loom-browser 0.0.1 → 0.0.2

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

@@ -1,885 +0,0 @@
-import type { ChromSizes, CumulativeOffsets } from './genome/chromSizes';
-/** Genomic locus — a chromosome region. */
-export interface Locus {
-    chr: string;
-    start: number;
-    end: number;
-}
-/** Axis information for the left-hand axis column in GenomeBrowser. */
-export interface AxisInfo {
-    /** Track label (e.g., track name). */
-    label?: string;
-    /** Data range for quantitative tracks (min at bottom, max at top). */
-    dataRange?: {
-        min: number;
-        max: number;
-    };
-    /** Color for the axis color strip indicator. */
-    color?: string;
-    /** If true, swap min/max label positions (used by GWAS/QTL tracks). */
-    flipAxis?: boolean;
-    /** If true, use logarithmic scale for tick placement and labels. */
-    logScale?: boolean;
-    /** Background color for the axis cell. Defaults to 'white'. */
-    backgroundColor?: string;
-    /** Foreground color for labels, ticks, and axis lines. Defaults to 'black'. */
-    labelColor?: string;
-}
-/**
- * State + callbacks for a numeric (quantitative) track.
- *
- * Returned by `Track.getNumericState()` so the browser can build shared
- * menu items (set data range, log scale, autoscale) via `numericDataMenuItems()`.
- * Mirrors igv.js `TrackBase.numericDataMenuItems()` (js/trackBase.ts).
- */
-export interface NumericState {
-    /** Whether autoscale is currently enabled. */
-    autoscale: boolean;
-    /** Whether log scale is currently enabled. Undefined = not supported. */
-    logScale?: boolean;
-    /** Current data range (min/max). */
-    dataRange: {
-        min: number;
-        max: number;
-    };
-    /** Toggle autoscale on/off. */
-    setAutoscale(enabled: boolean): void;
-    /** Toggle log scale on/off. Only present if log scale is supported. */
-    setLogScale?(enabled: boolean): void;
-    /** Set the data range (min/max). */
-    setDataRange(min: number, max: number): void;
-}
-/**
- * Generic track interface for canvas-based genomic tracks.
- * Each track manages its own canvas and knows how to render given a locus.
- */
-export interface Track {
-    /** Track type identifier (e.g. 'gene', 'ruler'). */
-    readonly type: string;
-    /** The canvas element managed by this track. */
-    readonly canvas: HTMLCanvasElement;
-    /** Current locus. */
-    readonly locus: Locus;
-    /** Track height in CSS pixels (after last render). */
-    readonly height: number;
-    /** Update the locus and re-render. */
-    setLocus(locus: Locus): void;
-    /** Render the track at its current state. */
-    render(): void;
-    /** Suspend rendering — calls to render() will be deferred until resumeRendering(). */
-    suspendRendering(): void;
-    /** Resume rendering and flush any deferred render. */
-    resumeRendering(): void;
-    /** Attach to a container (appends canvas, sets up ResizeObserver). */
-    attachTo(container: HTMLElement): void;
-    /** Detach from container, clean up. */
-    detach(): void;
-    /** Set an error state to render on the track canvas. Pass null to clear. */
-    setError(error: Error | null): void;
-    /**
-     * Hit-test at canvas-relative pixel coordinates.
-     * Returns features at that point with pre-formatted popup data.
-     * Default implementation returns [] (no interactive features).
-     */
-    hitTest(x: number, y: number): HitTestResult[];
-    /**
-     * Serialize this track's config for session save/restore.
-     * Returns the serializable subset of config, diffed against theme defaults.
-     * Each track type implements this with its own typed return value.
-     */
-    serializeConfig(theme: import('./themes/renderTheme').RenderTheme): TrackSessionConfig;
-    /**
-     * Return axis information for the left-hand label column.
-     * Optional — tracks that return undefined get an empty axis cell.
-     */
-    getAxisInfo?(): AxisInfo | undefined;
-    /**
-     * Return context menu items for a right-click at canvas-relative coordinates.
-     * Optional — tracks that return undefined get only common items (set height, remove).
-     */
-    getContextMenuItems?(x: number, y: number): ContextMenuItem[] | undefined;
-    /**
-     * Return current numeric/quantitative state and callbacks for shared menu items.
-     *
-     * When defined, the browser adds shared numeric menu items (set data range,
-     * log scale, autoscale) via `numericDataMenuItems()`. Mirrors igv.js
-     * `TrackBase.numericDataMenuItems()` (js/trackBase.ts lines 510-552)
-     * which is shared by WigTrack, BAMTrack, QTLTrack, GCNVTrack, etc.
-     *
-     * Undefined = track is not numeric (no items added).
-     */
-    getNumericState?(): NumericState | undefined;
-    /**
-     * Visibility window in base pairs. When the viewport spans more than this
-     * many bp, data fetching is skipped and "Zoom in to see features" is shown.
-     * Mirrors igv.js TrackBase.visibilityWindow (js/trackViewport.ts checkZoomIn).
-     *
-     * - undefined or 0: no limit (always fetch)
-     * - > 0: skip fetch when bpPerPixel * viewportWidth > visibilityWindow
-     */
-    /**
-     * Render this track onto an arbitrary context (e.g. SVG export).
-     * Unlike render(), this skips DPR scaling and canvas-element lifecycle —
-     * it draws directly onto the provided context at the given dimensions.
-     */
-    renderToContext?(ctx: CanvasRenderingContext2D, width: number, height: number): void;
-    visibilityWindow?: number;
-}
-/** A single exon within a gene feature. */
-export interface Exon {
-    start: number;
-    end: number;
-    /** True if entire exon is untranslated region. */
-    utr?: boolean;
-    /** CDS start within this exon (when exon is partially UTR at the start). */
-    cdStart?: number;
-    /** CDS end within this exon (when exon is partially UTR at the end). */
-    cdEnd?: number;
-    /** Codon reading frame offset (0, 1, or 2). Undefined for non-coding exons. */
-    readingFrame?: number;
-    /** Exon number (1-based). Assigned by GFF assembly based on strand direction. */
-    number?: number;
-}
-/** An annotation feature with optional exon structure and row assignment from packing. */
-export interface AnnotationFeature {
-    start: number;
-    end: number;
-    strand?: '+' | '-';
-    /** Gene name (e.g., "TP53"). */
-    name?: string;
-    /** Transcript ID (e.g., "NM_000546.6"). */
-    id?: string;
-    /** Chromosome (e.g., "chr17"). */
-    chr?: string;
-    /** CDS start position. Equal to cdsEnd for non-coding transcripts. */
-    cdStart?: number;
-    /** CDS end position. Equal to cdStart for non-coding transcripts. */
-    cdEnd?: number;
-    exons?: Exon[];
-    /** Per-feature color (e.g., from BED itemRgb column 8). */
-    color?: string;
-    /** Score from source annotation. */
-    score?: number;
-    /** CDS start completeness: "cmpl", "incmpl", or "unk". */
-    cdsStartStat?: string;
-    /** CDS end completeness: "cmpl", "incmpl", or "unk". */
-    cdsEndStat?: string;
-    /** Assigned by pack() — the row this feature is placed in. */
-    row?: number;
-}
-/** Display mode for gene features. */
-export type DisplayMode = 'COLLAPSED' | 'SQUISHED' | 'EXPANDED';
-/** Configuration controlling how annotation features (gene, BED, GFF, peaks) are rendered. */
-export interface AnnotationRenderConfig {
-    displayMode: DisplayMode;
-    featureHeight: number;
-    margin: number;
-    /** Row height in EXPANDED mode (featureHeight + label space + padding). */
-    expandedRowHeight: number;
-    /** Row height in SQUISHED mode. */
-    squishedRowHeight: number;
-    /** Pixel spacing between strand-direction arrows. */
-    arrowSpacing: number;
-    /** Default fill color for CDS exons. */
-    color: string;
-    /** Color for features on the opposite strand (if desired). */
-    altColor?: string;
-    /** Which feature property to use as the label. */
-    labelField: string;
-    /** CSS font string for labels, e.g. "10px sans-serif". */
-    font: string;
-    /** Whether to draw labels. */
-    drawLabels: boolean;
-    /** Label display mode — "SLANT" rotates labels 45°. */
-    labelDisplayMode?: 'SLANT';
-    /** UTR fill color. Defaults to main color. */
-    utrColor?: string;
-    /** Alt UTR color (for - strand when altColor is set). */
-    altUtrColor?: string;
-    /** Exon stroke outline color. No outline when undefined. */
-    borderColor?: string;
-    /** Exon outline width. Default: 0 (no outline). */
-    borderWidth?: number;
-    /** Rounded corner radius for exon rects. Default: 0 (square). */
-    borderRadius?: number;
-    /** Intron line color. Defaults to main color. */
-    intronColor?: string;
-    /** Intron line width. Default: 1. */
-    intronLineWidth?: number;
-    /** Dash pattern for intron lines, e.g. [3, 3]. Default: [] (solid). */
-    intronDash?: number[];
-    /** Strand arrow color on intron lines. Defaults to current stroke color. */
-    arrowColor?: string;
-    /** Strand arrow color inside exons. Default: 'white'. */
-    arrowInExonColor?: string;
-    /** Label text color. Defaults to feature color. */
-    labelColor?: string;
-    /** Background color behind labels. When set, fills behind labels instead of clearing to transparent. */
-    labelBackground?: string;
-    /** Separate CSS font string for labels. Defaults to `font`. */
-    labelFont?: string;
-}
-/** Rendering context — describes the viewport being drawn into. */
-export interface RenderContext {
-    /** Total pixel width of the canvas. */
-    pixelWidth: number;
-    /** Genomic coordinate of the left edge. */
-    bpStart: number;
-    /** Scale: base pairs per pixel. */
-    bpPerPixel: number;
-    /** Visible viewport width (may be less than pixelWidth for overscanning). */
-    viewportWidth: number;
-}
-/** Returns sensible defaults for annotation feature rendering. */
-export declare function defaultAnnotationRenderConfig(): AnnotationRenderConfig;
-/** Configuration for ruler track rendering. */
-export interface RulerRenderConfig {
-    /** Total height in CSS pixels. Default: 40. */
-    height: number;
-    /** Font for tick labels. Default: 'bold 10px sans-serif'. */
-    font: string;
-    /** Tick line color. Default: 'rgb(150, 150, 150)'. */
-    tickColor: string;
-    /** Label text color. Default: 'rgb(0, 0, 0)'. */
-    labelColor: string;
-    /** Baseline (bottom rule) color. Default: 'rgb(150, 150, 150)'. */
-    baselineColor: string;
-    /** Background color. Default: 'white'. */
-    background: string;
-}
-/** A single wig data point: a chromosome region with a numeric value. */
-export interface WigFeature {
-    chr: string;
-    start: number;
-    end: number;
-    value: number;
-    /** Human-readable summary description (e.g. "mean of 12 values"). */
-    description?: string;
-    /** DNA sequence for this region (populated for dynseq rendering). */
-    sequence?: string;
-}
-/** Graph type for wig track rendering. */
-export type WigGraphType = 'bar' | 'line' | 'points' | 'dynseq';
-/** A function that fetches DNA sequence for a genomic region. */
-export type SequenceProvider = (locus: Locus, signal?: AbortSignal) => Promise<string>;
-/**
- * Chromosome metadata.
- * Mirrors igv.js Chromosome (js/genome/chromosome.ts).
- */
-export interface Chromosome {
-    /** Canonical chromosome name (e.g., "chr1"). */
-    name: string;
-    /** Length in base pairs. */
-    bpLength: number;
-    /** Sort order (chr1=0, chr2=1, ..., chrX=22, chrY=23, chrM=24). */
-    order: number;
-}
-/**
- * Genome assembly providing chromosome metadata and optional sequence access.
- *
- * Mirrors igv.js Genome (js/genome/genome.ts) — the central object that
- * provides chromosome sizes, coordinate conversion, and sequence retrieval.
- * In our architecture this is a Layer 1 (Data + Layout) interface: pure data,
- * no DOM, no canvas.
- */
-export interface Genome {
-    /** Genome identifier (e.g., "hg38", "mm10"). */
-    readonly id: string;
-    /** Human-readable name (e.g., "Human (GRCh38/hg38)"). */
-    readonly name?: string;
-    /** Ordered main chromosome names (chr1-22, X, Y, M). */
-    readonly chromosomeNames: string[];
-    /** Full chromosome sizes record (chr → bp length). */
-    readonly chromSizes: ChromSizes;
-    /** Precomputed cumulative offsets for whole genome view. */
-    readonly cumulativeOffsets: CumulativeOffsets;
-    /** Get chromosome metadata by name. Returns undefined if not found. */
-    getChromosome(name: string): Chromosome | undefined;
-    /** Get chromosome length by name. Returns undefined if not found. */
-    getChromosomeLength(name: string): number | undefined;
-    /** Optional sequence provider. Undefined when genome has no sequence source. */
-    readonly sequence?: SequenceProvider;
-    /** Resolve a chromosome alias to the canonical name. Returns the input unchanged if no alias found. */
-    getChromosomeName(alias: string): string;
-    /** Get the full alias record for a chromosome. Returns undefined if not found. */
-    getAliasRecord(chr: string): ChromAliasRecord | undefined;
-}
-/**
- * Chromosome alias record mapping naming conventions to chromosome names.
- * `.chr` is always the canonical name in the genome's own namespace.
- *
- * Mirrors igv.js alias records (js/genome/chromAliasDefaults.ts) which use
- * `Record<string, string>` with named keys like "ncbi", "ucsc", "_chrprefix_".
- */
-export interface ChromAliasRecord {
-    /** Canonical chromosome name in this genome. Always present. */
-    chr: string;
-    /** Additional naming convention mappings (e.g., ncbi, ucsc, assembly, _chrprefix_). */
-    [nameSet: string]: string;
-}
-/**
- * Configuration for creating a Genome.
- *
- * Mirrors a subset of igv.js GenomeConfig (js/types/genome.ts).
- * Supports: built-in IDs, inline chromSizes, URL-based chromSizes,
- * and optional sequence providers.
- */
-export interface GenomeConfig {
-    /** Genome ID. Required for built-in genomes (e.g., "hg38"). */
-    id?: string;
-    /** Human-readable name. */
-    name?: string;
-    /** Inline chromosome sizes. Mutually exclusive with chromSizesURL. */
-    chromSizes?: ChromSizes;
-    /** URL to a chrom.sizes file (tab-separated: name\tlength). */
-    chromSizesURL?: string;
-    /** Sequence provider function. When set, genome.sequence is available. */
-    sequenceProvider?: SequenceProvider;
-    /**
-     * UCSC genome name for automatic sequence API access (e.g., "hg38").
-     * Defaults to `id` when not set. When a built-in genome is used,
-     * a CachedSequence wrapping the UCSC API is created automatically.
-     */
-    ucscGenome?: string;
-    /** URL to a chromosome alias file (tab-delimited). For future file-based alias loading. */
-    chromAliasURL?: string;
-}
-/** Aggregation function for resolution-aware data summarization. */
-export type WindowFunction = 'mean' | 'min' | 'max' | 'none';
-/** A horizontal guide line drawn at a specific data value. */
-export interface WigGuideLine {
-    /** The data value at which to draw the line. */
-    y: number;
-    /** Line color. */
-    color: string;
-    /** Whether to draw a dashed line. */
-    dotted: boolean;
-}
-/** Color value for wig features: a static CSS color string or a function mapping value → color. */
-export type WigColorValue = string | ((value: number) => string);
-/** Configuration controlling how wig features are rendered. */
-export interface WigRenderConfig {
-    /** Track height in CSS pixels. Default: 50. */
-    height: number;
-    /** Graph rendering style. Default: 'bar'. */
-    graphType: WigGraphType;
-    /** Data aggregation when zoomed out. Default: 'mean'. */
-    windowFunction: WindowFunction;
-    /** Y-axis data range. Features are scaled to this range. */
-    dataRange: {
-        min: number;
-        max: number;
-    };
-    /** Whether to auto-compute dataRange from features. Default: true. */
-    autoscale: boolean;
-    /** Fill/stroke color for positive values. String or (value) => color function. Default: 'rgb(150, 150, 150)'. */
-    color: WigColorValue;
-    /** Fill/stroke color for negative values. String or (value) => color function. Uses `color` when undefined. */
-    altColor?: WigColorValue;
-    /** Alpha transparency for feature colors (0–1). Applied on top of resolved color. Default: undefined (fully opaque). */
-    alpha?: number;
-    /** Flip the y-axis (values grow downward). Default: false. */
-    flipAxis: boolean;
-    /** Use logarithmic scale for the y-axis. Default: false. */
-    logScale: boolean;
-    /** Color for the zero-line baseline. Default: 'lightGray'. */
-    baselineColor: string;
-    /** Color for out-of-range value indicators. Default: 'rgb(255, 32, 255)'. */
-    overflowColor: string;
-    /** Point diameter in pixels (for 'points' graphType). Default: 3. */
-    pointSize: number;
-    /** Background color. Default: '#ffffff'. */
-    background: string;
-    /** Optional horizontal guide lines. */
-    guideLines?: WigGuideLine[];
-    /** Nucleotide colors for dynseq rendering. Keys: A, C, G, T, N. */
-    nucleotideColors?: Record<string, string>;
-    /** Multiply all feature values by this factor before rendering. Default: undefined (no scaling). */
-    scaleFactor?: number;
-    /**
-     * Normalization factor applied to all feature values (e.g. reads-per-million from TDF).
-     * When set, all values are multiplied by this factor before scaleFactor is applied.
-     * Typically provided by the data source rather than set manually.
-     */
-    normalizationFactor?: number;
-    /** Whether to draw min/max data range labels on the track. Default: true. */
-    showDataRange: boolean;
-    /** Color for data range label text. Default: palette.foreground. */
-    labelColor: string;
-    /** Font for data range labels. Default: 'bold 9px sans-serif'. */
-    labelFont: string;
-    /** Track name to display as an overlay label (igv.js style, top-left). */
-    trackName?: string;
-}
-/** Sequence type for the sequence track. */
-export type SequenceType = 'dna' | 'rna' | 'prot';
-/** Configuration controlling how sequence features are rendered. */
-export interface SequenceRenderConfig {
-    /** Sequence type (affects coloring). Default: 'dna'. */
-    sequenceType: SequenceType;
-    /** Show reverse complement. Default: false. */
-    reversed: boolean;
-    /** Show three-frame amino acid translation. Default: false. */
-    frameTranslate: boolean;
-    /** Override color for all bases. When set, ignores nucleotide color map. */
-    color?: string;
-    /** Background color. Default: '#ffffff'. */
-    background: string;
-    /** Nucleotide color mapping (A, C, G, T, N). Used when sequenceType is 'dna'. */
-    nucleotideColors: Record<string, string>;
-    /** Default color for RNA/protein bases. Default: 'rgb(0, 0, 150)'. */
-    nonDnaColor: string;
-    /** Track height without translation frames. Default: 25. */
-    defaultHeight: number;
-    /** Track height with translation frames. Default: 115. */
-    translatedHeight: number;
-    /** Height of the sequence row. Default: 15. */
-    sequenceHeight: number;
-    /** Height of each translation frame row. Default: 25. */
-    frameHeight: number;
-    /** Border/padding between elements. Default: 5. */
-    frameBorder: number;
-    /** Alternating background color 1 for translation frames. Default: 'rgb(160,160,160)'. */
-    frameColor1: string;
-    /** Alternating background color 2 for translation frames. Default: 'rgb(224,224,224)'. */
-    frameColor2: string;
-    /** Stop codon highlight color. Default: 'rgb(255, 0, 0)'. */
-    stopCodonColor: string;
-    /** Start codon (M) highlight color. Default: 'rgb(0, 153, 0)'. */
-    startCodonColor: string;
-    /** Use fillText instead of strokeText for base and amino acid labels. Default: false (strokeText, matching igv.js). */
-    useFillText: boolean;
-    /** Color for amino acid labels in translation frames. Default: '#000000'. */
-    frameLabelColor: string;
-    /** Color for amino acid labels on start/stop codon backgrounds. Default: same as frameLabelColor. */
-    codonLabelColor?: string;
-    /** Font for amino acid labels in translation frames. Default: 'bold 10px sans-serif'. */
-    frameFont: string;
-    /** Border radius for start/stop codon highlights (roundRect). 0 = sharp rectangles. Default: 0. */
-    codonBorderRadius: number;
-}
-/** Returns sensible defaults for sequence rendering. */
-export declare function defaultSequenceRenderConfig(): SequenceRenderConfig;
-/** Returns sensible defaults for wig rendering. */
-export declare function defaultWigRenderConfig(): WigRenderConfig;
-/** An interaction feature representing a pairwise genomic contact (Hi-C, ChIA-PET, etc.). */
-export interface InteractionFeature {
-    /** Bounding chromosome (same as chr1 for intra-chr; set per-copy for inter-chr). */
-    chr: string;
-    /** Bounding start (min of start1, start2 for intra-chr). */
-    start: number;
-    /** Bounding end (max of end1, end2 for intra-chr). */
-    end: number;
-    /** First region chromosome. */
-    chr1: string;
-    /** First region start. */
-    start1: number;
-    /** First region end. */
-    end1: number;
-    /** Second region chromosome. */
-    chr2: string;
-    /** Second region start. */
-    start2: number;
-    /** Second region end. */
-    end2: number;
-    name?: string;
-    score?: number;
-    value?: number;
-    color?: string;
-    strand1?: string;
-    strand2?: string;
-    type?: string;
-    thickness?: number;
-    extras?: string[];
-    /** True if this is a duplicated copy of an inter-chr feature (for the other chromosome). */
-    dup?: boolean;
-}
-/** Arc orientation: arcs open upward or downward. */
-export type ArcOrientation = 'UP' | 'DOWN';
-/** Display mode for interaction arcs. */
-export type ArcDisplayMode = 'nested' | 'proportional';
-/** Configuration controlling how interaction features are rendered as arcs. */
-export interface InteractionRenderConfig {
-    /** Track height in CSS pixels. Default: 250. */
-    height: number;
-    /** Arc direction. Default: 'UP'. */
-    arcOrientation: ArcOrientation;
-    /** Display mode. Default: 'nested'. */
-    displayMode: ArcDisplayMode;
-    /** Show small rectangles at feature endpoints. Default: true. */
-    showBlocks: boolean;
-    /** Height of endpoint rectangles in pixels. Default: 3. */
-    blockHeight: number;
-    /** Arc stroke width in pixels. Default: 1. */
-    thickness: number;
-    /** Default arc color. Default: 'rgb(180,25,137)'. */
-    color: string;
-    /** Fill alpha for arcs. Default: 0.02. */
-    alpha: number;
-    /** Use log scale for proportional arc heights. Default: true. */
-    logScale: boolean;
-    /** Background color. Default: '#ffffff'. */
-    background: string;
-    /** Font for inter-chromosome labels. Default: '8px sans-serif'. */
-    font: string;
-    /** Whether to use score-based shading. Default: false. */
-    useScore: boolean;
-}
-/** Returns sensible defaults for interaction rendering. */
-export declare function defaultInteractionRenderConfig(): InteractionRenderConfig;
-/** A single item in a feature popup (key-value pair). */
-export interface PopupDataItem {
-    name: string;
-    value: string | number;
-    /** Draw a border above this item (visual section separator). */
-    borderTop?: boolean;
-}
-/** Result of a hit test at a pixel coordinate within a track canvas. */
-export interface HitTestResult<F = unknown> {
-    feature: F;
-    popupData: PopupDataItem[];
-}
-/** Payload for trackclick / trackhover browser events. */
-export interface TrackInteractionEvent {
-    track: Track;
-    /** Genomic position at the interaction point. */
-    genomicLocation: number;
-    /** Features found at the interaction point. */
-    features: unknown[];
-    /** Pre-formatted popup data items from all hit features. */
-    popupData: PopupDataItem[];
-    /** Canvas-relative X in CSS pixels. */
-    x: number;
-    /** Canvas-relative Y in CSS pixels. */
-    y: number;
-}
-/** A single Region of Interest — a highlighted genomic region spanning all tracks. */
-export interface ROI {
-    /** Unique identifier. */
-    id: string;
-    /** Chromosome name. */
-    chr: string;
-    /** Start position (0-based). */
-    start: number;
-    /** End position. */
-    end: number;
-    /** Display name. */
-    name?: string;
-    /** Description text. */
-    description?: string;
-    /** Fill color (CSS color with alpha). */
-    color?: string;
-}
-/** Serializable config for an ROI set — used in SessionConfig. */
-export interface ROISetConfig {
-    /** Set display name. */
-    name: string;
-    /** Default color for ROIs in this set. */
-    color?: string;
-    /** Whether this set was created by the user (vs loaded from config). */
-    isUserDefined?: boolean;
-    /** The ROI features in this set. */
-    features: ROI[];
-}
-/** Payload for ROI interaction events (click, hover). */
-export interface ROIInteractionEvent {
-    /** The ROI that was interacted with. */
-    roi: ROI;
-    /** Genomic position at the interaction point. */
-    genomicLocation: number;
-    /** Container-relative X in CSS pixels. */
-    x: number;
-    /** Container-relative Y in CSS pixels. */
-    y: number;
-}
-/** A single item in a track context menu. */
-export interface ContextMenuItem {
-    /** Display label text. */
-    label: string;
-    /** Action to execute when clicked. */
-    action?: () => void;
-    /** Item type. Default: 'action'. */
-    type?: 'action' | 'checkbox' | 'separator';
-    /** For checkbox items: whether currently checked. */
-    checked?: boolean;
-    /** Submenu items (one level of nesting). */
-    children?: ContextMenuItem[];
-    /** If true, item is grayed out and not clickable. */
-    disabled?: boolean;
-}
-/** Payload for the trackcontextmenu browser event. */
-export interface TrackContextMenuEvent {
-    track: Track;
-    /** Genomic position at the right-click point. */
-    genomicLocation: number;
-    /** Features found at the right-click point. */
-    features: unknown[];
-    /** Menu items contributed by the track. */
-    trackItems: ContextMenuItem[];
-    /** Common menu items (set height, remove, etc). */
-    commonItems: ContextMenuItem[];
-    /** Canvas-relative X in CSS pixels. */
-    x: number;
-    /** Canvas-relative Y in CSS pixels. */
-    y: number;
-}
-/** Generic async data fetcher for a track. */
-export interface DataSource<F = unknown> {
-    /**
-     * Fetch features for a genomic region at a given resolution.
-     * @param locus - The buffered region to fetch (already padded by the browser)
-     * @param bpPerPixel - Current resolution for zoom-level selection
-     * @param signal - AbortSignal for cancellation of stale requests
-     */
-    fetch(locus: Locus, bpPerPixel: number, signal: AbortSignal): Promise<F[]>;
-}
-/** Cached features for a track, stored and managed by GenomeBrowser. */
-export interface FeatureCacheEntry<F = unknown> {
-    locus: Locus;
-    bpPerPixel: number;
-    features: F[];
-}
-/** A track that can receive features from a DataSource. */
-export interface DataDrivenTrack<F = unknown> extends Track {
-    setFeatures(features: F[]): void;
-}
-/** Returns sensible defaults for ruler rendering. */
-export declare function defaultRulerRenderConfig(): RulerRenderConfig;
-/** Base for all track feature summaries. */
-interface FeatureSummaryBase {
-    /** Number of features in the current view. */
-    featureCount: number;
-}
-/** Summary for quantitative signal tracks (BigWig, GTX). */
-export interface WigFeatureSummary extends FeatureSummaryBase {
-    /** Signal range in the current view. */
-    signalRange: {
-        min: number;
-        max: number;
-    };
-}
-/** Summary for annotation/gene/BED tracks. */
-export interface AnnotationFeatureSummary extends FeatureSummaryBase {
-    /** Unique names of visible features (genes, peaks, etc.), up to a limit. */
-    featureNames: string[];
-    /** Number of display rows (packing density indicator). */
-    packingDepth: number;
-}
-/** Summary for interaction (arc/BEDPE) tracks. */
-export interface InteractionFeatureSummary extends FeatureSummaryBase {
-    /** Value range of visible interactions. */
-    valueRange: {
-        min: number;
-        max: number;
-    };
-}
-/** Union of all track feature summaries. */
-export type TrackFeatureSummary = WigFeatureSummary | AnnotationFeatureSummary | InteractionFeatureSummary;
-/** First-party session config — fully typed, JSON-serializable browser state. */
-export interface SessionConfig {
-    version: string;
-    locus: Locus;
-    viewportWidth?: number;
-    theme?: Partial<import('./themes/renderTheme').RenderTheme>;
-    /** Genome config for restoring the assembly. */
-    genome?: GenomeConfig;
-    tracks: TrackSessionConfig[];
-    /** ROI sets for region highlighting. */
-    rois?: ROISetConfig[];
-}
-/** Discriminated union — each track type has its own typed config shape. */
-export type TrackSessionConfig = WigTrackSessionConfig | AnnotationTrackSessionConfig | RulerTrackSessionConfig | SequenceTrackSessionConfig | InteractionTrackSessionConfig;
-interface TrackSessionBase {
-    /** Stable string identifier for the track. Auto-generated if not provided. */
-    id?: string;
-    name?: string;
-    order?: number;
-    /** Arbitrary key-value metadata (e.g., assay, biosample, tissue). */
-    metadata?: Record<string, string>;
-}
-export interface WigTrackSessionConfig extends TrackSessionBase {
-    type: 'wig';
-    dataSource?: DataSourceConfig;
-    config?: WigSessionOverrides;
-}
-export interface AnnotationTrackSessionConfig extends TrackSessionBase {
-    type: 'annotation';
-    dataSource?: DataSourceConfig;
-    config?: AnnotationSessionOverrides;
-}
-export interface RulerTrackSessionConfig extends TrackSessionBase {
-    type: 'ruler';
-    config?: RulerSessionOverrides;
-}
-export interface SequenceTrackSessionConfig extends TrackSessionBase {
-    type: 'sequence';
-    config?: SequenceSessionOverrides;
-}
-export interface InteractionTrackSessionConfig extends TrackSessionBase {
-    type: 'interact';
-    dataSource?: DataSourceConfig;
-    config?: InteractionSessionOverrides;
-}
-/** Serializable subset of WigRenderConfig — functions replaced with strings. */
-export type WigSessionOverrides = Omit<Partial<WigRenderConfig>, 'color' | 'altColor'> & {
-    color?: string;
-    altColor?: string;
-};
-/** Serializable subset of AnnotationRenderConfig (all fields are already serializable). */
-export type AnnotationSessionOverrides = Partial<AnnotationRenderConfig>;
-/** Serializable subset of RulerRenderConfig (all fields are already serializable). */
-export type RulerSessionOverrides = Partial<RulerRenderConfig>;
-/** Serializable subset of SequenceRenderConfig (all fields are already serializable). */
-export type SequenceSessionOverrides = Partial<SequenceRenderConfig>;
-/** Serializable subset of InteractionRenderConfig (all fields are already serializable). */
-export type InteractionSessionOverrides = Partial<InteractionRenderConfig>;
-/** Discriminated union for data source reconstruction. */
-export type DataSourceConfig = BigWigDataSourceConfig | GtxDataSourceConfig | UCSCDataSourceConfig | TextDataSourceConfig;
-export interface BigWigDataSourceConfig {
-    type: 'bigwig';
-    url: string;
-    windowFunction?: WindowFunction;
-}
-export interface GtxDataSourceConfig {
-    type: 'gtx';
-    url: string;
-    experimentId: string;
-    windowFunction?: WindowFunction;
-}
-export interface UCSCDataSourceConfig {
-    type: 'ucsc';
-    genome?: string;
-    track?: string;
-}
-export interface TextDataSourceConfig {
-    type: 'text';
-    url: string;
-    /** Explicit format override. When absent, inferred from URL. */
-    format?: TextFileFormat;
-    /** Index URL override. Defaults to url + '.tbi'. */
-    indexURL?: string;
-    /** Whether the file is indexed (tabix). When absent, auto-detected from indexURL presence. */
-    indexed?: boolean;
-}
-/** Strand value for genomic features. */
-export type Strand = '+' | '-' | '.';
-/** Known text genomic file formats supported by the format detection system. */
-export type TextFileFormat = 'bed' | 'narrowpeak' | 'broadpeak' | 'peaks' | 'gappedpeak' | 'bedgraph' | 'wig' | 'gff3' | 'gff' | 'gtf' | 'genepred' | 'genepredext' | 'refgene' | 'refflat' | 'ensgene' | 'vcf' | 'bedpe' | 'interact' | 'longrange' | 'seg' | 'mut' | 'maf' | 'gwas' | 'snp' | 'rmsk';
-/**
- * Feature decoded from BED format (3-12 columns).
- *
- * Structurally compatible with GeneFeature for rendering on the gene track
- * (shares chr, start, end, strand, name, exons, cdStart, cdEnd).
- */
-export interface BedFeature {
-    chr: string;
-    start: number;
-    end: number;
-    name?: string;
-    score?: number;
-    strand?: Strand;
-    cdStart?: number;
-    cdEnd?: number;
-    color?: string;
-    exons?: Exon[];
-    /** Row assigned by feature packing. */
-    row?: number;
-    /** Extra attributes from GFF-style column 4 (when gffTags is true). */
-    attributes?: Record<string, string>;
-    /** Line thickness (from #columns directive). */
-    thickness?: number;
-}
-/** Peak feature from narrowPeak or broadPeak ENCODE formats. */
-export interface PeakFeature extends BedFeature {
-    signal?: number;
-    pValue?: number;
-    qValue?: number;
-    /** Peak point-source position (narrowPeak only, column 10). */
-    peak?: number;
-}
-/** BedGraph feature — a BED3+value for quantitative data. */
-export interface BedGraphFeature {
-    chr: string;
-    start: number;
-    end: number;
-    value: number;
-}
-/** A single GFF/GTF record before transcript assembly. */
-export interface GFFRecord {
-    chr: string;
-    start: number;
-    end: number;
-    source: string;
-    type: string;
-    score?: number;
-    strand?: Strand;
-    phase?: number;
-    /** Raw attribute string from column 9. */
-    attributeString: string;
-    /** Parsed attribute key-value pairs (lazily populated). */
-    attributes: Record<string, string>;
-    /** ID extracted from attributes. */
-    id?: string;
-    /** Parent ID extracted from attributes. */
-    parent?: string;
-    color?: string;
-}
-/**
- * Assembled GFF transcript — a gene/transcript with exon structure.
- * Built by combining GFFRecords sharing parent/ID relationships.
- *
- * Structurally compatible with GeneFeature for rendering on the gene track
- * (shares chr, start, end, strand, name, exons, cdStart, cdEnd).
- */
-export interface GFFFeature {
-    chr: string;
-    start: number;
-    end: number;
-    name?: string;
-    id?: string;
-    strand?: '+' | '-';
-    type: string;
-    source: string;
-    score?: number;
-    cdStart?: number;
-    cdEnd?: number;
-    exons?: Exon[];
-    /** Row assigned by feature packing. */
-    row?: number;
-    /** All attributes from the top-level record. */
-    attributes?: Record<string, string>;
-    color?: string;
-}
-/** Union of all feature types produced by text format decoders. */
-export type TextFeature = BedFeature | PeakFeature | BedGraphFeature | GFFFeature;
-/** Minimal igv.js session shape — just enough to parse/produce sessions. */
-export interface IgvSessionObject {
-    version?: string;
-    reference?: IgvReferenceConfig;
-    genome?: string;
-    locus?: string | string[];
-    tracks?: IgvTrackConfig[];
-}
-export interface IgvReferenceConfig {
-    id?: string;
-    fastaURL?: string;
-    indexURL?: string;
-}
-export interface IgvTrackConfig {
-    type?: string;
-    format?: string;
-    url?: string;
-    indexURL?: string;
-    name?: string;
-    color?: string;
-    altColor?: string;
-    height?: number;
-    min?: number;
-    max?: number;
-    autoscale?: boolean;
-    displayMode?: string;
-    order?: number;
-    visibilityWindow?: number;
-    windowFunction?: string;
-}
-export {};