@genome-spy/core 0.29.0 → 0.30.2

package/src/encoder/encoder.js

@@ -1,394 +0,0 @@
-import { isDiscrete } from "vega-scale";
-import createIndexer from "../utils/indexer";
-
-/**
- * @typedef {Object} EncoderMetadata
- * @prop {boolean} constant True if the accessor returns the same value for all objects
- * @prop {boolean} constantValue True the encoder returns a "value" without a scale
- * @prop {(value: import("../spec/channel").Scalar) => import("../spec/channel").Scalar} invert
- * @prop {VegaScale} [scale]
- * @prop {import("./accessor").Accessor} accessor 
- * @prop {function(any):number} [indexer] Converts ordinal values to index numbers
- * @prop {import("../view/viewUtils").ChannelDef} channelDef
- * @prop {function(function):void} applyMetadata Copies metadata to the target function
- *
- * @typedef {(function(object):(string|number)) & EncoderMetadata} Encoder
- * @typedef {(function(object):number) & EncoderMetadata} NumberEncoder
- *
- * @typedef {object} ScaleMetadata
- * @prop {string} type Scale type
- * @prop {boolean} [fp64] Whether to use emulated 64 bit floating point in WebGL
- * 
- * @typedef {(
-    import("d3-scale").ScaleContinuousNumeric<any, any> |
-    import("d3-scale").ScaleLinear<any, any> |
-    import("d3-scale").ScalePower<any, any> |
-    import("d3-scale").ScaleLogarithmic<any, any> |
-    import("d3-scale").ScaleSymLog<any, any> |
-    import("d3-scale").ScaleIdentity |
-    import("d3-scale").ScaleTime<any, any> |
-    import("d3-scale").ScaleSequential<any> |
-    import("d3-scale").ScaleDiverging<any> | 
-    import("d3-scale").ScaleQuantize<any> |
-    import("d3-scale").ScaleQuantile<any> |
-    import("d3-scale").ScaleThreshold<any, any> |
-    import("d3-scale").ScaleOrdinal<any, any> |
-    import("d3-scale").ScaleBand<any> |
-    import("d3-scale").ScalePoint<any>
-    )} D3Scale
- * 
- * @typedef {(D3Scale | import("../genome/scaleIndex").ScaleIndex | import("../genome/scaleLocus").ScaleLocus) & ScaleMetadata} VegaScale
- * 
- * @typedef {import("../spec/channel").Channel} Channel
- */
-
-/**
- * Creates an object that contains encoders for every channel of a mark
- *
- * TODO: This should actually receive the mark as parameter
- *
- * TODO: This method should have a test. But how to mock Mark...
- *
- * @param {import("../marks/mark").default} mark
- * @param {import("../spec/channel").Encoding} [encoding] Taken from the mark if not provided
- * @returns {Partial<Record<Channel, Encoder>>}
- */
-export default function createEncoders(mark, encoding) {
-    /** @type {Partial<Record<Channel, Encoder>>} */
-    const encoders = {};
-
-    if (!encoding) {
-        encoding = mark.encoding;
-    }
-
-    for (const [channel, channelDef] of Object.entries(encoding)) {
-        if (!channelDef) {
-            continue;
-        }
-
-        const resolution = mark.unitView.getScaleResolution(
-            (isChannelDefWithScale(channelDef) &&
-                channelDef.resolutionChannel) ||
-                channel
-        );
-
-        encoders[channel] = createEncoder(
-            encoding[channel],
-            resolution?.getScale(),
-            mark.unitView.getAccessor(channel),
-            channel
-        );
-    }
-
-    return encoders;
-}
-
-/**
- *
- * @param {import("../spec/channel").ChannelDef} channelDef
- * @param {any} scale
- * @param {import("./accessor").Accessor} accessor
- * @param {Channel} channel
- * @returns {Encoder}
- */
-export function createEncoder(channelDef, scale, accessor, channel) {
-    /** @type {Encoder} */
-    let encoder;
-
-    if (isValueDef(channelDef)) {
-        const value = channelDef.value;
-        encoder = /** @type {Encoder} */ ((datum) => value);
-        encoder.constant = true;
-        encoder.constantValue = true;
-        encoder.accessor = undefined;
-    } else if (accessor) {
-        if (channel == "text") {
-            // TODO: Define somewhere channels that don't use a scale
-            encoder = /** @type {Encoder} */ ((datum) => undefined);
-            encoder.accessor = accessor;
-            encoder.constant = accessor.constant;
-        } else {
-            if (!scale) {
-                throw new Error(
-                    `Missing scale! "${channel}": ${JSON.stringify(channelDef)}`
-                );
-            }
-
-            encoder = /** @type {Encoder} */ (
-                (datum) => scale(accessor(datum))
-            );
-
-            if (isDiscrete(scale.type)) {
-                // TODO: pass the found values back to the scale/resolution
-                const indexer = createIndexer();
-                indexer.addAll(scale.domain());
-                encoder.indexer = indexer;
-            }
-
-            encoder.constant = accessor.constant;
-            encoder.accessor = accessor;
-            encoder.scale = scale;
-        }
-    } else {
-        throw new Error(
-            `Missing value or accessor (field, expr, datum) on channel "${channel}": ${JSON.stringify(
-                channelDef
-            )}`
-        );
-    }
-
-    // TODO: Modifier should be inverted too
-    encoder.invert = scale
-        ? (value) => scale.invert(value)
-        : (value) => {
-              throw new Error(
-                  "No scale available, cannot invert: " +
-                      JSON.stringify(channelDef)
-              );
-          };
-
-    // Just to provide a convenient access to the config
-    encoder.channelDef = channelDef;
-
-    /** @param {Encoder} target */
-    encoder.applyMetadata = (target) => {
-        for (const prop in encoder) {
-            if (prop in encoder) {
-                // @ts-ignore
-                target[prop] = encoder[prop];
-            }
-        }
-        return target;
-    };
-
-    return encoder;
-}
-
-/**
- * TODO: Move to a more generic place
- *
- * @param {import("../spec/channel").ChannelDef} channelDef
- * @returns {channelDef is import("../spec/channel").ValueDef}
- */
-export function isValueDef(channelDef) {
-    return channelDef && "value" in channelDef;
-}
-
-/**
- * @param {import("../spec/channel").ChannelDef} channelDef
- * @returns {channelDef is import("../spec/channel").FieldDefBase<string>}
- */
-export function isFieldDef(channelDef) {
-    return channelDef && "field" in channelDef;
-}
-
-/**
- * @param {import("../spec/channel").ChannelDef} channelDef
- * @returns {channelDef is import("../spec/channel").DatumDef}
- */
-export function isDatumDef(channelDef) {
-    return channelDef && "datum" in channelDef;
-}
-
-/**
- * @param {import("../spec/channel").ChannelDef} channelDef
- * @returns {channelDef is import("../spec/channel").ChannelDefWithScale}
- */
-export function isChannelDefWithScale(channelDef) {
-    // TODO: Not accurate, fix
-    return (
-        isFieldDef(channelDef) ||
-        isDatumDef(channelDef) ||
-        isExprDef(channelDef) ||
-        isChromPosDef(channelDef)
-    );
-}
-
-/**
- * @param {import("../view/unitView").default} view
- * @param {Channel} channel
- */
-export function getChannelDefWithScale(view, channel) {
-    const channelDef = view.mark.encoding[channel];
-    if (isChannelDefWithScale(channelDef)) {
-        return channelDef;
-    } else {
-        throw new Error("Not a channel def with scale!");
-    }
-}
-
-/**
- * @param {import("../spec/channel").ChannelDef} channelDef
- * @returns {channelDef is import("../spec/channel").ChromPosDef}
- */
-export function isChromPosDef(channelDef) {
-    return channelDef && "chrom" in channelDef;
-}
-
-/**
- * @param {import("../spec/channel").ChannelDef} channelDef
- * @returns {channelDef is import("../spec/channel").ExprDef}
- */
-export function isExprDef(channelDef) {
-    return channelDef && "expr" in channelDef;
-}
-
-/**
- * @type {import("../spec/channel").PrimaryPositionalChannel[]}
- */
-export const primaryPositionalChannels = ["x", "y"];
-
-/**
- * @type {import("../spec/channel").SecondaryPositionalChannel[]}
- */
-export const secondaryPositionalChannels = ["x2", "y2"];
-
-/**
- * @type {import("../spec/channel").PositionalChannel[]}
- */
-export const positionalChannels = [
-    ...primaryPositionalChannels,
-    ...secondaryPositionalChannels,
-];
-
-/**
- * @param {Channel} channel
- * @returns {channel is import("../spec/channel").PrimaryPositionalChannel}
- */
-export function isPrimaryPositionalChannel(channel) {
-    // @ts-expect-error
-    return primaryPositionalChannels.includes(channel);
-}
-
-/**
- * @param {Channel} channel
- * @returns {channel is import("../spec/channel").PositionalChannel}
- */
-export function isPositionalChannel(channel) {
-    // @ts-expect-error
-    return positionalChannels.includes(channel);
-}
-
-/**
- * Map primary channels to secondarys
- *
- * @type {Partial<Record<Channel, import("../spec/channel").SecondaryPositionalChannel>>}
- */
-export const secondaryChannels = {
-    x: "x2",
-    y: "y2",
-};
-
-/**
- * Map secondary channels to primaries
- *
- * @type {Partial<Record<Channel, Channel>>}
- */
-export const primaryChannels = Object.fromEntries(
-    Object.entries(secondaryChannels).map((entry) => [entry[1], entry[0]])
-);
-
-/**
- *
- * @param {string} channel
- */
-export function isSecondaryChannel(channel) {
-    return channel in primaryChannels;
-}
-
-/**
- * Return the matching secondary channel or throws if one does not exist.
- *
- * @param {Channel} primaryChannel
- */
-export function getSecondaryChannel(primaryChannel) {
-    const secondary = secondaryChannels[primaryChannel];
-    if (secondary) {
-        return secondary;
-    } else {
-        throw new Error(`${primaryChannel} has no secondary channel!`);
-    }
-}
-
-/**
- * Finds the primary channel for the provided channel, which may be
- * the primary or secondary.
- *
- * @param {Channel} channel
- */
-export function getPrimaryChannel(channel) {
-    return primaryChannels[channel] ?? channel;
-}
-
-/**
- * Returns an array that contains the given channel and its secondary channel if one exists.
- *
- * @param {Channel} channel
- */
-export function getChannelWithSecondarys(channel) {
-    return secondaryChannels[channel]
-        ? [channel, secondaryChannels[channel]]
-        : [channel];
-}
-
-/**
- * @param {Channel} channel
- */
-export function isColorChannel(channel) {
-    return ["color", "fill", "stroke"].includes(getPrimaryChannel(channel));
-}
-
-/**
- * Returns true if the channel has a discrete range.
- *
- * @param {Channel} channel
- */
-export function isDiscreteChannel(channel) {
-    return ["shape", "squeeze"].includes(channel);
-}
-
-/**
- * Returns valid discrete values for a discrete channel.
- *
- * @param {Channel} channel
- * @returns {any[]}
- */
-export function getDiscreteRange(channel) {
-    // TODO: This is not easily extendable. Figure out a more dynamic approach.
-    switch (channel) {
-        case "shape":
-            return [
-                "circle",
-                "square",
-                "triangle-up",
-                "cross",
-                "diamond",
-                "triangle-down",
-                "triangle-right",
-                "triangle-left",
-            ];
-        default:
-    }
-}
-
-/**
- * @param {Channel} channel
- * @returns {function(any):number}
- */
-export function getDiscreteRangeMapper(channel) {
-    if (!isDiscreteChannel(channel)) {
-        throw new Error("Not a discrete channel: " + channel);
-    }
-
-    const valueMap = new Map(
-        getDiscreteRange(channel).map((value, i) => [value, i])
-    );
-
-    return (value) => {
-        const mapped = valueMap.get(value);
-        if (mapped !== undefined) {
-            return mapped;
-        }
-        throw new Error(`Invalid value for "${channel}" channel: ${value}`);
-    };
-}

package/src/encoder/encoder.test.js

@@ -1,98 +0,0 @@
-import { describe, expect, test } from "vitest";
-import AccessorFactory from "./accessor";
-import { scale as vegaScale } from "vega-scale";
-
-import { createEncoder } from "./encoder";
-
-describe("Encoder", () => {
-    /** @type {Record<string, import("../view/viewUtils").ChannelDef>} */
-    const encodingSpecs = {
-        x: { value: 0 },
-        y: { field: "a" },
-        z: { datum: 2 },
-        size: { value: 5 },
-    };
-
-    const scaleLinear = vegaScale("linear");
-
-    /** @type {Record<string, import("./encoder").VegaScale>} */
-    const scales = {
-        y: scaleLinear().domain([0, 10]),
-        z: scaleLinear().domain([0, 20]),
-    };
-
-    const accessorFactory = new AccessorFactory();
-
-    /** @param {Record<string, import("../view/viewUtils").ChannelDef>} encoding */
-    function createEncoders(encoding) {
-        /** @type {Record<string, import("./encoder").Encoder>} */
-        const encoders = {};
-        for (const [channel, channelDef] of Object.entries(encoding)) {
-            encoders[channel] = createEncoder(
-                channelDef,
-                scales[channel],
-                accessorFactory.createAccessor(encodingSpecs[channel]),
-                channel
-            );
-        }
-        return encoders;
-    }
-
-    const datum = {
-        a: 5,
-        b: 6,
-        c: "Pink Floyd",
-    };
-
-    test("Throws on a broken spec", () =>
-        expect(() => createEncoders({ x: {} })).toThrow());
-
-    const encoders = createEncoders(encodingSpecs);
-
-    test("The encoder object contains all channels", () =>
-        expect(
-            ["x", "y", "z", "size"].every(
-                (channel) => typeof encoders[channel] === "function"
-            )
-        ).toBeTruthy());
-
-    test("Returns a value", () => expect(encoders.x(datum)).toEqual(0));
-
-    test("Encodes and returns a constant using a scale", () =>
-        expect(encoders.z(datum)).toBeCloseTo(0.1));
-
-    test("Accesses a field and uses a scale", () =>
-        expect(encoders.y(datum)).toBeCloseTo(0.5));
-
-    /*
-    test("Accesses a field on a secondary channel and uses the scale from the primary", () =>
-        expect(encoders.y2(datum)).toBeCloseTo(0.6));
-        */
-
-    test("Constant encoder is annotated", () => {
-        expect(encoders.y.constant).toBeFalsy();
-        expect(encoders.z.constant).toBeTruthy();
-        expect(encoders.size.constant).toBeTruthy();
-    });
-
-    test("Constant value encoder is annotated", () => {
-        expect(encoders.y.constantValue).toBeFalsy();
-        expect(encoders.z.constantValue).toBeFalsy();
-        expect(encoders.size.constantValue).toBeTruthy();
-    });
-
-    test("Inverts a value", () => {
-        expect(encoders.y.invert(0.5)).toBeCloseTo(5);
-        expect(encoders.z.invert(0.5)).toBeCloseTo(10);
-        // A value, no scale, can't invert
-        expect(() => encoders.size.invert(123)).toThrow();
-    });
-
-    test("Accessors are provided", () => {
-        expect(encoders.y.accessor).toBeDefined();
-        expect(encoders.z.accessor).toBeDefined();
-        expect(encoders.x.accessor).toBeUndefined();
-    });
-
-    // TODO: Test indexer
-});