@genome-spy/core 0.73.0 → 0.74.0

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

@@ -3,6 +3,7 @@ import {
     withoutExprRef,
 } from "../../../paramRuntime/paramUtils.js";
 import addBaseUrl from "../../../utils/addBaseUrl.js";
+import { registerBuiltInLazyDataSource } from "./lazyDataSourceRegistry.js";
 import SingleAxisWindowedSource from "./singleAxisWindowedSource.js";
 
 /**
@@ -165,6 +166,16 @@ export default class BigWigSource extends SingleAxisWindowedSource {
     }
 }
 
+/**
+ * @param {import("../../../spec/data.js").LazyDataParams} params
+ * @returns {params is import("../../../spec/data.js").BigWigData}
+ */
+function isBigWigSource(params) {
+    return params?.type == "bigwig";
+}
+
+registerBuiltInLazyDataSource(isBigWigSource, BigWigSource);
+
 /**
  * @param {number[]} domain
  * @param {number} widthInPixels view width in pixels

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":"AAEA;;GAEG;AACH;;;CAuBC;wBA5BuB,kBAAkB"}
+{"version":3,"file":"gff3Source.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/gff3Source.js"],"names":[],"mappings":"AAGA;;GAEG;AACH;;;CAuBC;wBA5BuB,kBAAkB"}

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

@@ -1,3 +1,4 @@
+import { registerBuiltInLazyDataSource } from "./lazyDataSourceRegistry.js";
 import TabixSource from "./tabixSource.js";
 
 /**
@@ -22,8 +23,18 @@ export default class Gff3Source extends TabixSource {
      * @param {string[]} lines
      */
     _parseFeatures(lines) {
-        const features = this.#gff?.parseArraySync(lines);
+        const features = this.#gff?.parseStringSync(lines.join("\n"));
 
         return features;
     }
 }
+
+/**
+ * @param {import("../../../spec/data.js").LazyDataParams} params
+ * @returns {params is import("../../../spec/data.js").Gff3Data}
+ */
+function isGff3Source(params) {
+    return params?.type == "gff3";
+}
+
+registerBuiltInLazyDataSource(isGff3Source, Gff3Source);

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":"AAGA;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,EAwCjD;IA1BG,yDAAgC;IAQhC,iCAiBE;IATM,iDAKE;CAwCjB;qCAhFoC,+BAA+B"}

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

@@ -1,4 +1,5 @@
 import addBaseUrl from "../../../utils/addBaseUrl.js";
+import { registerBuiltInLazyDataSource } from "./lazyDataSourceRegistry.js";
 import SingleAxisWindowedSource from "./singleAxisWindowedSource.js";
 
 export default class IndexedFastaSource extends SingleAxisWindowedSource {
@@ -80,3 +81,13 @@ export default class IndexedFastaSource extends SingleAxisWindowedSource {
         this.publishData([features.filter((f) => f !== undefined)]);
     }
 }
+
+/**
+ * @param {import("../../../spec/data.js").LazyDataParams} params
+ * @returns {params is import("../../../spec/data.js").IndexedFastaData}
+ */
+function isIndexedFastaSource(params) {
+    return params?.type == "indexedFasta";
+}
+
+registerBuiltInLazyDataSource(isIndexedFastaSource, IndexedFastaSource);

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

@@ -0,0 +1,27 @@
+/**
+ * Registers a lazy data source for a custom type.
+ *
+ * @template {import("../../../spec/data.js").LazyDataParams} P
+ * @param {LazySourceEntry<P>["guard"]} guard
+ * @param {LazySourceEntry<P>["Source"]} Source
+ * @returns {() => void}
+ */
+export function registerLazyDataSource<P extends import("../../../spec/data.js").LazyDataParams>(guard: LazySourceEntry<P>["guard"], Source: LazySourceEntry<P>["Source"]): () => void;
+/**
+ * Registers a built-in lazy data source.
+ *
+ * @template {import("../../../spec/data.js").LazyDataParams} P
+ * @param {LazySourceEntry<P>["guard"]} guard
+ * @param {LazySourceEntry<P>["Source"]} Source
+ */
+export function registerBuiltInLazyDataSource<P extends import("../../../spec/data.js").LazyDataParams>(guard: LazySourceEntry<P>["guard"], Source: LazySourceEntry<P>["Source"]): void;
+/**
+ * @param {import("../../../spec/data.js").LazyDataParams} params
+ * @param {import("../../../view/view.js").default} view
+ */
+export function createLazyDataSource(params: import("../../../spec/data.js").LazyDataParams, view: import("../../../view/view.js").default): import("../dataSource.js").default;
+export type LazySourceEntry<P extends import("../../../spec/data.js").LazyDataParams> = {
+    guard: (params: import("../../../spec/data.js").LazyDataParams) => params is P;
+    Source: new (params: any, view: import("../../../view/view.js").default) => import("../dataSource.js").default;
+};
+//# sourceMappingURL=lazyDataSourceRegistry.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"lazyDataSourceRegistry.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/lazyDataSourceRegistry.js"],"names":[],"mappings":"AAcA;;;;;;;GAOG;AACH,uCAL8D,CAAC,SAAlD,OAAQ,uBAAuB,EAAE,cAAe,SAClD,eAAe,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,UAC3B,eAAe,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAC1B,MAAM,IAAI,CAYtB;AAED;;;;;;GAMG;AACH,8CAJ8D,CAAC,SAAlD,OAAQ,uBAAuB,EAAE,cAAe,SAClD,eAAe,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,UAC3B,eAAe,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,QAItC;AAED;;;GAGG;AACH,6CAHW,OAAO,uBAAuB,EAAE,cAAc,QAC9C,OAAO,uBAAuB,EAAE,OAAO,sCAiBjD;4BA/D6D,CAAC,SAAlD,OAAQ,uBAAuB,EAAE,cAAe,IAChD;IACR,KAAK,EAAE,CAAC,MAAM,EAAE,OAAO,uBAAuB,EAAE,cAAc,KAAK,MAAM,IAAI,CAAC,CAAC;IAC/E,MAAM,EAAE,KAAK,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,OAAO,uBAAuB,EAAE,OAAO,KAAK,OAAO,kBAAkB,EAAE,OAAO,CAAA;CAC/G"}

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

@@ -0,0 +1,65 @@
+/**
+ * @template {import("../../../spec/data.js").LazyDataParams} P
+ * @typedef {{
+ *   guard: (params: import("../../../spec/data.js").LazyDataParams) => params is P,
+ *   Source: new (params: any, view: import("../../../view/view.js").default) => import("../dataSource.js").default
+ * }} LazySourceEntry
+ */
+
+/** @type {LazySourceEntry<any>[]} */
+const customLazySources = [];
+
+/** @type {LazySourceEntry<any>[]} */
+const builtinLazySources = [];
+
+/**
+ * Registers a lazy data source for a custom type.
+ *
+ * @template {import("../../../spec/data.js").LazyDataParams} P
+ * @param {LazySourceEntry<P>["guard"]} guard
+ * @param {LazySourceEntry<P>["Source"]} Source
+ * @returns {() => void}
+ */
+export function registerLazyDataSource(guard, Source) {
+    /** @type {LazySourceEntry<any>} */
+    const entry = { guard, Source };
+    customLazySources.push(entry);
+    return () => {
+        const index = customLazySources.indexOf(entry);
+        if (index >= 0) {
+            customLazySources.splice(index, 1);
+        }
+    };
+}
+
+/**
+ * Registers a built-in lazy data source.
+ *
+ * @template {import("../../../spec/data.js").LazyDataParams} P
+ * @param {LazySourceEntry<P>["guard"]} guard
+ * @param {LazySourceEntry<P>["Source"]} Source
+ */
+export function registerBuiltInLazyDataSource(guard, Source) {
+    builtinLazySources.push({ guard, Source });
+}
+
+/**
+ * @param {import("../../../spec/data.js").LazyDataParams} params
+ * @param {import("../../../view/view.js").default} view
+ */
+export function createLazyDataSource(params, view) {
+    for (const entry of customLazySources) {
+        if (entry.guard(params)) {
+            return new entry.Source(/** @type {any} */ (params), view);
+        }
+    }
+    for (const entry of builtinLazySources) {
+        if (entry.guard(params)) {
+            return new entry.Source(/** @type {any} */ (params), view);
+        }
+    }
+
+    throw new Error(
+        "Cannot figure out the data source type: " + JSON.stringify(params)
+    );
+}

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

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

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

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

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

@@ -0,0 +1,8 @@
+import "./axisTickSource.js";
+import "./axisGenomeSource.js";
+import "./indexedFastaSource.js";
+import "./bigWigSource.js";
+import "./bigBedSource.js";
+import "./bamSource.js";
+import "./gff3Source.js";
+import "./vcfSource.js";

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

@@ -1 +1 @@
-{"version":3,"file":"singleAxisLazySource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/singleAxisLazySource.js"],"names":[],"mappings":"AAGA;;GAEG;AAEH;;GAEG;AAEH;;;;;GAKG;AACH,wEAFgB,sBAAsB;IAelC;;;OAGG;IACH,kBAHW,OAAO,uBAAuB,EAAE,OAAO,WACvC,OAAO,0BAA0B,EAAE,wBAAwB,EA+CrE;IA7DD;;;OAGG;IACH,4CAAuC;IAEvC;;;OAGG;IACH,6BAHU,MAAM,EAAE,GAAG,SAAS,CAGZ;IAmBd,2EAA2E;IAC3E,SADW,OAAO,0BAA0B,EAAE,wBAAwB,CAChD;IAEtB,sEAA4D;IA+BhE;;;;OAIG;IACH,oEASC;IAED;;;;;;OAMG;IACH,wBAJW,MAAM,EAAE,iBACR,OAAO,yBAAyB,EAAE,gBAAgB,EAAE,QAK9D;IAED;;;;;OAKG;IACH,gCAGC;IAQD;;;;;;;;OAQG;IACH,8BAHW,OAAO,mBAAmB,EAAE,KAAK,EAAE,EAAE,QAe/C;IAED;;;OAGG;IACH,8BAHW,oBAAoB,GAClB,OAAO,CAenB;CACJ;mCAlKY,OAAO,CAAC,MAAM,CAAC,OAAO,0BAA0B,EAAE,wBAAwB,EAAE,MAAM,EAAE,CAAC,CAAC;qCAItF;IAAC,oBAAoB,EAAE,CAAC,OAAO,EAAE,oBAAoB,KAAK,OAAO,CAAA;CAAC;uBAPxD,kBAAkB"}
+{"version":3,"file":"singleAxisLazySource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/singleAxisLazySource.js"],"names":[],"mappings":"AAEA;;GAEG;AAEH;;GAEG;AAEH;;;;;GAKG;AACH,wEAFgB,sBAAsB;IAelC;;;OAGG;IACH,kBAHW,OAAO,uBAAuB,EAAE,OAAO,WACvC,OAAO,0BAA0B,EAAE,wBAAwB,EA+CrE;IA7DD;;;OAGG;IACH,4CAAuC;IAEvC;;;OAGG;IACH,6BAHU,MAAM,EAAE,GAAG,SAAS,CAGZ;IAmBd,2EAA2E;IAC3E,SADW,OAAO,0BAA0B,EAAE,wBAAwB,CAChD;IAEtB,sEAA4D;IA+BhE;;;;OAIG;IACH,oEASC;IAED;;;;;;OAMG;IACH,wBAJW,MAAM,EAAE,iBACR,OAAO,yBAAyB,EAAE,gBAAgB,EAAE,QAK9D;IAED;;;;;OAKG;IACH,gCAGC;IAQD;;;;;;;;OAQG;IACH,8BAHW,OAAO,mBAAmB,EAAE,KAAK,EAAE,EAAE,QAe/C;IAED;;;OAGG;IACH,8BAHW,oBAAoB,GAClB,OAAO,CAenB;CACJ;mCAlKY,OAAO,CAAC,MAAM,CAAC,OAAO,0BAA0B,EAAE,wBAAwB,EAAE,MAAM,EAAE,CAAC,CAAC;qCAItF;IAAC,oBAAoB,EAAE,CAAC,OAAO,EAAE,oBAAoB,KAAK,OAAO,CAAA;CAAC;uBAPxD,kBAAkB"}

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

@@ -1,4 +1,3 @@
-import UnitView from "../../../view/unitView.js";
 import DataSource from "../dataSource.js";
 
 /**
@@ -53,7 +52,7 @@ export default class SingleAxisLazySource extends DataSource {
             const sentences = [
                 `The lazy data source cannot find a resolved scale for channel "${channel}".`,
             ];
-            if (!(this.view instanceof UnitView)) {
+            if (!isUnitViewLike(this.view)) {
                 sentences.push(
                     `Make sure the view has a "shared" scale resolution as it is not a unit view.`
                 );
@@ -165,3 +164,13 @@ export default class SingleAxisLazySource extends DataSource {
         return min >= loadedMin && max <= loadedMax;
     }
 }
+
+/**
+ * Unit views expose `getMarkType()`, while container and helper views do not.
+ *
+ * @param {import("../../../view/view.js").default} view
+ * @returns {view is import("../../../view/unitView.js").default}
+ */
+function isUnitViewLike(view) {
+    return typeof (/** @type {any} */ (view).getMarkType) == "function";
+}

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

@@ -1 +1 @@
-{"version":3,"file":"vcfSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/vcfSource.js"],"names":[],"mappings":"AAEA;;GAEG;AACH;;;CAgCC;wBArCuB,kBAAkB"}
+{"version":3,"file":"vcfSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/vcfSource.js"],"names":[],"mappings":"AAGA;;GAEG;AACH;;;CAgCC;wBAtCuB,kBAAkB"}

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

@@ -1,4 +1,5 @@
 import TabixSource from "./tabixSource.js";
+import { registerBuiltInLazyDataSource } from "./lazyDataSourceRegistry.js";
 
 /**
  * @extends {TabixSource<import("./vcfTypes.js").ParsedVariant>}
@@ -36,3 +37,13 @@ export default class VcfSource extends TabixSource {
         });
     }
 }
+
+/**
+ * @param {import("../../../spec/data.js").LazyDataParams} params
+ * @returns {params is import("../../../spec/data.js").VcfData}
+ */
+function isVcfSource(params) {
+    return params?.type == "vcf";
+}
+
+registerBuiltInLazyDataSource(isVcfSource, VcfSource);

package/dist/src/data/sources/urlSource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"urlSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/urlSource.js"],"names":[],"mappings":"AA+IA;;;GAGG;AACH,gCAHW,OAAO,CAAC,OAAO,oBAAoB,EAAE,IAAI,CAAC,GACxC,IAAI,IAAI,OAAO,oBAAoB,EAAE,OAAO,CAIxD;AAzID;;;GAGG;AACH;IACI;;;OAGG;IACH,oBAHW,OAAO,oBAAoB,EAAE,OAAO,QACpC,OAAO,oBAAoB,EAAE,OAAO,EAc9C;IATG,6CAMC;IAED,gBAAiC;;CA6GxC;uBA3IsB,iBAAiB"}
+{"version":3,"file":"urlSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/urlSource.js"],"names":[],"mappings":"AAkJA;;;GAGG;AACH,gCAHW,OAAO,CAAC,OAAO,oBAAoB,EAAE,IAAI,CAAC,GACxC,IAAI,IAAI,OAAO,oBAAoB,EAAE,OAAO,CAIxD;AA5ID;;;GAGG;AACH;IACI;;;OAGG;IACH,oBAHW,OAAO,oBAAoB,EAAE,OAAO,QACpC,OAAO,oBAAoB,EAAE,OAAO,EAc9C;IATG,6CAMC;IAED,gBAAiC;;CAgHxC;uBA9IsB,iBAAiB"}

package/dist/src/data/sources/urlSource.js

@@ -101,7 +101,8 @@ export default class UrlSource extends DataSource {
                 return await readResponseBody(result, url, type);
             } catch (e) {
                 throw new Error(
-                    `Could not load data: ${url}. Reason: ${e.message}`
+                    `Could not load data: ${url}. Reason: ${e.message}`,
+                    { cause: e }
                 );
             }
         };
@@ -124,7 +125,9 @@ export default class UrlSource extends DataSource {
                 }
             } catch (e) {
                 console.warn(e);
-                throw new Error(`Cannot parse: ${url}: ${e.message}`);
+                throw new Error(`Cannot parse: ${url}: ${e.message}`, {
+                    cause: e,
+                });
             }
         };
 

package/dist/src/data/transforms/aggregate.d.ts

@@ -16,6 +16,7 @@ export default class AggregateTransform extends Transform {
      * @type {string[]}
      */
     as: string[];
+    #private;
 }
 import Transform from "./transform.js";
 //# sourceMappingURL=aggregate.d.ts.map

package/dist/src/data/transforms/aggregate.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"aggregate.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/aggregate.js"],"names":[],"mappings":"AAOA;IAKI;;;;OAIG;IACH,oBAJW,OAAO,yBAAyB,EAAE,eAAe,EA6C3D;IAvCG,0DAAoB;IAEpB,oBAAoB;IACpB,QADW,GAAG,EAAE,CACA;IAEhB;;OAEG;IACH,KAFU,CAAC,CAAC,GAAG,EAAE,gCAAO,KAAK,MAAM,CAAC,EAAE,CAEzB;IACb;;OAEG;IACH,IAFU,MAAM,EAAE,CAEN;CAiFnB;sBA5GqB,gBAAgB"}
+{"version":3,"file":"aggregate.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/aggregate.js"],"names":[],"mappings":"AAOA;IAKI;;;;OAIG;IACH,oBAJW,OAAO,yBAAyB,EAAE,eAAe,EA6C3D;IAvCG,0DAAoB;IAEpB,oBAAoB;IACpB,QADW,GAAG,EAAE,CACA;IAEhB;;OAEG;IACH,KAFU,CAAC,CAAC,GAAG,EAAE,gCAAO,KAAK,MAAM,CAAC,EAAE,CAEzB;IACb;;OAEG;IACH,IAFU,MAAM,EAAE,CAEN;;CAuGnB;sBAlIqB,gBAAgB"}

package/dist/src/data/transforms/aggregate.js

@@ -64,16 +64,10 @@ export default class AggregateTransform extends Transform {
     }
 
     /**
-     *
-     * @param {import("../flowNode.js").Datum} datum
+     * Propagate the current buffer as one aggregated batch.
      */
-    handle(datum) {
-        this.buffer.push(datum);
-    }
-
-    complete() {
+    #flushBuffer() {
         const params = this.params;
-
         const groupby = params?.groupby;
 
         if (groupby?.length > 0) {
@@ -107,6 +101,34 @@ export default class AggregateTransform extends Transform {
 
             this._propagate(datum);
         }
+    }
+
+    /**
+     *
+     * @param {import("../flowNode.js").Datum} datum
+     */
+    handle(datum) {
+        this.buffer.push(datum);
+    }
+
+    /**
+     * Flush the current batch before downstream nodes switch to a new facet.
+     *
+     * @param {import("../../types/flowBatch.js").FlowBatch} flowBatch
+     */
+    beginBatch(flowBatch) {
+        if (this.buffer.length > 0) {
+            this.#flushBuffer();
+            this.buffer = [];
+        }
+
+        super.beginBatch(flowBatch);
+    }
+
+    complete() {
+        if (this.buffer.length > 0) {
+            this.#flushBuffer();
+        }
 
         super.complete();
     }

package/dist/src/data/transforms/aggregateOps.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"aggregateOps.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/aggregateOps.js"],"names":[],"mappings":";AAEA;;GAEG;AACH,6BAFU,MAAM,CAAC,OAAO,yBAAyB,EAAE,WAAW,EAAE,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE,QAAQ,CAAC,EAAE,CAAC,KAAK,EAAE,GAAG,KAAK,MAAM,KAAK,MAAM,CAAC,CAWxH"}
+{"version":3,"file":"aggregateOps.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/aggregateOps.js"],"names":[],"mappings":";AAWA;;GAEG;AACH,6BAFU,MAAM,CAAC,OAAO,yBAAyB,EAAE,WAAW,EAAE,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE,QAAQ,CAAC,EAAE,CAAC,KAAK,EAAE,GAAG,KAAK,MAAM,KAAK,MAAM,CAAC,CAaxH"}

package/dist/src/data/transforms/aggregateOps.js

@@ -1,4 +1,13 @@
-import { count, max, mean, median, min, sum, variance } from "d3-array";
+import {
+    count,
+    max,
+    mean,
+    median,
+    min,
+    quantile,
+    sum,
+    variance,
+} from "d3-array";
 
 /**
  * @type {Record<import("../../spec/transform.js").AggregateOp, (arr: any[], accessor?: (datum: any) => number) => number>}
@@ -10,7 +19,9 @@ const AGGREGATE_OPS = {
     min,
     max,
     mean,
+    q1: (arr, accessor) => quantile(arr, 0.25, accessor),
     median,
+    q3: (arr, accessor) => quantile(arr, 0.75, accessor),
     variance,
 };
 

package/dist/src/data/transforms/coverage.js

@@ -147,7 +147,7 @@ export default class CoverageTransform extends Transform {
         };
 
         const flushQueue = () => {
-            let edge = 0;
+            let edge;
             while ((edge = ends.peekValue()) !== undefined) {
                 pushSegment(prevEdge, edge, coverage);
                 prevEdge = edge;
@@ -166,7 +166,7 @@ export default class CoverageTransform extends Transform {
         this.handle = (datum) => {
             const start = startAccessor(datum);
 
-            let edge = 0;
+            let edge;
             while ((edge = ends.peekValue()) !== undefined && edge < start) {
                 pushSegment(prevEdge, edge, coverage);
                 prevEdge = edge;

package/dist/src/data/transforms/filter.js

@@ -17,7 +17,7 @@ export default class FilterTransform extends Transform {
     }
 
     initialize() {
-        let expression = "";
+        let expression;
 
         if (isExprFilterParams(this.params)) {
             expression = this.params.expr;

package/dist/src/data/transforms/filterScoredLabels.d.ts

@@ -5,6 +5,12 @@ export default class FilterScoredLabelsTransform extends Transform {
      * @param {import("../../view/view.js").default} view
      */
     constructor(params: import("../../spec/transform.js").FilterScoredLabelsParams, view: import("../../view/view.js").default);
+    /**
+     * The transform emits only labels that fit in the current visible interval,
+     * so downstream x/y values derived from its output must not feed back into
+     * shared-domain resolution.
+     */
+    get domainSensitiveScaleChannels(): ("x" | "y")[];
     params: import("../../spec/transform.js").FilterScoredLabelsParams;
     /** @type {any[]} */
     _data: any[];

package/dist/src/data/transforms/filterScoredLabels.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"filterScoredLabels.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/filterScoredLabels.js"],"names":[],"mappings":"AAOA;IAKI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,wBAAwB,QAC1D,OAAO,oBAAoB,EAAE,OAAO,EAkD9C;IA7CG,mEAAoB;IAEpB,oBAAoB;IACpB,OADW,GAAG,EAAE,CACD;IAEf,mBAAoC;IAMpC,sDAA8C;IAC9C,oDAAgE;IAChE,wDAAuD;IACvD,sDAAmD;IACnD,mDAA6C;IAC7C,mDAA6C;IAC7C,gCAAgC;IAChC,cADW,CAAS,IAAG,EAAH,GAAG,KAAE,GAAG,CAGd;IACd,gBAAuC;IAEvC,uCAAuC;IACvC,iBADW,GAAG,CAAC,GAAG,EAAE,cAAc,CAAC,CACH;IAEhC,8DAAuD;IAIvD,qBAAuE;IA8B3E,4BAsEC;IAKG,sBAAuB;CAU9B;sBAhKqB,gBAAgB;2BAFX,+BAA+B"}
+{"version":3,"file":"filterScoredLabels.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/filterScoredLabels.js"],"names":[],"mappings":"AAOA;IAcI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,wBAAwB,QAC1D,OAAO,oBAAoB,EAAE,OAAO,EAkD9C;IA9DD;;;;OAIG;IACH,kDAEC;IAUG,mEAAoB;IAEpB,oBAAoB;IACpB,OADW,GAAG,EAAE,CACD;IAEf,mBAAoC;IAMpC,sDAA8C;IAC9C,oDAAgE;IAChE,wDAAuD;IACvD,sDAAmD;IACnD,mDAA6C;IAC7C,mDAA6C;IAC7C,gCAAgC;IAChC,cADW,CAAS,IAAG,EAAH,GAAG,KAAE,GAAG,CAGd;IACd,gBAAuC;IAEvC,uCAAuC;IACvC,iBADW,GAAG,CAAC,GAAG,EAAE,cAAc,CAAC,CACH;IAEhC,8DAAuD;IAIvD,qBAAuE;IA8B3E,4BAsEC;IAKG,sBAAuB;CAU9B;sBAzKqB,gBAAgB;2BAFX,+BAA+B"}

package/dist/src/data/transforms/filterScoredLabels.js

@@ -10,6 +10,15 @@ export default class FilterScoredLabelsTransform extends Transform {
         return BEHAVIOR_COLLECTS;
     }
 
+    /**
+     * The transform emits only labels that fit in the current visible interval,
+     * so downstream x/y values derived from its output must not feed back into
+     * shared-domain resolution.
+     */
+    get domainSensitiveScaleChannels() {
+        return [this.channel];
+    }
+
     /**
      *
      * @param {import("../../spec/transform.js").FilterScoredLabelsParams} params

package/dist/src/data/transforms/measureText.d.ts

@@ -14,6 +14,7 @@ export default class MeasureTextTransform extends Transform {
      * @param {any} datum
      */
     handle: (datum: any) => void;
+    font: import("../../fonts/bmFontManager.js").FontEntry;
 }
 import Transform from "./transform.js";
 //# sourceMappingURL=measureText.d.ts.map

package/dist/src/data/transforms/measureText.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"measureText.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/measureText.js"],"names":[],"mappings":"AAOA;;GAEG;AACH;IAKI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,iBAAiB,wBACnD,OAAO,gBAAgB,EAAE,oBAAoB,EA8CvD;IAzCG,4DAAoB;IA4BpB;;;OAGG;IACH,gBAFW,GAAG,UAUb;CAER;sBA7DqB,gBAAgB"}
+{"version":3,"file":"measureText.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/measureText.js"],"names":[],"mappings":"AAKA;;GAEG;AACH;IAKI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,iBAAiB,wBACnD,OAAO,gBAAgB,EAAE,oBAAoB,EA4CvD;IAvCG,4DAAoB;IA0BpB;;;OAGG;IACH,gBAFW,GAAG,UAUb;IAOD,uDAMkC;CAEzC;sBAxEqB,gBAAgB"}

package/dist/src/data/transforms/measureText.js

@@ -1,6 +1,4 @@
 import { BEHAVIOR_MODIFIES } from "../flowNode.js";
-import fontMetadata from "../../fonts/Lato-Regular.json" with { type: "json" };
-import getMetrics from "../../fonts/bmFontMetrics.js";
 import { field } from "../../utils/field.js";
 import Transform from "./transform.js";
 import { isExprRef } from "../../paramRuntime/paramUtils.js";
@@ -23,10 +21,8 @@ export default class MeasureTextTransform extends Transform {
 
         this.params = params;
 
-        const metrics = getMetrics(fontMetadata);
         const accessor = field(params.field);
         const as = params.as;
-        // TODO: Support custom fonts.
 
         let size = 0;
 
@@ -56,11 +52,24 @@ export default class MeasureTextTransform extends Transform {
         this.handle = (datum) => {
             const text = accessor(datum);
             if (text !== undefined) {
-                datum[as] = metrics.measureWidth(text, size);
+                datum[as] = this.font.metrics.measureWidth(text, size);
             } else {
                 datum[as] = 0;
             }
             this._propagate(datum);
         };
     }
+
+    initialize() {
+        const fontManager = this.paramRuntimeProvider.context.fontManager;
+        // Resolve the font during flow initialization so viewDataInit's global
+        // font wait also covers measureText before any rows are propagated.
+        this.font = this.params.font
+            ? fontManager.getFont(
+                  this.params.font,
+                  this.params.fontStyle,
+                  this.params.fontWeight
+              )
+            : fontManager.getDefaultFont();
+    }
 }

package/dist/src/data/transforms/pileup.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"pileup.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/pileup.js"],"names":[],"mappings":"AASA;IAKI;;;OAGG;IACH,oBAFW,OAAO,yBAAyB,EAAE,YAAY,EAMxD;IADG,uDAAoB;CAyG3B;sBAzHqB,gBAAgB"}
+{"version":3,"file":"pileup.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/pileup.js"],"names":[],"mappings":"AAQA;IAKI;;;OAGG;IACH,oBAFW,OAAO,yBAAyB,EAAE,YAAY,EAMxD;IADG,uDAAoB;CAyG3B;sBAzHqB,gBAAgB"}

package/dist/src/data/transforms/pileup.js

@@ -1,4 +1,3 @@
-/* eslint-disable no-unmodified-loop-condition */
 import FlatQueue from "flatqueue";
 import { isNumber } from "vega-util";
 import { field } from "../../utils/field.js";
@@ -68,7 +67,7 @@ export default class PileupTransform extends Transform {
                 const preferredLane = preferredOrder.indexOf(
                     preferenceAccessor(datum)
                 );
-                let lane = -1;
+                let lane;
                 if (preferredLane >= 0 && freeLaneMap[preferredLane] < start) {
                     lane = preferredLane;
                 } else {

package/dist/src/data/transforms/regexFold.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"regexFold.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/regexFold.js"],"names":[],"mappings":"AAIA;;;;GAIG;AACH;IAKI;;OAEG;IACH,oBAFW,OAAO,yBAAyB,EAAE,eAAe,EA6I3D;IAxIG,0DAAoB;IAyHhB,gBALO,GAAG,UAKe;CAgBpC;sBA3JqB,gBAAgB"}
+{"version":3,"file":"regexFold.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/regexFold.js"],"names":[],"mappings":"AAIA;;;;GAIG;AACH;IAKI;;OAEG;IACH,oBAFW,OAAO,yBAAyB,EAAE,eAAe,EA4I3D;IAvIG,0DAAoB;IAwHhB,gBALO,GAAG,UAKe;CAgBpC;sBA1JqB,gBAAgB"}

package/dist/src/data/transforms/regexFold.js

@@ -107,7 +107,6 @@ export default class RegexFoldTransform extends Transform {
                 ...as.map((a, i) => JSON.stringify(a) + `: datum[attrs[${i}]]`),
             ];
 
-            // eslint-disable-next-line no-new-func
             create = /** @type {any} */ (
                 new Function(
                     "datum",

package/dist/src/embedFactory.d.ts

@@ -0,0 +1,13 @@
+/**
+ * @param {new (container: HTMLElement, spec: import("./spec/root.js").RootSpec, options?: import("./types/embedApi.js").EmbedOptions) => import("./genomeSpy.js").default} GenomeSpy
+ * @returns {(el: HTMLElement | string, spec: import("./spec/root.js").RootSpec | string, options?: import("./types/embedApi.js").EmbedOptions) => Promise<import("./types/embedApi.js").EmbedResult>}
+ */
+export function createEmbed(GenomeSpy: new (container: HTMLElement, spec: import("./spec/root.js").RootSpec, options?: import("./types/embedApi.js").EmbedOptions) => import("./genomeSpy.js").default): (el: HTMLElement | string, spec: import("./spec/root.js").RootSpec | string, options?: import("./types/embedApi.js").EmbedOptions) => Promise<import("./types/embedApi.js").EmbedResult>;
+/**
+ * Loads the spec from the given url and sets the baseUrl if it is not
+ * defined in the spec.
+ *
+ * @param {string} url
+ */
+export function loadSpec(url: string): Promise<any>;
+//# sourceMappingURL=embedFactory.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"embedFactory.d.ts","sourceRoot":"","sources":["../../src/embedFactory.js"],"names":[],"mappings":"AAKA;;;GAGG;AACH,uCAHW,KAAK,SAAS,EAAE,WAAW,EAAE,IAAI,EAAE,OAAO,gBAAgB,EAAE,QAAQ,EAAE,OAAO,CAAC,EAAE,OAAO,qBAAqB,EAAE,YAAY,KAAK,OAAO,gBAAgB,EAAE,OAAO,GAC7J,CAAC,EAAE,EAAE,WAAW,GAAG,MAAM,EAAE,IAAI,EAAE,OAAO,gBAAgB,EAAE,QAAQ,GAAG,MAAM,EAAE,OAAO,CAAC,EAAE,OAAO,qBAAqB,EAAE,YAAY,KAAK,OAAO,CAAC,OAAO,qBAAqB,EAAE,WAAW,CAAC,CAmFpM;AAaD;;;;;GAKG;AACH,8BAFW,MAAM,gBAmBhB"}