@genome-spy/core 0.65.0 → 0.67.0

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

@@ -0,0 +1,18 @@
+/**
+ * @typedef {import("../types/viewContext.js").default} ViewContext
+ */
+/**
+ * Creates a ViewContext from a partial input. Omitted fields default to
+ * "fail-fast" placeholders that throw when called. This lets tests supply only
+ * what they need while keeping production usage explicit.
+ *
+ * @param {Partial<ViewContext> & {
+ *   createOrImportViewWithContext?: (context: ViewContext, spec: import("../spec/view.js").ViewSpec | import("../spec/view.js").ImportSpec, layoutParent?: import("../view/containerView.js").default, dataParent?: import("../view/view.js").default, defaultName?: string, validator?: (spec: import("../spec/view.js").ViewSpec) => void) => Promise<import("../view/view.js").default>
+ * }} options
+ * @returns {ViewContext}
+ */
+export function createViewContext(options: Partial<ViewContext> & {
+    createOrImportViewWithContext?: (context: ViewContext, spec: import("../spec/view.js").ViewSpec | import("../spec/view.js").ImportSpec, layoutParent?: import("../view/containerView.js").default, dataParent?: import("../view/view.js").default, defaultName?: string, validator?: (spec: import("../spec/view.js").ViewSpec) => void) => Promise<import("../view/view.js").default>;
+}): ViewContext;
+export type ViewContext = import("../types/viewContext.js").default;
+//# sourceMappingURL=viewContextFactory.d.ts.map

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

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

@@ -0,0 +1,79 @@
+/**
+ * @typedef {import("../types/viewContext.js").default} ViewContext
+ */
+
+/**
+ * Creates a ViewContext from a partial input. Omitted fields default to
+ * "fail-fast" placeholders that throw when called. This lets tests supply only
+ * what they need while keeping production usage explicit.
+ *
+ * @param {Partial<ViewContext> & {
+ *   createOrImportViewWithContext?: (context: ViewContext, spec: import("../spec/view.js").ViewSpec | import("../spec/view.js").ImportSpec, layoutParent?: import("../view/containerView.js").default, dataParent?: import("../view/view.js").default, defaultName?: string, validator?: (spec: import("../spec/view.js").ViewSpec) => void) => Promise<import("../view/view.js").default>
+ * }} options
+ * @returns {ViewContext}
+ */
+export function createViewContext(options) {
+    /** @param {string} name */
+    const missing = (name) => {
+        throw new Error("ViewContext." + name + " is not configured.");
+    };
+    /** @type {Partial<ViewContext>} */
+    const context = {
+        dataFlow: options.dataFlow ?? missing("dataFlow"),
+        glHelper: options.glHelper ?? missing("glHelper"),
+        animator: options.animator ?? missing("animator"),
+        genomeStore: options.genomeStore,
+        fontManager: options.fontManager ?? missing("fontManager"),
+        createOrImportView: async function (
+            spec,
+            layoutParent,
+            dataParent,
+            defaultName,
+            validator
+        ) {
+            const create = options.createOrImportViewWithContext;
+            if (!create) {
+                return Promise.reject(
+                    new Error(
+                        "ViewContext.createOrImportView is not configured."
+                    )
+                );
+            }
+
+            // Needs the fully wired context for recursive view creation.
+            return create(
+                /** @type {ViewContext} */ (context),
+                spec,
+                layoutParent,
+                dataParent,
+                defaultName,
+                validator
+            );
+        },
+    };
+
+    /** @type {(keyof ViewContext)[]} */
+    const methodNames = [
+        "requestLayoutReflow",
+        "updateTooltip",
+        "getNamedDataFromProvider",
+        "getCurrentHover",
+        "setDataLoadingStatus",
+        "addKeyboardListener",
+        "addBroadcastListener",
+        "removeBroadcastListener",
+        "highlightView",
+        "isViewConfiguredVisible",
+        "isViewSpec",
+    ];
+
+    /** @type {Partial<ViewContext>} */
+    const optionValues = options;
+    const contextAny = /** @type {any} */ (context);
+
+    for (const name of methodNames) {
+        contextAny[name] = optionValues[name] ?? (() => missing(name));
+    }
+
+    return /** @type {ViewContext} */ (context);
+}

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

@@ -0,0 +1,22 @@
+/**
+ * Initializes the view data pipeline: builds the flow graph, awaits fonts,
+ * loads sources, and finalizes graphics for rendering.
+ *
+ * @param {import("../view/view.js").default} viewRoot
+ * @param {import("../data/dataFlow.js").default} dataFlow
+ * @param {import("../fonts/bmFontManager.js").default} fontManager
+ * @param {(dataFlow: import("../data/dataFlow.js").default) => void} onDataFlowBuilt
+ * @returns {Promise<import("../data/dataFlow.js").default>}
+ */
+export function initializeViewData(viewRoot: import("../view/view.js").default, dataFlow: import("../data/dataFlow.js").default, fontManager: import("../fonts/bmFontManager.js").default, onDataFlowBuilt: (dataFlow: import("../data/dataFlow.js").default) => void): Promise<import("../data/dataFlow.js").default>;
+/**
+ * Initializes data flow and graphics for visible views that were previously
+ * skipped. Intended for view-visibility toggles.
+ *
+ * @param {import("../view/view.js").default} viewRoot
+ * @param {import("../data/dataFlow.js").default} dataFlow
+ * @param {import("../fonts/bmFontManager.js").default} fontManager
+ * @returns {Promise<import("../data/dataFlow.js").default>}
+ */
+export function initializeVisibleViewData(viewRoot: import("../view/view.js").default, dataFlow: import("../data/dataFlow.js").default, fontManager: import("../fonts/bmFontManager.js").default): Promise<import("../data/dataFlow.js").default>;
+//# sourceMappingURL=viewDataInit.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"viewDataInit.d.ts","sourceRoot":"","sources":["../../../src/genomeSpy/viewDataInit.js"],"names":[],"mappings":"AAOA;;;;;;;;;GASG;AACH,6CANW,OAAO,iBAAiB,EAAE,OAAO,YACjC,OAAO,qBAAqB,EAAE,OAAO,eACrC,OAAO,2BAA2B,EAAE,OAAO,mBAC3C,CAAC,QAAQ,EAAE,OAAO,qBAAqB,EAAE,OAAO,KAAK,IAAI,GACvD,OAAO,CAAC,OAAO,qBAAqB,EAAE,OAAO,CAAC,CAkC1D;AAED;;;;;;;;GAQG;AACH,oDALW,OAAO,iBAAiB,EAAE,OAAO,YACjC,OAAO,qBAAqB,EAAE,OAAO,eACrC,OAAO,2BAA2B,EAAE,OAAO,GACzC,OAAO,CAAC,OAAO,qBAAqB,EAAE,OAAO,CAAC,CAgD1D"}

package/dist/src/genomeSpy/viewDataInit.js

@@ -0,0 +1,160 @@
+import {
+    initializeViewSubtree,
+    loadViewSubtreeData,
+} from "../data/flowInit.js";
+import { finalizeSubtreeGraphics } from "../view/viewUtils.js";
+import { VISIT_SKIP } from "../view/view.js";
+
+/**
+ * Initializes the view data pipeline: builds the flow graph, awaits fonts,
+ * loads sources, and finalizes graphics for rendering.
+ *
+ * @param {import("../view/view.js").default} viewRoot
+ * @param {import("../data/dataFlow.js").default} dataFlow
+ * @param {import("../fonts/bmFontManager.js").default} fontManager
+ * @param {(dataFlow: import("../data/dataFlow.js").default) => void} onDataFlowBuilt
+ * @returns {Promise<import("../data/dataFlow.js").default>}
+ */
+export async function initializeViewData(
+    viewRoot,
+    dataFlow,
+    fontManager,
+    onDataFlowBuilt
+) {
+    const visibilityPredicate = (
+        /** @type {import("../view/view.js").default} */ view
+    ) => view.isConfiguredVisible();
+    const { dataFlow: builtDataFlow, graphicsPromises } = initializeViewSubtree(
+        viewRoot,
+        dataFlow,
+        visibilityPredicate
+    );
+    onDataFlowBuilt(builtDataFlow);
+
+    // Have to wait until asynchronous font loading is complete.
+    // Text mark's geometry builder needs font metrics before data can be
+    // converted into geometries.
+    // TODO: Make updateGraphicsData async and await font loading there.
+    await fontManager.waitUntilReady();
+
+    // Find all data sources and initiate loading.
+    await loadViewSubtreeData(
+        viewRoot,
+        new Set(builtDataFlow.dataSources),
+        visibilityPredicate
+    );
+
+    await finalizeSubtreeGraphics(graphicsPromises);
+
+    return builtDataFlow;
+}
+
+/**
+ * Initializes data flow and graphics for visible views that were previously
+ * skipped. Intended for view-visibility toggles.
+ *
+ * @param {import("../view/view.js").default} viewRoot
+ * @param {import("../data/dataFlow.js").default} dataFlow
+ * @param {import("../fonts/bmFontManager.js").default} fontManager
+ * @returns {Promise<import("../data/dataFlow.js").default>}
+ */
+export async function initializeVisibleViewData(
+    viewRoot,
+    dataFlow,
+    fontManager
+) {
+    const visibilityPredicate = (
+        /** @type {import("../view/view.js").default} */ view
+    ) => view.isConfiguredVisible();
+    const visibleViews = collectVisibleViews(viewRoot, visibilityPredicate);
+    const viewsToInitialize = visibleViews.filter(
+        (view) => view.getDataInitializationState() === "none"
+    );
+
+    if (viewsToInitialize.length === 0) {
+        return dataFlow;
+    }
+
+    const viewsToInitializeSet = new Set(viewsToInitialize);
+    const viewInitializationPredicate = (
+        /** @type {import("../view/view.js").default} */ view
+    ) => viewsToInitializeSet.has(view);
+
+    const { dataFlow: builtDataFlow, graphicsPromises } = initializeViewSubtree(
+        viewRoot,
+        dataFlow,
+        visibilityPredicate,
+        viewInitializationPredicate
+    );
+
+    await fontManager.waitUntilReady();
+
+    const dataSourceRoots = collectDataSourceRoots(viewsToInitialize);
+    await Promise.all(
+        Array.from(dataSourceRoots.entries()).map(
+            ([subtreeRoot, dataSources]) =>
+                loadViewSubtreeData(subtreeRoot, dataSources, undefined, {
+                    // If a source is already loading, schedule a reload so new branches
+                    // added during lazy init receive a complete data propagation.
+                    queueReload: true,
+                })
+        )
+    );
+
+    await finalizeSubtreeGraphics(graphicsPromises);
+
+    return builtDataFlow;
+}
+
+/**
+ * @param {import("../view/view.js").default} viewRoot
+ * @param {(view: import("../view/view.js").default) => boolean} viewFilter
+ * @returns {import("../view/view.js").default[]}
+ */
+function collectVisibleViews(viewRoot, viewFilter) {
+    /** @type {import("../view/view.js").default[]} */
+    const views = [];
+    viewRoot.visit((view) => {
+        if (!viewFilter(view)) {
+            return VISIT_SKIP;
+        }
+        views.push(view);
+    });
+    return views;
+}
+
+/**
+ * @param {import("../view/view.js").default[]} views
+ * @returns {Map<import("../view/view.js").default, Set<import("../data/sources/dataSource.js").default>>}
+ */
+function collectDataSourceRoots(views) {
+    /** @type {Map<import("../view/view.js").default, Set<import("../data/sources/dataSource.js").default>>} */
+    const roots = new Map();
+
+    for (const view of views) {
+        let current = view;
+        while (current && !current.flowHandle?.dataSource) {
+            current = current.dataParent;
+        }
+
+        if (!current?.flowHandle?.dataSource) {
+            if (view.spec.data) {
+                throw new Error(
+                    "No data source found for view " + view.getPathString()
+                );
+            }
+            // Some views are data-less (constants or references); they don't
+            // participate in data loading but still need graphics init.
+            continue;
+        }
+
+        let dataSources = roots.get(current);
+        if (!dataSources) {
+            dataSources = new Set();
+            roots.set(current, dataSources);
+        }
+        dataSources.add(current.flowHandle.dataSource);
+    }
+
+    return roots;
+}

package/dist/src/genomeSpy/viewDataInit.test.d.ts

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

package/dist/src/genomeSpy/viewDataInit.test.d.ts.map

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

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

@@ -0,0 +1,14 @@
+/**
+ * @param {import("../view/view.js").default} viewRoot
+ */
+export function configureViewHierarchy(viewRoot: import("../view/view.js").default): void;
+/**
+ * Configures view opacity after scale/axis resolution has stabilized.
+ *
+ * NOTE: This is a separate pass because dynamic opacity needs resolved scales.
+ * If we end up with more post-resolve work, consider a post-resolve thunk queue.
+ *
+ * @param {import("../view/view.js").default} viewRoot
+ */
+export function configureViewOpacity(viewRoot: import("../view/view.js").default): void;
+//# sourceMappingURL=viewHierarchyConfig.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"viewHierarchyConfig.d.ts","sourceRoot":"","sources":["../../../src/genomeSpy/viewHierarchyConfig.js"],"names":[],"mappings":"AAKA;;GAEG;AACH,iDAFW,OAAO,iBAAiB,EAAE,OAAO,QAK3C;AAED;;;;;;;GAOG;AACH,+CAFW,OAAO,iBAAiB,EAAE,OAAO,QAI3C"}

package/dist/src/genomeSpy/viewHierarchyConfig.js

@@ -0,0 +1,24 @@
+import {
+    checkForDuplicateScaleNames,
+    setImplicitScaleNames,
+} from "../view/viewUtils.js";
+
+/**
+ * @param {import("../view/view.js").default} viewRoot
+ */
+export function configureViewHierarchy(viewRoot) {
+    checkForDuplicateScaleNames(viewRoot);
+    setImplicitScaleNames(viewRoot);
+}
+
+/**
+ * Configures view opacity after scale/axis resolution has stabilized.
+ *
+ * NOTE: This is a separate pass because dynamic opacity needs resolved scales.
+ * If we end up with more post-resolve work, consider a post-resolve thunk queue.
+ *
+ * @param {import("../view/view.js").default} viewRoot
+ */
+export function configureViewOpacity(viewRoot) {
+    viewRoot.getDescendants().forEach((view) => view.configureViewOpacity());
+}

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

@@ -0,0 +1,5 @@
+/**
+ * @param {HTMLElement} container
+ */
+export function createViewHighlighter(container: HTMLElement): (view: import("../view/view.js").default | null) => void;
+//# sourceMappingURL=viewHighlight.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"viewHighlight.d.ts","sourceRoot":"","sources":["../../../src/genomeSpy/viewHighlight.js"],"names":[],"mappings":"AAAA;;GAEG;AACH,iDAFW,WAAW,IAMV,MAFG,OAAO,iBAAiB,EAAE,OAAO,GAAG,IAEnC,UAsBf"}

package/dist/src/genomeSpy/viewHighlight.js

@@ -0,0 +1,30 @@
+/**
+ * @param {HTMLElement} container
+ */
+export function createViewHighlighter(container) {
+    /**
+     * @param {import("../view/view.js").default | null} view
+     */
+    return (view) => {
+        container.querySelector(".view-highlight")?.remove();
+        if (view) {
+            if (!view.isConfiguredVisible()) {
+                return;
+            }
+            const coords = view.coords;
+            if (coords) {
+                const div = document.createElement("div");
+                div.className = "view-highlight";
+                div.style.position = "absolute";
+                div.style.left = coords.x + "px";
+                div.style.top = coords.y + "px";
+                div.style.width = coords.width + "px";
+                div.style.height = coords.height + "px";
+                div.style.border = "1px solid green";
+                div.style.backgroundColor = "rgba(0, 255, 0, 0.1)";
+                div.style.pointerEvents = "none";
+                container.appendChild(div);
+            }
+        }
+    };
+}

package/dist/src/genomeSpy.d.ts

@@ -14,8 +14,6 @@ export default class GenomeSpy {
     constructor(container: HTMLElement, spec: import("./spec/root.js").RootSpec, options?: import("./types/embedApi.js").EmbedOptions);
     container: HTMLElement;
     options: import("./types/embedApi.js").EmbedOptions;
-    /** @type {(() => void)[]} */
-    _destructionCallbacks: (() => void)[];
     /** Root level configuration object */
     spec: import("./spec/root.js").RootSpec;
     viewFactory: ViewFactory;
@@ -31,59 +29,10 @@ export default class GenomeSpy {
      * @type {(view: View) => boolean}
      */
     viewVisibilityPredicate: (view: import("./view/view.js").default) => boolean;
-    /** @type {BufferedViewRenderingContext} */
-    _renderingContext: BufferedViewRenderingContext;
-    /** @type {BufferedViewRenderingContext} */
-    _pickingContext: BufferedViewRenderingContext;
-    /** Does picking buffer need to be rendered again */
-    _dirtyPickingBuffer: boolean;
-    /**
-     * Currently hovered mark and datum
-     * @type {{ mark: import("./marks/mark.js").default, datum: import("./data/flowNode.js").Datum, uniqueId: number }}
-     */
-    _currentHover: {
-        mark: import("./marks/mark.js").default;
-        datum: import("./data/flowNode.js").Datum;
-        uniqueId: number;
-    };
-    _wheelInertia: Inertia;
-    /**
-     * Keeping track so that these can be cleaned up upon finalization.
-     * @type {Map<string, (function(KeyboardEvent):void)[]>}
-     */
-    _keyboardListeners: Map<string, ((arg0: KeyboardEvent) => void)[]>;
-    /**
-     * Listers for exposed high-level events such as click on a mark instance.
-     * These should probably be in the View class and support bubbling through
-     * the hierarchy.
-     *
-     * @type {Map<string, Set<(event: any) => void>>}
-     */
-    _eventListeners: Map<string, Set<(event: any) => void>>;
-    /**
-     *
-     * @type {Map<string, Set<(event: any) => void>>}
-     */
-    _extraBroadcastListeners: Map<string, Set<(event: any) => void>>;
     /** @type {Record<string, import("./tooltip/tooltipHandler.js").TooltipHandler>}> */
     tooltipHandlers: Record<string, import("./tooltip/tooltipHandler.js").TooltipHandler>;
     /** @type {View} */
     viewRoot: import("./view/view.js").default;
-    /**
-     * Views that are currently loading data using lazy sources.
-     *
-     * @type {Map<View, { status: import("./types/viewContext.js").DataLoadingStatus, detail?: string }>}
-     */
-    _loadingViews: Map<import("./view/view.js").default, {
-        status: import("./types/viewContext.js").DataLoadingStatus;
-        detail?: string;
-    }>;
-    /**
-     * @type {HTMLElement}
-     */
-    _inputBindingContainer: HTMLElement;
-    /** @type {Point} */
-    _mouseDownCoords: Point;
     dpr: number;
     /**
      *
@@ -100,6 +49,16 @@ export default class GenomeSpy {
      * @param {any[]} data
      */
     updateNamedData(name: string, data: any[]): void;
+    /**
+     * @param {string} type
+     * @param {(event: any) => void} listener
+     */
+    addEventListener(type: string, listener: (event: any) => void): void;
+    /**
+     * @param {string} type
+     * @param {(event: any) => void} listener
+     */
+    removeEventListener(type: string, listener: (event: any) => void): void;
     /**
      * Broadcast a message to all views
      
@@ -107,32 +66,20 @@ export default class GenomeSpy {
      * @param {any} [payload]
      */
     broadcast(type: BroadcastEventType, payload?: any): void;
-    /**
-     * Draw some layers on top of the canvas. It's easier to do fancy spinning
-     * animations with html elements than with WebGL.
-     */
-    _updateLoadingIndicators(): void;
-    _glHelper: WebGLHelper;
     loadingMessageElement: HTMLElement;
     loadingIndicatorsElement: HTMLElement;
-    tooltip: Tooltip;
+    tooltip: import("./utils/ui/tooltip.js").default;
     /**
      * Unregisters all listeners, removes all created dom elements, removes all css classes from the container
      */
     destroy(): void;
-    _prepareViewsAndData(): Promise<void>;
     /**
      * 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
      */
     launch(): Promise<boolean>;
+    initializeVisibleViewData(): Promise<void>;
     registerMouseEvents(): void;
-    _tooltipUpdateRequested: boolean;
-    /**
-     * @param {number} x
-     * @param {number} y
-     */
-    _handlePicking(x: number, y: number): void;
     /**
      * This method should be called in a mouseMove handler. If not called, the
      * tooltip will be hidden.
@@ -152,11 +99,15 @@ export default class GenomeSpy {
      * @returns A PNG data Url
      */
     exportCanvas(logicalWidth?: number, logicalHeight?: number, devicePixelRatio?: number, clearColor?: string): string;
+    getLogicalCanvasSize(): {
+        width: any;
+        height: any;
+    };
     computeLayout(): void;
     renderAll(): void;
     renderPickingFramebuffer(): void;
     getSearchableViews(): UnitView[];
-    getNamedScaleResolutions(): Map<string, import("./view/scaleResolution.js").default>;
+    getNamedScaleResolutions(): Map<string, import("./scales/scaleResolution.js").default>;
     #private;
 }
 /**
@@ -166,10 +117,5 @@ export type BroadcastEventType = "dataFlowBuilt" | "layout" | "layoutComputed" |
 import { ViewFactory } from "./view/viewFactory.js";
 import Animator from "./utils/animator.js";
 import GenomeStore from "./genome/genomeStore.js";
-import BufferedViewRenderingContext from "./view/renderingContext/bufferedViewRenderingContext.js";
-import Inertia from "./utils/inertia.js";
-import Point from "./view/layout/point.js";
-import WebGLHelper from "./gl/webGLHelper.js";
-import Tooltip from "./utils/ui/tooltip.js";
 import UnitView from "./view/unitView.js";
 //# sourceMappingURL=genomeSpy.d.ts.map

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

@@ -1 +1 @@
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