@jbrowse/plugin-linear-genome-view 3.6.5 → 4.0.0

package/dist/LinearGenomeView/svgcomponents/SVGBackground.d.ts

@@ -1,5 +0,0 @@
-export default function SVGBackground({ width, height, shift, }: {
-    width: number;
-    height: number;
-    shift: number;
-}): import("react/jsx-runtime").JSX.Element;

package/dist/LinearGenomeView/svgcomponents/SVGBackground.js

@@ -1,10 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SVGBackground;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const util_1 = require("@jbrowse/core/util");
-const material_1 = require("@mui/material");
-function SVGBackground({ width, height, shift, }) {
-    const theme = (0, material_1.useTheme)();
-    return ((0, jsx_runtime_1.jsx)("rect", { width: width + shift * 2, height: height, fill: (0, util_1.stripAlpha)(theme.palette.background.default) }));
-}

package/dist/LinearGenomeView/svgcomponents/SVGHeader.d.ts

@@ -1,7 +0,0 @@
-import type { LinearGenomeViewModel } from '..';
-export default function SVGHeader({ model, fontSize, cytobandHeight, rulerHeight, }: {
-    model: LinearGenomeViewModel;
-    rulerHeight: number;
-    fontSize: number;
-    cytobandHeight: number;
-}): import("react/jsx-runtime").JSX.Element | null;

package/dist/LinearGenomeView/svgcomponents/SVGHeader.js

@@ -1,47 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SVGHeader;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const util_1 = require("@jbrowse/core/util");
-const Base1DViewModel_1 = __importDefault(require("@jbrowse/core/util/Base1DViewModel"));
-const material_1 = require("@mui/material");
-const SVGRuler_1 = __importDefault(require("./SVGRuler"));
-const SVGScalebar_1 = __importDefault(require("./SVGScalebar"));
-const Cytobands_1 = __importDefault(require("../components/Cytobands"));
-const OverviewScalebarPolygon_1 = __importDefault(require("../components/OverviewScalebarPolygon"));
-const consts_1 = require("../consts");
-function SVGHeader({ model, fontSize, cytobandHeight, rulerHeight, }) {
-    const { width, assemblyNames, showCytobands, displayedRegions } = model;
-    const { assemblyManager } = (0, util_1.getSession)(model);
-    const assemblyName = assemblyNames.length > 1 ? '' : assemblyNames[0];
-    const assembly = assemblyManager.get(assemblyName);
-    const theme = (0, material_1.useTheme)();
-    const c = (0, util_1.stripAlpha)(theme.palette.text.primary);
-    const overview = Base1DViewModel_1.default.create({
-        displayedRegions: JSON.parse(JSON.stringify(displayedRegions)),
-        interRegionPaddingWidth: 0,
-        minimumBlockWidth: model.minimumBlockWidth,
-    });
-    const visibleRegions = model.dynamicBlocks.contentBlocks;
-    if (!visibleRegions.length) {
-        return null;
-    }
-    overview.setVolatileWidth(width);
-    overview.showAllRegions();
-    const block = overview.dynamicBlocks.contentBlocks[0];
-    const first = visibleRegions.at(0);
-    const last = visibleRegions.at(-1);
-    const firstOverviewPx = overview.bpToPx({
-        ...first,
-        coord: first.reversed ? first.end : first.start,
-    }) || 0;
-    const lastOverviewPx = overview.bpToPx({
-        ...last,
-        coord: last.reversed ? last.start : last.end,
-    }) || 0;
-    const y = +showCytobands * cytobandHeight;
-    return ((0, jsx_runtime_1.jsxs)("g", { id: "header", children: [(0, jsx_runtime_1.jsx)("text", { x: 0, y: 0, dominantBaseline: "hanging", fontSize: fontSize, fill: c, children: assemblyName }), showCytobands ? ((0, jsx_runtime_1.jsxs)("g", { transform: `translate(0 ${rulerHeight})`, children: [(0, jsx_runtime_1.jsx)(Cytobands_1.default, { overview: overview, assembly: assembly, block: block }), (0, jsx_runtime_1.jsx)("rect", { stroke: "red", fill: "rgb(255,0,0)", fillOpacity: 0.1, width: Math.max(lastOverviewPx - firstOverviewPx, 0.5), height: consts_1.HEADER_OVERVIEW_HEIGHT - 1, x: firstOverviewPx, y: 0.5 }), (0, jsx_runtime_1.jsx)("g", { transform: `translate(0,${consts_1.HEADER_OVERVIEW_HEIGHT})`, children: (0, jsx_runtime_1.jsx)(OverviewScalebarPolygon_1.default, { overview: overview, model: model, useOffset: false }) })] })) : null, (0, jsx_runtime_1.jsx)("g", { transform: `translate(0 ${fontSize + y})`, children: (0, jsx_runtime_1.jsx)(SVGScalebar_1.default, { model: model, fontSize: fontSize }) }), (0, jsx_runtime_1.jsx)("g", { transform: `translate(0 ${rulerHeight + y})`, children: (0, jsx_runtime_1.jsx)(SVGRuler_1.default, { model: model, fontSize: fontSize }) })] }));
-}

package/dist/LinearGenomeView/svgcomponents/SVGLinearGenomeView.d.ts

@@ -1,6 +0,0 @@
-import type { LinearGenomeViewModel } from '..';
-import type { ExportSvgOptions } from '../types';
-type LGV = LinearGenomeViewModel;
-export declare function renderToSvg(model: LGV, opts: ExportSvgOptions): Promise<string>;
-export { default as SVGRuler } from './SVGRuler';
-export { default as SVGTracks } from './SVGTracks';

package/dist/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js

@@ -1,42 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.SVGTracks = exports.SVGRuler = void 0;
-exports.renderToSvg = renderToSvg;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const ui_1 = require("@jbrowse/core/ui");
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-const material_1 = require("@mui/material");
-const mobx_1 = require("mobx");
-const SVGBackground_1 = __importDefault(require("./SVGBackground"));
-const SVGHeader_1 = __importDefault(require("./SVGHeader"));
-const SVGTracks_1 = __importDefault(require("./SVGTracks"));
-const util_2 = require("./util");
-async function renderToSvg(model, opts) {
-    await (0, mobx_1.when)(() => model.initialized);
-    const { textHeight = 18, headerHeight = 40, rulerHeight = 50, fontSize = 13, cytobandHeight = 100, trackLabels = 'offset', themeName = 'default', Wrapper = ({ children }) => children, } = opts;
-    const session = (0, util_1.getSession)(model);
-    const { allThemes } = session;
-    const theme = allThemes === null || allThemes === void 0 ? void 0 : allThemes()[themeName];
-    const { width, pinnedTracks, unpinnedTracks, tracks, showCytobands } = model;
-    const shift = 50;
-    const c = +showCytobands * cytobandHeight;
-    const offset = headerHeight + rulerHeight + c + 10;
-    const height = (0, util_2.totalHeight)(tracks, textHeight, trackLabels) + offset + 100;
-    const displayResults = await Promise.all([...pinnedTracks, ...unpinnedTracks].map(async (track) => {
-        const display = track.displays[0];
-        await (0, mobx_1.when)(() => !display.renderProps().notReady);
-        return { track, result: await display.renderSvg({ ...opts, theme }) };
-    }));
-    const trackLabelMaxLen = (0, util_1.max)(tracks.map(t => (0, util_1.measureText)((0, tracks_1.getTrackName)(t.configuration, session), fontSize)), 0) + 40;
-    const trackLabelOffset = trackLabels === 'left' ? trackLabelMaxLen : 0;
-    const w = width + trackLabelOffset;
-    return (0, util_1.renderToStaticMarkup)((0, jsx_runtime_1.jsx)(material_1.ThemeProvider, { theme: (0, ui_1.createJBrowseTheme)(theme), children: (0, jsx_runtime_1.jsx)(Wrapper, { children: (0, jsx_runtime_1.jsxs)("svg", { width: w, height: height, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w + shift * 2, height].toString(), children: [(0, jsx_runtime_1.jsx)(SVGBackground_1.default, { width: w, height: height, shift: shift }), (0, jsx_runtime_1.jsxs)("g", { transform: `translate(${shift} 0)`, children: [(0, jsx_runtime_1.jsx)("g", { transform: `translate(${trackLabelOffset})`, children: (0, jsx_runtime_1.jsx)(SVGHeader_1.default, { model: model, fontSize: fontSize, rulerHeight: rulerHeight, cytobandHeight: cytobandHeight }) }), (0, jsx_runtime_1.jsx)("g", { transform: `translate(0 ${offset})`, children: (0, jsx_runtime_1.jsx)(SVGTracks_1.default, { textHeight: textHeight, fontSize: fontSize, model: model, displayResults: displayResults, trackLabels: trackLabels, trackLabelOffset: trackLabelOffset }) })] })] }) }) }));
-}
-var SVGRuler_1 = require("./SVGRuler");
-Object.defineProperty(exports, "SVGRuler", { enumerable: true, get: function () { return __importDefault(SVGRuler_1).default; } });
-var SVGTracks_2 = require("./SVGTracks");
-Object.defineProperty(exports, "SVGTracks", { enumerable: true, get: function () { return __importDefault(SVGTracks_2).default; } });

package/dist/LinearGenomeView/svgcomponents/SVGRegionSeparators.js

@@ -1,8 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SVGRegionSeparators;
-const jsx_runtime_1 = require("react/jsx-runtime");
-function SVGRegionSeparators({ model, height, }) {
-    const { dynamicBlocks, offsetPx, interRegionPaddingWidth } = model;
-    return ((0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: dynamicBlocks.contentBlocks.slice(1).map(block => ((0, jsx_runtime_1.jsx)("rect", { x: block.offsetPx - offsetPx - interRegionPaddingWidth, width: interRegionPaddingWidth, y: 0, height: height, fill: "grey" }, block.key))) }));
-}

package/dist/LinearGenomeView/svgcomponents/SVGRuler.d.ts

@@ -1,7 +0,0 @@
-import type { LinearGenomeViewModel } from '..';
-type LGV = LinearGenomeViewModel;
-export default function SVGRuler({ model, fontSize, }: {
-    model: LGV;
-    fontSize: number;
-}): import("react/jsx-runtime").JSX.Element;
-export {};

package/dist/LinearGenomeView/svgcomponents/SVGRuler.js

@@ -1,39 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SVGRuler;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const util_1 = require("@jbrowse/core/util");
-const material_1 = require("@mui/material");
-const util_2 = require("../util");
-const SVGRegionSeparators_1 = __importDefault(require("./SVGRegionSeparators"));
-function Ruler({ start, end, bpPerPx, reversed = false, major = true, minor = true, hideText = false, }) {
-    const ticks = (0, util_2.makeTicks)(start, end, bpPerPx, major, minor);
-    const theme = (0, material_1.useTheme)();
-    const c = (0, util_1.stripAlpha)(theme.palette.text.secondary);
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [ticks.map(tick => {
-                const x = (reversed ? end - tick.base : tick.base - start) / bpPerPx;
-                return ((0, jsx_runtime_1.jsx)("line", { x1: x, x2: x, y1: 0, y2: tick.type === 'major' ? 6 : 4, strokeWidth: 1, stroke: c }, `tick-${tick.base}`));
-            }), !hideText
-                ? ticks
-                    .filter(tick => tick.type === 'major')
-                    .map(tick => {
-                    const x = (reversed ? end - tick.base : tick.base - start) / bpPerPx;
-                    return ((0, jsx_runtime_1.jsx)("text", { x: x - 3, y: 7 + 11, fontSize: 11, fill: c, children: (0, util_1.getTickDisplayStr)(tick.base + 1, bpPerPx) }, `label-${tick.base}`));
-                })
-                : null] }));
-}
-function SVGRuler({ model, fontSize, }) {
-    const { dynamicBlocks: { contentBlocks }, offsetPx: viewOffsetPx, bpPerPx, } = model;
-    const renderRuler = contentBlocks.length < 5;
-    const theme = (0, material_1.useTheme)();
-    const c = (0, util_1.stripAlpha)(theme.palette.text.primary);
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(SVGRegionSeparators_1.default, { model: model, height: 30 }), contentBlocks.map(block => {
-                const { start, end, key, reversed, offsetPx, refName, widthPx } = block;
-                const offset = offsetPx - viewOffsetPx;
-                const clipid = `clip-${key}`;
-                return ((0, jsx_runtime_1.jsxs)("g", { children: [(0, jsx_runtime_1.jsx)("defs", { children: (0, jsx_runtime_1.jsx)("clipPath", { id: clipid, children: (0, jsx_runtime_1.jsx)("rect", { x: 0, y: 0, width: widthPx, height: 100 }) }) }), (0, jsx_runtime_1.jsx)("g", { transform: `translate(${offset} 0)`, children: (0, jsx_runtime_1.jsxs)("g", { clipPath: `url(#${clipid})`, children: [(0, jsx_runtime_1.jsx)("text", { x: 4, y: fontSize, fontSize: fontSize, fill: c, children: refName }), (0, jsx_runtime_1.jsx)("g", { transform: "translate(0 20)", children: (0, jsx_runtime_1.jsx)(Ruler, { hideText: !renderRuler, start: start, end: end, bpPerPx: bpPerPx, reversed: reversed }) })] }) })] }, key));
-            })] }));
-}

package/dist/LinearGenomeView/svgcomponents/SVGScalebar.d.ts

@@ -1,7 +0,0 @@
-import type { LinearGenomeViewModel } from '..';
-type LGV = LinearGenomeViewModel;
-export default function SVGScalebar({ model, fontSize, }: {
-    model: LGV;
-    fontSize: number;
-}): import("react/jsx-runtime").JSX.Element;
-export {};

package/dist/LinearGenomeView/svgcomponents/SVGScalebar.js

@@ -1,17 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SVGScalebar;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const util_1 = require("@jbrowse/core/util");
-const material_1 = require("@mui/material");
-function SVGScalebar({ model, fontSize, }) {
-    const { offsetPx, dynamicBlocks: { totalWidthPxWithoutBorders: totalWidthPx, totalBp }, } = model;
-    const theme = (0, material_1.useTheme)();
-    const displayBp = (0, util_1.getBpDisplayStr)(totalBp);
-    const x0 = Math.max(-offsetPx, 0);
-    const x1 = x0 + totalWidthPx;
-    const c = (0, util_1.stripAlpha)(theme.palette.text.secondary);
-    const x = x0 + (x1 - x0) / 2;
-    const y = fontSize;
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("line", { x1: x0, x2: x1, y1: 10, y2: 10, stroke: c }), (0, jsx_runtime_1.jsx)("line", { x1: x0, x2: x0, y1: 5, y2: 15, stroke: c }), (0, jsx_runtime_1.jsx)("line", { x1: x1, x2: x1, y1: 5, y2: 15, stroke: c }), (0, jsx_runtime_1.jsx)("text", { x: x, y: y, textAnchor: "middle", dominantBaseline: "hanging", fontSize: fontSize, fill: c, children: displayBp })] }));
-}

package/dist/LinearGenomeView/svgcomponents/SVGTrackLabel.d.ts

@@ -1,7 +0,0 @@
-export default function SVGTrackLabel({ trackLabels, trackName, fontSize, trackLabelOffset, x, }: {
-    trackName: string;
-    trackLabels: string;
-    fontSize: number;
-    trackLabelOffset: number;
-    x: number;
-}): import("react/jsx-runtime").JSX.Element | null;

package/dist/LinearGenomeView/svgcomponents/SVGTrackLabel.js

@@ -1,14 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SVGTrackLabel;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const util_1 = require("@jbrowse/core/util");
-const material_1 = require("@mui/material");
-function SVGTrackLabel({ trackLabels, trackName, fontSize, trackLabelOffset, x, }) {
-    const theme = (0, material_1.useTheme)();
-    const fill = (0, util_1.stripAlpha)(theme.palette.text.primary);
-    const xoff = trackLabels === 'overlay' ? 5 : 0;
-    const yoff = trackLabels === 'offset' ? 5 : 0;
-    const name = (0, util_1.coarseStripHTML)(trackName);
-    return trackLabels !== 'none' ? ((0, jsx_runtime_1.jsx)("g", { children: trackLabels === 'left' ? ((0, jsx_runtime_1.jsx)("text", { x: trackLabelOffset - 40, y: 20, fill: fill, fontSize: fontSize, dominantBaseline: "hanging", textAnchor: "end", children: name })) : ((0, jsx_runtime_1.jsx)("text", { x: x + xoff, y: yoff, fill: fill, fontSize: fontSize, dominantBaseline: "hanging", children: name })) })) : null;
-}

package/dist/LinearGenomeView/svgcomponents/SVGTracks.d.ts

@@ -1,21 +0,0 @@
-import type { LinearGenomeViewModel } from '..';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-type LGV = LinearGenomeViewModel;
-interface DisplayResult {
-    track: {
-        configuration: AnyConfigurationModel;
-        displays: {
-            height: number;
-        }[];
-    };
-    result: string;
-}
-export default function SVGTracks({ displayResults, model, textHeight, fontSize, trackLabels, trackLabelOffset, }: {
-    displayResults: DisplayResult[];
-    model: LGV;
-    textHeight: number;
-    fontSize: number;
-    trackLabels?: string;
-    trackLabelOffset?: number;
-}): import("react/jsx-runtime").JSX.Element;
-export {};

package/dist/LinearGenomeView/svgcomponents/SVGTracks.js

@@ -1,32 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SVGTracks;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-const SVGRegionSeparators_1 = __importDefault(require("./SVGRegionSeparators"));
-const SVGTrackLabel_1 = __importDefault(require("./SVGTrackLabel"));
-function SVGTracks({ displayResults, model, textHeight, fontSize, trackLabels = 'offset', trackLabelOffset = 0, }) {
-    const session = (0, util_1.getSession)(model);
-    const textOffset = trackLabels === 'offset' ? textHeight : 0;
-    return ((0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: displayResults.reduce(({ prevOffset, reactElements }, { track, result }) => {
-            const conf = track.configuration;
-            const trackName = (0, tracks_1.getTrackName)(conf, session);
-            const display = track.displays[0];
-            const x = Math.max(-model.offsetPx, 0);
-            const currOffset = prevOffset + display.height + textOffset;
-            return {
-                prevOffset: currOffset,
-                reactElements: [
-                    ...reactElements,
-                    (0, jsx_runtime_1.jsxs)("g", { transform: `translate(0 ${prevOffset})`, children: [(0, jsx_runtime_1.jsxs)("g", { transform: `translate(${trackLabelOffset} ${textOffset})`, children: [(0, jsx_runtime_1.jsx)(SVGRegionSeparators_1.default, { model: model, height: display.height }), result] }), (0, jsx_runtime_1.jsx)(SVGTrackLabel_1.default, { trackName: trackName, fontSize: fontSize, trackLabels: trackLabels, trackLabelOffset: trackLabelOffset, x: x })] }, conf.trackId),
-                ],
-            };
-        }, {
-            prevOffset: 0,
-            reactElements: [],
-        }).reactElements }));
-}

package/dist/LinearGenomeView/svgcomponents/util.d.ts

@@ -1,8 +0,0 @@
-interface Display {
-    height: number;
-}
-interface Track {
-    displays: Display[];
-}
-export declare function totalHeight(tracks: Track[], textHeight: number, trackLabels: string): number;
-export {};

package/dist/LinearGenomeView/svgcomponents/util.js

@@ -1,8 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.totalHeight = totalHeight;
-const util_1 = require("@jbrowse/core/util");
-function totalHeight(tracks, textHeight, trackLabels) {
-    return (0, util_1.sum)(tracks.map(t => t.displays[0].height +
-        (['none', 'left'].includes(trackLabels) ? 0 : textHeight)));
-}

package/dist/LinearGenomeView/types.d.ts

@@ -1,43 +0,0 @@
-export interface BpOffset {
-    refName?: string;
-    index: number;
-    offset: number;
-    start?: number;
-    end?: number;
-    coord?: number;
-    reversed?: boolean;
-    assemblyName?: string;
-    oob?: boolean;
-}
-export interface ExportSvgOptions {
-    rasterizeLayers?: boolean;
-    filename?: string;
-    Wrapper?: React.FC<{
-        children: React.ReactNode;
-    }>;
-    fontSize?: number;
-    rulerHeight?: number;
-    textHeight?: number;
-    paddingHeight?: number;
-    headerHeight?: number;
-    cytobandHeight?: number;
-    trackLabels?: string;
-    themeName?: string;
-}
-export interface HighlightType {
-    start: number;
-    end: number;
-    assemblyName: string;
-    refName: string;
-}
-export interface NavLocation {
-    refName: string;
-    start?: number;
-    end?: number;
-    assemblyName?: string;
-}
-export interface InitState {
-    loc: string;
-    assembly: string;
-    tracks?: string[];
-}

package/dist/LinearGenomeView/types.js

@@ -1,2 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });

package/dist/LinearGenomeView/util.d.ts

@@ -1,26 +0,0 @@
-import type { AssemblyManager, ParsedLocString } from '@jbrowse/core/util';
-import type { BaseBlock } from '@jbrowse/core/util/blockTypes';
-export declare function chooseGridPitch(scale: number, minMajorPitchPx: number, minMinorPitchPx: number): {
-    majorPitch: number;
-    minorPitch: number;
-};
-export declare function makeTicks(start: number, end: number, bpPerPx: number, emitMajor?: boolean, emitMinor?: boolean): {
-    type: string;
-    base: number;
-    index: number;
-}[];
-export declare function generateLocations({ regions, assemblyManager, assemblyName, grow, }: {
-    regions: ParsedLocString[];
-    assemblyManager: AssemblyManager;
-    assemblyName?: string;
-    grow?: number;
-}): Promise<{
-    assemblyName: string;
-    parentRegion: import("@jbrowse/core/assemblyManager/assembly").BasicRegion;
-    end?: number | undefined;
-    start?: number | undefined;
-    refName: string;
-    reversed?: boolean | undefined;
-}[]>;
-export declare function parseLocStrings(input: string, assemblyName: string, isValidRefName: (str: string, assemblyName: string) => boolean): ParsedLocString[];
-export declare function calculateVisibleLocStrings(contentBlocks: BaseBlock[]): string;

package/dist/LinearGenomeView/util.js

@@ -1,138 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.chooseGridPitch = chooseGridPitch;
-exports.makeTicks = makeTicks;
-exports.generateLocations = generateLocations;
-exports.parseLocStrings = parseLocStrings;
-exports.calculateVisibleLocStrings = calculateVisibleLocStrings;
-const util_1 = require("@jbrowse/core/util");
-function chooseGridPitch(scale, minMajorPitchPx, minMinorPitchPx) {
-    scale = Math.abs(scale);
-    const minMajorPitchBp = minMajorPitchPx * scale;
-    const majorMagnitude = Number.parseInt(Number(minMajorPitchBp).toExponential().split(/e/i)[1], 10);
-    let majorPitch = 10 ** majorMagnitude;
-    while (majorPitch < minMajorPitchBp) {
-        majorPitch *= 2;
-        if (majorPitch >= minMajorPitchBp) {
-            break;
-        }
-        majorPitch *= 2.5;
-    }
-    majorPitch = Math.max(majorPitch, 5);
-    const majorPitchPx = majorPitch / scale;
-    let minorPitch = 0;
-    if (!(majorPitch % 10) && majorPitchPx / 10 >= minMinorPitchPx) {
-        minorPitch = majorPitch / 10;
-    }
-    else if (!(majorPitch % 5) && majorPitchPx / 5 >= minMinorPitchPx) {
-        minorPitch = majorPitch / 5;
-    }
-    else if (!(majorPitch % 2) && majorPitchPx / 2 >= minMinorPitchPx) {
-        minorPitch = majorPitch / 2;
-    }
-    return { majorPitch, minorPitch };
-}
-function makeTicks(start, end, bpPerPx, emitMajor = true, emitMinor = true) {
-    const gridPitch = chooseGridPitch(bpPerPx, 60, 15);
-    let minBase = start;
-    let maxBase = end;
-    if (bpPerPx < 0) {
-        ;
-        [minBase, maxBase] = [maxBase, minBase];
-    }
-    minBase -= Math.abs(20 * bpPerPx) - 1;
-    maxBase += Math.abs(20 * bpPerPx) + 1;
-    const iterPitch = gridPitch.minorPitch || gridPitch.majorPitch;
-    let index = 0;
-    const ticks = [];
-    for (let base = Math.floor(minBase / iterPitch) * iterPitch; base < Math.ceil(maxBase / iterPitch) * iterPitch + 1; base += iterPitch) {
-        if (emitMinor && base % (gridPitch.majorPitch * 2)) {
-            ticks.push({ type: 'minor', base: base - 1, index });
-            index += 1;
-        }
-        else if (emitMajor && !(base % (gridPitch.majorPitch * 2))) {
-            ticks.push({ type: 'major', base: base - 1, index });
-            index += 1;
-        }
-    }
-    return ticks;
-}
-async function generateLocations({ regions, assemblyManager, assemblyName, grow, }) {
-    return Promise.all(regions.map(async (region) => {
-        const asmName = region.assemblyName || assemblyName;
-        if (!asmName) {
-            throw new Error('no assembly provided');
-        }
-        const asm = await assemblyManager.waitForAssembly(asmName);
-        const { refName } = region;
-        if (!asm) {
-            throw new Error(`assembly ${asmName} not found`);
-        }
-        const { regions } = asm;
-        if (!regions) {
-            throw new Error(`regions not loaded yet for ${asmName}`);
-        }
-        const canonicalRefName = asm.getCanonicalRefName(region.refName);
-        if (!canonicalRefName) {
-            throw new Error(`Could not find refName ${refName} in ${asm.name}`);
-        }
-        const parentRegion = regions.find(r => r.refName === canonicalRefName);
-        if (!parentRegion) {
-            throw new Error(`Could not find refName ${refName} in ${asmName}`);
-        }
-        const { start, end } = region;
-        if (grow && start && end) {
-            const len = end - start;
-            const margin = len * grow;
-            return {
-                ...region,
-                start: Math.max(0, start - margin),
-                end: end + margin,
-                assemblyName: asmName,
-                parentRegion,
-            };
-        }
-        else {
-            return {
-                ...region,
-                assemblyName: asmName,
-                parentRegion,
-            };
-        }
-    }));
-}
-function parseLocStrings(input, assemblyName, isValidRefName) {
-    const inputs = input
-        .split(/(\s+)/)
-        .map(f => f.trim())
-        .filter(f => !!f);
-    try {
-        return inputs.map(loc => (0, util_1.parseLocString)(loc, ref => isValidRefName(ref, assemblyName)));
-    }
-    catch (e) {
-        const [refName, start, end] = inputs;
-        if (/Unknown reference sequence/.exec(`${e}`) &&
-            Number.isInteger(+start) &&
-            Number.isInteger(+end)) {
-            return [
-                (0, util_1.parseLocString)(`${refName}:${start}..${end}`, ref => isValidRefName(ref, assemblyName)),
-            ];
-        }
-        throw e;
-    }
-}
-function calculateVisibleLocStrings(contentBlocks) {
-    if (!contentBlocks.length) {
-        return '';
-    }
-    else {
-        const isSingleAssemblyName = contentBlocks.every(b => b.assemblyName === contentBlocks[0].assemblyName);
-        const locs = contentBlocks.map(block => (0, util_1.assembleLocString)({
-            ...block,
-            start: Math.round(block.start),
-            end: Math.round(block.end),
-            assemblyName: isSingleAssemblyName ? undefined : block.assemblyName,
-        }));
-        return locs.join(' ');
-    }
-}