@jbrowse/core 2.16.1 → 2.18.0

package/util/index.js

@@ -17,7 +17,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.blobToDataURL = exports.isFeature = exports.SimpleFeature = exports.defaultCodonTable = exports.defaultStops = exports.defaultStarts = exports.rIC = exports.complement = exports.isElectron = void 0;
+exports.makeAbortableReaction = exports.blobToDataURL = exports.isFeature = exports.SimpleFeature = exports.defaultCodonTable = exports.defaultStops = exports.defaultStarts = exports.rIC = exports.complementTable = exports.isElectron = void 0;
 exports.useDebounce = useDebounce;
 exports.useWidthSetter = useWidthSetter;
 exports.useDebouncedCallback = useDebouncedCallback;
@@ -45,7 +45,6 @@ exports.bpSpanPx = bpSpanPx;
 exports.iterMap = iterMap;
 exports.findLastIndex = findLastIndex;
 exports.findLast = findLast;
-exports.makeAbortableReaction = makeAbortableReaction;
 exports.renameRegionIfNeeded = renameRegionIfNeeded;
 exports.renameRegionsIfNeeded = renameRegionsIfNeeded;
 exports.minmax = minmax;
@@ -53,10 +52,12 @@ exports.shorten = shorten;
 exports.stringify = stringify;
 exports.revcom = revcom;
 exports.reverse = reverse;
+exports.complement = complement;
 exports.measureText = measureText;
 exports.getFrame = getFrame;
 exports.generateCodonTable = generateCodonTable;
 exports.updateStatus = updateStatus;
+exports.updateStatus2 = updateStatus2;
 exports.hashCode = hashCode;
 exports.objectHash = objectHash;
 exports.bytesForRegions = bytesForRegions;
@@ -88,20 +89,17 @@ exports.getStrokeProps = getStrokeProps;
 exports.getFillProps = getFillProps;
 exports.renderToStaticMarkup = renderToStaticMarkup;
 exports.isGzip = isGzip;
+exports.fetchAndMaybeUnzip = fetchAndMaybeUnzip;
 const react_1 = require("react");
+const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
+const useMeasure_1 = __importDefault(require("@jbrowse/core/util/useMeasure"));
 const is_object_1 = __importDefault(require("is-object"));
 const mobx_state_tree_1 = require("mobx-state-tree");
-const mobx_1 = require("mobx");
-const types_1 = require("./types");
-const aborting_1 = require("./aborting");
-const types_2 = require("./types");
-// has to be the full path and not the relative path to get the jest mock
-const useMeasure_1 = __importDefault(require("@jbrowse/core/util/useMeasure"));
-const colord_1 = require("./colord");
-// eslint-disable-next-line react/no-deprecated
 const react_dom_1 = require("react-dom");
+const colord_1 = require("./colord");
+const stopToken_1 = require("./stopToken");
+const types_1 = require("./types");
 __exportStar(require("./types"), exports);
-__exportStar(require("./aborting"), exports);
 __exportStar(require("./when"), exports);
 __exportStar(require("./range"), exports);
 __exportStar(require("./dedupe"), exports);
@@ -119,14 +117,10 @@ function useDebounce(value, delay) {
     }, [value, delay]);
     return debouncedValue;
 }
-// used in ViewContainer files to get the width
 function useWidthSetter(view, padding) {
     const [ref, { width }] = (0, useMeasure_1.default)();
     (0, react_1.useEffect)(() => {
         if (width && (0, mobx_state_tree_1.isAlive)(view)) {
-            // sets after a requestAnimationFrame
-            // https://stackoverflow.com/a/58701523/2129219
-            // avoids ResizeObserver loop error being shown during development
             requestAnimationFrame(() => {
                 view.setWidth(width - Number.parseInt(padding, 10) * 2);
             });
@@ -134,26 +128,19 @@ function useWidthSetter(view, padding) {
     }, [padding, view, width]);
     return ref;
 }
-// https://stackoverflow.com/questions/56283920/
 function useDebouncedCallback(callback, wait = 400) {
-    // track args & timeout handle between calls
     const argsRef = (0, react_1.useRef)();
     const timeout = (0, react_1.useRef)();
-    // make sure our timeout gets cleared if our consuming component gets
-    // unmounted
     (0, react_1.useEffect)(() => {
         if (timeout.current) {
             clearTimeout(timeout.current);
         }
     }, []);
     return function debouncedCallback(...args) {
-        // capture latest args
         argsRef.current = args;
-        // clear debounce timer
         if (timeout.current) {
             clearTimeout(timeout.current);
         }
-        // start waiting again
         timeout.current = setTimeout(() => {
             if (argsRef.current) {
                 callback(...argsRef.current);
@@ -161,9 +148,6 @@ function useDebouncedCallback(callback, wait = 400) {
         }, wait);
     };
 }
-/**
- * find the first node in the hierarchy that matches the given predicate
- */
 function findParentThat(node, predicate) {
     if (!(0, mobx_state_tree_1.hasParent)(node)) {
         throw new Error('node does not have parent');
@@ -182,7 +166,6 @@ function findParentThat(node, predicate) {
     }
     throw new Error('no matching node found');
 }
-// based on https://github.com/react-spring/react-spring/blob/cd5548a987383b8023efd620f3726a981f9e18ea/src/animated/FrameLoop.ts
 function springAnimate(fromValue, toValue, setValue, onFinish = () => { }, precision = 0, tension = 400, friction = 20, clamp = true) {
     const mass = 1;
     if (!precision) {
@@ -194,11 +177,9 @@ function springAnimate(fromValue, toValue, setValue, onFinish = () => { }, preci
         let position = animation.lastPosition;
         let lastTime = animation.lastTime || time;
         let velocity = animation.lastVelocity || 0;
-        // If we lost a lot of frames just jump to the end.
         if (time > lastTime + 64) {
             lastTime = time;
         }
-        // http://gafferongames.com/game-physics/fix-your-timestep/
         const numSteps = Math.floor(time - lastTime);
         for (let i = 0; i < numSteps; ++i) {
             const force = -tension * (position - toValue);
@@ -239,17 +220,9 @@ function springAnimate(fromValue, toValue, setValue, onFinish = () => { }, preci
         },
     ];
 }
-/**
- * find the first node in the hierarchy that matches the given 'is' typescript
- * type guard predicate
- */
 function findParentThatIs(node, predicate) {
     return findParentThat(node, predicate);
 }
-/**
- * get the current JBrowse session model, starting at any node in the state
- * tree
- */
 function getSession(node) {
     try {
         return findParentThatIs(node, types_1.isSessionModel);
@@ -258,10 +231,6 @@ function getSession(node) {
         throw new Error('no session model found!');
     }
 }
-/**
- * get the state model of the view in the state tree that contains the given
- * node
- */
 function getContainingView(node) {
     try {
         return findParentThatIs(node, types_1.isViewModel);
@@ -270,10 +239,6 @@ function getContainingView(node) {
         throw new Error('no containing view found');
     }
 }
-/**
- * get the state model of the view in the state tree that contains the given
- * node
- */
 function getContainingTrack(node) {
     try {
         return findParentThatIs(node, types_1.isTrackModel);
@@ -282,10 +247,6 @@ function getContainingTrack(node) {
         throw new Error('no containing track found');
     }
 }
-/**
- * get the state model of the display in the state tree that contains the given
- * node
- */
 function getContainingDisplay(node) {
     try {
         return findParentThatIs(node, types_1.isDisplayModel);
@@ -294,46 +255,9 @@ function getContainingDisplay(node) {
         throw new Error('no containing display found');
     }
 }
-/**
- * Assemble a 1-based "locString" from an interbase genomic location
- * @param region - Region
- * @example
- * ```ts
- * assembleLocString({ refName: 'chr1', start: 0, end: 100 })
- * // ↳ 'chr1:1..100'
- * ```
- * @example
- * ```ts
- * assembleLocString({ assemblyName: 'hg19', refName: 'chr1', start: 0, end: 100 })
- * // ↳ '{hg19}chr1:1..100'
- * ```
- * @example
- * ```ts
- * assembleLocString({ refName: 'chr1' })
- * // ↳ 'chr1'
- * ```
- * @example
- * ```ts
- * assembleLocString({ refName: 'chr1', start: 0 })
- * // ↳ 'chr1:1..'
- * ```
- * @example
- * ```ts
- * assembleLocString({ refName: 'chr1', end: 100 })
- * // ↳ 'chr1:1..100'
- * ```
- * @example
- * ```ts
- * assembleLocString({ refName: 'chr1', start: 0, end: 1 })
- * // ↳ 'chr1:1'
- * ```
- */
 function assembleLocString(region) {
     return assembleLocStringFast(region, toLocale);
 }
-// same as assembleLocString above, but does not perform toLocaleString which
-// can slow down the speed of block calculations which use assembleLocString
-// for block.key
 function assembleLocStringFast(region, cb = (n) => n) {
     const { assemblyName, refName, start, end, reversed } = region;
     const assemblyNameString = assemblyName ? `{${assemblyName}}` : '';
@@ -369,10 +293,7 @@ function parseLocStringOneBased(locString, isValidRefName) {
         reversed = true;
         locString = locString.replace(/\[rev]$/, '');
     }
-    // remove any whitespace
     locString = locString.replace(/\s/, '');
-    // refNames can have colons, refer to
-    // https://samtools.github.io/hts-specs/SAMv1.pdf Appendix A
     const assemblyMatch = /({(.+)})?(.+)/.exec(locString);
     if (!assemblyMatch) {
         throw new Error(`invalid location string: "${locString}"`);
@@ -402,9 +323,7 @@ function parseLocStringOneBased(locString, isValidRefName) {
     }
     else if (isValidRefName(prefix, assemblyName)) {
         if (suffix) {
-            // see if it's a range
             const rangeMatch = /^(-?(\d+|\d{1,3}(,\d{3})*))(\.\.|-)(-?(\d+|\d{1,3}(,\d{3})*))$/.exec(suffix);
-            // see if it's a single point
             const singleMatch = /^(-?(\d+|\d{1,3}(,\d{3})*))(\.\.|-)?$/.exec(suffix);
             if (rangeMatch) {
                 const [, start, , , , end] = rangeMatch;
@@ -422,7 +341,6 @@ function parseLocStringOneBased(locString, isValidRefName) {
                 const [, start, , , separator] = singleMatch;
                 if (start !== undefined) {
                     if (separator) {
-                        // indefinite end
                         return {
                             assemblyName,
                             refName: prefix,
@@ -460,43 +378,6 @@ function parseLocStringOneBased(locString, isValidRefName) {
     }
     throw new Error(`unknown reference sequence name in location "${locString}"`);
 }
-/**
- * Parse a 1-based location string into an interbase genomic location
- * @param locString - Location string
- * @param isValidRefName - Function that checks if a refName exists in the set
- * of all known refNames, or in the set of refNames for an assembly if
- * assemblyName is given
- * @example
- * ```ts
- * parseLocString('chr1:1..100', isValidRefName)
- * // ↳ { refName: 'chr1', start: 0, end: 100 }
- * ```
- * @example
- * ```ts
- * parseLocString('chr1:1-100', isValidRefName)
- * // ↳ { refName: 'chr1', start: 0, end: 100 }
- * ```
- * @example
- * ```ts
- * parseLocString(`{hg19}chr1:1..100`, isValidRefName)
- * // ↳ { assemblyName: 'hg19', refName: 'chr1', start: 0, end: 100 }
- * ```
- * @example
- * ```ts
- * parseLocString('chr1', isValidRefName)
- * // ↳ { refName: 'chr1' }
- * ```
- * @example
- * ```ts
- * parseLocString('chr1:1', isValidRefName)
- * // ↳ { refName: 'chr1', start: 0, end: 1 }
- * ```
- * @example
- * ```ts
- * parseLocString('chr1:1..', isValidRefName)
- * // ↳ { refName: 'chr1', start: 0}
- * ```
- */
 function parseLocString(locString, isValidRefName) {
     const parsed = parseLocStringOneBased(locString, isValidRefName);
     if (typeof parsed.start === 'number') {
@@ -536,13 +417,6 @@ function compareLocStrings(a, b, isValidRefName) {
     const locB = parseLocString(b, isValidRefName);
     return compareLocs(locA, locB);
 }
-/**
- * Ensure that a number is at least min and at most max.
- *
- * @param num -
- * @param min -
- * @param  max -
- */
 function clamp(num, min, max) {
     if (num < min) {
         return min;
@@ -555,11 +429,6 @@ function clamp(num, min, max) {
 function roundToNearestPointOne(num) {
     return Math.round(num * 10) / 10;
 }
-/**
- * @param bp -
- * @param region -
- * @param bpPerPx -
- */
 function bpToPx(bp, { reversed, end = 0, start = 0, }, bpPerPx) {
     return roundToNearestPointOne((reversed ? end - bp : bp - start) / bpPerPx);
 }
@@ -571,17 +440,9 @@ function radToDeg(radians) {
 function degToRad(degrees) {
     return (degrees * piOverOneEighty) % (2 * Math.PI);
 }
-/**
- * @returns [x, y]
- */
 function polarToCartesian(rho, theta) {
     return [rho * Math.cos(theta), rho * Math.sin(theta)];
 }
-/**
- * @param x - the x
- * @param y - the y
- * @returns [rho, theta]
- */
 function cartesianToPolar(x, y) {
     const rho = Math.sqrt(x * x + y * y);
     const theta = Math.atan(y / x);
@@ -595,7 +456,6 @@ function bpSpanPx(leftBp, rightBp, region, bpPerPx) {
     const end = bpToPx(rightBp, region, bpPerPx);
     return region.reversed ? [end, start] : [start, end];
 }
-// do an array map of an iterable
 function iterMap(iter, func, sizeHint) {
     const results = Array.from({ length: sizeHint || 0 });
     let counter = 0;
@@ -605,19 +465,6 @@ function iterMap(iter, func, sizeHint) {
     }
     return results;
 }
-/**
- * Returns the index of the last element in the array where predicate is true,
- * and -1 otherwise.
- * Based on https://stackoverflow.com/a/53187807
- *
- * @param array - The source array to search in
- *
- * @param predicate - find calls predicate once for each element of the array, in
- * descending order, until it finds one where predicate returns true.
- *
- * @returns findLastIndex returns element index where predicate is true.
- * Otherwise, findLastIndex returns -1.
- */
 function findLastIndex(array, predicate) {
     let l = array.length;
     while (l--) {
@@ -636,87 +483,14 @@ function findLast(array, predicate) {
     }
     return undefined;
 }
-/**
- * makes a mobx reaction with the given functions, that calls actions on the
- * model for each stage of execution, and to abort the reaction function when
- * the model is destroyed.
- *
- * Will call startedFunction(signal), successFunction(result), and
- * errorFunction(error) when the async reaction function starts, completes, and
- * errors respectively.
- *
- * @param self -
- * @param dataFunction -
- * @param asyncReactionFunction -
- * @param reactionOptions -
- * @param startedFunction -
- * @param successFunction -
- * @param errorFunction -
- */
-function makeAbortableReaction(self, dataFunction, asyncReactionFunction, 
-// @ts-expect-error
-reactionOptions, startedFunction, successFunction, errorFunction) {
-    let inProgress;
-    function handleError(error) {
-        if (!(0, aborting_1.isAbortException)(error)) {
-            if ((0, mobx_state_tree_1.isAlive)(self)) {
-                errorFunction(error);
-            }
-            else {
-                console.error(error);
-            }
-        }
-    }
-    (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.reaction)(() => {
-        try {
-            return dataFunction(self);
-        }
-        catch (e) {
-            handleError(e);
-            return undefined;
-        }
-    }, async (data, mobxReactionHandle) => {
-        if (inProgress && !inProgress.signal.aborted) {
-            inProgress.abort();
-        }
-        if (!(0, mobx_state_tree_1.isAlive)(self)) {
-            return;
-        }
-        inProgress = new AbortController();
-        const thisInProgress = inProgress;
-        startedFunction(thisInProgress);
-        try {
-            const result = await asyncReactionFunction(data, thisInProgress.signal, self, 
-            // @ts-expect-error
-            mobxReactionHandle);
-            (0, aborting_1.checkAbortSignal)(thisInProgress.signal);
-            if ((0, mobx_state_tree_1.isAlive)(self)) {
-                successFunction(result);
-            }
-        }
-        catch (e) {
-            if (!thisInProgress.signal.aborted) {
-                thisInProgress.abort();
-            }
-            handleError(e);
-        }
-    }, reactionOptions));
-    (0, mobx_state_tree_1.addDisposer)(self, () => {
-        if (inProgress && !inProgress.signal.aborted) {
-            inProgress.abort();
-        }
-    });
-}
 function renameRegionIfNeeded(refNameMap, region) {
     if ((0, mobx_state_tree_1.isStateTreeNode)(region) && !(0, mobx_state_tree_1.isAlive)(region)) {
         return region;
     }
     if (refNameMap === null || refNameMap === void 0 ? void 0 : refNameMap[region.refName]) {
-        // clone the region so we don't modify it
         region = (0, mobx_state_tree_1.isStateTreeNode)(region)
             ? { ...(0, mobx_state_tree_1.getSnapshot)(region) }
             : { ...region };
-        // modify it directly in the container
         const newRef = refNameMap[region.refName];
         if (newRef) {
             return { ...region, refName: newRef, originalRefName: region.refName };
@@ -738,9 +512,7 @@ async function renameRegionsIfNeeded(assemblyManager, args) {
     })));
     return {
         ...args,
-        regions: regions.map((region, i) => 
-        // note: uses assemblyNames defined above since region could be dead now
-        renameRegionIfNeeded(assemblyMaps[assemblyNames[i]], region)),
+        regions: regions.map((region, i) => renameRegionIfNeeded(assemblyMaps[assemblyNames[i]], region)),
     };
 }
 function minmax(a, b) {
@@ -759,67 +531,66 @@ function stringify({ refName, coord, assemblyName, oob, }, useAssemblyName) {
             : '',
     ].join('');
 }
-// 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
-//
-// const isElectron = process.versions.electron
-// const i2 = process.versions.hasOwnProperty('electron')
 exports.isElectron = /electron/i.test(typeof navigator !== 'undefined' ? navigator.userAgent : '');
-function revcom(seqString) {
-    return reverse((0, exports.complement)(seqString));
-}
-function reverse(seqString) {
-    return seqString.split('').reverse().join('');
-}
-exports.complement = (() => {
-    const complementRegex = /[ACGT]/gi;
-    // from bioperl: tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/
-    // generated with:
-    // perl -MJSON -E '@l = split "","acgtrymkswhbvdnxACGTRYMKSWHBVDNX"; print to_json({ map { my $in = $_; tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/; $in => $_ } @l})'
-    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',
-    };
-    return (seqString) => {
-        return seqString.replaceAll(complementRegex, m => complementTable[m] || '');
-    };
-})();
-// requires immediate execution in jest environment, because (hypothesis) it
-// otherwise listens for prerendered_canvas but reads empty pixels, and doesn't
-// get the contents of the canvas
+exports.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',
+};
+function revcom(str) {
+    var _a;
+    let revcomped = '';
+    for (let i = str.length - 1; i >= 0; i--) {
+        revcomped += (_a = exports.complementTable[str[i]]) !== null && _a !== void 0 ? _a : str[i];
+    }
+    return revcomped;
+}
+function reverse(str) {
+    let reversed = '';
+    for (let i = str.length - 1; i >= 0; i--) {
+        reversed += str[i];
+    }
+    return reversed;
+}
+function complement(str) {
+    var _a;
+    let comp = '';
+    for (let i = 0; i < str.length; i++) {
+        comp += (_a = exports.complementTable[str[i]]) !== null && _a !== void 0 ? _a : str[i];
+    }
+    return comp;
+}
 exports.rIC = typeof jest === 'undefined'
-    ? // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+    ?
         typeof window !== 'undefined' && window.requestIdleCallback
             ? window.requestIdleCallback
             : (cb) => setTimeout(() => {
@@ -828,9 +599,7 @@ exports.rIC = typeof jest === 'undefined'
     : (cb) => {
         cb();
     };
-// prettier-ignore
 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];
-// xref https://gist.github.com/tophtucker/62f93a4658387bb61e4510c37e2e97cf
 function measureText(str, fontSize = 10) {
     var _a;
     const avg = 0.5279276315789471;
@@ -915,10 +684,6 @@ exports.defaultCodonTable = {
     GGG: 'G',
     GGT: 'G',
 };
-/**
- * take CodonTable above and generate larger codon table that includes all
- * permutations of upper and lower case nucleotides
- */
 function generateCodonTable(table) {
     const tempCodonTable = {};
     Object.keys(table).forEach(codon => {
@@ -944,13 +709,19 @@ function generateCodonTable(table) {
     });
     return tempCodonTable;
 }
-// call statusCallback with current status and clear when finished
 async function updateStatus(msg, cb, fn) {
     cb(msg);
     const res = await fn();
     cb('');
     return res;
 }
+async function updateStatus2(msg, cb, stopToken, fn) {
+    cb(msg);
+    const res = await fn();
+    (0, stopToken_1.checkStopToken)(stopToken);
+    cb('');
+    return res;
+}
 function hashCode(str) {
     let hash = 0;
     if (str.length === 0) {
@@ -959,7 +730,7 @@ function hashCode(str) {
     for (let i = 0; i < str.length; i++) {
         const chr = str.charCodeAt(i);
         hash = (hash << 5) - hash + chr;
-        hash |= 0; // Convert to 32bit integer
+        hash |= 0;
     }
     return hash;
 }
@@ -976,8 +747,6 @@ async function bytesForRegions(regions, index) {
     }))
         .reduce((a, b) => a + b.end - b.start, 0);
 }
-// supported adapter types by text indexer ensure that this matches the method
-// found in @jbrowse/text-indexing/util
 function isSupportedIndexingAdapter(type = '') {
     return [
         'Gff3TabixAdapter',
@@ -1006,7 +775,6 @@ function getTickDisplayStr(totalBp, bpPerPx) {
         : toLocale(Math.floor(totalBp));
 }
 function getViewParams(model, exportSVG) {
-    // @ts-expect-error
     const { dynamicBlocks, staticBlocks, offsetPx } = getContainingView(model);
     const b = (dynamicBlocks === null || dynamicBlocks === void 0 ? void 0 : dynamicBlocks.contentBlocks[0]) || {};
     const staticblock = (staticBlocks === null || staticBlocks === void 0 ? void 0 : staticBlocks.contentBlocks[0]) || {};
@@ -1021,7 +789,6 @@ function getViewParams(model, exportSVG) {
 function getLayoutId({ sessionId, layoutId, }) {
     return `${sessionId}-${layoutId}`;
 }
-// Hook from https://usehooks.com/useLocalStorage/
 function useLocalStorage(key, initialValue) {
     const [storedValue, setStoredValue] = (0, react_1.useState)(() => {
         if (typeof window === 'undefined') {
@@ -1063,23 +830,18 @@ function getUriLink(value) {
 }
 function getStr(obj) {
     return (0, is_object_1.default)(obj)
-        ? (0, types_2.isUriLocation)(obj)
+        ? (0, types_1.isUriLocation)(obj)
             ? getUriLink(obj)
             : JSON.stringify(obj)
         : String(obj);
 }
-// tries to measure grid width without HTML tags included
 function coarseStripHTML(s) {
     return s.replaceAll(/(<([^>]+)>)/gi, '');
 }
-// based on autolink-js, license MIT
-// https://github.com/bryanwoods/autolink-js/blob/1418049970152c56ced73d43dcc62d80b320fb71/autolink.js#L9
 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>');
 }
-// heuristic measurement for a column of a @mui/x-data-grid, pass in
-// values from a column
 function measureGridWidth(elements, args) {
     const { padding = 30, minWidth = 80, fontSize = 12, maxWidth = 1000, stripHTML = false, } = args || {};
     return max(elements
@@ -1140,27 +902,18 @@ function notEmpty(value) {
     return value !== null && value !== undefined;
 }
 function mergeIntervals(intervals, w = 5000) {
-    // test if there are at least 2 intervals
     if (intervals.length <= 1) {
         return intervals;
     }
     const stack = [];
     let top = null;
-    // sort the intervals based on their start values
     intervals = intervals.sort((a, b) => a.start - b.start);
-    // push the 1st interval into the stack
     stack.push(intervals[0]);
-    // start from the next interval and merge if needed
     for (let i = 1; i < intervals.length; i++) {
-        // get the top element
         top = stack.at(-1);
-        // if the current interval doesn't overlap with the
-        // stack top element, push it to the stack
         if (top.end + w < intervals[i].start - w) {
             stack.push(intervals[i]);
         }
-        // otherwise update the end value of the top element
-        // if end of current interval is higher
         else if (top.end < intervals[i].end) {
             top.end = Math.max(top.end, intervals[i].end);
             stack.pop();
@@ -1169,7 +922,6 @@ function mergeIntervals(intervals, w = 5000) {
     }
     return stack;
 }
-// returns new array non-overlapping features
 function gatherOverlaps(regions, w = 5000) {
     const memo = {};
     for (const x of regions) {
@@ -1197,7 +949,6 @@ function getFillProps(str) {
         fill: c.alpha(1).toHex(),
     };
 }
-// https://react.dev/reference/react-dom/server/renderToString#removing-rendertostring-from-the-client-code
 function renderToStaticMarkup(node, createRootFn) {
     const div = document.createElement('div');
     (0, react_dom_1.flushSync)(() => {
@@ -1213,8 +964,18 @@ function renderToStaticMarkup(node, createRootFn) {
 function isGzip(buf) {
     return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
 }
+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, () => (0, bgzf_filehandle_1.unzip)(buf))
+        : buf;
+}
 var simpleFeature_1 = require("./simpleFeature");
 Object.defineProperty(exports, "SimpleFeature", { enumerable: true, get: function () { return __importDefault(simpleFeature_1).default; } });
 Object.defineProperty(exports, "isFeature", { enumerable: true, get: function () { return simpleFeature_1.isFeature; } });
 var blobToDataURL_1 = require("./blobToDataURL");
 Object.defineProperty(exports, "blobToDataURL", { enumerable: true, get: function () { return blobToDataURL_1.blobToDataURL; } });
+var makeAbortableReaction_1 = require("./makeAbortableReaction");
+Object.defineProperty(exports, "makeAbortableReaction", { enumerable: true, get: function () { return makeAbortableReaction_1.makeAbortableReaction; } });
+__exportStar(require("./aborting"), exports);