@genome-spy/core 0.64.0 → 0.66.1

package/dist/src/view/unitView.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"unitView.d.ts","sourceRoot":"","sources":["../../../src/view/unitView.js"],"names":[],"mappings":"AA6BA;;;;GAIG;AACH,wBAHU,MAAM,CAAC,OAAO,iBAAiB,EAAE,QAAQ,EAAE,cAAc,kBAAkB,EAAE,OAAO,CAAC,CAc7F;AAEF;IAeI;;;;;;;;OAQG;IACH,kBAPW,OAAO,iBAAiB,EAAE,QAAQ,WAClC,OAAO,yBAAyB,EAAE,OAAO,gBACzC,OAAO,oBAAoB,EAAE,OAAO,cACpC,OAAO,WAAW,EAAE,OAAO,QAC3B,MAAM,YACN,OAAO,WAAW,EAAE,WAAW,EAyCzC;IApCG,yCAAgB;IAIZ,iDAAiD;IACjD,MADW,OAAO,kBAAkB,EAAE,OAAO,CACnB;IAoKlC,2DAIC;IAgBD;;;;;OAKG;IAEH,iEA0IC;IAUD;;;;;OAKG;IACH,4IAMC;IAkBD;;OAEG;IACH,uDAEC;IAED;;;;;;;;;;;;;OAaG;IACH,uEAHW,OAAO,oBAAoB,EAAE,IAAI,iDAqB3C;IAED,uBAQC;IAgBD;;;;OAIG;IACH,8BAJW,MAAM,+DAEJ,OAAO,iBAAiB,EAAE,kBAAkB,CAKxD;;CACJ;iBAxfgB,WAAW"}

package/dist/src/view/unitView.js

@@ -4,7 +4,7 @@ import RuleMark from "../marks/rule.js";
 import LinkMark from "../marks/link.js";
 import TextMark from "../marks/text.js";
 
-import ScaleResolution from "./scaleResolution.js";
+import ScaleResolution from "../scales/scaleResolution.js";
 import {
     isPositionalChannel,
     isChannelDefWithScale,
@@ -15,7 +15,7 @@ import {
     isValueDefWithCondition,
 } from "../encoder/encoder.js";
 import createDomain from "../utils/domainArray.js";
-import AxisResolution from "./axisResolution.js";
+import AxisResolution from "../scales/axisResolution.js";
 import View from "./view.js";
 import {
     asSelectionConfig,
@@ -88,14 +88,22 @@ export default class UnitView extends View {
             "zoomLevel",
             1.0
         );
-        /** @type {import("../spec/channel.js").ChannelWithScale[]} */ ([
+
+        for (const channel of /** @type {import("../spec/channel.js").ChannelWithScale[]} */ ([
             "x",
             "y",
-        ]).forEach((channel) =>
-            this.getScaleResolution(channel)?.addEventListener("domain", () =>
-                this.#zoomLevelSetter(Math.sqrt(this.getZoomLevel()))
-            )
-        );
+        ])) {
+            const resolution = this.getScaleResolution(channel);
+            if (resolution) {
+                const listener = () => {
+                    this.#zoomLevelSetter(Math.sqrt(this.getZoomLevel()));
+                };
+                resolution.addEventListener("domain", listener);
+                this.registerDisposer(() =>
+                    resolution.removeEventListener("domain", listener)
+                );
+            }
+        }
 
         this.needsAxes = { x: true, y: true };
 
@@ -340,11 +348,21 @@ export default class UnitView extends View {
                         targetChannel
                     );
                 }
-                view.resolutions[type][targetChannel].addMember({
+                const resolution = view.resolutions[type][targetChannel];
+                const unregister = resolution.registerMember({
                     view: this,
                     channel,
                     channelDef: channelDefWithScale,
                 });
+                this.registerDisposer(() => {
+                    // Unregister returns true when it removed the last member.
+                    if (
+                        unregister() &&
+                        view.resolutions[type][targetChannel] === resolution
+                    ) {
+                        delete view.resolutions[type][targetChannel];
+                    }
+                });
             } else if (type == "scale" && isChannelWithScale(channel)) {
                 if (!view.resolutions[type][targetChannel]) {
                     const resolution = new ScaleResolution(targetChannel);
@@ -370,16 +388,34 @@ export default class UnitView extends View {
                         ? undefined
                         : this.extractDataDomain.bind(this);
 
-                view.resolutions[type][targetChannel].addMember({
+                const resolution = view.resolutions[type][targetChannel];
+                const unregister = resolution.registerMember({
                     view: this,
                     channel,
                     channelDef: channelDefWithScale,
                     dataDomainSource,
                 });
+                this.registerDisposer(() => {
+                    // Unregister returns true when it removed the last member.
+                    if (
+                        unregister() &&
+                        view.resolutions[type][targetChannel] === resolution
+                    ) {
+                        delete view.resolutions[type][targetChannel];
+                    }
+                });
             }
         }
     }
 
+    /**
+     * @override
+     */
+    dispose() {
+        super.dispose();
+        this.mark.dispose();
+    }
+
     /**
      * Returns an accessor that accesses a field or an evaluated expression,
      * if there is one.
@@ -387,7 +423,11 @@ export default class UnitView extends View {
      * @param {Channel} channel
      */
     getDataAccessor(channel) {
-        return this.mark.encoders[channel]?.dataAccessor;
+        const encoders = this.mark.encoders;
+        if (!encoders) {
+            return undefined;
+        }
+        return encoders[channel]?.dataAccessor;
     }
 
     /**
@@ -410,7 +450,7 @@ export default class UnitView extends View {
      * Returns a collector that is associated with this view.
      */
     getCollector() {
-        return this.context.dataFlow.findCollectorByKey(this);
+        return this.flowHandle?.collector;
     }
 
     /**

package/dist/src/view/view.d.ts

@@ -65,14 +65,14 @@ export default class View {
     resolutions: {
         /**
          * Channel-specific scale resolutions
-         * @type {Partial<Record<import("../spec/channel.js").ChannelWithScale, import("./scaleResolution.js").default>>}
+         * @type {Partial<Record<import("../spec/channel.js").ChannelWithScale, import("../scales/scaleResolution.js").default>>}
          */
-        scale: Partial<Record<import("../spec/channel.js").ChannelWithScale, import("./scaleResolution.js").default>>;
+        scale: Partial<Record<import("../spec/channel.js").ChannelWithScale, import("../scales/scaleResolution.js").default>>;
         /**
          * Channel-specific axis resolutions
-         * @type {Partial<Record<import("../spec/channel.js").PrimaryPositionalChannel, import("./axisResolution.js").default>>}
+         * @type {Partial<Record<import("../spec/channel.js").PrimaryPositionalChannel, import("../scales/axisResolution.js").default>>}
          */
-        axis: Partial<Record<import("../spec/channel.js").PrimaryPositionalChannel, import("./axisResolution.js").default>>;
+        axis: Partial<Record<import("../spec/channel.js").PrimaryPositionalChannel, import("../scales/axisResolution.js").default>>;
     };
     options: {
         /**
@@ -90,6 +90,10 @@ export default class View {
          */
         layersChildren?: boolean;
     };
+    /**
+     * @type {import("../data/flowHandle.js").FlowHandle | undefined}
+     */
+    flowHandle: import("../data/flowHandle.js").FlowHandle | undefined;
     /**
      * Whether GridView or equivalent should draw axis and grid lines for this view.
      * TODO: Use view options for this.
@@ -210,9 +214,21 @@ export default class View {
      */
     visit(visitor: Visitor): VisitResult;
     /**
-     * Get all descendants of this view in depth-first order.
+     * Get this view and all descendants in depth-first order.
      */
     getDescendants(): View[];
+    /**
+     * Release resources owned by this view.
+     */
+    dispose(): void;
+    /**
+     * @param {() => void} disposer
+     */
+    registerDisposer(disposer: () => void): void;
+    /**
+     * Dispose this view and all descendants in post-order.
+     */
+    disposeSubtree(): void;
     /**
      * Called after all scales in the view hierarchy have been resolved.
      */
@@ -264,11 +280,11 @@ export default class View {
     /**
      * @param {import("../spec/channel.js").ChannelWithScale} channel
      */
-    getScaleResolution(channel: import("../spec/channel.js").ChannelWithScale): import("./scaleResolution.js").default;
+    getScaleResolution(channel: import("../spec/channel.js").ChannelWithScale): import("../scales/scaleResolution.js").default;
     /**
      * @param {import("../spec/channel.js").PositionalChannel} channel
      */
-    getAxisResolution(channel: import("../spec/channel.js").PositionalChannel): import("./axisResolution.js").default;
+    getAxisResolution(channel: import("../spec/channel.js").PositionalChannel): import("../scales/axisResolution.js").default;
     /**
      * @param {import("../spec/channel.js").Channel | "default"} channel
      * @param {import("../spec/view.js").ResolutionTarget} resolutionType

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

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package/dist/src/view/view.js

@@ -86,6 +86,11 @@ export default class View {
      */
     opacityFunction = defaultOpacityFunction;
 
+    /**
+     * @type {(() => void)[]}
+     */
+    #disposers = [];
+
     /**
      * Coords of the view for each facet, recorded during the last layout rendering pass.
      * Most views have only one facet, so the map is usually of size 1.
@@ -118,12 +123,12 @@ export default class View {
         this.resolutions = {
             /**
              * Channel-specific scale resolutions
-             * @type {Partial<Record<import("../spec/channel.js").ChannelWithScale, import("./scaleResolution.js").default>>}
+             * @type {Partial<Record<import("../spec/channel.js").ChannelWithScale, import("../scales/scaleResolution.js").default>>}
              */
             scale: {},
             /**
              * Channel-specific axis resolutions
-             * @type {Partial<Record<import("../spec/channel.js").PrimaryPositionalChannel, import("./axisResolution.js").default>>}
+             * @type {Partial<Record<import("../spec/channel.js").PrimaryPositionalChannel, import("../scales/axisResolution.js").default>>}
              */
             axis: {},
         };
@@ -136,6 +141,11 @@ export default class View {
             ...options,
         };
 
+        /**
+         * @type {import("../data/flowHandle.js").FlowHandle | undefined}
+         */
+        this.flowHandle = undefined;
+
         /**
          * Whether GridView or equivalent should draw axis and grid lines for this view.
          * TODO: Use view options for this.
@@ -266,7 +276,7 @@ export default class View {
 
             const scale = this.getScaleResolution(
                 dimension == "width" ? "x" : "y"
-            )?.scale;
+            )?.getScale();
 
             if (scale) {
                 // Note: this and all ancestral views need to be refreshed when the domain is changed.
@@ -497,7 +507,7 @@ export default class View {
     }
 
     /**
-     * Get all descendants of this view in depth-first order.
+     * Get this view and all descendants in depth-first order.
      */
     getDescendants() {
         /** @type {View[]} */
@@ -508,6 +518,52 @@ export default class View {
         return descendants;
     }
 
+    /**
+     * Release resources owned by this view.
+     */
+    dispose() {
+        for (const disposer of this.#disposers) {
+            disposer();
+        }
+        this.#disposers.length = 0;
+
+        const handle = this.flowHandle;
+
+        if (handle?.collector) {
+            this.context.dataFlow.pruneCollectorBranch(handle.collector);
+            this.context.dataFlow.removeCollector(handle.collector);
+        }
+
+        if (
+            handle?.dataSource &&
+            handle.dataSource.view === this &&
+            !handle.dataSource.identifier
+        ) {
+            this.context.dataFlow.removeDataSource(handle.dataSource);
+        }
+
+        this.flowHandle = undefined;
+    }
+
+    /**
+     * @param {() => void} disposer
+     */
+    registerDisposer(disposer) {
+        this.#disposers.push(disposer);
+    }
+
+    /**
+     * Dispose this view and all descendants in post-order.
+     */
+    disposeSubtree() {
+        /** @type {Visitor} */
+        const visitor = () => undefined;
+        visitor.postOrder = (view) => {
+            view.dispose();
+        };
+        this.visit(visitor);
+    }
+
     /**
      * Called after all scales in the view hierarchy have been resolved.
      */
@@ -787,7 +843,7 @@ function createViewOpacityFunction(view) {
         } else if (isDynamicOpacity(opacityDef)) {
             /** @type {(channel: import("../spec/channel.js").ChannelWithScale) => any} */
             const getScale = (channel) => {
-                const scale = view.getScaleResolution(channel)?.scale;
+                const scale = view.getScaleResolution(channel)?.getScale();
                 // Only works on linear scales
                 if (["linear", "index", "locus"].includes(scale?.type)) {
                     return scale;

package/dist/src/view/viewDispose.test.d.ts

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

package/dist/src/view/viewDispose.test.d.ts.map

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

package/dist/src/view/viewUtils.d.ts

@@ -35,11 +35,11 @@ export function checkForDuplicateScaleNames(root: View): void;
  */
 export function setImplicitScaleNames(root: View): void;
 /**
- * @param {View} root
- * @param {import("../data/dataFlow.js").default<View>} [existingFlow] Add data flow
- *      graphs to an existing DataFlow object.
+ * @param {Promise<import("../marks/mark.js").default>[]} graphicsPromises
+ * @param {() => boolean} [shouldFinalize]
+ * @returns {Promise<void>}
  */
-export function initializeData(root: View, existingFlow?: import("../data/dataFlow.js").default<View>): Promise<import("../data/dataFlow.js").default<View>>;
+export function finalizeSubtreeGraphics(graphicsPromises: Promise<import("../marks/mark.js").default>[], shouldFinalize?: () => boolean): Promise<void>;
 /**
  *
  * @param {View} view

package/dist/src/view/viewUtils.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"viewUtils.d.ts","sourceRoot":"","sources":["../../../src/view/viewUtils.js"],"names":[],"mappings":"AASA;;;;GAIG;AACH,qCAHW,OAAO,oBAAoB,EAAE,UAAU,GAAG,OAAO,iBAAiB,EAAE,YAAY,GAC9E,IAAI,IAAI,aAAa,CAIjC;AAED;;;;GAIG;AACH,oCAHW,OAAO,oBAAoB,EAAE,aAAa,GAAG,OAAO,iBAAiB,EAAE,YAAY,GACjF,IAAI,IAAI,YAAY,CAOhC;AAED;;;GAGG;AACH,+BAFW,IAAI,6EAMd;AAED;;;;GAIG;AACH,wCAFW,IAAI,UASd;AAED;;GAEG;AACH,kDAFW,IAAI,QAiBd;AAED;;;;;;;GAOG;AACH,4CAFW,IAAI,QAUd;AAED;;;;GAIG;AACH,0DAJW,OAAO,CAAC,OAAO,kBAAkB,EAAE,OAAO,CAAC,EAAE,mBAC7C,MAAM,OAAO,GACX,OAAO,CAAC,IAAI,CAAC,CAmBzB;AAED;;;GAGG;AACH,wCAFW,IAAI;UAGO,QAAQ;aAAW,OAAO,oBAAoB,EAAE,OAAO;WAAS,OAAO,oBAAoB,EAAE,KAAK;UAAQ,OAAO,oBAAoB,EAAE,IAAI;IAqBhK;AAED;;;;;GAKG;AACH,2CALW,OAAO,iBAAiB,EAAE,UAAU,WACpC,MAAM,eACN,OAAO,yBAAyB,EAAE,OAAO,GACvC,OAAO,CAAC,OAAO,iBAAiB,EAAE,QAAQ,CAAC,CAsCvD;AAED;;GAEG;AACH,yCAFW,CAAS,IAAI,EAAJ,IAAI,EAAE,IAAM,EAAN,IAAI,EAAE,KAAE,IAAI,+BAkBrC;AAED;;;;;;GAMG;AACH,4CAJW,IAAI,QACJ,MAAM,GACJ,IAAI,EAAE,CAalB;AAED;;;GAGG;AACH,0CAFW,IAAI,eAqBd;AAED;;GAEG;AACH,8CAFW,OAAO,WAAW,EAAE,OAAO;;;EAoBrC;iBA/Q4C,WAAW;qBAFnC,eAAe"}

package/dist/src/view/viewUtils.js

@@ -3,8 +3,6 @@ import { isObject, isString } from "vega-util";
 import UnitView from "./unitView.js";
 // eslint-disable-next-line no-unused-vars
 import View, { VISIT_SKIP, VISIT_STOP } from "./view.js";
-import { buildDataFlow } from "./flowBuilder.js";
-import { optimizeDataFlow } from "../data/flowOptimizer.js";
 import { isFieldDef, primaryPositionalChannels } from "../encoder/encoder.js";
 import { rollup } from "d3-array";
 import { concatUrl, getDirectory } from "../utils/url.js";
@@ -93,21 +91,27 @@ export function setImplicitScaleNames(root) {
 }
 
 /**
- * @param {View} root
- * @param {import("../data/dataFlow.js").default<View>} [existingFlow] Add data flow
- *      graphs to an existing DataFlow object.
+ * @param {Promise<import("../marks/mark.js").default>[]} graphicsPromises
+ * @param {() => boolean} [shouldFinalize]
+ * @returns {Promise<void>}
  */
-export async function initializeData(root, existingFlow) {
-    const flow = buildDataFlow(root, existingFlow);
-    optimizeDataFlow(flow);
-    flow.initialize();
-
-    /** @type {Promise<void>[]} */
-    const promises = flow.dataSources.map((dataSource) => dataSource.load());
-
-    await Promise.all(promises);
+export function finalizeSubtreeGraphics(
+    graphicsPromises,
+    shouldFinalize = () => true
+) {
+    return Promise.allSettled(graphicsPromises).then((results) => {
+        if (!shouldFinalize()) {
+            return;
+        }
 
-    return flow;
+        for (const result of results) {
+            if ("value" in result) {
+                result.value.finalizeGraphicsInitialization();
+            } else if ("reason" in result) {
+                console.error(result.reason);
+            }
+        }
+    });
 }
 
 /**

package/dist/src/view/viewUtils.test.d.ts

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

package/dist/src/view/viewUtils.test.d.ts.map

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

package/package.json

@@ -7,7 +7,7 @@
   },
   "contributors": [],
   "license": "MIT",
-  "version": "0.64.0",
+  "version": "0.66.1",
   "jsdelivr": "dist/bundle/index.js",
   "unpkg": "dist/bundle/index.js",
   "browser": "dist/bundle/index.js",
@@ -36,14 +36,12 @@
     "postpack": "node scripts/postpack.mjs"
   },
   "dependencies": {
-    "@gmod/bam": "^4.0.1",
-    "@gmod/bbi": "^5.0.2",
-    "@gmod/bed": "^2.1.3",
-    "@gmod/bgzf-filehandle": "^1.5.5",
-    "@gmod/gff": "^1.3.0",
-    "@gmod/indexedfasta": "^2.1.1",
-    "@gmod/tabix": "^1.6.1",
-    "@gmod/vcf": "^6.0.0",
+    "@gmod/bam": "^7.0.5",
+    "@gmod/bbi": "^7.1.0",
+    "@gmod/bed": "^2.1.7",
+    "@gmod/indexedfasta": "^4.0.7",
+    "@gmod/tabix": "^3.1.2",
+    "@gmod/vcf": "^6.1.0",
     "@types/d3-array": "^3.2.2",
     "@types/d3-dsv": "^3.0.7",
     "@types/d3-ease": "^3.0.2",
@@ -56,6 +54,8 @@
     "d3-format": "^3.1.0",
     "events": "^3.3.0",
     "flatqueue": "^2.0.3",
+    "generic-filehandle2": "^2.0.14",
+    "gff-nostream": "^2.0.0",
     "internmap": "^2.0.3",
     "lit": "^3.3.0",
     "twgl.js": "^4.19.1",
@@ -67,5 +67,5 @@
   "devDependencies": {
     "@types/long": "^4.0.1"
   },
-  "gitHead": "a1edb39d7a50b3a2b05c9ee0d860170065fd5ad6"
+  "gitHead": "fa34fedd04f743754e79c0bcdcada56ba5846769"
 }

package/dist/bundle/__vite-browser-external-C--ziKoh.js

@@ -1,8 +0,0 @@
-const e = {}, t = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProperty({
-  __proto__: null,
-  default: e
-}, Symbol.toStringTag, { value: "Module" }));
-export {
-  e as L,
-  t as _
-};

package/dist/bundle/_commonjsHelpers-DjF3Plf2.js

@@ -1,26 +0,0 @@
-function n(e) {
-  return e && e.__esModule && Object.prototype.hasOwnProperty.call(e, "default") ? e.default : e;
-}
-function c(e) {
-  if (e.__esModule) return e;
-  var o = e.default;
-  if (typeof o == "function") {
-    var t = function r() {
-      return this instanceof r ? Reflect.construct(o, arguments, this.constructor) : o.apply(this, arguments);
-    };
-    t.prototype = o.prototype;
-  } else t = {};
-  return Object.defineProperty(t, "__esModule", { value: !0 }), Object.keys(e).forEach(function(r) {
-    var u = Object.getOwnPropertyDescriptor(e, r);
-    Object.defineProperty(t, r, u.get ? u : {
-      enumerable: !0,
-      get: function() {
-        return e[r];
-      }
-    });
-  }), t;
-}
-export {
-  c as a,
-  n as g
-};