@jbrowse/plugin-breakpoint-split-view 3.7.0 → 4.0.0

package/dist/BreakpointSplitView/svgcomponents/SVGBreakpointSplitView.js

@@ -1,41 +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.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 plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const material_1 = require("@mui/material");
-const mobx_1 = require("mobx");
-const SVGBackground_1 = __importDefault(require("./SVGBackground"));
-const util_2 = require("./util");
-const Overlay_1 = __importDefault(require("../components/Overlay"));
-async function renderToSvg(model, opts) {
-    var _a;
-    const { textHeight = 18, headerHeight = 30, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', Wrapper = ({ children }) => children, themeName = 'default', } = 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, views } = model;
-    const shift = 50;
-    const offset = headerHeight + rulerHeight;
-    const heights = views.map(v => (0, plugin_linear_genome_view_1.totalHeight)(v.tracks, textHeight, trackLabels) + offset);
-    const totalHeightSvg = (0, util_1.sum)(heights) + 100;
-    const displayResults = await Promise.all(views.map(async (view) => ({
-        view,
-        data: await Promise.all(view.tracks.map(async (track) => {
-            const d = track.displays[0];
-            await (0, mobx_1.when)(() => (d.ready !== undefined ? d.ready : true));
-            return { track, result: await d.renderSvg({ ...opts, theme }) };
-        })),
-    })));
-    const trackLabelMaxLen = (0, util_2.getTrackNameMaxLen)(views, fontSize, session) + 40;
-    const trackLabelOffset = trackLabels === 'left' ? trackLabelMaxLen : 0;
-    const textOffset = trackLabels === 'offset' ? textHeight : 0;
-    const trackOffsets = views.map((view, idx) => (0, util_2.getTrackOffsets)(view, textOffset, fontSize + (idx > 0 ? heights[idx - 1] : 0) + offset));
-    const w = width + trackLabelOffset;
-    const t = (0, ui_1.createJBrowseTheme)(theme);
-    return (0, util_1.renderToStaticMarkup)((0, jsx_runtime_1.jsx)(material_1.ThemeProvider, { theme: t, children: (0, jsx_runtime_1.jsx)(Wrapper, { children: (0, jsx_runtime_1.jsxs)("svg", { width: width, height: totalHeightSvg, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w + shift * 2, totalHeightSvg].toString(), children: [(0, jsx_runtime_1.jsx)(SVGBackground_1.default, { width: w, height: totalHeightSvg, shift: shift }), views[0] ? ((0, jsx_runtime_1.jsxs)("g", { transform: `translate(${shift} ${fontSize})`, children: [(0, jsx_runtime_1.jsxs)("g", { transform: `translate(${trackLabelOffset})`, children: [(0, jsx_runtime_1.jsx)("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary, children: views[0].assemblyNames.join(', ') }), (0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.SVGRuler, { model: displayResults[0].view, fontSize: fontSize })] }), (0, jsx_runtime_1.jsx)("g", { transform: `translate(0 ${offset})`, children: (0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[0].view, displayResults: displayResults[0].data, trackLabelOffset: trackLabelOffset }) })] })) : null, views[1] ? ((0, jsx_runtime_1.jsxs)("g", { transform: `translate(${shift} ${fontSize + heights[0]})`, children: [(0, jsx_runtime_1.jsxs)("g", { transform: `translate(${trackLabelOffset})`, children: [(0, jsx_runtime_1.jsx)("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary, children: views[1].assemblyNames.join(', ') }), (0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.SVGRuler, { model: displayResults[1].view, fontSize: fontSize })] }), (0, jsx_runtime_1.jsx)("g", { transform: `translate(0 ${offset})`, children: (0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[1].view, displayResults: displayResults[1].data, trackLabelOffset: trackLabelOffset }) })] })) : null, (0, jsx_runtime_1.jsx)("defs", { children: (0, jsx_runtime_1.jsx)("clipPath", { id: "clip-bsv", children: (0, jsx_runtime_1.jsx)("rect", { x: 0, y: 0, width: width, height: totalHeightSvg }) }) }), (0, jsx_runtime_1.jsx)("g", { transform: `translate(${trackLabelOffset + shift})`, clipPath: "url(#clip-bsv)", children: model.matchedTracks.map(track => ((0, jsx_runtime_1.jsx)(Overlay_1.default, { parentRef: { current: null }, model: model, trackId: track.configuration.trackId, getTrackYPosOverride: (id, level) => trackOffsets[level][id] }, track.configuration.trackId))) })] }) }) }));
-}

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

@@ -1,4 +0,0 @@
-import type { AbstractSessionModel } from '@jbrowse/core/util';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export declare function getTrackNameMaxLen(views: LinearGenomeViewModel[], fontSize: number, session: AbstractSessionModel): number;
-export declare function getTrackOffsets(view: LinearGenomeViewModel, textOffset: number, extra?: number): Record<string, number>;

package/dist/BreakpointSplitView/svgcomponents/util.js

@@ -1,18 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getTrackNameMaxLen = getTrackNameMaxLen;
-exports.getTrackOffsets = getTrackOffsets;
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-function getTrackNameMaxLen(views, fontSize, session) {
-    return (0, util_1.max)(views.flatMap(view => view.tracks.map(t => (0, util_1.measureText)((0, tracks_1.getTrackName)(t.configuration, session), fontSize))), 0);
-}
-function getTrackOffsets(view, textOffset, extra = 0) {
-    const offsets = {};
-    let curr = textOffset;
-    for (const track of view.tracks) {
-        offsets[track.configuration.trackId] = curr + extra;
-        curr += track.displays[0].height + textOffset;
-    }
-    return offsets;
-}

package/dist/BreakpointSplitView/types.d.ts

@@ -1,22 +0,0 @@
-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 Breakend {
-    MateDirection: string;
-    Join: string;
-    Replacement: string;
-    MatePosition: string;
-}
-export type LayoutRecord = [number, number, number, number];

package/dist/BreakpointSplitView/types.js

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

package/dist/BreakpointSplitView/util.d.ts

@@ -1,28 +0,0 @@
-import type { LayoutRecord } from './types';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Feature } from '@jbrowse/core/util';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-type LGV = LinearGenomeViewModel;
-interface Display {
-    height: number;
-    scrollTop: number;
-    SNPCoverageDisplay?: {
-        height: number;
-    };
-    notReady?: () => boolean;
-    searchFeatureByID?: (str: string) => LayoutRecord;
-}
-interface Track {
-    displays: Display[];
-    configuration: AnyConfigurationModel;
-}
-export declare function heightFromSpecificLevel(views: LGV[], trackId: string, level: number, getYPosOverride?: (trackId: string, level: number) => number): number;
-export declare function getPxFromCoordinate(view: LGV, refName: string, coord: number): number;
-export declare function yPos(trackId: string, level: number, views: LGV[], tracks: Track[], c: LayoutRecord, getYPosOverride?: (trackId: string, level: number) => number): number;
-export declare const useNextFrame: (variable: unknown) => void;
-export declare function intersect<T>(cb: (l: T) => string, a1?: T[], a2?: T[], ...rest: T[][]): T[];
-export declare function calc(track: Track, f: Feature): LayoutRecord | undefined;
-export declare function getBlockFeatures(model: {
-    views: LinearGenomeViewModel[];
-}, track: Track): Promise<Feature[][][]>;
-export {};

package/dist/BreakpointSplitView/util.js

@@ -1,67 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.useNextFrame = void 0;
-exports.heightFromSpecificLevel = heightFromSpecificLevel;
-exports.getPxFromCoordinate = getPxFromCoordinate;
-exports.yPos = yPos;
-exports.intersect = intersect;
-exports.calc = calc;
-exports.getBlockFeatures = getBlockFeatures;
-const react_1 = require("react");
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-const [, TOP, , BOTTOM] = [0, 1, 2, 3];
-function cheight(chunk) {
-    return chunk[BOTTOM] - chunk[TOP];
-}
-function heightFromSpecificLevel(views, trackId, level, getYPosOverride) {
-    var _a;
-    return getYPosOverride
-        ? getYPosOverride(trackId, level)
-        : ((_a = views[level].trackRefs[trackId]) === null || _a === void 0 ? void 0 : _a.getBoundingClientRect().top) || 0;
-}
-function getPxFromCoordinate(view, refName, coord) {
-    var _a;
-    return (((_a = view.bpToPx({ refName, coord })) === null || _a === void 0 ? void 0 : _a.offsetPx) || 0) - view.offsetPx;
-}
-function yPos(trackId, level, views, tracks, c, getYPosOverride) {
-    const display = tracks[level].displays[0];
-    const min = 0;
-    const max = display.height;
-    let offset = 0;
-    const { SNPCoverageDisplay } = display;
-    if (SNPCoverageDisplay) {
-        offset = SNPCoverageDisplay.height;
-    }
-    const yPos = getYPosOverride ? 0 : display.scrollTop;
-    return ((0, util_1.clamp)(c[TOP] - yPos + cheight(c) / 2 + offset, min, max) +
-        heightFromSpecificLevel(views, trackId, level, getYPosOverride) +
-        display.scrollTop);
-}
-const useNextFrame = (variable) => {
-    const [, setNextFrameState] = (0, react_1.useState)();
-    (0, react_1.useEffect)(() => {
-        setNextFrameState(variable);
-    }, [variable]);
-};
-exports.useNextFrame = useNextFrame;
-function intersect(cb, a1 = [], a2 = [], ...rest) {
-    const ids = new Set(a2.map(elt => cb(elt)));
-    const a12 = a1.filter(value => ids.has(cb(value)));
-    return rest.length === 0 ? a12 : intersect(cb, a12, ...rest);
-}
-function calc(track, f) {
-    var _a, _b;
-    return (_b = (_a = track.displays[0]).searchFeatureByID) === null || _b === void 0 ? void 0 : _b.call(_a, f.id());
-}
-async function getBlockFeatures(model, track) {
-    const { views } = model;
-    const { rpcManager } = (0, util_1.getSession)(model);
-    const sessionId = (0, tracks_1.getRpcSessionId)(track);
-    return Promise.all(views.flatMap(async (view) => (await rpcManager.call(sessionId, 'CoreGetFeatures', {
-        adapterConfig: (0, configuration_1.getConf)(track, ['adapter']),
-        sessionId,
-        regions: view.staticBlocks.contentBlocks,
-    }))));
-}

package/dist/index.d.ts

@@ -1,7 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin';
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default class BreakpointSplitViewPlugin extends Plugin {
-    name: string;
-    install(pluginManager: PluginManager): void;
-    configure(): void;
-}

package/dist/index.js

@@ -1,20 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const BreakpointAlignmentsFeatureDetail_1 = __importDefault(require("./BreakpointAlignmentsFeatureDetail"));
-const BreakpointSplitView_1 = __importDefault(require("./BreakpointSplitView"));
-class BreakpointSplitViewPlugin extends Plugin_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'BreakpointSplitViewPlugin';
-    }
-    install(pluginManager) {
-        (0, BreakpointSplitView_1.default)(pluginManager);
-        (0, BreakpointAlignmentsFeatureDetail_1.default)(pluginManager);
-    }
-    configure() { }
-}
-exports.default = BreakpointSplitViewPlugin;