@genome-spy/core 0.36.1 → 0.37.1

package/dist/src/view/view.js

@@ -0,0 +1,691 @@
+import {
+    parseSizeDef,
+    FlexDimensions,
+    ZERO_FLEXDIMENSIONS,
+} from "../utils/layout/flexLayout";
+import Padding from "../utils/layout/padding";
+import {
+    getCachedOrCall,
+    initPropertyCache,
+    invalidatePrefix,
+} from "../utils/propertyCacher";
+import { isNumber, isString, span } from "vega-util";
+import { scaleLog } from "d3-scale";
+import { isFieldDef, getPrimaryChannel } from "../encoder/encoder";
+import { appendToBaseUrl } from "../utils/url";
+import { isDiscrete, bandSpace } from "vega-scale";
+import { peek } from "../utils/arrayUtils";
+
+// TODO: View classes have too many responsibilities. Come up with a way
+// to separate the concerns. However, most concerns are tightly tied to
+// the hierarchy, which makes the separation quite tricky.
+// Separation of concerns would also make the code more easily testable.
+
+/** Skip children */
+export const VISIT_SKIP = "VISIT_SKIP";
+/** Stop further visits */
+export const VISIT_STOP = "VISIT_STOP";
+
+/** @type {function(number):number} */
+const defaultOpacityFunction = (parentOpacity) => parentOpacity;
+
+/**
+ * @typedef {VISIT_SKIP|VISIT_STOP|void} VisitResult
+ *
+ * @callback VisitorCallback
+ * @param {View} view
+ * @returns {VisitResult}
+ *
+ * @typedef {VisitorCallback & {
+ *      postOrder?: function(View):void,
+ *      beforeChildren?: function(View):void,
+ *      afterChildren?: function(View):void}
+ * } Visitor
+ *
+ * @typedef {object} BroadcastMessage
+ * @prop {import("../genomeSpy").BroadcastEventType} type Broadcast type
+ * @prop {any} [payload] Anything
+ *
+ * @callback InteractionEventListener
+ * @param {import("../utils/layout/rectangle").default} coords
+ *      Coordinates of the view
+ * @param {import("../utils/interactionEvent").default} event
+ */
+export default class View {
+    /** @type {Record<string, (function(BroadcastMessage):void)[]>} */
+    #broadcastHandlers = {};
+
+    /** @type {Record<string, InteractionEventListener[]>} */
+    #capturingInteractionEventListeners = {};
+
+    /** @type {Record<string, InteractionEventListener[]>} */
+    #nonCapturingInteractionEventListeners = {};
+
+    /**
+     * @type {function(number):number}
+     */
+    opacityFunction = defaultOpacityFunction;
+
+    /**
+     *
+     * @param {import("../spec/view").ViewSpec} spec
+     * @param {import("../types/viewContext").default} context
+     * @param {import("./containerView").default} layoutParent Parent that handles rendering of this view
+     * @param {import("./view").default} dataParent Parent that provides data, encodings, and is used in scale resolution
+     * @param {string} name
+     */
+    constructor(spec, context, layoutParent, dataParent, name) {
+        if (!spec) {
+            throw new Error("View spec must be defined!");
+        }
+
+        this.context = context;
+        this.layoutParent = layoutParent;
+        this.dataParent = dataParent;
+        this.name = spec.name || name;
+        this.spec = spec;
+
+        this.resolutions = {
+            /**
+             * Channel-specific scale resolutions
+             * @type {Partial<Record<import("../spec/channel").ChannelWithScale, import("./scaleResolution").default>>}
+             */
+            scale: {},
+            /**
+             * Channel-specific axis resolutions
+             * @type {Partial<Record<import("../spec/channel").PrimaryPositionalChannel, import("./axisResolution").default>>}
+             */
+            axis: {},
+        };
+
+        initPropertyCache(this);
+
+        /**
+         * Don't inherit encodings from parent.
+         * TODO: Make configurable through spec. Allow more fine-grained control.
+         */
+        this.blockEncodingInheritance = false;
+
+        /**
+         * Whether ScaleResolution should include this view or its children in the domain.
+         * This is mainly used to block axis views from contributing to the domain.
+         */
+        this.contributesToScaleDomain = true;
+
+        /**
+         * Whether GridView or equivalent should draw axis and grid lines for this view.
+         * @type {Record<import("../spec/channel").PrimaryPositionalChannel, boolean>}
+         */
+        this.needsAxes = { x: false, y: false };
+    }
+
+    getPadding() {
+        return this._cache("size/padding", () =>
+            Padding.createFromConfig(this.spec.padding)
+        );
+    }
+
+    /**
+     * Returns a padding that indicates how much axes and titles extend over the plot area.
+     *
+     * @returns {Padding}
+     */
+    getOverhang() {
+        return Padding.zero();
+    }
+
+    /**
+     * Returns the configured size, if present. Otherwise a computed or default
+     * height is returned.
+     *
+     * @returns {FlexDimensions}
+     */
+    getSize() {
+        return this._cache("size/size", () =>
+            this.isConfiguredVisible()
+                ? this.#getSizeFromSpec()
+                : ZERO_FLEXDIMENSIONS
+        );
+    }
+
+    /**
+     * @return {FlexDimensions}
+     */
+    #getSizeFromSpec() {
+        /**
+         * @param {"width" | "height"} dimension
+         * @return {import("../utils/layout/flexLayout").SizeDef}
+         */
+        const handleSize = (dimension) => {
+            let value = this.spec[dimension];
+
+            if (isStepSize(value)) {
+                const stepSize = value.step;
+
+                const scale = this.getScaleResolution(
+                    dimension == "width" ? "x" : "y"
+                )?.getScale();
+
+                if (scale) {
+                    // Note: this and all ancestral views need to be refreshed when the domain is changed.
+                    let steps = 0;
+                    if (isDiscrete(scale.type)) {
+                        steps = scale.domain().length;
+                    } else if (["locus", "index"].includes(scale.type)) {
+                        const domain = scale.domain();
+                        steps = peek(domain) - domain[0];
+                    } else {
+                        throw new Error(
+                            `Cannot use step-based size with "${scale.type}" scale!`
+                        );
+                    }
+
+                    // TODO: Type guards maybe?
+                    const _scale =
+                        /** @type {import("d3-scale").ScaleBand<any> | import("../genome/scaleLocus").ScaleLocus | import("../genome/scaleIndex").ScaleIndex} */ (
+                            scale
+                        );
+
+                    steps = bandSpace(
+                        steps,
+                        _scale.paddingInner(),
+                        _scale.paddingOuter()
+                    );
+
+                    return { px: steps * stepSize, grow: 0 };
+                } else {
+                    throw new Error(
+                        "Cannot use 'step' size with missing scale!"
+                    );
+                }
+            } else {
+                return (value && parseSizeDef(value)) ?? { px: 0, grow: 1 };
+            }
+        };
+
+        return this._cache(
+            "size/sizeFromSpec",
+            () => new FlexDimensions(handleSize("width"), handleSize("height"))
+        );
+    }
+
+    isConfiguredVisible() {
+        return this.context.isViewConfiguredVisible(this);
+    }
+
+    isVisibleInSpec() {
+        return this.spec.visible ?? true;
+    }
+
+    /**
+     * Returns the effective visibility of this view, e.g., whether this view
+     * and all its ancestors are visible.
+     *
+     * When doing a depth-first traversal on the view hierarchy, it's best to
+     * use `isConfiguredVisible()` instead of this method.
+     *
+     * @returns {boolean}
+     */
+    isVisible() {
+        return this.getLayoutAncestors().every((view) =>
+            view.isConfiguredVisible()
+        );
+    }
+
+    /**
+     * Returns the effective opacity of this view, e.g., view's opacity multiplied
+     * by opacities of its ancestors.
+     *
+     * TODO: This methods makes sense only in Unit and Layer views.
+     *
+     * @returns {number}
+     */
+    getEffectiveOpacity() {
+        return this.opacityFunction(
+            this.layoutParent?.getEffectiveOpacity() ?? 1.0
+        );
+    }
+
+    getPathString() {
+        return this.getLayoutAncestors()
+            .map((v) => v.name)
+            .reverse()
+            .join("/");
+    }
+
+    /**
+     * @param {"dataParent" | "layoutParent"} prop
+     * @returns {View[]}
+     */
+    #getAncestors(prop) {
+        /** @type {View[]} */
+        const ancestors = [];
+        // eslint-disable-next-line consistent-this
+        let view = /** @type {View} */ (this);
+        do {
+            ancestors.push(view);
+            view = view[prop];
+        } while (view);
+        return ancestors;
+    }
+
+    /**
+     * Returns the ancestor views, starting with this view.
+     */
+    getLayoutAncestors() {
+        return this.#getAncestors("layoutParent");
+    }
+
+    /**
+     * Returns the ancestor views, starting with this view.
+     */
+    getDataAncestors() {
+        return this.#getAncestors("dataParent");
+    }
+
+    /**
+     * Handles a broadcast message that is intended for the whole view hierarchy.
+     *
+     * @param {BroadcastMessage} message
+     */
+    handleBroadcast(message) {
+        // TODO: message types should be constants
+        for (const handler of this.#broadcastHandlers[message.type] || []) {
+            handler(message);
+        }
+    }
+
+    /**
+     *
+     * @param {string} type
+     * @param {function(BroadcastMessage):void} handler
+     */
+    _addBroadcastHandler(type, handler) {
+        let handlers = this.#broadcastHandlers[type];
+        if (!handlers) {
+            handlers = [];
+            this.#broadcastHandlers[type] = handlers;
+        }
+        handlers.push(handler);
+    }
+
+    /**
+     * Handles an interactionEvent
+     *
+     * @param {import("../utils/layout/rectangle").default} coords
+     *      Coordinates of the view
+     * @param {import("../utils/interactionEvent").default} event
+     * @param {boolean} capturing
+     */
+    handleInteractionEvent(coords, event, capturing) {
+        const listenersByType = capturing
+            ? this.#capturingInteractionEventListeners
+            : this.#nonCapturingInteractionEventListeners;
+        for (const listener of listenersByType[event.type] || []) {
+            listener(coords, event);
+        }
+    }
+
+    /**
+     * Add an "interaction" event listener that mimics DOM's event model inside
+     * the view hierarchy.
+     *
+     * This is intended for GenomeSpy's internal use. It allows the views to handle
+     * low level interactions such as dragging, wheeling, etc.
+     *
+     * @param {string} type
+     * @param {InteractionEventListener} listener
+     * @param {boolean} [useCapture]
+     */
+    addInteractionEventListener(type, listener, useCapture) {
+        const listenersByType = useCapture
+            ? this.#capturingInteractionEventListeners
+            : this.#nonCapturingInteractionEventListeners;
+        let listeners = listenersByType[type];
+        if (!listeners) {
+            listeners = [];
+            listenersByType[type] = listeners;
+        }
+
+        listeners.push(listener);
+    }
+
+    /**
+     * Visits child views in depth-first order. Visitor's return value
+     * controls the traversal.
+     *
+     * @param {Visitor} visitor
+     * @returns {VisitResult}
+     *
+     */
+    visit(visitor) {
+        try {
+            const result = visitor(this);
+
+            if (visitor.postOrder) {
+                visitor.postOrder(this);
+            }
+
+            if (result !== VISIT_STOP) {
+                return result;
+            }
+        } catch (e) {
+            // Augment the exception with the view
+            e.view = this;
+            throw e;
+        }
+    }
+
+    /**
+     * Get all descendants of this view in depth-first order.
+     */
+    getDescendants() {
+        /** @type {View[]} */
+        const descendants = [];
+        this.visit((view) => {
+            descendants.push(view);
+        });
+        return descendants;
+    }
+
+    /**
+     * Called after all scales in the view hierarchy have been resolved.
+     */
+    onScalesResolved() {
+        // Only set the opacity function once. The idea is to allow custom functions
+        // and prevent accidental overwrites.
+        if (
+            !this.opacityFunction ||
+            this.opacityFunction === defaultOpacityFunction
+        ) {
+            this.opacityFunction = createViewOpacityFunction(this);
+        }
+    }
+
+    /**
+     * ViewRenderingContext calls this method once for each view during each rendering
+     * pass. The order is depth first, pre order.
+     */
+    onBeforeRender() {
+        //
+    }
+
+    /**
+     * Recursively traverses the view hierarchy, computes the view coordinates,
+     * and coordinates the mark rendering.
+     *
+     * @type {import("../types/rendering").RenderMethod}
+     */
+    render(context, coords, options = {}) {
+        // override
+    }
+
+    /**
+     * Returns the encodings specified in this view combined with the inherited
+     * encodings. However, this does not contain any defaults or inferred/adjusted/fixed
+     * encodings. Those are available in Mark's encoding property.
+     *
+     * @return {import("../spec/channel").Encoding}
+     */
+    getEncoding() {
+        const pe =
+            this.dataParent && !this.blockEncodingInheritance
+                ? this.dataParent.getEncoding()
+                : {};
+        const te = this.spec.encoding || {};
+
+        /** @type {import("../spec/channel").Encoding} */
+        const combined = {
+            ...pe,
+            ...te,
+        };
+
+        for (const [channel, channelDef] of Object.entries(combined)) {
+            if (channelDef === null) {
+                // Prevent propagation
+                delete combined[channel];
+            }
+        }
+
+        return combined;
+    }
+
+    /**
+     * @param {View} [whoIsAsking] Passed to the immediate parent. Allows for
+     *      selectively breaking the inheritance.
+     * @return {function(object):any}
+     */
+    getFacetAccessor(whoIsAsking) {
+        if (this.layoutParent) {
+            return this.layoutParent.getFacetAccessor(this);
+        }
+    }
+
+    /**
+     * Returns the fields that should be used for partitioning the data for facets.
+     *
+     * @param {View} [whoIsAsking]
+     * @returns {string[]}
+     */
+    getFacetFields(whoIsAsking) {
+        const sampleFieldDef = this.getEncoding().sample;
+        if (isFieldDef(sampleFieldDef)) {
+            return [sampleFieldDef.field];
+        } else {
+            return this.layoutParent?.getFacetFields(this);
+        }
+    }
+
+    /**
+     * Returns a texture that has a mapping for the sample locations. This is implemented
+     * only in the SampleView of GenomeSpy App.
+     *
+     * Background:
+     * There are to ways to manage how sample facets are drawn in the App:
+     *
+     * 1) Use one draw call for each facet and pass the location data as a uniform.
+     * 2) Draw all facets with one call and pass the facet locations as a texture.
+     *
+     * The former is suitable for large datasets, which can be subsetted for better
+     * performance. The latter one is more performant for cases where each facet
+     * consists of few data items (sample attributes / metadata).
+     *
+     * @return {WebGLTexture}
+     */
+    getSampleFacetTexture() {
+        return undefined;
+    }
+
+    /**
+     * @param {import("../spec/channel").ChannelWithScale} channel
+     */
+    getScaleResolution(channel) {
+        const primaryChannel =
+            /** @type {import("../spec/channel").ChannelWithScale} */ (
+                getPrimaryChannel(channel)
+            );
+
+        return this.getDataAncestors()
+            .map((view) => view.resolutions.scale[primaryChannel])
+            .find((resolution) => resolution);
+    }
+
+    /**
+     * @param {import("../spec/channel").PositionalChannel} channel
+     */
+    getAxisResolution(channel) {
+        const primaryChannel =
+            /** @type {import("../spec/channel").PrimaryPositionalChannel} */ (
+                getPrimaryChannel(channel)
+            );
+
+        return this.getDataAncestors()
+            .map((view) => view.resolutions.axis[primaryChannel])
+            .find((resolution) => resolution);
+    }
+
+    /**
+     * @param {import("../spec/channel").Channel | "default"} channel
+     * @param {import("../spec/view").ResolutionTarget} resolutionType
+     * @returns {import("../spec/view").ResolutionBehavior}
+     */
+    getConfiguredResolution(channel, resolutionType) {
+        return this.spec.resolve?.[resolutionType]?.[channel];
+    }
+
+    /**
+     * @param {import("../spec/channel").Channel} channel
+     * @param {import("../spec/view").ResolutionTarget} resolutionType
+     * @returns {import("../spec/view").ResolutionBehavior}
+     */
+    getConfiguredOrDefaultResolution(channel, resolutionType) {
+        return (
+            this.getConfiguredResolution(channel, resolutionType) ??
+            this.getConfiguredResolution("default", resolutionType) ??
+            this.getDefaultResolution(channel, resolutionType)
+        );
+    }
+
+    /**
+     * @param {import("../spec/channel").Channel} channel
+     * @param {import("../spec/view").ResolutionTarget} resolutionType
+     * @returns {import("../spec/view").ResolutionBehavior}
+     */
+    getDefaultResolution(channel, resolutionType) {
+        return "independent";
+    }
+
+    /**
+     * @returns {string}
+     */
+    getBaseUrl() {
+        return appendToBaseUrl(
+            () => this.dataParent?.getBaseUrl(),
+            this.spec.baseUrl
+        );
+    }
+
+    /**
+     * Returns `true` if this view and its children supports picking.
+     */
+    isPickingSupported() {
+        return true;
+    }
+
+    getTitleText() {
+        const title = this.spec.title;
+        if (title) {
+            return isString(title) ? title : title.text;
+        }
+    }
+
+    /**
+     * @param {any} key string
+     * @param {function(key?):T} callable A function that produces a value to be cached
+     * @returns {T}
+     * @template T
+     * @protected
+     */
+    _cache(key, callable) {
+        return getCachedOrCall(this, key, callable);
+    }
+
+    /**
+     *
+     * @param {string} key
+     * @param {"self" | "progeny" | "ancestors"} [direction]
+     */
+    _invalidateCacheByPrefix(key, direction = "self") {
+        switch (direction) {
+            case "self":
+                invalidatePrefix(this, key);
+                break;
+            case "ancestors":
+                for (const view of this.getLayoutAncestors()) {
+                    invalidatePrefix(view, key);
+                }
+                break;
+            case "progeny":
+                this.visit((view) => invalidatePrefix(view, key));
+                break;
+            default:
+        }
+    }
+
+    invalidateSizeCache() {
+        this._invalidateCacheByPrefix("size/", "ancestors");
+    }
+
+    /**
+     * Broadcasts a message to views that include the given (x, y) point.
+     * This is mainly intended for mouse events.
+     *
+     * @param {import("../utils/interactionEvent").default} event
+     */
+    propagateInteractionEvent(event) {
+        // Subclasses must implement proper handling
+    }
+}
+
+/**
+ *
+ * @param {any} opacity
+ * @returns {opacity is import("../spec/view").DynamicOpacity}
+ */
+function isDynamicOpacity(opacity) {
+    return "unitsPerPixel" in opacity;
+}
+
+/**
+ *
+ * @param {View} view
+ * @returns {function(number):number}
+ */
+function createViewOpacityFunction(view) {
+    const opacityDef = view.spec.opacity;
+
+    if (opacityDef !== undefined) {
+        if (isNumber(opacityDef)) {
+            return (parentOpacity) => parentOpacity * opacityDef;
+        } else if (isDynamicOpacity(opacityDef)) {
+            /** @type {(channel: import("../spec/channel").ChannelWithScale) => any} */
+            const getScale = (channel) => {
+                const scale = view.getScaleResolution(channel)?.getScale();
+                // Only works on linear scales
+                if (["linear", "index", "locus"].includes(scale?.type)) {
+                    return scale;
+                }
+            };
+
+            const scale = opacityDef.channel
+                ? getScale(opacityDef.channel)
+                : getScale("x") || getScale("y");
+
+            if (!scale) {
+                throw new Error(
+                    "Cannot find a resolved quantitative scale for dynamic opacity!"
+                );
+            }
+
+            const interpolate = scaleLog()
+                .domain(opacityDef.unitsPerPixel)
+                .range(opacityDef.values)
+                .clamp(true);
+
+            return (parentOpacity) => {
+                const rangeSpan = 1000; //TODO: span(scale.range());
+                const unitsPerPixel = span(scale.domain()) / rangeSpan;
+
+                return interpolate(unitsPerPixel) * parentOpacity;
+            };
+        }
+    }
+    return (parentOpacity) => parentOpacity;
+}
+
+/**
+ *
+ * @param {any} size
+ * @return {size is import("../spec/view").Step}
+ */
+export const isStepSize = (size) => !!size?.step;