@genome-spy/core 0.36.1 → 0.37.0

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

@@ -0,0 +1,370 @@
+/*!
+ * 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 { Axis } from "./axis";
+import { FieldName, PrimaryPositionalChannel } 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
+    | LazyData;
+
+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 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;
+}
+
+export interface LazyData {
+    lazy: LazyDataParams;
+}
+
+export type LazyDataParams =
+    | AxisTicksData
+    | AxisGenomeData
+    | IndexedFastaData
+    | BigWigData
+    | BigBedData
+    | BamData
+    | Gff3Data;
+
+export interface AxisTicksData {
+    type: "axisTicks";
+
+    /** Optional axis properties */
+    axis?: Axis;
+
+    /** Which channel's scale domain to listen to */
+    channel: PrimaryPositionalChannel;
+}
+
+export interface AxisGenomeData {
+    type: "axisGenome";
+
+    /** Which channel's scale domain to use */
+    channel: PrimaryPositionalChannel;
+}
+
+export interface IndexedFastaData {
+    type: "indexedFasta";
+
+    /**
+     * Which channel's scale domain to monitor.
+     *
+     * __Default value:__ `"x"`
+     */
+    channel?: PrimaryPositionalChannel;
+
+    /**
+     * URL of the fasta file.
+     */
+    url: string;
+
+    /**
+     * URL of the index file.
+     *
+     * __Default value:__ `url` + `".fai"`.
+     */
+    indexUrl?: string;
+
+    /**
+     * Size of each chunk when fetching the fasta file. Data is only fetched
+     * when the length of the visible domain smaller than the window size.
+     *
+     * __Default value:__ `7000`
+     */
+    windowSize?: number;
+}
+
+export interface BigWigData {
+    type: "bigwig";
+
+    /**
+     * Which channel's scale domain to monitor.
+     *
+     * __Default value:__ `"x"`
+     */
+    channel?: PrimaryPositionalChannel;
+
+    /**
+     * URL of the BigWig file.
+     */
+    url: string;
+
+    /**
+     * The approximate minimum width of each data bin, in pixels.
+     *
+     * __Default value:__ `2`
+     */
+    pixelsPerBin?: number;
+}
+
+export interface BigBedData {
+    type: "bigbed";
+
+    /**
+     * Which channel's scale domain to monitor.
+     *
+     * __Default value:__ `"x"`
+     */
+    channel?: PrimaryPositionalChannel;
+
+    /**
+     * URL of the BigBed file.
+     */
+    url: string;
+
+    /**
+     * Size of each chunk when fetching the BigBed file. Data is only fetched
+     * when the length of the visible domain smaller than the window size.
+     *
+     * __Default value:__ `1000000`
+     */
+    windowSize?: number;
+}
+
+export interface BamData {
+    type: "bam";
+
+    /**
+     * Which channel's scale domain to monitor.
+     *
+     * __Default value:__ `"x"`
+     */
+    channel?: PrimaryPositionalChannel;
+
+    /**
+     * URL of the BigBed file.
+     */
+    url: string;
+
+    /**
+     * URL of the index file.
+     *
+     * __Default value:__ `url` + `".bai"`.
+     */
+    indexUrl?: string;
+
+    /**
+     * Size of each chunk when fetching the BigBed file. Data is only fetched
+     * when the length of the visible domain smaller than the window size.
+     *
+     * __Default value:__ `10000`
+     */
+    windowSize?: number;
+}
+
+export interface TabixData {
+    /**
+     * Which channel's scale domain to monitor.
+     *
+     * __Default value:__ `"x"`
+     */
+    channel?: PrimaryPositionalChannel;
+
+    /**
+     * Url of the bgzip compressed file.
+     */
+    url: string;
+
+    /**
+     * Url of the tabix index file.
+     *
+     * __Default value:__ `url` + `".tbi"`.
+     */
+    indexUrl?: string;
+
+    /**
+     * Size of each chunk when fetching the Tabix file. Data is only fetched
+     * when the length of the visible domain smaller than the window size.
+     *
+     * __Default value:__ `30000000`
+     */
+    windowSize?: number;
+
+    /**
+     * The debounce time for domain changes, in milliseconds. Debouncing prevents
+     * data fetches while the user is still panning around.
+     *
+     * __Default value:__ `200`
+     */
+    debounceDomainChange?: number;
+}
+
+export interface Gff3Data extends TabixData {
+    type: "gff3";
+}

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

@@ -0,0 +1,15 @@
+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/dist/src/spec/genome.d.ts

@@ -0,0 +1,35 @@
+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;
+}