@genome-spy/core 0.72.0 → 0.74.0

package/dist/src/genomeSpy/cursorManager.d.ts

@@ -0,0 +1,69 @@
+/**
+ * @typedef {{
+ *   owner: object,
+ *   raw: unknown,
+ *   evaluate: () => string | undefined,
+ *   watch: (registerDisposer: (dispose: () => void) => void, listener: () => void) => void,
+ * }} CursorSource
+ */
+/**
+ * @param {CursorView | undefined} target
+ * @param {{ mark?: CursorOwner } | undefined} hover
+ * @returns {CursorSource | undefined}
+ */
+export function resolveCursorSource(target: CursorView | undefined, hover: {
+    mark?: CursorOwner;
+} | undefined): CursorSource | undefined;
+/**
+ * Resolves and applies the active canvas cursor based on the current mark hover
+ * and interaction target path.
+ */
+/**
+ * @typedef {{
+ *   getCursorSpec?: () => unknown,
+ *   getCursor: () => string | undefined,
+ *   watchCursor?: (listener: () => void, registerDisposer: (dispose: () => void) => void) => void,
+ * }} CursorOwner
+ */
+/**
+ * @typedef {CursorOwner & {
+ *   getLayoutAncestors: () => CursorView[],
+ * }} CursorView
+ */
+export default class CursorManager {
+    /**
+     * @param {object} options
+     * @param {HTMLCanvasElement} options.canvas
+     */
+    constructor({ canvas }: {
+        canvas: HTMLCanvasElement;
+    });
+    /**
+     * @param {object} options
+     * @param {CursorView | undefined} options.target
+     * @param {{ mark?: CursorOwner } | undefined} options.hover
+     */
+    update({ target, hover }: {
+        target: CursorView | undefined;
+        hover: {
+            mark?: CursorOwner;
+        } | undefined;
+    }): void;
+    clear(): void;
+    #private;
+}
+export type CursorSource = {
+    owner: object;
+    raw: unknown;
+    evaluate: () => string | undefined;
+    watch: (registerDisposer: (dispose: () => void) => void, listener: () => void) => void;
+};
+export type CursorOwner = {
+    getCursorSpec?: () => unknown;
+    getCursor: () => string | undefined;
+    watchCursor?: (listener: () => void, registerDisposer: (dispose: () => void) => void) => void;
+};
+export type CursorView = CursorOwner & {
+    getLayoutAncestors: () => CursorView[];
+};
+//# sourceMappingURL=cursorManager.d.ts.map

package/dist/src/genomeSpy/cursorManager.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/genomeSpy/cursorManager.js

@@ -0,0 +1,131 @@
+/**
+ * Resolves and applies the active canvas cursor based on the current mark hover
+ * and interaction target path.
+ */
+
+/**
+ * @typedef {{
+ *   getCursorSpec?: () => unknown,
+ *   getCursor: () => string | undefined,
+ *   watchCursor?: (listener: () => void, registerDisposer: (dispose: () => void) => void) => void,
+ * }} CursorOwner
+ */
+
+/**
+ * @typedef {CursorOwner & {
+ *   getLayoutAncestors: () => CursorView[],
+ * }} CursorView
+ */
+
+export default class CursorManager {
+    /** @type {HTMLCanvasElement} */
+    #canvas;
+
+    /** @type {CursorSource | undefined} */
+    #activeSource;
+
+    /** @type {(() => void) | undefined} */
+    #disposeActiveSource;
+
+    /**
+     * @param {object} options
+     * @param {HTMLCanvasElement} options.canvas
+     */
+    constructor({ canvas }) {
+        this.#canvas = canvas;
+    }
+
+    /**
+     * @param {object} options
+     * @param {CursorView | undefined} options.target
+     * @param {{ mark?: CursorOwner } | undefined} options.hover
+     */
+    update({ target, hover }) {
+        this.#setActiveSource(resolveCursorSource(target, hover));
+    }
+
+    clear() {
+        this.#setActiveSource(undefined);
+    }
+
+    /**
+     * @param {CursorSource | undefined} source
+     */
+    #setActiveSource(source) {
+        if (sameSource(this.#activeSource, source)) {
+            this.#applyActiveCursor();
+            return;
+        }
+
+        this.#disposeActiveSource?.();
+        this.#disposeActiveSource = undefined;
+        this.#activeSource = source;
+
+        source?.watch(
+            (dispose) => {
+                this.#disposeActiveSource = dispose;
+            },
+            () => this.#applyActiveCursor()
+        );
+
+        this.#applyActiveCursor();
+    }
+
+    #applyActiveCursor() {
+        const cursor = this.#activeSource?.evaluate();
+        this.#canvas.style.cursor = typeof cursor === "string" ? cursor : "";
+    }
+}
+
+/**
+ * @typedef {{
+ *   owner: object,
+ *   raw: unknown,
+ *   evaluate: () => string | undefined,
+ *   watch: (registerDisposer: (dispose: () => void) => void, listener: () => void) => void,
+ * }} CursorSource
+ */
+
+/**
+ * @param {CursorView | undefined} target
+ * @param {{ mark?: CursorOwner } | undefined} hover
+ * @returns {CursorSource | undefined}
+ */
+export function resolveCursorSource(target, hover) {
+    const mark = hover?.mark;
+    const markCursor = mark?.getCursorSpec?.();
+    if (markCursor !== undefined) {
+        return {
+            owner: mark,
+            raw: markCursor,
+            evaluate: () => mark.getCursor(),
+            watch: (registerDisposer, listener) =>
+                mark.watchCursor?.(listener, registerDisposer),
+        };
+    }
+
+    for (const view of target?.getLayoutAncestors() ?? []) {
+        const cursor = view.getCursorSpec?.();
+        if (cursor !== undefined) {
+            return {
+                owner: view,
+                raw: cursor,
+                evaluate: () => view.getCursor(),
+                watch: (registerDisposer, listener) =>
+                    view.watchCursor?.(listener, registerDisposer),
+            };
+        }
+    }
+}
+
+/**
+ * @param {CursorSource | undefined} a
+ * @param {CursorSource | undefined} b
+ */
+function sameSource(a, b) {
+    if (!a || !b) {
+        return a === b;
+    }
+
+    return a.owner === b.owner && a.raw === b.raw;
+}

package/dist/src/genomeSpy/headlessBootstrap.d.ts

@@ -0,0 +1,113 @@
+/**
+ * @param {{
+ *   viewFactoryOptions?: import("../view/viewFactory.js").ViewFactoryOptions,
+ *   dataFlow?: DataFlow,
+ *   genomeStore?: GenomeStore,
+ *   fontManager?: BmFontManager,
+ *   animator?: import("../utils/animator.js").default,
+ *   baseConfig?: ReturnType<typeof resolveBaseConfig>,
+ *   getNamedDataFromProvider?: (name: string) => any[] | undefined,
+ *   getCurrentHover?: () => any,
+ *   updateTooltip?: <T>(datum: T, converter?: (datum: T) => Promise<any>) => void,
+ *   requestLayoutReflow?: () => void,
+ *   suspendHoverTracking?: () => void,
+ *   resumeHoverTracking?: (event?: MouseEvent) => void,
+ *   addKeyboardListener?: (
+ *     type: "keydown" | "keyup",
+ *     listener: (event: KeyboardEvent) => void
+ *   ) => void,
+ *   addBroadcastListener?: (
+ *     type: import("../genomeSpy.js").BroadcastEventType,
+ *     listener: (message: import("../view/view.js").BroadcastMessage) => void
+ *   ) => void,
+ *   removeBroadcastListener?: (
+ *     type: import("../genomeSpy.js").BroadcastEventType,
+ *     listener: (message: import("../view/view.js").BroadcastMessage) => void
+ *   ) => void,
+ *   highlightView?: (view: import("../view/view.js").default | null) => void,
+ *   isViewConfiguredVisible?: (view: import("../view/view.js").default) => boolean,
+ *   isViewSpec?: (spec: any) => boolean,
+ *   glHelper?: import("../gl/webGLHelper.js").default,
+ * }} [options]
+ * @returns {ViewContext}
+ */
+export function createHeadlessViewContext(options?: {
+    viewFactoryOptions?: import("../view/viewFactory.js").ViewFactoryOptions;
+    dataFlow?: DataFlow;
+    genomeStore?: GenomeStore;
+    fontManager?: BmFontManager;
+    animator?: import("../utils/animator.js").default;
+    baseConfig?: ReturnType<typeof resolveBaseConfig>;
+    getNamedDataFromProvider?: (name: string) => any[] | undefined;
+    getCurrentHover?: () => any;
+    updateTooltip?: <T>(datum: T, converter?: (datum: T) => Promise<any>) => void;
+    requestLayoutReflow?: () => void;
+    suspendHoverTracking?: () => void;
+    resumeHoverTracking?: (event?: MouseEvent) => void;
+    addKeyboardListener?: (type: "keydown" | "keyup", listener: (event: KeyboardEvent) => void) => void;
+    addBroadcastListener?: (type: import("../genomeSpy.js").BroadcastEventType, listener: (message: import("../view/view.js").BroadcastMessage) => void) => void;
+    removeBroadcastListener?: (type: import("../genomeSpy.js").BroadcastEventType, listener: (message: import("../view/view.js").BroadcastMessage) => void) => void;
+    highlightView?: (view: import("../view/view.js").default | null) => void;
+    isViewConfiguredVisible?: (view: import("../view/view.js").default) => boolean;
+    isViewSpec?: (spec: any) => boolean;
+    glHelper?: import("../gl/webGLHelper.js").default;
+}): ViewContext;
+/**
+ * Shared view-hierarchy preparation that does not require a browser shell.
+ *
+ * @param {import("../view/view.js").default} viewRoot
+ */
+export function prepareViewHierarchy(viewRoot: import("../view/view.js").default): void;
+/**
+ * Creates a real view hierarchy and initializes its dataflow without touching
+ * browser-only subsystems such as WebGL or DOM event wiring.
+ *
+ * @param {RootSpec} spec
+ * @param {{
+ *   context?: ViewContext,
+ *   contextOptions?: Parameters<typeof createHeadlessViewContext>[0],
+ *   onDataFlowBuilt?: (dataFlow: DataFlow) => void,
+ * }} [options]
+ * @returns {Promise<{ view: import("../view/view.js").default, context: ViewContext }>}
+ */
+export function createHeadlessEngine(spec: RootSpec, options?: {
+    context?: ViewContext;
+    contextOptions?: Parameters<typeof createHeadlessViewContext>[0];
+    onDataFlowBuilt?: (dataFlow: DataFlow) => void;
+}): Promise<{
+    view: import("../view/view.js").default;
+    context: ViewContext;
+}>;
+/**
+ * Creates a resolved view hierarchy without initializing dataflow or loading
+ * assemblies ahead of time.
+ *
+ * @param {RootSpec} spec
+ * @param {{
+ *   context?: ViewContext,
+ *   contextOptions?: Parameters<typeof createHeadlessViewContext>[0],
+ *   viewFactoryOptions?: import("../view/viewFactory.js").ViewFactoryOptions,
+ * }} [options]
+ * @returns {Promise<{ view: import("../view/view.js").default, context: ViewContext }>}
+ */
+export function createHeadlessViewHierarchy(spec: RootSpec, options?: {
+    context?: ViewContext;
+    contextOptions?: Parameters<typeof createHeadlessViewContext>[0];
+    viewFactoryOptions?: import("../view/viewFactory.js").ViewFactoryOptions;
+}): Promise<{
+    view: import("../view/view.js").default;
+    context: ViewContext;
+}>;
+/**
+ * Shared helpers for creating a GenomeSpy runtime without DOM or WebGL.
+ */
+export type RootSpec = import("../spec/root.js").RootSpec;
+/**
+ * Shared helpers for creating a GenomeSpy runtime without DOM or WebGL.
+ */
+export type ViewContext = import("../types/viewContext.js").default;
+import DataFlow from "../data/dataFlow.js";
+import GenomeStore from "../genome/genomeStore.js";
+import BmFontManager from "../fonts/bmFontManager.js";
+import { resolveBaseConfig } from "../config/resolveConfig.js";
+//# sourceMappingURL=headlessBootstrap.d.ts.map

package/dist/src/genomeSpy/headlessBootstrap.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/genomeSpy/headlessBootstrap.js

@@ -0,0 +1,246 @@
+/**
+ * Shared helpers for creating a GenomeSpy runtime without DOM or WebGL.
+ *
+ * @typedef {import("../spec/root.js").RootSpec} RootSpec
+ * @typedef {import("../types/viewContext.js").default} ViewContext
+ */
+
+import DataFlow from "../data/dataFlow.js";
+import GenomeStore from "../genome/genomeStore.js";
+import BmFontManager from "../fonts/bmFontManager.js";
+import Animator from "../utils/animator.js";
+import { INTERNAL_DEFAULT_CONFIG } from "../config/defaultConfig.js";
+import { resolveBaseConfig } from "../config/resolveConfig.js";
+import { createViewContext } from "./viewContextFactory.js";
+import { ViewFactory, VIEW_ROOT_NAME } from "../view/viewFactory.js";
+import { ensureAssembliesForView } from "../genome/assemblyPreflight.js";
+import {
+    configureViewHierarchy,
+    configureViewOpacity,
+} from "./viewHierarchyConfig.js";
+import { initializeViewData } from "./viewDataInit.js";
+
+/**
+ * @returns {GenomeStore}
+ */
+function createTestGenomeStore() {
+    const genomeStore = new GenomeStore(".");
+    genomeStore.initialize({
+        name: "hg38",
+    });
+    return genomeStore;
+}
+
+/**
+ * @returns {import("../utils/animator.js").default}
+ */
+function createHeadlessAnimator() {
+    class HeadlessAnimator extends Animator {
+        constructor() {
+            super(() => undefined);
+        }
+
+        requestRender() {
+            //
+        }
+
+        /**
+         * @param {(timestamp: number) => void} callback
+         */
+        requestTransition(callback) {
+            callback(0);
+        }
+
+        /**
+         * @param {import("../utils/transition.js").TransitionOptions} options
+         */
+        transition(options) {
+            const to = typeof options.to === "number" ? options.to : 1;
+            options.onUpdate(to);
+            return Promise.resolve();
+        }
+    }
+
+    return new HeadlessAnimator();
+}
+
+/**
+ * @param {{
+ *   viewFactoryOptions?: import("../view/viewFactory.js").ViewFactoryOptions,
+ *   dataFlow?: DataFlow,
+ *   genomeStore?: GenomeStore,
+ *   fontManager?: BmFontManager,
+ *   animator?: import("../utils/animator.js").default,
+ *   baseConfig?: ReturnType<typeof resolveBaseConfig>,
+ *   getNamedDataFromProvider?: (name: string) => any[] | undefined,
+ *   getCurrentHover?: () => any,
+ *   updateTooltip?: <T>(datum: T, converter?: (datum: T) => Promise<any>) => void,
+ *   requestLayoutReflow?: () => void,
+ *   suspendHoverTracking?: () => void,
+ *   resumeHoverTracking?: (event?: MouseEvent) => void,
+ *   addKeyboardListener?: (
+ *     type: "keydown" | "keyup",
+ *     listener: (event: KeyboardEvent) => void
+ *   ) => void,
+ *   addBroadcastListener?: (
+ *     type: import("../genomeSpy.js").BroadcastEventType,
+ *     listener: (message: import("../view/view.js").BroadcastMessage) => void
+ *   ) => void,
+ *   removeBroadcastListener?: (
+ *     type: import("../genomeSpy.js").BroadcastEventType,
+ *     listener: (message: import("../view/view.js").BroadcastMessage) => void
+ *   ) => void,
+ *   highlightView?: (view: import("../view/view.js").default | null) => void,
+ *   isViewConfiguredVisible?: (view: import("../view/view.js").default) => boolean,
+ *   isViewSpec?: (spec: any) => boolean,
+ *   glHelper?: import("../gl/webGLHelper.js").default,
+ * }} [options]
+ * @returns {ViewContext}
+ */
+export function createHeadlessViewContext(options = {}) {
+    const viewFactory = new ViewFactory({
+        allowImport: false,
+        wrapRoot: false,
+        ...options.viewFactoryOptions,
+    });
+
+    const dataFlow = options.dataFlow ?? new DataFlow();
+    const genomeStore = options.genomeStore ?? createTestGenomeStore();
+    const baseConfig =
+        options.baseConfig ??
+        resolveBaseConfig({
+            defaultConfig: INTERNAL_DEFAULT_CONFIG,
+        });
+
+    return createViewContext({
+        allowMissingGlHelper: true,
+        dataFlow,
+        genomeStore,
+        glHelper: options.glHelper,
+        fontManager: options.fontManager ?? new BmFontManager(),
+        animator: options.animator ?? createHeadlessAnimator(),
+        requestLayoutReflow: options.requestLayoutReflow ?? (() => undefined),
+        updateTooltip: options.updateTooltip ?? (() => undefined),
+        getNamedDataFromProvider:
+            options.getNamedDataFromProvider ?? (() => undefined),
+        getCurrentHover: options.getCurrentHover ?? (() => undefined),
+        suspendHoverTracking: options.suspendHoverTracking ?? (() => undefined),
+        resumeHoverTracking: options.resumeHoverTracking ?? (() => undefined),
+        addKeyboardListener: options.addKeyboardListener ?? (() => undefined),
+        addBroadcastListener: options.addBroadcastListener ?? (() => undefined),
+        removeBroadcastListener:
+            options.removeBroadcastListener ?? (() => undefined),
+        highlightView: options.highlightView ?? (() => undefined),
+        isViewConfiguredVisible:
+            options.isViewConfiguredVisible ?? (() => true),
+        isViewSpec:
+            options.isViewSpec ?? viewFactory.isViewSpec.bind(viewFactory),
+        getBaseConfig: () => baseConfig,
+        createOrImportViewWithContext: (
+            context,
+            spec,
+            layoutParent,
+            dataParent,
+            defaultName,
+            validator,
+            createOptions
+        ) =>
+            viewFactory.createOrImportView(
+                spec,
+                context,
+                layoutParent,
+                dataParent,
+                defaultName,
+                validator,
+                createOptions
+            ),
+    });
+}
+
+/**
+ * Shared view-hierarchy preparation that does not require a browser shell.
+ *
+ * @param {import("../view/view.js").default} viewRoot
+ */
+export function prepareViewHierarchy(viewRoot) {
+    configureViewHierarchy(viewRoot);
+    configureViewOpacity(viewRoot);
+}
+
+/**
+ * Creates a real view hierarchy and initializes its dataflow without touching
+ * browser-only subsystems such as WebGL or DOM event wiring.
+ *
+ * @param {RootSpec} spec
+ * @param {{
+ *   context?: ViewContext,
+ *   contextOptions?: Parameters<typeof createHeadlessViewContext>[0],
+ *   onDataFlowBuilt?: (dataFlow: DataFlow) => void,
+ * }} [options]
+ * @returns {Promise<{ view: import("../view/view.js").default, context: ViewContext }>}
+ */
+export async function createHeadlessEngine(spec, options = {}) {
+    const context =
+        options.context ?? createHeadlessViewContext(options.contextOptions);
+
+    if (spec.datasets) {
+        const getNamedDataFromProvider = context.getNamedDataFromProvider;
+        context.getNamedDataFromProvider = (name) =>
+            spec.datasets[name] ?? getNamedDataFromProvider(name);
+    }
+
+    const view = await context.createOrImportView(
+        /** @type {import("../spec/view.js").ViewSpec} */ (spec),
+        null,
+        null,
+        VIEW_ROOT_NAME
+    );
+
+    await ensureAssembliesForView(view, context.genomeStore);
+    prepareViewHierarchy(view);
+
+    await initializeViewData(
+        view,
+        context.dataFlow,
+        context.fontManager,
+        options.onDataFlowBuilt ?? (() => undefined)
+    );
+
+    return { view, context };
+}
+
+/**
+ * Creates a resolved view hierarchy without initializing dataflow or loading
+ * assemblies ahead of time.
+ *
+ * @param {RootSpec} spec
+ * @param {{
+ *   context?: ViewContext,
+ *   contextOptions?: Parameters<typeof createHeadlessViewContext>[0],
+ *   viewFactoryOptions?: import("../view/viewFactory.js").ViewFactoryOptions,
+ * }} [options]
+ * @returns {Promise<{ view: import("../view/view.js").default, context: ViewContext }>}
+ */
+export async function createHeadlessViewHierarchy(spec, options = {}) {
+    const context =
+        options.context ??
+        createHeadlessViewContext({
+            ...options.contextOptions,
+            viewFactoryOptions: options.viewFactoryOptions,
+        });
+
+    if (spec.datasets) {
+        const getNamedDataFromProvider = context.getNamedDataFromProvider;
+        context.getNamedDataFromProvider = (name) =>
+            spec.datasets[name] ?? getNamedDataFromProvider(name);
+    }
+
+    const view = await context.createOrImportView(
+        /** @type {import("../spec/view.js").ViewSpec} */ (spec),
+        null,
+        null,
+        VIEW_ROOT_NAME
+    );
+
+    return { view, context };
+}

package/dist/src/genomeSpy/interactionController.d.ts

@@ -25,7 +25,12 @@ export default class InteractionController {
         datum: import("../data/flowNode.js").Datum;
         uniqueId: number;
     };
-    registerMouseEvents(): void;
+    suspendHoverTracking(): void;
+    /**
+     * @param {MouseEvent} [mouseEvent]
+     */
+    resumeHoverTracking(mouseEvent?: MouseEvent): void;
+    registerInteractionEvents(): void;
     /**
      * This method should be called in a mouseMove handler. If not called, the
      * tooltip will be hidden.
@@ -37,4 +42,8 @@ export default class InteractionController {
     updateTooltip<T>(datum: T, converter?: (arg0: T) => Promise<string | HTMLElement | import("lit").TemplateResult>): void;
     #private;
 }
+export type ClientPointLike = {
+    clientX: number;
+    clientY: number;
+};
 //# sourceMappingURL=interactionController.d.ts.map

package/dist/src/genomeSpy/interactionController.d.ts.map

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