@genome-spy/core 0.71.0 → 0.73.0

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":"AASA;;;GAGG;AACH,gCAHW,OAAO,CAAC,OAAO,oBAAoB,EAAE,IAAI,CAAC,GACxC,IAAI,IAAI,OAAO,oBAAoB,EAAE,OAAO,CAIxD;AAED;IACI;;;OAGG;IACH,oBAHW,OAAO,oBAAoB,EAAE,OAAO,QACpC,OAAO,oBAAoB,EAAE,OAAO,EAc9C;IATG,6CAMC;IAED,gBAAiC;;CAuGxC;uBAtIsB,iBAAiB"}
+{"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"}

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

@@ -1,5 +1,5 @@
 import { read } from "vega-loader";
-import { getFormat, responseType } from "./dataUtils.js";
+import { getFormat, hasGzipExtension, responseType } from "./dataUtils.js";
 import DataSource from "./dataSource.js";
 import {
     activateExprRefProps,
@@ -7,14 +7,13 @@ import {
 } from "../../paramRuntime/paramUtils.js";
 import { concatUrl } from "../../utils/url.js";
 
+const gzipMimeTypes = new Set(["application/gzip", "application/x-gzip"]);
+const textDecoder = new TextDecoder();
+
 /**
- * @param {Partial<import("../../spec/data.js").Data>} data
- * @returns {data is import("../../spec/data.js").UrlData}
+ * Loads eager data from URLs and transparently decompresses gzip-compatible
+ * payloads before handing them to the registered format reader.
  */
-export function isUrlData(data) {
-    return "url" in data;
-}
-
 export default class UrlSource extends DataSource {
     /**
      * @param {import("../../spec/data.js").UrlData} params
@@ -48,6 +47,7 @@ export default class UrlSource extends DataSource {
      */
     async #loadUrlsFromFile(props) {
         const listUrl = concatUrl(this.baseUrl, props.urlsFromFile);
+        const format = { type: props.type ?? "tsv" };
 
         const result = await fetch(listUrl);
 
@@ -56,10 +56,14 @@ export default class UrlSource extends DataSource {
                 `Cannot load "${listUrl}": ${result.status} ${result.statusText}`
             );
         }
-        const text = await result.text();
+        const content = await readResponseBody(
+            result,
+            listUrl,
+            responseType(format.type)
+        );
 
         const files = /** @type {string[] | {url: string}[]} */ (
-            read(text, { type: props.type ?? "tsv" })
+            read(content, format)
         )
             .map((u) => (typeof u === "string" ? u : u.url))
             .map((u) => concatUrl(listUrl, u));
@@ -94,11 +98,7 @@ export default class UrlSource extends DataSource {
                 if (!result.ok) {
                     throw new Error(`${result.status} ${result.statusText}`);
                 }
-                // @ts-ignore
-                return typeof result[type] == "function"
-                    ? // @ts-ignore
-                      result[type]()
-                    : result.text();
+                return await readResponseBody(result, url, type);
             } catch (e) {
                 throw new Error(
                     `Could not load data: ${url}. Reason: ${e.message}`
@@ -110,15 +110,20 @@ export default class UrlSource extends DataSource {
          * @param {any} content
          * @param {string} [url]
          */
-        const readAndParse = (content, url) => {
+        const readAndParse = async (content, url) => {
             try {
-                /** @type {any[]} */
-                const data = read(content, format);
+                /** @type {any[] | Promise<any[]>} */
+                const dataOrPromise = read(content, format);
+                const data =
+                    dataOrPromise instanceof Promise
+                        ? await dataOrPromise
+                        : dataOrPromise;
                 this.beginBatch({ type: "file", url: url });
                 for (const d of data) {
                     this._propagate(d);
                 }
             } catch (e) {
+                console.warn(e);
                 throw new Error(`Cannot parse: ${url}: ${e.message}`);
             }
         };
@@ -135,3 +140,122 @@ export default class UrlSource extends DataSource {
         this.complete();
     }
 }
+
+/**
+ * @param {Partial<import("../../spec/data.js").Data>} data
+ * @returns {data is import("../../spec/data.js").UrlData}
+ */
+export function isUrlData(data) {
+    return "url" in data;
+}
+
+/**
+ * @param {Uint8Array} bytes
+ */
+function hasGzipMagic(bytes) {
+    return (
+        bytes.length >= 10 &&
+        bytes[0] == 0x1f &&
+        bytes[1] == 0x8b &&
+        bytes[2] == 0x08 &&
+        (bytes[3] & 0xe0) == 0
+    );
+}
+
+/**
+ * @param {string | null} contentType
+ */
+function isGzipMimeType(contentType) {
+    if (!contentType) {
+        return false;
+    }
+
+    return gzipMimeTypes.has(contentType.split(";")[0].trim().toLowerCase());
+}
+
+/**
+ * @param {string | null} contentEncoding
+ */
+function hasGzipContentEncoding(contentEncoding) {
+    if (!contentEncoding) {
+        return false;
+    }
+
+    return contentEncoding
+        .toLowerCase()
+        .split(",")
+        .some((encoding) => encoding.trim() == "gzip");
+}
+
+/**
+ * @param {Uint8Array} bytes
+ * @returns {ArrayBuffer}
+ */
+function toArrayBuffer(bytes) {
+    return new Uint8Array(bytes).buffer;
+}
+
+/**
+ * @param {Uint8Array} bytes
+ */
+async function decompressGzip(bytes) {
+    if (typeof DecompressionStream != "function") {
+        throw new Error(
+            "Gzip-compressed URL data requires DecompressionStream support."
+        );
+    }
+
+    const body = new Response(toArrayBuffer(bytes)).body;
+    if (!body) {
+        throw new Error(
+            "Cannot create a readable stream for gzip decompression."
+        );
+    }
+
+    const stream = body.pipeThrough(new DecompressionStream("gzip"));
+    return new Uint8Array(await new Response(stream).arrayBuffer());
+}
+
+/**
+ * @param {Response} response
+ * @param {string} url
+ * @param {string} type
+ */
+async function readResponseBody(response, url, type) {
+    const gzipHint =
+        hasGzipExtension(url) ||
+        isGzipMimeType(response.headers.get("content-type")) ||
+        hasGzipContentEncoding(response.headers.get("content-encoding"));
+
+    if (!gzipHint) {
+        return readResponseUsingType(response, type);
+    }
+
+    const bytes = new Uint8Array(await response.arrayBuffer());
+    const bodyBytes = hasGzipMagic(bytes) ? await decompressGzip(bytes) : bytes;
+    return deserializeBytes(bodyBytes, type);
+}
+
+/**
+ * @param {Response} response
+ * @param {string} type
+ */
+function readResponseUsingType(response, type) {
+    // @ts-ignore
+    return typeof response[type] == "function"
+        ? // @ts-ignore
+          response[type]()
+        : response.text();
+}
+
+/**
+ * @param {Uint8Array} bytes
+ * @param {string} type
+ */
+function deserializeBytes(bytes, type) {
+    if (type == "arrayBuffer") {
+        return toArrayBuffer(bytes);
+    } else {
+        return textDecoder.decode(bytes);
+    }
+}

package/dist/src/encoder/encoder.d.ts

@@ -54,12 +54,12 @@ export function isChannelDefWithScale(channelDef: import("../spec/channel.js").C
 /**
  * @param {import("../spec/channel.js").ChannelDef} channelDef
  */
-export function findChannelDefWithScale(channelDef: import("../spec/channel.js").ChannelDef): import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, string> | import("../spec/channel.js").PositionFieldDef | import("../spec/channel.js").PositionDatumDef | import("../spec/channel.js").ChromPosDef | import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, number> | (import("../spec/channel.js").ParameterPredicate & import("../spec/channel.js").FieldDefBase & import("../spec/channel.js").TitleMixins & import("../spec/channel.js").DomainContributionMixins & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type>) | (import("../spec/channel.js").ParameterPredicate & import("../spec/channel.js").DatumDef<import("../spec/parameter.js").ExprRef | import("../spec/channel.js").Scalar> & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type> & import("../spec/channel.js").DomainContributionMixins) | (import("../spec/channel.js").ParameterPredicate & import("../spec/channel.js").ValueDefBase<string | import("../spec/parameter.js").ExprRef> & import("../spec/channel.js").TitleMixins & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type> & import("../spec/channel.js").DomainContributionMixins) | (import("../spec/channel.js").ParameterPredicate & import("../spec/channel.js").ValueDefBase<number | import("../spec/parameter.js").ExprRef> & import("../spec/channel.js").TitleMixins & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type> & import("../spec/channel.js").DomainContributionMixins);
+export function findChannelDefWithScale(channelDef: import("../spec/channel.js").ChannelDef): import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, string> | import("../spec/channel.js").PositionFieldDef | import("../spec/channel.js").ChromPosDef | import("../spec/channel.js").PositionDatumDef | import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, number> | (import("../spec/channel.js").ParameterPredicate & import("../spec/channel.js").ValueDefBase<string | import("../spec/parameter.js").ExprRef> & import("../spec/channel.js").TitleMixins & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type> & import("../spec/channel.js").DomainContributionMixins) | (import("../spec/channel.js").ParameterPredicate & import("../spec/channel.js").ValueDefBase<number | import("../spec/parameter.js").ExprRef> & import("../spec/channel.js").TitleMixins & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type> & import("../spec/channel.js").DomainContributionMixins) | (import("../spec/channel.js").ParameterPredicate & import("../spec/channel.js").FieldDefBase & import("../spec/channel.js").TitleMixins & import("../spec/channel.js").DomainContributionMixins & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type>) | (import("../spec/channel.js").ParameterPredicate & import("../spec/channel.js").DatumDef<import("../spec/parameter.js").ExprRef | import("../spec/channel.js").Scalar> & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type> & import("../spec/channel.js").DomainContributionMixins);
 /**
  * @param {import("../view/unitView.js").default} view
  * @param {import("../spec/channel.js").Channel} channel
  */
-export function getChannelDefWithScale(view: import("../view/unitView.js").default, channel: import("../spec/channel.js").Channel): import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, string> | import("../spec/channel.js").PositionFieldDef | import("../spec/channel.js").PositionDatumDef | import("../spec/channel.js").ChromPosDef | import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, number> | import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").TypeForShape>, string> | (import("../spec/channel.js").FieldDefBase & import("../spec/channel.js").TitleMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type> & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").DomainContributionMixins & import("../spec/channel.js").PositionMixins & import("../spec/channel.js").XIndexDef) | (import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").DatumDef<import("../spec/parameter.js").ExprRef | import("../spec/channel.js").Scalar> & import("../spec/channel.js").DomainContributionMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type> & import("../spec/channel.js").PositionMixins & import("../spec/channel.js").XIndexDef) | (import("../spec/channel.js").ChromPosDefBase & import("../spec/channel.js").TitleMixins & import("../spec/channel.js").PositionMixins & import("../spec/channel.js").DomainContributionMixins & import("../spec/channel.js").TypeMixins<"locus"> & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").XIndexDef);
+export function getChannelDefWithScale(view: import("../view/unitView.js").default, channel: import("../spec/channel.js").Channel): import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, string> | import("../spec/channel.js").PositionFieldDef | import("../spec/channel.js").ChromPosDef | import("../spec/channel.js").PositionDatumDef | (import("../spec/channel.js").FieldDefBase & import("../spec/channel.js").TitleMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type> & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").DomainContributionMixins & import("../spec/channel.js").PositionMixins & import("../spec/channel.js").XIndexDef) | (import("../spec/channel.js").ChromPosDefBase & import("../spec/channel.js").TitleMixins & import("../spec/channel.js").PositionMixins & import("../spec/channel.js").DomainContributionMixins & import("../spec/channel.js").TypeMixins<"locus"> & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").XIndexDef) | (import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").DatumDef<import("../spec/parameter.js").ExprRef | import("../spec/channel.js").Scalar> & import("../spec/channel.js").DomainContributionMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type> & import("../spec/channel.js").PositionMixins & import("../spec/channel.js").XIndexDef) | import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, number> | import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").TypeForShape>, string>;
 /**
  * @param {import("../spec/channel.js").ChannelDef} channelDef
  * @returns {channelDef is import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type>}

package/dist/src/fonts/bmFontManager.d.ts

@@ -51,7 +51,7 @@ export default class BmFontManager {
      * @param {FontWeight | keyof WEIGHTS} weight
      * @returns {FontEntry}
      */
-    getFont(family: string, style?: FontStyle, weight?: FontWeight | ("bold" | "normal" | "medium" | "thin" | "light" | "regular" | "black")): FontEntry;
+    getFont(family: string, style?: FontStyle, weight?: FontWeight | ("bold" | "normal" | "thin" | "light" | "regular" | "medium" | "black")): FontEntry;
     /**
      *
      * @param {FontEntry} fontEntry An uninitialized font entry

package/dist/src/genome/assemblyPreflight.d.ts

@@ -0,0 +1,31 @@
+/**
+ * @typedef {import("../spec/scale.js").Scale["assembly"]} AssemblyReference
+ */
+/**
+ * @typedef {object} AssemblyPreflightResult
+ * @prop {AssemblyReference[]} assemblies
+ * @prop {boolean} needsDefaultAssembly
+ */
+/**
+ * @param {import("../view/view.js").default} viewRoot
+ * @returns {AssemblyPreflightResult}
+ */
+export function collectAssembliesFromViewHierarchy(viewRoot: import("../view/view.js").default): AssemblyPreflightResult;
+/**
+ * Ensures that all assemblies required by the given view hierarchy are loaded
+ * before any scale initialization path can run.
+ *
+ * Reminder: call this immediately after view hierarchy creation and before
+ * operations that can implicitly initialize scales (for example, step-based
+ * size resolution, dynamic opacity setup, or encoder initialization).
+ *
+ * @param {import("../view/view.js").default} viewRoot
+ * @param {import("./genomeStore.js").default} genomeStore
+ */
+export function ensureAssembliesForView(viewRoot: import("../view/view.js").default, genomeStore: import("./genomeStore.js").default): Promise<void>;
+export type AssemblyReference = import("../spec/scale.js").Scale["assembly"];
+export type AssemblyPreflightResult = {
+    assemblies: AssemblyReference[];
+    needsDefaultAssembly: boolean;
+};
+//# sourceMappingURL=assemblyPreflight.d.ts.map

package/dist/src/genome/assemblyPreflight.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"assemblyPreflight.d.ts","sourceRoot":"","sources":["../../../src/genome/assemblyPreflight.js"],"names":[],"mappings":"AAEA;;GAEG;AAEH;;;;GAIG;AAEH;;;GAGG;AACH,6DAHW,OAAO,iBAAiB,EAAE,OAAO,GAC/B,uBAAuB,CAsBnC;AAED;;;;;;;;;;GAUG;AACH,kDAHW,OAAO,iBAAiB,EAAE,OAAO,eACjC,OAAO,kBAAkB,EAAE,OAAO,iBAgB5C;gCA5DY,OAAO,kBAAkB,EAAE,KAAK,CAAC,UAAU,CAAC;;gBAK/C,iBAAiB,EAAE;0BACnB,OAAO"}

package/dist/src/genome/assemblyPreflight.js

@@ -0,0 +1,99 @@
+import { visitAddressableViews } from "../view/viewSelectors.js";
+
+/**
+ * @typedef {import("../spec/scale.js").Scale["assembly"]} AssemblyReference
+ */
+
+/**
+ * @typedef {object} AssemblyPreflightResult
+ * @prop {AssemblyReference[]} assemblies
+ * @prop {boolean} needsDefaultAssembly
+ */
+
+/**
+ * @param {import("../view/view.js").default} viewRoot
+ * @returns {AssemblyPreflightResult}
+ */
+export function collectAssembliesFromViewHierarchy(viewRoot) {
+    /** @type {AssemblyReference[]} */
+    const assemblies = [];
+    let needsDefaultAssembly = false;
+
+    const resolutions = collectRelevantScaleResolutions(viewRoot);
+    for (const resolution of resolutions) {
+        const requirement = resolution.getAssemblyRequirement();
+        if (requirement.assembly) {
+            assemblies.push(requirement.assembly);
+        }
+        if (requirement.needsDefaultAssembly) {
+            needsDefaultAssembly = true;
+        }
+    }
+
+    return {
+        assemblies,
+        needsDefaultAssembly,
+    };
+}
+
+/**
+ * Ensures that all assemblies required by the given view hierarchy are loaded
+ * before any scale initialization path can run.
+ *
+ * Reminder: call this immediately after view hierarchy creation and before
+ * operations that can implicitly initialize scales (for example, step-based
+ * size resolution, dynamic opacity setup, or encoder initialization).
+ *
+ * @param {import("../view/view.js").default} viewRoot
+ * @param {import("./genomeStore.js").default} genomeStore
+ */
+export async function ensureAssembliesForView(viewRoot, genomeStore) {
+    const { assemblies, needsDefaultAssembly } =
+        collectAssembliesFromViewHierarchy(viewRoot);
+    if (needsDefaultAssembly) {
+        const defaultAssembly = genomeStore.getDefaultAssemblyName();
+        if (!defaultAssembly) {
+            throw new Error(
+                "No default assembly has been configured. Set root `assembly`, define exactly one entry in root `genomes`, or set `scale.assembly` on each locus scale."
+            );
+        }
+        assemblies.push(defaultAssembly);
+    }
+
+    await genomeStore.ensureAssemblies(assemblies);
+}
+
+/**
+ * Collects scale resolutions that can influence user-authored views while
+ * excluding internal helper subtrees (axis/grid/etc.).
+ *
+ * Reminder: implicit root wrappers are marked non-addressable, so include the
+ * root ancestry explicitly before traversing addressable views.
+ *
+ * @param {import("../view/view.js").default} viewRoot
+ * @returns {Set<import("../scales/scaleResolution.js").default>}
+ */
+function collectRelevantScaleResolutions(viewRoot) {
+    /** @type {Set<import("../scales/scaleResolution.js").default>} */
+    const resolutions = new Set();
+
+    /** @type {import("../spec/channel.js").PrimaryPositionalChannel[]} */
+    const locusChannels = ["x", "y"];
+
+    /**
+     * @param {import("../view/view.js").default} view
+     */
+    const collectFromView = (view) => {
+        for (const channel of locusChannels) {
+            const resolution = view.getScaleResolution(channel);
+            if (resolution) {
+                resolutions.add(resolution);
+            }
+        }
+    };
+
+    collectFromView(viewRoot);
+    visitAddressableViews(viewRoot, collectFromView);
+
+    return resolutions;
+}

package/dist/src/genome/genome.d.ts

@@ -62,11 +62,11 @@ export default class Genome {
     config: {
         name: string;
     } | {
-        url: string;
         name: string;
+        url: string;
     } | {
-        contigs: import("../spec/genome.js").Contig[];
         name: string;
+        contigs: import("../spec/genome.js").Contig[];
     };
     /** @type {(Chromosome & ChromosomeAnnotation)[]} */
     chromosomes: (Chromosome & ChromosomeAnnotation)[];

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

@@ -1 +1 @@
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package/dist/src/genome/genome.js

@@ -111,6 +111,10 @@ export default class Genome {
      * @param {Chromosome[]} chromSizes
      */
     setChromSizes(chromSizes) {
+        this.chromosomes = [];
+        this.cumulativeChromPositions = new Map();
+        this.chromosomesByName = new Map();
+
         let pos = 0;
         this.startByIndex = [0];
 

package/dist/src/genome/genomeStore.d.ts

@@ -1,3 +1,15 @@
+/**
+ * Resolves genome assemblies for locus scales.
+ *
+ * Keeps configured genome definitions and loaded `Genome` instances, supports
+ * named and inline assemblies, and deduplicates concurrent URL loads.
+ *
+ * `ensureAssembly(...)` is the async loading boundary. `getGenome(...)` is
+ * synchronous and expects required URL-backed assemblies to be ensured first.
+ *
+ * The default assembly comes from root `assembly`, a single configured genome,
+ * or a single already-loaded built-in genome.
+ */
 export default class GenomeStore {
     /**
      * @param {string} baseUrl
@@ -9,12 +21,31 @@ export default class GenomeStore {
     /**
      * @param {import("../spec/genome.js").GenomeConfig} genomeConfig
      */
-    initialize(genomeConfig: import("../spec/genome.js").GenomeConfig): Promise<void[]>;
+    initialize(genomeConfig: import("../spec/genome.js").GenomeConfig): Promise<void>;
     /**
-     * @param {string} [name] If not given, a default genome is returned.
+     * @param {Map<string, import("../spec/root.js").NamedGenomeConfig>} genomesByName
+     * @param {string} [defaultAssembly]
+     */
+    configureGenomes(genomesByName: Map<string, import("../spec/root.js").NamedGenomeConfig>, defaultAssembly?: string): void;
+    /**
+     * @returns {string | undefined}
+     */
+    getDefaultAssemblyName(): string | undefined;
+    /**
+     * @param {(string | import("../spec/scale.js").InlineLocusAssembly | undefined)[]} assemblies
+     */
+    ensureAssemblies(assemblies: (string | import("../spec/scale.js").InlineLocusAssembly | undefined)[]): Promise<void>;
+    /**
+     * @param {string | import("../spec/scale.js").InlineLocusAssembly} assembly
+     * @returns {Promise<Genome>}
+     */
+    ensureAssembly(assembly: string | import("../spec/scale.js").InlineLocusAssembly): Promise<Genome>;
+    /**
+     * @param {string | import("../spec/scale.js").InlineLocusAssembly} [name] If not given, a default genome is returned.
      * @returns {Genome}
      */
-    getGenome(name?: string): Genome;
+    getGenome(name?: string | import("../spec/scale.js").InlineLocusAssembly): Genome;
+    #private;
 }
 import Genome from "./genome.js";
 //# sourceMappingURL=genomeStore.d.ts.map

package/dist/src/genome/genomeStore.d.ts.map

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