@genome-spy/core 0.72.0 → 0.74.0

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

@@ -18,6 +18,14 @@ export function isChromosomalLocus(value: any): value is ChromosomalLocus;
  * @return {value is ChromosomalLocus[]}
  */
 export function isChromosomalLocusInterval(value: any[]): value is ChromosomalLocus[];
+/**
+ * Returns true when the right bound is an explicit locus position rather than a
+ * chromosome shortcut such as `{ chrom: "chr2" }`.
+ *
+ * @param {any} value
+ * @returns {value is ChromosomalLocus[]}
+ */
+export function hasExplicitLocusUpperBound(value: any): value is ChromosomalLocus[];
 /**
  * @param {any} value
  * @returns {value is GenomeConfig}
@@ -60,13 +68,13 @@ export default class Genome {
      */
     constructor(config: GenomeConfig);
     config: {
-        url: string;
         name: 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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+{"version":3,"file":"genome.d.ts","sourceRoot":"","sources":["../../../src/genome/genome.js"],"names":[],"mappings":"AA2XA;;;GAGG;AACH,gDAFW,MAAM;;;IAOhB;AAED;;;;GAIG;AACH,0CAHW,GAAG,GACF,KAAK,IAAI,gBAAgB,CAIpC;AAED;;;;GAIG;AACH,kDAHW,GAAG,EAAE,GACJ,KAAK,IAAI,gBAAgB,EAAE,CAItC;AAED;;;;;;GAMG;AACH,kDAHW,GAAG,GACD,KAAK,IAAI,gBAAgB,EAAE,CAOvC;AAED;;;GAGG;AACH,sCAHW,GAAG,GACD,KAAK,IAAI,YAAY,CASjC;AAED;;;GAGG;AACH,yCAHW,GAAG,GACD,KAAK,IAAI,OAAO,mBAAmB,EAAE,eAAe,CAIhE;AAED;;;GAGG;AACH,4CAHW,GAAG,GACD,KAAK,IAAI,OAAO,mBAAmB,EAAE,kBAAkB,CAInE;AA1bD;;;;;;;;;;;;;;;;;;;;GAoBG;AAEH;IACI;;OAEG;IACH,oBAFW,YAAY,EA6CtB;IA1CG;;;;;;;;MAA2C;IAc3C,oDAAoD;IACpD,aADW,CAAC,UAAU,GAAG,oBAAoB,CAAC,EAAE,CAC3B;IAErB,2CAA2C;IAC3C,0BADW,GAAG,CAAC,MAAM,GAAG,MAAM,EAAE,MAAM,CAAC,CACE;IAEzC,sEAAsE;IACtE,mBADW,GAAG,CAAC,MAAM,GAAG,MAAM,EAAE,UAAU,GAAG,oBAAoB,CAAC,CAChC;IAElC,uBAAuB;IACvB,cADW,MAAM,EAAE,CACG;IAEtB,kBAAkB;IAkBtB,mBAEC;IAED;;OAEG;IACH,cAFW,MAAM,iBAoBhB;IAED,wBAEC;IAED;;;OAGG;IACH,0BAFW,UAAU,EAAE,QA8CtB;IAED,sBAEC;IAED;;;;;OAKG;IACH,oBAHW,MAAM,GAAG,MAAM,OACf,MAAM,UAShB;IAED;;;OAGG;IACH,4BAFW,MAAM,qCAgBhB;IAED;;;;OAIG;IACH,6BAHW,MAAM,GACJ,gBAAgB,CAY5B;IAED;;;OAGG;IACH,oBAFW,MAAM,qCAIhB;IAED;;;;;;;;;;OAUG;IACH,yBAHW,MAAM,EAAE,GACN,MAAM,CAIlB;IAED;;;;;;OAMG;IACH,2BAHW,MAAM,GACJ,MAAM,CAQlB;IAED;;;OAGG;IACH,gCAHW,MAAM,EAAE,GACN,CAAC,gBAAgB,EAAE,gBAAgB,CAAC,CAUhD;IAED;;;;;;OAMG;IACH,kCAFW,gBAAgB,EAAE,YAgB5B;IAED;;;;;OAKG;IACH,wCAHW,CAAC,gBAAgB,EAAE,gBAAgB,CAAC,GAClC,0BAA0B,EAAE,CAiCxC;IAED;;;;OAIG;IACH,4DAFW,MAAM,EAAE,gCAOlB;IAED;;;;OAIG;IACH,mBAHW,MAAM,GACJ,CAAC,MAAM,EAAE,MAAM,CAAC,CAgC5B;CACJ;2BAjXY,OAAO,mBAAmB,EAAE,YAAY;+BACxC,OAAO,mBAAmB,EAAE,gBAAgB;;UAG/C,MAAM;UACN,MAAM;;;;;;WAGN,MAAM;;;;YACN,MAAM;;;;qBACN,MAAM;;;;mBACN,MAAM;wBACN,MAAM,EAAE;;;;SACR,OAAO;;;WAGP,MAAM;cACN,MAAM;YACN,MAAM"}

package/dist/src/genome/genome.js

@@ -97,7 +97,8 @@ export default class Genome {
             this.setChromSizes(parseChromSizes(await result.text()));
         } catch (e) {
             throw new Error(
-                `Could not load chrom sizes: ${this.config.url}. Reason: ${e.message}`
+                `Could not load chrom sizes: ${this.config.url}. Reason: ${e.message}`,
+                { cause: e }
             );
         }
     }
@@ -111,6 +112,10 @@ 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];
 
@@ -125,7 +130,6 @@ export default class Genome {
                 continuousInterval: [pos, pos + size],
                 index: i,
                 number: i + 1,
-                // eslint-disable-next-line no-bitwise
                 odd: !(i & 1),
             };
 
@@ -402,6 +406,20 @@ export function isChromosomalLocusInterval(value) {
     return value.every(isChromosomalLocus);
 }
 
+/**
+ * Returns true when the right bound is an explicit locus position rather than a
+ * chromosome shortcut such as `{ chrom: "chr2" }`.
+ *
+ * @param {any} value
+ * @returns {value is ChromosomalLocus[]}
+ */
+export function hasExplicitLocusUpperBound(value) {
+    return (
+        isChromosomalLocusInterval(value) &&
+        (value[1] ?? value[0]).pos !== undefined
+    );
+}
+
 /**
  * @param {any} value
  * @returns {value is GenomeConfig}

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

@@ -1 +1 @@
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+{"version":3,"file":"genomeStore.d.ts","sourceRoot":"","sources":["../../../src/genome/genomeStore.js"],"names":[],"mappings":"AAEA;;;;;;;;;;;GAWG;AACH;IACI;;OAEG;IACH,qBAFW,MAAM,EAahB;IAVG,kCAAkC;IAClC,SADW,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CACN;IAQxB,gBAAsB;IAkB1B;;OAEG;IACH,yBAFW,OAAO,mBAAmB,EAAE,YAAY,iBAMlD;IAED;;;OAGG;IACH,gCAHW,GAAG,CAAC,MAAM,EAAE,OAAO,iBAAiB,EAAE,iBAAiB,CAAC,oBACxD,MAAM,QAShB;IAED;;OAEG;IACH,0BAFa,MAAM,GAAG,SAAS,CAmB9B;IAED;;OAEG;IACH,6BAFW,CAAC,MAAM,GAAG,OAAO,kBAAkB,EAAE,mBAAmB,GAAG,SAAS,CAAC,EAAE,iBAuBjF;IAED;;;OAGG;IACH,yBAHW,MAAM,GAAG,OAAO,kBAAkB,EAAE,mBAAmB,GACrD,OAAO,CAAC,MAAM,CAAC,CAuB3B;IAED;;;OAGG;IACH,iBAHW,MAAM,GAAG,OAAO,kBAAkB,EAAE,mBAAmB,GACrD,MAAM,CAuDlB;;CAwOJ;mBAhbkB,aAAa"}