@genome-spy/core 0.30.0 → 0.30.2

package/src/spec/transform.d.ts

@@ -1,479 +0,0 @@
-/**
- * The name of the field or a JavaScript expression for accessing nested properties.
- * Dots and brackets in the field name must be escaped.
- */
-export type Field = string;
-
-export interface TransformParamsBase {
-    /** The type of the transform to be applied */
-    type: string;
-}
-
-export interface IdentifierParams extends TransformParamsBase {
-    type: "identifier";
-
-    /**
-     * **Default:** `"_uniqueId"`
-     */
-    as?: string;
-}
-export interface FilterParams extends TransformParamsBase {
-    type: "filter";
-
-    /** An expression string. The data object is removed if the expression evaluates to false. */
-    expr: string;
-}
-
-export interface FormulaParams extends TransformParamsBase {
-    type: "formula";
-
-    /** An expression string */
-    expr: string;
-
-    /** The (new) field where the computed value is written to */
-    as: string;
-}
-
-export interface ProjectParams extends TransformParamsBase {
-    type: "project";
-
-    /**
-     * The fields to be projected.
-     */
-    fields: Field[];
-
-    /**
-     * New names for the projected fields. If omitted, the names of the source fields are used.
-     */
-    as?: string[];
-}
-
-export interface RegexExtractParams extends TransformParamsBase {
-    type: "regexExtract";
-
-    /**
-     * A valid JavaScript regular expression with at least one group. For example: `"^Sample(\\d+)$"`.
-     *
-     * Read more at: https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions
-     **/
-    regex: string;
-
-    /**
-     * The source field
-     */
-    field: Field;
-
-    /**
-     * The new field or an array of fields where the extracted values are written.
-     */
-    as: string | string[];
-
-    /**
-     * Do not complain about invalid input. Just skip it and leave the new fields undefined on the affected datum.
-     *
-     * **Default:** `false`
-     **/
-    skipInvalidInput?: boolean;
-}
-
-export interface RegexFoldParams extends TransformParamsBase {
-    type: "regexFold";
-
-    /**
-     * A regular expression that matches to column names. The regex must have one
-     * capturing group that is used for extracting the key (e.g., a sample id)
-     * from the column name.
-     */
-    columnRegex: string[] | string;
-
-    /**
-     * A new column name for the extracted values.
-     */
-    asValue: string[] | string;
-
-    /**
-     * An optional regex that matches to fields that should not be included
-     * in the new folded data objects.
-     */
-    skipRegex?: string;
-
-    /**
-     * **Default:** `"sample"`
-     */
-    asKey?: string;
-}
-
-export type SortOrder = "ascending" | "descending";
-
-export interface CompareParams {
-    /**
-     * The field(s) to sort by
-     */
-    field: Field[] | Field;
-
-    /**
-     * The order(s) to use: `"ascending"` (default), `"descending"`.
-     */
-    order?: SortOrder[] | SortOrder;
-}
-
-export interface StackParams extends TransformParamsBase {
-    type: "stack";
-
-    /**
-     * The field to stack. If no field is defined, a constant value of one is assumed.
-     */
-    field?: Field;
-
-    /**
-     * The fields to be used for forming groups for different stacks.
-     */
-    groupby: Field[];
-
-    /**
-     * The sort order of data in each stack.
-     */
-    sort?: CompareParams;
-
-    /**
-     * How to offset the values in a stack.
-     * `"zero"` (default) starts stacking at 0.
-     * `"center"` centers the values around zero.
-     * `"normalize"` computes intra-stack percentages and normalizes the values to the range of `[0, 1]`.
-     * `"information"` computes a layout for a sequence logo. The total height of the stack reflects
-     * the group's information content.
-     */
-    offset?: "zero" | "center" | "normalize" | "information";
-
-    /**
-     * Fields to write the stacked values.
-     *
-     * **Default:** `["y0", "y1"]`
-     */
-    as: string[];
-
-    /**
-     * Cardinality, e.g., the number if distinct bases or amino acids. Used for
-     * information content calculation when the offset is `"information"`.
-     *
-     * **Default:** `4`
-     */
-    cardinality?: number;
-
-    /**
-     * The field that contains the base or amino acid. Used for
-     * information content calculation when the offset is `"information"`.
-     * The data objects that have `null` in the baseField are considered gaps
-     * and they are taken into account when scaling the the locus' information
-     * content.
-     */
-    baseField?: Field;
-}
-
-export interface AggregateParams extends TransformParamsBase {
-    type: "aggregate";
-
-    /**
-     * Which fields to use for grouping. Missing `groupby` results in a single
-     * group that includes all the data items.
-     */
-    groupby?: Field[];
-}
-
-export interface FlattenDelimitedParams extends TransformParamsBase {
-    type: "flattenDelimited";
-
-    /**
-     * The field(s) to split and flatten
-     */
-    field: Field[] | Field;
-
-    /**
-     * Separator(s) used on the field(s)
-     * TODO: Rename to delimiter
-     */
-    separator: string[] | string;
-
-    /**
-     * The output field name(s) for the flattened field.
-     *
-     * **Default:** the input fields.
-     */
-    as?: string[] | string;
-}
-
-export interface FlattenSequenceParams extends TransformParamsBase {
-    type: "flattenSequence";
-
-    /**
-     * The field to flatten.
-     *
-     * **Default:** `"sequence"`
-     */
-    field?: Field;
-
-    /**
-     * Name of the fields where the zero-based index number and flattened
-     * sequence letter are written to.
-     *
-     * **Default:** `["pos", "sequence"]`
-     */
-    as?: [string, string];
-}
-
-export interface PileupParams extends TransformParamsBase {
-    type: "pileup";
-
-    /**
-     * The field representing the start coordinate of the segment (inclusive).
-     */
-    start: Field;
-
-    /**
-     * The field representing the end coordinate of the segment (exclusive).
-     */
-    end: Field;
-
-    /**
-     * The output field name for the computed lane.
-     *
-     * **Default:** `"lane"`.
-     */
-    as?: string;
-
-    /**
-     * The spacing between adjacent segments on the same lane in coordinate units.
-     *
-     * **Default:** `1`.
-     */
-    spacing?: number;
-
-    /**
-     * An optional field indicating the preferred lane. Use together with the
-     * `preferredOrder` property.
-     */
-    preference?: Field;
-
-    /**
-     * The order of the lane preferences. The first element contains the value that
-     * should place the segment on the first lane and so forth.
-     * If the preferred lane is occupied, the first available lane is taken.
-     */
-    preferredOrder?: string[] | number[] | boolean[];
-}
-
-export interface CoverageParams extends TransformParamsBase {
-    type: "coverage";
-
-    /**
-     * An optional chromosome field that is passed through. TODO: groupby
-     */
-    chrom?: Field;
-
-    /**
-     * The field representing the start coordinate of the segment (inclusive).
-     */
-    start: Field;
-
-    /**
-     * The field representing the end coordinate of the segment (exclusive).
-     */
-    end: Field;
-
-    /**
-     * A field representing an optional weight for the segment. Can be used with
-     * copy ratios, for example.
-     */
-    weight?: Field;
-
-    /**
-     * The output field for the computed coverage.
-     */
-    as?: string;
-
-    /**
-     * The output field for the chromosome.
-     *
-     * **Default:** Same as `chrom`
-     */
-    asChrom?: string;
-
-    /**
-     * The output field for the start coordinate.
-     *
-     * **Default:** Same as `start`
-     */
-    asStart?: string;
-
-    /**
-     * The output field for the end coordinate.
-     *
-     * **Default:** Same as `end`
-     */
-    asEnd?: string;
-}
-
-export interface CollectParams extends TransformParamsBase {
-    type: "collect";
-
-    /**
-     * Arranges the data into consecutive batches based on the groups.
-     * This is mainly intended for internal use so that faceted data can
-     * be handled as batches.
-     */
-    groupby?: Field[];
-
-    /**
-     * The sort order.
-     */
-    sort?: CompareParams;
-}
-
-export interface SampleParams extends TransformParamsBase {
-    type: "sample";
-
-    /**
-     * The maximum sample size.
-     *
-     * **Default:** `500`
-     */
-    size?: number;
-}
-
-export interface MeasureTextParams extends TransformParamsBase {
-    type: "measureText";
-
-    field: Field;
-
-    fontSize: number;
-
-    as: string;
-
-    // TODO: FontFamily etc
-}
-
-export interface MergeFacetsParams extends TransformParamsBase {
-    type: "mergeFacets";
-}
-
-export interface LinearizeGenomicCoordinateParams extends TransformParamsBase {
-    type: "linearizeGenomicCoordinate";
-
-    /**
-     * Get the genome assembly from the scale of the channel.
-     *
-     * **Default:** `"x"`
-     */
-    channel?: "x" | "y";
-
-    /**
-     * The chromosome/contig field
-     */
-    chrom: Field;
-
-    /**
-     * The field or fields that contain intra-chromosomal positions
-     */
-    pos: Field | Field[];
-
-    /**
-     * 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 | number[];
-
-    /**
-     * The output field or fields for linearized coordinates.
-     */
-    as: string | string[];
-}
-
-export interface FilterScoredLabelsParams extends TransformParamsBase {
-    type: "filterScoredLabels";
-
-    /**
-     * The field representing the score used for prioritization.
-     */
-    score: Field;
-
-    /**
-     * The field representing element's width in pixels
-     */
-    width: Field;
-
-    /**
-     * The field representing element's position on the domain.
-     */
-    pos: Field;
-
-    /**
-     * An optional field representing element's lane, e.g., if transcripts
-     * are shown using a piled up layout.
-     */
-    lane?: Field;
-
-    /**
-     * Padding (in pixels) around the element.
-     *
-     * **Default:** `0`
-     */
-    padding?: number;
-
-    /**
-     * **Default:** `"x"`
-     */
-    channel?: "x" | "y";
-}
-
-export interface FlattenCompressedExonsParams extends TransformParamsBase {
-    type: "flattenCompressedExons";
-
-    /**
-     * The field containing the exons.
-     *
-     * **Default:** `"exons"`
-     */
-    exons?: Field;
-
-    /**
-     * Start coordinate of the gene body.
-     *
-     * **Default:** `"start"`
-     */
-    start?: Field;
-
-    /**
-     * Field names for the flattened exons.
-     *
-     * **Default:** `["exonStart", "exonEnd"]`
-     */
-    as?: [string, string];
-}
-
-export type TransformParams =
-    | AggregateParams
-    | CollectParams
-    | CoverageParams
-    | FlattenDelimitedParams
-    | FormulaParams
-    | FilterParams
-    | FilterScoredLabelsParams
-    | FlattenCompressedExonsParams
-    | FlattenSequenceParams
-    | IdentifierParams
-    | LinearizeGenomicCoordinateParams
-    | MeasureTextParams
-    | MergeFacetsParams
-    | PileupParams
-    | ProjectParams
-    | RegexExtractParams
-    | RegexFoldParams
-    | SampleParams
-    | StackParams;

package/src/spec/view.d.ts

@@ -1,201 +0,0 @@
-import { Data } from "./data";
-import { TransformParams } from "./transform";
-import {
-    Channel,
-    Encoding,
-    FacetFieldDef,
-    PrimaryPositionalChannel,
-} from "./channel";
-import {
-    FillAndStrokeProps,
-    MarkConfigAndType,
-    MarkType,
-    RectProps,
-} from "./mark";
-import { Title } from "./title";
-import { SampleSpec } from "./sampleView";
-
-export interface SizeDef {
-    /** Size in pixels */
-    px?: number;
-
-    /** Share of the remaining space */
-    grow?: number;
-}
-
-// TODO: Perhaps this should be in "utils"
-export type GeometricDimension = "width" | "height";
-
-export interface FacetMapping {
-    column?: FacetFieldDef;
-    row?: FacetFieldDef;
-}
-
-/**
- * DynamicOpacity specifies a zoom-dependent behavior for view opacity.
- * The opacity is interpolated between the specified stops.
- */
-export interface DynamicOpacity {
-    channel?: PrimaryPositionalChannel;
-    /** Stops expressed as units (base pairs, for example) per pixel. */
-    unitsPerPixel: number[];
-    /** Opacity values that match the given stops. */
-    values: number[];
-}
-
-export type ViewOpacityDef = number | DynamicOpacity;
-
-export interface Step {
-    step: number;
-}
-
-export type Side = "top" | "right" | "bottom" | "left";
-
-export type Paddings = Partial<Record<Side, number>>;
-
-export type PaddingConfig = Paddings | number;
-
-export interface ViewBackground extends RectProps, FillAndStrokeProps {
-    // TODO: style?: string | string[];
-
-    // TODO: Move to FillAndStrokeProps or something
-    strokeWidth?: number;
-}
-
-export interface ViewSpecBase extends ResolveSpec {
-    name?: string;
-
-    height?: SizeDef | number | Step | "container";
-    width?: SizeDef | number | Step | "container";
-
-    /**
-     * Padding in pixels.
-     *
-     * **Default:* `0`
-     */
-    padding?: PaddingConfig;
-
-    data?: Data;
-    transform?: TransformParams[];
-    encoding?: Encoding;
-    title?: string | Title;
-
-    /**
-     * A description of the view. Multiple lines can be provided as an array.
-     */
-    description?: string | string[];
-
-    baseUrl?: string;
-
-    /**
-     * Opacity of the view and all its children.
-     *
-     * **Default:* `1.0`
-     */
-    // TODO: Should be available only in Unit and Layer views.
-    opacity?: ViewOpacityDef;
-
-    /**
-     * Visibility of the view. An invisible view is removed from the layout
-     * and not rendered.
-     *
-     * **Default:** `true`
-     */
-    // TODO: Detach invisible views from the data flow.
-    visible?: boolean;
-
-    /**
-     * Is the visibility configurable interactively from the App.
-     * Configurability requires that the view has an explicitly specified name
-     * that is *unique* in within the view specification.
-     *
-     * **Default:** `false` for children of `layer`, `true` for others.
-     */
-    configurableVisibility?: boolean;
-}
-
-export interface UnitSpec extends ViewSpecBase, AggregateSamplesSpec {
-    view?: ViewBackground;
-    mark: MarkType | MarkConfigAndType;
-}
-
-export interface AggregateSamplesSpec {
-    // TODO: Introduce a type (UnitSpec | LayerSpec) that can ba used in SampleView and here
-    aggregateSamples?: (UnitSpec | LayerSpec)[];
-}
-
-export interface LayerSpec extends ViewSpecBase, AggregateSamplesSpec {
-    view?: ViewBackground;
-    layer: (LayerSpec | UnitSpec)[];
-}
-
-export interface FacetSpec extends ViewSpecBase {
-    facet: any; //FacetMapping | FacetFieldDef
-    spec: LayerSpec | UnitSpec;
-    columns?: number;
-    spacing?: number;
-}
-
-export type ResolutionTarget = "scale" | "axis";
-
-/**
- * `"independent"` and `"shared"` behave similarly to Vega-Lite.
- * `"excluded"` behaves like `"shared"`, but is not pulled towards the root.
- */
-export type ResolutionBehavior = "independent" | "shared" | "excluded";
-
-export interface ResolveSpec {
-    resolve?: Partial<
-        Record<
-            ResolutionTarget,
-            Partial<Record<Channel | "default", ResolutionBehavior>>
-        >
-    >;
-}
-
-export type ContainerSpec = (
-    | LayerSpec
-    //    | FacetSpec
-    | SampleSpec
-    | VConcatSpec
-    | HConcatSpec
-    | ConcatSpec
-    | UnitSpec
-) &
-    ResolveSpec;
-
-export type ViewSpec =
-    | UnitSpec
-    | LayerSpec
-    //    | FacetSpec
-    | SampleSpec
-    | VConcatSpec
-    | HConcatSpec
-    | ConcatSpec;
-
-export interface ImportConfig {
-    name?: string;
-    url?: string;
-    params?: object;
-}
-
-export interface ImportSpec {
-    import: ImportConfig;
-}
-
-export interface ConcatBase extends ViewSpecBase {
-    spacing?: number;
-}
-
-export interface VConcatSpec extends ConcatBase {
-    vconcat: (ViewSpec | ImportSpec)[];
-}
-
-export interface HConcatSpec extends ConcatBase {
-    hconcat: (ViewSpec | ImportSpec)[];
-}
-
-export interface ConcatSpec extends ConcatBase {
-    concat: (ViewSpec | ImportSpec)[];
-    columns: number;
-}