@genome-spy/core 0.30.0 → 0.30.2

package/src/spec/mark.d.ts

@@ -1,429 +0,0 @@
-import { Scalar } from "./channel";
-import { Align, Baseline, FontStyle, FontWeight } from "./font";
-import { Tooltip } from "./tooltip";
-
-export type MarkType = "rect" | "point" | "rule" | "text" | "link";
-
-export interface FillAndStrokeProps {
-    fill?: string;
-    fillOpacity?: number;
-
-    stroke?: string;
-    strokeOpacity?: number;
-}
-
-export interface SecondaryPositionProps {
-    x2?: number;
-    y2?: number;
-}
-
-export interface AngleProps {
-    /**
-     * The rotation angle in degrees.
-     *
-     * **Default value:** `0`
-     */
-    angle?: number;
-}
-
-/**
- * Specifies how mark should be faded at the viewport edges.
- * This is mainly used to make axis labels pretty.
- */
-export interface ViewportEdgeFadeProps {
-    viewportEdgeFadeWidthTop?: number;
-    viewportEdgeFadeWidthRight?: number;
-    viewportEdgeFadeWidthBottom?: number;
-    viewportEdgeFadeWidthLeft?: number;
-
-    viewportEdgeFadeDistanceTop?: number;
-    viewportEdgeFadeDistanceRight?: number;
-    viewportEdgeFadeDistanceBottom?: number;
-    viewportEdgeFadeDistanceLeft?: number;
-}
-
-export interface RectProps extends SecondaryPositionProps {
-    /**
-     * Clamps the minimum size-dependent opacity. The property does not affect the
-     * `opacity` channel. Valid values are between `0` and `1`.
-     *
-     * When a rectangle would be smaller than what is specified in `minHeight` and
-     * `minWidth`, it is faded out proportionally. Example: a rectangle would be
-     * rendered as one pixel wide, but `minWidth` clamps it to five pixels. The
-     * rectangle is actually rendered as five pixels wide, but its opacity is
-     * multiplied by 0.2. With this setting, you can limit the factor to, for
-     * example, 0.5 to keep the rectangles more clearly visible.
-     *
-     * **Default value:** `0`
-     */
-    // TODO: Rename to minCompensatedOpacity or something like that
-    minOpacity?: number;
-
-    /**
-     * The minimum width of a rectangle in pixels. The property clamps rectangles'
-     * widths when the viewport is zoomed out.
-     *
-     * This property also reduces flickering of very narrow rectangles when zooming.
-     * The value should generally be at least one.
-     *
-     * **Default value:** `1`
-     */
-    minWidth?: number;
-
-    /**
-     * The minimum height of a rectangle in pixels. The property clamps rectangles' heights.
-     *
-     * **Default value:** `0`
-     */
-    minHeight?: number;
-
-    /**
-     * Radius of the rounded corners.
-     *
-     * **Default value:** `0`
-     */
-    cornerRadius?: number;
-
-    /**
-     * Radius of the top left rounded corner. Has higher precedence than `cornerRadius`.
-     *
-     * **Default value:** (None)
-     */
-    cornerRadiusTopLeft?: number;
-
-    /**
-     * Radius of the top right rounded corner. Has higher precedence than `cornerRadius`.
-     *
-     * **Default value:** (None)
-     */
-    cornerRadiusTopRight?: number;
-
-    /**
-     * Radius of the bottom left rounded corner. Has higher precedence than `cornerRadius`.
-     *
-     * **Default value:** (None)
-     */
-    cornerRadiusBottomLeft?: number;
-
-    /**
-     * Radius of the bottom right rounded corner. Has higher precedence than `cornerRadius`.
-     *
-     * **Default value:** (None)
-     */
-    cornerRadiusBottomRight?: number;
-}
-
-export interface RuleProps extends SecondaryPositionProps {
-    /**
-     * 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.
-     *
-     * **Default value:** `0`
-     */
-    minLength?: number;
-
-    /**
-     * An array of of alternating stroke and gap lengths or `null` for solid strokes.
-     *
-     * **Default value:** `null`
-     */
-    strokeDash?: number[];
-
-    /**
-     * An offset for the stroke dash pattern.
-     *
-     * **Default value:** `0`
-     */
-    strokeDashOffset?: number;
-
-    /**
-     * The style of stroke ends. Available choices: `"butt"`, `"round`", and `"square"`.
-     *
-     * **Default value:** `"butt"`
-     */
-    strokeCap?: "butt" | "square" | "round";
-}
-
-export interface TextProps
-    extends SecondaryPositionProps,
-        AngleProps,
-        ViewportEdgeFadeProps {
-    /**
-     * 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)
-     * to channel definition's `format` property.
-     *
-     * **Default value:** `""`
-     */
-    text?: Scalar;
-
-    /**
-     * The font size in pixels.
-     *
-     * **Default value:** `11`
-     */
-    size?: number;
-
-    /**
-     * The font typeface. GenomeSpy uses [SDF](https://github.com/Chlumsky/msdfgen)
-     * versions of [Google Fonts](https://fonts.google.com/). Check their
-     * availability at the [A-Frame
-     * Fonts](https://github.com/etiennepinchon/aframe-fonts/tree/master/fonts)
-     * repository. System fonts are **not** supported.
-     *
-     * **Default value:** `"Lato"`
-     */
-    font?: string;
-
-    /**
-     * The font style. Valid values: `"normal"` and `"italic"`.
-     *
-     * **Default value:** `"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 value:** `"regular"`
-     */
-    fontWeight?: FontWeight;
-
-    /**
-     * The horizontal alignment of the text. One of `"left"`, `"center"`, or `"right"`.
-     *
-     * **Default value:** `"left"`
-     */
-    align?: Align;
-
-    /**
-     * The vertical alignment of the text.  One of `"top"`, `"middle"`, `"bottom"`.
-     *
-     * **Default value:** `"bottom"`
-     */
-    baseline?: Baseline;
-
-    /**
-     * The horizontal offset between the text and its anchor point, in pixels.
-     * Applied after the rotation by `angle`.
-     */
-    dx?: number;
-
-    /**
-     * The vertical offset between the text and its anchor point, in pixels.
-     * Applied after the rotation by `angle`.
-     */
-    dy?: number;
-
-    /**
-     * If true, sets the secondary positional channel that allows the text to be squeezed
-     * (see the `squeeze` property).
-     * Can be used when:
-     * 1) `"band"`, `"index"`, or `"locus"` scale is being used and
-     * 2) only the primary positional channel is specified.
-     *
-     * **Default value:** `false`
-     */
-    fitToBand?: boolean;
-
-    /**
-     * The horizontal padding, in pixels, when the `x2` channel is used for ranged text.
-     *
-     * **Default value:** `0`
-     */
-    paddingX?: number;
-
-    /**
-     * The vertical padding, in pixels, when the `y2` channel is used for ranged text.
-     *
-     * **Default value:** `0`
-     */
-    paddingY?: number;
-
-    /**
-     * If true, the text is kept inside the viewport when the range of `x` and `x2`
-     * intersect the viewport.
-     */
-    flushX?: boolean;
-
-    /**
-     * If true, the text is kept inside the viewport when the range of `y` and `y2`
-     * intersect the viewport.
-     */
-    flushY?: boolean;
-
-    /**
-     * If the `squeeze` property is true and secondary positional channels (`x2` and/or `y2`)
-     * are used, the text is scaled to fit mark's width and/or height.
-     *
-     * **Default value:** `true`
-     */
-    squeeze?: boolean;
-
-    /**
-     * Stretch letters so that they can be used with [sequence logos](https://en.wikipedia.org/wiki/Sequence_logo), etc...
-     */
-    logoLetters?: boolean;
-}
-
-export interface PointProps extends AngleProps {
-    /**
-     * One of `"circle"`, `"square"`, `"cross"`, `"diamond"`, `"triangle-up"`,
-     * `"triangle-down"`, `"triangle-right"`, or `"triangle-left"`.
-     *
-     * **Default value:** `"circle"`
-     */
-    shape?: string;
-
-    /**
-     * Should the stroke only grow inwards, e.g, the diameter/outline is not affected by the stroke width.
-     * Thus, a point that has a zero size has no visible stroke. This allows strokes to be used with
-     * geometric zoom, etc.
-     *
-     * **Default value:** `false`
-     */
-    inwardStroke?: boolean;
-
-    /**
-     * Gradient strength controls the amount of the gradient eye-candy effect in the fill color.
-     * Valid values are between 0 and 1.
-     *
-     * **Default value:** `0`
-     */
-    fillGradientStrength?: number;
-
-    /**
-     * Padding between sample facet's upper/lower edge and the maximum point size. This property
-     * controls how tightly points are squeezed when facet's height is smaller than the maximum
-     * point size. The unit is a proportion of facet's height. The value must be between `0`
-     * and `0.5`. This property has no effect when sample faceting is not used.
-     *
-     * **Default value:** `0.1`
-     */
-    sampleFacetPadding?: number;
-
-    /**
-     * TODO
-     *
-     * **Default value:** `0.02`
-     */
-    semanticZoomFraction?: number;
-
-    /**
-     * Enables geometric zooming. The value is the base two logarithmic zoom level where the maximum
-     * point size is reached.
-     *
-     * **Default value:** `0`
-     */
-    geometricZoomBound?: number;
-}
-
-export interface LinkProps extends SecondaryPositionProps {
-    /**
-     * 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`
-     */
-    segments?: number;
-
-    /**
-     * Scaling factor of the arc's sagitta. The default value `1.0` produces roughly circular arcs.
-     *
-     * **Default value:** `1.0`
-     */
-    sagittaScaleFactor?: number;
-
-    /**
-     * Minimum length of the arc's sagitta. Makes very short links more clearly visible.
-     *
-     * **Default value:** `1.5`
-     */
-    minSagittaLength?: number;
-
-    /**
-     * TODO
-     */
-    color2?: string;
-
-    /**
-     * TODO
-     */
-    size2?: number;
-}
-
-// TODO: Mark-specific configs
-export interface MarkConfig
-    extends PointProps,
-        RectProps,
-        TextProps,
-        RuleProps,
-        LinkProps,
-        FillAndStrokeProps {
-    // Channels.
-    x?: number;
-    y?: number;
-    color?: string;
-    opacity?: number;
-    size?: number;
-
-    /**
-     * 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;
-
-    /**
-     * 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;
-
-    /**
-     * Minimum size for WebGL buffers (number of data items).
-     * Allows for using `bufferSubData()` to update graphics.
-     *
-     * This property is intended for internal use.
-     */
-    minBufferSize?: number;
-
-    /**
-     * Builds and index for efficient rendering of subsets of the data.
-     * The data must be sorted by the x coordinate.
-     *
-     * TODO: This should be enabled automatically if the data are sorted.
-     */
-    buildIndex?: boolean;
-}
-
-export interface MarkConfigAndType extends MarkConfig {
-    type: MarkType;
-}

package/src/spec/root.d.ts

@@ -1,17 +0,0 @@
-import { GenomeConfig } from "./genome";
-import { ViewSpec } from "./view";
-
-interface RootConfig {
-    $schema?: string;
-
-    genome?: GenomeConfig;
-
-    baseUrl?: string;
-
-    /**
-     * https://vega.github.io/vega-lite/docs/data.html#datasets
-     */
-    datasets?: Record<string, any[]>;
-}
-
-export type RootSpec = ViewSpec & RootConfig;

package/src/spec/sampleView.d.ts

@@ -1,180 +0,0 @@
-import { Type } from "./channel";
-import { Data } from "./data";
-import { Align, FontStyle, FontWeight } from "./font";
-import { Scale } from "./scale";
-import { LayerSpec, UnitSpec, ViewSpecBase } from "./view";
-
-// TODO: Figure out how this could be moved to the app package and excluded
-// from the core package.
-
-/**
- * A view specification for a SampleView.
- * This is only functional in the GenomeSpy app.
- */
-export interface SampleSpec extends ViewSpecBase {
-    /**
-     * Sample metadata definition.
-     * If the object is empty, the sample identifiers will be inferred from the data.
-     */
-    samples: SampleDef;
-
-    /**
-     * The view specification to be repeated for each sample.
-     */
-    spec: LayerSpec | UnitSpec;
-
-    stickySummaries?: boolean;
-}
-
-export interface SampleAttributeDef {
-    /**
-     * The attribute type. One of `"nominal"`, `"ordinal"`, or `"quantitative"`.
-     */
-    type: Type; // TODO: Omit index/locus from available types
-
-    /**
-     * Scale definition for the (default) color channel
-     */
-    scale?: Scale;
-
-    /**
-     * An optional scale definition for mapping the attribute to
-     * the width of a metadata rectangle.
-     */
-    barScale?: Scale;
-
-    /**
-     * Width of the column in pixels.
-     */
-    width?: number;
-
-    /**
-     * Whether the attribute is visible by default.
-     */
-    visible?: boolean;
-}
-
-export interface SampleDef {
-    /**
-     * Optional metadata about the samples.
-     */
-    data?: Data;
-
-    /**
-     * Explicitly specify the sample attributes.
-     */
-    attributes?: Record<string, SampleAttributeDef>;
-
-    /**
-     * Text in the label title
-     *
-     * **Default:** `"Sample name"`
-     */
-    labelTitleText?: string;
-
-    /**
-     * How much space in pixels to reserve for the labels.
-     *
-     * **Default:** `140`
-     */
-    labelLength?: number;
-
-    /**
-     * The font typeface. GenomeSpy uses [SDF](https://github.com/Chlumsky/msdfgen)
-     * versions of [Google Fonts](https://fonts.google.com/). Check their
-     * availability at the [A-Frame
-     * Fonts](https://github.com/etiennepinchon/aframe-fonts/tree/master/fonts)
-     * repository. System fonts are **not** supported.
-     *
-     * **Default value:** `"Lato"`
-     */
-    labelFont?: string;
-
-    /**
-     * The font style. Valid values: `"normal"` and `"italic"`.
-     *
-     * **Default value:** `"normal"`
-     */
-    labelFontStyle?: 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 value:** `"regular"`
-     */
-    labelFontWeight?: FontWeight;
-
-    /**
-     * The font size in pixels.
-     *
-     * **Default value:** `11`
-     */
-    labelFontSize?: number;
-
-    /**
-     * The horizontal alignment of the text. One of `"left"`, `"center"`, or `"right"`.
-     *
-     * **Default value:** `"left"`
-     */
-    labelAlign?: Align;
-
-    /**
-     * Default size (width) of the metadata attribute columns.
-     * Can be configured per attribute using the `attributes` property.
-     *
-     * **Default value:** `10`
-     */
-    attributeSize?: number;
-
-    /**
-     * The font typeface. GenomeSpy uses [SDF](https://github.com/Chlumsky/msdfgen)
-     * versions of [Google Fonts](https://fonts.google.com/). Check their
-     * availability at the [A-Frame
-     * Fonts](https://github.com/etiennepinchon/aframe-fonts/tree/master/fonts)
-     * repository. System fonts are **not** supported.
-     *
-     * **Default value:** `"Lato"`
-     */
-    attributeLabelFont?: string;
-
-    /**
-     * The font style. Valid values: `"normal"` and `"italic"`.
-     *
-     * **Default value:** `"normal"`
-     */
-    attributeLabelFontStyle?: 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 value:** `"regular"`
-     */
-    attributeLabelFontWeight?: FontWeight;
-
-    /**
-     * The font size in pixels.
-     *
-     * **Default value:** `11`
-     */
-    attributeLabelFontSize?: number;
-
-    /**
-     * Angle to be added to the default label angle (-90).
-     *
-     * **Default value:** `0`
-     */
-    attributeLabelAngle?: number;
-
-    /**
-     * Spacing between attribute columns in pixels.
-     *
-     * **Default value:** `1`
-     */
-    attributeSpacing?: number;
-}