loom-browser 0.0.9 → 0.0.11

package/dist/types/types.d.ts

@@ -1,4 +1,15 @@
 import type { ChromSizes, CumulativeOffsets } from './genome/chromSizes';
+export type { DisplayMode, AnnotationRenderConfig } from './tracks/annotation/config';
+export { defaultAnnotationRenderConfig } from './tracks/annotation/config';
+export type { RulerRenderConfig } from './tracks/ruler/config';
+export { defaultRulerRenderConfig } from './tracks/ruler/config';
+export type { WigGraphType, WigGuideLine, WigColorValue, WigRenderConfig } from './tracks/wig/config';
+export { defaultWigRenderConfig } from './tracks/wig/config';
+export type { SequenceType, SequenceRenderConfig } from './tracks/sequence/config';
+export { defaultSequenceRenderConfig } from './tracks/sequence/config';
+export type { ArcOrientation, ArcDisplayMode, InteractionRenderConfig } from './tracks/interaction/config';
+export { defaultInteractionRenderConfig } from './tracks/interaction/config';
+export type { DataSourceConfig, BigWigDataSourceConfig, GtxDataSourceConfig, UCSCDataSourceConfig, TextDataSourceConfig, MemoryDataSourceConfig, } from './dataSources/config';
 /** Genomic locus — a chromosome region. */
 export interface Locus {
     chr: string;
@@ -78,6 +89,16 @@ export interface Track {
     setError(error: Error | null): void;
     /** Apply a new render theme and re-render. Replaces all theme-derived config values. */
     setTheme(theme: import('./themes/renderTheme').RenderTheme): void;
+    /**
+     * Callback invoked just before config changes (e.g. setConfig()).
+     * The browser registers this to snapshot state for undo (capturing pre-mutation state).
+     */
+    onBeforeConfigChange?: (() => void) | undefined;
+    /**
+     * Callback invoked after config changes (e.g. setConfig()).
+     * The browser registers this to emit TrackConfigChanged.
+     */
+    onConfigChanged?: (() => void) | undefined;
     /**
      * Hit-test at canvas-relative pixel coordinates.
      * Returns features at that point with pre-formatted popup data.
@@ -127,6 +148,12 @@ export interface Track {
     renderToContext?(ctx: CanvasRenderingContext2D, width: number, height: number): void;
     visibilityWindow?: number;
 }
+/** Track that supports zoom-level awareness (shows "zoom in" notice when zoomed out). */
+export interface ZoomAwareTrack extends Track {
+    setZoomedOut(zoomed: boolean): void;
+}
+/** Type guard for tracks that implement setZoomedOut(). */
+export declare function isZoomAware(track: Track): track is ZoomAwareTrack;
 /** A single exon within a gene feature. */
 export interface Exon {
     start: number;
@@ -169,58 +196,6 @@ export interface AnnotationFeature {
     /** 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. */
@@ -232,23 +207,6 @@ export interface RenderContext {
     /** 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;
@@ -260,8 +218,6 @@ export interface WigFeature {
     /** 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>;
 /**
@@ -348,122 +304,6 @@ export interface GenomeConfig {
 }
 /** 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). */
@@ -496,39 +336,6 @@ export interface InteractionFeature {
     /** 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;
@@ -652,7 +459,22 @@ export interface DataSource<F = unknown> {
      * @param signal - AbortSignal for cancellation of stale requests
      */
     fetch(locus: Locus, bpPerPixel: number, signal: AbortSignal): Promise<F[]>;
+    /** Optional cleanup — release file handles, caches, or other resources. */
+    dispose?(): void;
 }
+/**
+ * Optional configuration methods that DataSource implementations may support.
+ *
+ * Used by `configureDataSource()` to safely dispatch setter calls by name.
+ * Implementations should declare `implements ConfigurableDataSource` to opt in.
+ */
+export interface ConfigurableDataSource {
+    setCumulativeOffsets?(offsets: CumulativeOffsets): void;
+    setChromNameResolver?(resolver: (chr: string) => string): void;
+    setWindowFunction?(wf: WindowFunction): void;
+}
+/** Known setter method names on ConfigurableDataSource. */
+export type DataSourceConfigMethod = keyof ConfigurableDataSource;
 /** Cached features for a track, stored and managed by GenomeBrowser. */
 export interface FeatureCacheEntry<F = unknown> {
     locus: Locus;
@@ -663,8 +485,6 @@ export interface FeatureCacheEntry<F = unknown> {
 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. */
@@ -695,6 +515,12 @@ export interface InteractionFeatureSummary extends FeatureSummaryBase {
 }
 /** Union of all track feature summaries. */
 export type TrackFeatureSummary = WigFeatureSummary | AnnotationFeatureSummary | InteractionFeatureSummary;
+import type { AnnotationRenderConfig } from './tracks/annotation/config';
+import type { RulerRenderConfig } from './tracks/ruler/config';
+import type { WigRenderConfig } from './tracks/wig/config';
+import type { SequenceRenderConfig } from './tracks/sequence/config';
+import type { InteractionRenderConfig } from './tracks/interaction/config';
+import type { DataSourceConfig } from './dataSources/config';
 /** First-party session config — fully typed, JSON-serializable browser state. */
 export interface SessionConfig {
     version: string;
@@ -753,37 +579,6 @@ export type RulerSessionOverrides = Partial<RulerRenderConfig>;
 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 | MemoryDataSourceConfig;
-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;
-}
-export interface MemoryDataSourceConfig {
-    type: 'memory';
-}
 /** Strand value for genomic features. */
 export type Strand = '+' | '-' | '.';
 /** Known text genomic file formats supported by the format detection system. */
@@ -875,34 +670,3 @@ export interface GFFFeature {
 }
 /** 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 {};

package/dist/types/ui/components/LoomBrowserShell.d.ts

@@ -12,8 +12,8 @@
  * Or use the createShell() helper:
  *   const shell = createShell(container, { locus, theme: 'modern' })
  */
-import { GenomeBrowser } from '../../genomeBrowser';
-import type { GenomeBrowserOptions, BrowserEvents } from '../../genomeBrowser';
+import { GenomeBrowser } from '../../browser/dom/genomeBrowser';
+import type { GenomeBrowserOptions, BrowserEvents } from '../../browser/dom/genomeBrowser';
 import type { Locus, Track } from '../../types';
 import type { ShellTheme } from '../themes';
 export declare class LoomBrowserShell extends HTMLElement {

package/dist/types/ui/components/LoomChromosomeSelect.d.ts

@@ -4,7 +4,7 @@
  * Lists main chromosomes (chr1-22, X, Y, M) plus "All" for whole genome view.
  * Updates automatically when the browser locus changes.
  */
-import type { GenomeBrowser } from '../../genomeBrowser';
+import type { GenomeBrowser } from '../../browser/dom/genomeBrowser';
 export declare class LoomChromosomeSelect extends HTMLElement {
     private select;
     private unsubscribe;

package/dist/types/ui/components/LoomContextMenu.d.ts

@@ -17,6 +17,7 @@ export declare class LoomContextMenu extends HTMLElement {
     private menuDiv;
     constructor();
     connectedCallback(): void;
+    disconnectedCallback(): void;
     /** Populate the menu from typed ContextMenuItem data. */
     setItems(items: ContextMenuItem[]): void;
     private buildItems;

package/dist/types/ui/components/LoomExportControls.d.ts

@@ -4,7 +4,7 @@
  * Adds "Save SVG" and "Save PNG" buttons to the shell navbar.
  * Calls GenomeBrowser.saveSVGtoFile() and savePNGtoFile() respectively.
  */
-import type { GenomeBrowser } from '../../genomeBrowser';
+import type { GenomeBrowser } from '../../browser/dom/genomeBrowser';
 export declare class LoomExportControls extends HTMLElement {
     private _browser;
     constructor();

package/dist/types/ui/components/LoomLocusInput.d.ts

@@ -4,7 +4,7 @@
  * Shows the current locus as a formatted string. User can type a new locus
  * and press Enter to navigate. Updates automatically on locuschange events.
  */
-import type { GenomeBrowser } from '../../genomeBrowser';
+import type { GenomeBrowser } from '../../browser/dom/genomeBrowser';
 export declare class LoomLocusInput extends HTMLElement {
     private input;
     private unsubscribe;

package/dist/types/ui/components/LoomNavbar.d.ts

@@ -1,7 +1,7 @@
 /**
  * <loom-navbar> — Horizontal navigation bar composing locus input, window size, and zoom controls.
  */
-import type { GenomeBrowser } from '../../genomeBrowser';
+import type { GenomeBrowser } from '../../browser/dom/genomeBrowser';
 export declare class LoomNavbar extends HTMLElement {
     private chromSelect;
     private locusInput;

package/dist/types/ui/components/LoomWindowSize.d.ts

@@ -1,7 +1,7 @@
 /**
  * <loom-window-size> — Read-only display of current viewport bp range.
  */
-import type { GenomeBrowser } from '../../genomeBrowser';
+import type { GenomeBrowser } from '../../browser/dom/genomeBrowser';
 export declare class LoomWindowSize extends HTMLElement {
     private label;
     private unsubscribe;

package/dist/types/ui/components/LoomZoomControls.d.ts

@@ -1,7 +1,7 @@
 /**
  * <loom-zoom-controls> — Zoom in/out buttons.
  */
-import type { GenomeBrowser } from '../../genomeBrowser';
+import type { GenomeBrowser } from '../../browser/dom/genomeBrowser';
 export declare class LoomZoomControls extends HTMLElement {
     private _browser;
     constructor();

package/dist/types/undoManager.d.ts

@@ -0,0 +1,49 @@
+/**
+ * Undo/redo manager for HeadlessGenomeBrowser.
+ *
+ * Maintains two stacks of tagged session snapshots. Each entry records the
+ * mutation type so consumers can filter (e.g., skip navigation-only entries).
+ *
+ * Decoupled from the browser — operates purely on SessionConfig objects.
+ */
+import type { SessionConfig } from './types';
+/** Category of mutation that produced an undo entry. */
+export type UndoEntryType = 'navigation' | 'track-add' | 'track-remove' | 'track-reorder' | 'track-config' | 'roi' | 'theme' | 'session-load';
+/** A single undo/redo stack entry. */
+export interface UndoEntry {
+    type: UndoEntryType;
+    session: SessionConfig;
+}
+export declare class UndoManager {
+    readonly maxHistory: number;
+    private undoStack;
+    private redoStack;
+    private _paused;
+    constructor(maxHistory?: number);
+    /** Whether snapshot calls are currently suppressed. */
+    get paused(): boolean;
+    /** Suppress snapshot calls (e.g., during loadSession restoration). */
+    pause(): void;
+    /** Resume snapshot calls. */
+    resume(): void;
+    /** Push the current state before a mutation. Clears the redo stack. */
+    snapshot(type: UndoEntryType, session: SessionConfig): void;
+    /**
+     * Undo: pop from undo stack, push currentSession to redo, return the entry to restore.
+     * Optionally skip entries matching a predicate (they are discarded).
+     */
+    undo(currentSession: SessionConfig, skip?: (e: UndoEntry) => boolean): UndoEntry | undefined;
+    /**
+     * Redo: pop from redo stack, push currentSession to undo, return the entry to restore.
+     * Optionally skip entries matching a predicate (they are discarded).
+     */
+    redo(currentSession: SessionConfig, skip?: (e: UndoEntry) => boolean): UndoEntry | undefined;
+    canUndo(skip?: (e: UndoEntry) => boolean): boolean;
+    canRedo(skip?: (e: UndoEntry) => boolean): boolean;
+    /** Number of entries in the undo stack. */
+    get undoSize(): number;
+    /** Number of entries in the redo stack. */
+    get redoSize(): number;
+    /** Clear all history. */
+    clear(): void;
+}

package/dist/types/worker/dataSourceRegistry.d.ts

@@ -7,7 +7,7 @@
  * Runs inside a web worker or Node worker_threads context.
  * Layer 1 (Data + Layout): no DOM.
  */
-import type { DataSourceConfig, Locus } from '../types';
+import type { DataSourceConfig, DataSourceConfigMethod, Locus } from '../types';
 export declare class DataSourceRegistry {
     private readonly instances;
     private readonly inflightAborts;
@@ -27,7 +27,7 @@ export declare class DataSourceRegistry {
      * Call a setter method on a registered DataSource.
      * Used for serializable configuration updates (setCumulativeOffsets, setWindowFunction, etc.).
      */
-    configure(instanceId: string, method: string, args: unknown[]): void;
+    configure(instanceId: string, method: DataSourceConfigMethod, args: unknown[]): void;
     /** Destroy a DataSource instance and clean up. */
     destroy(instanceId: string): void;
 }

package/dist/types/worker/serializedError.d.ts

@@ -0,0 +1,16 @@
+/**
+ * Serialized error for cross-worker-boundary error propagation.
+ *
+ * Workers can't transfer Error objects via postMessage. This type carries
+ * the error message, name, and stack trace across the boundary so the
+ * receiving side can reconstruct a meaningful Error.
+ */
+export interface SerializedError {
+    message: string;
+    name: string;
+    stack?: string;
+}
+/** Extract serializable fields from an error. */
+export declare function serializeError(err: unknown): SerializedError;
+/** Reconstruct an Error from serialized fields (preserves name and stack). */
+export declare function deserializeError(se: SerializedError): Error;

package/dist/types/worker/taskTimeout.d.ts

@@ -0,0 +1,21 @@
+/**
+ * Timeout utility for worker task execution.
+ *
+ * Wraps a promise with a configurable timeout. If the promise doesn't settle
+ * within the timeout, it rejects with a TaskTimeoutError.
+ *
+ * Layer 1 (Data): no DOM, no canvas.
+ */
+/** Default timeout for worker tasks (30 seconds). */
+export declare const DEFAULT_TASK_TIMEOUT_MS = 30000;
+/** Error thrown when a worker task exceeds its timeout. */
+export declare class TaskTimeoutError extends Error {
+    constructor(taskName: string, ms: number);
+}
+/**
+ * Race a promise against a timeout. Returns the promise result if it settles
+ * first, or rejects with TaskTimeoutError if the timeout fires first.
+ *
+ * Pass `ms <= 0` to disable the timeout (returns the promise as-is).
+ */
+export declare function withTimeout<T>(promise: Promise<T>, ms: number, taskName: string): Promise<T>;

package/dist/types/worker/webWorkerPool.d.ts

@@ -19,7 +19,7 @@
  */
 import type { WorkerProvider, WorkerTask, WorkerTaskResultMap } from '../workerProvider';
 import type { DataSourceWorkerProvider } from '../dataSourceWorkerProvider';
-import type { DataSourceConfig, Locus } from '../types';
+import type { DataSourceConfig, DataSourceConfigMethod, Locus } from '../types';
 export interface WebWorkerPoolOptions {
     /**
      * URL to the worker pool script.
@@ -37,10 +37,13 @@ export interface WebWorkerPoolOptions {
      * Number of workers in the pool. Default: 1.
      */
     poolSize?: number;
+    /** Task timeout in ms. Default: 30000. Set to 0 to disable. */
+    taskTimeoutMs?: number;
 }
 export declare class WebWorkerPool implements WorkerProvider, DataSourceWorkerProvider {
     private workers;
     private readyPromises;
+    private readonly taskTimeoutMs;
     private nextId;
     private nextWorker;
     private pending;
@@ -53,7 +56,7 @@ export declare class WebWorkerPool implements WorkerProvider, DataSourceWorkerPr
     execute<T extends WorkerTask>(task: T, transfer?: Transferable[]): Promise<WorkerTaskResultMap[T['task']]>;
     create(instanceId: string, config: DataSourceConfig): void;
     fetch<F>(instanceId: string, locus: Locus, bpPerPixel: number, signal: AbortSignal): Promise<F[]>;
-    configure(instanceId: string, method: string, ...args: unknown[]): void;
+    configure(instanceId: string, method: DataSourceConfigMethod, ...args: unknown[]): void;
     destroy(instanceId: string): void;
     dispose(): void;
     /**

package/dist/types/worker/webWorkerProvider.d.ts

@@ -33,12 +33,15 @@ export interface WebWorkerProviderOptions {
      * Default: 1.
      */
     poolSize?: number;
+    /** Task timeout in ms. Default: 30000. Set to 0 to disable. */
+    taskTimeoutMs?: number;
 }
 export declare class WebWorkerProvider implements WorkerProvider {
     private workers;
     private nextId;
     private nextWorker;
     private pending;
+    private readonly taskTimeoutMs;
     /**
      * @param optionsOrUrl - Options object with workerUrl and poolSize,
      *   or a URL string/URL for backward compatibility (single worker).

package/dist/types/workerDataSource.d.ts

@@ -10,11 +10,11 @@
  *
  * Layer 1 (Data + Layout): no DOM.
  */
-import type { DataSource, Locus } from './types';
+import type { DataSource, ConfigurableDataSource, Locus } from './types';
 import type { CumulativeOffsets } from './genome/chromSizes';
 import type { DataSourceWorkerProvider } from './dataSourceWorkerProvider';
 import type { WindowFunction } from './types';
-export declare class WorkerDataSource<F = unknown> implements DataSource<F> {
+export declare class WorkerDataSource<F = unknown> implements DataSource<F>, ConfigurableDataSource {
     private readonly provider;
     readonly instanceId: string;
     private resolver?;