@genome-spy/core 0.73.0 → 0.74.0

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

@@ -0,0 +1,51 @@
+import { ShadowProps } from "./mark.js";
+
+export interface ZIndexProps {
+    /**
+     * Z-order relative to the view content.
+     *
+     * Values greater than `0` render after the view marks. Values less than or
+     * equal to `0` render before the marks.
+     * The default value depends on the element type.
+     */
+    zindex?: number;
+}
+
+export interface StrokeZIndexProps {
+    /**
+     * Z-order of the stroke relative to the view content.
+     *
+     * Values greater than `0` render the stroke after the view marks. Values
+     * less than or equal to `0` render before the marks.
+     * The default value depends on the element type.
+     */
+    strokeZindex?: number;
+}
+
+export interface ViewBackgroundProps
+    extends ShadowProps, ZIndexProps, StrokeZIndexProps {
+    /**
+     * Fill color of the view background.
+     */
+    fill?: string;
+
+    /**
+     * Opacity of the view background fill.
+     */
+    fillOpacity?: number;
+
+    /**
+     * Stroke color of the view background.
+     */
+    stroke?: string;
+
+    /**
+     * Stroke width of the view background border.
+     */
+    strokeWidth?: number;
+
+    /**
+     * Opacity of the view background stroke.
+     */
+    strokeOpacity?: number;
+}

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

@@ -0,0 +1,12 @@
+/**
+ * Collects shared example specs used by the offline example suite.
+ *
+ * @returns {string[]}
+ */
+export function collectSharedExamplePaths(): string[];
+/**
+ * @param {string} examplePath
+ * @returns {any}
+ */
+export function loadSharedExampleSpec(examplePath: string): any;
+//# sourceMappingURL=exampleFiles.d.ts.map

package/dist/src/spec/exampleFiles.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"exampleFiles.d.ts","sourceRoot":"","sources":["../../../src/spec/exampleFiles.js"],"names":[],"mappings":"AASA;;;;GAIG;AACH,6CAFa,MAAM,EAAE,CAcpB;AAED;;;GAGG;AACH,mDAHW,MAAM,GACJ,GAAG,CAMf"}

package/dist/src/spec/exampleFiles.js

@@ -0,0 +1,52 @@
+import fs from "fs";
+import path from "path";
+import { fileURLToPath } from "url";
+
+const packageDir = path.dirname(fileURLToPath(import.meta.url));
+const repoRoot = path.resolve(packageDir, "..", "..", "..", "..");
+
+const sharedExampleDirs = ["examples/core", "examples/docs"];
+
+/**
+ * Collects shared example specs used by the offline example suite.
+ *
+ * @returns {string[]}
+ */
+export function collectSharedExamplePaths() {
+    /** @type {string[]} */
+    const paths = [];
+
+    for (const dir of sharedExampleDirs) {
+        visit(path.join(repoRoot, dir), (absolutePath) => {
+            const relativePath = path.relative(repoRoot, absolutePath);
+            paths.push(relativePath.split(path.sep).join("/"));
+        });
+    }
+
+    return paths.sort();
+}
+
+/**
+ * @param {string} examplePath
+ * @returns {any}
+ */
+export function loadSharedExampleSpec(examplePath) {
+    return JSON.parse(
+        fs.readFileSync(path.join(repoRoot, examplePath), "utf8")
+    );
+}
+
+/**
+ * @param {string} dir
+ * @param {(absolutePath: string) => void} visitor
+ */
+function visit(dir, visitor) {
+    for (const entry of fs.readdirSync(dir, { withFileTypes: true })) {
+        const absolutePath = path.join(dir, entry.name);
+        if (entry.isDirectory()) {
+            visit(absolutePath, visitor);
+        } else if (entry.isFile() && entry.name.endsWith(".json")) {
+            visitor(absolutePath);
+        }
+    }
+}

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

@@ -12,4 +12,4 @@ export type FontWeight =
 
 export type Align = "left" | "center" | "right";
 
-export type Baseline = "top" | "middle" | "bottom" | "alphabetic";
+export type Baseline = "top" | "middle" | "bottom" | "alphabetic" | "baseline";

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

@@ -3,11 +3,25 @@ import { ExprRef } from "./parameter.js";
 import { Align, Baseline, FontStyle, FontWeight } from "./font.js";
 import { Tooltip } from "./tooltip.js";
 
-export type MarkType = "rect" | "point" | "rule" | "text" | "link";
+export type MarkType = "rect" | "point" | "rule" | "tick" | "text" | "link";
 
 export interface MarkPropsBase {
     type: MarkType;
 
+    /**
+     * Named style reference(s) resolved from `config.style`.
+     * If an array is provided, later styles override earlier ones.
+     */
+    style?: string | string[];
+
+    /**
+     * Mouse cursor shown while the pointer is over the mark.
+     * Mark cursor takes precedence over enclosing view cursors.
+     *
+     * __Default value:__ browser default
+     */
+    cursor?: string | ExprRef;
+
     // Channels.
 
     /**
@@ -62,6 +76,14 @@ export interface MarkPropsBase {
      */
     minBufferSize?: number;
 
+    /**
+     * Whether the x channel should build an index for efficient subset rendering.
+     * If omitted, GenomeSpy enables indexing automatically for positional x encodings.
+     *
+     * @internal
+     */
+    buildIndex?: boolean;
+
     /**
      * Tooltip handler. If `null`, no tooltip is shown. If string, specifies
      * the [tooltip handler](https://genomespy.app/docs/api/#custom-tooltip-handlers)
@@ -196,7 +218,8 @@ export interface ViewportEdgeFadeProps {
 }
 
 export interface RectProps
-    extends MarkPropsBase,
+    extends
+        MarkPropsBase,
         SecondaryPositionProps,
         FillAndStrokeProps,
         ShadowProps {
@@ -291,15 +314,10 @@ export interface RectProps
         | ExprRef;
 }
 
-export interface RuleProps
-    extends MarkPropsBase,
-        SecondaryPositionProps,
-        SizeProps {
-    type: "rule";
-
+export interface StrokeStyleProps {
     /**
-     * The minimum length of the rule in pixels. Use this property to ensure that
-     * very short ranged rules remain visible even when the user zooms out.
+     * The minimum stroke length in pixels. Use this property to ensure that
+     * very short strokes remain visible even when the user zooms out.
      *
      * **Default value:** `0`
      */
@@ -327,8 +345,38 @@ export interface RuleProps
     strokeCap?: "butt" | "square" | "round" | ExprRef;
 }
 
+export interface RuleProps
+    extends MarkPropsBase, SecondaryPositionProps, SizeProps, StrokeStyleProps {
+    type: "rule";
+}
+
+export interface TickProps extends MarkPropsBase, StrokeStyleProps {
+    type: "tick";
+
+    /**
+     * The orientation of the tick mark.
+     *
+     * If omitted, GenomeSpy infers the orientation when one positional channel
+     * uses a band-like scale and the other does not, or when the orthogonal
+     * channel is omitted. Specify `orient` explicitly when both `x` and `y`
+     * use band-like scales.
+     *
+     * **Default value:** inferred
+     */
+    orient?: "vertical" | "horizontal";
+
+    /**
+     * The thickness of the tick mark in pixels.
+     * Equivalent to the `size` of the underlying rule mark.
+     *
+     * **Default value:** `1`
+     */
+    thickness?: number;
+}
+
 export interface TextProps
-    extends MarkPropsBase,
+    extends
+        MarkPropsBase,
         SecondaryPositionProps,
         AngleProps,
         ViewportEdgeFadeProps,
@@ -457,7 +505,8 @@ export interface TextProps
 }
 
 export interface PointProps
-    extends MarkPropsBase,
+    extends
+        MarkPropsBase,
         FillAndStrokeProps,
         AngleProps,
         SizeProps,
@@ -482,6 +531,29 @@ export interface PointProps
      */
     inwardStroke?: boolean | ExprRef;
 
+    /**
+     * Horizontal offset in pixels.
+     *
+     * **Default value:** `0`
+     */
+    dx?: number | ExprRef;
+
+    /**
+     * Vertical offset in pixels.
+     *
+     * **Default value:** `0`
+     */
+    dy?: number | ExprRef;
+
+    /**
+     * Additional padding used by sample facets.
+     *
+     * **Default value:** `0.1`
+     *
+     * @internal
+     */
+    sampleFacetPadding?: number;
+
     /**
      * Gradient strength controls the amount of the gradient eye-candy effect in the fill color.
      * Valid values are between `0` and `1`.
@@ -490,6 +562,16 @@ export interface PointProps
      */
     fillGradientStrength?: number | ExprRef;
 
+    /**
+     * The semantic score used by semantic zooming in the point mark.
+     * This is primarily intended for internal use.
+     *
+     * **Default value:** `0`
+     *
+     * @internal
+     */
+    semanticScore?: number | ExprRef;
+
     /**
      * TODO
      *
@@ -507,7 +589,8 @@ export interface PointProps
 }
 
 export interface LinkProps
-    extends MarkPropsBase,
+    extends
+        MarkPropsBase,
         SecondaryPositionProps,
         SizeProps,
         MinPickingSizeProps {
@@ -603,5 +686,6 @@ export type MarkProps =
     | RectProps
     | TextProps
     | RuleProps
+    | TickProps
     | LinkProps
     | PointProps;

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

@@ -1,5 +1,6 @@
 import { PrimaryPositionalChannel, Scalar } from "./channel.js";
 import { ShadowProps } from "./mark.js";
+import { ZIndexProps } from "./decoration.js";
 
 export interface ExprRef {
     /**
@@ -180,22 +181,17 @@ export type SelectionInitInterval =
 export type InteractionEventType =
     | "click"
     | "dblclick"
+    | "mouseenter"
+    | "mouseleave"
     | "mouseover"
     | "mousedown"
     | "wheel";
 
-// TODO: merge with InteractionEventType
-export type DomEventType =
-    | "click"
-    | "dblclick"
-    | "mouseover"
-    | "pointerover"
-    | "mousedown"
-    | "wheel";
+export type DomEventType = InteractionEventType | "pointerover";
 
 export interface EventConfig {
     /**
-     * The type of event to listen to. For example, `"click"` or `"mouseover"`.
+     * The type of event to listen to. For example, `"click"` or `"mouseenter"`.
      */
     type: DomEventType;
 
@@ -286,7 +282,14 @@ export interface IntervalSelectionConfig extends BaseSelectionConfig<"interval">
     zoom?: DomEventType | EventConfig | string | boolean;
 }
 
-export interface BrushConfig extends ShadowProps {
+export interface BrushConfig extends ShadowProps, ZIndexProps {
+    /**
+     * Mouse cursor shown while the pointer is over the interval mark.
+     *
+     * __Default value:__ `{ expr: "intervalDragActive ? 'grabbing' : 'move'" }`
+     */
+    cursor?: string | ExprRef;
+
     /**
      * The fill color of the interval mark.
      *
@@ -323,6 +326,23 @@ export interface BrushConfig extends ShadowProps {
      */
     strokeWidth?: number;
 
+    /**
+     * Whether the brush rectangle should be clipped to the viewport.
+     *
+     * __Default value:__ `true`
+     */
+    clip?: boolean | "never";
+
+    /**
+     * Z-order of the interval mark relative to the view content.
+     *
+     * Values greater than `0` render after the view marks. Values less than or
+     * equal to `0` render before the marks.
+     *
+     * __Default value:__ `1`
+     */
+    zindex?: number;
+
     /**
      * Where to display the measurement text (e.g., number of base pairs) for the interval selection.
      *

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

@@ -1,4 +1,5 @@
 import { GenomeConfig, GenomeDefinition } from "./genome.js";
+import { BuiltInThemeName, GenomeSpyConfig } from "./config.js";
 import { ViewSpec } from "./view.js";
 
 export type NamedGenomeConfig = GenomeDefinition | Record<string, never>;
@@ -36,6 +37,19 @@ export interface RootConfig {
      * https://vega.github.io/vega-lite/docs/data.html#datasets
      */
     datasets?: Record<string, any[]>;
+
+    /**
+     * Global configuration defaults and theme tokens.
+     *
+     * The configuration is inherited by descendant views and can be overridden
+     * by view-local `config` objects.
+     */
+    config?: GenomeSpyConfig;
+
+    /**
+     * Selects built-in theme preset(s) for the whole visualization.
+     */
+    theme?: BuiltInThemeName | BuiltInThemeName[];
 }
 
 export type RootSpec = ViewSpec & RootConfig;

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

@@ -234,6 +234,13 @@ export interface Scale {
      * If `true` and the scale is used on a positional channel, it can bee zoomed and translated interactively.
      */
     zoom?: boolean | ZoomParams;
+
+    /**
+     * The numbering offset used when formatting tick labels on index and locus scales.
+     *
+     * __Default value:__ `0`
+     */
+    numberingOffset?: number;
 }
 
 export type InlineLocusAssembly = GenomeDefinition;
@@ -245,25 +252,23 @@ export interface SelectionDomainRef {
     param: string;
 
     /**
-     * Selection interval channel to use.
+     * Initial configured domain for the linked scale when the linked interval
+     * selection is empty.
      *
-     * If omitted, GenomeSpy infers the channel from the scale channel when
-     * possible (e.g., `x` -> `x`, `x2` -> `x`, `y` -> `y`, `y2` -> `y`).
+     * Only supported when the linked scale is zoomable.
+     *
+     * Clearing the linked interval selection resets the domain to the normal
+     * default/data-derived domain instead of restoring `initial`.
      */
-    encoding?: "x" | "y";
+    initial?: ScalarDomain | ComplexDomain;
 
     /**
-     * Domain synchronization mode.
-     *
-     * - `"oneWay"`: selection drives the domain.
-     * - `"twoWay"`: selection drives the domain and zoom/pan updates selection.
-     *
-     * __Default value:__ implicit auto mode:
+     * Selection interval channel to use.
      *
-     * - `"twoWay"` when the linked scale is zoomable
-     * - `"oneWay"` otherwise
+     * If omitted, GenomeSpy infers the channel from the scale channel when
+     * possible (e.g., `x` -> `x`, `x2` -> `x`, `y` -> `y`, `y2` -> `y`).
      */
-    sync?: "oneWay" | "twoWay";
+    encoding?: "x" | "y";
 }
 
 export interface SchemeParams {

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

@@ -10,12 +10,13 @@
 
 import { Align, Baseline, FontStyle, FontWeight } from "./font.js";
 import { ExprRef } from "./parameter.js";
+import { ZIndexProps } from "./decoration.js";
 
 export type TitleOrient = "none" | "left" | "right" | "top" | "bottom";
 export type TitleAnchor = null | "start" | "middle" | "end";
 export type TitleFrame = "bounds" | "group";
 
-export interface Title {
+export interface Title extends ZIndexProps {
     /**
      * The title text.
      */
@@ -24,7 +25,7 @@ export interface Title {
     /**
      * A mark style property to apply to the title text mark. If not specified, a default style of `"group-title"` is applied.
      */
-    style?: string;
+    style?: string | string[];
 
     /**
      * The anchor position for placing the title and subtitle text. One of `"start"`, `"middle"`, or `"end"`. For example, with an orientation of top these anchor positions map to a left-, center-, or right-aligned title.
@@ -41,6 +42,16 @@ export interface Title {
      */
     offset?: number;
 
+    /**
+     * Z-order of the title relative to the view content.
+     *
+     * Values greater than `0` render after the view marks. Values less than or
+     * equal to `0` render before the marks.
+     *
+     * __Default value:__ `1`
+     */
+    zindex?: number;
+
     /**
      * Default title orientation (`"none"`, `"top"`, `"bottom"`, `"left"`, or `"right"`)
      */

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

@@ -6,4 +6,4 @@ export interface HandledTooltip {
 
 // TODO: Encoding / data: https://vega.github.io/vega-lite/docs/tooltip.html#encoding
 
-export type Tooltip = HandledTooltip | null;
+export type Tooltip = HandledTooltip | null | false;

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

@@ -1,4 +1,5 @@
 import { PositionalChannel } from "./channel.js";
+import { FontStyle, FontWeight } from "./font.js";
 import { ExprRef } from "./parameter.js";
 
 /**
@@ -177,7 +178,7 @@ export interface StackParams extends TransformParamsBase {
      *
      * **Default:** `["y0", "y1"]`
      */
-    as: string[];
+    as?: string[];
 
     /**
      * Cardinality, e.g., the number if distinct bases or amino acids. Used for
@@ -204,7 +205,9 @@ export type AggregateOp =
     | "min"
     | "max"
     | "mean"
+    | "q1"
     | "median"
+    | "q3"
     | "variance";
 
 export interface AggregateParams extends TransformParamsBase {
@@ -225,7 +228,7 @@ export interface AggregateParams extends TransformParamsBase {
 
     /**
      * The aggregation operations to be performed on the fields, such as `"sum"`,
-     * `"average"`, or `"count"`.
+     * `"q1"`, `"median"`, `"q3"`, or `"count"`.
      */
     ops?: AggregateOp[];
 
@@ -424,13 +427,45 @@ export interface SampleParams extends TransformParamsBase {
 export interface MeasureTextParams extends TransformParamsBase {
     type: "measureText";
 
+    /**
+     * The field that contains the text to be measured.
+     */
     field: Field;
 
+    /**
+     * The font size in pixels.
+     */
     fontSize: number | ExprRef;
 
-    as: string;
+    /**
+     * The font typeface. Uses the same asynchronously loaded SDF fonts as the
+     * `"text"` mark.
+     *
+     * **Default:** `"Lato"`
+     */
+    font?: string;
+
+    /**
+     * The font style. Valid values: `"normal"` and `"italic"`.
+     *
+     * **Default:** `"normal"`
+     */
+    fontStyle?: FontStyle;
+
+    /**
+     * The font weight. The following strings and numbers are valid values:
+     * `"thin"` (`100`), `"light"` (`300`), `"regular"` (`400`),
+     * `"normal"` (`400`), `"medium"` (`500`), `"bold"` (`700`),
+     * `"black"` (`900`)
+     *
+     * **Default:** `"regular"`
+     */
+    fontWeight?: FontWeight;
 
-    // TODO: FontFamily etc
+    /**
+     * The output field where the measured width is written.
+     */
+    as: string;
 }
 
 export interface MergeFacetsParams extends TransformParamsBase {