@genome-spy/core 0.77.0 → 0.79.0

package/dist/src/data/sources/lazy/gff3Source.d.ts

@@ -1,9 +1,13 @@
 /**
- * @extends {TabixSource<import("gff-nostream").GFF3Feature>}
+ * @extends {TabixSource<import("gff-nostream").GFF3Feature, import("gff-nostream")>}
  */
-export default class Gff3Source extends TabixSource<import("gff-nostream").GFF3Feature> {
+export default class Gff3Source extends TabixSource<import("gff-nostream").GFF3Feature, typeof import("gff-nostream")> {
     constructor(params: import("../../../spec/data.js").TabixData, view: import("../../../view/view.js").default);
-    #private;
+    /**
+     * @param {string} header
+     * @returns {Promise<import("gff-nostream")>}
+     */
+    _createParser(header: string): Promise<typeof import("gff-nostream")>;
 }
 import TabixSource from "./tabixSource.js";
 //# sourceMappingURL=gff3Source.d.ts.map

package/dist/src/data/sources/lazy/gff3Source.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"gff3Source.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/gff3Source.js"],"names":[],"mappings":"AAGA;;GAEG;AACH;;;CAuBC;wBA5BuB,kBAAkB"}
+{"version":3,"file":"gff3Source.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/gff3Source.js"],"names":[],"mappings":"AAGA;;GAEG;AACH;;IAKI;;;OAGG;IACH,sBAHW,MAAM,GACJ,OAAO,CAAC,6BAAsB,CAAC,CAI3C;CAWJ;wBA3BuB,kBAAkB"}

package/dist/src/data/sources/lazy/gff3Source.js

@@ -2,28 +2,27 @@ import { registerBuiltInLazyDataSource } from "./lazyDataSourceRegistry.js";
 import TabixSource from "./tabixSource.js";
 
 /**
- * @extends {TabixSource<import("gff-nostream").GFF3Feature>}
+ * @extends {TabixSource<import("gff-nostream").GFF3Feature, import("gff-nostream")>}
  */
 export default class Gff3Source extends TabixSource {
-    /** @type {import("gff-nostream")} */
-    #gff;
-
     get label() {
         return "gff3Source";
     }
 
     /**
      * @param {string} header
+     * @returns {Promise<import("gff-nostream")>}
      */
-    async _handleHeader(header) {
-        this.#gff = await import("gff-nostream");
+    async _createParser(header) {
+        return await import("gff-nostream");
     }
 
     /**
      * @param {string[]} lines
+     * @param {import("gff-nostream")} gff
      */
-    _parseFeatures(lines) {
-        const features = this.#gff?.parseStringSync(lines.join("\n"));
+    _parseFeatures(lines, gff) {
+        const features = gff.parseStringSync(lines.join("\n"));
 
         return features;
     }

package/dist/src/data/sources/lazy/indexedFastaSource.d.ts

@@ -5,8 +5,8 @@ export default class IndexedFastaSource extends SingleAxisWindowedSource {
      */
     constructor(params: import("../../../spec/data.js").IndexedFastaData, view: import("../../../view/view.js").default);
     params: import("../../../spec/data.js").IndexedFastaData;
-    initializedPromise: Promise<any>;
     fasta: import("@gmod/indexedfasta").IndexedFasta;
+    #private;
 }
 import SingleAxisWindowedSource from "./singleAxisWindowedSource.js";
 //# sourceMappingURL=indexedFastaSource.d.ts.map

package/dist/src/data/sources/lazy/indexedFastaSource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"indexedFastaSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/indexedFastaSource.js"],"names":[],"mappings":"AAIA;IACI;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,gBAAgB,QAChD,OAAO,uBAAuB,EAAE,OAAO,EAwCjD;IA1BG,yDAAgC;IAQhC,iCAiBE;IATM,iDAKE;CAwCjB;qCAhFoC,+BAA+B"}
+{"version":3,"file":"indexedFastaSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/indexedFastaSource.js"],"names":[],"mappings":"AAIA;IACI;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,gBAAgB,QAChD,OAAO,uBAAuB,EAAE,OAAO,EAuBjD;IATG,yDAAgC;IAmChC,iDAGE;;CAgCT;qCAzFoC,+BAA+B"}

package/dist/src/data/sources/lazy/indexedFastaSource.js

@@ -1,4 +1,4 @@
-import addBaseUrl from "../../../utils/addBaseUrl.js";
+import { normalizeSingleUrlDescriptor } from "../urlDescriptor.js";
 import { registerBuiltInLazyDataSource } from "./lazyDataSourceRegistry.js";
 import SingleAxisWindowedSource from "./singleAxisWindowedSource.js";
 
@@ -27,30 +27,39 @@ export default class IndexedFastaSource extends SingleAxisWindowedSource {
 
         this.setupDebouncing(this.params);
 
-        this.initializedPromise = new Promise((resolve) => {
-            Promise.all([
-                import("@gmod/indexedfasta"),
-                import("generic-filehandle2"),
-            ]).then(([{ IndexedFasta }, { RemoteFile }]) => {
-                const withBase = (/** @type {string} */ uri) =>
-                    new RemoteFile(addBaseUrl(uri, this.view.getBaseUrl()));
-
-                this.fasta = new IndexedFasta({
-                    fasta: withBase(this.params.url),
-                    fai: withBase(
-                        this.params.indexUrl ?? this.params.url + ".fai"
-                    ),
-                });
-
-                resolve();
-            });
-        });
+        this.#initialize();
     }
 
     get label() {
         return "bigWigSource";
     }
 
+    #initialize() {
+        this.initializedPromise = this.#doInitialize();
+        return this.initializedPromise;
+    }
+
+    async #doInitialize() {
+        const descriptor = await normalizeSingleUrlDescriptor(
+            {
+                url: this.params.url,
+                indexUrl: this.params.indexUrl,
+                baseUrl: this.view.getBaseUrl(),
+                paramRuntime: this.paramRuntime,
+            },
+            "IndexedFastaSource"
+        );
+        const [{ IndexedFasta }, { RemoteFile }] = await Promise.all([
+            import("@gmod/indexedfasta"),
+            import("generic-filehandle2"),
+        ]);
+
+        this.fasta = new IndexedFasta({
+            fasta: new RemoteFile(descriptor.url),
+            fai: new RemoteFile(descriptor.indexUrl ?? descriptor.url + ".fai"),
+        });
+    }
+
     /**
      * @param {number[]} interval linearized domain
      */

package/dist/src/data/sources/lazy/legendEntriesSource.d.ts

@@ -0,0 +1,24 @@
+/**
+ * @param {import("../../../view/view.js").default} view
+ * @param {import("../../../spec/channel.js").ChannelWithScale} channel
+ */
+export function findLegendScaleResolution(view: import("../../../view/view.js").default, channel: import("../../../spec/channel.js").ChannelWithScale): import("../../../scales/scaleResolution.js").default;
+export default class LegendEntriesSource extends DataSource {
+    /**
+     * @param {import("../../../spec/data.js").LegendEntriesData} params
+     * @param {import("../../../view/view.js").default} view
+     */
+    constructor(params: import("../../../spec/data.js").LegendEntriesData, view: import("../../../view/view.js").default);
+    params: import("../../../spec/data.js").LegendEntriesData;
+    scaleResolution: import("../../../scales/scaleResolution.js").default;
+    /**
+     * Defers size-entry updates caused by scale range changes. The live scale
+     * still updates marks; only the layout helper fields are republished later.
+     *
+     * @returns {() => void}
+     */
+    suspendRangeUpdates(): () => void;
+    #private;
+}
+import DataSource from "../dataSource.js";
+//# sourceMappingURL=legendEntriesSource.d.ts.map

package/dist/src/data/sources/lazy/legendEntriesSource.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"legendEntriesSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/legendEntriesSource.js"],"names":[],"mappings":"AAiMA;;;GAGG;AACH,gDAHW,OAAO,uBAAuB,EAAE,OAAO,WACvC,OAAO,0BAA0B,EAAE,gBAAgB,wDAW7D;AAhMD;IAUI;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,iBAAiB,QACjD,OAAO,uBAAuB,EAAE,OAAO,EAmCjD;IA9BG,0DAAoB;IACpB,sEAAsE;IA4C1E;;;;;OAKG;IACH,uBAFa,MAAM,IAAI,CAQtB;;CAuGJ;uBAxLsB,kBAAkB"}

package/dist/src/data/sources/lazy/legendEntriesSource.js

@@ -0,0 +1,217 @@
+import { format as numberFormat } from "d3-format";
+
+import { tickFormat, tickValues, validTicks } from "../../../scale/ticks.js";
+import { shallowArrayEquals } from "../../../utils/arrayUtils.js";
+import { createDiscreteLegendEntries } from "../../../view/legend/legendEntries.js";
+import { isChromeView } from "../../../view/viewSelectors.js";
+import Suspension from "../../../utils/suspension.js";
+import DataSource from "../dataSource.js";
+import { registerBuiltInLazyDataSource } from "./lazyDataSourceRegistry.js";
+
+const DEFAULT_QUANTITATIVE_ENTRY_COUNT = 5;
+const LEGEND_SYMBOL_SIZE_FIELD = "_legendSymbolSize";
+const LEGEND_STROKE_WIDTH_FIELD = "_legendStrokeWidth";
+
+export default class LegendEntriesSource extends DataSource {
+    /** @type {import("../../../spec/channel.js").Scalar[] | undefined} */
+    #domain = undefined;
+
+    #rangeUpdatePending = false;
+
+    #rangeUpdateSuspension = new Suspension(() =>
+        this.#flushPendingRangeUpdate()
+    );
+
+    /**
+     * @param {import("../../../spec/data.js").LegendEntriesData} params
+     * @param {import("../../../view/view.js").default} view
+     */
+    constructor(params, view) {
+        super(view);
+
+        this.params = params;
+        this.scaleResolution = findLegendScaleResolution(view, params.channel);
+        if (!this.scaleResolution) {
+            throw new Error(
+                `The legend entries data source cannot find a resolved scale for channel "${params.channel}".`
+            );
+        }
+
+        const publish = () => this.#publishEntries();
+        this.scaleResolution.addEventListener("domain", publish);
+        if (params.channel == "size") {
+            const publishSizeEntries = () => {
+                if (this.#deferRangeUpdateIfSuspended()) {
+                    return;
+                }
+
+                this.#domain = undefined;
+                this.#publishEntries();
+            };
+            this.scaleResolution.addEventListener("range", publishSizeEntries);
+            this.view.registerDisposer(() =>
+                this.scaleResolution.removeEventListener(
+                    "range",
+                    publishSizeEntries
+                )
+            );
+        }
+        this.view.registerDisposer(() =>
+            this.scaleResolution.removeEventListener("domain", publish)
+        );
+    }
+
+    get label() {
+        return "legendEntriesSource";
+    }
+
+    async load() {
+        if (this.#deferRangeUpdateIfSuspended()) {
+            return;
+        }
+
+        this.#domain = undefined;
+        this.#publishEntries();
+    }
+
+    /**
+     * Defers size-entry updates caused by scale range changes. The live scale
+     * still updates marks; only the layout helper fields are republished later.
+     *
+     * @returns {() => void}
+     */
+    suspendRangeUpdates() {
+        if (this.params.channel != "size") {
+            return () => undefined;
+        }
+
+        return this.#rangeUpdateSuspension.suspend();
+    }
+
+    #deferRangeUpdateIfSuspended() {
+        if (
+            this.params.channel != "size" ||
+            !this.#rangeUpdateSuspension.active ||
+            !this.#domain
+        ) {
+            return false;
+        }
+
+        this.#rangeUpdatePending = true;
+        return true;
+    }
+
+    #flushPendingRangeUpdate() {
+        if (this.#rangeUpdatePending) {
+            this.#rangeUpdatePending = false;
+            this.#domain = undefined;
+            this.#publishEntries();
+        }
+    }
+
+    #publishEntries() {
+        const domain = this.scaleResolution.getDomain();
+
+        if (!this.#domain || !shallowArrayEquals(domain, this.#domain)) {
+            this.#domain = domain.slice();
+            this.reset();
+            this.beginBatch({ type: "file" });
+
+            for (const datum of this.#createEntries()) {
+                this._propagate(datum);
+            }
+
+            this.complete();
+        }
+    }
+
+    #createEntries() {
+        const entries =
+            this.params.dataType == "quantitative"
+                ? this.#createQuantitativeEntries()
+                : this.#createDiscreteEntries();
+
+        if (this.params.channel == "size") {
+            const scale = this.scaleResolution.getScale();
+            for (const entry of entries) {
+                if (this.params.sizeMode == "strokeWidth") {
+                    /** @type {Record<string, any>} */ (entry)[
+                        LEGEND_STROKE_WIDTH_FIELD
+                    ] = scale(entry.value);
+                } else {
+                    /** @type {Record<string, any>} */ (entry)[
+                        LEGEND_SYMBOL_SIZE_FIELD
+                    ] = scale(entry.value);
+                }
+            }
+        }
+
+        return entries;
+    }
+
+    #createDiscreteEntries() {
+        const format = this.params.format;
+        const formatter = format
+            ? (
+                  /** @type {import("../../../spec/channel.js").Scalar} */ value
+              ) => numberFormat(format)(Number(value))
+            : undefined;
+
+        const entries = createDiscreteLegendEntries(
+            this.scaleResolution,
+            formatter
+        );
+
+        if (!this.params.values) {
+            return entries;
+        }
+
+        const entriesByValue = new Map(
+            entries.map((entry) => [entry.value, entry])
+        );
+
+        return this.params.values.flatMap((value) =>
+            entriesByValue.has(value) ? [entriesByValue.get(value)] : []
+        );
+    }
+
+    #createQuantitativeEntries() {
+        const scale = this.scaleResolution.getScale();
+        const count = this.params.count ?? DEFAULT_QUANTITATIVE_ENTRY_COUNT;
+        const format = tickFormat(scale, count, this.params.format);
+        const values = this.params.values
+            ? validTicks(scale, this.params.values, count)
+            : tickValues(scale, count);
+
+        return values.map((value, index) => ({
+            value,
+            label: format(value),
+            _legendIndex: index,
+        }));
+    }
+}
+
+/**
+ * @param {import("../../../view/view.js").default} view
+ * @param {import("../../../spec/channel.js").ChannelWithScale} channel
+ */
+export function findLegendScaleResolution(view, channel) {
+    let parent = view.dataParent;
+    while (parent && isChromeView(parent)) {
+        parent = parent.dataParent;
+    }
+
+    return (
+        parent?.getScaleResolution(channel) ?? view.getScaleResolution(channel)
+    );
+}
+
+/**
+ * @param {import("../../../spec/data.js").LazyDataParams} params
+ * @returns {params is import("../../../spec/data.js").LegendEntriesData}
+ */
+function isLegendEntriesSource(params) {
+    return params?.type == "legendEntries";
+}
+
+registerBuiltInLazyDataSource(isLegendEntriesSource, LegendEntriesSource);

package/dist/src/data/sources/lazy/legendGradientSource.d.ts

@@ -0,0 +1,30 @@
+export default class LegendGradientSource extends LegendGradientBaseSource {
+    #private;
+}
+export type NormalizedPositionScale = ((value: number) => number) & {
+    invert: (position: number) => number;
+};
+export type LegendGradientSourceData = import("../../../spec/data.js").LegendGradientData | import("../../../spec/data.js").LegendGradientTicksData;
+export type QuantizeScale = import("../../../types/encoder.js").VegaScale & {
+    range: () => unknown[];
+    invertExtent: (value: unknown) => [unknown, unknown];
+    thresholds: () => unknown[];
+};
+declare class LegendGradientBaseSource extends DataSource {
+    /**
+     * @param {LegendGradientSourceData} params
+     * @param {import("../../../view/view.js").default} view
+     */
+    constructor(params: LegendGradientSourceData, view: import("../../../view/view.js").default);
+    params: LegendGradientSourceData;
+    scaleResolution: import("../../../scales/scaleResolution.js").default;
+    /**
+     * @param {number} start
+     * @param {number} stop
+     */
+    publishData(start: number, stop: number): void;
+    #private;
+}
+import DataSource from "../dataSource.js";
+export {};
+//# sourceMappingURL=legendGradientSource.d.ts.map

package/dist/src/data/sources/lazy/legendGradientSource.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"legendGradientSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/legendGradientSource.js"],"names":[],"mappings":"AAuOA;;CAiFC;sCA7SY,CAAC,CAAC,KAAK,EAAE,MAAM,KAAK,MAAM,CAAC,GAAG;IAAE,MAAM,EAAE,CAAC,QAAQ,EAAE,MAAM,KAAK,MAAM,CAAA;CAAE;uCACtE,OAAO,uBAAuB,EAAE,kBAAkB,GAAG,OAAO,uBAAuB,EAAE,uBAAuB;4BAC5G,OAAO,2BAA2B,EAAE,SAAS,GAAG;IACtD,KAAK,EAAE,MAAM,OAAO,EAAE,CAAC;IACvB,YAAY,EAAE,CAAC,KAAK,EAAE,OAAO,KAAK,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;IACrD,UAAU,EAAE,MAAM,OAAO,EAAE,CAAA;CAC9B;AAwJJ;IAII;;;OAGG;IACH,oBAHW,wBAAwB,QACxB,OAAO,uBAAuB,EAAE,OAAO,EAkBjD;IAbG,iCAAoB;IACpB,sEAAsE;IAuC1E;;;OAGG;IACH,mBAHW,MAAM,QACN,MAAM,QAMhB;;CACJ;uBAjOsB,kBAAkB"}