@genome-spy/core 0.64.0 → 0.66.1

package/dist/src/scales/scaleResolution.js

@@ -0,0 +1,658 @@
+import scaleLocus, {
+    fromComplexInterval as locusFromComplexInterval,
+    fromComplexValue,
+    getGenomeExtent,
+    toComplexInterval,
+    toComplexValue,
+} from "../genome/scaleLocus.js";
+import scaleIndex from "../genome/scaleIndex.js";
+import scaleNull from "../utils/scaleNull.js";
+
+import { scale as vegaScale, isDiscrete, isContinuous } from "vega-scale";
+import { configureDomain } from "../scale/scale.js";
+
+import ScaleInstanceManager from "./scaleInstanceManager.js";
+import { resolveScalePropsBase } from "./scalePropsResolver.js";
+import ScaleDomainAggregator from "./scaleDomainAggregator.js";
+import ScaleInteractionController from "./scaleInteractionController.js";
+import {
+    INDEX,
+    LOCUS,
+    NOMINAL,
+    ORDINAL,
+    QUANTITATIVE,
+} from "./scaleResolutionConstants.js";
+
+import { isSecondaryChannel } from "../encoder/encoder.js";
+import { NominalDomain } from "../utils/domainArray.js";
+import { asArray, shallowArrayEquals } from "../utils/arrayUtils.js";
+
+// Register scaleLocus to Vega-Scale.
+// Loci are discrete but the scale's domain can be adjusted in a continuous manner.
+vegaScale("index", scaleIndex, ["continuous"]);
+vegaScale("locus", scaleLocus, ["continuous"]);
+vegaScale("null", scaleNull, []);
+
+export { INDEX, LOCUS, NOMINAL, ORDINAL, QUANTITATIVE };
+
+/**
+ * @template {ChannelWithScale}[T=ChannelWithScale]
+ *
+ * @typedef {object} ScaleResolutionMember
+ * @prop {import("../view/unitView.js").default} view TODO: Get rid of the view reference
+ * @prop {T} channel
+ * @prop {import("../spec/channel.js").ChannelDefWithScale} channelDef
+ * @prop {(channel: ChannelWithScale, type: import("../spec/channel.js").Type) => DomainArray} dataDomainSource
+ */
+/**
+ * Resolves a shared scale for a channel by merging scale properties and domains
+ * across participating views, then coordinating range updates and zoom/pan
+ * interactions. It is the central wiring point for scale-related state and
+ * notifications, while delegating domain aggregation, scale instance setup, and
+ * interaction logic to focused helpers.
+ *
+ * @implements {ScaleResolutionApi}
+ */
+export default class ScaleResolution {
+    /**
+     * @typedef {import("../types/scaleResolutionApi.js").ScaleResolutionApi} ScaleResolutionApi
+     * @typedef {import("../types/scaleResolutionApi.js").ScaleResolutionEventType} ScaleResolutionEventType
+     * @typedef {import("../spec/channel.js").Channel} Channel
+     * @typedef {import("../spec/channel.js").ChannelWithScale} ChannelWithScale
+     * @typedef {import("../spec/scale.js").NumericDomain} NumericDomain
+     * @typedef {import("../spec/scale.js").ScalarDomain} ScalarDomain
+     * @typedef {import("../spec/scale.js").ComplexDomain} ComplexDomain
+     * @typedef {import("../view/unitView.js").default} UnitView
+     * @typedef {import("../types/encoder.js").VegaScale} VegaScale
+     * @typedef {import("../utils/domainArray.js").DomainArray} DomainArray
+     * @typedef {import("../genome/genome.js").ChromosomalLocus} ChromosomalLocus
+     * @typedef {import("../types/scaleResolutionApi.js").ScaleResolutionListener} ScaleResolutionListener
+     *
+     * @typedef {VegaScale & { props: import("../spec/scale.js").Scale }} ScaleWithProps
+     */
+
+    /** @type {Set<ScaleResolutionMember>} The involved views */
+    #members = new Set();
+
+    /**
+     * @type {Record<ScaleResolutionEventType, Set<ScaleResolutionListener>>}
+     */
+    #listeners = {
+        domain: new Set(),
+        range: new Set(),
+    };
+
+    /** @type {ScaleInstanceManager} */
+    #scaleManager;
+
+    /** @type {ScaleDomainAggregator} */
+    #domainAggregator;
+
+    /** @type {ScaleInteractionController} */
+    #interactionController;
+
+    /**
+     * @param {Channel} channel
+     */
+    constructor(channel) {
+        this.channel = channel;
+        /** @type {import("../spec/channel.js").Type} Data type (quantitative, nominal, etc...) */
+        this.type = null;
+
+        /** @type {string} An optional unique identifier for the scale */
+        this.name = undefined;
+
+        this.#domainAggregator = new ScaleDomainAggregator({
+            getMembers: () => this.#members,
+            getType: () => this.type,
+            getLocusExtent: () => this.#getLocusExtent(),
+            fromComplexInterval: this.fromComplexInterval.bind(this),
+        });
+
+        this.#scaleManager = new ScaleInstanceManager({
+            getParamMediator: () => this.#firstMemberView.paramMediator,
+            onRangeChange: () => this.#notifyListeners("range"),
+            onDomainChange: () => this.#notifyListeners("domain"),
+            getGenomeStore: () => this.#viewContext.genomeStore,
+        });
+
+        this.#interactionController = new ScaleInteractionController({
+            getScale: () => this.getScale(),
+            getAnimator: () => this.#viewContext.animator,
+            getInitialDomainSnapshot: () =>
+                this.#domainAggregator.initialDomainSnapshot,
+            getResetDomain: () =>
+                this.#domainAggregator.getConfiguredOrDefaultDomain(),
+            fromComplexInterval: this.fromComplexInterval.bind(this),
+            getGenomeExtent: () => this.#getLocusExtent(),
+        });
+    }
+
+    /**
+     * @returns {import("../view/view.js").default}
+     */
+    get #firstMemberView() {
+        const first = this.#members.values().next().value;
+        if (!first) {
+            throw new Error("ScaleResolution has no members!");
+        }
+        return first.view;
+    }
+
+    get #viewContext() {
+        return this.#firstMemberView.context;
+    }
+
+    get zoomExtent() {
+        return (
+            (this.#scaleManager.scale &&
+                isContinuous(this.#scaleManager.scale.type) &&
+                this.#interactionController.getZoomExtent()) ?? [
+                -Infinity,
+                Infinity,
+            ]
+        );
+    }
+
+    /**
+     * @returns {number[]}
+     */
+    #getLocusExtent() {
+        return getGenomeExtent(this.#getGenomeSource());
+    }
+
+    /**
+     * @returns {import("../genome/scaleLocus.js").GenomeSource}
+     */
+    #getGenomeSource() {
+        if (this.type !== LOCUS) {
+            return undefined;
+        }
+        return /** @type {import("../genome/scaleLocus.js").GenomeSource} */ (
+            this.#scaleManager.scale ?? this.#scaleManager.getLocusGenome()
+        );
+    }
+
+    /**
+     * Adds a listener that is called when the scale domain is changed,
+     * e.g., zoomed. The call is synchronous and happens before the views
+     * are rendered.
+     *
+     * @param {ScaleResolutionEventType} type
+     * @param {ScaleResolutionListener} listener function
+     */
+    addEventListener(type, listener) {
+        this.#listeners[type].add(listener);
+    }
+
+    /**
+     * @param {ScaleResolutionEventType} type
+     * @param {ScaleResolutionListener} listener function
+     */
+    removeEventListener(type, listener) {
+        this.#listeners[type].delete(listener);
+    }
+
+    /**
+     * @param {ScaleResolutionEventType} type
+     */
+    #notifyListeners(type) {
+        for (const listener of this.#listeners[type].values()) {
+            listener({
+                type,
+                scaleResolution: this,
+            });
+        }
+    }
+
+    /**
+     * Add a view to this resolution.
+     * N.B. This is expected to be called in depth-first order
+     *
+     * @param {ScaleResolutionMember} newMember
+     */
+    #addMember(newMember) {
+        const { channel, channelDef } = newMember;
+
+        // A convenience hack for cases where the new member should adapt
+        // the scale type to the existing one. For example: SelectionRect
+        // TODO: Add test
+        const adapt = channelDef.type == null && this.type;
+
+        if (
+            // @ts-expect-error "sample" is not really a channel with scale
+            channel != "sample" &&
+            !channelDef.type &&
+            !isSecondaryChannel(channel) &&
+            !adapt
+        ) {
+            throw new Error(
+                `The "type" property must be defined in channel definition: "${channel}": ${JSON.stringify(
+                    channelDef
+                )}. Must be one of: "quantitative", "ordinal", "nominal", "locus", "index"`
+            );
+        }
+
+        // A hack for sample channel, which really doesn't have a scale but the
+        // domain is needed when samples are not specified explicitly.
+        // @ts-expect-error "sample" is not really a channel with scale
+        const type = channel == "sample" ? "nominal" : channelDef.type;
+        const name = channelDef?.scale?.name;
+
+        if (name) {
+            if (this.name !== undefined && name != this.name) {
+                throw new Error(
+                    `Shared scales have conflicting names: "${name}" vs. "${this.name}"!`
+                );
+            }
+            this.name = name;
+        }
+
+        if (!adapt) {
+            if (!this.type) {
+                this.type = type;
+            } else if (type !== this.type && !isSecondaryChannel(channel)) {
+                // TODO: Include a reference to the layer
+                throw new Error(
+                    `Can not use shared scale for different data types: ${this.type} vs. ${type}. Use "resolve: independent" for channel ${this.channel}`
+                );
+                // Actually, point scale could be changed into band scale
+                // TODO: Use the same merging logic as in: https://github.com/vega/vega-lite/blob/master/src/scale.ts
+            }
+        }
+
+        this.#members.add(newMember);
+    }
+
+    /**
+     * @param {ScaleResolutionMember} member
+     * @returns {() => boolean}
+     */
+    registerMember(member) {
+        this.#addMember(member);
+        return () => {
+            const removed = this.#members.delete(member);
+            return removed && this.#members.size === 0;
+        };
+    }
+
+    /**
+     * Returns true if the domain has been defined explicitly, i.e. not extracted from the data.
+     */
+    #isExplicitDomain() {
+        return this.#domainAggregator.hasConfiguredDomain();
+    }
+
+    #isDomainInitialized() {
+        const s = this.#scaleManager.scale;
+        if (!s) {
+            return false;
+        }
+
+        const domain = s.domain();
+
+        // We could alternatively have a flag that is set when the domain is initialized.
+        if (isContinuous(s.type)) {
+            return (
+                domain.length > 2 ||
+                (domain.length == 2 && (domain[0] !== 0 || domain[1] !== 0))
+            );
+        } else {
+            return domain.length > 0;
+        }
+    }
+
+    /**
+     * Collects and merges scale properties from the participating views.
+     * Does not include inferred default values such as schemes etc.
+     *
+     * @returns {import("../spec/scale.js").Scale}
+     */
+    #getMergedScaleProps() {
+        return resolveScalePropsBase({
+            channel: this.channel,
+            dataType: this.type,
+            members: this.#members,
+            isExplicitDomain: this.#isExplicitDomain(),
+        });
+    }
+
+    /**
+     * Returns the merged scale properties supplemented with inferred properties
+     * and domain.
+     *
+     * @param {boolean} [extractDataDomain]
+     * @returns {import("../spec/scale.js").Scale}
+     */
+    #getScaleProps(extractDataDomain = false) {
+        const props = this.#getMergedScaleProps();
+        if (props === null || props.type == "null") {
+            // No scale (pass-thru)
+            // TODO: Check that the channel is compatible
+            return { type: "null" };
+        }
+
+        const domain =
+            this.#domainAggregator.getConfiguredOrDefaultDomain(
+                extractDataDomain
+            );
+
+        if (domain && domain.length > 0) {
+            props.domain = domain;
+        } else if (isDiscrete(props.type)) {
+            props.domain = new NominalDomain();
+        }
+
+        if (!props.domain && props.domainMid !== undefined) {
+            // Initialize with a bogus domain so that scale.js can inject the domainMid.
+            // The number of domain elements must be know before the glsl scale is generated.
+            props.domain = [props.domainMin ?? 0, props.domainMax ?? 1];
+        }
+
+        return props;
+    }
+
+    /**
+     * Reconfigures the scale: updates domain and other settings.
+     *
+     * Use this when the set of participating members changes (views added or removed),
+     * or when scale properties are otherwise re-resolved from the view hierarchy.
+     */
+    reconfigure() {
+        const props = this.#getScaleProps(true);
+        this.#reconfigureWith(() => this.#scaleManager.reconfigureScale(props));
+    }
+
+    /**
+     * Reconfigures only the effective domain (configured + data-derived).
+     *
+     * Use this when data changes but the scale membership and properties are stable.
+     */
+    reconfigureDomain() {
+        const props = this.#getScaleProps(true);
+        this.#reconfigureWith(() => {
+            configureDomain(this.#scaleManager.scale, props);
+        });
+    }
+
+    /**
+     * @param {() => void} apply
+     */
+    #reconfigureWith(apply) {
+        const scale = this.#scaleManager.scale;
+
+        if (!scale || scale.type == "null") {
+            return;
+        }
+
+        const domainWasInitialized = this.#isDomainInitialized();
+        const previousDomain = scale.domain();
+
+        this.#scaleManager.withDomainNotificationsSuppressed(apply);
+
+        if (
+            this.#domainAggregator.captureInitialDomain(
+                scale,
+                domainWasInitialized
+            )
+        ) {
+            // Domain changes were suppressed during reconfigure; notify explicitly.
+            this.#notifyListeners("domain");
+            return;
+        }
+
+        const newDomain = scale.domain();
+        if (!shallowArrayEquals(newDomain, previousDomain)) {
+            if (this.isZoomable()) {
+                // Don't mess with zoomed views, restore the previous domain
+                this.#scaleManager.withDomainNotificationsSuppressed(() => {
+                    scale.domain(previousDomain);
+                });
+            } else if (this.#interactionController.isZoomingSupported()) {
+                // It can be zoomed, so lets make a smooth transition.
+                // Restore the previous domain and zoom smoothly to the new domain.
+                this.#scaleManager.withDomainNotificationsSuppressed(() => {
+                    scale.domain(previousDomain);
+                });
+                this.zoomTo(newDomain, 500); // TODO: Configurable duration
+            } else {
+                // Update immediately if the previous domain was the initial domain [0, 0]
+                // Notifications were suppressed during reconfigure; notify explicitly.
+                this.#notifyListeners("domain");
+            }
+        }
+    }
+
+    /**
+     * @returns {ScaleWithProps}
+     */
+    get scale() {
+        if (this.#scaleManager.scale) {
+            return this.#scaleManager.scale;
+        }
+        throw new Error(
+            "ScaleResolution.scale accessed before initialization. Call initializeScale()."
+        );
+    }
+
+    /**
+     * Returns the scale instance, creating it if needed.
+     *
+     * Use this from call sites that may run before explicit initialization.
+     *
+     * @returns {ScaleWithProps}
+     */
+    getScale() {
+        return this.#scaleManager.scale ?? this.initializeScale();
+    }
+
+    /**
+     * Initializes the scale instance once resolution has stabilized.
+     *
+     * @returns {ScaleWithProps}
+     */
+    initializeScale() {
+        if (this.#scaleManager.scale) {
+            return this.#scaleManager.scale;
+        }
+
+        const props = this.#getScaleProps();
+        const scale = this.#scaleManager.createScale(props);
+
+        return scale;
+    }
+
+    getDomain() {
+        return this.getScale().domain();
+    }
+
+    /**
+     * Extracts and unions the data domains of all participating views.
+     *
+     * @return { DomainArray }
+     */
+    getDataDomain() {
+        return this.#domainAggregator.getDataDomain();
+    }
+
+    /**
+     * @returns {NumericDomain | ComplexDomain}
+     */
+    getComplexDomain() {
+        return /** @type {NumericDomain | ComplexDomain} */ (
+            toComplexInterval(this.#getGenomeSource(), this.getDomain())
+        );
+    }
+
+    /**
+     * Return true if the scale is zoomable and the current domain differs from the initial domain.
+     *
+     * @returns true if zoomed
+     */
+    isZoomed() {
+        return this.#interactionController.isZoomed();
+    }
+
+    /**
+     * Returns true if zooming is supported and allowed in view spec.
+     */
+    isZoomable() {
+        // Check explicit configuration
+        return this.#interactionController.isZoomable();
+    }
+
+    /**
+     * Pans (translates) and zooms using a specified scale factor.
+     *
+     * @param {number} scaleFactor
+     * @param {number} scaleAnchor
+     * @param {number} pan
+     * @returns {boolean} true if the scale was zoomed
+     */
+    zoom(scaleFactor, scaleAnchor, pan) {
+        return this.#interactionController.zoom(scaleFactor, scaleAnchor, pan);
+    }
+
+    /**
+     * Immediately zooms to the given interval.
+     *
+     * @param {NumericDomain | ComplexDomain} domain
+     * @param {boolean | number} [duration] an approximate duration for transition.
+     *      Zero duration zooms immediately. Boolean `true` indicates a default duration.
+     */
+    async zoomTo(domain, duration = false) {
+        return this.#interactionController.zoomTo(domain, duration);
+    }
+
+    /**
+     * Resets the current domain to the initial one
+     *
+     * @returns true if the domain was changed
+     */
+    resetZoom() {
+        return this.#interactionController.resetZoom();
+    }
+
+    /**
+     * Returns the zoom level with respect to the reference domain span (the original domain).
+     *
+     * In principle, this is highly specific to positional channels. However, zooming can
+     * be generalized to other quantitative channels such as color, opacity, size, etc.
+     */
+    getZoomLevel() {
+        return this.#interactionController.getZoomLevel();
+    }
+
+    /**
+     * Returns the length of the axis in pixels. Chooses the smallest of the views.
+     * They should all be the same, but some exotic configuration might break that assumption.
+     *
+     * This method is needed because positional channels have unit ranges and the
+     * length of the axis is not directly available from the scale. Ideally, ranges would
+     * be configured as pixels, but that is yet to be materialized.
+     */
+    getAxisLength() {
+        if (this.channel !== "x" && this.channel !== "y") {
+            throw new Error(
+                "Axis length is only defined for x and y channels!"
+            );
+        }
+
+        // Here's a problem: if the view has been hidden, it may have stale coords.
+        // TODO: They should be cleared when the layout is invalidated.
+        // Alternatively, scale ranges could be set in pixels.
+        const lengths = Array.from(this.#members)
+            .map(
+                (m) =>
+                    m.view.coords?.[this.channel === "x" ? "width" : "height"]
+            )
+            .filter((len) => len > 0);
+
+        return lengths.length
+            ? lengths.reduce((a, b) => Math.min(a, b), 10000)
+            : 0;
+    }
+
+    /**
+     * Inverts a value in range to a value on domain. Returns an object in
+     * case of locus scale.
+     *
+     * @param {number} value
+     */
+    invertToComplex(value) {
+        const scale = this.getScale();
+        if ("invert" in scale) {
+            const inverted = /** @type {number} */ (scale.invert(value));
+            return this.toComplex(inverted);
+        } else {
+            throw new Error("The scale does not support inverting!");
+        }
+    }
+
+    /**
+     * @param {number} value
+     */
+    toComplex(value) {
+        return toComplexValue(this.#getGenomeSource(), value);
+    }
+
+    /**
+     * @param {number | ChromosomalLocus} complex
+     * @returns {number}
+     */
+    fromComplex(complex) {
+        return fromComplexValue(this.#getGenomeSource(), complex);
+    }
+
+    /**
+     * @param {ScalarDomain | ComplexDomain} interval
+     * @returns {number[]}
+     */
+    fromComplexInterval(interval) {
+        if (this.type == LOCUS) {
+            return locusFromComplexInterval(this.#getGenomeSource(), interval);
+        }
+        return /** @type {number[]} */ (interval);
+    }
+}
+
+/**
+ * Reconfigures scale domains, starting from the given view.
+ *
+ * Use this for data-driven updates where only domains need refreshing.
+ *
+ * TODO: This should be made unnecessary. Collectors should trigger the reconfiguration
+ * for those views that get their data from the collector.
+ *
+ * TODO: This may reconfigure channels that are not affected by the change.
+ * Causes performance issues with domains that are extracted from data.
+ *
+ * @param {import("../view/view.js").default | import("../view/view.js").default[]} fromViews
+ */
+export function reconfigureScaleDomains(fromViews) {
+    /** @type {Set<ScaleResolution>} */
+    const uniqueResolutions = new Set();
+
+    /** @param {import("../view/view.js").default} view */
+    function collectResolutions(view) {
+        for (const resolution of Object.values(view.resolutions.scale)) {
+            uniqueResolutions.add(resolution);
+        }
+    }
+
+    for (const fromView of asArray(fromViews)) {
+        // Descendants
+        fromView.visit(collectResolutions);
+
+        // Ancestors
+        for (const view of fromView.getDataAncestors()) {
+            // Skip axis views etc. They should not mess with the domains.
+            if (!view.options.contributesToScaleDomain) {
+                break;
+            }
+            collectResolutions(view);
+        }
+    }
+
+    uniqueResolutions.forEach((resolution) => resolution.reconfigureDomain());
+}

package/dist/src/scales/scaleResolution.test.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/scales/scaleResolutionConstants.d.ts

@@ -0,0 +1,6 @@
+export const QUANTITATIVE: "quantitative";
+export const ORDINAL: "ordinal";
+export const NOMINAL: "nominal";
+export const LOCUS: "locus";
+export const INDEX: "index";
+//# sourceMappingURL=scaleResolutionConstants.d.ts.map

package/dist/src/scales/scaleResolutionConstants.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/scales/scaleResolutionConstants.js

@@ -0,0 +1,5 @@
+export const QUANTITATIVE = "quantitative";
+export const ORDINAL = "ordinal";
+export const NOMINAL = "nominal";
+export const LOCUS = "locus";
+export const INDEX = "index";

package/dist/src/scales/scaleRules.d.ts

@@ -0,0 +1,16 @@
+/**
+ * @typedef {import("../spec/channel.js").Channel} Channel
+ */
+/**
+ * @param {Channel} channel
+ * @param {import("../spec/channel.js").Type} dataType
+ * @returns {import("../spec/scale.js").ScaleType}
+ */
+export function getDefaultScaleType(channel: Channel, dataType: import("../spec/channel.js").Type): import("../spec/scale.js").ScaleType;
+/**
+ * @param {import("../spec/scale.js").Scale} props
+ * @param {Channel} channel
+ */
+export function applyLockedProperties(props: import("../spec/scale.js").Scale, channel: Channel): void;
+export type Channel = import("../spec/channel.js").Channel;
+//# sourceMappingURL=scaleRules.d.ts.map

package/dist/src/scales/scaleRules.d.ts.map

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