@genome-spy/core 0.50.0 → 0.50.1

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

@@ -1 +1 @@
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+{"version":3,"file":"genomeSpy.d.ts","sourceRoot":"","sources":["../../src/genomeSpy.js"],"names":[],"mappings":"AA6CA;IACI;;;;;OAKG;IAEH;;;;;OAKG;IACH,uBAJW,WAAW,qDAEX,OAAO,qBAAqB,EAAE,YAAY,EA6FpD;IA1FG,uBAA0B;IAC1B,oDAAsB;IAItB,6BAA6B;IAC7B,uBADW,CAAC,MAAM,IAAI,CAAC,EAAE,CACM;IAE/B,sCAAsC;IACtC,wCAAgB;IAEhB,yBAAoC;IAEpC,4CAA4C;IAC5C,oBADW,QAAU,MAAM,KAAE,MAAM,EAAE,CAAC,EAAE,CACZ;IAE5B,mBAAoD;IAEpD,0BAA0B;IAC1B,aADW,WAAW,CACM;IAE5B;;;;;OAKG;IACH,qEAF0B,OAAO,CAE8B;IAE/D,2CAA2C;IAC3C,mBADW,4BAA4B,CACL;IAClC,2CAA2C;IAC3C,iBADW,4BAA4B,CACP;IAEhC,oDAAoD;IACpD,6BAAgC;IAEhC;;;OAGG;IACH,eAFU;QAAE,IAAI,EAAE,OAAO,iBAAiB,EAAE,OAAO,CAAC;QAAC,KAAK,EAAE,OAAO,oBAAoB,EAAE,KAAK,CAAC;QAAC,QAAQ,EAAE,MAAM,CAAA;KAAE,CAEpF;IAE9B,uBAA+C;IAE/C;;;OAGG;IACH,oBAFU,IAAI,MAAM,EAAE,QAAU,aAAa,KAAE,IAAI,CAAC,EAAE,CAAC,CAEpB;IAEnC;;;;;;OAMG;IACH,yCAFkC,GAAG,KAAK,IAAI,GAEd;IAEhC;;;OAGG;IACH,kDAFkC,GAAG,KAAK,IAAI,GAEL;IAEzC,oFAAoF;IACpF,iBADW,OAAO,MAAM,EAAE,OAAO,6BAA6B,EAAE,cAAc,CAAC,CAK9E;IAED,mBAAmB;IACnB,2CAAyB;IAEzB;;;;OAIG;IACH;gBAF8B,OAAO,wBAAwB,EAAE,iBAAiB;iBAAW,MAAM;OAEnE;IAE9B;;OAEG;IACH,wBAFU,WAAW,CAEkB;IAEvC,oBAAoB;IACpB,kBADW,KAAK,CACiB;IA2CrC;;;OAGG;IACH,2CAFkB,MAAM,KAAK,GAAG,EAAE,QAIjC;IAED;;OAEG;IACH,+BAFW,MAAM,YAShB;IAED;;;;OAIG;IACH,sBAHW,MAAM,QACN,GAAG,EAAE,QAaf;IAED;;;;;OAKG;IACH,gBAHW,kBAAkB,YAClB,GAAG,QAQb;IAED;;;OAGG;IACH,iCAwDC;IA4DG,uBAQC;IAGD,mCAGE;IAOF,sCAEE;IAGF,iBAA0C;IAW9C;;OAEG;IACH,gBAuBC;IAED,sCA6MC;IAED;;;OAGG;IACH,UAFa,QAAQ,OAAO,CAAC,CA6B5B;IAED,4BA8JC;IAvIe,iCAAoC;IAyIpD;;;OAGG;IACH,kBAHW,MAAM,KACN,MAAM,QAqEhB;IAED;;;;;;;OAOG;IACH,oDAHuB,QAAQ,MAAM,GAAG,WAAW,GAAG,OAAO,KAAK,EAAE,cAAc,CAAC,QAYlF;IAED,sBA6CC;IAED,kBAIC;IAED,iCAOC;IAED,iCASC;IAED,qFAWC;;CACJ;;;;iCAt8BY,eAAe,GAAG,YAAY,GAAG,QAAQ,GAAG,gBAAgB;4BAP7B,uBAAuB;qBAZ9C,qBAAqB;wBAIlB,yBAAyB;yCARR,yDAAyD;oBAYvD,oBAAoB;kBAT7C,wBAAwB;wBALlB,qBAAqB;oBATzB,uBAAuB;qBAOtB,oBAAoB"}

package/dist/src/genomeSpy.js

@@ -10,7 +10,6 @@ import {
     checkForDuplicateScaleNames,
     setImplicitScaleNames,
     calculateCanvasSize,
-    calculateViewRootSize,
 } from "./view/viewUtils.js";
 import UnitView from "./view/unitView.js";
 
@@ -288,6 +287,9 @@ export default class GenomeSpy {
         // Do some hacks to stop css animations of the loading indicators.
         // Otherwise they fire animation frames even when their opacity is zero.
         // TODO: Instead of this, replace the animated spinners with static images.
+        // Or even better, once more widely supported, use `allow-discrete`
+        // https://developer.mozilla.org/en-US/docs/Web/CSS/transition-behavior
+        // to enable transition of the display property.
         if (isSomethingVisible()) {
             this.loadingIndicatorsElement.style.display = "block";
         } else {
@@ -316,10 +318,12 @@ export default class GenomeSpy {
             this.renderAll();
         };
 
-        // 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());
+        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;
@@ -362,7 +366,7 @@ export default class GenomeSpy {
             canvasWrapper,
             () =>
                 this.viewRoot
-                    ? calculateCanvasSize(calculateViewRootSize(this.viewRoot))
+                    ? calculateCanvasSize(this.viewRoot.getSize())
                     : { width: undefined, height: undefined },
             this.spec.background,
             { powerPreference: this.options.powerPreference ?? "default" }
@@ -384,7 +388,7 @@ export default class GenomeSpy {
         });
         canvasWrapper.appendChild(this.loadingIndicatorsElement);
 
-        this.tooltip = new Tooltip(canvasWrapper);
+        this.tooltip = new Tooltip(this.container);
 
         this.loadingMessageElement
             .querySelector(".message")
@@ -539,7 +543,7 @@ export default class GenomeSpy {
         );
 
         this.#canvasWrapper.style.flexGrow =
-            calculateViewRootSize(this.viewRoot).height.grow > 0 ? "1" : "0";
+            this.viewRoot.getSize().height.grow > 0 ? "1" : "0";
 
         this.#initializeParameterBindings();
 

package/dist/src/marks/mark.d.ts

@@ -236,6 +236,7 @@ export default class Mark<P extends import("../spec/mark.js").MarkProps = import
     /**
      * @param {DrawFunction} draw A function that draws a range of vertices
      * @param {import("./mark.js").MarkRenderingOptions} options
+     * @returns {function():void}
      */
     createRenderCallback(draw: DrawFunction, options: import("./mark.js").MarkRenderingOptions): () => void;
     /**

package/dist/src/marks/mark.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"mark.d.ts","sourceRoot":"","sources":["../../../src/marks/mark.js"],"names":[],"mappings":";AAoDA,0DAA2D;AAC3D,0DAA2D;AAE3D;;;;;;;;;;;GAWG;AAEH;;GAEG;AACH;IAgBI;;OAEG;IACH,sBAFW,OAAO,qBAAqB,EAAE,OAAO,EAoG/C;IAjGG,gDAAwB;IAExB,8EAA8E;IAC9E,uGAAyB;IAIzB;;;OAGG;IACH,sBAHU,OAAO,SAAS,EAAE,UAAU,GAAG;QAAE,iBAAiB,CAAC,EAAE,MAAM,CAAA;KAAE,CAG5C;IAE3B;;;;;;;OAOG;IACH,2BAHU,IAAI,MAAM,EAAE,MAAM,CAAC,CAGG;IAEhC;;;OAGG;IACH,uBAHU,OAAO,SAAS,EAAE,WAAW,CAGX;IAE5B;;;OAGG;IACH,2BAHU,OAAO,SAAS,EAAE,eAAe,CAGX;IAEhC;;;OAGG;IACH,2BAHU,OAAO,SAAS,EAAE,gBAAgB,CAGZ;IAEhC;;;;;OAKG;IACH,2BAHU,OAAO,SAAS,EAAE,gBAAgB,CAGZ;IAEhC;;;;;OAKG;IACH,uCAA+B;IAE/B,kFAAkF;IAClF,UADW,SAAS,GAAG,CAAC,CACM;IAG9B,qBAqBE;IAEF;;;;;;OAMG;IACH,qBAHU,CAAC,CAQV;IAGL;;;OAGG;IACH,0CAHW,QAAQ,CAAC,CAAC,QAQpB;IAED,sBAEC;IAED;;;;;OAKG;IACH,2BAHa,OAAO,oBAAoB,EAAE,OAAO,EAAE,CAMlD;IAED;;OAEG;IACH,+DAWC;IAED;;OAEG;IACH,4DAcC;IAED;;;;;OAKG;IACH,oGAEC;IAED;;;;;;OAMG;IACH,oDAHW,CAAC,MAAM,CAAC,CAAC,EAAE,QAqCrB;IAED;;;;OAIG;IACH,sDAiDC;IAED,wDAEC;IAED,uDAEC;IAED,uBAEC;IAED;;;OAGG;IACH,2BAEC;IAED;;OAEG;IACH,oCAEC;IAED;;OAEG;IACH,2BAEC;IAED,sEAeC;IAED;;;;;;OAMG;IAEH,6CANW,MAAM,kBACN,MAAM,iBACN,MAAM,EAAE,QA8UlB;IALG;;;;;;MAIC;IAGL;;;;;;OAMG;IACH,uCA6CC;IAED;;;;;;OAMG;IACH,+CAHW,MAAM,UACK,GAAG,KAAE,IAAI,CAe9B;IAED;;;;;;;;;;OAUG;IACH,mDAJW,MAAM,sFAEsB,GAAG,QA6BzC;IAED;;OAEG;IACH,2BAwBC;IAED;;;OAGG;IACH,6BAFW,GAAG,QAyCb;IAED,yBAAyB;IACzB,uDAEC;IAED,yBAAyB;IACzB,iCAEC;IAED,gCAEC;IAED,+BAEC;IAED,yCAEC;IAED;;OAEG;IACH,gCAgBC;IAED;;OAEG;IACH,4CAOC;IAED;;;;;;;;OAQG;IAEH,uBAJW,OAAO,uBAAuB,EAAE,sBAAsB,GACpD,CAAC,MAAM,IAAI,CAAC,EAAE,CAsF1B;IAED;;;;;;OAMG;IACH,qCAJW,oBAAoB,GAClB,OAAO,CAqCnB;IAED;;;;;;;OAOG;IACH,gBAJW,oBAAoB,SACP,IAAI,CAM3B;IAED;;;;OAIG;IACH,2BAJW,YAAY,WACZ,OAAO,WAAW,EAAE,oBAAoB,SAC3B,IAAI,CAmE3B;IAED;;;;;;OAMG;IACH,oBAJW,OAAO,6BAA6B,EAAE,OAAO,aAC7C,OAAO,6BAA6B,EAAE,OAAO,GAC3C,OAAO,CAuHnB;IAED;;;;;;;;;OASG;IACH,qBAJW,MAAM,KACN,OAAO,oBAAoB,EAAE,MAAM,GACjC,GAAG,CAIf;;CACJ;+BArxCY,OAAO,uBAAuB,EAAE,gBAAgB;;;;;;wBAEnD,OAAO;;mCAEJ,gBAAgB,GAAG,qBAAqB;oCAG1C,MAAM,SACN,MAAM;AA+wCjB;;;GAGG;AACH;IACI,cAEC;IAkBD;;;OAGG;IACH,2BAFW,IAAI,CAAC,EAAE,OAAO,yBAAyB,EAAE,UAAU,CAAC,QAiB9D;CACJ;0BA/0CyB,WAAW"}

package/dist/src/marks/mark.js

@@ -1148,13 +1148,16 @@ export default class Mark {
     /**
      * @param {DrawFunction} draw A function that draws a range of vertices
      * @param {import("./mark.js").MarkRenderingOptions} options
+     * @returns {function():void}
      */
     createRenderCallback(draw, options) {
         if (!this.bufferInfo) {
-            throw new ViewError(
-                `${this.getType()} mark has no data. This is bug.`,
-                this.unitView
-            );
+            // This happens if the layout is computed before the data flow has propagated.
+            // However, it's not a big deal, because this will be called again at the end
+            // of the initialization process.
+
+            // Return no operation
+            return () => undefined;
         }
 
         // eslint-disable-next-line consistent-this

package/dist/src/spec/mark.d.ts

@@ -10,9 +10,24 @@ export interface MarkPropsBase {
 
     // Channels.
 
+    /**
+     * Position on the x axis.
+     */
     x?: number | ExprRef;
+
+    /**
+     * Position on the y axis.
+     */
     y?: number | ExprRef;
+
+    /**
+     * Color of the mark. Affects either `fill` or `stroke`, depending on the `filled` property.
+     */
     color?: string | ExprRef;
+
+    /**
+     * Opacity of the mark. Affects `fillOpacity` or `strokeOpacity`, depending on the `filled` property.
+     */
     opacity?: number | ExprRef;
 
     /**
@@ -48,7 +63,9 @@ export interface MarkPropsBase {
     minBufferSize?: number;
 
     /**
-     * Tooltip handler. If `null`, no tooltip is shown.
+     * Tooltip handler. If `null`, no tooltip is shown. If string, specifies
+     * the [tooltip handler](https://genomespy.app/docs/api/#custom-tooltip-handlers)
+     * to use.
      */
     tooltip?: Tooltip;
 }
@@ -73,12 +90,12 @@ export interface FillAndStrokeProps {
     filled?: boolean;
 
     /**
-     * The fill color
+     * The fill color.
      */
     fill?: string | ExprRef;
 
     /**
-     * The fill opacity. Value between [0, 1].
+     * The fill opacity. Value between `0` and `1`.
      */
     fillOpacity?: number | ExprRef;
 
@@ -88,13 +105,20 @@ export interface FillAndStrokeProps {
     stroke?: string | ExprRef;
 
     /**
-     * The stroke opacity. Value between [0, 1].
+     * The stroke opacity. Value between `0` and `1`.
      */
     strokeOpacity?: number | ExprRef;
 }
 
 export interface SecondaryPositionProps {
+    /**
+     * The secondary position on the x axis.
+     */
     x2?: number | ExprRef;
+
+    /**
+     * The secondary position on the y axis.
+     */
     y2?: number | ExprRef;
 }
 
@@ -385,11 +409,12 @@ export interface PointProps
 
     /**
      * One of `"circle"`, `"square"`, `"cross"`, `"diamond"`, `"triangle-up"`,
-     * `"triangle-down"`, `"triangle-right"`, or `"triangle-left"`.
+     * `"triangle-down"`, `"triangle-right"`, `"triangle-left"`, `"tick-up"`,
+     * `"tick-down"`, `"tick-right"`, or `"tick-left"`
      *
      * **Default value:** `"circle"`
      */
-    shape?: string;
+    shape?: string | ExprRef;
 
     /**
      * Should the stroke only grow inwards, e.g, the diameter/outline is not affected by the stroke width.
@@ -402,7 +427,7 @@ export interface PointProps
 
     /**
      * Gradient strength controls the amount of the gradient eye-candy effect in the fill color.
-     * Valid values are between 0 and 1.
+     * Valid values are between `0` and `1`.
      *
      * **Default value:** `0`
      */
@@ -432,7 +457,16 @@ export interface LinkProps
     type: "link";
 
     /**
-     * The shape of the link path. Either `"arc"`, `"diagonal"`, `"line"`, or `"dome"`.
+     * The shape of the link path.
+     *
+     * The `"arc"` shape draws a circular arc between the two points. The apex of the
+     * arc resides on the left side of the line that connects the two points.
+     * The `"dome"` shape draws a vertical or horizontal arc with a specific height.
+     * The primary positional channel determines the apex of the arc and the secondary
+     * determines the endpoint placement.
+     * The `"diagonal"` shape draws an "S"-shaped curve between the two points.
+     * The `"line"` shape draws a straight line between the two points. See an
+     * [example](#different-link-shapes-and-orientations) of the different shapes below.
      *
      * **Default value:** `"arc"`
      */
@@ -459,7 +493,7 @@ export interface LinkProps
      * The number of segments in the bézier curve. Affects the rendering quality and performance.
      * Use a higher value for a smoother curve.
      *
-     * **Default value:* `101`
+     * **Default value:** `101`
      */
     segments?: number | ExprRef;
 

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

@@ -13,10 +13,16 @@ import { SampleSpec } from "./sampleView.js";
 import { Parameter } from "./parameter.js";
 
 export interface SizeDef {
-    /** Size in pixels */
+    /**
+     * Size in pixels
+     */
     px?: number;
 
-    /** Share of the remaining space */
+    /**
+     * Share of the remaining space. See [child
+     * sizing](https://genomespy.app/docs/grammar/composition/concat/#child-sizing)
+     * for details.
+     */
     grow?: number;
 }
 
@@ -34,9 +40,15 @@ export interface FacetMapping {
  */
 export interface DynamicOpacity {
     channel?: PrimaryPositionalChannel;
-    /** Stops expressed as units (base pairs, for example) per pixel. */
+
+    /**
+     * Stops expressed as units (base pairs, for example) per pixel.
+     */
     unitsPerPixel: number[];
-    /** Opacity values that match the given stops. */
+
+    /**
+     * Opacity values that match the given stops.
+     */
     values: number[];
 }
 
@@ -65,17 +77,25 @@ export type ViewBackground = Pick<
 >;
 
 export interface ViewSpecBase extends ResolveSpec {
+    /**
+     * An internal name that can be used for referring the view. For referencing
+     * purposes, the name should be unique within the view hierarchy.
+     */
     name?: string;
 
     /**
      * Height of the view. If a number, it is interpreted as pixels.
+     * Check [child sizing](https://genomespy.app/docs/grammar/composition/concat/#child-sizing)
+     * for details.
      *
-     * **Default:** `"container"`
+     * **Default value:** `"container"`
      */
     height?: SizeDef | number | Step | "container";
 
     /**
      * Width of the view. If a number, it is interpreted as pixels.
+     * Check [child sizing](https://genomespy.app/docs/grammar/composition/concat/#child-sizing)
+     * for details.
      *
      * **Default:** `"container"`
      */
@@ -83,7 +103,8 @@ export interface ViewSpecBase extends ResolveSpec {
 
     /**
      * Optional viewport height of the view. If the view size exceeds the viewport height,
-     * it will be shown with scrollbars. This property implicitly enables clipping.
+     * it will be shown with [scrollbars](https://genomespy.app/docs/grammar/composition/concat/#scrollable-viewports).
+     * This property implicitly enables clipping.
      *
      * **Default:** `null` (same as `height`)
      */
@@ -91,85 +112,140 @@ export interface ViewSpecBase extends ResolveSpec {
 
     /**
      * Optional viewport width of the view. If the view size exceeds the viewport width,
-     * it will be shown with scrollbars. This property implicitly enables clipping.
+     * it will be shown with [scrollbars](https://genomespy.app/docs/grammar/composition/concat/#scrollable-viewports).
+     * This property implicitly enables clipping.
      *
      * **Default:** `null` (same as `width`)
      */
     viewportWidth?: SizeDef | number | "container";
 
     /**
-     * Padding in pixels.
+     * Padding applied to the view. Accepts either a number representing pixels or an
+     * object specifying separate paddings for each edge.
+     *
+     * Examples:
+     * - `padding: 10`
+     * - `padding: { top: 10, right: 20, bottom: 10, left: 20 }`
      *
-     * **Default:* `0`
+     * **Default value:** `0`
      */
     padding?: PaddingConfig;
 
     /**
-     * Dynamic variables that parameterize a visualization.
+     * Dynamic variables that [parameterize](https://genomespy.app/docs/grammar/parameters/)
+     * a visualization.
      */
     params?: Parameter[];
 
+    /**
+     * Specifies a [data source](https://genomespy.app/docs/grammar/data/).
+     * If omitted, the data source is inherited from the parent view.
+     */
     data?: Data;
+
+    /**
+     * An array of [transformations](https://genomespy.app/docs/grammar/transform/)
+     * applied to the data before visual encoding.
+     */
     transform?: TransformParams[];
+
+    /**
+     * Specifies how data are [encoded](https://genomespy.app/docs/grammar/mark/#encoding)
+     * using the visual channels.
+     */
     encoding?: Encoding;
-    title?: string | Title;
 
     /**
-     * A description of the view. Multiple lines can be provided as an array.
+     * View title.
+     * N.B.: Currently, GenomeSpy doesn't do bound calculation, and you need to
+     * manually specify proper padding for the view to ensure that the title is
+     * visible.
      */
-    description?: string | string[];
+    title?: string | Title;
 
     /**
-     * Optional base URL for constructing request URLs. When set, all views
-     * deeper in the hierarchy inherit this base URL, using it for importing
-     * loading data and importing specifications.
+     * A description of the view. Can be used for documentation. The description
+     * of the top-level view is shown in the toolbar of the [GenomeSpy
+     * App](https://genomespy.app/docs/sample-collections/).
      */
-    baseUrl?: string;
+    description?: string | string[];
 
     /**
-     * Opacity of the view and all its children.
-     *
-     * **Default:** `1.0`
+     * The base URL for relative URL data sources and URL
+     * [imports](https://genomespy.app/docs/grammar/import/#importing-from-a-url).
+     * The base URLs are inherited in the view hierarchy unless overridden with
+     * this property. By default, the top-level view's base URL equals to the
+     * visualization specification's base URL.
      */
-    // TODO: Should be available only in Unit and Layer views.
-    opacity?: ViewOpacityDef;
+    baseUrl?: string;
 
     /**
-     * Visibility of the view. An invisible view is removed from the layout
-     * and not rendered.
+     * The default visibility of the view. An invisible view is removed from the
+     * layout and not rendered. For context, see [toggleable view
+     * visibility](https://genomespy.app/docs/sample-collections/visualizing/#toggleable-view-visibility).
      *
      * **Default:** `true`
      */
-    // TODO: Detach invisible views from the data flow.
     visible?: boolean;
 
     /**
-     * Is the visibility configurable interactively from the App.
+     * Is the visibility configurable interactively from the [GenomeSpy
+     * App](https://genomespy.app/docs/sample-collections/).
      * Configurability requires that the view has an explicitly specified name
-     * that is *unique* in within the view specification.
+     * that is *unique* in within the view hierarchy.
      *
      * **Default:** `false` for children of `layer`, `true` for others.
      */
     configurableVisibility?: boolean;
 
     /**
-     * Templates that can be reused within the view specification by importing
-     * them with the template key.
+     * [Templates](https://genomespy.app/docs/grammar/import/#repeating-with-named-templates)
+     * that can be reused within the view specification by importing them with the template key.
      */
     templates?: Record<string, ViewSpec>;
 }
 
-export interface UnitSpec extends ViewSpecBase, AggregateSamplesSpec {
+export interface DynamicOpacitySpec {
+    /**
+     * Opacity of the view and all its children. Allows implementing semantic
+     * zooming where the layers are faded in and out as the user zooms in and out.
+     *
+     * TODO: Write proper documentation with examples.
+     *
+     * **Default:** `1.0`
+     */
+    opacity?: ViewOpacityDef;
+}
+
+export interface UnitSpec
+    extends ViewSpecBase,
+        DynamicOpacitySpec,
+        AggregateSamplesSpec {
+    /**
+     * The background of the view, including fill, stroke, and stroke width.
+     */
     view?: ViewBackground;
+
+    /**
+     * The graphical mark presenting the data objects.
+     */
     mark: MarkType | MarkProps;
 }
 
+// TODO: Some fancy generic typing that would make Aggregating available only
+// inside SampleSpec.
 export interface AggregateSamplesSpec {
-    // TODO: Introduce a type (UnitSpec | LayerSpec) that can ba used in SampleView and here
+    /**
+     * Specifies views that [aggregate](https://genomespy.app/docs/sample-collections/visualizing/#aggregation)
+     * multiple samples within the GenomeSpy App.
+     */
     aggregateSamples?: (UnitSpec | LayerSpec)[];
 }
 
-export interface LayerSpec extends ViewSpecBase, AggregateSamplesSpec {
+export interface LayerSpec
+    extends ViewSpecBase,
+        DynamicOpacitySpec,
+        AggregateSamplesSpec {
     view?: ViewBackground;
     layer: (LayerSpec | UnitSpec | ImportSpec)[];
 }
@@ -196,6 +272,11 @@ export type ResolutionBehavior =
     | "forced";
 
 export interface ResolveSpec {
+    /**
+     * Specifies how scales and axes are
+     * [resolved](https://genomespy.app/docs/grammar/composition/#scale-and-axis-resolution)
+     * in the view hierarchy.
+     */
     resolve?: Partial<
         Record<
             ResolutionTarget,

package/dist/src/styles/genome-spy.css.d.ts

@@ -1,3 +1,3 @@
 export default css;
-declare const css: "\n.genome-spy {\n  font-family: system-ui, \"Segoe UI\", Roboto, Helvetica, Arial, sans-serif, \"Apple Color Emoji\", \"Segoe UI Emoji\", \"Segoe UI Symbol\";\n  position: relative;\n  display: flex;\n  flex-direction: column;\n}\n.genome-spy .canvas-wrapper {\n  position: relative;\n  flex-grow: 1;\n  overflow: hidden;\n}\n.genome-spy canvas {\n  transform: scale(1, 1);\n  opacity: 1;\n  transition: transform 0.6s, opacity 0.6s;\n}\n.genome-spy .loading-message {\n  position: absolute;\n  inset: 0;\n  display: flex;\n  align-items: center;\n  justify-content: center;\n}\n.genome-spy .loading-message .message {\n  color: #666;\n  opacity: 0;\n  transition: opacity 0.7s;\n}\n.genome-spy .loading > canvas {\n  transform: scale(0.95, 0.95);\n  opacity: 0;\n}\n.genome-spy .loading > .loading-message .message {\n  opacity: 1;\n}\n.genome-spy .loading > .loading-message .message .ellipsis {\n  animation: blinker 1s linear infinite;\n}\n@keyframes blinker {\n  50% {\n    opacity: 0;\n  }\n}\n.genome-spy .loading-indicators {\n  position: absolute;\n  inset: 0;\n  user-select: none;\n  pointer-events: none;\n}\n.genome-spy .loading-indicators div {\n  position: absolute;\n  display: flex;\n  align-items: center;\n  justify-content: center;\n}\n.genome-spy .loading-indicators div > div {\n  font-size: 11px;\n  transition: opacity 0.2s;\n  background: white;\n  padding: 2px 5px;\n  display: flex;\n  border-radius: 3px;\n  gap: 0.5em;\n  opacity: 0;\n}\n.genome-spy .loading-indicators div > div.loading {\n  opacity: 0.5;\n}\n.genome-spy .loading-indicators div > div.error {\n  opacity: 0.8;\n  color: firebrick;\n}\n.genome-spy .loading-indicators div > div > * {\n  display: block;\n}\n.genome-spy .loading-indicators div > div img {\n  width: 1.5em;\n  height: 1.5em;\n}\n.genome-spy .tooltip {\n  position: absolute;\n  max-width: 450px;\n  overflow: hidden;\n  background: #f6f6f6;\n  padding: 10px;\n  font-size: 13px;\n  box-shadow: 0px 3px 15px 0px rgba(0, 0, 0, 0.21);\n  pointer-events: none;\n  z-index: 100;\n}\n.genome-spy .tooltip > :last-child {\n  margin-bottom: 0;\n}\n.genome-spy .tooltip > .title {\n  padding-bottom: 5px;\n  margin-bottom: 5px;\n  border-bottom: 1px dashed #b6b6b6;\n}\n.genome-spy .tooltip .summary {\n  font-size: 12px;\n}\n.genome-spy .tooltip table {\n  border-collapse: collapse;\n}\n.genome-spy .tooltip table:first-child {\n  margin-top: 0;\n}\n.genome-spy .tooltip table th,\n.genome-spy .tooltip table td {\n  padding: 2px 0.4em;\n  vertical-align: top;\n}\n.genome-spy .tooltip table th:first-child,\n.genome-spy .tooltip table td:first-child {\n  padding-left: 0;\n}\n.genome-spy .tooltip table th {\n  text-align: left;\n  font-weight: bold;\n}\n.genome-spy .tooltip .color-legend {\n  display: inline-block;\n  width: 0.8em;\n  height: 0.8em;\n  margin-left: 0.4em;\n  box-shadow: 0px 0px 3px 1px white;\n}\n.genome-spy .tooltip .attributes .hovered {\n  background-color: #e0e0e0;\n}\n.genome-spy .tooltip .na {\n  color: #aaa;\n  font-style: italic;\n  font-size: 80%;\n}\n.genome-spy .gene-track-tooltip .summary {\n  font-size: 90%;\n}\n.genome-spy .message-box {\n  display: flex;\n  align-items: center;\n  justify-content: center;\n  position: absolute;\n  top: 0;\n  height: 100%;\n  width: 100%;\n}\n.genome-spy .message-box > div {\n  border: 1px solid red;\n  padding: 10px;\n  background: #fff0f0;\n}\n\n.gs-input-binding {\n  display: grid;\n  grid-template-columns: max-content max-content;\n  column-gap: 1em;\n  row-gap: 0.3em;\n  justify-items: start;\n}\n.gs-input-binding > select,\n.gs-input-binding > input:not([type=checkbox]) {\n  width: 100%;\n}\n.gs-input-binding input[type=range] + span {\n  display: inline-block;\n  margin-left: 0.3em;\n  min-width: 2.2em;\n  font-variant-numeric: tabular-nums;\n}\n.gs-input-binding input[type=range],\n.gs-input-binding input[type=radio] {\n  vertical-align: text-bottom;\n}\n.gs-input-binding .radio-group {\n  display: flex;\n  align-items: center;\n}\n.gs-input-binding .description {\n  max-width: 26em;\n  grid-column: 1/-1;\n  color: #777;\n  font-size: 90%;\n  margin-top: -0.5em;\n}\n\n.gs-input-bindings {\n  flex-basis: content;\n  font-size: 14px;\n  padding: 10px;\n}\n";
+declare const css: "\n.genome-spy {\n  font-family: system-ui, \"Segoe UI\", Roboto, Helvetica, Arial, sans-serif, \"Apple Color Emoji\", \"Segoe UI Emoji\", \"Segoe UI Symbol\";\n  position: relative;\n  display: flex;\n  flex-direction: column;\n}\n.genome-spy .canvas-wrapper {\n  position: relative;\n  flex-grow: 1;\n  overflow: hidden;\n}\n.genome-spy canvas {\n  display: block;\n  transform: scale(1, 1);\n  opacity: 1;\n  transition: transform 0.6s, opacity 0.6s;\n}\n.genome-spy .loading-message {\n  position: absolute;\n  inset: 0;\n  display: flex;\n  align-items: center;\n  justify-content: center;\n}\n.genome-spy .loading-message .message {\n  color: #666;\n  opacity: 0;\n  transition: opacity 0.7s;\n}\n.genome-spy .loading > canvas {\n  transform: scale(0.95, 0.95);\n  opacity: 0;\n}\n.genome-spy .loading > .loading-message .message {\n  opacity: 1;\n}\n.genome-spy .loading > .loading-message .message .ellipsis {\n  animation: blinker 1s linear infinite;\n}\n@keyframes blinker {\n  50% {\n    opacity: 0;\n  }\n}\n.genome-spy .loading-indicators {\n  position: absolute;\n  inset: 0;\n  user-select: none;\n  pointer-events: none;\n}\n.genome-spy .loading-indicators div {\n  position: absolute;\n  display: flex;\n  align-items: center;\n  justify-content: center;\n}\n.genome-spy .loading-indicators div > div {\n  font-size: 11px;\n  transition: opacity 0.2s;\n  background: white;\n  padding: 2px 5px;\n  display: flex;\n  border-radius: 3px;\n  gap: 0.5em;\n  opacity: 0;\n}\n.genome-spy .loading-indicators div > div.loading {\n  opacity: 0.5;\n}\n.genome-spy .loading-indicators div > div.error {\n  opacity: 0.8;\n  color: firebrick;\n}\n.genome-spy .loading-indicators div > div > * {\n  display: block;\n}\n.genome-spy .loading-indicators div > div img {\n  width: 1.5em;\n  height: 1.5em;\n}\n.genome-spy .tooltip {\n  position: absolute;\n  max-width: 450px;\n  overflow: hidden;\n  background: #f6f6f6;\n  padding: 10px;\n  font-size: 13px;\n  box-shadow: 0px 3px 15px 0px rgba(0, 0, 0, 0.21);\n  pointer-events: none;\n  z-index: 100;\n}\n.genome-spy .tooltip > :last-child {\n  margin-bottom: 0;\n}\n.genome-spy .tooltip > .title {\n  padding-bottom: 5px;\n  margin-bottom: 5px;\n  border-bottom: 1px dashed #b6b6b6;\n}\n.genome-spy .tooltip .summary {\n  font-size: 12px;\n}\n.genome-spy .tooltip table {\n  border-collapse: collapse;\n}\n.genome-spy .tooltip table:first-child {\n  margin-top: 0;\n}\n.genome-spy .tooltip table th,\n.genome-spy .tooltip table td {\n  padding: 2px 0.4em;\n  vertical-align: top;\n}\n.genome-spy .tooltip table th:first-child,\n.genome-spy .tooltip table td:first-child {\n  padding-left: 0;\n}\n.genome-spy .tooltip table th {\n  text-align: left;\n  font-weight: bold;\n}\n.genome-spy .tooltip .color-legend {\n  display: inline-block;\n  width: 0.8em;\n  height: 0.8em;\n  margin-left: 0.4em;\n  box-shadow: 0px 0px 3px 1px white;\n}\n.genome-spy .tooltip .attributes .hovered {\n  background-color: #e0e0e0;\n}\n.genome-spy .tooltip .na {\n  color: #aaa;\n  font-style: italic;\n  font-size: 80%;\n}\n.genome-spy .gene-track-tooltip .summary {\n  font-size: 90%;\n}\n.genome-spy .message-box {\n  display: flex;\n  align-items: center;\n  justify-content: center;\n  position: absolute;\n  top: 0;\n  height: 100%;\n  width: 100%;\n}\n.genome-spy .message-box > div {\n  border: 1px solid red;\n  padding: 10px;\n  background: #fff0f0;\n}\n\n.gs-input-binding {\n  display: grid;\n  grid-template-columns: max-content max-content;\n  column-gap: 1em;\n  row-gap: 0.3em;\n  justify-items: start;\n}\n.gs-input-binding > select,\n.gs-input-binding > input:not([type=checkbox]) {\n  width: 100%;\n}\n.gs-input-binding input[type=range] + span {\n  display: inline-block;\n  margin-left: 0.3em;\n  min-width: 2.2em;\n  font-variant-numeric: tabular-nums;\n}\n.gs-input-binding input[type=range],\n.gs-input-binding input[type=radio] {\n  vertical-align: text-bottom;\n}\n.gs-input-binding .radio-group {\n  display: flex;\n  align-items: center;\n}\n.gs-input-binding .description {\n  max-width: 26em;\n  grid-column: 1/-1;\n  color: #777;\n  font-size: 90%;\n  margin-top: -0.5em;\n}\n\n.gs-input-bindings {\n  flex-basis: content;\n  font-size: 14px;\n  padding: 10px;\n}\n";
 //# sourceMappingURL=genome-spy.css.d.ts.map

package/dist/src/styles/genome-spy.css.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"genome-spy.css.d.ts","sourceRoot":"","sources":["../../../src/styles/genome-spy.css.js"],"names":[],"mappings":";AAAA,yoIAgME"}
+{"version":3,"file":"genome-spy.css.d.ts","sourceRoot":"","sources":["../../../src/styles/genome-spy.css.js"],"names":[],"mappings":";AAAA,4pIAiME"}

package/dist/src/styles/genome-spy.css.js

@@ -11,6 +11,7 @@ const css = `
   overflow: hidden;
 }
 .genome-spy canvas {
+  display: block;
   transform: scale(1, 1);
   opacity: 1;
   transition: transform 0.6s, opacity 0.6s;

package/dist/src/styles/genome-spy.scss

@@ -20,6 +20,7 @@ $font-family: system-ui, "Segoe UI", Roboto, Helvetica, Arial, sans-serif,
     }
 
     canvas {
+        display: block;
         transform: scale(1, 1);
         opacity: 1;
         transition: transform 0.6s, opacity 0.6s;

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

@@ -123,6 +123,12 @@ export class FlexDimensions {
      * @param {import("./padding.js").default} padding
      */
     subtractPadding(padding: import("./padding.js").default): FlexDimensions;
+    /**
+     * Returns true if either of the dimensions is growing
+     *
+     * @returns {boolean}
+     */
+    isGrowing(): boolean;
     #private;
 }
 /**

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

@@ -1 +1 @@
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+{"version":3,"file":"flexLayout.d.ts","sourceRoot":"","sources":["../../../../src/view/layout/flexLayout.js"],"names":[],"mappings":"AAGA;;;;;;;;;;;;;;;;;;;;;;;;;;;GA2BG;AACH,wCALW,OAAO,EAAE,iBACT,MAAM,mDACN,WAAW,GACT,OAAO,EAAE,CAqGrB;AAED;;;;;GAKG;AACH,sCAHW,SAAS,OAAO,CAAC,gBACjB,WAAW,UAQrB;AAED;;;GAGG;AACH,sCAHW,SAAS,OAAO,CAAC,GACf,OAAO,CAWnB;AAED;;;GAGG;AACH,oCAFW,OAAO,EAAE,WAInB;AAED;;;GAGG;AACH,sCAFW,OAAO,EAAE;;;EASnB;AA4ED;;;;GAIG;AACH,uCAFW,OAAO,WAIjB;AAWD;;;;GAIG;AACH,sDAEC;AAED;;;;GAIG;AACH,mCAHW,WAAW,GAAG,MAAM,GAAG,OAAO,GAAG,OAAO,oBAAoB,EAAE,IAAI,GAChE,OAAO,CAiBnB;AAID;;;;;;;GAOG;AACH,0CALW,OAAO,MACP,OAAO,eACI,MAAM,GACf,OAAO,CA4BnB;AAED;;;;;;GAMG;AACH,0CAJW,OAAO,UACP,MAAM,UAAc,MAAM,CAAA,GACxB,OAAO,CAanB;AAED;;;;;;GAMG;AACH,sCAJW,OAAO,UACP,MAAM,UAAc,MAAM,CAAA,GACxB,OAAO,CAanB;AAED;;;GAGG;AACH,yCAHW,OAAO,SACP,MAAM,WAIhB;AA/MD;IACI;;;;OAIG;IACH,mBAHW,OAAO,UACP,OAAO,EAQjB;IAJG,gBAAgB;IAChB,wBAAkB;IAClB,gBAAgB;IAChB,yBAAoB;IAGxB;;;;OAIG;IACH,oBAFW,OAAO,cAAc,EAAE,OAAO,kBAIxC;IAED;;;;OAIG;IACH,yBAFW,OAAO,cAAc,EAAE,OAAO,kBAIxC;IAmBD;;;;OAIG;IACH,aAFa,OAAO,CAInB;;CACJ;AAED;;;;GAIG;AACH,2BAFU,OAAO,CAKd;AAEH,iDAGE;;;;;;;;SAlPQ,MAAM;;;;WACN,MAAM;;;;;;cAGN,MAAM;UACN,MAAM;;;;;;;;;;;;;;cAGN,MAAM;;;;;uBACN,MAAM;;;;aAEN,MAAM;;;;cACN,OAAO"}

package/dist/src/view/layout/flexLayout.js

@@ -228,6 +228,15 @@ export class FlexDimensions {
             }
         );
     }
+
+    /**
+     * Returns true if either of the dimensions is growing
+     *
+     * @returns {boolean}
+     */
+    isGrowing() {
+        return !!(this.width.grow || this.height.grow);
+    }
 }
 
 /**

package/dist/src/view/view.js

@@ -732,7 +732,7 @@ function isDynamicOpacity(opacity) {
  * @returns {function(number):number}
  */
 function createViewOpacityFunction(view) {
-    const opacityDef = view.spec.opacity;
+    const opacityDef = "opacity" in view.spec ? view.spec.opacity : undefined;
 
     if (opacityDef !== undefined) {
         if (isNumber(opacityDef)) {

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

@@ -74,10 +74,6 @@ export function findDescendantsByPath(root: View, name: string): View[];
  * @param {View} root
  */
 export function findUniqueViewNames(root: View): Set<string>;
-/**
- * @param {View} viewRoot
- */
-export function calculateViewRootSize(viewRoot: View): import("./layout/flexLayout.js").FlexDimensions;
 /**
  * @param {import("./layout/flexLayout.js").FlexDimensions} viewRootSize
  */

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

@@ -1 +1 @@
-{"version":3,"file":"viewUtils.d.ts","sourceRoot":"","sources":["../../../src/view/viewUtils.js"],"names":[],"mappings":"AAWA;;;;GAIG;AACH,qCAHW,OAAO,oBAAoB,EAAE,UAAU,GAAG,OAAO,iBAAiB,EAAE,YAAY,yBAK1F;AAED;;;;GAIG;AACH,oCAHW,OAAO,oBAAoB,EAAE,aAAa,GAAG,OAAO,iBAAiB,EAAE,YAAY,wBAQ7F;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,qCAJW,IAAI,iBACJ,OAAO,qBAAqB,EAAE,OAAO,CAAC,IAAI,CAAC,wDAcrD;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,QAAQ,OAAO,iBAAiB,EAAE,QAAQ,CAAC,CA6BvD;AAED;;GAEG;AACH,gDAFoB,IAAI,QAAE,IAAI,EAAE,KAAE,IAAI,+BAkBrC;AAED;;;;;;GAMG;AACH,4CAJW,IAAI,QACJ,MAAM,GACJ,IAAI,EAAE,CAalB;AAED;;;GAGG;AACH,0CAFW,IAAI,eAqBd;AAOD;;GAEG;AACH,gDAFW,IAAI,mDAId;AAED;;GAEG;AACH,kDAFW,OAAO,wBAAwB,EAAE,cAAc;;;EAczD;AAxBM,uCAFI,MAAM,WAE0D;iBA/O9B,WAAW;qBAFnC,eAAe"}
+{"version":3,"file":"viewUtils.d.ts","sourceRoot":"","sources":["../../../src/view/viewUtils.js"],"names":[],"mappings":"AAWA;;;;GAIG;AACH,qCAHW,OAAO,oBAAoB,EAAE,UAAU,GAAG,OAAO,iBAAiB,EAAE,YAAY,yBAK1F;AAED;;;;GAIG;AACH,oCAHW,OAAO,oBAAoB,EAAE,aAAa,GAAG,OAAO,iBAAiB,EAAE,YAAY,wBAQ7F;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,qCAJW,IAAI,iBACJ,OAAO,qBAAqB,EAAE,OAAO,CAAC,IAAI,CAAC,wDAcrD;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,QAAQ,OAAO,iBAAiB,EAAE,QAAQ,CAAC,CA6BvD;AAED;;GAEG;AACH,gDAFoB,IAAI,QAAE,IAAI,EAAE,KAAE,IAAI,+BAkBrC;AAED;;;;;;GAMG;AACH,4CAJW,IAAI,QACJ,MAAM,GACJ,IAAI,EAAE,CAalB;AAED;;;GAGG;AACH,0CAFW,IAAI,eAqBd;AAOD;;GAEG;AACH,kDAFW,OAAO,wBAAwB,EAAE,cAAc;;;EAczD;AAjBM,uCAFI,MAAM,WAE0D;iBA/O9B,WAAW;qBAFnC,eAAe"}

package/dist/src/view/viewUtils.js

@@ -244,13 +244,6 @@ export function findUniqueViewNames(root) {
  */
 export const isCustomViewName = (name) => !/^(layer|concat)\d+$/.test(name);
 
-/**
- * @param {View} viewRoot
- */
-export function calculateViewRootSize(viewRoot) {
-    return viewRoot.getSize().addPadding(viewRoot.getOverhang());
-}
-
 /**
  * @param {import("./layout/flexLayout.js").FlexDimensions} viewRootSize
  */

package/package.json

@@ -7,7 +7,7 @@
   },
   "contributors": [],
   "license": "MIT",
-  "version": "0.50.0",
+  "version": "0.50.1",
   "jsdelivr": "dist/bundle/index.js",
   "unpkg": "dist/bundle/index.js",
   "browser": "dist/bundle/index.js",
@@ -67,5 +67,5 @@
   "devDependencies": {
     "@types/long": "^4.0.1"
   },
-  "gitHead": "39de1ffdcfdaefe9f34a4d6e092378ccffd267c9"
+  "gitHead": "f21b0f12e961366c12c1d514017c6270246801cc"
 }