@genome-spy/core 0.29.0 → 0.30.2

package/src/spec/channel.d.ts

@@ -1,430 +0,0 @@
-/*!
- * Partially based on
- * https://github.com/vega/vega-lite/blob/master/src/channeldef.ts
- *
- * Copyright (c) 2015-2018, University of Washington Interactive Data Lab
- * All rights reserved.
- *
- * BSD-3-Clause License: https://github.com/vega/vega-lite/blob/master/LICENSE
- */
-
-import { Scale } from "./scale";
-import { Axis } from "./axis";
-
-export type Scalar = string | number | boolean;
-export type Value = Scalar | null;
-
-export type FieldName = string;
-export type Field = FieldName;
-
-export type PrimaryPositionalChannel = "x" | "y";
-export type SecondaryPositionalChannel = "x2" | "y2";
-
-export type PositionalChannel =
-    | PrimaryPositionalChannel
-    | SecondaryPositionalChannel;
-
-export type Channel =
-    | PositionalChannel
-    | "color"
-    | "fill"
-    | "stroke"
-    | "opacity"
-    | "fillOpacity"
-    | "strokeOpacity"
-    | "strokeWidth"
-    | "size"
-    | "shape"
-    | "text"
-    | "angle"
-    | "sample"
-    | "uniqueId"
-    | "search"
-    | "facetIndex"
-    | "semanticScore"
-    | "dx"
-    | "dy"
-    | "uniqueId";
-
-// TODO
-export type FacetFieldDef = any;
-
-// TODO: Belongs to "guide"
-export interface TitleMixins {
-    /**
-     * A title for the field. If `null`, the title will be removed.
-     */
-    title?: string | null;
-}
-
-export interface BandMixins {
-    /**
-     * Relative position on band scale. For example, the marks will be positioned at the beginning of the band if set to `0`, and at the middle of the band if set to `0.5`.
-     *
-     * @minimum 0
-     * @maximum 1
-     */
-    // TODO: rename to bandPosition: https://github.com/vega/vega-lite/pull/7190
-    // bandPosition?: number;
-    band?: number;
-}
-
-export interface FormatMixins {
-    /**
-     * When used with the default `"number"` format type, the text formatting pattern for labels of guides (axes, legends, headers) and text marks.
-     *
-     * - If the format type is `"number"` (e.g., for quantitative fields), this is D3's [number format pattern](https://github.com/d3/d3-format#locale_format).
-     *
-     * See the [format documentation](https://vega.github.io/vega-lite/docs/format.html) for more examples.
-     */
-    format?: string;
-}
-
-export type StringDatumDef = DatumDef & FormatMixins;
-
-export type Type = "quantitative" | "ordinal" | "nominal" | "index" | "locus";
-
-export type TypeForShape = "ordinal" | "nominal";
-
-export interface TypeMixins<T extends Type> {
-    type: T;
-}
-
-export interface FieldDefBase<F> {
-    /**
-     * __Required.__ A string defining the name of the field from which to pull a data value
-     * or an object defining iterated values from the [`repeat`](https://vega.github.io/vega-lite/docs/repeat.html) operator.
-     *
-     * __See also:__ [`field`](https://vega.github.io/vega-lite/docs/field.html) documentation.
-     *
-     * __Notes:__
-     * 1)  Dots (`.`) and brackets (`[` and `]`) can be used to access nested objects (e.g., `"field": "foo.bar"` and `"field": "foo['bar']"`).
-     * If field names contain dots or brackets but are not nested, you can use `\\` to escape dots and brackets (e.g., `"a\\.b"` and `"a\\[0\\]"`).
-     * See more details about escaping in the [field documentation](https://vega.github.io/vega-lite/docs/field.html).
-     * 2) `field` is not required if `aggregate` is `count`.
-     */
-    field?: F;
-}
-
-export type TypedFieldDef<
-    F extends Field,
-    T extends Type = any
-> = FieldDefBase<F> & TitleMixins & TypeMixins<T>;
-
-export type ScaleFieldDef<F extends Field, T extends Type> = TypedFieldDef<
-    F,
-    T
-> &
-    ScaleMixins;
-
-export type FieldDefWithoutScale<F extends Field> = FieldDefBase<F> &
-    TitleMixins;
-
-export interface ScaleMixins {
-    /**
-     * An object defining properties of the channel's scale, which is the function that transforms values in the data domain (numbers, dates, strings, etc) to visual values (pixels, colors, sizes) of the encoding channels.
-     *
-     * If `null`, the scale will be [disabled and the data value will be directly encoded](https://vega.github.io/vega-lite/docs/scale.html#disable).
-     *
-     * __Default value:__ If undefined, default [scale properties](https://vega.github.io/vega-lite/docs/scale.html) are applied.
-     *
-     * __See also:__ [`scale`](https://vega.github.io/vega-lite/docs/scale.html) documentation.
-     */
-    scale?: Scale | null;
-
-    /**
-     * An alternative channel for scale resolution.
-     *
-     * This is mainly for internal use and allows using `color` channel to resolve `fill` and `stroke` channels under certain circumstances.
-     */
-    resolutionChannel?: Channel;
-}
-
-export interface ValueDef<V extends Value = Scalar> {
-    /**
-     * A constant value in visual domain (e.g., `"red"` / `"#0099ff"`, values between `0` to `1` for opacity).
-     */
-    value: V;
-}
-
-export interface DatumDef extends TitleMixins {
-    /**
-     * A constant value in data domain.
-     */
-    datum?: Scalar;
-}
-
-export interface ExprDef {
-    /** An expression. Properties of the data can be accessed through the `datum` object. */
-    expr: string;
-}
-
-/**
- * Field definition of a mark property, which can contain a legend.
- */
-export type MarkPropFieldDef<
-    F extends Field,
-    T extends Type = Type
-> = ScaleFieldDef<F, T> & LegendMixins;
-
-export type MarkPropExprDef<T extends Type = Type> = ExprDef &
-    TypeMixins<T> &
-    ScaleMixins;
-
-export type MarkPropDatumDef<T extends Type> = LegendMixins &
-    ScaleDatumDef &
-    TypeMixins<T>;
-
-export type MarkPropFieldOrDatumOrExprDef<
-    F extends Field,
-    T extends Type = Type
-> = MarkPropFieldDef<F, T> | MarkPropDatumDef<T> | MarkPropExprDef;
-
-export interface LegendMixins {
-    /**
-     * An object defining properties of the legend.
-     * If `null`, the legend for the encoding channel will be removed.
-     *
-     * __Default value:__ If undefined, default [legend properties](https://vega.github.io/vega-lite/docs/legend.html) are applied.
-     *
-     * __See also:__ [`legend`](https://vega.github.io/vega-lite/docs/legend.html) documentation.
-     */
-    // TODO: legend?: Legend<ExprRef | SignalRef> | null;
-}
-
-export type MarkPropDef<
-    F extends Field,
-    V extends Value,
-    T extends Type = Type
-> = MarkPropFieldOrDatumOrExprDef<F, T> | ValueDef<V>;
-
-export type ColorDef<F extends Field> = MarkPropDef<F, string | null>;
-
-export type SecondaryFieldDef<F extends Field> = FieldDefBase<F> & TitleMixins;
-
-export type NumericValueDef = ValueDef<number>;
-
-export type ScaleDatumDef = ScaleMixins & DatumDef;
-
-export type PositionDatumDefBase = ScaleDatumDef & TypeMixins<Type>;
-
-export type PositionFieldDef<F extends Field> = PositionFieldDefBase<F> &
-    PositionMixins;
-
-export type PositionDatumDef = PositionDatumDefBase & PositionMixins;
-
-export type PositionExprDef = ExprDef &
-    PositionMixins &
-    BandMixins &
-    TypeMixins<Type>;
-
-export type PositionValueDef = NumericValueDef;
-
-export interface PositionMixins extends BandMixins {
-    /**
-     * An object defining properties of axis's gridlines, ticks and labels.
-     * If `null`, the axis for the encoding channel will be removed.
-     *
-     * __Default value:__ If undefined, default [axis properties](https://vega.github.io/vega-lite/docs/axis.html) are applied.
-     *
-     * __See also:__ [`axis`](https://vega.github.io/vega-lite/docs/axis.html) documentation.
-     */
-    axis?: Axis | null;
-}
-
-export type PositionFieldDefBase<F extends Field> = ScaleFieldDef<F, Type>;
-
-export interface ChromPosDefBase extends BandMixins {
-    /**
-     * The field having the chromosome or contig.
-     */
-    chrom: FieldName;
-
-    /**
-     * The field having an intra-chromosomal position.
-     */
-    pos?: FieldName;
-
-    /**
-     * An offset or offsets that allow for adjusting the numbering base. The offset
-     * is subtracted from the positions.
-     *
-     * GenomeSpy uses internally zero-based indexing with half-open intervals.
-     * UCSC-based formats (BED, etc.) generally use this scheme. However, for example,
-     * VCF files use one-based indexing and must be adjusted by setting the offset to
-     * `1`.
-     *
-     * **Default:** `0`
-     */
-    offset?: number;
-}
-
-export type SecondaryChromPosDef = ChromPosDefBase &
-    TitleMixins &
-    PositionMixins;
-
-export type ChromPosDef = SecondaryChromPosDef &
-    TypeMixins<"locus"> &
-    ScaleMixins;
-
-export type PositionDef<F extends Field> =
-    | PositionFieldDef<F>
-    | ChromPosDef
-    | PositionDatumDef
-    | PositionExprDef
-    | PositionValueDef;
-
-export type Position2Def<F extends Field> =
-    | (SecondaryFieldDef<F> & BandMixins)
-    | SecondaryChromPosDef
-    | (DatumDef & BandMixins)
-    | (ExprDef & BandMixins)
-    | PositionValueDef;
-
-export type NumericMarkPropDef<F extends Field> = MarkPropDef<F, number>;
-
-export type ShapeDef<F extends Field> = MarkPropDef<
-    F,
-    string | null,
-    TypeForShape
->;
-
-export interface StringFieldDef<F extends Field>
-    extends FieldDefWithoutScale<F>,
-        FormatMixins {}
-
-export type TextDef<F extends Field> =
-    | StringFieldDef<F>
-    | StringDatumDef
-    | ExprDef;
-
-export type ChannelDef<F extends Field = string> =
-    Encoding<F>[keyof Encoding<F>];
-
-// TODO: Does this make sense?
-export type ChannelDefWithScale = ScaleMixins & TypeMixins<Type>;
-
-export interface Encoding<F extends Field = string> {
-    /**
-     * X coordinates of the marks.
-     *
-     * The `value` of this channel can be a number between zero and one.
-     */
-    x?: PositionDef<F>;
-
-    /**
-     * Y coordinates of the marks.
-     *
-     * The `value` of this channel can be a number between zero and one.
-     */
-    y?: PositionDef<F>;
-
-    /**
-     * X2 coordinates of the marks.
-     *
-     * The `value` of this channel can be a number between zero and one.
-     */
-    x2?: Position2Def<F>;
-
-    /**
-     * Y2 coordinates of the marks.
-     *
-     * The `value` of this channel can be a number between zero and one.
-     */
-    y2?: Position2Def<F>;
-
-    dx?: NumericMarkPropDef<F>;
-    dy?: NumericMarkPropDef<F>;
-
-    /**
-     * Color of the marks – either fill or stroke color based on  the `filled` property of mark definition.
-     *
-     * _Note:_
-     * 1) For fine-grained control over both fill and stroke colors of the marks, please use the `fill` and `stroke` channels. The `fill` or `stroke` encodings have higher precedence than `color`, thus may override the `color` encoding if conflicting encodings are specified.
-     * 2) See the scale documentation for more information about customizing [color scheme](https://vega.github.io/vega-lite/docs/scale.html#scheme).
-     */
-    color?: ColorDef<F>;
-
-    /**
-     * Fill color of the marks.
-     *
-     * _Note:_ The `fill` encoding has higher precedence than `color`, thus may override the `color` encoding if conflicting encodings are specified.
-     */
-    fill?: ColorDef<F>;
-
-    /**
-     * Stroke color of the marks.
-     *
-     * _Note:_ The `stroke` encoding has higher precedence than `color`, thus may override the `color` encoding if conflicting encodings are specified.
-     */
-
-    stroke?: ColorDef<F>;
-
-    /**
-     * Opacity of the marks.
-     */
-    opacity?: NumericMarkPropDef<F>;
-
-    /**
-     * Fill opacity of the marks.
-     */
-    fillOpacity?: NumericMarkPropDef<F>;
-
-    /**
-     * Stroke opacity of the marks.
-     */
-    strokeOpacity?: NumericMarkPropDef<F>;
-
-    /**
-     * Stroke width of the marks.
-     */
-    strokeWidth?: NumericMarkPropDef<F>;
-
-    /**
-     * Size of the mark.
-     * - For `"point"` – the symbol size, or pixel area of the mark.
-     * - For `"text"` – the text's font size.
-     */
-    size?: NumericMarkPropDef<F>;
-
-    /**
-     * Rotation angle of point and text marks.
-     */
-    angle?: NumericMarkPropDef<F>;
-
-    /**
-     * Shape of the mark.
-     *
-     * For `point` marks the supported values include:
-     * - plotting shapes: `"circle"`, `"square"`, `"cross"`, `"diamond"`, `"triangle-up"`, `"triangle-down"`, `"triangle-right"`, or `"triangle-left"`.
-     * - centered directional shape `"triangle"`
-     */
-    shape?: ShapeDef<F>;
-
-    /**
-     * Text of the `text` mark.
-     */
-    text?: TextDef<F>;
-
-    /**
-     * Facet identifier for interactive filtering, sorting, and grouping in the App.
-     */
-    sample?: FieldDefWithoutScale<F>;
-
-    /**
-     * For internal use
-     */
-    // TODO: proper type
-    uniqueId?: FieldDefWithoutScale<F>;
-
-    // TODO: proper type
-    search?: FieldDefWithoutScale<F>;
-
-    /**
-     * For internal use
-     */
-    // TODO: proper type
-    facetIndex?: FieldDefWithoutScale<F>;
-
-    semanticScore?: FieldDefWithoutScale<F>;
-}

package/src/spec/data.d.ts

@@ -1,196 +0,0 @@
-/*!
- * Adapted from
- * https://github.com/vega/vega-lite/blob/master/src/data.ts
- *
- * Copyright (c) 2015-2018, University of Washington Interactive Data Lab
- * All rights reserved.
- *
- * BSD-3-Clause License: https://github.com/vega/vega-lite/blob/master/LICENSE
- */
-
-/*
- * Constants and utilities for data.
- */
-import { FieldName } from "./channel";
-
-export type ParseValue =
-    | null
-    | string
-    | "string"
-    | "boolean"
-    | "date"
-    | "number";
-
-export interface Parse {
-    [field: string]: ParseValue;
-}
-
-export interface DataFormatBase {
-    /**
-     * If set to `null`, disable type inference based on the spec and only use type inference based on the data.
-     * Alternatively, a parsing directive object can be provided for explicit data types. Each property of the object corresponds to a field name, and the value to the desired data type (one of `"number"`, `"boolean"`, `"date"`, or null (do not parse the field)).
-     * For example, `"parse": {"modified_on": "date"}` parses the `modified_on` field in each input record a Date value.
-     *
-     * For `"date"`, we parse data based using Javascript's [`Date.parse()`](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Date/parse).
-     * For Specific date formats can be provided (e.g., `{foo: "date:'%m%d%Y'"}`), using the [d3-time-format syntax](https://github.com/d3/d3-time-format#locale_format). UTC date format parsing is supported similarly (e.g., `{foo: "utc:'%m%d%Y'"}`). See more about [UTC time](https://vega.github.io/vega-lite/docs/timeunit.html#utc)
-     */
-    parse?: Parse | null;
-
-    /**
-     * Type of input data: `"json"`, `"csv"`, `"tsv"`, `"dsv"`.
-     *
-     * __Default value:__  The default format type is determined by the extension of the file URL.
-     * If no extension is detected, `"json"` will be used by default.
-     */
-    type?: DataFormatType;
-}
-
-export interface CsvDataFormat extends DataFormatBase {
-    type?: "csv" | "tsv";
-}
-
-export interface DsvDataFormat extends DataFormatBase {
-    type?: "dsv";
-
-    /**
-     * The delimiter between records. The delimiter must be a single character (i.e., a single 16-bit code unit); so, ASCII delimiters are fine, but emoji delimiters are not.
-     *
-     * @minLength 1
-     * @maxLength 1
-     */
-    delimiter: string;
-}
-
-export interface JsonDataFormat extends DataFormatBase {
-    type?: "json";
-
-    /**
-     * The JSON property containing the desired data.
-     * This parameter can be used when the loaded JSON file may have surrounding structure or meta-data.
-     * For example `"property": "values.features"` is equivalent to retrieving `json.values.features`
-     * from the loaded JSON object.
-     */
-    property?: string;
-}
-
-/**
- * Other data format, such as `"fasta"`
- */
-export interface OtherDataFormat {
-    type: string;
-}
-
-export type DataFormat =
-    | CsvDataFormat
-    | DsvDataFormat
-    | JsonDataFormat
-    | OtherDataFormat;
-
-export type DataFormatType = "json" | "csv" | "tsv" | "dsv" | string;
-
-export type DataSource =
-    | UrlData
-    | InlineData
-    | NamedData
-    | DynamicCallbackData
-    | DynamicData;
-
-export type Data = DataSource | Generator;
-
-export type InlineDataset =
-    | number[]
-    | string[]
-    | boolean[]
-    | object[]
-    | string
-    | object;
-
-export interface DataBase {
-    /**
-     * An object that specifies the format for parsing the data.
-     */
-    format?: DataFormat;
-
-    /**
-     * Provide a placeholder name and bind data at runtime.
-     */
-    name?: string;
-}
-
-export interface UrlData extends DataBase {
-    /**
-     * An URL or an array of URLs from which to load the data set.
-     * Use the `format.type` property to ensure the loaded data is correctly parsed.
-     */
-    url: string | string[];
-}
-
-export interface InlineData extends DataBase {
-    /**
-     * The full data set, included inline. This can be an array of objects or primitive values, an object, or a string.
-     * Arrays of primitive values are ingested as objects with a `data` property. Strings are parsed according to the specified format type.
-     */
-    values: InlineDataset;
-}
-
-export interface NamedData extends DataBase {
-    /**
-     * Provide a placeholder name and bind data at runtime.
-     */
-    name: string;
-}
-
-export interface DynamicCallbackData extends DataBase {
-    /**
-     * The View class has `getDynamicData()` methods that provides the data.
-     * This is intended for internal use.
-     */
-    dynamicCallbackSource: boolean;
-}
-
-export interface DynamicData extends DataBase {
-    /**
-     * For internal use.
-     */
-    dynamicSource: boolean;
-}
-
-export type Generator = SequenceGenerator;
-
-export interface GeneratorBase {
-    /**
-     * Provide a placeholder name and bind data at runtime.
-     */
-    name?: string;
-}
-
-export interface SequenceGenerator extends GeneratorBase {
-    /**
-     * Generate a sequence of numbers.
-     */
-    sequence: SequenceParams;
-}
-
-export interface SequenceParams {
-    /**
-     * The starting value of the sequence (inclusive).
-     */
-    start: number;
-    /**
-     * The ending value of the sequence (exclusive).
-     */
-    stop: number;
-    /**
-     * The step value between sequence entries.
-     *
-     * __Default value:__ `1`
-     */
-    step?: number;
-
-    /**
-     * The name of the generated sequence field.
-     *
-     * __Default value:__ `"data"`
-     */
-    as?: FieldName;
-}

package/src/spec/font.d.ts

@@ -1,15 +0,0 @@
-export type FontStyle = "normal" | "italic";
-
-export type FontWeight =
-    | number
-    | "thin"
-    | "light"
-    | "regular"
-    | "normal"
-    | "medium"
-    | "bold"
-    | "black";
-
-export type Align = "left" | "center" | "right";
-
-export type Baseline = "top" | "middle" | "bottom" | "alphabetic";

package/src/spec/genome.d.ts

@@ -1,35 +0,0 @@
-export interface Contig {
-    name: string;
-    size: number;
-}
-
-export interface GenomeConfig {
-    /**
-     * Name of the genome assembly, e.g., `hg19` or `hg38`.
-     */
-    name: string;
-
-    /**
-     * Base url of data files: chromsizes, cytobands, and gene annotations.
-     *
-     * **Default:** `"https://genomespy.app/data/genomes/"`
-     */
-    baseUrl?: string;
-
-    /**
-     * As an alternative for chromSizes, the contigs can be provided inline.
-     */
-    contigs?: Contig[];
-}
-
-export interface ChromosomalLocus {
-    /**
-     * The name of the chromosome. For example: `"chr1"`, `"CHR1"`, or `"1"`.
-     */
-    chrom: string;
-
-    /**
-     * The zero-based position inside the chromosome or contig.
-     */
-    pos?: number;
-}