@genome-spy/core 0.65.0 → 0.67.0

package/dist/src/genome/scaleLocus.js

@@ -1,6 +1,8 @@
 import { tickStep } from "d3-array";
 import { format as d3format } from "d3-format";
+
 import scaleIndex from "./scaleIndex.js";
+import { isChromosomalLocus, isChromosomalLocusInterval } from "./genome.js";
 
 export default function scaleLocus() {
     /** @type {import("./scaleLocus.js").ScaleLocus} */
@@ -99,3 +101,77 @@ export default function scaleLocus() {
 export function isScaleLocus(scale) {
     return scale.type == "locus";
 }
+
+/**
+ * @param {import("./genome.js").default | { genome?: () => import("./genome.js").default } | undefined} scaleOrGenome
+ * @param {number} value
+ * @returns {number | import("./genome.js").ChromosomalLocus}
+ */
+export function toComplexValue(scaleOrGenome, value) {
+    const genome = resolveGenome(scaleOrGenome);
+    return genome ? genome.toChromosomal(value) : value;
+}
+
+/**
+ * @param {import("./genome.js").default | { genome?: () => import("./genome.js").default } | undefined} scaleOrGenome
+ * @param {number | import("./genome.js").ChromosomalLocus} complex
+ * @returns {number}
+ */
+export function fromComplexValue(scaleOrGenome, complex) {
+    const genome = resolveGenome(scaleOrGenome);
+    if (genome && isChromosomalLocus(complex)) {
+        return genome.toContinuous(complex.chrom, complex.pos);
+    }
+    return /** @type {number} */ (complex);
+}
+
+/**
+ * @param {import("./genome.js").default | { genome?: () => import("./genome.js").default } | undefined} scaleOrGenome
+ * @param {import("../spec/scale.js").ScalarDomain | import("../spec/scale.js").ComplexDomain} interval
+ * @returns {number[]}
+ */
+export function fromComplexInterval(scaleOrGenome, interval) {
+    const genome = resolveGenome(scaleOrGenome);
+    if (genome && isChromosomalLocusInterval(interval)) {
+        return genome.toContinuousInterval(interval);
+    }
+    return /** @type {number[]} */ (interval);
+}
+
+/**
+ * @param {import("./genome.js").default | { genome?: () => import("./genome.js").default } | undefined} scaleOrGenome
+ * @param {import("../spec/scale.js").ScalarDomain | import("../spec/scale.js").ComplexDomain} interval
+ * @returns {import("../spec/scale.js").ScalarDomain | import("../spec/scale.js").ComplexDomain}
+ */
+export function toComplexInterval(scaleOrGenome, interval) {
+    const genome = resolveGenome(scaleOrGenome);
+    return genome
+        ? genome.toChromosomalInterval(/** @type {number[]} */ (interval))
+        : interval;
+}
+
+/**
+ * @param {import("./genome.js").default | { genome?: () => import("./genome.js").default } | undefined} scaleOrGenome
+ * @returns {number[]}
+ */
+export function getGenomeExtent(scaleOrGenome) {
+    const genome = resolveGenome(scaleOrGenome);
+    if (!genome) {
+        throw new Error("No genome has been defined!");
+    }
+    return genome.getExtent();
+}
+
+/**
+ * @param {import("./genome.js").default | { genome?: () => import("./genome.js").default } | undefined} scaleOrGenome
+ * @returns {import("./genome.js").default | undefined}
+ */
+function resolveGenome(scaleOrGenome) {
+    if (scaleOrGenome && "toChromosomal" in scaleOrGenome) {
+        return scaleOrGenome;
+    }
+    if (scaleOrGenome && "genome" in scaleOrGenome) {
+        return scaleOrGenome.genome();
+    }
+    return undefined;
+}

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

@@ -0,0 +1,19 @@
+/**
+ * @param {object} options
+ * @param {import("../gl/webGLHelper.js").default} options.glHelper
+ * @param {import("../view/view.js").default} options.viewRoot
+ * @param {number} [options.logicalWidth]
+ * @param {number} [options.logicalHeight]
+ * @param {number} [options.devicePixelRatio]
+ * @param {string} [options.clearColor]
+ * @returns {string}
+ */
+export function exportCanvas({ glHelper, viewRoot, logicalWidth, logicalHeight, devicePixelRatio, clearColor, }: {
+    glHelper: import("../gl/webGLHelper.js").default;
+    viewRoot: import("../view/view.js").default;
+    logicalWidth?: number;
+    logicalHeight?: number;
+    devicePixelRatio?: number;
+    clearColor?: string;
+}): string;
+//# sourceMappingURL=canvasExport.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"canvasExport.d.ts","sourceRoot":"","sources":["../../../src/genomeSpy/canvasExport.js"],"names":[],"mappings":"AAMA;;;;;;;;;GASG;AACH,iHARG;IAAwD,QAAQ,EAAxD,OAAO,sBAAsB,EAAE,OAAO;IACK,QAAQ,EAAnD,OAAO,iBAAiB,EAAE,OAAO;IAChB,YAAY,GAA7B,MAAM;IACW,aAAa,GAA9B,MAAM;IACW,gBAAgB,GAAjC,MAAM;IACW,UAAU,GAA3B,MAAM;CACd,GAAU,MAAM,CAmDlB"}

package/dist/src/genomeSpy/canvasExport.js

@@ -0,0 +1,66 @@
+import { createFramebufferInfo } from "twgl.js";
+
+import BufferedViewRenderingContext from "../view/renderingContext/bufferedViewRenderingContext.js";
+import Rectangle from "../view/layout/rectangle.js";
+import { framebufferToDataUrl } from "../gl/webGLHelper.js";
+
+/**
+ * @param {object} options
+ * @param {import("../gl/webGLHelper.js").default} options.glHelper
+ * @param {import("../view/view.js").default} options.viewRoot
+ * @param {number} [options.logicalWidth]
+ * @param {number} [options.logicalHeight]
+ * @param {number} [options.devicePixelRatio]
+ * @param {string} [options.clearColor]
+ * @returns {string}
+ */
+export function exportCanvas({
+    glHelper,
+    viewRoot,
+    logicalWidth,
+    logicalHeight,
+    devicePixelRatio,
+    clearColor = "white",
+}) {
+    logicalWidth ??= glHelper.getLogicalCanvasSize().width;
+    logicalHeight ??= glHelper.getLogicalCanvasSize().height;
+    devicePixelRatio ??= window.devicePixelRatio ?? 1;
+
+    const gl = glHelper.gl;
+
+    const width = Math.floor(logicalWidth * devicePixelRatio);
+    const height = Math.floor(logicalHeight * devicePixelRatio);
+
+    const framebufferInfo = createFramebufferInfo(
+        gl,
+        [
+            {
+                format: gl.RGBA,
+                type: gl.UNSIGNED_BYTE,
+                minMag: gl.LINEAR,
+                wrap: gl.CLAMP_TO_EDGE,
+            },
+        ],
+        width,
+        height
+    );
+
+    const renderingContext = new BufferedViewRenderingContext(
+        { picking: false },
+        {
+            webGLHelper: glHelper,
+            canvasSize: { width: logicalWidth, height: logicalHeight },
+            devicePixelRatio,
+            clearColor,
+            framebufferInfo,
+        }
+    );
+
+    viewRoot.render(
+        renderingContext,
+        Rectangle.create(0, 0, logicalWidth, logicalHeight)
+    );
+    renderingContext.render();
+
+    return framebufferToDataUrl(gl, framebufferInfo, "image/png");
+}

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

@@ -0,0 +1,17 @@
+/**
+ * @param {HTMLElement} container
+ */
+export function createContainerUi(container: HTMLElement): {
+    canvasWrapper: HTMLElement;
+    loadingMessageElement: HTMLElement;
+    loadingIndicatorsElement: HTMLElement;
+    tooltip: Tooltip;
+    styleElement: HTMLStyleElement;
+};
+/**
+ * @param {HTMLElement} container
+ * @param {string} message
+ */
+export function createMessageBox(container: HTMLElement, message: string): void;
+import Tooltip from "../utils/ui/tooltip.js";
+//# sourceMappingURL=containerUi.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"containerUi.d.ts","sourceRoot":"","sources":["../../../src/genomeSpy/containerUi.js"],"names":[],"mappings":"AAGA;;GAEG;AACH,6CAFW,WAAW;;;;;;EA2CrB;AAED;;;GAGG;AACH,4CAHW,WAAW,WACX,MAAM,QAUhB;oBA5DmB,wBAAwB"}

package/dist/src/genomeSpy/containerUi.js

@@ -0,0 +1,78 @@
+import css from "../styles/genome-spy.css.js";
+import Tooltip from "../utils/ui/tooltip.js";
+
+/**
+ * @param {HTMLElement} container
+ */
+export function createContainerUi(container) {
+    container.classList.add("genome-spy");
+
+    const styleElement = document.createElement("style");
+    styleElement.innerHTML = css;
+    container.appendChild(styleElement);
+
+    const canvasWrapper = element("div", {
+        class: "canvas-wrapper",
+    });
+    container.appendChild(canvasWrapper);
+
+    canvasWrapper.classList.add("loading");
+
+    const loadingMessageElement = element("div", {
+        class: "loading-message",
+        innerHTML: `<div class="message">Loading<span class="ellipsis">...</span></div>`,
+    });
+    canvasWrapper.appendChild(loadingMessageElement);
+
+    const loadingIndicatorsElement = element("div", {
+        class: "loading-indicators",
+    });
+    canvasWrapper.appendChild(loadingIndicatorsElement);
+
+    const tooltip = new Tooltip(container);
+
+    loadingMessageElement
+        .querySelector(".message")
+        .addEventListener("transitionend", () => {
+            /** @type {HTMLElement} */ (loadingMessageElement).style.display =
+                "none";
+        });
+
+    return {
+        canvasWrapper,
+        loadingMessageElement,
+        loadingIndicatorsElement,
+        tooltip,
+        styleElement,
+    };
+}
+
+/**
+ * @param {HTMLElement} container
+ * @param {string} message
+ */
+export function createMessageBox(container, message) {
+    // Uh, need a templating thingy
+    const messageBox = document.createElement("div");
+    messageBox.className = "message-box";
+    const messageText = document.createElement("div");
+    messageText.textContent = message;
+    messageBox.appendChild(messageText);
+    container.appendChild(messageBox);
+}
+
+/**
+ * @param {string} tag
+ * @param {Record<string, any>} attrs
+ */
+function element(tag, attrs) {
+    const el = document.createElement(tag);
+    for (const [key, value] of Object.entries(attrs)) {
+        if (["innerHTML", "innerText", "className"].includes(key)) {
+            // @ts-ignore
+            el[key] = value;
+        }
+        el.setAttribute(key, value);
+    }
+    return el;
+}

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

@@ -0,0 +1,19 @@
+export default class EventListenerRegistry {
+    /**
+     * @param {string} type
+     * @param {(event: any) => void} listener
+     */
+    add(type: string, listener: (event: any) => void): void;
+    /**
+     * @param {string} type
+     * @param {(event: any) => void} listener
+     */
+    remove(type: string, listener: (event: any) => void): void;
+    /**
+     * @param {string} type
+     * @param {any} event
+     */
+    emit(type: string, event: any): void;
+    #private;
+}
+//# sourceMappingURL=eventListenerRegistry.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"eventListenerRegistry.d.ts","sourceRoot":"","sources":["../../../src/genomeSpy/eventListenerRegistry.js"],"names":[],"mappings":"AAAA;IAQI;;;OAGG;IACH,UAHW,MAAM,YACN,CAAC,KAAK,EAAE,GAAG,KAAK,IAAI,QAU9B;IAED;;;OAGG;IACH,aAHW,MAAM,YACN,CAAC,KAAK,EAAE,GAAG,KAAK,IAAI,QAI9B;IAED;;;OAGG;IACH,WAHW,MAAM,SACN,GAAG,QAIb;;CACJ"}

package/dist/src/genomeSpy/eventListenerRegistry.js

@@ -0,0 +1,38 @@
+export default class EventListenerRegistry {
+    /** @type {Map<string, Set<(event: any) => void>>} */
+    #listeners;
+
+    constructor() {
+        this.#listeners = new Map();
+    }
+
+    /**
+     * @param {string} type
+     * @param {(event: any) => void} listener
+     */
+    add(type, listener) {
+        let listeners = this.#listeners.get(type);
+        if (!listeners) {
+            listeners = new Set();
+            this.#listeners.set(type, listeners);
+        }
+
+        listeners.add(listener);
+    }
+
+    /**
+     * @param {string} type
+     * @param {(event: any) => void} listener
+     */
+    remove(type, listener) {
+        this.#listeners.get(type)?.delete(listener);
+    }
+
+    /**
+     * @param {string} type
+     * @param {any} event
+     */
+    emit(type, event) {
+        this.#listeners.get(type)?.forEach((listener) => listener(event));
+    }
+}

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

@@ -0,0 +1,14 @@
+export default class InputBindingManager {
+    /**
+     * @param {HTMLElement} container
+     * @param {import("../types/embedApi.js").EmbedOptions} options
+     */
+    constructor(container: HTMLElement, options: import("../types/embedApi.js").EmbedOptions);
+    /**
+     * @param {import("../view/view.js").default} viewRoot
+     */
+    initialize(viewRoot: import("../view/view.js").default): void;
+    remove(): void;
+    #private;
+}
+//# sourceMappingURL=inputBindingManager.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"inputBindingManager.d.ts","sourceRoot":"","sources":["../../../src/genomeSpy/inputBindingManager.js"],"names":[],"mappings":"AAIA;IAQI;;;OAGG;IACH,uBAHW,WAAW,WACX,OAAO,sBAAsB,EAAE,YAAY,EAOrD;IAED;;OAEG;IACH,qBAFW,OAAO,iBAAiB,EAAE,OAAO,QAiC3C;IAED,eAEC;;CACJ"}

package/dist/src/genomeSpy/inputBindingManager.js

@@ -0,0 +1,63 @@
+import { html, render } from "lit";
+
+import createBindingInputs from "../utils/inputBinding.js";
+
+export default class InputBindingManager {
+    /** @type {HTMLElement} */
+    #container;
+    /** @type {import("../types/embedApi.js").EmbedOptions} */
+    #options;
+    /** @type {HTMLElement} */
+    #inputBindingContainer;
+
+    /**
+     * @param {HTMLElement} container
+     * @param {import("../types/embedApi.js").EmbedOptions} options
+     */
+    constructor(container, options) {
+        this.#container = container;
+        this.#options = options;
+
+        this.#inputBindingContainer = undefined;
+    }
+
+    /**
+     * @param {import("../view/view.js").default} viewRoot
+     */
+    initialize(viewRoot) {
+        /** @type {import("lit").TemplateResult[]} */
+        const inputs = [];
+
+        viewRoot.visit((view) => {
+            const mediator = view.paramMediator;
+            inputs.push(...createBindingInputs(mediator));
+        });
+        const ibc = this.#options.inputBindingContainer;
+
+        if (!ibc || ibc == "none" || !inputs.length) {
+            return;
+        }
+
+        this.#inputBindingContainer = document.createElement("div");
+        this.#inputBindingContainer.className = "gs-input-bindings";
+
+        if (ibc == "default") {
+            this.#container.appendChild(this.#inputBindingContainer);
+        } else if (ibc instanceof HTMLElement) {
+            ibc.appendChild(this.#inputBindingContainer);
+        } else {
+            throw new Error("Invalid inputBindingContainer");
+        }
+
+        if (inputs.length) {
+            render(
+                html`<div class="gs-input-binding">${inputs}</div>`,
+                this.#inputBindingContainer
+            );
+        }
+    }
+
+    remove() {
+        this.#inputBindingContainer?.remove();
+    }
+}

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

@@ -0,0 +1,40 @@
+export default class InteractionController {
+    /**
+     * @param {object} options
+     * @param {import("../view/view.js").default} options.viewRoot
+     * @param {import("../gl/webGLHelper.js").default} options.glHelper
+     * @param {import("../utils/ui/tooltip.js").default} options.tooltip
+     * @param {import("../utils/animator.js").default} options.animator
+     * @param {(type: string, event: any) => void} options.emitEvent
+     * @param {Record<string, import("../tooltip/tooltipHandler.js").TooltipHandler>} options.tooltipHandlers
+     * @param {() => void} options.renderPickingFramebuffer
+     * @param {() => number} options.getDevicePixelRatio
+     */
+    constructor({ viewRoot, glHelper, tooltip, animator, emitEvent, tooltipHandlers, renderPickingFramebuffer, getDevicePixelRatio, }: {
+        viewRoot: import("../view/view.js").default;
+        glHelper: import("../gl/webGLHelper.js").default;
+        tooltip: import("../utils/ui/tooltip.js").default;
+        animator: import("../utils/animator.js").default;
+        emitEvent: (type: string, event: any) => void;
+        tooltipHandlers: Record<string, import("../tooltip/tooltipHandler.js").TooltipHandler>;
+        renderPickingFramebuffer: () => void;
+        getDevicePixelRatio: () => number;
+    });
+    getCurrentHover(): {
+        mark: import("../marks/mark.js").default;
+        datum: import("../data/flowNode.js").Datum;
+        uniqueId: number;
+    };
+    registerMouseEvents(): void;
+    /**
+     * 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<T>(datum: T, converter?: (arg0: T) => Promise<string | HTMLElement | import("lit").TemplateResult>): void;
+    #private;
+}
+//# sourceMappingURL=interactionController.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"interactionController.d.ts","sourceRoot":"","sources":["../../../src/genomeSpy/interactionController.js"],"names":[],"mappings":"AAQA;IA2BI;;;;;;;;;;OAUG;IACH,mIATG;QAAmD,QAAQ,EAAnD,OAAO,iBAAiB,EAAE,OAAO;QACe,QAAQ,EAAxD,OAAO,sBAAsB,EAAE,OAAO;QACY,OAAO,EAAzD,OAAO,wBAAwB,EAAE,OAAO;QACQ,QAAQ,EAAxD,OAAO,sBAAsB,EAAE,OAAO;QACM,SAAS,EAArD,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,IAAI;QAC6C,eAAe,EAA9F,MAAM,CAAC,MAAM,EAAE,OAAO,8BAA8B,EAAE,cAAc,CAAC;QACjD,wBAAwB,EAA5C,MAAM,IAAI;QACY,mBAAmB,EAAzC,MAAM,MAAM;KACtB,EAgCA;IAED;cArDkB,OAAO,kBAAkB,EAAE,OAAO;eAAS,OAAO,qBAAqB,EAAE,KAAK;kBAAY,MAAM;MAuDjH;IAED,4BAgMC;IA6ED;;;;;;;OAOG;IACH,cAFa,CAAC,SAFH,CAAC,cACD,CAAS,IAAC,EAAD,CAAC,KAAE,OAAO,CAAC,MAAM,GAAG,WAAW,GAAG,OAAO,KAAK,EAAE,cAAc,CAAC,QAYlF;;CACJ"}