@genome-spy/core 0.48.2 → 0.50.0

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

@@ -5,17 +5,91 @@ import { Tooltip } from "./tooltip.js";
 
 export type MarkType = "rect" | "point" | "rule" | "text" | "link";
 
+export interface MarkPropsBase {
+    type: MarkType;
+
+    // Channels.
+
+    x?: number | ExprRef;
+    y?: number | ExprRef;
+    color?: string | ExprRef;
+    opacity?: number | ExprRef;
+
+    /**
+     * If true, the mark is clipped to the UnitView's rectangle. By default, clipping
+     * is enabled for marks that have zoomable positional scales.
+     */
+    clip?: boolean | "never";
+
+    /**
+     * Offsets of the `x` and `x2` coordinates in pixels. The offset is applied
+     * after the viewport scaling and translation.
+     *
+     * **Default value:** `0`
+     */
+    xOffset?: number;
+
+    /**
+     * Offsets of the `y` and `y2` coordinates in pixels. The offset is applied
+     * after the viewport scaling and translation.
+     *
+     * **Default value:** `0`
+     */
+    yOffset?: number;
+
+    /**
+     * Minimum size for WebGL buffers (number of data items).
+     * Allows for using `bufferSubData()` to update graphics.
+     *
+     * This property is intended for internal use.
+     *
+     * @internal
+     */
+    minBufferSize?: number;
+
+    /**
+     * Tooltip handler. If `null`, no tooltip is shown.
+     */
+    tooltip?: Tooltip;
+}
+
+export interface SizeProps {
+    /**
+     * Stroke width of `"link"` and `"rule"` marks in pixels, the area of the
+     * bounding square of `"point"` mark, or the font size of `"text"` mark.
+     */
+    size?: number | ExprRef;
+}
+
 export interface FillAndStrokeProps {
-    /** The fill color */
+    /**
+     * The stroke width in pixels.
+     */
+    strokeWidth?: number | ExprRef;
+
+    /**
+     * Whether the `color` represents the `fill` color (`true`) or the `stroke` color (`false`).
+     */
+    filled?: boolean;
+
+    /**
+     * The fill color
+     */
     fill?: string | ExprRef;
 
-    /** The fill opacity. Value between [0, 1]. */
+    /**
+     * The fill opacity. Value between [0, 1].
+     */
     fillOpacity?: number | ExprRef;
 
-    /** The stroke color */
+    /**
+     * The stroke color
+     */
     stroke?: string | ExprRef;
 
-    /** The stroke opacity. Value between [0, 1]. */
+    /**
+     * The stroke opacity. Value between [0, 1].
+     */
     strokeOpacity?: number | ExprRef;
 }
 
@@ -33,6 +107,17 @@ export interface AngleProps {
     angle?: number | ExprRef;
 }
 
+export interface MinPickingSizeProps {
+    /**
+     * The minimum picking size invisibly increases the stroke width or point diameter
+     * of marks when pointing them with the mouse cursor, making it easier to select them.
+     * The valus is the minimum size in pixels.
+     *
+     * **Default value:** `3.0` for `"link"` and `2.0` for `"point"`
+     */
+    minPickingSize?: number | ExprRef;
+}
+
 /**
  * Specifies how mark should be faded at the viewport edges.
  * This is mainly used to make axis labels pretty.
@@ -49,7 +134,12 @@ export interface ViewportEdgeFadeProps {
     viewportEdgeFadeDistanceLeft?: number;
 }
 
-export interface RectProps extends SecondaryPositionProps {
+export interface RectProps
+    extends MarkPropsBase,
+        SecondaryPositionProps,
+        FillAndStrokeProps {
+    type: "rect";
+
     /**
      * Clamps the minimum size-dependent opacity. The property does not affect the
      * `opacity` channel. Valid values are between `0` and `1`.
@@ -120,7 +210,12 @@ export interface RectProps extends SecondaryPositionProps {
     cornerRadiusBottomRight?: number | ExprRef;
 }
 
-export interface RuleProps extends SecondaryPositionProps {
+export interface RuleProps
+    extends MarkPropsBase,
+        SecondaryPositionProps,
+        SizeProps {
+    type: "rule";
+
     /**
      * 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.
@@ -152,9 +247,13 @@ export interface RuleProps extends SecondaryPositionProps {
 }
 
 export interface TextProps
-    extends SecondaryPositionProps,
+    extends MarkPropsBase,
+        SecondaryPositionProps,
         AngleProps,
-        ViewportEdgeFadeProps {
+        ViewportEdgeFadeProps,
+        SizeProps {
+    type: "text";
+
     /**
      * The text to display. The format of numeric data can be customized by
      * setting a [format specifier](https://github.com/d3/d3-format#locale_format)
@@ -276,7 +375,14 @@ export interface TextProps
     logoLetters?: boolean | ExprRef;
 }
 
-export interface PointProps extends AngleProps {
+export interface PointProps
+    extends MarkPropsBase,
+        FillAndStrokeProps,
+        AngleProps,
+        SizeProps,
+        MinPickingSizeProps {
+    type: "point";
+
     /**
      * One of `"circle"`, `"square"`, `"cross"`, `"diamond"`, `"triangle-up"`,
      * `"triangle-down"`, `"triangle-right"`, or `"triangle-left"`.
@@ -318,7 +424,13 @@ export interface PointProps extends AngleProps {
     geometricZoomBound?: number;
 }
 
-export interface LinkProps extends SecondaryPositionProps {
+export interface LinkProps
+    extends MarkPropsBase,
+        SecondaryPositionProps,
+        SizeProps,
+        MinPickingSizeProps {
+    type: "link";
+
     /**
      * The shape of the link path. Either `"arc"`, `"diagonal"`, `"line"`, or `"dome"`.
      *
@@ -387,75 +499,18 @@ export interface LinkProps extends SecondaryPositionProps {
     arcFadingDistance?: [number, number] | false | ExprRef;
 
     /**
-     * The minimum stroke width of the links when pointing with the mouse cursor.
-     * Allows making very thin links easier to point at.
+     * Disables fading of the link when an mark instance is subject to any point selection.
+     * As the fading distance is unavailable as a visual channel, this property allows for
+     * enhancing the visibility of the selected links.
      *
-     * **Default value:** `3.0`
-     */
-    minPickingSize?: number | ExprRef;
-}
-
-// TODO: Mark-specific configs
-export interface MarkProps
-    extends PointProps,
-        RectProps,
-        TextProps,
-        RuleProps,
-        LinkProps,
-        FillAndStrokeProps {
-    // Channels.
-    x?: number | ExprRef;
-    y?: number | ExprRef;
-    color?: string | ExprRef;
-    opacity?: number | ExprRef;
-    size?: number | ExprRef;
-
-    /**
-     * Whether the `color` represents the `fill` color (`true`) or the `stroke` color (`false`).
-     */
-    filled?: boolean;
-
-    /**
-     * If true, the mark is clipped to the UnitView's rectangle. By default, clipping
-     * is enabled for marks that have zoomable positional scales.
-     */
-    clip?: boolean | "never";
-
-    /**
-     * Offsets of the `x` and `x2` coordinates in pixels. The offset is applied
-     * after the viewport scaling and translation.
-     *
-     * **Default value:** `0`
-     */
-    xOffset?: number;
-
-    /**
-     * Offsets of the `y` and `y2` coordinates in pixels. The offset is applied
-     * after the viewport scaling and translation.
-     *
-     * **Default value:** `0`
-     */
-    yOffset?: number;
-
-    /**
-     * TODO
-     */
-    tooltip?: Tooltip;
-
-    /**
-     * The stroke width in pixels.
-     */
-    strokeWidth?: number | ExprRef;
-
-    /**
-     * Minimum size for WebGL buffers (number of data items).
-     * Allows for using `bufferSubData()` to update graphics.
-     *
-     * This property is intended for internal use.
+     * **Default value:** `true`
      */
-    minBufferSize?: number;
+    noFadingOnPointSelection?: boolean | ExprRef;
 }
 
-export interface MarkConfigAndType extends MarkProps {
-    type: MarkType;
-}
+export type MarkProps =
+    | RectProps
+    | TextProps
+    | RuleProps
+    | LinkProps
+    | PointProps;

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

@@ -1,3 +1,5 @@
+import { ChannelWithScale, Scalar } from "./channel.js";
+
 export interface ExprRef {
     /**
      * The expression string.
@@ -5,9 +7,7 @@ export interface ExprRef {
     expr: string;
 }
 
-// Adapted from: https://github.com/vega/vega-lite/blob/main/src/parameter.ts
-
-export interface VariableParameter {
+export interface ParameterBase {
     /**
      * A unique name for the variable parameter. Parameter names should be valid
      * JavaScript identifiers: they should contain only alphanumeric characters
@@ -16,6 +16,12 @@ export interface VariableParameter {
      */
     name: string;
 
+    push?: "outer";
+}
+
+// Adapted from: https://github.com/vega/vega-lite/blob/main/src/parameter.ts
+
+export interface VariableParameter extends ParameterBase {
     /**
      * The [initial value](http://vega.github.io/vega-lite/docs/value.html) of the parameter.
      *
@@ -144,3 +150,106 @@ export interface BindDirect {
 }
 
 export type Binding = BindCheckbox | BindRadioSelect | BindRange | BindInput;
+
+// ----------------------------------------------------------------------------
+// Adapted from: https://github.com/vega/vega-lite/blob/main/src/selection.ts
+
+type Vector2<T> = [T, T];
+
+export type SelectionType = "point" | "interval";
+export type SelectionInit = Scalar;
+export type SelectionInitInterval =
+    | Vector2<boolean>
+    | Vector2<number>
+    | Vector2<string>;
+
+export type InteractionEventType = "click" | "dblclick" | "mouseover";
+
+export interface BaseSelectionConfig<T extends SelectionType = SelectionType> {
+    /**
+     * Determines the default event processing and data query for the selection. Vega-Lite currently supports two selection types:
+     *
+     * - `"point"` -- to select multiple discrete data values; the first value is selected on `click` and additional values toggled on shift-click.
+     * - `"interval"` -- to select a continuous range of data values on `drag`.
+     */
+    type: T;
+
+    /**
+     */
+    on?: "click" | "mouseover" | "pointerover";
+
+    /**
+     * An array of encoding channels. The corresponding data field values
+     * must match for a data tuple to fall within the selection.
+     *
+     * __See also:__ The [projection with `encodings` and `fields` section](https://vega.github.io/vega-lite/docs/selection.html#project) in the documentation.
+     */
+    encodings?: ChannelWithScale[];
+
+    /**
+     * An array of field names whose values must match for a data tuple to
+     * fall within the selection.
+     *
+     * __See also:__ The [projection with `encodings` and `fields` section](https://vega.github.io/vega-lite/docs/selection.html#project) in the documentation.
+     */
+    fields?: string[];
+}
+
+export interface PointSelectionConfig extends BaseSelectionConfig<"point"> {
+    /**
+     * Controls whether data values should be toggled (inserted or removed from a point selection)
+     * when clicking with the shift key pressed.
+     *
+     * - `true` -- additional values can be selected by shift-clicking.
+     * - `false` -- only a single value can be selected at a time.
+     *
+     * __Default value:__ `true`
+     */
+    // TODO TODO TODO TODO TODO TODO TODO TODO
+    //toggle?: boolean;
+    /**
+     * A set of fields that uniquely identify a tuple. Used for bookmarking point selections
+     * in the GenomeSpy App. Still work in progress.
+     *
+     * TODO: Or maybe use the `key` channel? https://vega.github.io/vega-lite/docs/encoding.html#key
+     */
+    //keyFields?: string[];
+}
+
+export interface IntervalSelectionConfig
+    extends BaseSelectionConfig<"interval"> {
+    // TODO
+}
+
+export interface SelectionParameter<T extends SelectionType = SelectionType>
+    extends ParameterBase {
+    /**
+     * Determines the default event processing and data query for the selection. Vega-Lite currently supports two selection types:
+     *
+     * - `"point"` -- to select multiple discrete data values; the first value is selected on `click` and additional values toggled on shift-click.
+     * - `"interval"` -- to select a continuous range of data values on `drag`.
+     */
+    select:
+        | T
+        | (T extends "point"
+              ? PointSelectionConfig
+              : T extends "interval"
+              ? IntervalSelectionConfig
+              : never);
+
+    /*
+     * Initialize the selection with a mapping between [projected channels or field names](https://vega.github.io/vega-lite/docs/selection.html#project) and initial values.
+     *
+     * __See also:__ [`init`](https://vega.github.io/vega-lite/docs/value.html) documentation.
+     */
+    /*
+    // TODO TODO TODO TODO TODO TODO TODO TODO 
+    value?: T extends "point"
+        ? SelectionInit | SelectionInitMapping[]
+        : T extends "interval"
+        ? SelectionInitIntervalMapping
+        : never;
+        */
+}
+
+export type Parameter = VariableParameter | SelectionParameter;

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

@@ -1,5 +1,4 @@
 import { GenomeConfig } from "./genome.js";
-import { VariableParameter } from "./parameter.js";
 import { ViewSpec } from "./view.js";
 
 interface RootConfig {

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

@@ -17,13 +17,31 @@ export interface IdentifierParams extends TransformParamsBase {
      */
     as?: string;
 }
-export interface FilterParams extends TransformParamsBase {
+export interface ExprFilterParams extends TransformParamsBase {
     type: "filter";
 
     /** An expression string. The data object is removed if the expression evaluates to false. */
     expr: string;
 }
 
+export interface SelectionFilterParams extends TransformParamsBase {
+    type: "filter";
+
+    /**
+     * A selection parameter. The data object is removed if it is not part of the selection.
+     */
+    param: string;
+
+    /**
+     * If true, the filter retains all data objects when the selection is empty.
+
+     * **Default:** `true`
+     */
+    empty?: boolean;
+}
+
+export type FilterParams = ExprFilterParams | SelectionFilterParams;
+
 export interface FormulaParams extends TransformParamsBase {
     type: "formula";
 

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

@@ -6,16 +6,11 @@ import {
     FacetFieldDef,
     PrimaryPositionalChannel,
 } from "./channel.js";
-import {
-    FillAndStrokeProps,
-    MarkConfigAndType,
-    MarkType,
-    RectProps,
-} from "./mark.js";
+import { FillAndStrokeProps, MarkProps, MarkType, RectProps } from "./mark.js";
 import { ExprRef } from "./parameter.js";
 import { Title } from "./title.js";
 import { SampleSpec } from "./sampleView.js";
-import { VariableParameter } from "./parameter.js";
+import { Parameter } from "./parameter.js";
 
 export interface SizeDef {
     /** Size in pixels */
@@ -112,7 +107,7 @@ export interface ViewSpecBase extends ResolveSpec {
     /**
      * Dynamic variables that parameterize a visualization.
      */
-    params?: VariableParameter[];
+    params?: Parameter[];
 
     data?: Data;
     transform?: TransformParams[];
@@ -166,7 +161,7 @@ export interface ViewSpecBase extends ResolveSpec {
 
 export interface UnitSpec extends ViewSpecBase, AggregateSamplesSpec {
     view?: ViewBackground;
-    mark: MarkType | MarkConfigAndType;
+    mark: MarkType | MarkProps;
 }
 
 export interface AggregateSamplesSpec {
@@ -255,7 +250,7 @@ export interface ImportSpec {
      * Dynamic variables that parameterize a visualization. Parameters defined
      * here override the parameters defined in the imported specification.
      */
-    params?: VariableParameter[] | Record<string, any>;
+    params?: Parameter[] | Record<string, any>;
 
     /**
      * The method to import a specification.

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

@@ -1,2 +1,2 @@
-export default function dataTooltipHandler(datum: Record<string, any>, mark: import("../marks/mark.js").default, params?: Record<string, any>): Promise<string | HTMLElement | import("lit-html").TemplateResult>;
+export default function dataTooltipHandler(datum: Record<string, any>, mark: import("../marks/mark.js").default<import("../spec/mark.js").MarkProps>, params?: Record<string, any>): Promise<string | HTMLElement | import("lit-html").TemplateResult>;
 //# sourceMappingURL=dataTooltipHandler.d.ts.map

package/dist/src/tooltip/dataTooltipHandler.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"dataTooltipHandler.d.ts","sourceRoot":"","sources":["../../../src/tooltip/dataTooltipHandler.js"],"names":[],"mappings":"AAMoC,kNAMa"}
+{"version":3,"file":"dataTooltipHandler.d.ts","sourceRoot":"","sources":["../../../src/tooltip/dataTooltipHandler.js"],"names":[],"mappings":"AAMoC,uPAMa"}

package/dist/src/tooltip/dataTooltipHandler.js

@@ -11,7 +11,7 @@ export default async function dataTooltipHandler(datum, mark, params) {
      */
     const legend = (key, datum) => {
         for (const [channel, encoder] of Object.entries(mark.encoders)) {
-            if (encoder?.accessor?.fields.includes(key)) {
+            if (encoder?.dataAccessor?.fields.includes(key)) {
                 switch (channel) {
                     case "color":
                     case "fill":

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

@@ -1,2 +1,2 @@
-export default function refseqGeneTooltipHandler(datum: Record<string, any>, mark: import("../marks/mark.js").default, params?: Record<string, any>): Promise<string | HTMLElement | import("lit-html").TemplateResult>;
+export default function refseqGeneTooltipHandler(datum: Record<string, any>, mark: import("../marks/mark.js").default<import("../spec/mark.js").MarkProps>, params?: Record<string, any>): Promise<string | HTMLElement | import("lit-html").TemplateResult>;
 //# sourceMappingURL=refseqGeneTooltipHandler.d.ts.map

package/dist/src/tooltip/refseqGeneTooltipHandler.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"refseqGeneTooltipHandler.d.ts","sourceRoot":"","sources":["../../../src/tooltip/refseqGeneTooltipHandler.js"],"names":[],"mappings":"AAOC,wNAQW"}
+{"version":3,"file":"refseqGeneTooltipHandler.d.ts","sourceRoot":"","sources":["../../../src/tooltip/refseqGeneTooltipHandler.js"],"names":[],"mappings":"AAOC,6PAQW"}

package/dist/src/types/encoder.d.ts

@@ -15,57 +15,109 @@ import {
     ScaleDiverging,
     ScaleContinuousNumeric,
 } from "d3-scale";
-import { ChannelDef } from "../spec/channel.js";
+import { Channel, ChannelDef, ChannelWithScale } from "../spec/channel.js";
 import { ScaleLocus } from "../genome/scaleLocus.js";
 import { ScaleIndex } from "../genome/scaleIndex.js";
 import { Scalar } from "../spec/channel.js";
+import { Datum } from "../data/flowNode.js";
+import { ExprRefFunction } from "../view/paramMediator.js";
 
-export interface AccessorMetadata {
-    /** True if the accessor returns the same value for all objects */
+export interface Accessor<T = Scalar> {
+    (datum: Datum): T;
+
+    /**
+     * Returns a new accessor that returns the same value as this accessor,
+     * but typed as a number
+     */
+    asNumberAccessor(): Accessor<number>;
+
+    /**
+     * True if the accessor returns the same value for all objects
+     */
     constant: boolean;
 
-    /** The fields that the return value is based on (if any) */
+    /**
+     * The fields that the return value is based on (if any)
+     */
     fields: string[];
-}
 
-export type Accessor = ((datum: any) => any) & AccessorMetadata;
+    /**
+     * The channel that the accessor is based on
+     */
+    channel: Channel;
+
+    /**
+     * If the accessed data needs to be passed to a scale function
+     * before visual encoding, indicates with channel has the scale.
+     * If no scale is needed, this is undefined.
+     */
+    scaleChannel: ChannelWithScale;
+
+    /**
+     * The ChannelDef that the accessor is based on
+     */
+    channelDef: ChannelDef;
 
-export interface EncoderMetadata {
-    /** True if the accessor returns the same value for all objects */
-    constant: boolean;
+    /**
+     * This accessor should be used when the predicate is true
+     */
+    predicate: Predicate;
+}
+
+export interface Predicate extends ExprRefFunction {
+    /**
+     * The parameter the predicate is based on
+     */
+    param?: string;
+
+    /**
+     * If true, the predicate is true for empty selections.
+     *
+     * **Default:** `true`
+     */
+    empty?: boolean;
+}
 
-    /** True the encoder returns a "value" without a scale */
-    constantValue: boolean;
+/**
+ * Wraps one or more accessors, uses an optional scale to encode the data.
+ */
+export interface Encoder {
+    (datum: Datum): Scalar;
 
-    invert: (value: Scalar) => Scalar;
+    /**
+     * True if the accessor returns the same value for all objects
+     */
+    constant: boolean;
 
+    /**
+     * Scale, if the encoder has one
+     */
     scale?: VegaScale;
 
-    accessor: Accessor;
+    /**
+     * An accessor, or if the ChannelDef has conditions, all the accessors.
+     */
+    accessors: Accessor[];
 
-    /** Converts ordinal values to index numbers */
-    indexer?: (value: any) => number;
+    /**
+     * The encoded channel may have a maximum of one accessor accessing the
+     * data fields. It's this one.
+     */
+    dataAccessor?: Accessor;
 
+    /**
+     * The ChannelDef that the encoder is based on
+     */
     channelDef: ChannelDef;
-
-    /** Copies metadata to the target function */
-    applyMetadata: (target: Function) => void;
 }
 
-export type Encoder = ((datum: object) => Scalar) & EncoderMetadata;
-
-export type NumberEncoder = ((datum: object) => number) & EncoderMetadata;
-
 export interface ScaleMetadata {
     /** Scale type */
     type: string;
-
-    /** Whether to use emulated 64 bit floating point in WebGL */
-    fp64?: boolean;
 }
 
 export type D3Scale =
-    | ScaleContinuousNumeric<any, any>
+    | ScaleContinuousNumeric<any, any, any>
     | ScaleLinear<any, any>
     | ScalePower<any, any>
     | ScaleLogarithmic<any, any>
@@ -81,4 +133,6 @@ export type D3Scale =
     | ScaleBand<any>
     | ScalePoint<any>;
 
+export type GenericScale = any;
+
 export type VegaScale = (D3Scale | ScaleIndex | ScaleLocus) & ScaleMetadata;

package/dist/src/types/rendering.d.ts

@@ -1,6 +1,7 @@
 import Mark from "../marks/mark.js";
 import { LocSize } from "../view/layout/flexLayout.js";
 import Rectangle from "../view/layout/rectangle.js";
+import ViewRenderingContext from "../view/renderingContext/viewRenderingContext.js";
 
 /**
  * Describes the location of a sample facet. Left is the primary pos, right is for