@jbrowse/core 4.3.0 → 5.0.0-beta.2

package/esm/util/index.js

@@ -1,765 +1,128 @@
-import { useEffect, useRef, useState } from 'react';
-import { unzip } from '@gmod/bgzf-filehandle';
-import useMeasure from '@jbrowse/core/util/useMeasure';
-import { getEnv as getEnvMST, getParent, getSnapshot, hasParent, isAlive, isStateTreeNode, } from '@jbrowse/mobx-state-tree';
-import { flushSync } from 'react-dom';
-import { createRoot } from 'react-dom/client';
-import { coarseStripHTML } from "./coarseStripHTML.js";
-import { colord } from "./colord.js";
-import { parseLocString } from "./locString.js";
-import { checkStopToken } from "./stopToken.js";
-import { isDisplayModel, isSessionModel, isTrackModel, isUriLocation, isViewModel, } from "./types/index.js";
-export * from "./types/index.js";
-export * from "./when.js";
-export * from "./range.js";
-export * from "./dedupe.js";
-export * from "./coarseStripHTML.js";
-export * from "./offscreenCanvasPonyfill.js";
-export * from "./offscreenCanvasUtils.js";
-export * from "./rpc.js";
-export * from "./crypto.js";
-const containingDisplayCache = new WeakMap();
-const containingTrackCache = new WeakMap();
-const containingViewCache = new WeakMap();
-const sessionCache = new WeakMap();
-export function useDebounce(value, delay) {
-    const [debouncedValue, setDebouncedValue] = useState(value);
-    useEffect(() => {
-        const handle = setTimeout(() => {
-            setDebouncedValue(value);
-        }, delay);
-        return () => {
-            clearTimeout(handle);
-        };
-    }, [value, delay]);
-    return debouncedValue;
-}
-export function useWidthSetter(view, padding) {
-    const [ref, { width }] = useMeasure();
-    useEffect(() => {
-        let token;
-        if (width && isAlive(view)) {
-            token = requestAnimationFrame(() => {
-                view.setWidth(width);
-            });
-        }
-        return () => {
-            if (token) {
-                cancelAnimationFrame(token);
-            }
-        };
-    }, [padding, view, width]);
-    return ref;
-}
-export function useDebouncedCallback(callback, wait = 400) {
-    const argsRef = useRef(null);
-    const timeout = useRef(null);
-    useEffect(() => {
-        if (timeout.current) {
-            clearTimeout(timeout.current);
-        }
-    }, []);
-    return function debouncedCallback(...args) {
-        argsRef.current = args;
-        if (timeout.current) {
-            clearTimeout(timeout.current);
-        }
-        timeout.current = setTimeout(() => {
-            if (argsRef.current) {
-                callback(...argsRef.current);
-            }
-        }, wait);
-    };
-}
-export function findParentThat(node, predicate) {
-    if (!hasParent(node)) {
-        throw new Error('node does not have parent');
-    }
-    let currentNode = getParent(node);
-    while (currentNode && isAlive(currentNode)) {
-        if (predicate(currentNode)) {
-            return currentNode;
-        }
-        if (hasParent(currentNode)) {
-            currentNode = getParent(currentNode);
-        }
-        else {
-            break;
-        }
-    }
-    throw new Error('no matching node found');
-}
-export function springAnimate(fromValue, toValue, setValue, onFinish = () => { }, precision = 0, tension = 400, friction = 20, clamp = true) {
-    const mass = 1;
-    if (!precision) {
-        precision = Math.abs(toValue - fromValue) / 1000;
-    }
-    let animationFrameId;
-    function update(animation) {
-        const time = performance.now();
-        let position = animation.lastPosition;
-        let lastTime = animation.lastTime || time;
-        let velocity = animation.lastVelocity || 0;
-        if (time > lastTime + 64) {
-            lastTime = time;
-        }
-        const numSteps = Math.floor(time - lastTime);
-        for (let i = 0; i < numSteps; ++i) {
-            const force = -tension * (position - toValue);
-            const damping = -friction * velocity;
-            const acceleration = (force + damping) / mass;
-            velocity += (acceleration * 1) / 1000;
-            position += (velocity * 1) / 1000;
-        }
-        const isVelocity = Math.abs(velocity) <= precision;
-        const isDisplacement = tension !== 0 ? Math.abs(toValue - position) <= precision : true;
-        const isOvershooting = clamp && tension !== 0
-            ? fromValue < toValue
-                ? position > toValue
-                : position < toValue
-            : false;
-        const endOfAnimation = isOvershooting || (isVelocity && isDisplacement);
-        if (endOfAnimation) {
-            setValue(toValue);
-            onFinish();
-        }
-        else {
-            setValue(position);
-            animationFrameId = requestAnimationFrame(() => {
-                update({
-                    lastPosition: position,
-                    lastTime: time,
-                    lastVelocity: velocity,
-                });
-            });
-        }
-    }
-    return [
-        () => {
-            update({ lastPosition: fromValue });
-        },
-        () => {
-            cancelAnimationFrame(animationFrameId);
-        },
-    ];
-}
-export function findParentThatIs(node, predicate) {
-    return findParentThat(node, predicate);
-}
-export function getSession(node) {
-    const cached = sessionCache.get(node);
-    if (cached && isAlive(cached)) {
-        return cached;
-    }
-    try {
-        const result = findParentThatIs(node, isSessionModel);
-        sessionCache.set(node, result);
-        return result;
-    }
-    catch (e) {
-        throw new Error('no session model found!');
-    }
-}
-export function getContainingView(node) {
-    const cached = containingViewCache.get(node);
-    if (cached && isAlive(cached)) {
-        return cached;
-    }
-    try {
-        const result = findParentThatIs(node, isViewModel);
-        containingViewCache.set(node, result);
-        return result;
-    }
-    catch (e) {
-        throw new Error('no containing view found');
-    }
-}
-export function getContainingTrack(node) {
-    const cached = containingTrackCache.get(node);
-    if (cached && isAlive(cached)) {
-        return cached;
-    }
-    try {
-        const result = findParentThatIs(node, isTrackModel);
-        containingTrackCache.set(node, result);
-        return result;
-    }
-    catch (e) {
-        throw new Error('no containing track found');
-    }
-}
-export function getContainingDisplay(node) {
-    const cached = containingDisplayCache.get(node);
-    if (cached && isAlive(cached)) {
-        return cached;
-    }
-    try {
-        const result = findParentThatIs(node, isDisplayModel);
-        containingDisplayCache.set(node, result);
-        return result;
-    }
-    catch (e) {
-        throw new Error('no containing display found');
-    }
-}
-export function assembleLocString(region) {
-    return assembleLocStringFast(region, toLocale);
-}
-export function assembleLocStringFast(region, cb = (n) => n) {
-    const { assemblyName, refName, start, end, reversed } = region;
-    const assemblyNameString = assemblyName ? `{${assemblyName}}` : '';
-    let startString;
-    if (start !== undefined) {
-        startString = `:${cb(start + 1)}`;
-    }
-    else if (end !== undefined) {
-        startString = ':1';
-    }
-    else {
-        startString = '';
-    }
-    let endString;
-    if (end !== undefined) {
-        endString = start !== undefined && start + 1 === end ? '' : `..${cb(end)}`;
-    }
-    else {
-        endString = start !== undefined ? '..' : '';
-    }
-    let rev = '';
-    if (reversed) {
-        rev = '[rev]';
-    }
-    return `${assemblyNameString}${refName}${startString}${endString}${rev}`;
-}
-export function compareLocs(locA, locB) {
-    const assemblyComp = locA.assemblyName || locB.assemblyName
-        ? (locA.assemblyName || '').localeCompare(locB.assemblyName || '')
-        : 0;
-    if (assemblyComp) {
-        return assemblyComp;
-    }
-    const refComp = locA.refName || locB.refName
-        ? (locA.refName || '').localeCompare(locB.refName || '')
-        : 0;
-    if (refComp) {
-        return refComp;
-    }
-    if (locA.start !== undefined && locB.start !== undefined) {
-        const startComp = locA.start - locB.start;
-        if (startComp) {
-            return startComp;
-        }
-    }
-    if (locA.end !== undefined && locB.end !== undefined) {
-        const endComp = locA.end - locB.end;
-        if (endComp) {
-            return endComp;
-        }
-    }
-    return 0;
-}
-export function compareLocStrings(a, b, isValidRefName) {
-    const locA = parseLocString(a, isValidRefName);
-    const locB = parseLocString(b, isValidRefName);
-    return compareLocs(locA, locB);
-}
-export function clamp(num, min, max) {
-    if (num < min) {
-        return min;
-    }
-    if (num > max) {
-        return max;
-    }
-    return num;
-}
-function roundToNearestPointOne(num) {
-    return Math.round(num * 10) / 10;
-}
-export function bpToPx(bp, { reversed, end = 0, start = 0, }, bpPerPx) {
-    return roundToNearestPointOne((reversed ? end - bp : bp - start) / bpPerPx);
-}
-const oneEightyOverPi = 180 / Math.PI;
-const piOverOneEighty = Math.PI / 180;
-export function radToDeg(radians) {
-    return (radians * oneEightyOverPi) % 360;
-}
-export function degToRad(degrees) {
-    return (degrees * piOverOneEighty) % (2 * Math.PI);
-}
-export function polarToCartesian(rho, theta) {
-    return [rho * Math.cos(theta), rho * Math.sin(theta)];
-}
-export function cartesianToPolar(x, y) {
-    const rho = Math.sqrt(x * x + y * y);
-    const theta = Math.atan(y / x);
-    return [rho, theta];
-}
-export function featureSpanPx(feature, region, bpPerPx) {
-    return bpSpanPx(feature.get('start'), feature.get('end'), region, bpPerPx);
-}
-export function bpSpanPx(leftBp, rightBp, region, bpPerPx) {
-    const start = bpToPx(leftBp, region, bpPerPx);
-    const end = bpToPx(rightBp, region, bpPerPx);
-    return region.reversed ? [end, start] : [start, end];
-}
-export function calculateLayoutBounds(featureStart, featureEnd, layoutWidthBp, reversed) {
-    const featureWidthBp = featureEnd - featureStart;
-    const labelOverhangBp = Math.max(0, layoutWidthBp - featureWidthBp);
-    return reversed
-        ? [featureStart - labelOverhangBp, featureEnd]
-        : [featureStart, featureStart + layoutWidthBp];
-}
-export function iterMap(iter, func, sizeHint) {
-    const results = Array.from({ length: sizeHint || 0 });
-    let counter = 0;
-    for (const item of iter) {
-        results[counter] = func(item);
-        counter += 1;
-    }
-    return results;
-}
-export function findLastIndex(array, predicate) {
-    let l = array.length;
-    while (l--) {
-        if (predicate(array[l], l, array)) {
-            return l;
-        }
-    }
-    return -1;
-}
-export function findLast(array, predicate) {
-    let l = array.length;
-    while (l--) {
-        if (predicate(array[l], l, array)) {
-            return array[l];
-        }
-    }
-    return undefined;
-}
-export function renameRegionIfNeeded(refNameMap, region, getSeqAdapterRefName) {
-    if (isStateTreeNode(region) && !isAlive(region)) {
-        return region;
-    }
-    const newRef = refNameMap?.[region.refName];
-    if (newRef) {
+import { isElectron } from './environment.js';
+import { storeBlobLocation } from './tracks.js';
+// `unzip` is deliberately NOT re-exported here — it lives at
+// '@jbrowse/core/util/unzip' so this barrel does not reach bgzf/pako. See that
+// file for why a re-export of it cannot be tree-shaken.
+//
+// Same weight, other direction: don't `await import('@jbrowse/core/util')` to
+// defer something. A dynamic namespace request re-inflates what the named
+// static imports tree-shook away — 231KB against 145KB, measured. Point the
+// dynamic import at the module instead ('@jbrowse/core/svg/saveSvgAsImage').
+export { capitalizeFirst, pluralize, shorten, shorten2, truncateMiddle, } from './stringUtils.js';
+export { formatBytes } from './formatBytes.js';
+export { getFillProps, getStrokeProps, stripAlpha } from './svgColorProps.js';
+export { fetchAndMaybeUnzip, fetchAndMaybeUnzipText, isGzip, } from './fetchAndMaybeUnzip.js';
+export { AuthNeededError, addOrReplaceView, canReplaceView, isAbstractMenuManager, isAppRootModel, isAuthNeededException, isBlobLocation, isDisplayModel, isFileHandleLocation, isLocalPathLocation, isRootModelWithInternetAccounts, isSelectionContainer, isSessionModel, isSessionServices, isSessionModelWithConfigEditing, isSessionModelWithConnectionEditing, isSessionModelWithConnections, isSessionModelWithWidgets, isSessionWithAddAssembly, isSessionWithAddSessionTrack, isSessionWithAddTracks, isSessionWithPublishTrackConf, isSessionWithDeleteTrackConf, isSessionWithMultipleViews, isSessionWithPermanentPlugins, isSessionWithSessionPlugins, isSessionWithSessionTracks, isSessionWithShareURL, isSessionWithViewReplacement, isTrackModel, isTrackViewModel, isUriLocation, isViewContainer, isViewModel, } from './types/index.js';
+export { getPluginUpdate, installablePlugins, installedVersionFromUrl, isPluginInstalled, resolvePlugin, resolveStorePluginRefs, resolveStoreRefs, } from './pluginStore.js';
+export { createProgressReporter, createStatusFanOut, createStatusWindow, downloadStatus, progressLabel, statusFraction, statusMessageText, statusProgressLabel, statusReading, statusSource, throttleStatusEmits, updateStatus, withProgress, } from './progress.js';
+export { calculateRedispatchRange, doesIntersect2, intersection2, } from './range.js';
+export { dedupe } from './dedupe.js';
+export { MAX_GLOB_REGIONS, matchRefNames, parseRegionNames, resolveNamedRegions, selectNamedRegions, } from './selectNamedRegions.js';
+export { isValidTag, tagRegex } from './tags.js';
+export { formatRelativeTime } from './formatRelativeTime.js';
+export { fetchJson } from './fetchJson.js';
+export { ENCODED_PREFIX, JSON_PREFIX, SHARE_PREFIX, b64PadSuffix, encodeSessionParam, fromUrlSafeB64, readSessionFromDynamo, shareEndpoint, toUrlSafeB64, } from './sessionSharing.js';
+export { coarseStripHTML } from './coarseStripHTML.js';
+export { measureText, measuredFont } from './measureText.js';
+export { createScrollLatch } from './scrollLatch.js';
+export { MAX_ZOOM_RATE_PER_MS, SCROLL_ZOOM_FACTOR_DIVISOR, ZOOM_ACTIVE_WINDOW_MS, accumulateScroll, applyZoomAccum, getZoomNormalizer, isActivelyZooming, normalizeWheelDelta, wheelFrameElapsedMs, wheelZoomAccum, } from './wheelZoom.js';
+export { avg, clamp, getDisplayStr, getNumberGrouping, max, maxFinite, min, minmax, polarToCartesian, radToDeg, reducePrecision, setNumberGrouping, sum, toLocale, } from './numericUtils.js';
+export { bpSpanPx, bpToPx, bytesForRegions, featureSpanPx, getBpDisplayStr, getTickDisplayStr, parseBpString, } from './bpUtils.js';
+export { gatherOverlaps, mergeIntervals, } from './intervals.js';
+export { clampToContig } from './clampToContig.js';
+export { animationAllowed } from './animationAllowed.js';
+export { springAnimate } from './springAnimate.js';
+export { localStorageAvailable, localStorageGetBoolean, localStorageGetItem, localStorageGetJSON, localStorageGetNumber, localStorageGetStringArray, localStorageRemoveItem, localStorageSetBoolean, localStorageSetItem, localStorageSetJSON, localStorageSetNumber, notifyLocalStorageKey, subscribeToLocalStorageKey, } from './localStorage.js';
+export { renameRegionIfNeeded, renameRegionsIfNeeded } from './renameRegions.js';
+export { addAndShowTrack } from './addAndShowTrack.js';
+export { addTrackFromWidget, containerDisplaysAssembly, finishAddTrack, } from './addTrackFromWidget.js';
+export { namesTemporaryAssembly } from './temporaryAssembly.js';
+export { makeTrackId } from './makeTrackId.js';
+export { matchTrackId } from './matchTrackId.js';
+export { drawImageOntoCanvasContext } from './offscreenCanvasPonyfill.js';
+export { indexedDBAvailable, isElectron, isNode, rIC } from './environment.js';
+export { isWebWorker } from './isWebWorker.js';
+export { sessionStorageAvailable, sessionStorageGetItem, sessionStorageRemoveItem, sessionStorageSetItem, } from './sessionStorage.js';
+export { isObject } from './objectUtils.js';
+export { openPromotableDisplays } from './openDisplays.js';
+export { applyOrderWithin, reorder, reorderWithin, } from './reorder.js';
+export { getStr } from './getStr.js';
+export { downloadPhase, getLocationUri, resolveUri } from './getLocationUri.js';
+export { measureGridWidth, resolveSelectedIds } from './dataGridUtils.js';
+export { isRpcResult } from './rpc.js';
+export { aesDecrypt, aesEncrypt, sha256, sha256Base64, sha256Base64Url, toBase64, toBase64Url, } from './crypto.js';
+export { notifyFeatureDetailsMiss, openFeatureWidget, } from './openFeatureWidget.js';
+export { withFeatureDetails } from './withFeatureDetails.js';
+export { canonicalizeViewRefName, findParentThat, findParentThatIs, getAssemblyHost, getContainingDisplay, getContainingTrack, getContainingView, getEnv, getRenderingServices, launchOrReplaceView, getSession, hashCode, objectHash, } from './mstUtils.js';
+export { getDialogHost, getNotificationSink, getPaletteHost, getRpcHost, getSessionServices, } from './sessionServices.js';
+// this is recommended in a later comment in
+// https://github.com/electron/electron/issues/2288 for detecting electron in a
+// renderer process, which is the one that has node enabled for us
+//
+/**
+ * Convert a browser File (from a drop zone or file input) into a FileLocation:
+ * a native local path under electron, or an in-memory blob location otherwise.
+ */
+export function fileToLocation(file) {
+    if (isElectron) {
         return {
-            ...(isStateTreeNode(region) ? getSnapshot(region) : region),
-            refName: newRef,
-            originalRefName: getSeqAdapterRefName?.(region.refName) ?? region.refName,
+            // @ts-ignore - electron injects require onto window, needs to be ignore not expect-error for now
+            localPath: window.require('electron').webUtils.getPathForFile(file),
+            locationType: 'LocalPathLocation',
         };
     }
-    return region;
-}
-export async function renameRegionsIfNeeded(assemblyManager, args) {
-    const { regions = [], adapterConfig } = args;
-    if (!args.sessionId) {
-        throw new Error('sessionId is required');
-    }
-    const assemblyNames = regions.map(r => r.assemblyName);
-    const uniqueAssemblyNames = [...new Set(assemblyNames)];
-    const assemblyData = Object.fromEntries(await Promise.all(uniqueAssemblyNames.map(async (name) => [
-        name,
-        {
-            refNameMap: await assemblyManager.getRefNameMapForAdapter(adapterConfig, name, args),
-            assembly: assemblyManager.get(name),
-        },
-    ])));
-    return {
-        ...args,
-        regions: regions.map((region, i) => {
-            const { refNameMap, assembly } = assemblyData[assemblyNames[i]];
-            return renameRegionIfNeeded(refNameMap, region, assembly ? r => assembly.getSeqAdapterRefName(r) : undefined);
-        }),
-    };
-}
-export function minmax(a, b) {
-    return [Math.min(a, b), Math.max(a, b)];
-}
-export function shorten(name, max = 70, short = 30) {
-    return name.length > max
-        ? `${name.slice(0, short)}...${name.slice(-short)}`
-        : name;
-}
-export function shorten2(name, max = 70) {
-    return name.length > max ? `${name.slice(0, max)}...` : name;
-}
-export function stringify({ refName, coord, assemblyName, oob, }, useAssemblyName) {
-    return [
-        assemblyName && useAssemblyName ? `{${assemblyName}}` : '',
-        refName
-            ? `${shorten(refName)}:${toLocale(coord)}${oob ? ' (out of bounds)' : ''}`
-            : '',
-    ].join('');
-}
-export const isElectron = /electron/i.test(typeof navigator !== 'undefined' ? navigator.userAgent : '');
-export const complementTable = {
-    S: 'S',
-    w: 'w',
-    T: 'A',
-    r: 'y',
-    a: 't',
-    N: 'N',
-    K: 'M',
-    x: 'x',
-    d: 'h',
-    Y: 'R',
-    V: 'B',
-    y: 'r',
-    M: 'K',
-    h: 'd',
-    k: 'm',
-    C: 'G',
-    g: 'c',
-    t: 'a',
-    A: 'T',
-    n: 'n',
-    W: 'W',
-    X: 'X',
-    m: 'k',
-    v: 'b',
-    B: 'V',
-    s: 's',
-    H: 'D',
-    c: 'g',
-    D: 'H',
-    b: 'v',
-    R: 'Y',
-    G: 'C',
-};
-export function revcom(str) {
-    const revcomped = [];
-    for (let i = str.length - 1; i >= 0; i--) {
-        revcomped.push(complementTable[str[i]] ?? str[i]);
-    }
-    return revcomped.join('');
-}
-export function reverse(str) {
-    const reversed = [];
-    for (let i = str.length - 1; i >= 0; i--) {
-        reversed.push(str[i]);
-    }
-    return reversed.join('');
-}
-export function complement(str) {
-    const comp = [];
-    for (let i = 0, l = str.length; i < l; i++) {
-        comp.push(complementTable[str[i]] ?? str[i]);
-    }
-    return comp.join('');
-}
-export const rIC = typeof jest === 'undefined'
-    ?
-        typeof window !== 'undefined' && window.requestIdleCallback
-            ? window.requestIdleCallback
-            : (cb) => setTimeout(() => {
-                cb();
-            }, 1)
-    : (cb) => {
-        cb();
-    };
-const widths = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.2796875, 0.2765625, 0.3546875, 0.5546875, 0.5546875, 0.8890625, 0.665625, 0.190625, 0.3328125, 0.3328125, 0.3890625, 0.5828125, 0.2765625, 0.3328125, 0.2765625, 0.3015625, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.2765625, 0.2765625, 0.584375, 0.5828125, 0.584375, 0.5546875, 1.0140625, 0.665625, 0.665625, 0.721875, 0.721875, 0.665625, 0.609375, 0.7765625, 0.721875, 0.2765625, 0.5, 0.665625, 0.5546875, 0.8328125, 0.721875, 0.7765625, 0.665625, 0.7765625, 0.721875, 0.665625, 0.609375, 0.721875, 0.665625, 0.94375, 0.665625, 0.665625, 0.609375, 0.2765625, 0.3546875, 0.2765625, 0.4765625, 0.5546875, 0.3328125, 0.5546875, 0.5546875, 0.5, 0.5546875, 0.5546875, 0.2765625, 0.5546875, 0.5546875, 0.221875, 0.240625, 0.5, 0.221875, 0.8328125, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.3328125, 0.5, 0.2765625, 0.5546875, 0.5, 0.721875, 0.5, 0.5, 0.5, 0.3546875, 0.259375, 0.353125, 0.5890625];
-const avgWidth = 0.5279276315789471;
-export function measureText(str, fontSize = 10) {
-    const s = String(str);
-    let total = 0;
-    for (let i = 0, l = s.length; i < l; i++) {
-        total += widths[s.charCodeAt(i)] ?? avgWidth;
-    }
-    return total * fontSize;
-}
-export function getFrame(start, end, strand, phase) {
-    return strand === 1
-        ? (((start + phase) % 3) + 1)
-        : (-1 * ((end - phase) % 3) - 1);
-}
-export const defaultStarts = ['ATG'];
-export const defaultStops = ['TAA', 'TAG', 'TGA'];
-export const defaultCodonTable = {
-    TCA: 'S',
-    TCC: 'S',
-    TCG: 'S',
-    TCT: 'S',
-    TTC: 'F',
-    TTT: 'F',
-    TTA: 'L',
-    TTG: 'L',
-    TAC: 'Y',
-    TAT: 'Y',
-    TAA: '*',
-    TAG: '*',
-    TGC: 'C',
-    TGT: 'C',
-    TGA: '*',
-    TGG: 'W',
-    CTA: 'L',
-    CTC: 'L',
-    CTG: 'L',
-    CTT: 'L',
-    CCA: 'P',
-    CCC: 'P',
-    CCG: 'P',
-    CCT: 'P',
-    CAC: 'H',
-    CAT: 'H',
-    CAA: 'Q',
-    CAG: 'Q',
-    CGA: 'R',
-    CGC: 'R',
-    CGG: 'R',
-    CGT: 'R',
-    ATA: 'I',
-    ATC: 'I',
-    ATT: 'I',
-    ATG: 'M',
-    ACA: 'T',
-    ACC: 'T',
-    ACG: 'T',
-    ACT: 'T',
-    AAC: 'N',
-    AAT: 'N',
-    AAA: 'K',
-    AAG: 'K',
-    AGC: 'S',
-    AGT: 'S',
-    AGA: 'R',
-    AGG: 'R',
-    GTA: 'V',
-    GTC: 'V',
-    GTG: 'V',
-    GTT: 'V',
-    GCA: 'A',
-    GCC: 'A',
-    GCG: 'A',
-    GCT: 'A',
-    GAC: 'D',
-    GAT: 'D',
-    GAA: 'E',
-    GAG: 'E',
-    GGA: 'G',
-    GGC: 'G',
-    GGG: 'G',
-    GGT: 'G',
-};
-export function generateCodonTable(table) {
-    const tempCodonTable = {};
-    for (const codon of Object.keys(table)) {
-        const aa = table[codon];
-        const nucs = [];
-        for (let i = 0; i < 3; i++) {
-            const nuc = codon.charAt(i);
-            nucs[i] = [];
-            nucs[i][0] = nuc.toUpperCase();
-            nucs[i][1] = nuc.toLowerCase();
-        }
-        for (let i = 0; i < 2; i++) {
-            const n0 = nucs[0][i];
-            for (let j = 0; j < 2; j++) {
-                const n1 = nucs[1][j];
-                for (let k = 0; k < 2; k++) {
-                    const n2 = nucs[2][k];
-                    const triplet = n0 + n1 + n2;
-                    tempCodonTable[triplet] = aa;
-                }
-            }
+    else {
+        const loc = storeBlobLocation({ blob: file });
+        if ('blobId' in loc) {
+            return loc;
         }
-    }
-    return tempCodonTable;
-}
-export async function updateStatus(msg, cb, fn) {
-    cb?.(msg);
-    const res = await fn();
-    cb?.('');
-    return res;
-}
-export async function updateStatus2(msg, cb, stopToken, fn) {
-    cb(msg);
-    const res = await fn();
-    checkStopToken(stopToken);
-    cb('');
-    return res;
-}
-export function hashCode(str) {
-    let hash = 0;
-    if (str.length === 0) {
-        return hash;
-    }
-    for (let i = 0; i < str.length; i++) {
-        const chr = str.charCodeAt(i);
-        hash = (hash << 5) - hash + chr;
-        hash |= 0;
-    }
-    return hash;
-}
-export function objectHash(obj) {
-    return `${hashCode(JSON.stringify(obj))}`;
-}
-export async function bytesForRegions(regions, index) {
-    const blockResults = await Promise.all(regions.map(r => index.blocksForRange(r.refName, r.start, r.end)));
-    return sum(blockResults
-        .flat()
-        .map(block => block.maxv.blockPosition + 65535 - block.minv.blockPosition));
-}
+        else {
+            throw new Error('could not store file as a blob location');
+        }
+    }
+}
+export { complement, complementTable, defaultStarts, getFrame, revcom, reverse, stitch, } from './seqUtils.js';
+export { revlist } from './revlist.js';
+// Part of the published ABI at v4.0.0 and v4.3.0 and dropped by a barrel
+// split, which is the same way `defaultCodonTable` went (ac47890743). Nothing in
+// this repo imports them from here, but the barrel is what external plugins
+// resolve against at runtime: jbrowse-plugin-msaview and jbrowse-plugin-mafviewer
+// both `import { useLocalStorage } from '@jbrowse/core/util'`, and on a host
+// without it that is `(0, PR.useLocalStorage) is not a function` when the panel
+// renders. The implementations never went anywhere -- only these lines did.
+export { useCreateOnce, useDebounce, useFinalUnmount, useLocalStorage, useWidthSetter, } from './hooks.js';
+export { codonTable, defaultCodonTable, generateCodonTable, } from './geneticCodes.js';
+export { IUPAC_MOTIF_REGEX, isPalindromic, iupacToRegex, reverseComplementIupac, } from './iupac.js';
+export { parseMotifList, } from './parseMotifList.js';
+// Browser-safe mirror of `indexableAdapters` in @jbrowse/text-indexing-core,
+// which cannot be imported here (it pulls in node:fs). Pinned by the parity
+// test in packages/text-indexing/src/util.test.ts — the one place that depends
+// on both packages. NOT text-indexing-core's own common.test.ts, which this
+// used to name: that one calls text-indexing-core's `isSupportedIndexingAdapter`
+// rather than this mirror, so it passes however far the two drift apart.
 export function isSupportedIndexingAdapter(type = '') {
     return [
-        'Gff3TabixAdapter',
-        'VcfTabixAdapter',
         'Gff3Adapter',
+        'Gff3TabixAdapter',
+        'GtfAdapter',
+        'GtfTabixAdapter',
         'VcfAdapter',
+        'VcfTabixAdapter',
     ].includes(type);
 }
-export function getBpDisplayStr(total) {
-    if (Math.floor(total / 1_000_000) > 0) {
-        return `${reducePrecision(total / 1_000_000)}Mbp`;
-    }
-    else if (Math.floor(total / 1_000) > 0) {
-        return `${reducePrecision(total / 1_000)}Kbp`;
-    }
-    else {
-        return `${Math.floor(total)}bp`;
-    }
-}
-export function reducePrecision(s, n = 3) {
-    return toLocale(Number.parseFloat(s.toPrecision(n)));
-}
-export function getProgressDisplayStr(current, total) {
-    if (Math.floor(total / 1_000_000) > 0) {
-        return `${reducePrecision(current / 1_000_000)}/${reducePrecision(total / 1_000_000)}Mb`;
-    }
-    else if (Math.floor(total / 1_000) > 0) {
-        return `${reducePrecision(current / 1_000)}/${reducePrecision(total / 1_000)}Kb`;
-    }
-    else {
-        return `${reducePrecision(current)}/${reducePrecision(total)} bytes`;
-    }
-}
-export function toLocale(n) {
-    if (n < 1000) {
-        return String(n);
-    }
-    const str = String(n);
-    const len = str.length;
-    let result = '';
-    for (let i = 0; i < len; i++) {
-        if (i > 0 && (len - i) % 3 === 0) {
-            result += ',';
-        }
-        result += str[i];
-    }
-    return result;
-}
-export function getTickDisplayStr(totalBp, bpPerPx) {
-    return Math.floor(bpPerPx / 1_000) > 0
-        ? `${toLocale(Number.parseFloat((totalBp / 1_000_000).toFixed(2)))}M`
-        : toLocale(Math.floor(totalBp));
-}
-export function getLayoutId({ sessionId, trackInstanceId, }) {
-    return `${sessionId}-${trackInstanceId}`;
-}
-export function getStatsId({ sessionId, trackInstanceId, }) {
-    return `${sessionId}-${trackInstanceId}`;
-}
-export function useLocalStorage(key, initialValue, enabled = true) {
-    const [storedValue, setStoredValue] = useState(() => {
-        if (typeof window === 'undefined' || !enabled) {
-            return initialValue;
-        }
-        try {
-            const item = window.localStorage.getItem(key);
-            return item ? JSON.parse(item) : initialValue;
-        }
-        catch (error) {
-            console.error(error);
-            return initialValue;
-        }
-    });
-    const setValue = (value) => {
-        try {
-            const valueToStore = value instanceof Function ? value(storedValue) : value;
-            setStoredValue(valueToStore);
-            if (typeof window !== 'undefined' && enabled) {
-                window.localStorage.setItem(key, JSON.stringify(valueToStore));
-            }
-        }
-        catch (error) {
-            console.error(error);
-        }
-    };
-    return [storedValue, setValue];
-}
-export function getUriLink(value) {
-    const { uri, baseUri = '' } = value;
-    let href;
-    try {
-        href = new URL(uri, baseUri).href;
-    }
-    catch (e) {
-        href = uri;
-    }
-    return href;
-}
-export function getStr(obj) {
-    return isObject(obj)
-        ? isUriLocation(obj)
-            ? getUriLink(obj)
-            : JSON.stringify(obj)
-        : String(obj);
-}
-export function linkify(s) {
-    const pattern = /(^|[\s\n]|<[A-Za-z]*\/?>)((?:https?|ftp):\/\/[-A-Z0-9+\u0026\u2019@#/%?=()~_|!:,.;]*[-A-Z0-9+\u0026@#/%=~()_|])/gi;
-    return s.replaceAll(pattern, '$1<a href=\'$2\' target="_blank">$2</a>');
-}
-export function measureGridWidth(elements, args) {
-    const { padding = 30, minWidth = 80, fontSize = 12, maxWidth = 1000, stripHTML = false, } = args || {};
-    return max(elements
-        .map(element => getStr(element))
-        .map(str => (stripHTML ? coarseStripHTML(str) : str))
-        .map(str => measureText(str, fontSize))
-        .map(n => Math.min(Math.max(n + padding, minWidth), maxWidth)));
-}
-export function getEnv(obj) {
-    return getEnvMST(obj);
-}
-export function localStorageGetItem(item) {
-    return typeof localStorage !== 'undefined'
-        ? localStorage.getItem(item)
-        : undefined;
-}
-export function localStorageSetItem(str, item) {
-    if (typeof localStorage !== 'undefined') {
-        localStorage.setItem(str, item);
-    }
-}
-export function max(arr, init = Number.NEGATIVE_INFINITY) {
-    let max = init;
-    for (const entry of arr) {
-        max = Math.max(entry, max);
-    }
-    return max;
-}
-export function min(arr, init = Number.POSITIVE_INFINITY) {
-    let min = init;
-    for (const entry of arr) {
-        min = Math.min(entry, min);
-    }
-    return min;
-}
-export function sum(arr) {
-    let sum = 0;
-    for (const entry of arr) {
-        sum += entry;
-    }
-    return sum;
-}
-export function avg(arr) {
-    return sum(arr) / arr.length;
-}
+// Null prototype, not `{}`: keys are data (a BAM QNAME, a track category), and
+// on a plain object `result['constructor'] ??= []` finds Object and never
+// assigns, so the next line throws.
+//
+// Still an object rather than a Map because this is on the plugin ABI — a Map
+// would leave `Object.entries` on a published plugin returning [] and silently
+// doing nothing. So integer-like keys still hoist ahead of the rest; anything
+// needing insertion order builds its own Map (see tree-sidebar's CLAUDE.md).
 export function groupBy(array, predicate) {
-    const result = {};
+    const result = Object.create(null);
     for (const value of array) {
         const t = predicate(value);
-        if (!result[t]) {
-            result[t] = [];
-        }
+        result[t] ??= [];
         result[t].push(value);
     }
     return result;
@@ -767,110 +130,29 @@ export function groupBy(array, predicate) {
 export function notEmpty(value) {
     return value !== null && value !== undefined;
 }
-export function mergeIntervals(intervals, w = 5000) {
-    if (intervals.length <= 1) {
-        return intervals;
-    }
-    const stack = [];
-    let top = null;
-    intervals = intervals.sort((a, b) => a.start - b.start);
-    stack.push(intervals[0]);
-    for (let i = 1; i < intervals.length; i++) {
-        top = stack.at(-1);
-        if (top.end + w < intervals[i].start - w) {
-            stack.push(intervals[i]);
-        }
-        else if (top.end < intervals[i].end) {
-            top.end = Math.max(top.end, intervals[i].end);
-            stack.pop();
-            stack.push(top);
-        }
-    }
-    return stack;
-}
-export function gatherOverlaps(regions, w = 5000) {
-    const memo = {};
-    for (const x of regions) {
-        if (!memo[x.refName]) {
-            memo[x.refName] = [];
-        }
-        memo[x.refName].push(x);
-    }
-    return Object.values(memo).flatMap(group => mergeIntervals(group.sort((a, b) => a.start - b.start), w));
-}
-export function stripAlpha(str) {
-    return colord(str).alpha(1).toHex();
-}
-export function getStrokeProps(str) {
-    if (str) {
-        const c = colord(str);
-        return {
-            strokeOpacity: c.alpha(),
-            stroke: c.alpha(1).toHex(),
-        };
-    }
-    else {
-        return {};
-    }
-}
-export function getFillProps(str) {
-    if (str) {
-        const c = colord(str);
-        return {
-            fillOpacity: c.alpha(),
-            fill: c.alpha(1).toHex(),
-        };
-    }
-    else {
-        return {};
-    }
-}
-export function renderToStaticMarkup(node) {
-    const div = document.createElement('div');
-    flushSync(() => {
-        createRoot(div).render(node);
-    });
-    return div.innerHTML.replaceAll(/\brgba\((.+?),[^,]+?\)/g, 'rgb($1)');
-}
-export function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
-}
-export async function fetchAndMaybeUnzip(loc, opts = {}) {
-    const { statusCallback = () => { } } = opts;
-    const buf = await updateStatus('Downloading file', statusCallback, () => loc.readFile(opts));
-    return isGzip(buf)
-        ? await updateStatus('Unzipping', statusCallback, () => unzip(buf))
-        : buf;
-}
-export async function fetchAndMaybeUnzipText(loc, opts) {
-    const buffer = await fetchAndMaybeUnzip(loc, opts);
-    if (buffer.length > 536_870_888) {
-        throw new Error('Data exceeds maximum string length (512MB)');
-    }
-    return new TextDecoder('utf8', { fatal: true }).decode(buffer);
-}
-export function isObject(x) {
-    return typeof x === 'object' && x !== null;
-}
-export function localStorageGetNumber(key, defaultVal) {
-    return +(localStorageGetItem(key) ?? defaultVal);
-}
-export function localStorageGetBoolean(key, defaultVal) {
-    return Boolean(JSON.parse(localStorageGetItem(key) || JSON.stringify(defaultVal)));
-}
-export function localStorageSetBoolean(key, value) {
-    localStorageSetItem(key, JSON.stringify(value));
-}
 export function testAdapter(fileName, regex, adapterHint, expected) {
     return (regex.test(fileName) && !adapterHint) || adapterHint === expected;
 }
-export { default as SimpleFeature, isFeature, } from "./simpleFeature.js";
-export { blobToDataURL } from "./blobToDataURL.js";
-export { makeAbortableReaction } from "./makeAbortableReaction.js";
-export * from "./aborting.js";
-export * from "./linkify.js";
-export * from "./locString.js";
-export * from "./stopToken.js";
-export * from "./tracks.js";
-export * from "./fileHandleStore.js";
-export { IntervalTree } from "./IntervalTree.js";
+export { default as SimpleFeature, isFeature, } from './simpleFeature.js';
+export { saveAs } from './FileSaver/index.js';
+export { saveSvgAsImage, svgHtmlToPngBlob, } from '../svg/saveSvgAsImage.js';
+export { createStatusChannel, createStopTokenRotation, } from './createStopTokenRotation.js';
+// `installFetch` is deliberately NOT re-exported here: it reaches `getSession`
+// through `fetchContext.ts`, which imports this barrel, so exporting it makes
+// the barrel initialize itself. Import it from `@jbrowse/core/util/installFetch`.
+export { createSharedSetup } from './cachedSetup.js';
+export { isDataCurrent } from './isDataCurrent.js';
+export { handleFetchError, isAbortException, makeAbortError, } from './aborting.js';
+export { linkify } from './linkify.js';
+export { locStringsToRegions } from './locStringsToRegions.js';
+export { UnknownRefNameError, assembleLocString, assembleLocStringRaw, assembleLocStrings, compareLocStrings, compareLocs, parseLocString, parseLocStringOneBased, stringify, } from './locString.js';
+export { checkStopToken, checkStopTokenThrottled, createStopToken, createStopTokenChecker, hasSharedArrayBuffer, isStopToken, isStopped, markStopTokenStopped, registerStopTokenBroadcaster, stopStopToken, stopTokenSignal, withStopTokenCheck, withStopTokenSignal, } from './stopToken.js';
+export { adapterNeedsAddTrackComponent, addAddTrackComponent, } from './addTrackComponent.js';
+export { adapterConfigFromSpec } from './formatGuessers.js';
+export { UNKNOWN, UNSUPPORTED, addAdapterGuesser, addTrackTypeGuesser, clearFileFromCache, ensureFileHandleReady, expandLooseTrackConfig, findFileHandleIds, generateUnknownTrackConf, generateUnsupportedTrackConf, getBlob, getBlobMap, getConfAssemblyNames, getFileFromCache, getFileName, getRpcSessionId, getTrackAssemblyNames, getTrackName, guessAdapter, guessTrackConf, guessTrackType, hasFileHandlesInCache, hideTrackGeneric, isLooseTrackConfig, makeIndex, makeIndexType, restoreFileHandles, restoreFileHandlesFromSnapshot, setBlobMap, setFileInCache, showTrackGeneric, storeBlobLocation, storeFileHandleLocation, stripFileExtension, stripTrackIds, toggleTrackGeneric, } from './tracks.js';
+export { getFileHandle, isFileSystemAccessSupported, storeFileHandle, verifyPermission, } from './fileHandleStore.js';
+export { IntervalTree } from './IntervalTree.js';
+export { cmpStr } from './cmpStr.js';
+export { diffTrackConfig, flattenTrackConfigDelta, mergeTrackConfig, } from './trackConfigDelta.js';
+export { BEZIER_CONNECTOR_MAX_REACH_PX, bezierConnectorPath, } from './bezierConnector.js';
+export { diagonalizeRegions, } from './diagonalizeRegions.js';