@genome-spy/core 0.29.0 → 0.30.2

package/src/gl/webGLHelper.js

@@ -1,489 +0,0 @@
-import {
-    addExtensionsToContext,
-    createFramebufferInfo,
-    createTexture,
-    getContext,
-    isWebGL2,
-    resizeFramebufferInfo,
-    setTextureFromArray,
-} from "twgl.js";
-import { isArray, isString } from "vega-util";
-
-import { isDiscrete, isDiscretizing, isInterpolating } from "vega-scale";
-import {
-    createDiscreteColorTexture,
-    createDiscreteTexture,
-    createInterpolatedColorTexture,
-    createSchemeTexture,
-} from "../scale/colorUtils";
-import {
-    getDiscreteRangeMapper,
-    isColorChannel,
-    isDiscreteChannel,
-} from "../encoder/encoder";
-
-export default class WebGLHelper {
-    /**
-     *
-     * @param {HTMLElement} container
-     * @param {() => {width: number, height: number}} [sizeSource]
-     *      A function that returns the content size. If a dimension is undefined,
-     *      the canvas fills the container, otherwise the canvas is adjusted to the content size.
-     */
-    constructor(container, sizeSource) {
-        this._container = container;
-        this._sizeSource = sizeSource;
-
-        /** @type {Map<string, WebGLShader>} */
-        this._shaderCache = new Map();
-
-        /** @type {{ type: string, listener: function}[]} */
-        this._listeners = [];
-
-        /** @type {WeakMap<import("../view/scaleResolution").default, WebGLTexture>} */
-        this.rangeTextures = new WeakMap();
-
-        // --------------------------------------------------------
-
-        const canvas = document.createElement("canvas");
-
-        container.appendChild(canvas);
-
-        // TODO: Consider using high-performance powerPreference:
-        // https://www.khronos.org/webgl/public-mailing-list/public_webgl/1912/msg00001.php
-
-        const gl = /** @type {WebGL2RenderingContext} */ (
-            getContext(canvas, {
-                antialias: true,
-                // Disable depth writes. We don't use depth testing.
-                depth: false,
-                premultipliedAlpha: true,
-            })
-        );
-
-        if (!gl) {
-            throw new Error(
-                "Unable to initialize WebGL. Your browser or machine may not support it."
-            );
-        }
-
-        if (!isWebGL2(gl)) {
-            throw new Error(
-                "Your web browser does not support WebGL 2.0. Chrome, Firefox, and Safari Tech Preview should work."
-            );
-        }
-
-        addExtensionsToContext(gl);
-
-        // TODO: view background: https://vega.github.io/vega-lite/docs/spec.html#view-background
-
-        // Always use pre-multiplied alpha
-        gl.blendFunc(gl.ONE, gl.ONE_MINUS_SRC_ALPHA);
-
-        this.canvas = canvas;
-        this.gl = gl;
-
-        // Setup framebuffer for piccking
-        /** @type {import("twgl.js").AttachmentOptions[]} */
-        this._pickingAttachmentOptions = [
-            {
-                format: gl.RGBA,
-                type: gl.UNSIGNED_BYTE,
-                minMag: gl.LINEAR,
-                wrap: gl.CLAMP_TO_EDGE,
-            },
-        ];
-        this._pickingBufferInfo = createFramebufferInfo(
-            gl,
-            this._pickingAttachmentOptions
-        );
-        gl.bindFramebuffer(gl.FRAMEBUFFER, null);
-
-        this.adjustGl();
-
-        // TODO: Size should be observed only if the content is not absolutely sized
-        this._resizeObserver = new ResizeObserver((entries) => {
-            this.invalidateSize();
-            this._emit("resize");
-        });
-        this._resizeObserver.observe(this._container);
-
-        // TODO: Observe devicePixelRatio
-        // https://developer.mozilla.org/en-US/docs/Web/API/Window/devicePixelRatio#Monitoring_screen_resolution_or_zoom_level_changes
-
-        this._updateDpr();
-    }
-
-    invalidateSize() {
-        this._logicalCanvasSize = undefined;
-        this._updateDpr();
-        this.adjustGl();
-    }
-
-    _updateDpr() {
-        this.dpr = window.devicePixelRatio;
-    }
-
-    /**
-     * Compiles and caches a shader. The shader source is used as a cache key.
-     *
-     * @param {number} type gl.VERTEX_SHADER or gl.FRAGMENT_SHADER
-     * @param {string | string[]} glsl
-     */
-    compileShader(type, glsl) {
-        const VERSION = "#version 300 es";
-        const PRECISION = "precision mediump float;";
-
-        if (isArray(glsl)) {
-            glsl = glsl.join("\n\n");
-        }
-
-        const gl = this.gl;
-        const cacheKey = glsl.replaceAll(/ {2,}|^\s*\/\/.*$/gm, "");
-
-        let shader = this._shaderCache.get(cacheKey);
-        if (!shader) {
-            const stitchedSource = [VERSION, PRECISION, glsl].join("\n\n");
-
-            shader = gl.createShader(type);
-            gl.shaderSource(shader, stitchedSource);
-            gl.compileShader(shader);
-
-            // Don't check errors here. Only check them if linking fails.
-
-            this._shaderCache.set(cacheKey, shader);
-        }
-
-        return shader;
-    }
-
-    adjustGl() {
-        const logicalSize = this.getLogicalCanvasSize();
-        this.canvas.style.width = `${logicalSize.width}px`;
-        this.canvas.style.height = `${logicalSize.height}px`;
-
-        const physicalSize = this.getPhysicalCanvasSize(logicalSize);
-        this.canvas.width = physicalSize.width;
-        this.canvas.height = physicalSize.height;
-
-        resizeFramebufferInfo(
-            this.gl,
-            this._pickingBufferInfo,
-            this._pickingAttachmentOptions
-        );
-    }
-
-    finalize() {
-        this._resizeObserver.unobserve(this._container);
-        this.canvas.remove();
-    }
-
-    /**
-     * Returns the canvas size in true display pixels
-     *
-     * @param {{ width: number, height: number }} [logicalSize]
-     */
-    getPhysicalCanvasSize(logicalSize) {
-        logicalSize = logicalSize || this.getLogicalCanvasSize();
-        return {
-            width: logicalSize.width * this.dpr,
-            height: logicalSize.height * this.dpr,
-        };
-    }
-
-    /**
-     * Returns the canvas size in logical pixels (without devicePixelRatio correction)
-     */
-    getLogicalCanvasSize() {
-        if (this._logicalCanvasSize) {
-            return this._logicalCanvasSize;
-        }
-
-        // TODO: The size should never be smaller than the minimum content size!
-        const contentSize = this._sizeSource?.() ?? {
-            width: undefined,
-            height: undefined,
-        };
-
-        const cs = window.getComputedStyle(this._container, null);
-        const width =
-            contentSize.width ??
-            this._container.clientWidth -
-                parseFloat(cs.paddingLeft) -
-                parseFloat(cs.paddingRight);
-
-        const height =
-            contentSize.height ??
-            this._container.clientHeight -
-                parseFloat(cs.paddingTop) -
-                parseFloat(cs.paddingBottom);
-
-        this._logicalCanvasSize = { width, height };
-        return this._logicalCanvasSize;
-    }
-
-    /**
-     * @param {"render"|"resize"} eventType
-     * @param {function} listener
-     */
-    addEventListener(eventType, listener) {
-        this._listeners.push({ type: eventType, listener });
-    }
-
-    /**
-     * @param {string} eventType
-     */
-    _emit(eventType) {
-        for (const entry of this._listeners) {
-            if (entry.type === eventType) {
-                entry.listener();
-            }
-        }
-    }
-
-    /**
-     *
-     * @param {number} x
-     * @param {number} y
-     */
-    readPickingPixel(x, y) {
-        const gl = this.gl;
-
-        x *= this.dpr;
-        y *= this.dpr;
-
-        const height = this.getPhysicalCanvasSize().height;
-
-        const pixel = new Uint8Array(4);
-        gl.bindFramebuffer(gl.FRAMEBUFFER, this._pickingBufferInfo.framebuffer);
-        gl.readPixels(
-            x,
-            height - y - 1,
-            1,
-            1,
-            gl.RGBA,
-            gl.UNSIGNED_BYTE,
-            pixel
-        );
-        gl.bindFramebuffer(gl.FRAMEBUFFER, null);
-
-        return pixel;
-    }
-
-    clearAll() {
-        const gl = this.gl;
-        const { width, height } = this.getPhysicalCanvasSize();
-        gl.viewport(0, 0, width, height);
-        gl.disable(gl.SCISSOR_TEST);
-        gl.clearColor(0, 0, 0, 0);
-        gl.clear(gl.COLOR_BUFFER_BIT);
-    }
-
-    /**
-     * Creates textures for color schemes and discrete/discretizing ranges.
-     * N.B. Discrete range textures need domain. Thus, this cannot be called
-     * before the final domains are resolved.
-     *
-     * TODO: This may be too specific to be included in WebGLHelper. Find a better place.
-     *
-     * @param {import("../view/scaleResolution").default} resolution
-     * @param {boolean} update Update the texture if it exists already.
-     */
-    createRangeTexture(resolution, update = false) {
-        const existingTexture = this.rangeTextures.get(resolution);
-        if (!update && existingTexture) {
-            return;
-        }
-
-        /**
-         * TODO: The count configuration logic etc should be combined
-         * with scale.js that configures d3 scales using vega specs
-         * @param {number} count
-         * @param {any} scale
-         * @returns {number}
-         */
-        function fixCount(count, scale) {
-            if (isDiscrete(scale.type)) {
-                return scale.domain().length;
-            } else if (scale.type == "threshold") {
-                return scale.domain().length + 1;
-            } else if (scale.type == "quantize") {
-                return count ?? 4;
-            } else if (scale.type == "quantile") {
-                return count ?? 4;
-            }
-            return count;
-        }
-
-        const channel = resolution.channel;
-
-        if (isColorChannel(channel)) {
-            const props = resolution.getScaleProps();
-
-            const scale = resolution.getScale();
-
-            /** @type {WebGLTexture} */
-            let texture;
-
-            if (props.scheme) {
-                let count = isString(props.scheme)
-                    ? undefined
-                    : props.scheme.count;
-
-                count = fixCount(count, scale);
-
-                texture = createSchemeTexture(
-                    props.scheme,
-                    this.gl,
-                    count,
-                    existingTexture
-                );
-            } else {
-                // No scheme, assume that colors are specified in the range
-
-                const range = /** @type {any[]} */ (scale.range());
-
-                if (isInterpolating(scale.type)) {
-                    texture = createInterpolatedColorTexture(
-                        range,
-                        props.interpolate,
-                        this.gl,
-                        existingTexture
-                    );
-                } else {
-                    texture = createDiscreteColorTexture(
-                        range,
-                        this.gl,
-                        scale.domain().length,
-                        existingTexture
-                    );
-                }
-            }
-
-            this.rangeTextures.set(resolution, texture);
-        } else {
-            const scale = resolution.getScale();
-
-            if (scale.type === "ordinal" || isDiscretizing(scale.type)) {
-                /** @type {function(any):number} Handle "shape" etc */
-                const mapper = isDiscreteChannel(channel)
-                    ? getDiscreteRangeMapper(channel)
-                    : (x) => x;
-
-                const range = /** @type {any[]} */ (
-                    resolution.getScale().range()
-                );
-
-                this.rangeTextures.set(
-                    resolution,
-                    createDiscreteTexture(
-                        range.map(mapper),
-                        this.gl,
-                        scale.domain().length,
-                        existingTexture
-                    )
-                );
-            }
-        }
-    }
-}
-
-/**
- * Copy-pasted from twgl.js:
- * https://github.com/greggman/twgl.js/blob/master/src/programs.js
- * Copyright 2019 Gregg Tavares, MIT license
- *
- * @param {string} src
- */
-function addLineNumbersWithError(src, log = "", lineOffset = 0) {
-    const errorRE = /ERROR:\s*\d+:(\d+)/gi;
-    // Note: Error message formats are not defined by any spec so this may or may not work.
-    const matches = [...log.matchAll(errorRE)];
-    const lineNoToErrorMap = new Map(
-        matches.map((m, ndx) => {
-            const lineNo = parseInt(m[1]);
-            const next = matches[ndx + 1];
-            const end = next ? next.index : log.length;
-            const msg = log.substring(m.index, end);
-            return [lineNo - 1, msg];
-        })
-    );
-    return src
-        .split("\n")
-        .map((line, lineNo) => {
-            const err = lineNoToErrorMap.get(lineNo);
-            return `${lineNo + 1 + lineOffset}: ${line}${
-                err ? `\n\n^^^ ${err}` : ""
-            }`;
-        })
-        .join("\n");
-}
-
-/**
- * @param {WebGL2RenderingContext} gl
- * @param {WebGLShader} vertexShader
- * @param {WebGLShader} fragmentShader
- */
-export function createProgram(gl, vertexShader, fragmentShader) {
-    const program = gl.createProgram();
-    gl.attachShader(program, vertexShader);
-    gl.attachShader(program, fragmentShader);
-    gl.linkProgram(program);
-
-    function getProgramErrors() {
-        /** @type {string} */
-        let errorMsg;
-        /** @type {string} */
-        let errorDetail;
-
-        const linked = gl.getProgramParameter(program, gl.LINK_STATUS);
-        if (!linked) {
-            errorMsg = gl.getProgramInfoLog(program);
-
-            for (const shader of [vertexShader, fragmentShader]) {
-                const compiled = gl.getShaderParameter(
-                    shader,
-                    gl.COMPILE_STATUS
-                );
-                if (!compiled) {
-                    errorMsg = gl.getShaderInfoLog(shader);
-                    errorDetail =
-                        addLineNumbersWithError(
-                            gl.getShaderSource(shader),
-                            errorMsg,
-                            0
-                        ) + `\nError compiling: ${errorMsg}`;
-                    gl.deleteShader(shader);
-                }
-            }
-            gl.deleteProgram(program);
-        }
-
-        if (errorMsg) {
-            return { message: errorMsg, detail: errorDetail };
-        }
-    }
-
-    return {
-        program,
-        getProgramErrors,
-    };
-}
-
-/**
- * @param {WebGLRenderingContext} gl
- * @param {Omit<import("twgl.js").TextureOptions, "src">} options
- * @param {number[] | ArrayBufferView} src
- * @param {WebGLTexture} [texture]
- */
-export function createOrUpdateTexture(gl, options, src, texture) {
-    if (texture) {
-        setTextureFromArray(gl, texture, src, options);
-    } else {
-        texture = createTexture(gl, {
-            ...options,
-            src,
-        });
-    }
-    return texture;
-}

package/src/img/bowtie.svg

@@ -1 +0,0 @@
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package/src/img/genomespy-favicon.svg

@@ -1,34 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<svg width="100%" height="100%" viewBox="0 0 64 64" version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" xml:space="preserve" xmlns:serif="http://www.serif.com/" style="fill-rule:evenodd;clip-rule:evenodd;stroke-linecap:round;stroke-linejoin:round;stroke-miterlimit:1.5;">
-    <g transform="matrix(0.10221,0.00683825,-0.0067136,0.100347,-8.03424,-13.2222)">
-        <path d="M208.629,548.17C208.629,548.17 219.768,594.389 239.814,619.222C259.86,644.055 319.119,680.831 319.119,680.831C319.119,680.831 385.557,622.915 437.87,498.346C437.87,498.346 456.021,499.236 473.808,486.446C491.594,473.656 490.239,478.534 494.883,461.62C494.883,461.62 551.848,467.937 625.826,451.863C667.634,442.778 710.238,425.649 747.382,393.142C747.382,393.142 721.992,360.244 689.422,291.45C677.029,265.275 647.518,257.098 590.747,203.309L438.083,391.273L208.629,548.17Z" style="fill-opacity:0.11;"/>
-    </g>
-    <g transform="matrix(0.081985,-0.0582493,0.0582493,0.081985,-40.4754,34.7668)">
-        <path d="M561.588,349.155C561.588,349.155 516.297,271.341 328.841,252.044C328.841,252.044 302.342,325.189 307.686,368.056C313.031,410.922 303.001,456.147 329.132,501.174C329.132,501.174 443.114,506.743 554.649,428.469L629.204,432.112C629.204,432.112 673.755,534.351 856.964,554.375C856.964,554.375 886.717,491.768 879.193,417.478C871.211,338.673 871.716,293.443 871.716,293.443C871.716,293.443 775.485,283.928 635.418,361.795L561.588,349.155Z" style="fill:rgb(127,187,221);"/>
-        <clipPath id="_clip1">
-            <path d="M561.588,349.155C561.588,349.155 516.297,271.341 328.841,252.044C328.841,252.044 302.342,325.189 307.686,368.056C313.031,410.922 303.001,456.147 329.132,501.174C329.132,501.174 443.114,506.743 554.649,428.469L629.204,432.112C629.204,432.112 673.755,534.351 856.964,554.375C856.964,554.375 886.717,491.768 879.193,417.478C871.211,338.673 871.716,293.443 871.716,293.443C871.716,293.443 775.485,283.928 635.418,361.795L561.588,349.155Z"/>
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-        <g clip-path="url(#_clip1)">
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-        <g clip-path="url(#_clip2)">
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-        </g>
-        <path d="M384.916,385.459C384.916,385.459 430.781,347.868 450.027,350.093C471.685,352.596 490.49,407.747 490.208,424.416C489.927,441.085 442.948,469.866 422.537,466.24C422.537,466.24 425.525,442.129 412.114,413.335C398.702,384.54 384.916,385.459 384.916,385.459Z" style="fill:none;stroke:black;stroke-width:16.57px;"/>
-    </g>
-</svg>

package/src/index.html

@@ -1,11 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
-  <head>
-    <meta charset="UTF-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>GenomeSpy</title>
-  </head>
-  <body>
-    <script type="module" src="/singlePageApp.js"></script>
-  </body>
-</html>

package/src/index.js

@@ -1,128 +0,0 @@
-import { isObject, isString } from "vega-util";
-import { loader as vegaLoader } from "vega-loader";
-import { html } from "lit-html";
-
-import GenomeSpy from "./genomeSpy.js";
-import icon from "./img/bowtie.svg";
-
-export { GenomeSpy, html, icon };
-
-/**
- * Embeds GenomeSpy into the DOM
- *
- * @type {import("./embedApi.js").EmbedFunction}
- * @returns {Promise<import("./embedApi").EmbedResult>}
- */
-export async function embed(el, spec, options = {}) {
-    /** @type {HTMLElement} */
-    let element;
-
-    if (isString(el)) {
-        element = document.querySelector(el);
-        if (!element) {
-            throw new Error(`No such element: ${el}`);
-        }
-    } else if (el instanceof HTMLElement) {
-        element = el;
-    } else {
-        throw new Error(`Invalid element: ${el}`);
-    }
-
-    /** @type {GenomeSpy} */
-    let genomeSpy;
-
-    try {
-        const specObject = isObject(spec) ? spec : await loadSpec(spec);
-
-        specObject.baseUrl ??= "";
-        specObject.width ??= "container";
-        specObject.padding ??= 10;
-
-        if (element == document.body) {
-            // Need to add a wrapper to make sizing behavior more stable
-            const wrapper = document.createElement("div");
-            wrapper.style.position = "fixed";
-            wrapper.style.inset = "0";
-            wrapper.style.overflow = "hidden";
-            element.appendChild(wrapper);
-            element = wrapper;
-        }
-
-        genomeSpy = new GenomeSpy(element, specObject, options);
-        applyOptions(genomeSpy, options);
-        await genomeSpy.launch();
-    } catch (e) {
-        // eslint-disable-next-line require-atomic-updates
-        element.innerText = e.toString();
-        console.error(e);
-    }
-
-    return {
-        finalize() {
-            genomeSpy.destroy();
-            while (element.firstChild) {
-                element.firstChild.remove();
-            }
-        },
-
-        addEventListener(type, listener) {
-            const listenersByType = genomeSpy._eventListeners;
-
-            let listeners = listenersByType.get(type);
-            if (!listeners) {
-                listeners = new Set();
-                listenersByType.set(type, listeners);
-            }
-
-            listeners.add(listener);
-        },
-
-        removeEventListener(type, listener) {
-            const listenersByType = genomeSpy._eventListeners;
-
-            listenersByType.get(type)?.delete(listener);
-        },
-
-        getScaleResolutionByName(name) {
-            return genomeSpy.getNamedScaleResolutions().get(name);
-        },
-
-        updateNamedData: genomeSpy.updateNamedData.bind(genomeSpy),
-    };
-}
-
-/**
- *
- * @param {import("./genomeSpy").default} genomeSpy
- * @param {import("./embedApi.js").EmbedOptions} options options
- */
-function applyOptions(genomeSpy, options) {
-    if (options.namedDataProvider) {
-        genomeSpy.registerNamedDataProvider(options.namedDataProvider);
-    }
-}
-
-/**
- * Loads the spec from the given url and sets the baseUrl if it is not
- * defined in the spec.
- *
- * @param {string} url
- */
-export async function loadSpec(url) {
-    let spec;
-
-    try {
-        spec = JSON.parse(await vegaLoader().load(url));
-    } catch (e) {
-        throw new Error(
-            `Could not load or parse configuration: ${url}, reason: ${e.message}`
-        );
-    }
-
-    if (!spec.baseUrl) {
-        const m = url.match(/^[^?#]*\//);
-        spec.baseUrl = (m && m[0]) || "./";
-    }
-
-    return spec;
-}