@genome-spy/core 0.29.0 → 0.30.2

package/src/marks/rule.js

@@ -1,250 +0,0 @@
-import Mark from "./mark.js";
-import {
-    createTexture,
-    drawBufferInfo,
-    setBuffersAndAttributes,
-    setUniforms,
-} from "twgl.js";
-import VERTEX_SHADER from "../gl/rule.vertex.glsl";
-import FRAGMENT_SHADER from "../gl/rule.fragment.glsl";
-import { RuleVertexBuilder } from "../gl/dataToVertices";
-import { isChannelDefWithScale } from "../encoder/encoder.js";
-
-export default class RuleMark extends Mark {
-    /**
-     * @param {import("../view/unitView").default} unitView
-     */
-    constructor(unitView) {
-        super(unitView);
-
-        this.dashTextureSize = 0;
-
-        Object.defineProperties(
-            this.defaultProperties,
-            Object.getOwnPropertyDescriptors({
-                x2: undefined,
-                y2: undefined,
-                size: 1,
-                color: "black",
-                opacity: 1.0,
-
-                minLength: 0.0,
-                /** @type {number[]} */
-                strokeDash: null,
-                strokeDashOffset: 0,
-                strokeCap: "butt",
-            })
-        );
-    }
-
-    getAttributes() {
-        return [
-            "uniqueId",
-            "facetIndex",
-            "x",
-            "x2",
-            "y",
-            "y2",
-            "size",
-            "color",
-            "opacity",
-        ];
-    }
-
-    /**
-     * @returns {import("../spec/channel").Channel[]}
-     */
-    getSupportedChannels() {
-        return [...super.getSupportedChannels(), "x2", "y2", "size"];
-    }
-
-    /**
-     * @param {import("../spec/channel").Encoding} encoding
-     * @returns {import("../spec/channel").Encoding}
-     */
-    // eslint-disable-next-line complexity
-    fixEncoding(encoding) {
-        // TODO: Write test for this mess
-        if (encoding.x && encoding.y && encoding.x2 && encoding.y2) {
-            // Everything is defined
-        } else if (encoding.x && encoding.x2 && !encoding.y) {
-            encoding.y = { value: 0.5 };
-            encoding.y2 = encoding.y;
-        } else if (encoding.y && encoding.y2 && !encoding.x) {
-            encoding.x = { value: 0.5 };
-            encoding.x2 = encoding.x;
-        } else if (encoding.x && !encoding.y) {
-            // Vertical rule
-            encoding.y = { value: 0 };
-            encoding.y2 = { value: 1 };
-            encoding.x2 = encoding.x;
-        } else if (encoding.y && !encoding.x) {
-            // Horizontal rule
-            encoding.x = { value: 0 };
-            encoding.x2 = { value: 1 };
-            encoding.y2 = encoding.y;
-        } else if (encoding.x && encoding.y && encoding.y2) {
-            // Limited vertical rule
-            encoding.x2 = encoding.x;
-        } else if (encoding.y && encoding.x && encoding.x2) {
-            // Limited horizontal rule
-            encoding.y2 = encoding.y;
-        } else if (encoding.y && encoding.x) {
-            if (
-                !encoding.x2 &&
-                isChannelDefWithScale(encoding.y) &&
-                encoding.y.type == "quantitative"
-            ) {
-                encoding.x2 = encoding.x;
-                encoding.y2 = { datum: 0 };
-            } else if (
-                !encoding.y2 &&
-                isChannelDefWithScale(encoding.x) &&
-                encoding.x.type == "quantitative"
-            ) {
-                encoding.y2 = encoding.y;
-                encoding.x2 = { datum: 0 };
-            } else {
-                throw new Error("A bug!"); // Should be unreachable
-            }
-        } else {
-            throw new Error(
-                "Invalid x and y encodings for rule mark: " +
-                    JSON.stringify(encoding)
-            );
-        }
-
-        return encoding;
-    }
-
-    async initializeGraphics() {
-        await super.initializeGraphics();
-
-        if (this.properties.strokeDash) {
-            const gl = this.gl;
-            const textureData = createDashTextureArray(
-                this.properties.strokeDash
-            );
-            this.dashTexture = createTexture(gl, {
-                mag: gl.NEAREST,
-                min: gl.NEAREST,
-                internalFormat: gl.R8,
-                format: gl.RED,
-                src: textureData,
-                height: 1,
-            });
-            this.dashTextureSize = textureData.length; // Not needed with WebGL2
-        }
-
-        this.createAndLinkShaders(VERTEX_SHADER, FRAGMENT_SHADER);
-    }
-
-    finalizeGraphicsInitialization() {
-        super.finalizeGraphicsInitialization();
-
-        this.gl.useProgram(this.programInfo.program);
-
-        const props = this.properties;
-
-        setUniforms(this.programInfo, {
-            uMinLength: props.minLength,
-            uDashTextureSize: this.dashTextureSize,
-            uStrokeCap: ["butt", "square", "round"].indexOf(props.strokeCap),
-        });
-    }
-
-    updateGraphicsData() {
-        const collector = this.unitView.getCollector();
-        const itemCount = collector.getItemCount();
-
-        const builder = new RuleVertexBuilder({
-            encoders: this.encoders,
-            attributes: this.getAttributes(),
-            numItems: Math.max(itemCount, this.properties.minBufferSize || 0),
-        });
-
-        builder.addBatches(collector.facetBatches);
-
-        const vertexData = builder.toArrays();
-        this.rangeMap.migrateEntries(vertexData.rangeMap);
-
-        this.updateBufferInfo(vertexData);
-    }
-
-    /**
-     * @param {import("../view/rendering").GlobalRenderingOptions} options
-     */
-    prepareRender(options) {
-        const ops = super.prepareRender(options);
-
-        if (this.dashTexture) {
-            ops.push(() =>
-                setUniforms(this.programInfo, {
-                    uDashTexture: this.dashTexture,
-                    uStrokeDashOffset: this.properties.strokeDashOffset,
-                })
-            );
-        }
-
-        ops.push(() =>
-            setBuffersAndAttributes(
-                this.gl,
-                this.programInfo,
-                this.vertexArrayInfo
-            )
-        );
-
-        return ops;
-    }
-
-    /**
-     * @param {import("./Mark").MarkRenderingOptions} options
-     */
-    render(options) {
-        const gl = this.gl;
-
-        return this.createRenderCallback(
-            (offset, count) =>
-                drawBufferInfo(
-                    gl,
-                    this.vertexArrayInfo,
-                    gl.TRIANGLE_STRIP,
-                    count,
-                    offset
-                ),
-            options
-        );
-    }
-}
-
-/**
- *
- * @param {number[]} pattern
- */
-function createDashTextureArray(pattern) {
-    if (
-        pattern.length == 0 ||
-        pattern.length % 2 ||
-        pattern.findIndex((s) => Math.round(s) != s || s < 1 || s > 1000) >= 0
-    ) {
-        throw new Error(
-            "Invalid stroke dash pattern: " + JSON.stringify(pattern)
-        );
-    }
-
-    const len = pattern.reduce((a, b) => a + b);
-
-    const texture = new Uint8Array(len);
-
-    let state = true;
-    let i = 0;
-    for (let segment of pattern) {
-        while (segment) {
-            texture[i++] = (state && 255) || 0;
-            segment--;
-        }
-        state = !state;
-    }
-
-    return texture;
-}

package/src/marks/text.js

@@ -1,278 +0,0 @@
-import { isString } from "vega-util";
-import { format } from "d3-format";
-import { drawBufferInfo, setBuffersAndAttributes, setUniforms } from "twgl.js";
-import VERTEX_SHADER from "../gl/text.vertex.glsl";
-import FRAGMENT_SHADER from "../gl/text.fragment.glsl";
-import { TextVertexBuilder } from "../gl/dataToVertices";
-
-import Mark from "./mark";
-import { fixPositional } from "./markUtils";
-import { primaryPositionalChannels } from "../encoder/encoder";
-
-/** For GLSL uniforms */
-const alignments = {
-    left: -1,
-    center: 0,
-    right: 1,
-};
-
-/** For GLSL uniforms */
-const baselines = {
-    top: -1,
-    middle: 0,
-    bottom: 1,
-    alphabetic: 1,
-};
-
-/**
- * Renders text using SDF fonts
- *
- * Some resources:
- * - Valve's SDF paper: https://doi.org/10.1145/1281500.1281665
- * - Multi-channel SDF fonts: https://github.com/Chlumsky/msdfgen
- * - Google's web fonts as SDFs: https://github.com/etiennepinchon/aframe-fonts
- */
-export default class TextMark extends Mark {
-    /**
-     * @param {import("../view/unitView").default} unitView
-     */
-    constructor(unitView) {
-        super(unitView);
-
-        Object.defineProperties(
-            this.defaultProperties,
-            Object.getOwnPropertyDescriptors({
-                x: 0.5,
-                y: 0.5,
-                x2: undefined,
-                y2: undefined,
-                text: "",
-                size: 11.0,
-                color: "black",
-                opacity: 1.0,
-
-                // Use the built-in default
-                font: undefined,
-                fontStyle: undefined,
-                fontWeight: undefined,
-
-                align: "center",
-                baseline: "middle",
-                dx: 0,
-                dy: 0,
-                angle: 0,
-
-                /** When only primary channel is defined with band/locus scale */
-                fitToBand: false,
-
-                squeeze: true,
-                paddingX: 0,
-                paddingY: 0,
-                flushX: true,
-                flushY: true,
-
-                /** Stretch letters so that they can be used with sequence logos etc... */
-                logoLetters: false,
-
-                viewportEdgeFadeWidthTop: 0,
-                viewportEdgeFadeWidthRight: 0,
-                viewportEdgeFadeWidthBottom: 0,
-                viewportEdgeFadeWidthLeft: 0,
-
-                viewportEdgeFadeDistanceTop: -Infinity,
-                viewportEdgeFadeDistanceRight: -Infinity,
-                viewportEdgeFadeDistanceBottom: -Infinity,
-                viewportEdgeFadeDistanceLeft: -Infinity,
-            })
-        );
-
-        this.font = this.properties.font
-            ? unitView.context.fontManager.getFont(
-                  this.properties.font,
-                  this.properties.fontStyle,
-                  this.properties.fontWeight
-              )
-            : unitView.context.fontManager.getDefaultFont();
-    }
-
-    getAttributes() {
-        return [
-            "uniqueId",
-            "facetIndex",
-            "x",
-            "x2",
-            "y",
-            "y2",
-            "color",
-            "size",
-            "opacity",
-            "angle",
-        ];
-    }
-
-    /**
-     * @returns {import("../spec/channel").Channel[]}
-     */
-    getSupportedChannels() {
-        return [
-            ...super.getSupportedChannels(),
-            "x2",
-            "y2",
-            "size",
-            "text",
-            "angle",
-        ];
-    }
-
-    /**
-     * @param {import("../spec/channel").Encoding} encoding
-     * @returns {import("../spec/channel").Encoding}
-     */
-    fixEncoding(encoding) {
-        // TODO: Ensure that both the primary and secondary channel are either variables or constants (values)
-
-        for (const channel of primaryPositionalChannels) {
-            if (this.properties.fitToBand) {
-                fixPositional(encoding, channel);
-            }
-        }
-
-        return encoding;
-    }
-
-    async initializeGraphics() {
-        await super.initializeGraphics();
-        this.createAndLinkShaders(VERTEX_SHADER, FRAGMENT_SHADER);
-    }
-
-    finalizeGraphicsInitialization() {
-        super.finalizeGraphicsInitialization();
-
-        this.gl.useProgram(this.programInfo.program);
-
-        const props = this.properties;
-
-        // TODO: Use uniform block.
-        setUniforms(this.programInfo, {
-            uPaddingX: props.paddingX,
-            uPaddingY: props.paddingY,
-            uFlushX: !!props.flushX,
-            uFlushY: !!props.flushY,
-
-            uAlign: [alignments[props.align], baselines[props.baseline]],
-
-            uD: [props.dx, -props.dy],
-
-            uLogoLetter: !!props.logoLetters,
-            uSqueeze: !!props.squeeze,
-
-            uViewportEdgeFadeWidth: [
-                props.viewportEdgeFadeWidthTop,
-                props.viewportEdgeFadeWidthRight,
-                props.viewportEdgeFadeWidthBottom,
-                props.viewportEdgeFadeWidthLeft,
-            ],
-
-            uViewportEdgeFadeDistance: [
-                props.viewportEdgeFadeDistanceTop,
-                props.viewportEdgeFadeDistanceRight,
-                props.viewportEdgeFadeDistanceBottom,
-                props.viewportEdgeFadeDistanceLeft,
-            ],
-        });
-    }
-
-    updateGraphicsData() {
-        const collector = this.unitView.getCollector();
-        const data = collector.getData();
-        const encoding = this.encoding;
-
-        // Count the total number of characters to that we can pre-allocate a typed array
-        const accessor = this.encoders.text.accessor || this.encoders.text; // accessor or constant value
-        let charCount = 0;
-        /** @type {function(any):any} */
-        const numberFormat = encoding.text.format
-            ? format(encoding.text.format)
-            : (d) => d;
-        for (const d of data) {
-            // TODO: Optimization: don't format twice (calculation and actual encoding)
-            const value = numberFormat(accessor(d));
-            const str = isString(value)
-                ? value
-                : value === null
-                ? ""
-                : "" + value;
-            charCount += (str && str.length) || 0;
-        }
-
-        const builder = new TextVertexBuilder({
-            encoders: this.encoders,
-            attributes: this.getAttributes(),
-            properties: this.properties,
-            fontMetrics: this.font.metrics,
-            numCharacters: Math.max(
-                charCount,
-                this.properties.minBufferSize || 0
-            ),
-        });
-
-        builder.addBatches(collector.facetBatches);
-
-        const vertexData = builder.toArrays();
-        this.rangeMap.migrateEntries(vertexData.rangeMap);
-
-        this.updateBufferInfo(vertexData);
-    }
-
-    /**
-     * @param {import("../view/rendering").GlobalRenderingOptions} options
-     */
-    prepareRender(options) {
-        const ops = super.prepareRender(options);
-
-        let q = 0.35; // TODO: Ensure that this makes sense. Now chosen by trial & error
-        if (this.properties.logoLetters) {
-            // Adjust to make stretched letters a bit less blurry
-            // A proper solution would probably be to compute gradients in the fragment shader
-            // to find a suitable divisor.
-            q /= 2;
-        }
-
-        ops.push(() =>
-            setUniforms(this.programInfo, {
-                uTexture: this.font.texture,
-                uSdfNumerator:
-                    this.font.metrics.common.base / (this.glHelper.dpr / q),
-            })
-        );
-
-        ops.push(() =>
-            setBuffersAndAttributes(
-                this.gl,
-                this.programInfo,
-                this.vertexArrayInfo
-            )
-        );
-
-        return ops;
-    }
-
-    /**
-     * @param {import("./Mark").MarkRenderingOptions} options
-     */
-    render(options) {
-        const gl = this.gl;
-
-        return this.createRenderCallback(
-            (offset, count) =>
-                drawBufferInfo(
-                    gl,
-                    this.vertexArrayInfo,
-                    gl.TRIANGLES,
-                    count,
-                    offset
-                ),
-            options
-        );
-    }
-}

package/src/node_modules/.vitest/results.json

@@ -1 +0,0 @@
-{"version":"0.23.1","results":[["/genome/genome.test.js",{"duration":5,"failed":false}],["/scale/scale.test.js",{"duration":12,"failed":false}],["/utils/layout/flexLayout.test.js",{"duration":7,"failed":false}],["/data/flowOptimizer.test.js",{"duration":3,"failed":false}],["/utils/layout/rectangle.test.js",{"duration":5,"failed":false}],["/utils/domainArray.test.js",{"duration":5,"failed":false}],["/data/transforms/regexFold.test.js",{"duration":5,"failed":false}],["/view/scaleResolution.test.js",{"duration":20,"failed":false}],["/view/view.test.js",{"duration":13,"failed":false}],["/view/axisResolution.test.js",{"duration":11,"failed":false}],["/view/flowBuilder.test.js",{"duration":5,"failed":false}],["/encoder/encoder.test.js",{"duration":6,"failed":false}],["/data/transforms/stack.test.js",{"duration":5,"failed":false}],["/data/transforms/identifier.test.js",{"duration":29,"failed":false}],["/data/transforms/coverage.test.js",{"duration":4,"failed":false}],["/data/transforms/flattenDelimited.test.js",{"duration":3,"failed":false}],["/genome/scaleIndex.test.js",{"duration":4,"failed":false}],["/utils/layout/grid.test.js",{"duration":4,"failed":false}],["/utils/topK.test.js",{"duration":50,"failed":false}],["/utils/binnedIndex.test.js",{"duration":4,"failed":false}],["/data/collector.test.js",{"duration":4,"failed":false}],["/data/flow.test.js",{"duration":5,"failed":false}],["/utils/propertyCacher.test.js",{"duration":3,"failed":false}],["/data/transforms/regexExtract.test.js",{"duration":5,"failed":false}],["/data/transforms/pileup.test.js",{"duration":4,"failed":false}],["/utils/indexer.test.js",{"duration":4,"failed":false}],["/encoder/accessor.test.js",{"duration":4,"failed":false}],["/data/sources/sequenceSource.test.js",{"duration":3,"failed":false}],["/data/sources/inlineSource.test.js",{"duration":8,"failed":false}],["/utils/mergeObjects.test.js",{"duration":5,"failed":false}],["/data/flowNode.test.js",{"duration":995,"failed":false}],["/scale/ticks.test.js",{"duration":5,"failed":false}],["/data/formats/fasta.test.js",{"duration":3,"failed":false}],["/data/transforms/flattenSequence.test.js",{"duration":3,"failed":false}],["/utils/addBaseUrl.test.js",{"duration":3,"failed":false}],["/data/transforms/project.test.js",{"duration":4,"failed":false}],["/utils/iterateNestedMaps.test.js",{"duration":7,"failed":false}],["/utils/reservationMap.test.js",{"duration":3,"failed":false}],["/utils/kWayMerge.test.js",{"duration":4,"failed":false}],["/data/transforms/sample.test.js",{"duration":33,"failed":false}],["/utils/propertyCoalescer.test.js",{"duration":3,"failed":false}],["/utils/coalesce.test.js",{"duration":5,"failed":false}],["/data/transforms/filter.test.js",{"duration":4,"failed":false}],["/utils/cloner.test.js",{"duration":2,"failed":false}],["/utils/variableTools.test.js",{"duration":3,"failed":false}],["/view/viewFactory.test.js",{"duration":3,"failed":false}],["/data/transforms/formula.test.js",{"duration":2,"failed":false}],["/utils/concatIterables.test.js",{"duration":5,"failed":false}],["/utils/numberExtractor.test.js",{"duration":2,"failed":false}],["/data/transforms/clone.test.js",{"duration":2,"failed":false}],["/genome/scaleLocus.test.js",{"duration":0,"failed":false}],["/data/dataFlow.test.js",{"duration":0,"failed":false}]]}