loom-browser 0.0.1 → 0.0.2

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

@@ -1,22 +0,0 @@
-/**
- * First-party zstd WASM decompression module.
- *
- * Directly instantiates the zstd WASM binary (from @bokuweb/zstd-wasm, MIT license)
- * without the Emscripten glue code that breaks webpack bundling.
- *
- * Only exposes decompression with dictionary — the minimum needed for GTX.
- */
-/**
- * Initialize the zstd WASM module. Idempotent — safe to call multiple times.
- * Loads the WASM binary from the same directory as this module.
- */
-export declare function initZstd(): Promise<void>;
-/** Create a decompression context. Returns an opaque handle. */
-export declare function createDCtx(): number;
-/** Free a decompression context. */
-export declare function freeDCtx(dctx: number): void;
-/**
- * Decompress a zstd-compressed buffer using a dictionary.
- * Returns a newly allocated Uint8Array with the decompressed data.
- */
-export declare function decompressUsingDict(dctx: number, compressed: Uint8Array, dictionary: Uint8Array): Uint8Array;

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

@@ -1,450 +0,0 @@
-/**
- * Headless GenomeBrowser — pure data/navigation/caching core with zero DOM dependencies.
- *
- * Manages locus state, track coordination, data lifecycle (buffered fetch, caching,
- * abort), events, and theming. Can run in Node.js, workers, or any environment.
- *
- * The DOM-attached `GenomeBrowser` extends this class to add pointer events,
- * ResizeObserver, canvas stacking, and sweep-to-zoom.
- *
- * Usage (headless):
- *   const browser = new HeadlessGenomeBrowser({
- *       locus: { chr: 'chr17', start: 7668000, end: 7688000 },
- *       viewportWidth: 800,
- *   })
- *   browser.addTrack(track, dataSource)
- *   browser.setLocus({ chr: 'chr17', start: 7670000, end: 7680000 })
- *   browser.dispose()
- */
-import type { Locus, Track, DataSource, FeatureCacheEntry, SessionConfig, TrackSessionConfig, DataSourceConfig, TrackInteractionEvent, TrackContextMenuEvent, WindowFunction, WigRenderConfig, AnnotationRenderConfig, RulerRenderConfig, SequenceRenderConfig, InteractionRenderConfig, TextFileFormat, SequenceProvider, Genome, ROI, ROISetConfig, ROIInteractionEvent } from './types';
-import { ROISet } from './roi/roiSet';
-import type { CanvasProvider } from './canvasProvider';
-import type { WorkerProvider } from './workerProvider';
-import type { PopupProvider } from './popupProvider';
-import type { ContextMenuProvider } from './contextMenuProvider';
-import type { RenderTheme } from './themes/renderTheme';
-import { EventEmitter } from './events';
-import type { ChromSizes, CumulativeOffsets } from './genome/chromSizes';
-import { type CreateTrackFromSessionOptions } from './session';
-import { RulerTrackCanvas } from './tracks/ruler/rulerTrackCanvas';
-import { WigTrackCanvas } from './tracks/wig/wigTrackCanvas';
-import { AnnotationTrackCanvas } from './tracks/annotation/annotationTrackCanvas';
-import { SequenceTrackCanvas } from './tracks/sequence/sequenceTrackCanvas';
-import { InteractionTrackCanvas } from './tracks/interaction/interactionTrackCanvas';
-import { StateProjection } from './stateProjection';
-import type { TrackSelector } from './trackSelector';
-export declare const BrowserEvent: {
-    readonly LocusChange: "locuschange";
-    readonly TrackAdded: "trackadded";
-    readonly TrackRemoved: "trackremoved";
-    readonly TrackOrderChanged: "trackorderchanged";
-    readonly DataLoaded: "dataloaded";
-    readonly DataError: "dataerror";
-    readonly RenderError: "rendererror";
-    readonly TrackClick: "trackclick";
-    readonly TrackHover: "trackhover";
-    readonly TrackContextMenu: "trackcontextmenu";
-    readonly ROIAdded: "roiadded";
-    readonly ROIRemoved: "roiremoved";
-    readonly ROIChanged: "roichanged";
-    readonly ROIClick: "roiclick";
-    readonly ROIContextMenu: "roicontextmenu";
-};
-export interface BrowserEvents {
-    [BrowserEvent.LocusChange]: {
-        locus: Locus;
-    };
-    [BrowserEvent.TrackAdded]: {
-        track: Track;
-    };
-    [BrowserEvent.TrackRemoved]: {
-        track: Track;
-    };
-    [BrowserEvent.TrackOrderChanged]: {
-        tracks: Track[];
-    };
-    [BrowserEvent.DataLoaded]: {
-        track: Track;
-    };
-    [BrowserEvent.DataError]: {
-        track: Track;
-        error: Error;
-    };
-    [BrowserEvent.RenderError]: {
-        track: Track;
-        error: Error;
-    };
-    [BrowserEvent.TrackClick]: TrackInteractionEvent;
-    [BrowserEvent.TrackHover]: TrackInteractionEvent;
-    [BrowserEvent.TrackContextMenu]: TrackContextMenuEvent;
-    [BrowserEvent.ROIAdded]: {
-        roi: ROI;
-        set: ROISet;
-    };
-    [BrowserEvent.ROIRemoved]: {
-        roi: ROI;
-        set: ROISet;
-    };
-    [BrowserEvent.ROIChanged]: {
-        roi: ROI;
-        changes: Partial<ROI>;
-        set: ROISet;
-    };
-    [BrowserEvent.ROIClick]: ROIInteractionEvent;
-    [BrowserEvent.ROIContextMenu]: ROIInteractionEvent;
-}
-/** Internal bookkeeping for a track + optional data source. */
-export interface ManagedTrack {
-    /** Stable string identifier. Auto-generated on addTrack if not provided. */
-    id: string;
-    track: Track;
-    dataSource: DataSource | null;
-    /** Serializable data source config — stored for session save/restore. */
-    dataSourceConfig: DataSourceConfig | null;
-    /** Track name for session serialization. */
-    name?: string;
-    /** Track ordering for session serialization. */
-    order?: number;
-    /** Arbitrary key-value metadata (e.g., assay, biosample, tissue). */
-    metadata?: Record<string, string>;
-    cache: FeatureCacheEntry | null;
-    abortController: AbortController | null;
-    /** Max visible height in pixels — enables scrollable container in DOM browser. */
-    maxTrackHeight?: number;
-}
-export interface HeadlessGenomeBrowserOptions {
-    locus: Locus;
-    /** Viewport width in CSS pixels. Required for headless; DOM browser reads from container. */
-    viewportWidth?: number;
-    /** Canvas provider for environment abstraction. Default: DOMCanvasProvider. */
-    canvasProvider?: CanvasProvider;
-    /** Worker provider for offloading CPU-intensive tasks. Default: main-thread execution. */
-    workerProvider?: WorkerProvider;
-    /** Popup provider for rendering feature popups on click/hover. Default in GenomeBrowser: DefaultPopupProvider. Pass null to disable. */
-    popupProvider?: PopupProvider | null;
-    /** Context menu provider for right-click menus. Default: DefaultContextMenuProvider. Pass null to disable. */
-    contextMenuProvider?: ContextMenuProvider | null;
-    /** Unified render theme. Palette drives default colors/fonts for all tracks. */
-    theme?: Partial<RenderTheme>;
-    /**
-     * Genome assembly. Provides chromosome sizes, cumulative offsets, and sequence.
-     * Default: hg38Genome. Pass null to disable clamping/sequence.
-     */
-    genome?: Genome | null;
-    /** Custom StateProjection subclass instance. Default: lazily created StateProjection. */
-    stateProjection?: StateProjection;
-}
-export interface AddRulerOptions {
-    config?: Partial<RulerRenderConfig>;
-    /** Max visible height — enables scrollable container in DOM browser. */
-    maxTrackHeight?: number;
-}
-export interface AddWigTrackOptions {
-    config?: Partial<WigRenderConfig>;
-    /** Fixed pixel height (overrides config.height). */
-    height?: number;
-    /** Background color. */
-    background?: string;
-    /** Window function for BigWig summarization. Default: 'mean'. */
-    windowFunction?: WindowFunction;
-    /** Max visible height — enables scrollable container in DOM browser. */
-    maxTrackHeight?: number;
-    /** Track name for axis label. */
-    name?: string;
-    /** Arbitrary key-value metadata (e.g., assay, biosample, tissue). */
-    metadata?: Record<string, string>;
-}
-export interface AddGtxTrackOptions {
-    /** Experiment ID within the GTX file. */
-    experimentId: string;
-    config?: Partial<WigRenderConfig>;
-    /** Fixed pixel height (overrides config.height). */
-    height?: number;
-    /** Background color. */
-    background?: string;
-    /** Window function for summarization. Default: 'mean'. */
-    windowFunction?: WindowFunction;
-    /** Max visible height — enables scrollable container in DOM browser. */
-    maxTrackHeight?: number;
-    /** Track name for axis label. */
-    name?: string;
-    /** Arbitrary key-value metadata (e.g., assay, biosample, tissue). */
-    metadata?: Record<string, string>;
-}
-export interface AddSequenceTrackOptions {
-    config?: Partial<SequenceRenderConfig>;
-    /** Max visible height — enables scrollable container in DOM browser. */
-    maxTrackHeight?: number;
-}
-export interface AddBedTrackOptions {
-    config?: Partial<AnnotationRenderConfig>;
-    /** Fixed pixel height. */
-    height?: number;
-    /** Background color. */
-    background?: string;
-    /** Explicit format override. When absent, inferred from URL. */
-    format?: TextFileFormat;
-    /** Index URL override for tabix-indexed files. */
-    indexURL?: string;
-    /** Whether the file is tabix-indexed. Auto-detected if absent. */
-    indexed?: boolean;
-    /** Max visible height — enables scrollable container in DOM browser. */
-    maxTrackHeight?: number;
-    /** Track name for axis label. */
-    name?: string;
-    /** Arbitrary key-value metadata (e.g., assay, biosample, tissue). */
-    metadata?: Record<string, string>;
-}
-export interface AddInteractionTrackOptions {
-    config?: Partial<InteractionRenderConfig>;
-    /** Background color. */
-    background?: string;
-    /** Explicit format override (e.g., 'bedpe', 'interact'). Inferred from URL if absent. */
-    format?: TextFileFormat;
-    /** Index URL override for tabix-indexed files. */
-    indexURL?: string;
-    /** Whether the file is tabix-indexed. Auto-detected if absent. */
-    indexed?: boolean;
-    /** Track name for axis label. */
-    name?: string;
-    /** Arbitrary key-value metadata (e.g., assay, biosample, tissue). */
-    metadata?: Record<string, string>;
-}
-export interface AddAnnotationTrackOptions {
-    config?: Partial<AnnotationRenderConfig>;
-    /** Fixed pixel height. */
-    height?: number;
-    /** Background color. */
-    background?: string;
-    /** Genome assembly for UCSC API. Default: 'hg38'. */
-    genome?: string;
-    /** UCSC track name. Default: 'ncbiRefSeq'. */
-    track?: string;
-    /** Max visible height — enables scrollable container in DOM browser. */
-    maxTrackHeight?: number;
-    /** Track name for axis label. Default: 'Genes'. */
-    name?: string;
-    /** Arbitrary key-value metadata (e.g., assay, biosample, tissue). */
-    metadata?: Record<string, string>;
-}
-export declare class HeadlessGenomeBrowser {
-    protected _locus: Locus;
-    protected _viewportWidth: number;
-    protected managedTracks: ManagedTrack[];
-    protected roiSets: ROISet[];
-    /** Inflight fetch promises keyed by (cacheKey + fetchRegion + bpPerPixel) for deduplication. */
-    private inflightFetches;
-    /** Canvas provider for environment abstraction. Available for convenience API / future use. */
-    readonly canvasProvider: CanvasProvider;
-    /** Worker provider for offloading CPU-intensive tasks. */
-    readonly workerProvider?: WorkerProvider;
-    /** Popup provider for rendering feature popups on click/hover. */
-    readonly popupProvider?: PopupProvider;
-    /** Context menu provider for right-click menus. */
-    readonly contextMenuProvider?: ContextMenuProvider;
-    /** Resolved render theme. Available for track creation in convenience API. */
-    readonly theme: RenderTheme;
-    /**
-     * Genome assembly. Provides chromosome sizes, cumulative offsets, and optional sequence.
-     * Undefined when genome/clamping is disabled (null was passed).
-     */
-    readonly genome?: Genome;
-    /** Chromosome sizes for locus clamping. Derived from genome. Undefined when clamping is disabled. */
-    readonly chromSizes?: ChromSizes;
-    /** Precomputed cumulative offsets for whole genome view. Derived from genome. Undefined when chromSizes is not set. */
-    readonly cumulativeOffsets?: CumulativeOffsets;
-    /** Sequence provider for dynseq rendering on wig tracks. Derived from genome.sequence unless overridden. */
-    readonly sequenceProvider?: SequenceProvider;
-    readonly events: EventEmitter<BrowserEvents>;
-    private _state?;
-    get locus(): Locus;
-    get viewportWidth(): number;
-    /** Agent-friendly state projection manager. Lazily created on first access. */
-    get state(): StateProjection;
-    constructor(options: HeadlessGenomeBrowserOptions);
-    /** Clamp a locus to valid chromosome bounds. No-op if chromSizes is not set. */
-    protected clamp(locus: Locus): Locus;
-    /** Subscribe to a browser event. Returns an unsubscribe function. */
-    on<K extends keyof BrowserEvents>(event: K, handler: (data: BrowserEvents[K]) => void): () => void;
-    /** Unsubscribe from a browser event. */
-    off<K extends keyof BrowserEvents>(event: K, handler?: (data: BrowserEvents[K]) => void): void;
-    /**
-     * Update the viewport width and re-render.
-     * In headless mode, call this when the logical viewport size changes.
-     * The DOM browser calls this automatically from ResizeObserver.
-     */
-    setViewportWidth(width: number): void;
-    /** Add a track with an optional data source for automatic data management. */
-    addTrack<F>(track: Track, dataSource?: DataSource<F>, dataSourceConfig?: DataSourceConfig, maxTrackHeight?: number): string;
-    /** Remove a track by reference or by stable string ID. */
-    removeTrack(trackOrId: Track | string): void;
-    /**
-     * Move a track to a new position in the track list.
-     * Emits BrowserEvent.TrackOrderChanged with the new track order.
-     */
-    moveTrack(track: Track, toIndex: number): void;
-    /** Get the current track order. */
-    getTrackOrder(): Track[];
-    /** Find a managed track by its stable string ID. Returns undefined if not found. */
-    getManagedTrack(id: string): ManagedTrack | undefined;
-    /** Find a Track by its stable string ID. Returns undefined if not found. */
-    getTrack(id: string): Track | undefined;
-    /** Get all managed tracks (read-only snapshot). */
-    getManagedTracks(): readonly ManagedTrack[];
-    /**
-     * Find all managed tracks matching a selector.
-     *
-     * ```ts
-     * browser.findTracks({ type: 'wig', where: { biosample: 'K562' } })
-     * browser.findTracks({ name: 'H3K27ac' })
-     * ```
-     */
-    findTracks(selector: TrackSelector): ManagedTrack[];
-    /**
-     * Remove all tracks matching a selector. Returns the number of tracks removed.
-     *
-     * ```ts
-     * browser.removeTracks({ where: { assay: 'ATAC-seq' } })  // remove all ATAC-seq tracks
-     * browser.removeTracks({ type: 'wig' })                    // remove all wig tracks
-     * ```
-     */
-    removeTracks(selector: TrackSelector): number;
-    /**
-     * Merge metadata into all tracks matching a selector. Returns the number of tracks updated.
-     * New keys are added; existing keys are overwritten.
-     *
-     * ```ts
-     * browser.updateTrackMetadata({ type: 'wig' }, { project: 'ENCODE' })
-     * ```
-     */
-    updateTrackMetadata(selector: TrackSelector, metadata: Record<string, string>): number;
-    /** Update the locus and re-render all tracks. Clamped to chromosome bounds. */
-    setLocus(locus: Locus): void;
-    /**
-     * Parse a locus string and navigate to it.
-     * e.g., "chr17:7,668,000-7,688,000"
-     * Returns true if navigation succeeded.
-     */
-    search(query: string): boolean;
-    /** Zoom in by a factor (default 2x) around the center. */
-    zoomIn(factor?: number): void;
-    /** Zoom out by a factor (default 2x) around the center. */
-    zoomOut(factor?: number): void;
-    private zoomByFactor;
-    /**
-     * Zoom by a scale factor around an optional genomic coordinate.
-     *
-     * If `centerBP` is omitted, zooms around the viewport center (default).
-     * When provided, the zoom keeps `centerBP` at the same relative position
-     * in the viewport — e.g. for pointer-anchored pinch/wheel zoom.
-     *
-     * @param factor - Scale factor. <1 = zoom in, >1 = zoom out.
-     * @param centerBP - Optional genomic coordinate to anchor the zoom on.
-     */
-    zoomAroundCenter(factor: number, centerBP?: number): void;
-    /** Force a data reload for all managed tracks (e.g., after config change). */
-    reloadData(): void;
-    /** Get the cached features for a track, if available. */
-    getCachedFeatures<F>(track: Track): F[] | undefined;
-    /** Re-render all tracks at current locus. */
-    render(): void;
-    /**
-     * Add a single ROI to a named set. Creates a user-defined set if it doesn't exist.
-     * Returns the ROI (with generated ID if none provided).
-     */
-    addROI(roi: ROI, setName?: string): ROI;
-    /** Add a full ROI set from config. Returns the created ROISet. */
-    addROISet(config: ROISetConfig): ROISet;
-    /** Remove an ROI by ID (searches all sets). Returns true if found and removed. */
-    removeROI(roiId: string): boolean;
-    /** Update an ROI by ID. Returns the updated ROI, or undefined if not found. */
-    updateROI(roiId: string, changes: Partial<Omit<ROI, 'id'>>): ROI | undefined;
-    /** Remove all ROI sets. */
-    clearROIs(): void;
-    /** Get all ROIs across all sets (flattened). */
-    getROIs(): ROI[];
-    /** Get all ROI sets. */
-    getROISets(): readonly ROISet[];
-    /** Find ROIs overlapping a genomic region (searches all sets). */
-    findROIsAtLocus(chr: string, start: number, end: number): ROI[];
-    /** Get ROIs visible in the current viewport. */
-    getVisibleROIs(): ROI[];
-    /**
-     * Export the current view as an SVG string.
-     *
-     * Creates a Canvas2SVG context, renders each track with clipped groups and
-     * vertical offsets, and returns the serialized SVG. Named entities are
-     * replaced with numeric equivalents for standalone SVG compatibility.
-     *
-     * Mirrors igv.js Browser.toSVG() (js/browser.ts lines 352-388).
-     *
-     * @param options.width — Override viewport width (defaults to current viewportWidth).
-     * @param options.backdropColor — Background color (defaults to 'white').
-     */
-    toSVG(options?: {
-        width?: number;
-        backdropColor?: string;
-    }): string;
-    /**
-     * Serialize browser state to a SessionConfig.
-     * Track configs are serialized via per-type serializers that drop
-     * non-serializable values (functions, Promises) and only include
-     * fields that differ from theme defaults.
-     */
-    toJSON(): SessionConfig;
-    /**
-     * Load a session, replacing all current tracks.
-     * Disposes existing state, sets locus, and recreates tracks + data sources.
-     *
-     * Tracks are created headlessly (not attached to the DOM). Subclasses like
-     * GenomeBrowser can override this to also attach track canvases to the DOM.
-     */
-    loadSession(session: SessionConfig, options?: CreateTrackFromSessionOptions): void;
-    /**
-     * Create a new HeadlessGenomeBrowser from a session config.
-     * Creates the browser and loads all tracks from the session.
-     */
-    static fromSession(session: SessionConfig, options?: HeadlessGenomeBrowserOptions & CreateTrackFromSessionOptions): HeadlessGenomeBrowser;
-    /**
-     * Add a track from a session config using the track registry.
-     *
-     * Mirrors igv.js `Browser.createTrack(config)` (js/browser.ts lines 1074-1151)
-     * which resolves type aliases via `getTrack()` and instantiates through the
-     * track factory. Our version delegates to `createTrackFromConfig()` in the
-     * registry, then registers the created track with this browser's data lifecycle.
-     *
-     * This is the generic entry point — the convenience methods below
-     * (addRuler, addWigTrack, addGeneTrack) are sugar for common cases.
-     */
-    addTrackFromConfig(trackConfig: TrackSessionConfig): Track;
-    /** Add a ruler track. */
-    addRuler(options?: AddRulerOptions): RulerTrackCanvas;
-    /** Add a BigWig signal track. */
-    addWigTrack(url: string, options?: AddWigTrackOptions): WigTrackCanvas;
-    /** Add a GTX signal track (single experiment from a multi-experiment GTX file). */
-    addGtxTrack(url: string, options: AddGtxTrackOptions): WigTrackCanvas;
-    /** Add a UCSC gene annotation track. */
-    addGeneTrack(options?: AddAnnotationTrackOptions): AnnotationTrackCanvas;
-    /** Add a BED/peak annotation track from a URL. Supports plain text and tabix-indexed files. */
-    addBedTrack(url: string, options?: AddBedTrackOptions): AnnotationTrackCanvas;
-    /** Add an interaction (arc/BEDPE) track from a URL. */
-    addInteractionTrack(url: string, options?: AddInteractionTrackOptions): InteractionTrackCanvas;
-    /** Add a DNA/RNA sequence track. Data fetching is handled automatically via the genome's sequence provider. */
-    addSequenceTrack(options?: AddSequenceTrackOptions): SequenceTrackCanvas;
-    /** Clean up event listeners, abort in-flight requests, clear tracks and ROIs. */
-    dispose(): void;
-    /**
-     * Resolve pixel coordinates on a track canvas to interaction data.
-     * Used by GenomeBrowser to build event payloads from pointer events.
-     * Returns null if the track has no features at the given point.
-     */
-    protected resolveInteraction(track: Track, x: number, y: number): TrackInteractionEvent | null;
-    protected loadAllTracksIfNeeded(): void;
-    /**
-     * Load data for a single track, deduplicating against inflight fetches
-     * from other tracks with the same data source identity.
-     *
-     * Works for both initial addTrack() loads and bulk loadAllTracksIfNeeded() calls.
-     */
-    private loadTrackWithDedup;
-}

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

@@ -1,123 +0,0 @@
-export type { CanvasProvider, CanvasAndContext } from './canvasProvider';
-export { DOMCanvasProvider, defaultCanvasProvider } from './canvasProvider';
-export type { PopupProvider } from './popupProvider';
-export type { ContextMenuProvider } from './contextMenuProvider';
-export type { ContextMenuCallbacks, ROIMenuCallbacks } from './contextMenu';
-export { commonContextMenuItems, numericDataMenuItems, roiContextMenuItems } from './contextMenu';
-export type { WorkerProvider, WorkerTask, WorkerTaskResultMap } from './workerProvider';
-export type { PackTask, SummarizeWigTask, ComputeWigRangeTask, ParseFeaturesTask, } from './workerProvider';
-export { MainThreadProvider, mainThreadProvider } from './workerProvider';
-export { WebWorkerProvider } from './worker/webWorkerProvider';
-export type { WebWorkerProviderOptions } from './worker/webWorkerProvider';
-export { NodeWorkerProvider } from './worker/nodeWorkerProvider';
-export { BaseTrackCanvas } from './tracks/baseTrackCanvas';
-export type { AnnotationFeature, Exon, AnnotationRenderConfig, RenderContext, DisplayMode, Locus, Track, RulerRenderConfig, AxisInfo, TrackFeatureSummary, WigFeatureSummary, AnnotationFeatureSummary, InteractionFeatureSummary } from './types';
-export type { WigFeature, WigRenderConfig, WigColorValue, WigGraphType, WindowFunction, WigGuideLine } from './types';
-export type { SequenceRenderConfig, SequenceType, SequenceTrackSessionConfig, SequenceSessionOverrides } from './types';
-export { defaultSequenceRenderConfig } from './types';
-export type { InteractionFeature, InteractionRenderConfig, ArcOrientation, ArcDisplayMode, InteractionTrackSessionConfig, InteractionSessionOverrides } from './types';
-export { defaultInteractionRenderConfig } from './types';
-export type { DataSource, FeatureCacheEntry, DataDrivenTrack } from './types';
-export type { PopupDataItem, HitTestResult, TrackInteractionEvent, ContextMenuItem, TrackContextMenuEvent, NumericState, ROI, ROISetConfig, ROIInteractionEvent } from './types';
-export type { SessionConfig, TrackSessionConfig, WigTrackSessionConfig, AnnotationTrackSessionConfig, RulerTrackSessionConfig, WigSessionOverrides, AnnotationSessionOverrides, RulerSessionOverrides, DataSourceConfig, BigWigDataSourceConfig, GtxDataSourceConfig, UCSCDataSourceConfig, TextDataSourceConfig, SequenceProvider, IgvSessionObject, IgvReferenceConfig, IgvTrackConfig, Chromosome, Genome, GenomeConfig, ChromAliasRecord, Strand, TextFileFormat, BedFeature, PeakFeature, BedGraphFeature, GFFRecord, GFFFeature, TextFeature, } from './types';
-export { defaultAnnotationRenderConfig, defaultRulerRenderConfig, defaultWigRenderConfig } from './types';
-export type { Packable } from './pack';
-export { packFeatures } from './pack';
-export { renderAnnotationTrack } from './tracks/annotation/annotationRenderer';
-export { AnnotationTrackCanvas } from './tracks/annotation/annotationTrackCanvas';
-export type { AnnotationTrackCanvasOptions } from './tracks/annotation/annotationTrackCanvas';
-export { renderRulerTrack, renderWholeGenomeRuler } from './tracks/ruler/rulerRenderer';
-export type { WholeGenomeRulerContext } from './tracks/ruler/rulerRenderer';
-export { RulerTrackCanvas } from './tracks/ruler/rulerTrackCanvas';
-export type { RulerTrackCanvasOptions } from './tracks/ruler/rulerTrackCanvas';
-export { renderQuantitativeAxis, renderLabelAxis, prettyPrintNumber } from './tracks/axis/axisRenderer';
-export { renderWigTrack } from './tracks/wig/wigRenderer';
-export { WigTrackCanvas } from './tracks/wig/wigTrackCanvas';
-export type { WigTrackCanvasOptions } from './tracks/wig/wigTrackCanvas';
-export { summarizeWigData, computeWigDataRange } from './tracks/wig/wigSummary';
-export { HeadlessGenomeBrowser, BrowserEvent } from './headlessGenomeBrowser';
-export type { HeadlessGenomeBrowserOptions, ManagedTrack, AddRulerOptions, AddWigTrackOptions, AddGtxTrackOptions, AddBedTrackOptions, AddAnnotationTrackOptions, AddInteractionTrackOptions, AddSequenceTrackOptions } from './headlessGenomeBrowser';
-export { GenomeBrowser } from './genomeBrowser';
-export type { GenomeBrowserOptions, BrowserEvents } from './genomeBrowser';
-export type { ChromSizes, CumulativeOffsets } from './genome/chromSizes';
-export { hg38ChromSizes, getChromLength, isMainChromosome, mainChromosomeNames, computeCumulativeOffsets, genomeToChromCoord, parseChromSizes } from './genome/chromSizes';
-export { hg38Genome, createGenome, createGenomeSync } from './genome/genome';
-export { ChromAliasDefaults, addCaseAliases } from './genome/chromAlias';
-export { EventEmitter } from './events';
-export { parseLocus, formatLocus, formatBpLength, clampLocus, isWholeGenomeView } from './locusUtils';
-export { LoomChromosomeSelect, LoomLocusInput, LoomZoomControls, LoomWindowSize, LoomExportControls, LoomNavbar, LoomBrowserShell, createShell, classicThemeCSS, modernThemeCSS, getThemeCSS, LoomPopup, DefaultPopupProvider, LoomContextMenu, DefaultContextMenuProvider, LoomInputDialog, } from './ui';
-export type { ShellTheme, CreateShellOptions } from './ui';
-export { decodeGenePred, decodeGenePredExt, decodeRefGeneJson } from './decode/ucsc';
-export type { RefGeneRecord } from './decode/ucsc';
-export { findUTRs, parseColorString, parseStrand } from './decode/exonUtils';
-export { decodeBed, decodeNarrowPeak, decodeBroadPeak, decodeBedGraph, decodeGappedPeak, decodeRefflat } from './decode/bed';
-export type { BedHeader } from './decode/bed';
-export { decodeGFF3, decodeGTF, assembleGFFTranscripts, parseGFFAttributes, decodeGFFAttribute, isTranscript, isExon, isCoding, isUTR, isIntron, isTranscriptPart, } from './decode/gff';
-export { decodeBedpe, fixBedPE, isHiccups } from './decode/bedpe';
-export type { BedpeHeader } from './decode/bedpe';
-export { decodeInteract } from './decode/interact';
-export { renderInteractionTrack, positionString } from './tracks/interaction/interactionRenderer';
-export type { DrawnInteractionFeature, InteractionDrawState } from './tracks/interaction/interactionRenderer';
-export { InteractionTrackCanvas } from './tracks/interaction/interactionTrackCanvas';
-export type { InteractionTrackCanvasOptions } from './tracks/interaction/interactionTrackCanvas';
-export type { ThemePalette, RenderTheme } from './themes/renderTheme';
-export { defaultRenderTheme, resolveTheme, resolveAnnotationConfig, resolveWigConfig, resolveRulerConfig, resolveSequenceConfig, resolveInteractionConfig } from './themes/renderTheme';
-export { modernRenderTheme, darkRenderTheme } from './themes/renderThemePresets';
-export { modernTheme, darkTheme } from './tracks/annotation/annotationThemes';
-export { modernWigTheme, darkWigTheme, warmWigTheme, lineWigTheme } from './tracks/wig/wigThemes';
-export { modernSequenceTheme, darkSequenceTheme } from './tracks/sequence/sequenceThemes';
-export { renderSequenceTrack } from './tracks/sequence/sequenceRenderer';
-export type { SequenceFeature } from './tracks/sequence/sequenceRenderer';
-export { SequenceTrackCanvas } from './tracks/sequence/sequenceTrackCanvas';
-export type { SequenceTrackCanvasOptions } from './tracks/sequence/sequenceTrackCanvas';
-export { complementBase, complementSequence, reverseComplementSequence, translateSequence, translationDict, } from './sequence/sequenceUtils';
-export type { CodonTranslation } from './sequence/sequenceUtils';
-export { renderDynSeqFeature, drawLetterGlyph, defaultNucleotideColors } from './tracks/dynseq/dynseqRenderer';
-export { fetchGeneFeatures } from './data/ucscApi';
-export type { FetchGenesOptions } from './data/ucscApi';
-export { fetchSequence } from './data/ucscSequence';
-export type { FetchSequenceOptions } from './data/ucscSequence';
-export { createCachedSequence } from './data/cachedSequence';
-export { fetchBigWigFeatures, fetchBigWigWGFeatures, clearBigWigCache, BigWigReader } from './bigwig';
-export type { FetchBigWigOptions, BigWigHeader, BigWigTotalSummary } from './bigwig';
-export { fetchGtxFeatures, fetchGtxWGFeatures, fetchGtxMultiFeatures, clearGtxCache, GtxReader } from './gtx';
-export type { FetchGtxOptions, GtxHeader, ChromEntry, ExperimentEntry } from './gtx';
-export { TabixReader } from './tabix';
-export type { TabixReaderOptions, TabixHeader } from './tabix';
-export { BinaryParser } from './io/binaryParser';
-export { fetchRange, BufferedRangeReader } from './io/rangeReader';
-export type { ByteRange } from './io/rangeReader';
-export { BigWigDataSource } from './dataSources/bigWigDataSource';
-export { GtxDataSource } from './dataSources/gtxDataSource';
-export { GeneDataSource } from './dataSources/geneDataSource';
-export { TextFeatureSource } from './dataSources/textFeatureSource';
-export type { TextFeatureSourceConfig } from './dataSources/textFeatureSource';
-export { SequenceDataSource } from './dataSources/sequenceDataSource';
-export { createFeatureSource } from './dataSources/featureSourceFactory';
-export type { FeatureSourceConfig, FeatureSourceResult } from './dataSources/featureSourceFactory';
-export { dataSourceCacheKey } from './dataSources/dataSourceCacheKey';
-export { inferFormatFromPath, isBinaryFormat, isLikelyIndexed, inferIndexURL, inferTrackType, knownFileExtensions } from './formats/formatDetection';
-export { parseFeatures, parseHeader, getDecoder } from './formats/featureParser';
-export type { FeatureHeader, DecoderFunction } from './formats/featureParser';
-export { cacheCoversViewport, bufferLocus } from './dataLifecycle';
-export { IntervalTree } from './intervalTree';
-export type { Interval } from './intervalTree';
-export { FeatureCache } from './featureCache';
-export type { CacheableFeature, CacheRange } from './featureCache';
-export { C2S } from './export/canvas2svg';
-export type { C2SConfig, C2SContext, C2SVGExtensions } from './export/canvas2svg';
-export { ROISet, ROI_DEFAULT_COLOR, ROI_USER_DEFINED_COLOR, generateROIId } from './roi';
-export { renderROIOverlays } from './roi';
-export type { ROIRenderOptions } from './roi';
-export { registerTrackCreator, registerTypeAlias, getTrackCreator, knownTrackTypes, createTrackFromConfig, } from './trackRegistry';
-export type { TrackCreatorContext, TrackCreator, CreatedTrack } from './trackRegistry';
-export { SESSION_VERSION, createDataSource, createTrackFromSession, fromIgvSession, toIgvSession, } from './session';
-export type { CreateDataSourceOptions, CreateTrackFromSessionOptions } from './session';
-export { StateProjection } from './stateProjection';
-export type { ZoomLevel, TrackSummary, ProjectedState, StateDiff, TrackChangeDiff, GetStateOptions } from './stateProjection';
-export { matchesSelector, selectTracks } from './trackSelector';
-export type { TrackSelector } from './trackSelector';
-export { CommandDispatcher, CommandError, toTrackSelector } from './commandDispatcher';
-export type { CommandArgs, CommandResultMap, CommandErrorCode, CommandDispatcherOptions, WireTrackSelector, ModifyTrackAction, ROIAction, GetBrowserStateArgs, NavigateArgs, ModifyTracksArgs, QueryFeaturesArgs, AnnotateArgs, SetLayoutArgs, ExportViewArgs, ManageROIsArgs, SubscribeEventsArgs, ModifyTracksResult, ModifyTrackActionResult, QueryFeaturesResult, SetLayoutResult, ManageROIsResult, SubscribeEventsResult, } from './commandDispatcher';
-export { RemoteConnection, READY_STATE_OPEN } from './remoteProtocol';
-export type { RemoteSocket, RequestMessage, ResponseMessage, ErrorMessage, EventMessage, OutboundMessage, } from './remoteProtocol';

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

@@ -1,56 +0,0 @@
-/**
- * Augmented red-black interval tree for efficient overlap queries.
- *
- * Port of igv.js `js/intervalTree.ts` (CLR-based implementation).
- * Typed generically — values stored in intervals are `T` instead of `unknown`.
- *
- * Each node stores augmented min/max for its subtree, enabling O(log n + k)
- * overlap queries via subtree pruning.
- *
- * Layer 1 (Data + Layout) — pure data structure, no DOM, no canvas.
- */
-/** An interval with an associated value. */
-export interface Interval<T = unknown> {
-    low: number;
-    high: number;
-    value: T;
-}
-interface TreeNode<T> {
-    color: number;
-    parent: TreeNode<T>;
-    left: TreeNode<T>;
-    right: TreeNode<T>;
-    interval: Interval<T>;
-    /** Augmented: maximum high value in this subtree. */
-    max: number;
-    /** Augmented: minimum low value in this subtree. */
-    min: number;
-}
-/**
- * Augmented red-black interval tree.
- *
- * Public API:
- * - `insert(start, end, value)` — O(log n) insertion
- * - `findOverlapping(start, end)` — O(log n + k) query, returns sorted intervals
- * - `mapIntervals(fn)` — apply function to every interval (in-order)
- */
-export declare class IntervalTree<T = unknown> {
-    #private;
-    root: TreeNode<T>;
-    constructor();
-    /**
-     * Insert an interval [start, end] with associated value.
-     * Maintains red-black balance and augmented min/max.
-     */
-    insert(start: number, end: number, value: T): void;
-    /**
-     * Find all intervals overlapping [start, end].
-     * Returns intervals sorted by `low` value.
-     */
-    findOverlapping(start: number, end: number): Interval<T>[];
-    /**
-     * Apply a function to every interval in the tree.
-     */
-    mapIntervals(fn: (interval: Interval<T>) => void): void;
-}
-export {};