@genome-spy/core 0.48.2 → 0.50.0

package/dist/src/view/scaleResolution.js

@@ -21,7 +21,6 @@ import mergeObjects from "../utils/mergeObjects.js";
 import createScale, { configureScale } from "../scale/scale.js";
 
 import {
-    getChannelDefWithScale,
     isColorChannel,
     isDiscreteChannel,
     isPositionalChannel,
@@ -32,7 +31,7 @@ import {
     isChromosomalLocus,
     isChromosomalLocusInterval,
 } from "../genome/genome.js";
-import { NominalDomain } from "../utils/domainArray.js";
+import createDomain, { NominalDomain } from "../utils/domainArray.js";
 import { easeCubicInOut } from "d3-ease";
 import { asArray, shallowArrayEquals } from "../utils/arrayUtils.js";
 import eerp from "../utils/eerp.js";
@@ -52,8 +51,12 @@ export const INDEX = "index";
 
 /**
  * @template {ChannelWithScale}[T=ChannelWithScale]
- * @typedef {{view: import("./unitView.js").default, channel: T}} ResolutionMember
  *
+ * @typedef {object} ScaleResolutionMember
+ * @prop {import("./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
  */
 /**
  * Resolution takes care of merging domains and scales from multiple views.
@@ -109,9 +112,9 @@ export default class ScaleResolution {
      */
     constructor(channel) {
         this.channel = channel;
-        /** @type {ResolutionMember[]} The involved views */
+        /** @type {ScaleResolutionMember[]} The involved views */
         this.members = [];
-        /** @type {string} Data type (quantitative, nominal, etc...) */
+        /** @type {import("../spec/channel.js").Type} Data type (quantitative, nominal, etc...) */
         this.type = null;
 
         /** @type {string} An optional unique identifier for the scale */
@@ -162,11 +165,10 @@ export default class ScaleResolution {
      * Add a view to this resolution.
      * N.B. This is expected to be called in depth-first order
      *
-     * @param {UnitView} view
-     * @param {ChannelWithScale} channel
+     * @param {ScaleResolutionMember} newMember
      */
-    pushUnitView(view, channel) {
-        const channelDef = getChannelDefWithScale(view, channel);
+    addMember(newMember) {
+        const { channel, channelDef } = newMember;
         const type = channelDef.type;
         const name = channelDef?.scale?.name;
 
@@ -190,14 +192,14 @@ export default class ScaleResolution {
             // TODO: Use the same merging logic as in: https://github.com/vega/vega-lite/blob/master/src/scale.ts
         }
 
-        this.members.push({ view, channel });
+        this.members.push(newMember);
     }
 
     /**
      * Returns true if the domain has been defined explicitly, i.e. not extracted from the data.
      */
     #isExplicitDomain() {
-        return !!this.getConfiguredDomain();
+        return !!this.#getConfiguredDomain();
     }
 
     #isDomainInitialized() {
@@ -227,10 +229,7 @@ export default class ScaleResolution {
      */
     #getMergedScaleProps() {
         const propArray = this.members
-            .map(
-                (member) =>
-                    getChannelDefWithScale(member.view, member.channel).scale
-            )
+            .map((member) => member.channelDef.scale)
             .filter((props) => props !== undefined);
 
         // TODO: Disabled scale: https://vega.github.io/vega-lite/docs/scale.html#disable
@@ -241,9 +240,10 @@ export default class ScaleResolution {
      * Returns the merged scale properties supplemented with inferred properties
      * and domain.
      *
+     * @param {boolean} [extractDataDomain]
      * @returns {import("../spec/scale.js").Scale}
      */
-    #getScaleProps() {
+    #getScaleProps(extractDataDomain = false) {
         const mergedProps = this.#getMergedScaleProps();
         if (mergedProps === null || mergedProps.type == "null") {
             // No scale (pass-thru)
@@ -260,7 +260,7 @@ export default class ScaleResolution {
             props.type = getDefaultScaleType(this.channel, this.type);
         }
 
-        const domain = this.#getInitialDomain();
+        const domain = this.#getInitialDomain(extractDataDomain);
 
         if (domain && domain.length > 0) {
             props.domain = domain;
@@ -360,13 +360,19 @@ export default class ScaleResolution {
         }
     }
 
-    #getInitialDomain() {
+    /**
+     *
+     * @param {boolean} extractDataDomain
+     */
+    #getInitialDomain(extractDataDomain = false) {
         // TODO: intersect the domain with zoom extent (if it's defined)
         return (
-            this.getConfiguredDomain() ??
+            this.#getConfiguredDomain() ??
             (this.type == LOCUS
                 ? this.getGenome().getExtent()
-                : this.getDataDomain())
+                : extractDataDomain
+                ? this.getDataDomain()
+                : [])
         );
     }
 
@@ -375,12 +381,22 @@ export default class ScaleResolution {
      *
      * @return { DomainArray }
      */
-    getConfiguredDomain() {
-        return this.#reduceDomains((member) =>
-            isSecondaryChannel(member.channel)
-                ? undefined
-                : member.view.getConfiguredDomain(member.channel)
-        );
+    #getConfiguredDomain() {
+        const domains = this.members
+            .map((member) => member.channelDef)
+            .filter((channelDef) => channelDef.scale?.domain)
+            .map((channelDef) =>
+                // TODO: Handle ExprRefs and Param in domain
+                createDomain(
+                    channelDef.type,
+                    // Chrom/pos must be linearized first
+                    this.fromComplexInterval(channelDef.scale.domain)
+                )
+            );
+
+        if (domains.length > 0) {
+            return domains.reduce((acc, curr) => acc.extendAll(curr));
+        }
     }
 
     /**
@@ -389,13 +405,12 @@ export default class ScaleResolution {
      * @return { DomainArray }
      */
     getDataDomain() {
-        // TODO: Optimize: extract domain only once if the views share the data.
-        // In fact, this should be a responsibility of collectors.
-        return this.#reduceDomains((member) =>
-            isSecondaryChannel(member.channel)
-                ? undefined
-                : member.view.extractDataDomain(member.channel)
-        );
+        return this.members
+            .map((member) =>
+                member.dataDomainSource?.(member.channel, this.type)
+            )
+            .filter((domain) => !!domain)
+            .reduce((acc, curr) => acc.extendAll(curr));
     }
 
     /**
@@ -411,7 +426,7 @@ export default class ScaleResolution {
         const domainWasInitialized = this.#isDomainInitialized();
         const previousDomain = scale.domain();
 
-        const props = this.#getScaleProps();
+        const props = this.#getScaleProps(true);
         configureScale({ ...props, range: undefined }, scale);
 
         // Annotate the scale with the new props
@@ -458,6 +473,11 @@ export default class ScaleResolution {
         // Annotate the scale with props
         scale.props = props;
 
+        if ("unknown" in scale) {
+            // Never allow implicit domain construction
+            scale.unknown(null);
+        }
+
         this.#scale = scale;
         this.#configureRange();
 
@@ -630,27 +650,37 @@ export default class ScaleResolution {
 
         // TODO: Intersect the domain with zoom extent
 
-        const animator = this.members[0]?.view.context.animator;
+        const animator = this.#viewContext.animator;
 
         const scale = this.scale;
         const from = /** @type {number[]} */ (scale.domain());
 
         if (duration > 0 && from.length == 2) {
+            // Spans
             const fw = from[1] - from[0];
-            const fc = from[0] + fw / 2;
-
             const tw = to[1] - to[0];
+
+            // Centers
+            const fc = from[0] + fw / 2;
             const tc = to[0] + tw / 2;
 
+            // Constant endpoints. Skip calculation to maintain precision.
+            const ac = from[0] == to[0];
+            const bc = from[1] == to[1];
+
             // TODO: Abort possible previous transition
             await animator.transition({
                 duration,
                 easingFunction: easeCubicInOut,
                 onUpdate: (t) => {
                     const w = eerp(fw, tw, t);
-                    const wt = (fw - w) / (fw - tw);
+                    const wt = fw == tw ? t : (fw - w) / (fw - tw);
                     const c = wt * tc + (1 - wt) * fc;
-                    scale.domain([c - w / 2, c + w / 2]);
+                    const domain = [
+                        ac ? from[0] : c - w / 2,
+                        bc ? from[1] : c + w / 2,
+                    ];
+                    scale.domain(domain);
                     this.#notifyListeners("domain");
                 },
             });
@@ -770,7 +800,7 @@ export default class ScaleResolution {
         }
 
         // TODO: Support multiple assemblies
-        const genome = this.members[0].view.context.genomeStore?.getGenome();
+        const genome = this.#viewContext.genomeStore?.getGenome();
         if (!genome) {
             throw new Error("No genome has been defined!");
         }
@@ -825,34 +855,6 @@ export default class ScaleResolution {
         }
         return /** @type {number[]} */ (interval);
     }
-
-    #getViewPaths() {
-        return this.members.map((v) => v.view.getPathString()).join(", ");
-    }
-
-    /**
-     * Iterate all participanting views and reduce (union) their domains using an accessor.
-     * Accessor may return the an explicitly configured domain or a domain extracted from the data.
-     *
-     * @param {function(ResolutionMember):DomainArray} domainAccessor
-     * @returns {DomainArray}
-     */
-    #reduceDomains(domainAccessor) {
-        const domains = this.members
-            .filter(
-                (member) =>
-                    !member.view
-                        .getLayoutAncestors()
-                        // TODO: Should check until the resolved scale resolution
-                        .some((view) => !view.options.contributesToScaleDomain)
-            )
-            .map(domainAccessor)
-            .filter((domain) => !!domain);
-
-        if (domains.length) {
-            return domains.reduce((acc, curr) => acc.extendAll(curr));
-        }
-    }
 }
 
 /**

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

@@ -0,0 +1,2 @@
+export type Channel = import("../spec/channel.js").Channel;
+//# sourceMappingURL=scaleResolution.test.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"scaleResolution.test.d.ts","sourceRoot":"","sources":["../../../src/view/scaleResolution.test.js"],"names":[],"mappings":"sBAWa,OAAO,oBAAoB,EAAE,OAAO"}

package/dist/src/view/scaleResolution.test.js

@@ -1,3 +1,5 @@
+// @ts-nocheck
+
 import { describe, expect, test } from "vitest";
 import { createAndInitialize } from "./testUtils.js";
 import createDomain, { toRegularArray as r } from "../utils/domainArray.js";

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

@@ -1 +1 @@
-{"version":3,"file":"testUtils.d.ts","sourceRoot":"","sources":["../../../src/view/testUtils.js"],"names":[],"mappings":"AAeA;;;GAGG;AACH,2DAHW,OAAO,kBAAkB,EAAE,kBAAkB,6CAqDvD;AAGS,oEAA8C,QAAQ,2BAA4B,GAAG,EAAE,6BAA6B,OAAO,kBAAkB,EAAE,kBAAkB,cAAe;AAgBhL,iFAA8C,QAAQ,2BAA4B,GAAG,EAAE,kBAAkB,WAAW,YAAY;IAAC,MAAM,EAAE,OAAO,CAAC;IAAC,YAAY,EAAE,OAAO,CAAA;CAAC,cAAe;;;;;uBApFpL,OAAO,iBAAiB,EAAE,QAAQ;;;;;0BAClC,OAAO,yBAAyB,EAAE,OAAO"}
+{"version":3,"file":"testUtils.d.ts","sourceRoot":"","sources":["../../../src/view/testUtils.js"],"names":[],"mappings":"AAiBA;;;GAGG;AACH,2DAHW,OAAO,kBAAkB,EAAE,kBAAkB,6CAmDvD;AAGS,oEAA8C,QAAQ,2BAA4B,GAAG,EAAE,6BAA6B,OAAO,kBAAkB,EAAE,kBAAkB,cAAe;AAgBhL,iFAA8C,QAAQ,2BAA4B,GAAG,EAAE,kBAAkB,WAAW,YAAY;IAAC,MAAM,EAAE,OAAO,CAAC;IAAC,YAAY,EAAE,OAAO,CAAA;CAAC,cAAe;;;;;uBApFpL,OAAO,iBAAiB,EAAE,QAAQ;;;;;0BAClC,OAAO,yBAAyB,EAAE,OAAO"}

package/dist/src/view/testUtils.js

@@ -7,11 +7,13 @@
  */
 
 import { checkForDuplicateScaleNames, initializeData } from "./viewUtils.js";
-import AccessorFactory from "../encoder/accessor.js";
 import DataFlow from "../data/dataFlow.js";
 import { VIEW_ROOT_NAME, ViewFactory } from "./viewFactory.js";
 import GenomeStore from "../genome/genomeStore.js";
 import BmFontManager from "../fonts/bmFontManager.js";
+import { reconfigureScales } from "./scaleResolution.js";
+import UnitView from "./unitView.js";
+import ContainerView from "./containerView.js";
 
 /**
  * @param {import("./viewFactory.js").ViewFactoryOptions} [viewFactoryOptions]
@@ -35,8 +37,6 @@ export function createTestViewContext(viewFactoryOptions = {}) {
 
     // @ts-expect-error
     const c = /** @type {ViewContext} */ ({
-        accessorFactory: new AccessorFactory(),
-
         createView: function (spec, parent, defaultName) {
             throw new Error("Not implemented: createView");
         },
@@ -92,6 +92,18 @@ export async function createAndInitialize(spec, viewClass) {
     const view = await create(spec, viewClass);
 
     checkForDuplicateScaleNames(view);
+
+    if (view instanceof UnitView) {
+        view.mark.initializeEncoders();
+    } else if (view instanceof ContainerView) {
+        view.visit((v) => {
+            if (v instanceof UnitView) {
+                v.mark.initializeEncoders();
+            }
+        });
+    }
+
     await initializeData(view, view.context.dataFlow);
+    reconfigureScales(view);
     return view;
 }

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

@@ -1,11 +1,9 @@
 /**
  *
- * @type {Object.<string, typeof import("../marks/mark.js").default>}
+ * @type {Record<import("../spec/mark.js").MarkType, typeof import("../marks/mark.js").default>}
  * TODO: Find a proper place, make extendible
  */
-export const markTypes: {
-    [x: string]: typeof import("../marks/mark.js").default;
-};
+export const markTypes: Record<import("../spec/mark.js").MarkType, typeof import("../marks/mark.js").default>;
 export default class UnitView extends View {
     /**
      *
@@ -20,13 +18,7 @@ export default class UnitView extends View {
     spec: import("../spec/view.js").UnitSpec;
     /** @type {import("../marks/mark.js").default} */
     mark: import("../marks/mark.js").default;
-    /**
-     * @param {import("./renderingContext/viewRenderingContext.js").default} context
-     * @param {import("./layout/rectangle.js").default} coords
-     * @param {import("../types/rendering.js").RenderingOptions} [options]
-     */
-    render(context: import("./renderingContext/viewRenderingContext.js").default, coords: import("./layout/rectangle.js").default, options?: import("../types/rendering.js").RenderingOptions): void;
-    getMarkType(): import("../spec/mark.js").MarkType;
+    getMarkType(): "link" | "rect" | "text" | "point" | "rule";
     /**
      * Pulls scales and axes up in the view hierarcy according to the resolution rules, using dataParents.
      * TODO: legends
@@ -35,21 +27,16 @@ export default class UnitView extends View {
      */
     resolve(type?: import("../spec/view.js").ResolutionTarget): void;
     /**
+     * Returns an accessor that accesses a field or an evaluated expression,
+     * if there is one.
      *
      * @param {Channel} channel
      */
-    getAccessor(channel: import("../spec/channel.js").Channel): import("../types/encoder.js").Accessor;
+    getDataAccessor(channel: import("../spec/channel.js").Channel): import("../types/encoder.js").Accessor<import("../spec/channel.js").Scalar>;
     /**
      * Returns a collector that is associated with this view.
      */
     getCollector(): import("../data/collector.js").default;
-    /**
-     * Returns the domain of the specified channel of this domain/mark.
-     *
-     * @param {import("../spec/channel.js").ChannelWithScale} channel A primary channel
-     * @returns {DomainArray}
-     */
-    getConfiguredDomain(channel: import("../spec/channel.js").ChannelWithScale): import("../utils/domainArray.js").DomainArray;
     /**
      * Extracts the domain from the data.
      *
@@ -61,9 +48,10 @@ export default class UnitView extends View {
      * (with aggregate and extent).
      *
      * @param {Channel} channel
+     * @param {import("../spec/channel.js").Type} type
      * @returns {DomainArray}
      */
-    extractDataDomain(channel: import("../spec/channel.js").Channel): import("../utils/domainArray.js").DomainArray;
+    extractDataDomain(channel: import("../spec/channel.js").Channel, type: import("../spec/channel.js").Type): import("../utils/domainArray.js").DomainArray;
     getZoomLevel(): number;
     /**
      * @param {string} channel

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

@@ -1 +1 @@
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+{"version":3,"file":"unitView.d.ts","sourceRoot":"","sources":["../../../src/view/unitView.js"],"names":[],"mappings":"AAsBA;;;;GAIG;AACH,wBAHU,OAAO,OAAO,iBAAiB,EAAE,QAAQ,EAAE,cAAc,kBAAkB,EAAE,OAAO,CAAC,CAc7F;AAEF;IAeI;;;;;;;;OAQG;IACH,kBAPW,OAAO,iBAAiB,EAAE,QAAQ,WAClC,OAAO,yBAAyB,EAAE,OAAO,gBACzC,OAAO,oBAAoB,EAAE,OAAO,cACpC,OAAO,WAAW,EAAE,OAAO,QAC3B,MAAM,YACN,OAAO,WAAW,EAAE,WAAW,EAiCzC;IA5BG,yCAAgB;IAIZ,iDAAiD;IACjD,MADW,OAAO,kBAAkB,EAAE,OAAO,CACnB;IAsFlC,2DAIC;IAED;;;;;OAKG;IAEH,iEA+FC;IAED;;;;;OAKG;IACH,4IAEC;IAkBD;;OAEG;IACH,uDAEC;IAED;;;;;;;;;;;;;OAaG;IACH,uEAHW,OAAO,oBAAoB,EAAE,IAAI,iDAqB3C;IAED,uBAQC;IAgBD;;;;OAIG;IACH,8BAJW,MAAM,+DAEJ,OAAO,iBAAiB,EAAE,kBAAkB,CAKxD;;CACJ;iBA/VgB,WAAW"}