@genome-spy/core 0.75.0 → 0.76.0

package/dist/src/config/defaults/markDefaults.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"markDefaults.d.ts","sourceRoot":"","sources":["../../../../src/config/defaults/markDefaults.js"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,4BADW,OAAO,sBAAsB,EAAE,UAAU,CAKlD;AAEF,yDAAyD;AACzD,kCADW,OAAO,sBAAsB,EAAE,WAAW,CAkBnD;AAEF,wDAAwD;AACxD,iCADW,OAAO,sBAAsB,EAAE,UAAU,CAYlD;AAEF,wDAAwD;AACxD,iCADW,OAAO,sBAAsB,EAAE,UAAU,CAWlD;AAEF,wDAAwD;AACxD,iCADW,OAAO,sBAAsB,EAAE,UAAU,CAUlD;AAEF,wDAAwD;AACxD,iCADW,OAAO,sBAAsB,EAAE,UAAU,CAiClD;AAEF,wDAAwD;AACxD,iCADW,OAAO,sBAAsB,EAAE,UAAU,CAmBlD"}
+{"version":3,"file":"markDefaults.d.ts","sourceRoot":"","sources":["../../../../src/config/defaults/markDefaults.js"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,4BADW,OAAO,sBAAsB,EAAE,UAAU,CAMlD;AAEF,yDAAyD;AACzD,kCADW,OAAO,sBAAsB,EAAE,WAAW,CAgBnD;AAEF,wDAAwD;AACxD,iCADW,OAAO,sBAAsB,EAAE,UAAU,CAUlD;AAEF,wDAAwD;AACxD,iCADW,OAAO,sBAAsB,EAAE,UAAU,CASlD;AAEF,wDAAwD;AACxD,iCADW,OAAO,sBAAsB,EAAE,UAAU,CAQlD;AAEF,wDAAwD;AACxD,iCADW,OAAO,sBAAsB,EAAE,UAAU,CA+BlD;AAEF,wDAAwD;AACxD,iCADW,OAAO,sBAAsB,EAAE,UAAU,CAiBlD"}

package/dist/src/config/defaults/markDefaults.js

@@ -3,15 +3,14 @@ export const MARK_DEFAULTS = {
     xOffset: 0,
     yOffset: 0,
     minBufferSize: 0,
+    opacity: 1.0,
 };
 
 /** @type {import("../../spec/config.js").PointConfig} */
 export const POINT_MARK_DEFAULTS = {
     x: 0.5,
     y: 0.5,
-    color: "#4c78a8",
     filled: true,
-    opacity: 1.0,
     size: 100.0,
     semanticScore: 0.0,
     shape: "circle",
@@ -30,8 +29,6 @@ export const RECT_MARK_DEFAULTS = {
     x2: undefined,
     y2: undefined,
     filled: true,
-    color: "#4c78a8",
-    opacity: 1.0,
     strokeWidth: 3,
     cornerRadius: 0.0,
     minWidth: 0.5,
@@ -44,8 +41,6 @@ export const RULE_MARK_DEFAULTS = {
     x2: undefined,
     y2: undefined,
     size: 1,
-    color: "black",
-    opacity: 1.0,
     minLength: 0.0,
     strokeDash: null,
     strokeDashOffset: 0,
@@ -54,8 +49,6 @@ export const RULE_MARK_DEFAULTS = {
 
 /** @type {import("../../spec/config.js").TickConfig} */
 export const TICK_MARK_DEFAULTS = {
-    color: "black",
-    opacity: 1.0,
     minLength: 0.0,
     strokeDash: null,
     strokeDashOffset: 0,
@@ -72,8 +65,6 @@ export const TEXT_MARK_DEFAULTS = {
     y2: undefined,
     text: "",
     size: 11.0,
-    color: "black",
-    opacity: 1.0,
     font: undefined,
     fontStyle: undefined,
     fontWeight: undefined,
@@ -106,8 +97,6 @@ export const LINK_MARK_DEFAULTS = {
     y: 0.0,
     y2: undefined,
     size: 1.0,
-    color: "black",
-    opacity: 1.0,
     segments: 101,
     arcHeightFactor: 1.0,
     minArcHeight: 1.5,

package/dist/src/config/defaults/scaleDefaults.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"scaleDefaults.d.ts","sourceRoot":"","sources":["../../../../src/config/defaults/scaleDefaults.js"],"names":[],"mappings":"AAAA,yDAAyD;AACzD,6BADW,OAAO,sBAAsB,EAAE,WAAW,CAUnD;AAEF,yDAAyD;AACzD,6BADW,OAAO,sBAAsB,EAAE,WAAW,CAKnD"}
+{"version":3,"file":"scaleDefaults.d.ts","sourceRoot":"","sources":["../../../../src/config/defaults/scaleDefaults.js"],"names":[],"mappings":"AAAA,yDAAyD;AACzD,6BADW,OAAO,sBAAsB,EAAE,WAAW,CAUnD;AAEF,yDAAyD;AACzD,6BADW,OAAO,sBAAsB,EAAE,WAAW,CAMnD"}

package/dist/src/config/defaults/scaleDefaults.js

@@ -15,4 +15,5 @@ export const RANGE_DEFAULTS = {
     shape: ["circle", "square", "triangle-up", "cross", "diamond"],
     size: [0, 400],
     angle: [0, 360],
+    heatmap: "yellowgreenblue",
 };

package/dist/src/config/markConfig.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"markConfig.d.ts","sourceRoot":"","sources":["../../../src/config/markConfig.js"],"names":[],"mappings":"AAGA;;;;;GAKG;AACH,kDALW,OAAO,mBAAmB,EAAE,eAAe,EAAE,YAC7C,OAAO,iBAAiB,EAAE,QAAQ,SAClC,MAAM,GAAG,MAAM,EAAE,GAAG,SAAS,GAC3B,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,CAmB/B"}
+{"version":3,"file":"markConfig.d.ts","sourceRoot":"","sources":["../../../src/config/markConfig.js"],"names":[],"mappings":"AAGA;;;;;GAKG;AACH,kDALW,OAAO,mBAAmB,EAAE,eAAe,EAAE,YAC7C,OAAO,iBAAiB,EAAE,QAAQ,SAClC,MAAM,GAAG,MAAM,EAAE,GAAG,SAAS,GAC3B,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,CA2B/B"}

package/dist/src/config/markConfig.js

@@ -12,16 +12,24 @@ export function getConfiguredMarkDefaults(scopes, markType, style) {
     // part of style resolution, and explicit mark.style entries augment it.
     const styles = [markType, ...normalizeStyle(style)];
 
-    return mergeConfigScopes(
-        scopes.flatMap((scope) => [
-            /** @type {Record<string, any> | undefined} */ (scope.mark),
-            /** @type {Record<string, any> | undefined} */ (scope[markType]),
-            ...styles.map(
+    const genericBuckets = scopes.map(
+        (scope) => /** @type {Record<string, any> | undefined} */ (scope.mark)
+    );
+    const markTypeBuckets = scopes.map(
+        (scope) =>
+            /** @type {Record<string, any> | undefined} */ (scope[markType])
+    );
+
+    return mergeConfigScopes([
+        ...genericBuckets,
+        ...markTypeBuckets,
+        ...scopes.flatMap((scope) =>
+            styles.map(
                 (styleName) =>
                     /** @type {Record<string, any> | undefined} */ (
                         scope.style?.[styleName]
                     )
-            ),
-        ])
-    );
+            )
+        ),
+    ]);
 }

package/dist/src/config/themes.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"themes.d.ts","sourceRoot":"","sources":["../../../src/config/themes.js"],"names":[],"mappings":"AA+QA;;;GAGG;AACH,gDAHW,OAAO,mBAAmB,EAAE,gBAAgB,GAC1C,MAAM,GAAG,SAAS,CAI9B;AAED;;;GAGG;AACH,iDAHW,OAAO,mBAAmB,EAAE,gBAAgB,GAAG,OAAO,mBAAmB,EAAE,gBAAgB,EAAE,GAAG,SAAS,GACvG,OAAO,mBAAmB,EAAE,eAAe,GAAG,SAAS,CAWnE;AA1BD;;GAEG;AACH,iCAFU,OAAO,mBAAmB,EAAE,gBAAgB,CAER"}
+{"version":3,"file":"themes.d.ts","sourceRoot":"","sources":["../../../src/config/themes.js"],"names":[],"mappings":"AA4RA;;;GAGG;AACH,gDAHW,OAAO,mBAAmB,EAAE,gBAAgB,GAC1C,MAAM,GAAG,SAAS,CAI9B;AAED;;;GAGG;AACH,iDAHW,OAAO,mBAAmB,EAAE,gBAAgB,GAAG,OAAO,mBAAmB,EAAE,gBAAgB,EAAE,GAAG,SAAS,GACvG,OAAO,mBAAmB,EAAE,eAAe,GAAG,SAAS,CAWnE;AA1BD;;GAEG;AACH,iCAFU,OAAO,mBAAmB,EAAE,gBAAgB,CAER"}

package/dist/src/config/themes.js

@@ -39,7 +39,7 @@ const VEGALITE_THEME = {
         quantitativeColorScheme: "blues",
     },
     range: {
-        heatmap: "viridis",
+        heatmap: "yellowgreenblue",
         ramp: "blues",
         diverging: "blueorange",
     },
@@ -59,7 +59,20 @@ const VEGALITE_THEME = {
  * @type {Record<import("../spec/config.js").BuiltInThemeName, import("../spec/config.js").GenomeSpyConfig & { background?: string}>}
  */
 const BUILT_IN_THEME_DEFINITIONS = {
-    genomespy: {},
+    genomespy: {
+        mark: {
+            color: "#4c78a8",
+        },
+        rule: {
+            color: "black",
+        },
+        text: {
+            color: "black",
+        },
+        link: {
+            color: "black",
+        },
+    },
     vegalite: VEGALITE_THEME,
     quartz: mergeConfigScopes([
         VEGALITE_THEME,

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

@@ -1,8 +1,8 @@
-import "./axisTickSource.js";
-import "./axisGenomeSource.js";
+import "./registerCoreLazySources.js";
 import "./indexedFastaSource.js";
 import "./bigWigSource.js";
 import "./bigBedSource.js";
 import "./bamSource.js";
+import "./tabixTsvSource.js";
 import "./gff3Source.js";
 import "./vcfSource.js";

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

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=registerCoreLazySources.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"registerCoreLazySources.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/registerCoreLazySources.js"],"names":[],"mappings":""}

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

@@ -0,0 +1,2 @@
+import "./axisTickSource.js";
+import "./axisGenomeSource.js";

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

@@ -14,6 +14,13 @@ export default class TabixSource<T> extends SingleAxisWindowedSource {
      * @protected
      */
     protected _handleHeader(header: string): Promise<void>;
+    /**
+     * Read a prefix of the Tabix file and decode it as text.
+     *
+     * @returns {Promise<string>}
+     * @protected
+     */
+    protected _readFilePrefix(): Promise<string>;
     /**
      * @abstract
      * @protected

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

@@ -1 +1 @@
-{"version":3,"file":"tabixSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/tabixSource.js"],"names":[],"mappings":"AAOA;;;GAGG;AACH,iCAHa,CAAC;IAOV;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,SAAS,QACzC,OAAO,uBAAuB,EAAE,OAAO,EAyCjD;IAzBG,kDAgBC;IA0FL;;;OAGG;IACH,gCAHW,MAAM,iBAKhB;IAED;;;;;OAKG;IACH,gCAHW,MAAM,EAAE,GACN,CAAC,EAAE,CAKf;;CACJ;qCAxJoC,+BAA+B"}
+{"version":3,"file":"tabixSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/tabixSource.js"],"names":[],"mappings":"AAQA;;;GAGG;AACH,iCAHa,CAAC;IAOV;;;OAGG;IACH,oBAHW,OAAO,uBAAuB,EAAE,SAAS,QACzC,OAAO,uBAAuB,EAAE,OAAO,EAyCjD;IAzBG,kDAgBC;IA0FL;;;OAGG;IACH,gCAHW,MAAM,iBAKhB;IAED;;;;;OAKG;IACH,6BAHa,OAAO,CAAC,MAAM,CAAC,CAY3B;IAED;;;;;OAKG;IACH,gCAHW,MAAM,EAAE,GACN,CAAC,EAAE,CAKf;;CACJ;qCAzKoC,+BAA+B"}

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

@@ -1,3 +1,4 @@
+import { unzip } from "@gmod/bgzf-filehandle";
 import {
     activateExprRefProps,
     withoutExprRef,
@@ -145,6 +146,23 @@ export default class TabixSource extends SingleAxisWindowedSource {
         //
     }
 
+    /**
+     * Read a prefix of the Tabix file and decode it as text.
+     *
+     * @returns {Promise<string>}
+     * @protected
+     */
+    async _readFilePrefix() {
+        const { maxBlockSize } = await this.#tbiIndex.getMetadata();
+        const tbiIndex = /** @type {any} */ (this.#tbiIndex);
+        const compressedPrefix = await tbiIndex.filehandle.read(
+            maxBlockSize,
+            0
+        );
+        const bytes = await unzip(compressedPrefix);
+        return new TextDecoder("utf-8").decode(bytes);
+    }
+
     /**
      * @abstract
      * @protected

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

@@ -0,0 +1,37 @@
+/**
+ * Extract a TSV header from a tabix file header.
+ *
+ * Tabix headers commonly end with a commented column line such as
+ * `#chrom\tstart\tend\tvalue`.
+ *
+ * @param {string} header
+ * @returns {string[] | undefined}
+ */
+export function extractTabixTsvColumns(header: string): string[] | undefined;
+/**
+ * Extract a TSV header from the first line of a plain tabix file prefix.
+ *
+ * This is used when the file does not have a commented header line, but the
+ * first physical line still contains column names.
+ *
+ * @param {string} text
+ * @returns {string[] | undefined}
+ */
+export function extractTabixTsvColumnsFromFirstLine(text: string): string[] | undefined;
+/**
+ * Parse tabix TSV records into plain objects.
+ *
+ * @param {string[]} lines
+ * @param {string[]} columns
+ * @param {import("../../../spec/data.js").Parse | null | undefined} [parse]
+ */
+export function parseTabixTsvLines(lines: string[], columns: string[], parse?: import("../../../spec/data.js").Parse | null | undefined): Record<string, any>[];
+/**
+ * @extends {TabixSource<Record<string, any>>}
+ */
+export default class TabixTsvSource extends TabixSource<Record<string, any>> {
+    constructor(params: import("../../../spec/data.js").TabixData, view: import("../../../view/view.js").default);
+    #private;
+}
+import TabixSource from "./tabixSource.js";
+//# sourceMappingURL=tabixTsvSource.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"tabixTsvSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/tabixTsvSource.js"],"names":[],"mappings":"AAMA;;;;;;;;GAQG;AACH,+CAHW,MAAM,GACJ,MAAM,EAAE,GAAG,SAAS,CAsBhC;AAED;;;;;;;;GAQG;AACH,0DAHW,MAAM,GACJ,MAAM,EAAE,GAAG,SAAS,CAkBhC;AAED;;;;;;GAMG;AACH,0CAJW,MAAM,EAAE,WACR,MAAM,EAAE,UACR,OAAO,uBAAuB,EAAE,KAAK,GAAG,IAAI,GAAG,SAAS,yBAgClE;AAED;;GAEG;AACH;;;CA8CC;wBApJuB,kBAAkB"}

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

@@ -0,0 +1,163 @@
+import { read } from "vega-loader";
+import { withoutExprRef } from "../../../paramRuntime/paramUtils.js";
+import { toVegaLoaderFormat } from "../dataUtils.js";
+import { registerBuiltInLazyDataSource } from "./lazyDataSourceRegistry.js";
+import TabixSource from "./tabixSource.js";
+
+/**
+ * Extract a TSV header from a tabix file header.
+ *
+ * Tabix headers commonly end with a commented column line such as
+ * `#chrom\tstart\tend\tvalue`.
+ *
+ * @param {string} header
+ * @returns {string[] | undefined}
+ */
+export function extractTabixTsvColumns(header) {
+    const lines = header.split(/\r?\n/);
+
+    for (let i = lines.length - 1; i >= 0; i--) {
+        const line = lines[i].trimEnd().replace(/\r$/, "");
+
+        if (!line || line.startsWith("##")) {
+            continue;
+        }
+
+        if (!line.startsWith("#")) {
+            continue;
+        }
+
+        const columns = line.slice(1).split("\t");
+
+        if (columns.length > 1) {
+            return columns;
+        }
+    }
+}
+
+/**
+ * Extract a TSV header from the first line of a plain tabix file prefix.
+ *
+ * This is used when the file does not have a commented header line, but the
+ * first physical line still contains column names.
+ *
+ * @param {string} text
+ * @returns {string[] | undefined}
+ */
+export function extractTabixTsvColumnsFromFirstLine(text) {
+    const lines = text.split(/\r?\n/);
+
+    const firstLine = lines.find((line) => {
+        const trimmed = line.trimStart();
+        return trimmed !== "" && !trimmed.startsWith("#");
+    });
+
+    if (!firstLine) {
+        return;
+    }
+
+    const columns = firstLine.trimEnd().replace(/\r$/, "").split("\t");
+    if (columns.length > 1) {
+        return columns;
+    }
+}
+
+/**
+ * Parse tabix TSV records into plain objects.
+ *
+ * @param {string[]} lines
+ * @param {string[]} columns
+ * @param {import("../../../spec/data.js").Parse | null | undefined} [parse]
+ */
+export function parseTabixTsvLines(lines, columns, parse) {
+    if (lines.length == 0) {
+        return [];
+    }
+
+    /** @type {any} */
+    const format = {
+        type: "tsv",
+        columns,
+        parse: parse ?? "auto",
+    };
+
+    /** @type {Record<string, any>[]} */
+    const data = read(lines.join("\n"), toVegaLoaderFormat(format));
+
+    const chromField = columns[0];
+    /** @type {unknown} */
+    let prev = null;
+    let stringChrom = "";
+
+    for (const datum of data) {
+        const value = datum[chromField];
+        if (value != prev) {
+            prev = value;
+            stringChrom = String(value);
+        }
+        datum[chromField] = stringChrom;
+    }
+
+    return data;
+}
+
+/**
+ * @extends {TabixSource<Record<string, any>>}
+ */
+export default class TabixTsvSource extends TabixSource {
+    /** @type {string[] | undefined} */
+    #columns;
+
+    get label() {
+        return "tabixSource";
+    }
+
+    /**
+     * @param {string} header
+     */
+    async _handleHeader(header) {
+        const params =
+            /** @type {import("../../../spec/data.js").TabixTsvData} */ (
+                this.params
+            );
+        const columns = withoutExprRef(params.columns);
+        this.#columns = columns ?? extractTabixTsvColumns(header);
+
+        if (!this.#columns?.length) {
+            this.#columns = extractTabixTsvColumnsFromFirstLine(
+                await this._readFilePrefix()
+            );
+        }
+
+        if (!this.#columns?.length) {
+            throw new Error(
+                "No columns available for Tabix TSV source. Provide data.lazy.columns or a tabix header line such as #chrom\\tstart\\tend, or a plain first row such as chrom\\tstart\\tend."
+            );
+        }
+    }
+
+    /**
+     * @param {string[]} lines
+     */
+    _parseFeatures(lines) {
+        const params =
+            /** @type {import("../../../spec/data.js").TabixTsvData} */ (
+                this.params
+            );
+        return parseTabixTsvLines(
+            lines,
+            this.#columns ?? [],
+            withoutExprRef(params.parse)
+        );
+    }
+}
+
+/**
+ * @param {import("../../../spec/data.js").LazyDataParams} params
+ * @returns {params is import("../../../spec/data.js").TabixTsvData}
+ */
+function isTabixTsvSource(params) {
+    return params?.type == "tabix";
+}
+
+registerBuiltInLazyDataSource(isTabixTsvSource, TabixTsvSource);

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

@@ -1 +1 @@
-{"version":3,"file":"genomeSpyBase.d.ts","sourceRoot":"","sources":["../../src/genomeSpyBase.js"],"names":[],"mappings":"AA8CA;;;GAGG;AAEH;IAoBI;;;;;OAKG;IAEH;;;;;OAKG;IACH,uBAJW,WAAW,qDAEX,OAAO,qBAAqB,EAAE,YAAY,EA0CpD;IAvCG,uBAA0B;IAC1B,oDAAsB;IAItB,sCAAsC;IACtC,wCAAgB;IAEhB,yBAAoC;IAEpC,4CAA4C;IAC5C,oBADW,CAAC,CAAS,IAAM,EAAN,MAAM,KAAE,MAAM,EAAE,CAAC,EAAE,CACZ;IAE5B,mBAAoD;IAEpD,0BAA0B;IAC1B,aADW,WAAW,CACM;IAE5B;;;;;OAKG;IACH,yBAFU,CAAC,IAAI,qEAAM,KAAK,OAAO,CAE8B;IAE/D,oFAAoF;IACpF,iBADW,MAAM,CAAC,MAAM,EAAE,OAAO,6BAA6B,EAAE,cAAc,CAAC,CAK9E;IAED,mBAAmB;IACnB,8EAAyB;IAIzB,YAAkC;IAatC;;;OAGG;IACH,oCAFW,CAAC,IAAI,EAAE,MAAM,KAAK,GAAG,EAAE,QAIjC;IAED;;OAEG;IACH,+BAFW,MAAM,YAShB;IAED;;;;OAIG;IACH,sBAHW,MAAM,QACN,GAAG,EAAE,QAYf;IAED;;;OAGG;IACH,uBAHW,MAAM,YACN,CAAC,KAAK,EAAE,GAAG,KAAK,IAAI,QAI9B;IAED;;;OAGG;IACH,0BAHW,MAAM,YACN,CAAC,KAAK,EAAE,GAAG,KAAK,IAAI,QAI9B;IAED;;;;;OAKG;IACH,gBAHW,kBAAkB,YAClB,GAAG,QAMb;IAgEG,iDAAsB;IAQ1B;;OAEG;IACH,gBAqBC;IAyND;;;OAGG;IACH,UAFa,OAAO,CAAC,OAAO,CAAC,CAyC5B;IAED,2CAiBC;IAED;;;;;OAKG;IACH,8BAFW,WAAW,iBAerB;IAED;;;;;;;OAOG;IACH,cAFa,CAAC,SAFH,CAAC,cACD,CAAS,IAAC,EAAD,CAAC,KAAE,OAAO,CAAC,MAAM,GAAG,WAAW,GAAG,OAAO,KAAK,EAAE,cAAc,CAAC,QAKlF;IAED;;;;;;;;OAQG;IACH,4BANW,MAAM,kBACN,MAAM,qBACN,MAAM,eACN,MAAM,UAuBhB;IAED;;;MAEC;IAED;eACwB,MAAM,GAAG,SAAS;gBAAU,MAAM,GAAG,SAAS;MAcrE;IAED,sBAGC;IAED,kBAEC;IAED,iCAEC;IAED,oEAYC;IAED,uFAWC;;CACJ;;;;iCA5oBY,eAAe,GAAG,QAAQ,GAAG,gBAAgB,GAAG,kBAAkB;4BAtBnC,uBAAuB;qBAP9C,qBAAqB;wBAElB,yBAAyB;qBAL5B,oBAAoB"}
+{"version":3,"file":"genomeSpyBase.d.ts","sourceRoot":"","sources":["../../src/genomeSpyBase.js"],"names":[],"mappings":"AA8CA;;;GAGG;AAEH;IAoBI;;;;;OAKG;IAEH;;;;;OAKG;IACH,uBAJW,WAAW,qDAEX,OAAO,qBAAqB,EAAE,YAAY,EA0CpD;IAvCG,uBAA0B;IAC1B,oDAAsB;IAItB,sCAAsC;IACtC,wCAAgB;IAEhB,yBAAoC;IAEpC,4CAA4C;IAC5C,oBADW,CAAC,CAAS,IAAM,EAAN,MAAM,KAAE,MAAM,EAAE,CAAC,EAAE,CACZ;IAE5B,mBAAoD;IAEpD,0BAA0B;IAC1B,aADW,WAAW,CACM;IAE5B;;;;;OAKG;IACH,yBAFU,CAAC,IAAI,qEAAM,KAAK,OAAO,CAE8B;IAE/D,oFAAoF;IACpF,iBADW,MAAM,CAAC,MAAM,EAAE,OAAO,6BAA6B,EAAE,cAAc,CAAC,CAK9E;IAED,mBAAmB;IACnB,8EAAyB;IAIzB,YAAkC;IAatC;;;OAGG;IACH,oCAFW,CAAC,IAAI,EAAE,MAAM,KAAK,GAAG,EAAE,QAIjC;IAED;;OAEG;IACH,+BAFW,MAAM,YAShB;IAED;;;;OAIG;IACH,sBAHW,MAAM,QACN,GAAG,EAAE,QAYf;IAED;;;OAGG;IACH,uBAHW,MAAM,YACN,CAAC,KAAK,EAAE,GAAG,KAAK,IAAI,QAI9B;IAED;;;OAGG;IACH,0BAHW,MAAM,YACN,CAAC,KAAK,EAAE,GAAG,KAAK,IAAI,QAI9B;IAED;;;;;OAKG;IACH,gBAHW,kBAAkB,YAClB,GAAG,QAMb;IAmEG,iDAAsB;IAQ1B;;OAEG;IACH,gBAqBC;IAyND;;;OAGG;IACH,UAFa,OAAO,CAAC,OAAO,CAAC,CAyC5B;IAED,2CAiBC;IAED;;;;;OAKG;IACH,8BAFW,WAAW,iBAerB;IAED;;;;;;;OAOG;IACH,cAFa,CAAC,SAFH,CAAC,cACD,CAAS,IAAC,EAAD,CAAC,KAAE,OAAO,CAAC,MAAM,GAAG,WAAW,GAAG,OAAO,KAAK,EAAE,cAAc,CAAC,QAKlF;IAED;;;;;;;;OAQG;IACH,4BANW,MAAM,kBACN,MAAM,qBACN,MAAM,eACN,MAAM,UAuBhB;IAED;;;MAEC;IAED;eACwB,MAAM,GAAG,SAAS;gBAAU,MAAM,GAAG,SAAS;MAcrE;IAED,sBAGC;IAED,kBAEC;IAED,iCAEC;IAED,oEAYC;IAED,uFAWC;;CACJ;;;;iCA/oBY,eAAe,GAAG,QAAQ,GAAG,gBAAgB,GAAG,kBAAkB;4BAtBnC,uBAAuB;qBAP9C,qBAAqB;wBAElB,yBAAyB;qBAL5B,oBAAoB"}

package/dist/src/genomeSpyBase.js

@@ -256,7 +256,10 @@ export default class GenomeSpy {
                 this.viewRoot
                     ? calculateCanvasSize(this.viewRoot)
                     : { width: undefined, height: undefined },
-            { powerPreference: this.options.powerPreference ?? "default" }
+            { powerPreference: this.options.powerPreference ?? "default" },
+            // Physical backing-store changes do not affect layout, but they
+            // clear the canvas and require repainting the existing render batch.
+            () => this.#renderCoordinator?.renderAll()
         );
 
         canvasWrapper.appendChild(loadingIndicatorsElement);

package/dist/src/gl/webGLHelper.d.ts

@@ -40,11 +40,12 @@ export default class WebGLHelper {
      *      A function that returns the content size. If a dimension is undefined,
      *      the canvas fills the container, otherwise the canvas is adjusted to the content size.
      * @param {WebGLContextAttributes} [webglContextAttributes]
+     * @param {() => void} [onCanvasResize]
      */
     constructor(container: HTMLElement, sizeSource?: () => {
         width: number;
         height: number;
-    }, webglContextAttributes?: WebGLContextAttributes);
+    }, webglContextAttributes?: WebGLContextAttributes, onCanvasResize?: () => void);
     /**
      * @type {CanvasSizeHelper}
      */
@@ -58,6 +59,8 @@ export default class WebGLHelper {
         physicalWidth: number;
         physicalHeight: number;
     } | undefined;
+    /** @type {() => void} */
+    _onCanvasResize: () => void;
     /** @type {Map<string, WebGLShader>} */
     _shaderCache: Map<string, WebGLShader>;
     /** @type {WeakMap<import("../types/encoder.js").VegaScale, WebGLTexture>} */
@@ -79,7 +82,7 @@ export default class WebGLHelper {
      * @param {string | string[]} glsl
      */
     compileShader(type: number, glsl: string | string[]): WebGLShader;
-    adjustGl(): void;
+    adjustGl(): boolean;
     finalize(): void;
     /**
      * Returns the canvas size in true display pixels

package/dist/src/gl/webGLHelper.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"webGLHelper.d.ts","sourceRoot":"","sources":["../../../src/gl/webGLHelper.js"],"names":[],"mappings":"AAybA;;;;GAIG;AACH,kCAJW,sBAAsB,gBACtB,WAAW,kBACX,WAAW;;;;;;EA8CrB;AAED;;;;;GAKG;AACH,0CALW,qBAAqB,WACrB,IAAI,CAAC,OAAO,SAAS,EAAE,cAAc,EAAE,KAAK,CAAC,OAC7C,MAAM,EAAE,GAAG,eAAe,YAC1B,YAAY,gBAYtB;AAED;;;;;;GAMG;AACH,qCALW,sBAAsB,mBACtB,OAAO,SAAS,EAAE,eAAe,KACjC,MAAM,KACN,MAAM,2BAWhB;AAED;;;;;GAKG;AACH,yCAJW,sBAAsB,mBACtB,OAAO,SAAS,EAAE,eAAe,SACjC,MAAM,UA4BhB;AA7gBD;IACI;;;;;;;OAOG;IACH,uBANW,WAAW,eACX,MAAM;QAAC,KAAK,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAA;KAAC,2BAGrC,sBAAsB,EAsGhC;IA5FG;;OAEG;IACH,mBAFU,gBAAgB,CAEQ;IAElC;;OAEG;IACH,oBAFU;QAAE,YAAY,EAAE,MAAM,CAAC;QAAC,aAAa,EAAE,MAAM,CAAC;QAAC,aAAa,EAAE,MAAM,CAAC;QAAC,cAAc,EAAE,MAAM,CAAA;KAAE,GAAG,SAAS,CAEjF;IAEnC,uCAAuC;IACvC,cADW,GAAG,CAAC,MAAM,EAAE,WAAW,CAAC,CACN;IAE7B,6EAA6E;IAC7E,eADW,OAAO,CAAC,OAAO,qBAAqB,EAAE,SAAS,EAAE,YAAY,CAAC,CACvC;IAElC;;OAEG;IACH,mBAFU,OAAO,CAAC,OAAO,4BAA4B,EAAE,mBAAmB,EAAE,YAAY,CAAC,CAEnD;IA8CtC,0BAAoB;IACpB,2BAAY;IAGZ,oDAAoD;IACpD,2BADW,OAAO,SAAS,EAAE,iBAAiB,EAAE,CAQ/C;IACD,sDAGC;IAaL,uBAGC;IAED;;;;;OAKG;IACH,oBAHW,MAAM,QACN,MAAM,GAAG,MAAM,EAAE,eA2B3B;IAED,iBAgCC;IAED,iBAGC;IAED;;;;OAIG;IACH,oCAFW;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAA;KAAE;;;MAI3C;IAED;;;;OAIG;IACH,kCAFW;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAA;KAAE,UAI3C;IAED;;;OAGG;IACH;;;MAEC;IAED;;;;;;;;;OASG;IACH,+BAHW,OAAO,8BAA8B,EAAE,OAAO,WAC9C,OAAO,QA2GjB;IAED;;OAEG;IACH,kCAFW,OAAO,4BAA4B,EAAE,mBAAmB,0BAwClE;CACJ;6BAvX4B,uBAAuB"}
+{"version":3,"file":"webGLHelper.d.ts","sourceRoot":"","sources":["../../../src/gl/webGLHelper.js"],"names":[],"mappings":"AA0cA;;;;GAIG;AACH,kCAJW,sBAAsB,gBACtB,WAAW,kBACX,WAAW;;;;;;EA8CrB;AAED;;;;;GAKG;AACH,0CALW,qBAAqB,WACrB,IAAI,CAAC,OAAO,SAAS,EAAE,cAAc,EAAE,KAAK,CAAC,OAC7C,MAAM,EAAE,GAAG,eAAe,YAC1B,YAAY,gBAYtB;AAED;;;;;;GAMG;AACH,qCALW,sBAAsB,mBACtB,OAAO,SAAS,EAAE,eAAe,KACjC,MAAM,KACN,MAAM,2BAWhB;AAED;;;;;GAKG;AACH,yCAJW,sBAAsB,mBACtB,OAAO,SAAS,EAAE,eAAe,SACjC,MAAM,UA4BhB;AA9hBD;IACI;;;;;;;;OAQG;IACH,uBAPW,WAAW,eACX,MAAM;QAAC,KAAK,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAA;KAAC,2BAGrC,sBAAsB,mBACtB,MAAM,IAAI,EAoHpB;IArGG;;OAEG;IACH,mBAFU,gBAAgB,CAEQ;IAElC;;OAEG;IACH,oBAFU;QAAE,YAAY,EAAE,MAAM,CAAC;QAAC,aAAa,EAAE,MAAM,CAAC;QAAC,aAAa,EAAE,MAAM,CAAC;QAAC,cAAc,EAAE,MAAM,CAAA;KAAE,GAAG,SAAS,CAEjF;IAEnC,yBAAyB;IACzB,iBADW,MAAM,IAAI,CAC8B;IAEnD,uCAAuC;IACvC,cADW,GAAG,CAAC,MAAM,EAAE,WAAW,CAAC,CACN;IAE7B,6EAA6E;IAC7E,eADW,OAAO,CAAC,OAAO,qBAAqB,EAAE,SAAS,EAAE,YAAY,CAAC,CACvC;IAElC;;OAEG;IACH,mBAFU,OAAO,CAAC,OAAO,4BAA4B,EAAE,mBAAmB,EAAE,YAAY,CAAC,CAEnD;IA8CtC,0BAAoB;IACpB,2BAAY;IAGZ,oDAAoD;IACpD,2BADW,OAAO,SAAS,EAAE,iBAAiB,EAAE,CAQ/C;IACD,sDAGC;IAmBL,uBAGC;IAED;;;;;OAKG;IACH,oBAHW,MAAM,QACN,MAAM,GAAG,MAAM,EAAE,eA2B3B;IAED,oBAkCC;IAED,iBAGC;IAED;;;;OAIG;IACH,oCAFW;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAA;KAAE;;;MAI3C;IAED;;;;OAIG;IACH,kCAFW;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAA;KAAE,UAI3C;IAED;;;OAGG;IACH;;;MAEC;IAED;;;;;;;;;OASG;IACH,+BAHW,OAAO,8BAA8B,EAAE,OAAO,WAC9C,OAAO,QA2GjB;IAED;;OAEG;IACH,kCAFW,OAAO,4BAA4B,EAAE,mBAAmB,0BAwClE;CACJ;6BAxY4B,uBAAuB"}

package/dist/src/gl/webGLHelper.js

@@ -41,8 +41,14 @@ export default class WebGLHelper {
      *      A function that returns the content size. If a dimension is undefined,
      *      the canvas fills the container, otherwise the canvas is adjusted to the content size.
      * @param {WebGLContextAttributes} [webglContextAttributes]
+     * @param {() => void} [onCanvasResize]
      */
-    constructor(container, sizeSource, webglContextAttributes = {}) {
+    constructor(
+        container,
+        sizeSource,
+        webglContextAttributes = {},
+        onCanvasResize
+    ) {
         const resolvedSizeSource =
             sizeSource ??
             (() => ({
@@ -60,6 +66,9 @@ export default class WebGLHelper {
          */
         this._appliedCanvasSize = undefined;
 
+        /** @type {() => void} */
+        this._onCanvasResize = onCanvasResize ?? (() => {});
+
         /** @type {Map<string, WebGLShader>} */
         this._shaderCache = new Map();
 
@@ -138,7 +147,13 @@ export default class WebGLHelper {
             container,
             canvas,
             resolvedSizeSource,
-            () => this.adjustGl()
+            () => {
+                // Assigning canvas.width/height clears the WebGL drawing buffer.
+                // The observer may fire after layout/render, so repaint immediately.
+                if (this.adjustGl()) {
+                    this._onCanvasResize();
+                }
+            }
         );
 
         this.adjustGl();
@@ -193,7 +208,7 @@ export default class WebGLHelper {
             this._appliedCanvasSize.physicalWidth == physicalSize.width &&
             this._appliedCanvasSize.physicalHeight == physicalSize.height
         ) {
-            return;
+            return false;
         }
 
         this.canvas.style.width = `${logicalSize.width}px`;
@@ -214,6 +229,8 @@ export default class WebGLHelper {
             physicalWidth: physicalSize.width,
             physicalHeight: physicalSize.height,
         };
+
+        return true;
     }
 
     finalize() {