@genome-spy/core 0.67.0 → 0.69.0

package/dist/src/view/view.d.ts

@@ -27,9 +27,6 @@ export const VISIT_STOP: "VISIT_STOP";
  * @typedef {object} ViewOptions
  * @prop {boolean} [blockEncodingInheritance]
  *      Don't inherit encodings from parent. Default: false.
- * @prop {boolean} [contributesToScaleDomain]
- *      Whether ScaleResolution should include this view or its children in the
- *      domain. Default: true
  * @prop {boolean} [layersChildren]
  *      View's children are layered on top of each other and they have the same
  *      coordinates as their parent.
@@ -60,7 +57,6 @@ export default class View {
     context: import("../types/viewContext.js").default;
     layoutParent: import("./containerView.js").default;
     dataParent: View;
-    name: string;
     spec: import("../spec/view.js").ViewSpec;
     resolutions: {
         /**
@@ -79,11 +75,6 @@ export default class View {
          * Don't inherit encodings from parent. Default: false.
          */
         blockEncodingInheritance: boolean;
-        /**
-         * Whether ScaleResolution should include this view or its children in the
-         * domain. Default: true
-         */
-        contributesToScaleDomain: boolean;
         /**
          * View's children are layered on top of each other and they have the same
          * coordinates as their parent.
@@ -100,8 +91,22 @@ export default class View {
      * @type {Record<import("../spec/channel.js").PrimaryPositionalChannel, boolean>}
      */
     needsAxes: Record<import("../spec/channel.js").PrimaryPositionalChannel, boolean>;
-    /** @type {ParamMediator} */
-    paramMediator: ParamMediator;
+    /** @type {ViewParamRuntime} */
+    paramRuntime: ViewParamRuntime;
+    /**
+     * Effective view name. Equals the explicit name (`spec.name`) when provided,
+     * otherwise falls back to an auto-generated default name.
+     */
+    get name(): string;
+    /**
+     * The explicit name from the spec (`spec.name`), if any.
+     */
+    get explicitName(): string;
+    /**
+     * The auto-generated default name that was assigned by the parent/factory.
+     * Intended for debugging only.
+     */
+    get defaultName(): string;
     /**
      * Returns the coords of the view. If view has been faceted, returns the coords
      * of an arbitrary facet. If all or specific facet coords are needed, use `facetCoords`.
@@ -134,6 +139,7 @@ export default class View {
      * @returns {FlexDimensions}
      */
     getViewportSize(): FlexDimensions;
+    registerStepSizeInvalidation(): void;
     isConfiguredVisible(): boolean;
     isVisibleInSpec(): boolean;
     /**
@@ -146,6 +152,12 @@ export default class View {
      * @returns {boolean}
      */
     isVisible(): boolean;
+    /**
+     * Returns true if this view or any ancestor is marked as domain inert.
+     *
+     * @returns {boolean}
+     */
+    isDomainInert(): boolean;
     /**
      * @returns {"none" | "pending" | "ready"}
      */
@@ -186,8 +198,9 @@ export default class View {
      *
      * @param {string} type
      * @param {function(BroadcastMessage):void} handler
+     * @returns {() => void}
      */
-    _addBroadcastHandler(type: string, handler: (arg0: BroadcastMessage) => void): void;
+    _addBroadcastHandler(type: string, handler: (arg0: BroadcastMessage) => void): () => void;
     /**
      * Handles an interactionEvent
      *
@@ -250,6 +263,7 @@ export default class View {
      * pass. The order is depth first, pre order.
      */
     onBeforeRender(): void;
+    hasRendered(): boolean;
     render(context: import("./renderingContext/viewRenderingContext.js").default, coords: import("./layout/rectangle.js").default, options?: import("../types/rendering.js").RenderingOptions): void;
     /**
      * Returns the encodings specified in this view combined with the inherited
@@ -372,18 +386,13 @@ export type ViewOptions = {
      * Don't inherit encodings from parent. Default: false.
      */
     blockEncodingInheritance?: boolean;
-    /**
-     * Whether ScaleResolution should include this view or its children in the
-     * domain. Default: true
-     */
-    contributesToScaleDomain?: boolean;
     /**
      * View's children are layered on top of each other and they have the same
      * coordinates as their parent.
      */
     layersChildren?: boolean;
 };
-import ParamMediator from "./paramMediator.js";
+import ViewParamRuntime from "../paramRuntime/viewParamRuntime.js";
 import Padding from "./layout/padding.js";
 import { FlexDimensions } from "./layout/flexLayout.js";
 //# sourceMappingURL=view.d.ts.map

package/dist/src/view/view.d.ts.map

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package/dist/src/view/view.js

@@ -9,14 +9,15 @@ import {
     initPropertyCache,
     invalidatePrefix,
 } from "../utils/propertyCacher.js";
-import { isNumber, isString, span } from "vega-util";
+import { isArray, isNumber, isString, span } from "vega-util";
 import { scaleLog } from "d3-scale";
 import { isFieldDef, getPrimaryChannel } from "../encoder/encoder.js";
 import { concatUrl } from "../utils/url.js";
 import { isDiscrete, bandSpace } from "vega-scale";
 import { peek } from "../utils/arrayUtils.js";
 import ViewError from "./viewError.js";
-import ParamMediator, { isExprRef } from "./paramMediator.js";
+import ViewParamRuntime from "../paramRuntime/viewParamRuntime.js";
+import { isExprRef } from "../paramRuntime/paramUtils.js";
 import { InternMap } from "internmap";
 import { endWithSlash } from "../utils/addBaseUrl.js";
 
@@ -58,14 +59,14 @@ const defaultOpacityFunction = (parentOpacity) => parentOpacity;
  * @typedef {object} ViewOptions
  * @prop {boolean} [blockEncodingInheritance]
  *      Don't inherit encodings from parent. Default: false.
- * @prop {boolean} [contributesToScaleDomain]
- *      Whether ScaleResolution should include this view or its children in the
- *      domain. Default: true
  * @prop {boolean} [layersChildren]
  *      View's children are layered on top of each other and they have the same
  *      coordinates as their parent.
  */
 export default class View {
+    /** @type {string | undefined} */
+    #defaultName;
+
     /** @type {Record<string, (function(BroadcastMessage):void)[]>} */
     #broadcastHandlers = {};
 
@@ -81,6 +82,9 @@ export default class View {
     /** @type {(value: number) => void} */
     #heightSetter;
 
+    /** @type {boolean} */
+    #hasRendered = false;
+
     /**
      * @type {function(number):number}
      */
@@ -122,7 +126,7 @@ export default class View {
         this.context = context;
         this.layoutParent = layoutParent;
         this.dataParent = dataParent;
-        this.name = spec.name || name;
+        this.#defaultName = name;
         this.spec = spec;
 
         this.resolutions = {
@@ -142,7 +146,6 @@ export default class View {
 
         this.options = {
             blockEncodingInheritance: false,
-            contributesToScaleDomain: true,
             ...options,
         };
 
@@ -158,15 +161,15 @@ export default class View {
          */
         this.needsAxes = { x: false, y: false };
 
-        /** @type {ParamMediator} */
-        this.paramMediator = new ParamMediator(
-            () => this.dataParent?.paramMediator
+        /** @type {ViewParamRuntime} */
+        this.paramRuntime = new ViewParamRuntime(
+            () => this.dataParent?.paramRuntime
         );
 
         if (spec.params) {
             for (const param of spec.params) {
                 // TODO: If interval selection, validate `encodings` or provides defaults
-                this.paramMediator.registerParam(param);
+                this.paramRuntime.registerParam(param);
             }
         }
 
@@ -176,14 +179,37 @@ export default class View {
             // doesn't make much sense, but it's used in the App's SampleView
             // to set the height to sample facets' height.
             const allocateIfFree = (/** @type {string} */ name) =>
-                this.paramMediator.findMediatorForParam(name)
+                this.paramRuntime.findRuntimeForParam(name)
                     ? undefined
-                    : this.paramMediator.allocateSetter(name, 0);
+                    : this.paramRuntime.allocateSetter(name, 0);
             this.#heightSetter = allocateIfFree("height");
             this.#widthSetter = allocateIfFree("width");
         }
     }
 
+    /**
+     * Effective view name. Equals the explicit name (`spec.name`) when provided,
+     * otherwise falls back to an auto-generated default name.
+     */
+    get name() {
+        return this.spec.name ?? this.#defaultName;
+    }
+
+    /**
+     * The explicit name from the spec (`spec.name`), if any.
+     */
+    get explicitName() {
+        return this.spec.name;
+    }
+
+    /**
+     * The auto-generated default name that was assigned by the parent/factory.
+     * Intended for debugging only.
+     */
+    get defaultName() {
+        return this.#defaultName;
+    }
+
     /**
      * Returns the coords of the view. If view has been faceted, returns the coords
      * of an arbitrary facet. If all or specific facet coords are needed, use `facetCoords`.
@@ -265,11 +291,12 @@ export default class View {
      */
     #getDimensionSize(dimension) {
         let value = this.spec[dimension];
+        const needsStepInvalidation = isStepSize(value);
 
         const viewport =
             dimension == "viewportWidth" || dimension == "viewportHeight";
 
-        if (isStepSize(value)) {
+        if (needsStepInvalidation) {
             if (viewport) {
                 throw new ViewError(
                     `Cannot use step-based size with "${dimension}"!`,
@@ -313,7 +340,7 @@ export default class View {
                 return { px: steps * stepSize, grow: 0 };
             } else {
                 throw new ViewError(
-                    "Cannot use 'step' size with missing scale!",
+                    `Cannot use step-based size with "${dimension}"!`,
                     this
                 );
             }
@@ -325,6 +352,36 @@ export default class View {
         }
     }
 
+    registerStepSizeInvalidation() {
+        this.#registerStepSizeInvalidationFor("width", "x");
+        this.#registerStepSizeInvalidationFor("height", "y");
+    }
+
+    /**
+     * @param {"width" | "height"} dimension
+     * @param {import("../spec/channel.js").PrimaryPositionalChannel} channel
+     */
+    #registerStepSizeInvalidationFor(dimension, channel) {
+        const value = this.spec[dimension];
+        if (!isStepSize(value)) {
+            return;
+        }
+
+        const resolution = this.getScaleResolution(channel);
+        if (!resolution) {
+            throw new ViewError(
+                "Cannot use 'step' size without a scale!",
+                this
+            );
+        }
+
+        const listener = () => this.invalidateSizeCache();
+        resolution.addEventListener("domain", listener);
+        this.registerDisposer(() =>
+            resolution.removeEventListener("domain", listener)
+        );
+    }
+
     isConfiguredVisible() {
         return this.context.isViewConfiguredVisible(this);
     }
@@ -348,6 +405,24 @@ export default class View {
         );
     }
 
+    /**
+     * Returns true if this view or any ancestor is marked as domain inert.
+     *
+     * @returns {boolean}
+     */
+    isDomainInert() {
+        if (this.spec.domainInert) {
+            return true;
+        }
+
+        const parent = this.dataParent;
+        if (!parent) {
+            return false;
+        }
+
+        return parent.isDomainInert();
+    }
+
     /**
      * @returns {"none" | "pending" | "ready"}
      */
@@ -436,6 +511,7 @@ export default class View {
      *
      * @param {string} type
      * @param {function(BroadcastMessage):void} handler
+     * @returns {() => void}
      */
     _addBroadcastHandler(type, handler) {
         let handlers = this.#broadcastHandlers[type];
@@ -444,6 +520,18 @@ export default class View {
             this.#broadcastHandlers[type] = handlers;
         }
         handlers.push(handler);
+
+        return () => {
+            const currentHandlers = this.#broadcastHandlers[type];
+            if (!currentHandlers) {
+                return;
+            }
+
+            const index = currentHandlers.indexOf(handler);
+            if (index >= 0) {
+                currentHandlers.splice(index, 1);
+            }
+        };
     }
 
     /**
@@ -568,6 +656,10 @@ export default class View {
             this.context.dataFlow.removeDataSource(handle.dataSource);
         }
 
+        this.paramRuntime.dispose();
+
+        this.context.dataFlow.loadingStatusRegistry.delete(this);
+
         this.flowHandle = undefined;
     }
 
@@ -609,7 +701,13 @@ export default class View {
      * pass. The order is depth first, pre order.
      */
     onBeforeRender() {
-        //
+        if (!this.#hasRendered) {
+            this.#hasRendered = true;
+        }
+    }
+
+    hasRendered() {
+        return this.#hasRendered;
     }
 
     /**
@@ -793,7 +891,7 @@ export default class View {
             return isString(title)
                 ? title
                 : isExprRef(title.text)
-                  ? this.paramMediator.evaluateAndGet(title.text.expr)
+                  ? this.paramRuntime.evaluateAndGet(title.text.expr)
                   : title.text;
         }
     }
@@ -832,7 +930,9 @@ export default class View {
     }
 
     invalidateSizeCache() {
-        this._invalidateCacheByPrefix("size/", "ancestors");
+        // Clear both "size" and "size/*" cache keys.
+        invalidatePrefix(this, "size");
+        this._invalidateCacheByPrefix("size", "ancestors");
     }
 
     /**
@@ -856,6 +956,16 @@ function isDynamicOpacity(opacity) {
 }
 
 /**
+ * Builds the effective opacity function for a view.
+ *
+ * The resulting function multiplies parent opacity with one of:
+ * 1. constant opacity (`number`)
+ * 2. zoom-driven dynamic opacity (`DynamicOpacity`) that maps the current
+ *    units-per-pixel metric through a log interpolation
+ * 3. expression-driven opacity (`ExprRef`) that is evaluated reactively
+ *
+ * Dynamic opacity supports scale selection via `channel` (`x`, `y`, or
+ * `"auto"`), where `"auto"` averages available x/y metrics.
  *
  * @param {View} view
  * @returns {function(number):number}
@@ -867,46 +977,197 @@ function createViewOpacityFunction(view) {
         if (isNumber(opacityDef)) {
             return (parentOpacity) => parentOpacity * opacityDef;
         } else if (isDynamicOpacity(opacityDef)) {
-            /** @type {(channel: import("../spec/channel.js").ChannelWithScale) => any} */
-            const getScale = (channel) => {
-                const scale = view.getScaleResolution(channel)?.getScale();
+            /**
+             * @param {import("../spec/channel.js").PrimaryPositionalChannel} channel
+             */
+            const getScaleContext = (channel) => {
+                const scaleResolution = view.getScaleResolution(channel);
+                const scale = scaleResolution?.getScale();
                 // Only works on linear scales
                 if (["linear", "index", "locus"].includes(scale?.type)) {
-                    return scale;
+                    return { scale, scaleResolution };
                 }
             };
 
-            const scale = opacityDef.channel
-                ? getScale(opacityDef.channel)
-                : (getScale("x") ?? getScale("y"));
+            const opacityValues = asFiniteNumberArray(
+                opacityDef.values,
+                "opacity.values",
+                view
+            );
 
-            if (!scale) {
+            if (!isArray(opacityDef.unitsPerPixel)) {
                 throw new ViewError(
-                    "Cannot find a resolved quantitative scale for dynamic opacity!",
+                    '"opacity.unitsPerPixel" must be an array.',
                     view
                 );
             }
 
-            const interpolate = scaleLog()
-                .domain(opacityDef.unitsPerPixel)
-                .range(opacityDef.values)
-                .clamp(true);
+            /** @type {function(number): number} */
+            let interpolate = () => 1;
 
-            return (parentOpacity) => {
-                const rangeSpan = 1000; //TODO: span(scale.range());
-                const unitsPerPixel = span(scale.domain()) / rangeSpan;
+            /** @type {(() => number)[]} */
+            let stopReaders = [];
 
-                return interpolate(unitsPerPixel) * parentOpacity;
+            const updateInterpolator = () => {
+                const unitsPerPixel = asFiniteNumberArray(
+                    stopReaders.map((readStop) => readStop()),
+                    "opacity.unitsPerPixel",
+                    view
+                );
+
+                validateDynamicOpacityStops(unitsPerPixel, opacityValues, view);
+
+                const scale = scaleLog()
+                    .domain(unitsPerPixel)
+                    .range(opacityValues)
+                    .clamp(true);
+
+                interpolate = (value) => scale(value);
+            };
+
+            stopReaders = opacityDef.unitsPerPixel.map((stop) => {
+                if (isExprRef(stop)) {
+                    const fn = view.paramRuntime.watchExpression(
+                        stop.expr,
+                        () => {
+                            updateInterpolator();
+                            view.context.animator.requestRender();
+                        }
+                    );
+                    return () => fn(null);
+                } else {
+                    return () => stop;
+                }
+            });
+
+            updateInterpolator();
+
+            /**
+             * @param {{ scale: any, scaleResolution: import("../scales/scaleResolution.js").default }} scaleContext
+             */
+            const getUnitsPerPixel = (scaleContext) => {
+                const axisLength = scaleContext.scaleResolution.getAxisLength();
+                const rangeSpan = axisLength || 1000;
+                return span(scaleContext.scale.domain()) / rangeSpan;
+            };
+
+            /** @type {() => number} */
+            let getMetric;
+
+            if (opacityDef.channel === "auto") {
+                const xScale = getScaleContext("x");
+                const yScale = getScaleContext("y");
+
+                if (xScale && yScale) {
+                    getMetric = () =>
+                        (getUnitsPerPixel(xScale) + getUnitsPerPixel(yScale)) /
+                        2;
+                } else if (xScale) {
+                    getMetric = () => getUnitsPerPixel(xScale);
+                } else if (yScale) {
+                    getMetric = () => getUnitsPerPixel(yScale);
+                } else {
+                    throw new ViewError(
+                        "Cannot find a resolved quantitative x or y scale for dynamic opacity!",
+                        view
+                    );
+                }
+            } else {
+                const scaleContext = opacityDef.channel
+                    ? getScaleContext(opacityDef.channel)
+                    : (getScaleContext("x") ?? getScaleContext("y"));
+
+                if (!scaleContext) {
+                    throw new ViewError(
+                        "Cannot find a resolved quantitative scale for dynamic opacity!",
+                        view
+                    );
+                }
+
+                getMetric = () => getUnitsPerPixel(scaleContext);
+            }
+
+            return (parentOpacity) => {
+                return interpolate(getMetric()) * parentOpacity;
             };
         } else if (isExprRef(opacityDef)) {
-            const fn = view.paramMediator.createExpression(opacityDef.expr);
-            fn.addListener(() => view.context.animator.requestRender());
+            const fn = view.paramRuntime.watchExpression(opacityDef.expr, () =>
+                view.context.animator.requestRender()
+            );
             return (parentOpacity) => fn(null) * parentOpacity;
         }
     }
     return (parentOpacity) => parentOpacity;
 }
 
+/**
+ * @param {number[]} unitsPerPixel
+ * @param {number[]} values
+ * @param {View} view
+ */
+function validateDynamicOpacityStops(unitsPerPixel, values, view) {
+    if (!unitsPerPixel.length) {
+        throw new ViewError(
+            '"opacity.unitsPerPixel" must contain at least one stop.',
+            view
+        );
+    }
+
+    if (unitsPerPixel.length !== values.length) {
+        throw new ViewError(
+            '"opacity.unitsPerPixel" and "opacity.values" must have the same length.',
+            view
+        );
+    }
+
+    unitsPerPixel.forEach((value, index) => {
+        if (value <= 0) {
+            throw new ViewError(
+                "Invalid opacity.unitsPerPixel value at index " +
+                    index +
+                    ". Stop values must be positive.",
+                view
+            );
+        }
+    });
+
+    for (let i = 1; i < unitsPerPixel.length; i++) {
+        if (unitsPerPixel[i - 1] <= unitsPerPixel[i]) {
+            throw new ViewError(
+                '"opacity.unitsPerPixel" must be strictly decreasing.',
+                view
+            );
+        }
+    }
+}
+
+/**
+ * @param {unknown} value
+ * @param {string} label
+ * @param {View} view
+ * @returns {number[]}
+ */
+function asFiniteNumberArray(value, label, view) {
+    if (!isArray(value)) {
+        throw new ViewError('"' + label + '" must evaluate to an array.', view);
+    }
+
+    return value.map((item, index) => {
+        if (!isNumber(item) || !Number.isFinite(item)) {
+            throw new ViewError(
+                "Invalid " +
+                    label +
+                    " value at index " +
+                    index +
+                    ". Expected a finite number.",
+                view
+            );
+        }
+
+        return item;
+    });
+}
+
 /**
  *
  * @param {any} size

package/dist/src/view/viewFactory.d.ts

@@ -16,12 +16,6 @@ export function isLayerSpec(spec: import("../spec/view.js").ViewSpec): spec is i
  * @returns {spec is LayerSpec}
  */
 export function isFacetSpec(spec: import("../spec/view.js").ViewSpec): spec is import("../spec/view.js").LayerSpec;
-/**
- *
- * @param {ViewSpec} spec
- * @returns {spec is import("../spec/view.js").AggregateSamplesSpec}
- */
-export function isAggregateSamplesSpec(spec: import("../spec/view.js").ViewSpec): spec is import("../spec/view.js").AggregateSamplesSpec;
 /**
  *
  * @param {object} spec
@@ -46,12 +40,6 @@ export function isHConcatSpec(spec: import("../spec/view.js").ViewSpec): spec is
  * @returns {spec is ConcatSpec}
  */
 export function isConcatSpec(spec: import("../spec/view.js").ViewSpec): spec is import("../spec/view.js").ConcatSpec;
-/**
- *
- * @param {ViewSpec} spec
- * @returns {spec is SampleSpec}
- */
-export function isSampleSpec(spec: import("../spec/view.js").ViewSpec): spec is import("../spec/sampleView.js").SampleSpec;
 export const VIEW_ROOT_NAME: "viewRoot";
 /**
  * @typedef {object} ViewFactoryOptions

package/dist/src/view/viewFactory.d.ts.map

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