@jbrowse/plugin-alignments 3.7.0 → 4.0.0

package/esm/LinearReadCloudDisplay/drawFeatsStack.js

@@ -1,30 +0,0 @@
-import GranularRectLayout from '@jbrowse/core/util/layouts/GranularRectLayout';
-import { drawFeatsCommon } from './drawFeatsCommon';
-function calculateStackYOffsets(computedChains, self, _view, featureHeight) {
-    var _a, _b;
-    const noSpacing = (_a = self.noSpacing) !== null && _a !== void 0 ? _a : false;
-    const maxHeight = (_b = self.trackMaxHeight) !== null && _b !== void 0 ? _b : 1200;
-    const layout = new GranularRectLayout({
-        pitchX: 1,
-        pitchY: 1,
-        maxHeight,
-    });
-    const layoutPadding = noSpacing ? 0 : 1;
-    for (const { id, minX, maxX, chain } of computedChains) {
-        layout.addRect(id, minX, maxX, featureHeight + layoutPadding, {
-            feat: chain[0],
-            fill: 'transparent',
-            stroke: 'transparent',
-            distance: maxX - minX,
-        });
-    }
-    const chainYOffsets = new Map();
-    for (const [id, rect] of layout.getRectangles()) {
-        const top = rect[1];
-        chainYOffsets.set(id, top);
-    }
-    return { chainYOffsets, layoutHeight: layout.getTotalHeight() };
-}
-export function drawFeats(self, ctx) {
-    drawFeatsCommon(self, ctx, calculateStackYOffsets);
-}

package/esm/PileupRPC/methods/GetReducedFeatures.d.ts

@@ -1,37 +0,0 @@
-import PileupBaseRPC from '../base';
-import type { Region } from '@jbrowse/core/util';
-export default class PileupGetReducedFeatures extends PileupBaseRPC {
-    name: string;
-    execute(args: {
-        adapterConfig: Record<string, unknown>;
-        stopToken?: string;
-        headers?: Record<string, string>;
-        regions: Region[];
-        sessionId: string;
-        tag: string;
-    }, rpcDriver: string): Promise<{
-        chains: {
-            id: string;
-            refName: string;
-            name: any;
-            start: number;
-            strand: any;
-            end: number;
-            flags: any;
-            tlen: any;
-            pair_orientation: any;
-            next_ref: any;
-            next_pos: any;
-            clipPos: number;
-            SA: any;
-        }[][];
-        stats: {
-            upper: number;
-            lower: number;
-            avg: number;
-            sd: number;
-        } | undefined;
-        hasPaired: boolean;
-        containsNoTransferables: boolean;
-    }>;
-}

package/esm/PileupRPC/methods/GetReducedFeatures.js

@@ -1,48 +0,0 @@
-import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import { dedupe, groupBy } from '@jbrowse/core/util';
-import { firstValueFrom } from 'rxjs';
-import { toArray } from 'rxjs/operators';
-import { getClip } from '../../MismatchParser';
-import PileupBaseRPC from '../base';
-import { filterForPairs, getInsertSizeStats } from '../util';
-export default class PileupGetReducedFeatures extends PileupBaseRPC {
-    constructor() {
-        super(...arguments);
-        this.name = 'PileupGetReducedFeatures';
-    }
-    async execute(args, rpcDriver) {
-        const deserializedArgs = await this.deserializeArguments(args, rpcDriver);
-        const { adapterConfig, sessionId, regions } = deserializedArgs;
-        const dataAdapter = (await getAdapter(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
-        const featuresArray = await firstValueFrom(dataAdapter
-            .getFeaturesInMultipleRegions(regions, deserializedArgs)
-            .pipe(toArray()));
-        const reduced = dedupe(featuresArray.map(f => {
-            var _a;
-            return ({
-                id: f.id(),
-                refName: f.get('refName'),
-                name: f.get('name'),
-                start: f.get('start'),
-                strand: f.get('strand'),
-                end: f.get('end'),
-                flags: f.get('flags'),
-                tlen: f.get('template_length'),
-                pair_orientation: f.get('pair_orientation'),
-                next_ref: f.get('next_ref'),
-                next_pos: f.get('next_pos'),
-                clipPos: getClip(f.get('CIGAR'), f.get('strand')),
-                SA: (_a = f.get('tags')) === null || _a === void 0 ? void 0 : _a.SA,
-            });
-        }), f => f.id);
-        const filtered = filterForPairs(reduced);
-        const stats = filtered.length ? getInsertSizeStats(filtered) : undefined;
-        const chains = groupBy(reduced, f => f.name);
-        return {
-            chains: Object.values(chains),
-            stats,
-            hasPaired: !!stats,
-            containsNoTransferables: true,
-        };
-    }
-}

package/esm/PileupRPC/util.d.ts

@@ -1,8 +0,0 @@
-import type { ReducedFeature } from '../shared/fetchChains';
-export declare function getInsertSizeStats(features: ReducedFeature[]): {
-    upper: number;
-    lower: number;
-    avg: number;
-    sd: number;
-};
-export declare function filterForPairs(features: ReducedFeature[]): ReducedFeature[];

package/esm/PileupRPC/util.js

@@ -1,14 +0,0 @@
-export function getInsertSizeStats(features) {
-    const filtered = features.map(f => Math.abs(f.tlen));
-    const sum = filtered.reduce((a, b) => a + b, 0);
-    const sum2 = filtered.map(a => a * a).reduce((a, b) => a + b, 0);
-    const total = filtered.length;
-    const avg = sum / total;
-    const sd = Math.sqrt((total * sum2 - sum * sum) / (total * total));
-    const upper = avg + 4 * sd;
-    const lower = avg - 3 * sd;
-    return { upper, lower, avg, sd };
-}
-export function filterForPairs(features) {
-    return features.filter(f => f.flags & 2 && !(f.flags & 256) && !(f.flags & 2048));
-}

package/esm/PileupRenderer/renderers/renderMismatches.d.ts

@@ -1,21 +0,0 @@
-import type { FlatbushItem, ProcessedRenderArgs } from '../types';
-import type { LayoutFeature } from '../util';
-export declare function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorMap, colorContrastMap, hideSmallIndels, canvasWidth, drawSNPsMuted, drawIndels, }: {
-    ctx: CanvasRenderingContext2D;
-    feat: LayoutFeature;
-    renderArgs: ProcessedRenderArgs;
-    colorMap: Record<string, string>;
-    colorContrastMap: Record<string, string>;
-    mismatchAlpha?: boolean;
-    drawIndels?: boolean;
-    drawSNPsMuted?: boolean;
-    minSubfeatureWidth: number;
-    largeInsertionIndicatorScale: number;
-    hideSmallIndels: boolean;
-    charWidth: number;
-    charHeight: number;
-    canvasWidth: number;
-}): {
-    coords: number[];
-    items: FlatbushItem[];
-};

package/esm/PileupRenderer/renderers/renderMismatches.js

@@ -1,145 +0,0 @@
-import { bpSpanPx, measureText } from '@jbrowse/core/util';
-import { colord } from '@jbrowse/core/util/colord';
-import { fillRect } from '../util';
-export function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorMap, colorContrastMap, hideSmallIndels, canvasWidth, drawSNPsMuted, drawIndels = true, }) {
-    var _a;
-    const items = [];
-    const coords = [];
-    const { bpPerPx, regions } = renderArgs;
-    const { heightPx, topPx, feature } = feat;
-    const region = regions[0];
-    const start = feature.get('start');
-    const pxPerBp = Math.min(1 / bpPerPx, 2);
-    const mismatches = (_a = feature.get('mismatches')) !== null && _a !== void 0 ? _a : [];
-    const heightLim = charHeight - 2;
-    const extraHorizontallyFlippedOffset = region.reversed ? 1 / bpPerPx + 1 : -1;
-    for (const mismatch of mismatches) {
-        const mstart = start + mismatch.start;
-        const mlen = mismatch.length;
-        const mbase = mismatch.base;
-        const [leftPx, rightPx] = bpSpanPx(mstart, mstart + mlen, region, bpPerPx);
-        const widthPx = Math.max(minSubfeatureWidth, rightPx - leftPx);
-        if (mismatch.type === 'mismatch') {
-            items.push({
-                type: 'mismatch',
-                seq: mismatch.base,
-            });
-            coords.push(leftPx, topPx, rightPx, topPx + heightPx);
-            if (!drawSNPsMuted) {
-                const baseColor = colorMap[mismatch.base] || '#888';
-                const c = mismatchAlpha && mismatch.qual !== undefined
-                    ? colord(baseColor)
-                        .alpha(Math.min(1, mismatch.qual / 50))
-                        .toHslString()
-                    : baseColor;
-                fillRect(ctx, Math.round(leftPx), topPx, widthPx, heightPx, canvasWidth, c);
-            }
-            if (widthPx >= charWidth && heightPx >= heightLim) {
-                const contrastColor = drawSNPsMuted
-                    ? 'black'
-                    : colorContrastMap[mismatch.base] || 'black';
-                ctx.fillStyle =
-                    mismatchAlpha && mismatch.qual !== undefined
-                        ? colord(contrastColor)
-                            .alpha(Math.min(1, mismatch.qual / 50))
-                            .toHslString()
-                        : contrastColor;
-                ctx.fillText(mbase, leftPx + (widthPx - charWidth) / 2 + 1, topPx + heightPx);
-            }
-        }
-        else if (mismatch.type === 'deletion' && drawIndels) {
-            const len = mismatch.length;
-            if (!hideSmallIndels || len >= 10) {
-                fillRect(ctx, leftPx, topPx, Math.abs(leftPx - rightPx), heightPx, canvasWidth, colorMap.deletion);
-                items.push({
-                    type: 'deletion',
-                    seq: `${mismatch.length}`,
-                });
-                coords.push(leftPx, topPx, rightPx, topPx + heightPx);
-                const txt = `${mismatch.length}`;
-                const rwidth = measureText(txt, 10);
-                if (widthPx >= rwidth && heightPx >= heightLim) {
-                    ctx.fillStyle = colorContrastMap.deletion;
-                    ctx.fillText(txt, (leftPx + rightPx) / 2 - rwidth / 2, topPx + heightPx);
-                }
-            }
-        }
-        else if (mismatch.type === 'insertion' && drawIndels) {
-            const pos = leftPx + extraHorizontallyFlippedOffset;
-            const len = +mismatch.base || mismatch.length;
-            const insW = Math.max(0, Math.min(1.2, 1 / bpPerPx));
-            if (len < 10) {
-                if (!hideSmallIndels) {
-                    fillRect(ctx, pos, topPx, insW, heightPx, canvasWidth, colorMap.insertion);
-                    if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {
-                        items.push({
-                            type: 'insertion',
-                            seq: mismatch.insertedBases || 'unknown',
-                        });
-                        coords.push(leftPx - 2, topPx, leftPx + insW + 2, topPx + heightPx);
-                        const l = Math.round(pos - insW);
-                        fillRect(ctx, l, topPx, insW * 3, 1, canvasWidth);
-                        fillRect(ctx, l, topPx + heightPx - 1, insW * 3, 1, canvasWidth);
-                        ctx.fillText(`(${mismatch.base})`, pos + 3, topPx + heightPx);
-                    }
-                }
-            }
-        }
-        else if (mismatch.type === 'hardclip' || mismatch.type === 'softclip') {
-            const pos = leftPx + extraHorizontallyFlippedOffset;
-            const c = colorMap[mismatch.type];
-            const clipW = Math.max(minSubfeatureWidth, pxPerBp);
-            fillRect(ctx, pos, topPx, clipW, heightPx, canvasWidth, c);
-            if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {
-                const l = pos - clipW;
-                fillRect(ctx, l, topPx, clipW * 3, 1, canvasWidth);
-                fillRect(ctx, l, topPx + heightPx - 1, clipW * 3, 1, canvasWidth);
-                ctx.fillText(`(${mismatch.base})`, pos + 3, topPx + heightPx);
-            }
-        }
-        else if (mismatch.type === 'skip') {
-            if (leftPx + widthPx > 0) {
-                const adjustPx = widthPx - (bpPerPx > 10 ? 1.5 : 0);
-                const l = Math.max(0, leftPx);
-                const t = topPx + heightPx / 2 - 1;
-                const w = adjustPx + Math.min(leftPx, 0);
-                const h = 1;
-                fillRect(ctx, l, t, w, h, canvasWidth, colorMap.skip);
-            }
-        }
-    }
-    if (drawIndels) {
-        for (const mismatch of mismatches) {
-            const mstart = start + mismatch.start;
-            const mlen = mismatch.length;
-            const len = +mismatch.base || mismatch.length;
-            if (mismatch.type === 'insertion' && len >= 10) {
-                const [leftPx] = bpSpanPx(mstart, mstart + mlen, region, bpPerPx);
-                const txt = `${len}`;
-                items.push({
-                    type: 'insertion',
-                    seq: mismatch.insertedBases || 'unknown',
-                });
-                coords.push(leftPx - 3, topPx, leftPx + 4, topPx + heightPx);
-                if (bpPerPx > largeInsertionIndicatorScale) {
-                    fillRect(ctx, leftPx - 1, topPx, 2, heightPx, canvasWidth, colorMap.insertion);
-                }
-                else if (heightPx > charHeight) {
-                    const rwidth = measureText(txt);
-                    const padding = 5;
-                    fillRect(ctx, leftPx - rwidth / 2 - padding, topPx, rwidth + 2 * padding, heightPx, canvasWidth, 'purple');
-                    ctx.fillStyle = colorContrastMap.insertion;
-                    ctx.fillText(txt, leftPx - rwidth / 2, topPx + heightPx);
-                }
-                else {
-                    const padding = 2;
-                    fillRect(ctx, leftPx - padding, topPx, 2 * padding, heightPx, canvasWidth, colorMap.insertion);
-                }
-            }
-        }
-    }
-    return {
-        coords,
-        items,
-    };
-}

package/esm/SNPCoverageAdapter/generateCoverageBins.d.ts

@@ -1,13 +0,0 @@
-import type { Opts } from './util';
-import type { PreBaseCoverageBin, SkipMap } from '../shared/types';
-import type { Feature } from '@jbrowse/core/util';
-import type { AugmentedRegion as Region } from '@jbrowse/core/util/types';
-export declare function generateCoverageBins({ fetchSequence, features, region, opts, }: {
-    features: Feature[];
-    region: Region;
-    opts: Opts;
-    fetchSequence: (arg: Region) => Promise<string>;
-}): Promise<{
-    bins: PreBaseCoverageBin[];
-    skipmap: SkipMap;
-}>;

package/esm/SNPCoverageAdapter/generateCoverageBins.js

@@ -1,84 +0,0 @@
-import { sum } from '@jbrowse/core/util';
-import { checkStopToken } from '@jbrowse/core/util/stopToken';
-import { processDepth } from './processDepth';
-import { processMismatches } from './processMismatches';
-import { processModifications } from './processModifications';
-import { processReferenceCpGs } from './processReferenceCpGs';
-export async function generateCoverageBins({ fetchSequence, features, region, opts, }) {
-    const { stopToken, colorBy } = opts;
-    const skipmap = {};
-    const bins = [];
-    const start2 = Math.max(0, region.start - 1);
-    const diff = region.start - start2;
-    let regionSequence;
-    let start = performance.now();
-    for (const feature of features) {
-        if (performance.now() - start > 400) {
-            checkStopToken(stopToken);
-            start = performance.now();
-        }
-        processDepth({
-            feature,
-            bins,
-            region,
-        });
-        if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
-            regionSequence !== null && regionSequence !== void 0 ? regionSequence : (regionSequence = (await fetchSequence({
-                ...region,
-                start: start2,
-                end: region.end + 1,
-            })) || '');
-            processModifications({
-                feature,
-                colorBy,
-                bins,
-                region,
-                regionSequence: regionSequence.slice(diff),
-            });
-        }
-        else if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation') {
-            regionSequence !== null && regionSequence !== void 0 ? regionSequence : (regionSequence = (await fetchSequence({
-                ...region,
-                start: start2,
-                end: region.end + 1,
-            })) || '');
-            processReferenceCpGs({
-                feature,
-                bins,
-                region,
-                regionSequence,
-            });
-        }
-        processMismatches({ feature, skipmap, bins, region });
-    }
-    for (const bin of bins) {
-        if (bin) {
-            bin.mods = Object.fromEntries(Object.entries(bin.mods).map(([key, val]) => {
-                return [
-                    key,
-                    {
-                        ...val,
-                        avgProbability: val.probabilities.length
-                            ? sum(val.probabilities) / val.probabilities.length
-                            : undefined,
-                    },
-                ];
-            }));
-            bin.nonmods = Object.fromEntries(Object.entries(bin.nonmods).map(([key, val]) => {
-                return [
-                    key,
-                    {
-                        ...val,
-                        avgProbability: val.probabilities.length
-                            ? sum(val.probabilities) / val.probabilities.length
-                            : undefined,
-                    },
-                ];
-            }));
-        }
-    }
-    return {
-        bins,
-        skipmap,
-    };
-}

package/esm/SNPCoverageAdapter/processDepth.d.ts

@@ -1,8 +0,0 @@
-import type { PreBaseCoverageBin } from '../shared/types';
-import type { Feature } from '@jbrowse/core/util';
-import type { AugmentedRegion } from '@jbrowse/core/util/types';
-export declare function processDepth({ feature, bins, region, }: {
-    feature: Feature;
-    bins: PreBaseCoverageBin[];
-    region: AugmentedRegion;
-}): void;

package/esm/SNPCoverageAdapter/processDepth.js

@@ -1,35 +0,0 @@
-export function processDepth({ feature, bins, region, }) {
-    const fstart = feature.get('start');
-    const fend = feature.get('end');
-    const fstrand = feature.get('strand');
-    const regionLength = region.end - region.start;
-    for (let j = fstart; j < fend + 1; j++) {
-        const i = j - region.start;
-        if (i >= 0 && i < regionLength) {
-            if (bins[i] === undefined) {
-                bins[i] = {
-                    depth: 0,
-                    readsCounted: 0,
-                    ref: {
-                        probabilities: [],
-                        entryDepth: 0,
-                        '-1': 0,
-                        0: 0,
-                        1: 0,
-                    },
-                    snps: {},
-                    mods: {},
-                    nonmods: {},
-                    delskips: {},
-                    noncov: {},
-                };
-            }
-            if (j !== fend) {
-                bins[i].depth++;
-                bins[i].readsCounted++;
-                bins[i].ref.entryDepth++;
-                bins[i].ref[fstrand]++;
-            }
-        }
-    }
-}

package/esm/SNPCoverageAdapter/processMismatches.d.ts

@@ -1,9 +0,0 @@
-import type { PreBaseCoverageBin, SkipMap } from '../shared/types';
-import type { Feature } from '@jbrowse/core/util';
-import type { AugmentedRegion } from '@jbrowse/core/util/types';
-export declare function processMismatches({ feature, region, bins, skipmap, }: {
-    region: AugmentedRegion;
-    bins: PreBaseCoverageBin[];
-    feature: Feature;
-    skipmap: SkipMap;
-}): void;

package/esm/SNPCoverageAdapter/processMismatches.js

@@ -1,55 +0,0 @@
-import { inc, isInterbase, mismatchLen } from './util';
-export function processMismatches({ feature, region, bins, skipmap, }) {
-    var _a;
-    const fstart = feature.get('start');
-    const fstrand = feature.get('strand');
-    const mismatches = (_a = feature.get('mismatches')) !== null && _a !== void 0 ? _a : [];
-    for (const mismatch of mismatches) {
-        const mstart = fstart + mismatch.start;
-        const mlen = mismatchLen(mismatch);
-        const mend = mstart + mlen;
-        for (let j = mstart; j < mstart + mlen; j++) {
-            const epos = j - region.start;
-            if (epos >= 0 && epos < bins.length) {
-                const bin = bins[epos];
-                const { base, altbase, type } = mismatch;
-                const interbase = isInterbase(type);
-                if (type === 'deletion' || type === 'skip') {
-                    inc(bin, fstrand, 'delskips', type);
-                    bin.depth--;
-                }
-                else if (!interbase) {
-                    inc(bin, fstrand, 'snps', base);
-                    bin.ref.entryDepth--;
-                    bin.ref[fstrand]--;
-                    bin.refbase = altbase;
-                }
-                else {
-                    inc(bin, fstrand, 'noncov', type);
-                }
-            }
-        }
-        if (mismatch.type === 'skip') {
-            const tags = feature.get('tags');
-            const xs = (tags === null || tags === void 0 ? void 0 : tags.XS) || (tags === null || tags === void 0 ? void 0 : tags.TS);
-            const ts = tags === null || tags === void 0 ? void 0 : tags.ts;
-            const effectiveStrand = xs === '+'
-                ? 1
-                : xs === '-'
-                    ? -1
-                    : (ts === '+' ? 1 : xs === '-' ? -1 : 0) * fstrand;
-            const hash = `${mstart}_${mend}_${effectiveStrand}`;
-            if (skipmap[hash] === undefined) {
-                skipmap[hash] = {
-                    feature: feature,
-                    start: mstart,
-                    end: mend,
-                    strand: fstrand,
-                    effectiveStrand,
-                    score: 0,
-                };
-            }
-            skipmap[hash].score++;
-        }
-    }
-}

package/esm/shared/chainToSimpleFeature.d.ts

@@ -1,3 +0,0 @@
-import { SimpleFeature } from '@jbrowse/core/util';
-import type { ReducedFeature } from './fetchChains';
-export declare function chainToSimpleFeature(chain: ReducedFeature[]): SimpleFeature;

package/esm/shared/components/BaseDisplayComponent.d.ts

@@ -1,16 +0,0 @@
-import type React from 'react';
-interface BaseDisplayModel {
-    error?: unknown;
-    regionTooLarge?: boolean;
-    reload: () => void;
-    regionCannotBeRendered: () => React.ReactElement | null;
-    drawn: boolean;
-    loading: boolean;
-    lastDrawnOffsetPx?: number;
-    message?: string;
-}
-declare const BaseDisplayComponent: ({ model, children, }: {
-    model: BaseDisplayModel;
-    children?: React.ReactNode;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default BaseDisplayComponent;

package/esm/shared/components/BaseDisplayComponent.js

@@ -1,42 +0,0 @@
-import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { LoadingEllipses } from '@jbrowse/core/ui';
-import { getContainingView } from '@jbrowse/core/util';
-import { BlockMsg } from '@jbrowse/plugin-linear-genome-view';
-import { Button, Tooltip } from '@mui/material';
-import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-const useStyles = makeStyles()(theme => ({
-    loading: {
-        backgroundColor: theme.palette.background.default,
-        backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${theme.palette.action.disabledBackground} 5px, ${theme.palette.action.disabledBackground} 10px)`,
-        position: 'absolute',
-        bottom: 0,
-        height: 50,
-        width: 300,
-        right: 0,
-        pointerEvents: 'none',
-        textAlign: 'center',
-    },
-}));
-const BlockError = observer(function ({ model }) {
-    const { error } = model;
-    return (_jsx(BlockMsg, { message: `${error}`, severity: "error", action: _jsx(Tooltip, { title: "Reload", children: _jsx(Button, { "data-testid": "reload_button", onClick: () => {
-                    model.reload();
-                }, children: "Reload" }) }) }));
-});
-const BaseDisplayComponent = observer(function ({ model, children, }) {
-    const { error, regionTooLarge } = model;
-    return error ? (_jsx(BlockError, { model: model })) : regionTooLarge ? (model.regionCannotBeRendered()) : (_jsx(DataDisplay, { model: model, children: children }));
-});
-const DataDisplay = observer(function ({ model, children, }) {
-    const { drawn, loading } = model;
-    const view = getContainingView(model);
-    const left = (model.lastDrawnOffsetPx || 0) - view.offsetPx;
-    return (_jsxs("div", { "data-testid": `drawn-${drawn}`, children: [_jsx("div", { style: { position: 'absolute', left }, children: children }), left !== 0 || loading ? _jsx(LoadingBar, { model: model }) : null] }));
-});
-const LoadingBar = observer(function ({ model }) {
-    const { classes } = useStyles();
-    const { message } = model;
-    return (_jsx("div", { className: classes.loading, children: _jsx(LoadingEllipses, { message: message }) }));
-});
-export default BaseDisplayComponent;

package/esm/shared/drawLongReadChains.d.ts

@@ -1,24 +0,0 @@
-import type { ChainData, ReducedFeature } from './fetchChains';
-import type { FlatbushEntry } from './flatbushType';
-import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-type LGV = LinearGenomeViewModel;
-export declare function drawLongReadChains({ ctx, chainData, view, asm, chainYOffsets, renderChevrons, featureHeight, featuresForFlatbush, computedChains, flipStrandLongReadChains, }: {
-    ctx: CanvasRenderingContext2D;
-    chainData: ChainData;
-    view: LGV;
-    asm: Assembly;
-    chainYOffsets: Map<string, number>;
-    renderChevrons: boolean;
-    featureHeight: number;
-    featuresForFlatbush: FlatbushEntry[];
-    computedChains: {
-        distance: number;
-        minX: number;
-        maxX: number;
-        chain: ReducedFeature[];
-        id: string;
-    }[];
-    flipStrandLongReadChains: boolean;
-}): void;
-export {};