix: ${toP(i / (data.length - 1))}%`);
-            progressStart = performance.now();
-        }
-        const row = [];
-        for (let j = 0; j < data.length; j++) {
-            row.push(distance(data[i], data[j]));
-        }
-        distances.push(row);
-    }
-    const clusters = data.map((_datum, index) => ({
-        height: 0,
-        indexes: [index],
-    }));
-    let clustersGivenK = [];
-    stopTokenCheckerStart = performance.now();
-    progressStart = performance.now();
-    for (let iteration = 0; iteration < data.length; iteration++) {
-        const r = performance.now();
-        if (r - stopTokenCheckerStart > 400) {
-            (0, stopToken_1.checkStopToken)(stopToken);
-            stopTokenCheckerStart = performance.now();
-        }
-        if (r - progressStart > 50) {
-            onProgress === null || onProgress === void 0 ? void 0 : onProgress(`Clustering: ${toP((iteration + 1) / data.length)}%`);
-            progressStart = performance.now();
-        }
-        clustersGivenK.push(clusters.map(cluster => cluster.indexes));
-        if (iteration >= data.length - 1) {
-            break;
-        }
-        let nearestDistance = Infinity;
-        let nearestRow = 0;
-        let nearestCol = 0;
-        for (let row = 0; row < clusters.length; row++) {
-            for (let col = row + 1; col < clusters.length; col++) {
-                const distance = linkage(clusters[row].indexes, clusters[col].indexes, distances);
-                if (distance < nearestDistance) {
-                    nearestDistance = distance;
-                    nearestRow = row;
-                    nearestCol = col;
-                }
-            }
-        }
-        const newCluster = {
-            indexes: [
-                ...clusters[nearestRow].indexes,
-                ...clusters[nearestCol].indexes,
-            ],
-            height: nearestDistance,
-            children: [clusters[nearestRow], clusters[nearestCol]],
-        };
-        clusters.splice(Math.max(nearestRow, nearestCol), 1);
-        clusters.splice(Math.min(nearestRow, nearestCol), 1);
-        clusters.push(newCluster);
-    }
-    clustersGivenK = [[], ...clustersGivenK.reverse()];
-    return {
-        clusters: clusters[0],
-        distances: distances,
-        order: clusters[0].indexes,
-        clustersGivenK: clustersGivenK,
-    };
-}