@genome-spy/core 0.73.0 → 0.74.0

package/dist/src/genomeSpy.js

@@ -1,694 +1,13 @@
-import { formats as vegaFormats } from "vega-loader";
-
-import {
-    createContainerUi,
-    createMessageBox,
-} from "./genomeSpy/containerUi.js";
-import LoadingIndicatorManager from "./genomeSpy/loadingIndicatorManager.js";
-import LoadingStatusRegistry from "./genomeSpy/loadingStatusRegistry.js";
-import { createViewHighlighter } from "./genomeSpy/viewHighlight.js";
-import KeyboardListenerManager from "./genomeSpy/keyboardListenerManager.js";
-import EventListenerRegistry from "./genomeSpy/eventListenerRegistry.js";
-import InputBindingManager from "./genomeSpy/inputBindingManager.js";
-
-import { calculateCanvasSize } from "./view/viewUtils.js";
-import {
-    initializeViewData,
-    initializeVisibleViewData,
-} from "./genomeSpy/viewDataInit.js";
-import UnitView from "./view/unitView.js";
-
-import WebGLHelper from "./gl/webGLHelper.js";
-import Animator from "./utils/animator.js";
-import DataFlow from "./data/dataFlow.js";
-import GenomeStore from "./genome/genomeStore.js";
-import BmFontManager from "./fonts/bmFontManager.js";
-import fasta from "./data/formats/fasta.js";
-import refseqGeneTooltipHandler from "./tooltip/refseqGeneTooltipHandler.js";
-import dataTooltipHandler from "./tooltip/dataTooltipHandler.js";
-import { invalidatePrefix } from "./utils/propertyCacher.js";
-import { VIEW_ROOT_NAME, ViewFactory } from "./view/viewFactory.js";
-import InteractionController from "./genomeSpy/interactionController.js";
-import RenderCoordinator from "./genomeSpy/renderCoordinator.js";
-import { createViewContext } from "./genomeSpy/viewContextFactory.js";
-import {
-    configureViewHierarchy,
-    configureViewOpacity,
-} from "./genomeSpy/viewHierarchyConfig.js";
-import { exportCanvas } from "./genomeSpy/canvasExport.js";
-import { validateSelectorConstraints } from "./view/viewSelectors.js";
-import parquet from "./data/formats/parquet.js";
-import bed from "./data/formats/bed.js";
-import bedpe from "./data/formats/bedpe.js";
-import SingleAxisWindowedSource from "./data/sources/lazy/singleAxisWindowedSource.js";
-import { ensureAssembliesForView } from "./genome/assemblyPreflight.js";
-import { resolveRootGenomeConfig } from "./genome/rootGenomeConfig.js";
-import { awaitSubtreeLazyReady } from "./view/dataReadiness.js";
-
 /**
  * Events that are broadcasted to all views.
  * @typedef {"dataFlowBuilt" | "layout" | "layoutComputed" | "subtreeDataReady"} BroadcastEventType
  */
 
-vegaFormats("fasta", fasta);
-vegaFormats("parquet", parquet);
-vegaFormats("bed", bed);
-vegaFormats("bedpe", bedpe);
-
-export default class GenomeSpy {
-    /** @type {(() => void)[]} */
-    #destructionCallbacks = [];
-    /** @type {RenderCoordinator} */
-    #renderCoordinator;
-    /** @type {LoadingIndicatorManager} */
-    #loadingIndicatorManager;
-    /** @type {LoadingStatusRegistry} */
-    #loadingStatusRegistry;
-    /** @type {InputBindingManager} */
-    #inputBindingManager;
-    /** @type {InteractionController} */
-    #interactionController;
-    /** @type {WebGLHelper} */
-    #glHelper;
-
-    #keyboardListenerManager = new KeyboardListenerManager();
-    #eventListeners = new EventListenerRegistry();
-    #extraBroadcastListeners = new EventListenerRegistry();
-
-    /**
-     * @typedef {import("./view/view.js").default} View
-     * @typedef {import("./spec/view.js").ViewSpec} ViewSpec
-     * @typedef {import("./spec/root.js").RootSpec} RootSpec
-     * @typedef {import("./spec/root.js").RootConfig} RootConfig
-     */
-
-    /**
-     *
-     * @param {HTMLElement} container
-     * @param {RootSpec} spec
-     * @param {import("./types/embedApi.js").EmbedOptions} [options]
-     */
-    constructor(container, spec, options = {}) {
-        this.container = container;
-        this.options = options;
-
-        options.inputBindingContainer ??= "default";
-
-        /** Root level configuration object */
-        this.spec = spec;
-
-        this.viewFactory = new ViewFactory();
-
-        /** @type {(function(string):object[])[]} */
-        this.namedDataProviders = [];
-
-        this.animator = new Animator(() => this.renderAll());
-
-        /** @type {GenomeStore} */
-        this.genomeStore = undefined;
-
-        /**
-         * View visibility is checked using a predicate that can be overridden
-         * for more dynamic visibility management.
-         *
-         * @type {(view: View) => boolean}
-         */
-        this.viewVisibilityPredicate = (view) => view.isVisibleInSpec();
-
-        /** @type {Record<string, import("./tooltip/tooltipHandler.js").TooltipHandler>}> */
-        this.tooltipHandlers = {
-            default: dataTooltipHandler,
-            refseqgene: refseqGeneTooltipHandler,
-            ...(options.tooltipHandlers ?? {}),
-        };
-
-        /** @type {View} */
-        this.viewRoot = undefined;
-
-        this.#inputBindingManager = new InputBindingManager(container, options);
-
-        this.dpr = window.devicePixelRatio;
-    }
-
-    get #canvasWrapper() {
-        return /** @type {HTMLElement} */ (
-            this.container.querySelector(".canvas-wrapper")
-        );
-    }
-
-    #initializeParameterBindings() {
-        this.#inputBindingManager.initialize(this.viewRoot);
-    }
-
-    /**
-     *
-     * @param {(name: string) => any[]} provider
-     */
-    registerNamedDataProvider(provider) {
-        this.namedDataProviders.unshift(provider);
-    }
-
-    /**
-     * @param {string} name
-     */
-    getNamedDataFromProvider(name) {
-        for (const provider of this.namedDataProviders) {
-            const data = provider(name);
-            if (data) {
-                return data;
-            }
-        }
-    }
-
-    /**
-     *
-     * @param {string} name
-     * @param {any[]} data
-     */
-    updateNamedData(name, data) {
-        const namedSource =
-            this.viewRoot.context.dataFlow.findNamedDataSource(name);
-        if (!namedSource) {
-            throw new Error("No such named data source: " + name);
-        }
-
-        namedSource.dataSource.updateDynamicData(data);
-
-        this.animator.requestRender();
-    }
-
-    /**
-     * @param {string} type
-     * @param {(event: any) => void} listener
-     */
-    addEventListener(type, listener) {
-        this.#eventListeners.add(type, listener);
-    }
-
-    /**
-     * @param {string} type
-     * @param {(event: any) => void} listener
-     */
-    removeEventListener(type, listener) {
-        this.#eventListeners.remove(type, listener);
-    }
-
-    /**
-     * Broadcast a message to all views
-     
-     * @param {BroadcastEventType} type
-     * @param {any} [payload]
-     */
-    broadcast(type, payload) {
-        const message = { type, payload };
-        this.viewRoot.visit((view) => view.handleBroadcast(message));
-        this.#extraBroadcastListeners.emit(type, message);
-    }
-
-    #setupDpr() {
-        this.dpr = this.#glHelper.getDevicePixelRatio();
-
-        const dprSetter = this.viewRoot.paramRuntime.allocateSetter(
-            "devicePixelRatio",
-            this.dpr
-        );
-
-        const resizeCallback = () => {
-            this.#glHelper.invalidateSize();
-            this.dpr = this.#glHelper.getDevicePixelRatio();
-            dprSetter(this.dpr);
-            this.computeLayout();
-            // Render immediately, without RAF
-            this.renderAll();
-        };
-
-        if (this.viewRoot.getSize().isGrowing()) {
-            // TODO: Size should be observed only if the content is not absolutely sized
-            const resizeObserver = new ResizeObserver(resizeCallback);
-            resizeObserver.observe(this.container);
-            this.#destructionCallbacks.push(() => resizeObserver.disconnect());
-        }
-
-        /** @type {() => void} */
-        let remove = null;
-
-        const updatePixelRatio = () => {
-            if (remove != null) {
-                remove();
-                resizeCallback();
-            }
-            const media = matchMedia(
-                `(resolution: ${window.devicePixelRatio}dppx)`
-            );
-            media.addEventListener("change", updatePixelRatio);
-            remove = () => {
-                media.removeEventListener("change", updatePixelRatio);
-            };
-        };
-        updatePixelRatio();
-
-        if (remove) {
-            this.#destructionCallbacks.push(remove);
-        }
-    }
-
-    #prepareContainer() {
-        const { canvasWrapper, loadingIndicatorsElement, tooltip } =
-            createContainerUi(this.container);
-
-        this.#glHelper = new WebGLHelper(
-            canvasWrapper,
-            () =>
-                this.viewRoot
-                    ? calculateCanvasSize(this.viewRoot)
-                    : { width: undefined, height: undefined },
-            { powerPreference: this.options.powerPreference ?? "default" }
-        );
-
-        canvasWrapper.appendChild(loadingIndicatorsElement);
-
-        this.tooltip = tooltip;
-        this.#loadingStatusRegistry = new LoadingStatusRegistry();
-        this.#loadingIndicatorManager = new LoadingIndicatorManager(
-            loadingIndicatorsElement,
-            this.#loadingStatusRegistry
-        );
-    }
-
-    /**
-     * Unregisters all listeners, removes all created dom elements, removes all css classes from the container
-     */
-    destroy() {
-        // TODO: There's a memory leak somewhere
-
-        const canvasWrapper = this.#canvasWrapper;
-
-        this.container.classList.remove("genome-spy");
-        canvasWrapper.classList.remove("loading");
-
-        this.#keyboardListenerManager.removeAll();
-
-        this.#destructionCallbacks.forEach((callback) => callback());
-
-        this.#glHelper.finalize();
-
-        this.#inputBindingManager.remove();
-
-        this.#loadingIndicatorManager.destroy();
-
-        while (this.container.firstChild) {
-            this.container.firstChild.remove();
-        }
-    }
-
-    async #prepareViewsAndData() {
-        await this.#initializeGenomeStore();
-        const context = this.#createViewContext();
-        await this.#initializeViewHierarchy(context);
-        await initializeViewData(
-            this.viewRoot,
-            context.dataFlow,
-            context.fontManager,
-            (flow) => this.broadcast("dataFlowBuilt", flow)
-        );
-        this.#finalizeViewInitialization(context);
-    }
-
-    async #initializeGenomeStore() {
-        this.genomeStore = new GenomeStore(this.spec.baseUrl);
-
-        const { genomesByName, defaultAssembly, deprecationWarning } =
-            resolveRootGenomeConfig(this.spec);
-        this.genomeStore.configureGenomes(genomesByName, defaultAssembly);
-
-        if (deprecationWarning) {
-            // eslint-disable-next-line no-console
-            console.warn(deprecationWarning);
-        }
-    }
-
-    #createViewContext() {
-        const dataFlow = new DataFlow();
-        dataFlow.loadingStatusRegistry = this.#loadingStatusRegistry;
-
-        return createViewContext({
-            dataFlow,
-            glHelper: this.#glHelper,
-            animator: this.animator,
-            genomeStore: this.genomeStore,
-            fontManager: new BmFontManager(this.#glHelper),
-            updateTooltip: this.updateTooltip.bind(this),
-            getNamedDataFromProvider: this.getNamedDataFromProvider.bind(this),
-            getCurrentHover: () =>
-                this.#interactionController.getCurrentHover(),
-            addKeyboardListener: (type, listener) => {
-                this.#keyboardListenerManager.add(type, (event) => {
-                    if (this.#shouldDispatchKeyboardEvent(type, event)) {
-                        listener(event);
-                    }
-                });
-            },
-            addBroadcastListener: (type, listener) =>
-                this.#extraBroadcastListeners.add(type, listener),
-            removeBroadcastListener: (type, listener) =>
-                this.#extraBroadcastListeners.remove(type, listener),
-            isViewConfiguredVisible: this.viewVisibilityPredicate,
-            isViewSpec: (spec) => this.viewFactory.isViewSpec(spec),
-            createOrImportViewWithContext: (
-                ctx,
-                spec,
-                layoutParent,
-                dataParent,
-                defaultName,
-                validator
-            ) =>
-                this.viewFactory.createOrImportView(
-                    spec,
-                    ctx,
-                    layoutParent,
-                    dataParent,
-                    defaultName,
-                    validator
-                ),
-            highlightView: createViewHighlighter(this.container),
-        });
-    }
-
-    /**
-     * Scopes keydown events to the active embed (focused container or hovered container).
-     * Keyup is always dispatched so key-state machines can reliably release keys.
-     *
-     * @param {"keydown" | "keyup"} type
-     * @param {KeyboardEvent} event
-     */
-    #shouldDispatchKeyboardEvent(type, event) {
-        if (type === "keyup") {
-            return true;
-        }
-
-        const activeElement = document.activeElement;
-        if (activeElement && activeElement !== document.body) {
-            return this.container.contains(activeElement);
-        } else {
-            return this.container.matches(":hover");
-        }
-    }
-
-    /**
-     * @param {import("./types/viewContext.js").default} context
-     */
-    async #initializeViewHierarchy(context) {
-        /** @type {ViewSpec & RootConfig} */
-        const rootSpec = this.spec;
-
-        if (rootSpec.datasets) {
-            this.registerNamedDataProvider((name) => rootSpec.datasets[name]);
-        }
-
-        // Create the view hierarchy.
-        // This also resolves scales and axes.
-        this.viewRoot = await context.createOrImportView(
-            rootSpec,
-            null,
-            null,
-            VIEW_ROOT_NAME
-        );
-
-        // Reminder: assemblies must be ensured after view creation (imports and
-        // inheritance resolved), but before any code path that may touch scales
-        // (e.g. step-based sizes, dynamic opacity, encoder initialization).
-        await ensureAssembliesForView(this.viewRoot, this.genomeStore);
-
-        this.#loadingStatusRegistry.set(this.viewRoot, "loading");
-
-        this.#canvasWrapper.style.flexGrow =
-            this.viewRoot.getSize().height.grow > 0 ? "1" : "0";
-
-        this.#initializeParameterBindings();
-
-        configureViewHierarchy(this.viewRoot);
-        configureViewOpacity(this.viewRoot);
-        this.#logSelectorConstraintWarnings();
-
-        // We should now have a complete view hierarchy. Let's update the canvas size
-        // and ensure that the loading message is visible.
-        this.#glHelper.invalidateSize();
-        this.#renderCoordinator = new RenderCoordinator({
-            viewRoot: this.viewRoot,
-            glHelper: this.#glHelper,
-            getBackground: () => this.spec.background,
-            broadcast: this.broadcast.bind(this),
-            onLayoutComputed: () =>
-                this.#loadingIndicatorManager.updateLayout(),
-        });
-
-        // Allow early layout requests from view subscriptions created during initialization.
-        // Layout will be recomputed anyway once launch completes.
-        context.requestLayoutReflow = this.computeLayout.bind(this);
-
-        this.#setupDpr();
-    }
-
-    #logSelectorConstraintWarnings() {
-        const issues = validateSelectorConstraints(this.viewRoot);
-        if (!issues.length) {
-            return;
-        }
-
-        for (const issue of issues) {
-            console.warn("Selector constraints warning:", issue.message);
-        }
-    }
-
-    /**
-     * @param {import("./types/viewContext.js").default} context
-     */
-    #finalizeViewInitialization(context) {
-        // Allow layout computation (in case a custom context overrode the early assignment).
-        // eslint-disable-next-line require-atomic-updates
-        context.requestLayoutReflow = this.computeLayout.bind(this);
-
-        // Invalidate cached sizes to ensure that step-based sizes are current.
-        // TODO: This should be done automatically when the domains of band/point scales are updated.
-        this.viewRoot.visit((view) => invalidatePrefix(view, "size"));
-        this.#glHelper.invalidateSize();
-
-        this.#interactionController = new InteractionController({
-            viewRoot: this.viewRoot,
-            glHelper: this.#glHelper,
-            tooltip: this.tooltip,
-            animator: this.animator,
-            emitEvent: this.#eventListeners.emit.bind(this.#eventListeners),
-            tooltipHandlers: this.tooltipHandlers,
-            renderPickingFramebuffer: this.renderPickingFramebuffer.bind(this),
-            getDevicePixelRatio: () => this.dpr,
-        });
-    }
-
-    /**
-     * TODO: Come up with a sensible name. And maybe this should be called at the end of the constructor.
-     * @returns {Promise<boolean>} true if the launch was successful
-     */
-    async launch() {
-        let launched = false;
-        try {
-            this.#prepareContainer();
-
-            await this.#prepareViewsAndData();
-
-            this.#interactionController.registerInteractionEvents();
-
-            this.computeLayout();
-            this.animator.requestRender();
-
-            launched = true;
-            return true;
-        } catch (reason) {
-            const message = `${
-                reason.view ? `At "${reason.view.getPathString()}": ` : ""
-            }${reason.toString()}`;
-            console.error(reason.stack);
-            const handled = this.options.onError?.(reason, this.container);
-            if (!handled) {
-                createMessageBox(this.container, message);
-            }
-
-            if (this.viewRoot) {
-                this.#loadingStatusRegistry.set(
-                    this.viewRoot,
-                    "error",
-                    message
-                );
-            }
-
-            return false;
-        } finally {
-            this.#canvasWrapper.classList.remove("loading");
-            if (launched && this.viewRoot) {
-                this.#loadingStatusRegistry.set(this.viewRoot, "complete");
-            }
-        }
-    }
-
-    async initializeVisibleViewData() {
-        if (!this.viewRoot) {
-            return;
-        }
-
-        await initializeVisibleViewData(
-            this.viewRoot,
-            this.viewRoot.context.dataFlow,
-            this.viewRoot.context.fontManager
-        );
-
-        // Visibility toggles can change sizes; ensure layout is recomputed even
-        // when callers don't explicitly request it.
-        this.viewRoot._invalidateCacheByPrefix("size", "progeny");
-        this.#glHelper.invalidateSize();
-        this.computeLayout();
-        this.animator.requestRender();
-    }
-
-    /**
-     * Waits until lazy sources under the root view have loaded data for the
-     * current visible positional domain.
-     *
-     * @param {AbortSignal} [signal]
-     */
-    async awaitVisibleLazyData(signal) {
-        if (!this.viewRoot) {
-            return;
-        }
-
-        await awaitSubtreeLazyReady(
-            this.viewRoot.context,
-            this.viewRoot,
-            undefined,
-            signal,
-            (view) =>
-                view.isConfiguredVisible() &&
-                hasWindowedLazyDataSource(view)
-        );
-    }
-
-    /**
-     * This method should be called in a mouseMove handler. If not called, the
-     * tooltip will be hidden.
-     *
-     * @param {T} datum
-     * @param {function(T):Promise<string | HTMLElement | import("lit").TemplateResult>} [converter]
-     * @template T
-     */
-    updateTooltip(datum, converter) {
-        this.#interactionController.updateTooltip(datum, converter);
-    }
-
-    /**
-     * Returns a PNG data URL of the current canvas.
-     *
-     * @param {number} [logicalWidth] defaults to canvas width
-     * @param {number} [logicalHeight] defaults to canvas height
-     * @param {number} [devicePixelRatio] defaults to window.devicePixelRatio
-     * @param {string} [clearColor] null for transparent
-     * @returns A PNG data Url
-     */
-    exportCanvas(
-        logicalWidth,
-        logicalHeight,
-        devicePixelRatio,
-        clearColor = "white"
-    ) {
-        const pngUrl = exportCanvas({
-            glHelper: this.#glHelper,
-            viewRoot: this.viewRoot,
-            logicalWidth,
-            logicalHeight,
-            devicePixelRatio,
-            clearColor,
-        });
-
-        // Clean up
-        this.computeLayout();
-        this.renderAll();
-
-        return pngUrl;
-    }
-
-    getLogicalCanvasSize() {
-        return this.#glHelper.getLogicalCanvasSize();
-    }
-
-    getRenderedBounds() {
-        /** @type {{ width: number | undefined, height: number | undefined }} */
-        const bounds = {
-            width: undefined,
-            height: undefined,
-        };
-
-        this.viewRoot.visit((view) => {
-            for (const coords of view.facetCoords.values()) {
-                bounds.width = Math.max(bounds.width ?? 0, coords.x2);
-                bounds.height = Math.max(bounds.height ?? 0, coords.y2);
-            }
-        });
-
-        return bounds;
-    }
-
-    computeLayout() {
-        this.#renderCoordinator.computeLayout();
-    }
-
-    renderAll() {
-        this.#renderCoordinator.renderAll();
-    }
-
-    renderPickingFramebuffer() {
-        this.#renderCoordinator.renderPickingFramebuffer();
-    }
-
-    getSearchableViews() {
-        /** @type {UnitView[]} */
-        const views = [];
-        this.viewRoot.visit((view) => {
-            if (
-                view instanceof UnitView &&
-                view.getSearchAccessors().length > 0
-            ) {
-                views.push(view);
-            }
-        });
-        return views;
-    }
-
-    getNamedScaleResolutions() {
-        /** @type {Map<string, import("./scales/scaleResolution.js").default>} */
-        const resolutions = new Map();
-        this.viewRoot.visit((view) => {
-            for (const resolution of Object.values(view.resolutions.scale)) {
-                if (resolution.name) {
-                    resolutions.set(resolution.name, resolution);
-                }
-            }
-        });
-        return resolutions;
-    }
-}
-
-/**
- * @param {View} view
- */
-function hasWindowedLazyDataSource(view) {
-    /** @type {View | null} */
-    let current = view;
-
-    while (current) {
-        const dataSource = current.flowHandle?.dataSource;
-        if (dataSource) {
-            return dataSource instanceof SingleAxisWindowedSource;
-        }
-        current = current.dataParent;
-    }
+import "./data/formats/parquet.js";
+import "./data/formats/bed.js";
+import "./data/formats/bedpe.js";
+import "./data/formats/fasta.js";
+// These side-effect imports make the default runtime fat for convenience.
+import "./data/sources/lazy/registerBuiltInLazySources.js";
 
-    return false;
-}
+export { default } from "./genomeSpyBase.js";