@jbrowse/plugin-linear-genome-view 2.3.4 → 2.4.1

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

@@ -0,0 +1,6 @@
+/// <reference types="react" />
+export default function SVGBackground({ width, height, shift, }: {
+    width: number;
+    height: number;
+    shift: number;
+}): JSX.Element;

package/dist/LinearGenomeView/svgcomponents/SVGBackground.js

@@ -0,0 +1,13 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const material_1 = require("@mui/material");
+function SVGBackground({ width, height, shift, }) {
+    const theme = (0, material_1.useTheme)();
+    return (react_1.default.createElement("rect", { width: width + shift * 2, height: height, fill: theme.palette.background.default }));
+}
+exports.default = SVGBackground;
+//# sourceMappingURL=SVGBackground.js.map

package/dist/LinearGenomeView/svgcomponents/SVGBackground.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SVGBackground.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/svgcomponents/SVGBackground.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,4CAAwC;AAExC,SAAwB,aAAa,CAAC,EACpC,KAAK,EACL,MAAM,EACN,KAAK,GAKN;IACC,MAAM,KAAK,GAAG,IAAA,mBAAQ,GAAE,CAAA;IACxB,OAAO,CACL,wCACE,KAAK,EAAE,KAAK,GAAG,KAAK,GAAG,CAAC,EACxB,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO,GACtC,CACH,CAAA;AACH,CAAC;AAjBD,gCAiBC"}

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

@@ -0,0 +1,10 @@
+/// <reference types="react" />
+import { LinearGenomeViewModel } from '..';
+type LGV = LinearGenomeViewModel;
+export default function SVGHeader({ model, fontSize, cytobandHeight, rulerHeight, }: {
+    model: LGV;
+    rulerHeight: number;
+    fontSize: number;
+    cytobandHeight: number;
+}): JSX.Element;
+export {};

package/dist/LinearGenomeView/svgcomponents/SVGHeader.js

@@ -0,0 +1,55 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const util_1 = require("@jbrowse/core/util");
+const Base1DViewModel_1 = __importDefault(require("@jbrowse/core/util/Base1DViewModel"));
+const material_1 = require("@mui/material");
+// locals
+const __1 = require("..");
+const Cytobands_1 = __importDefault(require("../components/Cytobands"));
+const OverviewScalebar_1 = require("../components/OverviewScalebar");
+const SVGRuler_1 = __importDefault(require("./SVGRuler"));
+const SVGScalebar_1 = __importDefault(require("./SVGScalebar"));
+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 overview = Base1DViewModel_1.default.create({
+        displayedRegions: JSON.parse(JSON.stringify(displayedRegions)),
+        interRegionPaddingWidth: 0,
+        minimumBlockWidth: model.minimumBlockWidth,
+    });
+    const visibleRegions = model.dynamicBlocks.contentBlocks;
+    overview.setVolatileWidth(width);
+    overview.showAllRegions();
+    const block = overview.dynamicBlocks.contentBlocks[0];
+    const first = visibleRegions[0];
+    const firstOverviewPx = overview.bpToPx({
+        ...first,
+        coord: first.reversed ? first.end : first.start,
+    }) || 0;
+    const last = visibleRegions[visibleRegions.length - 1];
+    const lastOverviewPx = overview.bpToPx({
+        ...last,
+        coord: last.reversed ? last.start : last.end,
+    }) || 0;
+    const c = +showCytobands * cytobandHeight;
+    return (react_1.default.createElement("g", { id: "header" },
+        react_1.default.createElement("text", { x: 0, y: fontSize, fontSize: fontSize, fill: theme.palette.text.primary }, assemblyName),
+        showCytobands ? (react_1.default.createElement("g", { transform: `translate(0 ${rulerHeight})` },
+            react_1.default.createElement(Cytobands_1.default, { overview: overview, assembly: assembly, block: block }),
+            react_1.default.createElement("rect", { stroke: "red", fill: "rgb(255,0,0,0.1)", width: Math.max(lastOverviewPx - firstOverviewPx, 0.5), height: __1.HEADER_OVERVIEW_HEIGHT - 1, x: firstOverviewPx, y: 0.5 }),
+            react_1.default.createElement("g", { transform: `translate(0,${__1.HEADER_OVERVIEW_HEIGHT})` },
+                react_1.default.createElement(OverviewScalebar_1.Polygon, { overview: overview, model: model, useOffset: false })))) : null,
+        react_1.default.createElement("g", { transform: `translate(0 ${fontSize + c})` },
+            react_1.default.createElement(SVGScalebar_1.default, { model: model, fontSize: fontSize })),
+        react_1.default.createElement("g", { transform: `translate(0 ${rulerHeight + c})` },
+            react_1.default.createElement(SVGRuler_1.default, { model: model, fontSize: fontSize }))));
+}
+exports.default = SVGHeader;
+//# sourceMappingURL=SVGHeader.js.map

package/dist/LinearGenomeView/svgcomponents/SVGHeader.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SVGHeader.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/svgcomponents/SVGHeader.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,6CAA+C;AAC/C,yFAA2D;AAC3D,4CAAwC;AAExC,SAAS;AACT,0BAAkE;AAClE,wEAA+C;AAC/C,qEAAwD;AACxD,0DAAiC;AACjC,gEAAuC;AAIvC,SAAwB,SAAS,CAAC,EAChC,KAAK,EACL,QAAQ,EACR,cAAc,EACd,WAAW,GAMZ;IACC,MAAM,EAAE,KAAK,EAAE,aAAa,EAAE,aAAa,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IACvE,MAAM,EAAE,eAAe,EAAE,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IAC7C,MAAM,YAAY,GAAG,aAAa,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,CAAA;IACrE,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;IAClD,MAAM,KAAK,GAAG,IAAA,mBAAQ,GAAE,CAAA;IAExB,MAAM,QAAQ,GAAG,yBAAU,CAAC,MAAM,CAAC;QACjC,gBAAgB,EAAE,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,gBAAgB,CAAC,CAAC;QAC9D,uBAAuB,EAAE,CAAC;QAC1B,iBAAiB,EAAE,KAAK,CAAC,iBAAiB;KAC3C,CAAC,CAAA;IACF,MAAM,cAAc,GAAG,KAAK,CAAC,aAAa,CAAC,aAAa,CAAA;IAExD,QAAQ,CAAC,gBAAgB,CAAC,KAAK,CAAC,CAAA;IAChC,QAAQ,CAAC,cAAc,EAAE,CAAA;IACzB,MAAM,KAAK,GAAG,QAAQ,CAAC,aAAa,CAAC,aAAa,CAAC,CAAC,CAAC,CAAA;IAErD,MAAM,KAAK,GAAG,cAAc,CAAC,CAAC,CAAC,CAAA;IAC/B,MAAM,eAAe,GACnB,QAAQ,CAAC,MAAM,CAAC;QACd,GAAG,KAAK;QACR,KAAK,EAAE,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK;KAChD,CAAC,IAAI,CAAC,CAAA;IAET,MAAM,IAAI,GAAG,cAAc,CAAC,cAAc,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;IACtD,MAAM,cAAc,GAClB,QAAQ,CAAC,MAAM,CAAC;QACd,GAAG,IAAI;QACP,KAAK,EAAE,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG;KAC7C,CAAC,IAAI,CAAC,CAAA;IACT,MAAM,CAAC,GAAG,CAAC,aAAa,GAAG,cAAc,CAAA;IACzC,OAAO,CACL,qCAAG,EAAE,EAAC,QAAQ;QACZ,wCACE,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,QAAQ,EACX,QAAQ,EAAE,QAAQ,EAClB,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,IAE/B,YAAY,CACR;QAEN,aAAa,CAAC,CAAC,CAAC,CACf,qCAAG,SAAS,EAAE,eAAe,WAAW,GAAG;YACzC,8BAAC,mBAAS,IAAC,QAAQ,EAAE,QAAQ,EAAE,QAAQ,EAAE,QAAQ,EAAE,KAAK,EAAE,KAAK,GAAI;YACnE,wCACE,MAAM,EAAC,KAAK,EACZ,IAAI,EAAC,kBAAkB,EACvB,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,cAAc,GAAG,eAAe,EAAE,GAAG,CAAC,EACtD,MAAM,EAAE,0BAAsB,GAAG,CAAC,EAClC,CAAC,EAAE,eAAe,EAClB,CAAC,EAAE,GAAG,GACN;YACF,qCAAG,SAAS,EAAE,eAAe,0BAAsB,GAAG;gBACpD,8BAAC,0BAAO,IAAC,QAAQ,EAAE,QAAQ,EAAE,KAAK,EAAE,KAAK,EAAE,SAAS,EAAE,KAAK,GAAI,CAC7D,CACF,CACL,CAAC,CAAC,CAAC,IAAI;QAER,qCAAG,SAAS,EAAE,eAAe,QAAQ,GAAG,CAAC,GAAG;YAC1C,8BAAC,qBAAW,IAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,QAAQ,GAAI,CAC/C;QACJ,qCAAG,SAAS,EAAE,eAAe,WAAW,GAAG,CAAC,GAAG;YAC7C,8BAAC,kBAAQ,IAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,QAAQ,GAAI,CAC5C,CACF,CACL,CAAA;AACH,CAAC;AA9ED,4BA8EC"}

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

@@ -0,0 +1,12 @@
+import { LinearGenomeViewModel, ExportSvgOptions } from '..';
+type LGV = LinearGenomeViewModel;
+interface Display {
+    height: number;
+}
+interface Track {
+    displays: Display[];
+}
+export declare function totalHeight(tracks: Track[], textHeight: number, trackLabels: string): number;
+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

@@ -0,0 +1,57 @@
+"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 = exports.renderToSvg = exports.totalHeight = void 0;
+const react_1 = __importDefault(require("react"));
+const server_1 = require("react-dom/server");
+const mobx_1 = require("mobx");
+const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
+const ui_1 = require("@jbrowse/core/ui");
+const SVGBackground_1 = __importDefault(require("./SVGBackground"));
+const SVGTracks_1 = __importDefault(require("./SVGTracks"));
+const SVGHeader_1 = __importDefault(require("./SVGHeader"));
+const tracks_1 = require("@jbrowse/core/util/tracks");
+function totalHeight(tracks, textHeight, trackLabels) {
+    return (0, util_1.sum)(tracks.map(t => t.displays[0].height +
+        (['none', 'left'].includes(trackLabels) ? 0 : textHeight)));
+}
+exports.totalHeight = totalHeight;
+// render LGV to SVG
+async function renderToSvg(model, opts) {
+    var _a;
+    await (0, mobx_1.when)(() => model.initialized);
+    const { textHeight = 18, headerHeight = 40, rulerHeight = 50, fontSize = 13, cytobandHeight = 100, trackLabels = 'offset', themeName = 'default', Wrapper = ({ children }) => react_1.default.createElement(react_1.default.Fragment, null, children), } = opts;
+    const session = (0, util_1.getSession)(model);
+    const theme = (_a = session.allThemes) === null || _a === void 0 ? void 0 : _a.call(session)[themeName];
+    const { width, tracks, showCytobands } = model;
+    const shift = 50;
+    const c = +showCytobands * cytobandHeight;
+    const offset = headerHeight + rulerHeight + c + 10;
+    const height = totalHeight(tracks, textHeight, trackLabels) + offset + 100;
+    const displayResults = await Promise.all(tracks.map(async (track) => {
+        const display = track.displays[0];
+        await (0, mobx_1.when)(() => (display.ready !== undefined ? display.ready : true));
+        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;
+    // the xlink namespace is used for rendering <image> tag
+    return (0, server_1.renderToStaticMarkup)(react_1.default.createElement(material_1.ThemeProvider, { theme: (0, ui_1.createJBrowseTheme)(theme) },
+        react_1.default.createElement(Wrapper, null,
+            react_1.default.createElement("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() },
+                react_1.default.createElement(SVGBackground_1.default, { width: w, height: height, shift: shift }),
+                react_1.default.createElement("g", { transform: `translate(${shift} 0)` },
+                    react_1.default.createElement("g", { transform: `translate(${trackLabelOffset})` },
+                        react_1.default.createElement(SVGHeader_1.default, { model: model, fontSize: fontSize, rulerHeight: rulerHeight, cytobandHeight: cytobandHeight })),
+                    react_1.default.createElement(SVGTracks_1.default, { textHeight: textHeight, fontSize: fontSize, model: model, displayResults: displayResults, offset: offset, trackLabels: trackLabels, trackLabelOffset: trackLabelOffset }))))));
+}
+exports.renderToSvg = renderToSvg;
+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; } });
+//# sourceMappingURL=SVGLinearGenomeView.js.map

package/dist/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js.map

@@ -0,0 +1 @@
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package/dist/LinearGenomeView/svgcomponents/SVGRegionSeparators.d.ts

@@ -0,0 +1,8 @@
+/// <reference types="react" />
+import { LinearGenomeViewModel } from '..';
+type LGV = LinearGenomeViewModel;
+export default function SVGRegionSeparators({ model, height, }: {
+    height: number;
+    model: LGV;
+}): JSX.Element;
+export {};

package/dist/LinearGenomeView/svgcomponents/SVGRegionSeparators.js

@@ -0,0 +1,13 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+// SVG component, region separator
+function SVGRegionSeparators({ model, height, }) {
+    const { dynamicBlocks, offsetPx, interRegionPaddingWidth } = model;
+    return (react_1.default.createElement(react_1.default.Fragment, null, dynamicBlocks.contentBlocks.slice(1).map(block => (react_1.default.createElement("rect", { key: block.key, x: block.offsetPx - offsetPx - interRegionPaddingWidth, width: interRegionPaddingWidth, y: 0, height: height, fill: "grey" })))));
+}
+exports.default = SVGRegionSeparators;
+//# sourceMappingURL=SVGRegionSeparators.js.map

package/dist/LinearGenomeView/svgcomponents/SVGRegionSeparators.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SVGRegionSeparators.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/svgcomponents/SVGRegionSeparators.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AAOzB,kCAAkC;AAClC,SAAwB,mBAAmB,CAAC,EAC1C,KAAK,EACL,MAAM,GAIP;IACC,MAAM,EAAE,aAAa,EAAE,QAAQ,EAAE,uBAAuB,EAAE,GAAG,KAAK,CAAA;IAClE,OAAO,CACL,8DACG,aAAa,CAAC,aAAa,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CACjD,wCACE,GAAG,EAAE,KAAK,CAAC,GAAG,EACd,CAAC,EAAE,KAAK,CAAC,QAAQ,GAAG,QAAQ,GAAG,uBAAuB,EACtD,KAAK,EAAE,uBAAuB,EAC9B,CAAC,EAAE,CAAC,EACJ,MAAM,EAAE,MAAM,EACd,IAAI,EAAC,MAAM,GACX,CACH,CAAC,CACD,CACJ,CAAA;AACH,CAAC;AAtBD,sCAsBC"}

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

@@ -0,0 +1,8 @@
+/// <reference types="react" />
+import { LinearGenomeViewModel } from '..';
+type LGV = LinearGenomeViewModel;
+export default function SVGRuler({ model, fontSize, }: {
+    model: LGV;
+    fontSize: number;
+}): JSX.Element;
+export {};

package/dist/LinearGenomeView/svgcomponents/SVGRuler.js

@@ -0,0 +1,51 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
+// locals
+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)();
+    return (react_1.default.createElement(react_1.default.Fragment, null,
+        ticks.map(tick => {
+            const x = (reversed ? end - tick.base : tick.base - start) / bpPerPx;
+            return (react_1.default.createElement("line", { key: tick.base, x1: x, x2: x, y1: 0, y2: tick.type === 'major' ? 6 : 4, strokeWidth: 1, stroke: theme.palette.text.secondary }));
+        }),
+        !hideText
+            ? ticks
+                .filter(tick => tick.type === 'major')
+                .map(tick => {
+                const x = (reversed ? end - tick.base : tick.base - start) / bpPerPx;
+                return (react_1.default.createElement("text", { x: x - 3, y: 7 + 11, key: `label-${tick.base}`, fontSize: 11, fill: theme.palette.text.primary }, (0, util_1.getTickDisplayStr)(tick.base + 1, bpPerPx)));
+            })
+            : null));
+}
+function SVGRuler({ model, fontSize, }) {
+    const { dynamicBlocks: { contentBlocks }, offsetPx: viewOffsetPx, bpPerPx, } = model;
+    const renderRuler = contentBlocks.length < 5;
+    const theme = (0, material_1.useTheme)();
+    return (react_1.default.createElement(react_1.default.Fragment, null,
+        react_1.default.createElement(SVGRegionSeparators_1.default, { model: model, height: 30 }),
+        contentBlocks.map(block => {
+            const { start, end, key, reversed, offsetPx, refName, widthPx } = block;
+            const offset = offsetPx - viewOffsetPx;
+            const clipid = `clip-${key}`;
+            return (react_1.default.createElement("g", { key: key },
+                react_1.default.createElement("defs", null,
+                    react_1.default.createElement("clipPath", { id: clipid },
+                        react_1.default.createElement("rect", { x: 0, y: 0, width: widthPx, height: 100 }))),
+                react_1.default.createElement("g", { transform: `translate(${offset} 0)` },
+                    react_1.default.createElement("g", { clipPath: `url(#${clipid})` },
+                        react_1.default.createElement("text", { x: 4, y: fontSize, fontSize: fontSize, fill: theme.palette.text.primary }, refName),
+                        react_1.default.createElement("g", { transform: "translate(0 20)" },
+                            react_1.default.createElement(Ruler, { hideText: !renderRuler, start: start, end: end, bpPerPx: bpPerPx, reversed: reversed }))))));
+        })));
+}
+exports.default = SVGRuler;
+//# sourceMappingURL=SVGRuler.js.map

package/dist/LinearGenomeView/svgcomponents/SVGRuler.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SVGRuler.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/svgcomponents/SVGRuler.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,6CAAsD;AACtD,4CAAwC;AAExC,SAAS;AACT,kCAAmC;AAGnC,gFAAuD;AAIvD,SAAS,KAAK,CAAC,EACb,KAAK,EACL,GAAG,EACH,OAAO,EACP,QAAQ,GAAG,KAAK,EAChB,KAAK,GAAG,IAAI,EACZ,KAAK,GAAG,IAAI,EACZ,QAAQ,GAAG,KAAK,GASjB;IACC,MAAM,KAAK,GAAG,IAAA,gBAAS,EAAC,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,CAAC,CAAA;IAC1D,MAAM,KAAK,GAAG,IAAA,mBAAQ,GAAE,CAAA;IACxB,OAAO,CACL;QACG,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;YAChB,MAAM,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,GAAG,KAAK,CAAC,GAAG,OAAO,CAAA;YACpE,OAAO,CACL,wCACE,GAAG,EAAE,IAAI,CAAC,IAAI,EACd,EAAE,EAAE,CAAC,EACL,EAAE,EAAE,CAAC,EACL,EAAE,EAAE,CAAC,EACL,EAAE,EAAE,IAAI,CAAC,IAAI,KAAK,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EACjC,WAAW,EAAE,CAAC,EACd,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,GACpC,CACH,CAAA;QACH,CAAC,CAAC;QACD,CAAC,QAAQ;YACR,CAAC,CAAC,KAAK;iBACF,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,IAAI,KAAK,OAAO,CAAC;iBACrC,GAAG,CAAC,IAAI,CAAC,EAAE;gBACV,MAAM,CAAC,GACL,CAAC,QAAQ,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,GAAG,KAAK,CAAC,GAAG,OAAO,CAAA;gBAC5D,OAAO,CACL,wCACE,CAAC,EAAE,CAAC,GAAG,CAAC,EACR,CAAC,EAAE,CAAC,GAAG,EAAE,EACT,GAAG,EAAE,SAAS,IAAI,CAAC,IAAI,EAAE,EACzB,QAAQ,EAAE,EAAE,EACZ,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,IAE/B,IAAA,wBAAiB,EAAC,IAAI,CAAC,IAAI,GAAG,CAAC,EAAE,OAAO,CAAC,CACrC,CACR,CAAA;YACH,CAAC,CAAC;YACN,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC;AAED,SAAwB,QAAQ,CAAC,EAC/B,KAAK,EACL,QAAQ,GAIT;IACC,MAAM,EACJ,aAAa,EAAE,EAAE,aAAa,EAAE,EAChC,QAAQ,EAAE,YAAY,EACtB,OAAO,GACR,GAAG,KAAK,CAAA;IACT,MAAM,WAAW,GAAG,aAAa,CAAC,MAAM,GAAG,CAAC,CAAA;IAC5C,MAAM,KAAK,GAAG,IAAA,mBAAQ,GAAE,CAAA;IACxB,OAAO,CACL;QACE,8BAAC,6BAAmB,IAAC,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,EAAE,GAAI;QAChD,aAAa,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE;YACzB,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,QAAQ,EAAE,QAAQ,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;YACvE,MAAM,MAAM,GAAG,QAAQ,GAAG,YAAY,CAAA;YACtC,MAAM,MAAM,GAAG,QAAQ,GAAG,EAAE,CAAA;YAC5B,OAAO,CACL,qCAAG,GAAG,EAAE,GAAG;gBACT;oBACE,4CAAU,EAAE,EAAE,MAAM;wBAClB,wCAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,OAAO,EAAE,MAAM,EAAE,GAAG,GAAI,CACxC,CACN;gBACP,qCAAG,SAAS,EAAE,aAAa,MAAM,KAAK;oBACpC,qCAAG,QAAQ,EAAE,QAAQ,MAAM,GAAG;wBAC5B,wCACE,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,QAAQ,EACX,QAAQ,EAAE,QAAQ,EAClB,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,IAE/B,OAAO,CACH;wBACP,qCAAG,SAAS,EAAC,iBAAiB;4BAC5B,8BAAC,KAAK,IACJ,QAAQ,EAAE,CAAC,WAAW,EACtB,KAAK,EAAE,KAAK,EACZ,GAAG,EAAE,GAAG,EACR,OAAO,EAAE,OAAO,EAChB,QAAQ,EAAE,QAAQ,GAClB,CACA,CACF,CACF,CACF,CACL,CAAA;QACH,CAAC,CAAC,CACD,CACJ,CAAA;AACH,CAAC;AAtDD,2BAsDC"}

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

@@ -0,0 +1,8 @@
+/// <reference types="react" />
+import { LinearGenomeViewModel } from '..';
+type LGV = LinearGenomeViewModel;
+export default function SVGScalebar({ model, fontSize, }: {
+    model: LGV;
+    fontSize: number;
+}): JSX.Element;
+export {};

package/dist/LinearGenomeView/svgcomponents/SVGScalebar.js

@@ -0,0 +1,22 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+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;
+    return (react_1.default.createElement(react_1.default.Fragment, null,
+        react_1.default.createElement("line", { x1: x0, x2: x1, y1: 10, y2: 10, stroke: theme.palette.text.secondary }),
+        react_1.default.createElement("line", { x1: x0, x2: x0, y1: 5, y2: 15, stroke: theme.palette.text.secondary }),
+        react_1.default.createElement("line", { x1: x1, x2: x1, y1: 5, y2: 15, stroke: theme.palette.text.secondary }),
+        react_1.default.createElement("text", { x: x0 + (x1 - x0) / 2, y: fontSize * 2, textAnchor: "middle", fontSize: fontSize, fill: theme.palette.text.primary }, displayBp)));
+}
+exports.default = SVGScalebar;
+//# sourceMappingURL=SVGScalebar.js.map

package/dist/LinearGenomeView/svgcomponents/SVGScalebar.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SVGScalebar.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/svgcomponents/SVGScalebar.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,6CAAoD;AACpD,4CAAwC;AAKxC,SAAwB,WAAW,CAAC,EAClC,KAAK,EACL,QAAQ,GAIT;IACC,MAAM,EACJ,QAAQ,EACR,aAAa,EAAE,EAAE,0BAA0B,EAAE,YAAY,EAAE,OAAO,EAAE,GACrE,GAAG,KAAK,CAAA;IACT,MAAM,KAAK,GAAG,IAAA,mBAAQ,GAAE,CAAA;IACxB,MAAM,SAAS,GAAG,IAAA,sBAAe,EAAC,OAAO,CAAC,CAAA;IAC1C,MAAM,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAA;IACjC,MAAM,EAAE,GAAG,EAAE,GAAG,YAAY,CAAA;IAC5B,OAAO,CACL;QACE,wCACE,EAAE,EAAE,EAAE,EACN,EAAE,EAAE,EAAE,EACN,EAAE,EAAE,EAAE,EACN,EAAE,EAAE,EAAE,EACN,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,GACpC;QACF,wCACE,EAAE,EAAE,EAAE,EACN,EAAE,EAAE,EAAE,EACN,EAAE,EAAE,CAAC,EACL,EAAE,EAAE,EAAE,EACN,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,GACpC;QACF,wCACE,EAAE,EAAE,EAAE,EACN,EAAE,EAAE,EAAE,EACN,EAAE,EAAE,CAAC,EACL,EAAE,EAAE,EAAE,EACN,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,GACpC;QACF,wCACE,CAAC,EAAE,EAAE,GAAG,CAAC,EAAE,GAAG,EAAE,CAAC,GAAG,CAAC,EACrB,CAAC,EAAE,QAAQ,GAAG,CAAC,EACf,UAAU,EAAC,QAAQ,EACnB,QAAQ,EAAE,QAAQ,EAClB,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,IAE/B,SAAS,CACL,CACN,CACJ,CAAA;AACH,CAAC;AAjDD,8BAiDC"}

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

@@ -0,0 +1,8 @@
+/// <reference types="react" />
+export default function SVGTrackLabel({ trackLabels, trackName, fontSize, trackLabelOffset, x, }: {
+    trackName: string;
+    trackLabels: string;
+    fontSize: number;
+    trackLabelOffset: number;
+    x: number;
+}): JSX.Element | null;

package/dist/LinearGenomeView/svgcomponents/SVGTrackLabel.js

@@ -0,0 +1,16 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const material_1 = require("@mui/material");
+function SVGTrackLabel({ trackLabels, trackName, fontSize, trackLabelOffset, x, }) {
+    const theme = (0, material_1.useTheme)();
+    const fill = theme.palette.text.primary;
+    const xoff = trackLabels === 'overlay' ? 5 : 0;
+    const yoff = trackLabels === 'offset' ? 5 : 0;
+    return trackLabels !== 'none' ? (react_1.default.createElement("g", null, trackLabels === 'left' ? (react_1.default.createElement("text", { x: trackLabelOffset - 40, y: 20, fill: fill, fontSize: fontSize, dominantBaseline: "hanging", textAnchor: "end" }, trackName)) : (react_1.default.createElement("text", { x: x + xoff, y: yoff, fill: fill, fontSize: fontSize, dominantBaseline: "hanging" }, trackName)))) : null;
+}
+exports.default = SVGTrackLabel;
+//# sourceMappingURL=SVGTrackLabel.js.map

package/dist/LinearGenomeView/svgcomponents/SVGTrackLabel.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SVGTrackLabel.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/svgcomponents/SVGTrackLabel.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,4CAAwC;AAExC,SAAwB,aAAa,CAAC,EACpC,WAAW,EACX,SAAS,EACT,QAAQ,EACR,gBAAgB,EAChB,CAAC,GAOF;IACC,MAAM,KAAK,GAAG,IAAA,mBAAQ,GAAE,CAAA;IACxB,MAAM,IAAI,GAAG,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,CAAA;IACvC,MAAM,IAAI,GAAG,WAAW,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9C,MAAM,IAAI,GAAG,WAAW,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC7C,OAAO,WAAW,KAAK,MAAM,CAAC,CAAC,CAAC,CAC9B,yCACG,WAAW,KAAK,MAAM,CAAC,CAAC,CAAC,CACxB,wCACE,CAAC,EAAE,gBAAgB,GAAG,EAAE,EACxB,CAAC,EAAE,EAAE,EACL,IAAI,EAAE,IAAI,EACV,QAAQ,EAAE,QAAQ,EAClB,gBAAgB,EAAC,SAAS,EAC1B,UAAU,EAAC,KAAK,IAEf,SAAS,CACL,CACR,CAAC,CAAC,CAAC,CACF,wCACE,CAAC,EAAE,CAAC,GAAG,IAAI,EACX,CAAC,EAAE,IAAI,EACP,IAAI,EAAE,IAAI,EACV,QAAQ,EAAE,QAAQ,EAClB,gBAAgB,EAAC,SAAS,IAEzB,SAAS,CACL,CACR,CACC,CACL,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC;AA3CD,gCA2CC"}

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

@@ -0,0 +1,23 @@
+/// <reference types="react" />
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { LinearGenomeViewModel } from '..';
+type LGV = LinearGenomeViewModel;
+interface DisplayResult {
+    track: {
+        configuration: AnyConfigurationModel;
+        displays: {
+            height: number;
+        }[];
+    };
+    result: string;
+}
+export default function SVGTracks({ displayResults, model, offset, textHeight, fontSize, trackLabels, trackLabelOffset, }: {
+    displayResults: DisplayResult[];
+    model: LGV;
+    offset: number;
+    textHeight: number;
+    fontSize: number;
+    trackLabels?: string;
+    trackLabelOffset?: number;
+}): JSX.Element;
+export {};

package/dist/LinearGenomeView/svgcomponents/SVGTracks.js

@@ -0,0 +1,30 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const util_1 = require("@jbrowse/core/util");
+const SVGRegionSeparators_1 = __importDefault(require("./SVGRegionSeparators"));
+const SVGTrackLabel_1 = __importDefault(require("./SVGTrackLabel"));
+// SVG component, tracks
+function SVGTracks({ displayResults, model, offset, textHeight, fontSize, trackLabels = 'offset', trackLabelOffset = 0, }) {
+    const session = (0, util_1.getSession)(model);
+    const textOffset = trackLabels === 'offset' ? textHeight : 0;
+    return (react_1.default.createElement(react_1.default.Fragment, null, displayResults.map(({ track, result }) => {
+        const current = offset;
+        const conf = track.configuration;
+        const trackName = (0, tracks_1.getTrackName)(conf, session);
+        const display = track.displays[0];
+        const x = Math.max(-model.offsetPx, 0);
+        offset += display.height + textOffset;
+        return (react_1.default.createElement("g", { key: conf.trackId, transform: `translate(0 ${current})` },
+            react_1.default.createElement("g", { transform: `translate(${trackLabelOffset} ${textOffset})` },
+                react_1.default.createElement(SVGRegionSeparators_1.default, { model: model, height: display.height }),
+                result),
+            react_1.default.createElement(SVGTrackLabel_1.default, { trackName: trackName, fontSize: fontSize, trackLabels: trackLabels, trackLabelOffset: trackLabelOffset, x: x })));
+    })));
+}
+exports.default = SVGTracks;
+//# sourceMappingURL=SVGTracks.js.map

package/dist/LinearGenomeView/svgcomponents/SVGTracks.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SVGTracks.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/svgcomponents/SVGTracks.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AAEzB,sDAAwD;AACxD,6CAA+C;AAG/C,gFAAuD;AACvD,oEAA2C;AAY3C,wBAAwB;AACxB,SAAwB,SAAS,CAAC,EAChC,cAAc,EACd,KAAK,EACL,MAAM,EACN,UAAU,EACV,QAAQ,EACR,WAAW,GAAG,QAAQ,EACtB,gBAAgB,GAAG,CAAC,GASrB;IACC,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IACjC,MAAM,UAAU,GAAG,WAAW,KAAK,QAAQ,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAA;IAC5D,OAAO,CACL,8DACG,cAAc,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,EAAE,MAAM,EAAE,EAAE,EAAE;QACxC,MAAM,OAAO,GAAG,MAAM,CAAA;QACtB,MAAM,IAAI,GAAG,KAAK,CAAC,aAAa,CAAA;QAChC,MAAM,SAAS,GAAG,IAAA,qBAAY,EAAC,IAAI,EAAE,OAAO,CAAC,CAAA;QAC7C,MAAM,OAAO,GAAG,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;QACjC,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAA;QACtC,MAAM,IAAI,OAAO,CAAC,MAAM,GAAG,UAAU,CAAA;QACrC,OAAO,CACL,qCAAG,GAAG,EAAE,IAAI,CAAC,OAAO,EAAE,SAAS,EAAE,eAAe,OAAO,GAAG;YACxD,qCAAG,SAAS,EAAE,aAAa,gBAAgB,IAAI,UAAU,GAAG;gBAC1D,8BAAC,6BAAmB,IAAC,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,OAAO,CAAC,MAAM,GAAI;gBAC5D,MAAM,CACL;YACJ,8BAAC,uBAAa,IACZ,SAAS,EAAE,SAAS,EACpB,QAAQ,EAAE,QAAQ,EAClB,WAAW,EAAE,WAAW,EACxB,gBAAgB,EAAE,gBAAgB,EAClC,CAAC,EAAE,CAAC,GACJ,CACA,CACL,CAAA;IACH,CAAC,CAAC,CACD,CACJ,CAAA;AACH,CAAC;AA9CD,4BA8CC"}

package/dist/LinearGenomeView/util.js

@@ -9,7 +9,7 @@ exports.makeTicks = exports.chooseGridPitch = void 0;
 function chooseGridPitch(scale, minMajorPitchPx, minMinorPitchPx) {
     scale = Math.abs(scale);
     const minMajorPitchBp = minMajorPitchPx * scale;
-    const majorMagnitude = parseInt(Number(minMajorPitchBp).toExponential().split(/e/i)[1], 10);
+    const majorMagnitude = Number.parseInt(Number(minMajorPitchBp).toExponential().split(/e/i)[1], 10);
     let majorPitch = 10 ** majorMagnitude;
     while (majorPitch < minMajorPitchBp) {
         majorPitch *= 2;
@@ -51,7 +51,7 @@ function makeTicks(start, end, bpPerPx, emitMajor = true, emitMinor = true) {
     const iterPitch = gridPitch.minorPitch || gridPitch.majorPitch;
     let index = 0;
     const ticks = [];
-    for (let base = Math.ceil(minBase / iterPitch) * iterPitch; base < maxBase; base += iterPitch) {
+    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;

package/dist/LinearGenomeView/util.js.map

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