loom-browser 0.0.1 → 0.0.2

package/dist/types/renderThemePresets.d.ts

@@ -1,16 +0,0 @@
-/**
- * Built-in RenderTheme presets.
- *
- * These are Partial<RenderTheme> objects — pass them to resolveTheme() to get
- * a fully resolved theme with defaults filled in.
- *
- * Usage:
- *   import {resolveTheme} from './renderTheme'
- *   import {modernRenderTheme} from './renderThemePresets'
- *   const theme = resolveTheme(modernRenderTheme)
- */
-import type { RenderTheme } from './renderTheme';
-/** Modern theme — blue/pink palette, rounded exons, system font. */
-export declare const modernRenderTheme: Partial<RenderTheme>;
-/** Dark theme — adapted for dark backgrounds, high contrast. */
-export declare const darkRenderTheme: Partial<RenderTheme>;

package/dist/types/rulerRenderer.d.ts

@@ -1,14 +0,0 @@
-/**
- * Stateless ruler track renderer.
- *
- * Draws genomic coordinate tick marks and labels onto a canvas context.
- * Ported from js/rulerTrack.ts but with no igv.js dependencies.
- */
-import type { RulerRenderConfig, RenderContext } from './types';
-/**
- * Render a genomic coordinate ruler onto a canvas context.
- *
- * Stateless — all state is passed as parameters.
- * Draws tick marks, labels with SI-prefix units, and a baseline.
- */
-export declare function renderRulerTrack(ctx: CanvasRenderingContext2D, config: RulerRenderConfig, rc: RenderContext): void;

package/dist/types/rulerTrackCanvas.d.ts

@@ -1,32 +0,0 @@
-/**
- * Canvas manager for rendering a genomic coordinate ruler.
- *
- * Extends BaseTrackCanvas — canvas lifecycle is handled by the base class.
- * This class only implements ruler-specific rendering.
- *
- * Usage:
- *   const canvas = document.createElement('canvas')
- *   const ruler = new RulerTrackCanvas(canvas, { locus })
- *   ruler.attachTo(containerDiv)
- */
-import type { Locus, RulerRenderConfig, RenderContext, RulerTrackSessionConfig } from './types';
-import type { CanvasProvider } from './canvasProvider';
-import type { RenderTheme } from './renderTheme';
-import { BaseTrackCanvas } from './baseTrackCanvas';
-export interface RulerTrackCanvasOptions {
-    locus: Locus;
-    /** Per-track config overrides. Applied after theme-derived defaults. */
-    config?: Partial<RulerRenderConfig>;
-    /** Unified render theme. Palette drives default colors/fonts. */
-    theme?: Partial<RenderTheme>;
-    /** Canvas provider for environment abstraction. Default: DOMCanvasProvider. */
-    canvasProvider?: CanvasProvider;
-}
-export declare class RulerTrackCanvas extends BaseTrackCanvas<RulerRenderConfig> {
-    readonly type = "ruler";
-    constructor(canvas: HTMLCanvasElement, options: RulerTrackCanvasOptions);
-    protected computeHeight(_width: number): number;
-    protected getBackground(): string;
-    protected doRender(ctx: CanvasRenderingContext2D, _width: number, _height: number, rc: RenderContext): void;
-    serializeConfig(theme: RenderTheme): RulerTrackSessionConfig;
-}

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

@@ -1,66 +0,0 @@
-/**
- * BigWig reader — public API.
- *
- * Thin wrapper around @gmod/bbi that preserves the existing public API.
- * All binary parsing, decompression, and zoom level selection is handled
- * by @gmod/bbi internally.
- */
-import type { WigFeature, WindowFunction, Locus } from '../types';
-import type { WorkerProvider } from '../workerProvider';
-export { BinaryParser } from '../io/binaryParser';
-export interface FetchBigWigOptions {
-    /** Resolution in base pairs per pixel. Used to select an appropriate zoom level. */
-    bpPerPixel?: number;
-    /** Aggregation function for zoom-level data. Default: 'mean'. */
-    windowFunction?: WindowFunction;
-    /** @deprecated Worker dispatch is handled internally by @gmod/bbi. */
-    workerProvider?: WorkerProvider;
-    /** AbortSignal for cancelling in-flight HTTP requests. */
-    signal?: AbortSignal;
-}
-/** Header metadata from a BigWig file. */
-export interface BigWigHeader {
-    bwVersion: number;
-    nZoomLevels: number;
-    chromTreeOffset: number;
-    fullDataOffset: number;
-    fullIndexOffset: number;
-    fieldCount: number;
-    definedFieldCount: number;
-    autoSqlOffset: number;
-    totalSummaryOffset: number;
-    uncompressBuffSize: number;
-    extensionOffset: number;
-}
-/** Summary statistics for the entire BigWig file. */
-export interface BigWigTotalSummary {
-    basesCovered: number;
-    minVal: number;
-    maxVal: number;
-    sumData: number;
-    sumSquares: number;
-    mean: number;
-    stddev: number;
-}
-/**
- * Thin wrapper around @gmod/bbi BigWig that preserves the legacy API.
- */
-export declare class BigWigReader {
-    private readonly bw;
-    constructor(url: string, _workerProvider?: WorkerProvider);
-    loadHeader(signal?: AbortSignal): Promise<BigWigHeader>;
-    getTotalSummary(signal?: AbortSignal): Promise<BigWigTotalSummary | undefined>;
-    readFeatures(chr: string, bpStart: number, bpEnd: number, bpPerPixel?: number, windowFunction?: WindowFunction, signal?: AbortSignal): Promise<WigFeature[]>;
-    readWGFeatures(chromNames: string[], bpPerPixel: number, windowFunction?: WindowFunction, signal?: AbortSignal): Promise<WigFeature[]>;
-}
-/**
- * Fetch BigWig features for a genomic locus.
- */
-export declare function fetchBigWigFeatures(url: string, locus: Locus, options?: FetchBigWigOptions): Promise<WigFeature[]>;
-/**
- * Fetch BigWig features across all specified chromosomes for whole genome view.
- * Returns features with per-chromosome coordinates (caller transforms to genome-wide).
- */
-export declare function fetchBigWigWGFeatures(url: string, chromNames: string[], bpPerPixel: number, options?: Pick<FetchBigWigOptions, 'windowFunction' | 'workerProvider' | 'signal'>): Promise<WigFeature[]>;
-/** Clear the BigWig reader cache (useful for testing or memory management). */
-export declare function clearBigWigCache(): void;

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

@@ -1,36 +0,0 @@
-/**
- * CanvasProvider — environment abstraction for canvas creation and DPR.
- *
- * Decouples track rendering from browser globals (document, window).
- * DOMCanvasProvider is the default for browser environments.
- * Future: NodeCanvasProvider (wrapping node-canvas) for server-side rendering,
- * MockCanvasProvider for tests.
- *
- * Reference: ai_docs/modernization/headless-v2.md (Phase 1)
- */
-/** A canvas and its 2D rendering context, returned by CanvasProvider.createCanvas(). */
-export interface CanvasAndContext {
-    canvas: HTMLCanvasElement;
-    ctx: CanvasRenderingContext2D;
-}
-/**
- * Abstraction over canvas creation and device pixel ratio.
- *
- * Implementations:
- *   - DOMCanvasProvider — browser (default)
- *   - Future: NodeCanvasProvider — server-side (wraps node-canvas)
- *   - Future: MockCanvasProvider — tests
- */
-export interface CanvasProvider {
-    /** Create a canvas element with the given logical (CSS) dimensions. */
-    createCanvas(width: number, height: number): CanvasAndContext;
-    /** Device pixel ratio for sharp rendering on high-DPI displays. */
-    readonly devicePixelRatio: number;
-}
-/** Browser-based CanvasProvider using DOM APIs. */
-export declare class DOMCanvasProvider implements CanvasProvider {
-    createCanvas(width: number, height: number): CanvasAndContext;
-    get devicePixelRatio(): number;
-}
-/** Default CanvasProvider for browser environments. */
-export declare const defaultCanvasProvider: CanvasProvider;

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

@@ -1,220 +0,0 @@
-/**
- * CommandDispatcher — transport-agnostic command dispatch for HeadlessGenomeBrowser.
- *
- * Maps a vocabulary of 8 commands (discriminated union on `command` field) to
- * browser method calls. Designed for reuse across WebSocket (remoteProtocol.ts)
- * and future MCP transport.
- *
- * Follows the discriminated-union + result-map pattern from workerProvider.ts.
- */
-import type { HeadlessGenomeBrowser } from './headlessGenomeBrowser';
-import type { ROI, ROISetConfig, TrackSessionConfig, SessionConfig } from './types';
-import type { TrackSelector } from './trackSelector';
-import type { ProjectedState, TrackSummary } from './stateProjection';
-export type CommandErrorCode = 'UNKNOWN_COMMAND' | 'INVALID_ARGS' | 'TRACK_NOT_FOUND' | 'NOT_IMPLEMENTED' | 'EXPORT_UNAVAILABLE' | 'NAVIGATION_FAILED' | 'INTERNAL_ERROR';
-export declare class CommandError extends Error {
-    readonly code: CommandErrorCode;
-    constructor(code: CommandErrorCode, message: string);
-}
-/** JSON-serializable variant of TrackSelector. */
-export interface WireTrackSelector {
-    /** Exact match against track ID. */
-    id?: string;
-    /** Case-insensitive substring match against track name. */
-    name?: string;
-    /** Regex pattern string — converted to RegExp(pattern, 'i'). Takes precedence over `name`. */
-    nameRegex?: string;
-    /** Exact match against track type (e.g. 'wig', 'annotation', 'interact'). */
-    type?: string;
-    /** Metadata key-value matching. AND semantics. */
-    where?: Record<string, string>;
-}
-/** Convert wire selector to internal TrackSelector. */
-export declare function toTrackSelector(wire: WireTrackSelector): TrackSelector;
-export interface GetBrowserStateArgs {
-    command: 'get_browser_state';
-    /** Record state under this snapshot key for future diff() calls. */
-    record?: string;
-}
-export interface NavigateArgs {
-    command: 'navigate';
-    /** Locus string (e.g. "chr17:7,668,000-7,688,000" or gene name "TP53"). */
-    locus?: string;
-    /** Zoom direction. */
-    zoom?: 'in' | 'out';
-    /** Zoom factor (default 2). */
-    factor?: number;
-}
-export interface ModifyTracksArgs {
-    command: 'modify_tracks';
-    actions: ModifyTrackAction[];
-}
-export type ModifyTrackAction = {
-    action: 'add';
-    config: TrackSessionConfig;
-} | {
-    action: 'remove';
-    selector: WireTrackSelector;
-} | {
-    action: 'find';
-    selector: WireTrackSelector;
-} | {
-    action: 'update_metadata';
-    selector: WireTrackSelector;
-    metadata: Record<string, string>;
-};
-export interface QueryFeaturesArgs {
-    command: 'query_features';
-    /** Track ID to query. */
-    trackId: string;
-    /** If true, return a feature summary instead of raw features. */
-    summarize?: boolean;
-}
-export interface AnnotateArgs {
-    command: 'annotate';
-}
-export interface SetLayoutArgs {
-    command: 'set_layout';
-    /** Desired track configuration. Reconciler diffs against current state. */
-    tracks: TrackSessionConfig[];
-    /** If provided, navigate to this locus. */
-    locus?: string;
-}
-export interface ExportViewArgs {
-    command: 'export_view';
-    format: 'svg' | 'png' | 'session';
-    /** Override width in pixels. */
-    width?: number;
-}
-export interface ManageROIsArgs {
-    command: 'manage_rois';
-    action: ROIAction;
-}
-export type ROIAction = {
-    action: 'add';
-    roi: ROI;
-    setName?: string;
-} | {
-    action: 'remove';
-    roiId: string;
-} | {
-    action: 'update';
-    roiId: string;
-    changes: Partial<Omit<ROI, 'id'>>;
-} | {
-    action: 'clear';
-} | {
-    action: 'list';
-} | {
-    action: 'list_sets';
-} | {
-    action: 'find_at_locus';
-    chr: string;
-    start: number;
-    end: number;
-} | {
-    action: 'get_visible';
-};
-export interface SubscribeEventsArgs {
-    command: 'subscribe_events';
-    /** Event names to subscribe to. Use `['*']` for all events, `[]` for none. */
-    events: string[];
-}
-export type CommandArgs = GetBrowserStateArgs | NavigateArgs | ModifyTracksArgs | QueryFeaturesArgs | AnnotateArgs | SetLayoutArgs | ExportViewArgs | ManageROIsArgs | SubscribeEventsArgs;
-export interface ModifyTrackActionResult {
-    action: string;
-    success: boolean;
-    trackId?: string;
-    tracks?: TrackSummary[];
-    count?: number;
-    error?: string;
-}
-export interface ModifyTracksResult {
-    results: ModifyTrackActionResult[];
-}
-export interface QueryFeaturesResult {
-    trackId: string;
-    featureCount: number;
-    features?: unknown[];
-    summary?: unknown;
-}
-export interface SetLayoutResult {
-    added: string[];
-    removed: string[];
-    unchanged: string[];
-}
-export type ManageROIsResult = {
-    action: 'add';
-    roi: ROI;
-} | {
-    action: 'remove';
-    success: boolean;
-} | {
-    action: 'update';
-    roi: ROI | undefined;
-} | {
-    action: 'clear';
-} | {
-    action: 'list';
-    rois: ROI[];
-} | {
-    action: 'list_sets';
-    sets: ROISetConfig[];
-} | {
-    action: 'find_at_locus';
-    rois: ROI[];
-} | {
-    action: 'get_visible';
-    rois: ROI[];
-};
-export interface SubscribeEventsResult {
-    subscribed: string[];
-}
-export interface CommandResultMap {
-    get_browser_state: ProjectedState;
-    navigate: boolean;
-    modify_tracks: ModifyTracksResult;
-    query_features: QueryFeaturesResult;
-    annotate: never;
-    set_layout: SetLayoutResult;
-    export_view: string | SessionConfig;
-    manage_rois: ManageROIsResult;
-    subscribe_events: SubscribeEventsResult;
-}
-export interface CommandDispatcherOptions {
-    /** Whether the browser supports PNG export (true for DOM GenomeBrowser). */
-    supportsPNG?: boolean;
-    /** Custom PNG exporter — called when format is 'png'. Allows GenomeBrowser to inject toPNG(). */
-    exportPNG?: () => Promise<string>;
-    /** Callback when agent subscribes to events. Used by RemoteConnection to filter forwarding. */
-    onSubscribeEvents?: (events: string[]) => void;
-}
-export declare class CommandDispatcher {
-    private browser;
-    private options;
-    constructor(browser: HeadlessGenomeBrowser, options?: CommandDispatcherOptions);
-    /** Dispatch a command to the appropriate handler. */
-    dispatch(args: GetBrowserStateArgs): Promise<ProjectedState>;
-    dispatch(args: NavigateArgs): Promise<boolean>;
-    dispatch(args: ModifyTracksArgs): Promise<ModifyTracksResult>;
-    dispatch(args: QueryFeaturesArgs): Promise<QueryFeaturesResult>;
-    dispatch(args: AnnotateArgs): Promise<never>;
-    dispatch(args: SetLayoutArgs): Promise<SetLayoutResult>;
-    dispatch(args: ExportViewArgs): Promise<string | SessionConfig>;
-    dispatch(args: ManageROIsArgs): Promise<ManageROIsResult>;
-    dispatch(args: SubscribeEventsArgs): Promise<SubscribeEventsResult>;
-    dispatch(args: CommandArgs): Promise<CommandResultMap[CommandArgs['command']]>;
-    private handleGetState;
-    private handleNavigate;
-    private handleModifyTracks;
-    private handleQueryFeatures;
-    private handleAnnotate;
-    private handleSetLayout;
-    /** Find a current track that matches a desired config. */
-    private findMatchingTrack;
-    /** Compute a stable match key from a track session config's data source. */
-    private layoutMatchKey;
-    private handleExportView;
-    private handleManageROIs;
-    private handleSubscribeEvents;
-}

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

@@ -1,64 +0,0 @@
-/**
- * Common context menu item factories.
- *
- * Stateless functions that return ContextMenuItem[] — no DOM, no side effects.
- * The ContextMenuCallbacks interface decouples menu items from browser-level
- * actions (removing tracks, showing dialogs).
- *
- * `numericDataMenuItems()` mirrors igv.js `TrackBase.numericDataMenuItems()`
- * (js/trackBase.ts lines 510-552), which is shared by WigTrack, BAMTrack,
- * QTLTrack, GCNVTrack, CNVPytorTrack, GWASTrack, InteractionTrack, and
- * MergedTrack — any track with a Y-axis data range.
- */
-import type { ContextMenuItem, NumericState, Track, ROI, Locus } from './types';
-/**
- * Callback interface for common menu actions that require browser-level
- * coordination. GenomeBrowser provides the implementation.
- */
-export interface ContextMenuCallbacks {
-    /** Set the track's pixel height and re-render. */
-    setTrackHeight(track: Track, height: number): void;
-    /** Remove the track from the browser. */
-    removeTrack(track: Track): void;
-    /** Show an input dialog. Returns the entered value, or null if cancelled. */
-    promptInput(label: string, currentValue: string | number): Promise<string | null>;
-}
-/** Common menu items that apply to all tracks (set height, remove). */
-export declare function commonContextMenuItems(track: Track, callbacks: ContextMenuCallbacks): ContextMenuItem[];
-/**
- * Menu items for quantitative/numeric tracks: set data range, log scale, autoscale.
- *
- * Mirrors igv.js `TrackBase.numericDataMenuItems()` (js/trackBase.ts lines 510-552).
- * In igv.js this is a method on TrackBase used by 8 track classes. In our
- * architecture it's a stateless factory that takes the track's NumericState
- * (state + callbacks combined), matching our separation of data from DOM.
- *
- * Items produced:
- * 1. "Set data range" — prompts for min/max, disables autoscale when set
- *    (mirrors igv.js DataRangeDialog → TrackBase.setDataRange)
- * 2. "Log scale" checkbox — only if logScale is supported (state.logScale !== undefined)
- *    (mirrors igv.js conditional on this.logScale !== undefined)
- * 3. "Autoscale" checkbox
- *    (mirrors igv.js autoScaleHandler)
- */
-export declare function numericDataMenuItems(state: NumericState, promptInput: ContextMenuCallbacks['promptInput']): ContextMenuItem[];
-/**
- * Callback interface for ROI menu actions that require browser-level coordination.
- */
-export interface ROIMenuCallbacks {
-    /** Navigate the browser to the ROI's genomic region. */
-    goToRegion(locus: Locus): void;
-    /** Update an ROI's properties. */
-    updateROI(roiId: string, changes: Partial<Omit<ROI, 'id'>>): void;
-    /** Remove an ROI by ID. */
-    removeROI(roiId: string): void;
-    /** Show an input dialog. Returns the entered value, or null if cancelled. */
-    promptInput(label: string, currentValue: string | number): Promise<string | null>;
-}
-/**
- * Context menu items for an ROI region.
- *
- * Mirrors igv.js ROIMenu (js/roi/ROIMenu.ts) but with stateless factory pattern.
- * Items: edit name, edit description, set color, separator, go to region, remove.
- */
-export declare function roiContextMenuItems(roi: ROI, callbacks: ROIMenuCallbacks): ContextMenuItem[];

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

@@ -1,25 +0,0 @@
-/**
- * ContextMenuProvider — abstraction for context menu rendering.
- *
- * Follows the PopupProvider / CanvasProvider / WorkerProvider pattern.
- * Provide a custom implementation to replace the default `<loom-context-menu>`
- * Web Component with your own React, Vue, or vanilla JS context menu.
- *
- * Unlike PopupProvider, a default context menu provider is created automatically
- * when none is specified. Pass `null` to disable context menus entirely.
- *
- * When no context menu provider is active, the browser still emits
- * `trackcontextmenu` events — consumers can handle menus entirely via events.
- */
-import type { ContextMenuItem } from './types';
-export interface ContextMenuProvider {
-    /** Show a context menu with the given items, positioned relative to the container. */
-    show(items: ContextMenuItem[], position: {
-        x: number;
-        y: number;
-    }, container: HTMLElement): void;
-    /** Hide/dismiss the context menu. */
-    hide(): void;
-    /** Clean up resources (remove DOM elements, event listeners, etc). */
-    dispose(): void;
-}

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

@@ -1,19 +0,0 @@
-/**
- * Interval-based sequence cache, matching igv.js CachedSequence.
- *
- * Wraps any SequenceProvider and adds:
- * - 100kb minimum query expansion (amortizes small requests)
- * - 10-slot interval cache with FIFO eviction
- * - Deduplication of concurrent in-flight requests
- * - Subsumption: new intervals evict smaller overlapping ones
- *
- * Module-level singleton pattern: call `createCachedSequence(provider)` once,
- * then pass the returned function as the SequenceProvider to WigTrackCanvas.
- */
-import type { SequenceProvider } from '../types';
-/**
- * Create a cached SequenceProvider wrapping a raw provider.
- *
- * The returned function is a drop-in SequenceProvider with transparent caching.
- */
-export declare function createCachedSequence(provider: SequenceProvider): SequenceProvider;

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

@@ -1,21 +0,0 @@
-/**
- * UCSC Genome Browser REST API client.
- *
- * Fetches gene annotation data from the UCSC REST API and decodes it
- * into GeneFeature objects using the same parsing logic as igv.js.
- *
- * API docs: https://genome.ucsc.edu/goldenPath/help/api.html
- */
-import type { AnnotationFeature, Locus } from '../types';
-export interface FetchGenesOptions {
-    /** Genome assembly, e.g. "hg38", "hg19", "mm10". Default: "hg38". */
-    genome?: string;
-    /** UCSC track name, e.g. "ncbiRefSeq", "knownGene". Default: "ncbiRefSeq". */
-    track?: string;
-}
-/**
- * Fetch gene features for a genomic region from the UCSC REST API.
- *
- * Uses the same ncbiRefSeq track that igv.js loads by default for hg38.
- */
-export declare function fetchGeneFeatures(locus: Locus, options?: FetchGenesOptions, signal?: AbortSignal): Promise<AnnotationFeature[]>;

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

@@ -1,19 +0,0 @@
-/**
- * UCSC Genome Browser REST API client for genomic sequences.
- *
- * Fetches DNA sequence data from the UCSC REST API.
- * API docs: https://genome.ucsc.edu/goldenPath/help/api.html
- */
-import type { Locus } from '../types';
-export interface FetchSequenceOptions {
-    /** Genome assembly, e.g. "hg38", "hg19", "mm10". Default: "hg38". */
-    genome?: string;
-}
-/**
- * Fetch DNA sequence for a genomic region from the UCSC REST API.
- *
- * @param locus - The genomic region to fetch
- * @param options - Optional genome assembly (default: hg38)
- * @returns The DNA sequence string (lowercase)
- */
-export declare function fetchSequence(locus: Locus, options?: FetchSequenceOptions, signal?: AbortSignal): Promise<string>;

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

@@ -1,16 +0,0 @@
-/**
- * Data lifecycle utilities for GenomeBrowser.
- *
- * Pure functions for cache validation and viewport buffering.
- * Used internally by GenomeBrowser to decide when to re-fetch track data.
- */
-import type { Locus, FeatureCacheEntry } from './types';
-/**
- * Check if a cache entry covers a viewport at a compatible resolution.
- */
-export declare function cacheCoversViewport<F>(cache: FeatureCacheEntry<F>, viewport: Locus, bpPerPixel: number): boolean;
-/**
- * Expand a locus by BUFFER_SCREENS on each side for pre-fetching.
- * Produces a 3x viewport region.
- */
-export declare function bufferLocus(locus: Locus): Locus;

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

@@ -1,24 +0,0 @@
-import type { DataSource, Locus, WigFeature, WindowFunction } from '../types';
-import type { WorkerProvider } from '../workerProvider';
-import type { CumulativeOffsets } from '../genome/chromSizes';
-export declare class BigWigDataSource implements DataSource<WigFeature> {
-    private url;
-    private _windowFunction;
-    private workerProvider?;
-    private _cumulativeOffsets?;
-    private _resolveChromName?;
-    constructor(url: string, windowFunction?: WindowFunction, workerProvider?: WorkerProvider);
-    get windowFunction(): WindowFunction;
-    /** Update the window function for future fetches. */
-    setWindowFunction(wf: WindowFunction): void;
-    /** Set cumulative offsets for whole genome view coordinate transformation. */
-    setCumulativeOffsets(offsets: CumulativeOffsets): void;
-    /** Set a chromosome name resolver for alias resolution (e.g., "1" → "chr1"). */
-    setChromNameResolver(resolver: (chr: string) => string): void;
-    fetch(locus: Locus, bpPerPixel: number, signal: AbortSignal): Promise<WigFeature[]>;
-    /**
-     * Fetch all chromosomes for whole genome view and transform to genome-wide coordinates.
-     * Port of js/bigwig/bwSource.ts getWGValues().
-     */
-    private fetchWG;
-}

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

@@ -1,9 +0,0 @@
-/**
- * Derive a stable cache key from a DataSourceConfig.
- *
- * Used by HeadlessGenomeBrowser to group tracks that share the same
- * underlying data source, enabling fetch deduplication when multiple
- * tracks point to the same URL/region.
- */
-import type { DataSourceConfig } from '../types';
-export declare function dataSourceCacheKey(config: DataSourceConfig): string;

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

@@ -1,46 +0,0 @@
-/**
- * Feature source factory — URL config → DataSource + inferred track type.
- *
- * Routes to the appropriate DataSource implementation based on detected format:
- * - Binary formats (bigwig, bigbed) → BigWigDataSource
- * - Text formats (bed, gff, narrowpeak, etc.) → TextFeatureSource
- *
- * Port of js/feature/featureSource.ts factory logic.
- *
- * Layer 1 (Data + Layout): no DOM.
- */
-import type { DataSource } from '../types';
-import type { WorkerProvider } from '../workerProvider';
-export interface FeatureSourceConfig {
-    /** URL to the data file. */
-    url: string;
-    /** Explicit format override. When absent, inferred from URL. */
-    format?: string;
-    /** Index URL override for tabix-indexed files. */
-    indexURL?: string;
-    /** Whether the file is indexed (tabix). Auto-detected if absent. */
-    indexed?: boolean;
-    /** For GFF: whether to assemble transcript models. Default: true. */
-    assembleGFF?: boolean;
-    /** Window function for BigWig/GTX summarization. Default: 'mean'. */
-    windowFunction?: 'mean' | 'min' | 'max';
-    /** Experiment ID within a GTX file. Required for GTX format. */
-    experimentId?: string;
-}
-export interface FeatureSourceResult {
-    /** The created DataSource. */
-    dataSource: DataSource;
-    /** Inferred track type string (e.g., 'wig', 'annotation', 'variant'). */
-    trackType: string;
-    /** Detected format string (e.g., 'bed', 'bigwig', 'gff3'). */
-    format: string;
-}
-/**
- * Create a DataSource from a URL config.
- *
- * Detects format from the URL, routes to the appropriate DataSource
- * implementation, and infers the track type.
- *
- * Port of js/feature/featureSource.ts factory routing logic.
- */
-export declare function createFeatureSource(config: FeatureSourceConfig, workerProvider?: WorkerProvider): FeatureSourceResult;

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

@@ -1,16 +0,0 @@
-import type { DataSource, Locus, AnnotationFeature } from '../types';
-import type { CumulativeOffsets } from '../genome/chromSizes';
-import type { FetchGenesOptions } from '../data/ucscApi';
-export declare class GeneDataSource implements DataSource<AnnotationFeature> {
-    private options;
-    private _cumulativeOffsets?;
-    constructor(options?: FetchGenesOptions);
-    /** Set cumulative offsets for whole genome view coordinate transformation. */
-    setCumulativeOffsets(offsets: CumulativeOffsets): void;
-    fetch(locus: Locus, _bpPerPixel: number, signal: AbortSignal): Promise<AnnotationFeature[]>;
-    /**
-     * Fetch genes for all main chromosomes and transform to genome-wide coordinates.
-     * Follows igv.js computeWGFeatures() pattern: strips exons, downsamples.
-     */
-    private fetchWG;
-}