loom-browser 0.0.1 → 0.0.3

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

@@ -1,52 +0,0 @@
-/**
- * <loom-browser> — Top-level shell combining navbar + GenomeBrowser.
- *
- * Usage:
- *   const shell = document.createElement('loom-browser')
- *   shell.setAttribute('theme', 'modern')
- *   container.appendChild(shell)
- *   shell.initialize({ locus: { chr: 'chr17', start: 7668000, end: 7688000 } })
- *   shell.addTrack(rulerTrack)
- *   shell.addTrack(geneTrack)
- *
- * Or use the createShell() helper:
- *   const shell = createShell(container, { locus, theme: 'modern' })
- */
-import { GenomeBrowser } from '../../genomeBrowser';
-import type { GenomeBrowserOptions, BrowserEvents } from '../../genomeBrowser';
-import type { Locus, Track } from '../../types';
-import type { ShellTheme } from '../themes';
-export declare class LoomBrowserShell extends HTMLElement {
-    private navbar;
-    private trackContainer;
-    private themeStyle;
-    private _browser;
-    static get observedAttributes(): string[];
-    constructor();
-    attributeChangedCallback(name: string, _oldValue: string | null, newValue: string | null): void;
-    private applyTheme;
-    connectedCallback(): void;
-    /** Initialize the GenomeBrowser inside this shell. */
-    initialize(options: GenomeBrowserOptions): GenomeBrowser;
-    /** Get the underlying GenomeBrowser instance. */
-    get browser(): GenomeBrowser | null;
-    /** Proxy: add a track to the browser. */
-    addTrack(track: Track): void;
-    /** Proxy: remove a track from the browser. */
-    removeTrack(track: Track): void;
-    /** Proxy: set the locus. */
-    setLocus(locus: Locus): void;
-    /** Proxy: subscribe to browser events. */
-    on<K extends keyof BrowserEvents>(event: K, handler: (data: BrowserEvents[K]) => void): (() => void) | undefined;
-    disconnectedCallback(): void;
-}
-/** Options for createShell(). */
-export interface CreateShellOptions extends GenomeBrowserOptions {
-    /** UI shell theme (CSS chrome). Separate from GenomeBrowserOptions.theme (render palette). */
-    shellTheme?: ShellTheme;
-}
-/**
- * Convenience function to create an <loom-browser> shell and initialize it.
- * Returns the shell element (with .browser for the underlying GenomeBrowser).
- */
-export declare function createShell(container: HTMLElement, options: CreateShellOptions): LoomBrowserShell;

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

@@ -1,18 +0,0 @@
-/**
- * <loom-chromosome-select> — Chromosome dropdown for quick navigation.
- *
- * 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';
-export declare class LoomChromosomeSelect extends HTMLElement {
-    private select;
-    private unsubscribe;
-    private _browser;
-    constructor();
-    set browser(b: GenomeBrowser | null);
-    get browser(): GenomeBrowser | null;
-    private populate;
-    private updateSelection;
-    disconnectedCallback(): void;
-}

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

@@ -1,39 +0,0 @@
-/**
- * <loom-context-menu> — Right-click context menu Web Component.
- *
- * Renders ContextMenuItem[] as a styled menu with action items, checkboxes,
- * separators, and one level of submenu nesting.
- *
- * Also exports DefaultContextMenuProvider which wraps this component and
- * implements the ContextMenuProvider interface.
- *
- * Customizable via CSS custom properties:
- *   --loom-menu-bg, --loom-menu-border, --loom-menu-radius, --loom-menu-shadow,
- *   --loom-menu-font, --loom-menu-color, --loom-menu-hover, --loom-menu-divider
- */
-import type { ContextMenuItem } from '../../types';
-import type { ContextMenuProvider } from '../../contextMenuProvider';
-export declare class LoomContextMenu extends HTMLElement {
-    private menuDiv;
-    constructor();
-    connectedCallback(): void;
-    /** Populate the menu from typed ContextMenuItem data. */
-    setItems(items: ContextMenuItem[]): void;
-    private buildItems;
-    /** Position and show the menu, clamping to container bounds. */
-    showAt(x: number, y: number): void;
-    hide(): void;
-}
-/**
- * Default ContextMenuProvider using the <loom-context-menu> Web Component.
- * Lazily creates the element on first show() call (same pattern as DefaultPopupProvider).
- */
-export declare class DefaultContextMenuProvider implements ContextMenuProvider {
-    private element;
-    show(items: ContextMenuItem[], position: {
-        x: number;
-        y: number;
-    }, container: HTMLElement): void;
-    hide(): void;
-    dispose(): void;
-}

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

@@ -1,13 +0,0 @@
-/**
- * <loom-export-controls> — SVG/PNG export buttons.
- *
- * Adds "Save SVG" and "Save PNG" buttons to the shell navbar.
- * Calls GenomeBrowser.saveSVGtoFile() and savePNGtoFile() respectively.
- */
-import type { GenomeBrowser } from '../../genomeBrowser';
-export declare class LoomExportControls extends HTMLElement {
-    private _browser;
-    constructor();
-    set browser(b: GenomeBrowser | null);
-    get browser(): GenomeBrowser | null;
-}

package/dist/types/src/ui/components/LoomInputDialog.d.ts

@@ -1,27 +0,0 @@
-/**
- * <loom-input-dialog> — Simple modal input dialog Web Component.
- *
- * Shows a label, text input, and OK/Cancel buttons. Returns the entered
- * value via a Promise. Used by the context menu's "Set track height" action.
- *
- * Customizable via CSS custom properties:
- *   --loom-dialog-bg, --loom-dialog-border, --loom-dialog-shadow,
- *   --loom-dialog-font, --loom-dialog-color, --loom-dialog-radius,
- *   --loom-dialog-btn-bg, --loom-dialog-btn-color
- */
-export declare class LoomInputDialog extends HTMLElement {
-    private labelEl;
-    private inputEl;
-    private okBtn;
-    private cancelBtn;
-    private resolve;
-    constructor();
-    connectedCallback(): void;
-    /**
-     * Show the dialog and return a Promise that resolves with the input value
-     * (on OK/Enter) or null (on Cancel/Escape).
-     */
-    prompt(label: string, currentValue: string | number): Promise<string | null>;
-    private confirm;
-    private cancel;
-}

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

@@ -1,18 +0,0 @@
-/**
- * <loom-locus-input> — Locus search/display input.
- *
- * 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';
-export declare class LoomLocusInput extends HTMLElement {
-    private input;
-    private unsubscribe;
-    private _browser;
-    constructor();
-    set browser(b: GenomeBrowser | null);
-    get browser(): GenomeBrowser | null;
-    private updateDisplay;
-    private doSearch;
-    disconnectedCallback(): void;
-}

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

@@ -1,15 +0,0 @@
-/**
- * <loom-navbar> — Horizontal navigation bar composing locus input, window size, and zoom controls.
- */
-import type { GenomeBrowser } from '../../genomeBrowser';
-export declare class LoomNavbar extends HTMLElement {
-    private chromSelect;
-    private locusInput;
-    private zoomControls;
-    private windowSize;
-    private exportControls;
-    private _browser;
-    constructor();
-    set browser(b: GenomeBrowser | null);
-    get browser(): GenomeBrowser | null;
-}

package/dist/types/src/ui/components/LoomPopup.d.ts

@@ -1,32 +0,0 @@
-/**
- * <loom-popup> — Feature popup / tooltip Web Component.
- *
- * Renders PopupDataItem[] as a name/value table. Positioned as a floating
- * element near the pointer, clamped to stay within the viewport.
- *
- * Also exports DefaultPopupProvider which wraps this component and
- * implements the PopupProvider interface.
- */
-import type { PopupDataItem } from '../../types';
-import type { PopupProvider } from '../../popupProvider';
-export declare class LoomPopup extends HTMLElement {
-    constructor();
-    /** Populate popup with data items and show it. */
-    setData(data: PopupDataItem[]): void;
-    /** Position relative to a parent container and show. */
-    showAt(x: number, y: number): void;
-    hide(): void;
-}
-/**
- * Default PopupProvider implementation using the <loom-popup> Web Component.
- * Creates and manages a single popup element within the browser container.
- */
-export declare class DefaultPopupProvider implements PopupProvider {
-    private element;
-    show(data: PopupDataItem[], position: {
-        x: number;
-        y: number;
-    }, container: HTMLElement): void;
-    hide(): void;
-    dispose(): void;
-}

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

@@ -1,14 +0,0 @@
-/**
- * <loom-window-size> — Read-only display of current viewport bp range.
- */
-import type { GenomeBrowser } from '../../genomeBrowser';
-export declare class LoomWindowSize extends HTMLElement {
-    private label;
-    private unsubscribe;
-    private _browser;
-    constructor();
-    set browser(b: GenomeBrowser | null);
-    get browser(): GenomeBrowser | null;
-    private update;
-    disconnectedCallback(): void;
-}

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

@@ -1,10 +0,0 @@
-/**
- * <loom-zoom-controls> — Zoom in/out buttons.
- */
-import type { GenomeBrowser } from '../../genomeBrowser';
-export declare class LoomZoomControls extends HTMLElement {
-    private _browser;
-    constructor();
-    set browser(b: GenomeBrowser | null);
-    get browser(): GenomeBrowser | null;
-}

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

@@ -1,21 +0,0 @@
-/**
- * UI Shell — Web components for interacting with the headless GenomeBrowser.
- *
- * Importing this module auto-registers all custom elements:
- *   <loom-browser>, <loom-navbar>, <loom-chromosome-select>, <loom-locus-input>, <loom-zoom-controls>, <loom-window-size>, <loom-export-controls>
- */
-export { EventEmitter } from '../events';
-export { parseLocus, formatLocus, formatBpLength } from '../locusUtils';
-export { classicThemeCSS, modernThemeCSS, getThemeCSS } from './themes';
-export type { ShellTheme } from './themes';
-export { LoomChromosomeSelect } from './components/LoomChromosomeSelect';
-export { LoomLocusInput } from './components/LoomLocusInput';
-export { LoomZoomControls } from './components/LoomZoomControls';
-export { LoomWindowSize } from './components/LoomWindowSize';
-export { LoomExportControls } from './components/LoomExportControls';
-export { LoomNavbar } from './components/LoomNavbar';
-export { LoomBrowserShell, createShell } from './components/LoomBrowserShell';
-export type { CreateShellOptions } from './components/LoomBrowserShell';
-export { LoomPopup, DefaultPopupProvider } from './components/LoomPopup';
-export { LoomContextMenu, DefaultContextMenuProvider } from './components/LoomContextMenu';
-export { LoomInputDialog } from './components/LoomInputDialog';

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

@@ -1,14 +0,0 @@
-/**
- * CSS custom property themes for UI shell web components.
- *
- * Themes are injected as <style> blocks into Shadow DOM roots.
- * Components reference CSS custom properties (--loom-*) for all visual styling.
- */
-export type ShellTheme = 'classic' | 'modern' | 'dark';
-/** Classic theme — matches igv.js navbar look. */
-export declare const classicThemeCSS = "\n:host {\n    --loom-navbar-bg: #f3f3f3;\n    --loom-navbar-height: 32px;\n    --loom-navbar-padding: 0 8px;\n    --loom-font: 12px Arial, sans-serif;\n    --loom-font-small: 11px Arial, sans-serif;\n    --loom-text-color: #333;\n    --loom-text-muted: #737373;\n    --loom-border: 1px solid #ccc;\n    --loom-border-radius: 4px;\n    --loom-button-bg: white;\n    --loom-button-hover: #e8e8e8;\n    --loom-button-border: 1px solid #b0b0b0;\n    --loom-button-size: 24px;\n    --loom-input-bg: white;\n    --loom-input-border: 1px solid #b0b0b0;\n    --loom-input-focus-border: 1px solid #4A90D9;\n    --loom-input-width: 220px;\n    --loom-input-height: 22px;\n    --loom-accent: #4A90D9;\n    --loom-icon-color: #555;\n    --loom-icon-size: 14px;\n    --loom-gap: 8px;\n}\n";
-/** Modern theme — softer colors, rounded corners, taller navbar. */
-export declare const modernThemeCSS = "\n:host {\n    --loom-navbar-bg: #fafbfc;\n    --loom-navbar-height: 40px;\n    --loom-navbar-padding: 0 12px;\n    --loom-font: 13px Inter, system-ui, -apple-system, sans-serif;\n    --loom-font-small: 11px Inter, system-ui, -apple-system, sans-serif;\n    --loom-text-color: #1a1a1a;\n    --loom-text-muted: #6b7280;\n    --loom-border: 1px solid rgba(0, 0, 0, 0.08);\n    --loom-border-radius: 8px;\n    --loom-button-bg: white;\n    --loom-button-hover: #f0f4ff;\n    --loom-button-border: 1px solid rgba(0, 0, 0, 0.1);\n    --loom-button-size: 28px;\n    --loom-input-bg: white;\n    --loom-input-border: 1px solid rgba(0, 0, 0, 0.12);\n    --loom-input-focus-border: 1px solid #4A90D9;\n    --loom-input-width: 260px;\n    --loom-input-height: 28px;\n    --loom-accent: #4A90D9;\n    --loom-icon-color: #6b7280;\n    --loom-icon-size: 16px;\n    --loom-gap: 10px;\n}\n";
-/** Dark theme — dark backgrounds, light text, high contrast. */
-export declare const darkThemeCSS = "\n:host {\n    --loom-shell-bg: #16162a;\n    --loom-navbar-bg: #1a1a2e;\n    --loom-navbar-height: 36px;\n    --loom-navbar-padding: 0 10px;\n    --loom-font: 12px Arial, sans-serif;\n    --loom-font-small: 11px Arial, sans-serif;\n    --loom-text-color: #e0e0e0;\n    --loom-text-muted: #888;\n    --loom-border: 1px solid #333;\n    --loom-border-radius: 4px;\n    --loom-button-bg: #2a2a3e;\n    --loom-button-hover: #3a3a50;\n    --loom-button-border: 1px solid #444;\n    --loom-button-size: 24px;\n    --loom-input-bg: #2a2a3e;\n    --loom-input-border: 1px solid #444;\n    --loom-input-focus-border: 1px solid #6a9fd9;\n    --loom-input-width: 220px;\n    --loom-input-height: 22px;\n    --loom-accent: #6a9fd9;\n    --loom-icon-color: #b0b0b0;\n    --loom-icon-size: 14px;\n    --loom-gap: 8px;\n}\n";
-export declare function getThemeCSS(theme: ShellTheme): string;

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

@@ -1,28 +0,0 @@
-/**
- * NodeWorkerProvider — Node.js worker_threads implementation of WorkerProvider.
- *
- * Same RPC pattern as WebWorkerProvider but uses Node.js worker_threads API.
- * All worker_threads references use dynamic import() to avoid requiring
- * @types/node in browser-targeted builds.
- *
- * Usage:
- *   import { NodeWorkerProvider } from './worker/nodeWorkerProvider'
- *   const provider = new NodeWorkerProvider(new URL('./nodeWorkerScript.js', import.meta.url))
- *   const browser = new HeadlessGenomeBrowser({ ..., workerProvider: provider })
- *   // ...
- *   provider.dispose()
- */
-import type { WorkerProvider, WorkerTask, WorkerTaskResultMap } from '../workerProvider';
-export declare class NodeWorkerProvider implements WorkerProvider {
-    private worker;
-    private nextId;
-    private pending;
-    private initPromise;
-    /**
-     * @param workerPath - Path or URL to the Node.js worker script.
-     */
-    constructor(workerPath: string | URL);
-    private init;
-    execute<T extends WorkerTask>(task: T, transfer?: Transferable[]): Promise<WorkerTaskResultMap[T['task']]>;
-    dispose(): void;
-}

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

@@ -1,15 +0,0 @@
-/**
- * Pure task dispatcher for worker threads.
- *
- * Maps WorkerTask → result using existing pure functions. No DOM, no
- * environment-specific APIs. Imported by both the Web Worker script
- * and the Node.js worker_threads script.
- */
-import type { WorkerTask, WorkerTaskResultMap } from '../workerProvider';
-/**
- * Handle a worker task and return the result.
- *
- * Each task is dispatched to the appropriate pure function. The return
- * value must be structured-clone-safe (or Transferable for ArrayBuffers).
- */
-export declare function handleTask(task: WorkerTask): Promise<WorkerTaskResultMap[WorkerTask['task']]>;

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

@@ -1,51 +0,0 @@
-/**
- * WebWorkerProvider — browser Web Worker implementation of WorkerProvider.
- *
- * Creates a pool of worker threads and dispatches tasks via round-robin.
- * Supports Transferable for zero-copy ArrayBuffer transfer.
- *
- * Usage:
- *   const provider = new WebWorkerProvider({ workerUrl: '/loom-worker.js', poolSize: 4 })
- *   const browser = new GenomeBrowser({ ..., workerProvider: provider })
- *   // ...
- *   provider.dispose()
- */
-import type { WorkerProvider, WorkerTask, WorkerTaskResultMap } from '../workerProvider';
-export interface WebWorkerProviderOptions {
-    /**
-     * URL to the worker script (built from workerScript.ts).
-     * Can be a blob URL, data URL, or path to a bundled worker script.
-     * Mutually exclusive with `workerFactory`.
-     */
-    workerUrl?: string | URL;
-    /**
-     * Factory function that creates Worker instances.
-     * Use this with bundlers like webpack 5 that require `new Worker(new URL(...))` in
-     * the same expression for static analysis:
-     *
-     *   workerFactory: () => new Worker(new URL('./workerScript.ts', import.meta.url))
-     *
-     * Mutually exclusive with `workerUrl`.
-     */
-    workerFactory?: () => Worker;
-    /**
-     * Number of workers in the pool. Tasks are distributed round-robin.
-     * Default: 1.
-     */
-    poolSize?: number;
-}
-export declare class WebWorkerProvider implements WorkerProvider {
-    private workers;
-    private nextId;
-    private nextWorker;
-    private pending;
-    /**
-     * @param optionsOrUrl - Options object with workerUrl and poolSize,
-     *   or a URL string/URL for backward compatibility (single worker).
-     */
-    constructor(optionsOrUrl: WebWorkerProviderOptions | string | URL);
-    /** Number of workers in the pool. */
-    get poolSize(): number;
-    execute<T extends WorkerTask>(task: T, transfer?: Transferable[]): Promise<WorkerTaskResultMap[T['task']]>;
-    dispose(): void;
-}

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

@@ -1,11 +0,0 @@
-/**
- * Web Worker entry point.
- *
- * This file is the script that runs inside the Web Worker. It listens
- * for messages from the main thread, dispatches them to the task handler,
- * and posts results back.
- *
- * Bundle this file as a standalone module (e.g. via Rollup/Vite worker plugin)
- * and pass the resulting URL to WebWorkerProvider.
- */
-export {};

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

@@ -1,76 +0,0 @@
-/**
- * WorkerProvider — environment abstraction for offloading CPU-intensive tasks.
- *
- * Follows the same injection pattern as CanvasProvider:
- *   - Interface with minimal methods
- *   - Concrete implementations for each environment
- *   - Optional injection with a sensible default (MainThreadProvider)
- *
- * Implementations:
- *   - MainThreadProvider  — synchronous fallback (runs tasks on main thread)
- *   - WebWorkerProvider   — browser (Web Workers)
- *   - NodeWorkerProvider  — Node.js (worker_threads)
- */
-import type { AnnotationFeature, WigFeature, WindowFunction, TextFileFormat } from './types';
-import type { FeatureHeader } from './formats/featureParser';
-export interface PackTask {
-    task: 'pack';
-    features: AnnotationFeature[];
-    maxRows?: number;
-}
-export interface SummarizeWigTask {
-    task: 'summarize';
-    features: WigFeature[];
-    startBP: number;
-    bpPerPixel: number;
-    windowFunction: WindowFunction;
-}
-export interface ComputeWigRangeTask {
-    task: 'computeWigRange';
-    features: WigFeature[];
-}
-export interface ParseFeaturesTask {
-    task: 'parseFeatures';
-    /** Raw text lines to parse. */
-    lines: string[];
-    /** File format (bed, gff3, narrowpeak, etc.). */
-    format: TextFileFormat;
-    /** Pre-parsed header metadata. */
-    header?: FeatureHeader;
-    /** Whether to assemble GFF transcripts. Default: true. */
-    assembleGFF?: boolean;
-}
-export type WorkerTask = PackTask | SummarizeWigTask | ComputeWigRangeTask | ParseFeaturesTask;
-/** Maps task name → result type. */
-export interface WorkerTaskResultMap {
-    pack: AnnotationFeature[];
-    summarize: WigFeature[];
-    computeWigRange: {
-        min: number;
-        max: number;
-    };
-    parseFeatures: unknown[];
-}
-/**
- * Execute CPU-intensive tasks, potentially in a worker thread.
- *
- * The `transfer` parameter accepts `Transferable` objects (e.g. `ArrayBuffer`)
- * for zero-copy transfer to the worker. After transfer, the original buffer
- * becomes detached on the sending side.
- */
-export interface WorkerProvider {
-    execute<T extends WorkerTask>(task: T, transfer?: Transferable[]): Promise<WorkerTaskResultMap[T['task']]>;
-    /** Terminate worker threads and release resources. */
-    dispose(): void;
-}
-/**
- * Runs all tasks on the main thread using direct function calls.
- * This is the default when no WorkerProvider is supplied.
- */
-export declare class MainThreadProvider implements WorkerProvider {
-    execute<T extends WorkerTask>(task: T): Promise<WorkerTaskResultMap[T['task']]>;
-    private dispatch;
-    dispose(): void;
-}
-/** Default worker provider: runs everything on the main thread. */
-export declare const mainThreadProvider: WorkerProvider;

package/dist/types/tabix/bgzBlockLoader.d.ts

@@ -1,60 +0,0 @@
-/**
- * BGZF block loader — fetches and decompresses BGZF blocks via HTTP range requests.
- *
- * Given two virtual offsets (from a tabix index), fetches the compressed bytes
- * covering those blocks, decompresses them, and returns the data between the
- * virtual offset boundaries.
- *
- * Caches the most recent compressed byte range so sequential/overlapping queries
- * (common when iterating through tabix chunks) avoid redundant HTTP requests.
- *
- * Port of js/bam/bgzBlockLoader.ts BGZBlockLoader.
- * Layer 1 (Data + Layout): pure data, no DOM.
- */
-import type { VirtualOffset } from './virtualOffset';
-import type { WorkerProvider } from '../workerProvider';
-export interface BgzBlockLoaderOptions {
-    /**
-     * Cache compressed blocks for sequential/overlapping queries.
-     * Default: true. Disable for memory-constrained environments.
-     * Matches igv.js BGZBlockLoader.cacheBlocks config.
-     */
-    cacheBlocks?: boolean;
-    /** Worker provider for offloading BGZF decompression. */
-    workerProvider?: WorkerProvider;
-}
-export declare class BgzBlockLoader {
-    private readonly url;
-    private readonly cacheEnabled;
-    private readonly workerProvider?;
-    private cache;
-    constructor(url: string, options?: BgzBlockLoaderOptions);
-    /**
-     * Fetch and decompress data between two virtual offsets.
-     *
-     * Uses a single-entry cache of compressed bytes. When the requested range
-     * overlaps or falls within the cached range, only the missing portions are
-     * fetched. This matches the igv.js pattern where sequential tabix chunks
-     * often share or overlap compressed block ranges.
-     *
-     * Port of js/bam/bgzBlockLoader.ts BGZBlockLoader.getData().
-     */
-    getData(minv: VirtualOffset, maxv: VirtualOffset, signal?: AbortSignal): Promise<Uint8Array>;
-    /**
-     * Return inflated blocks for the given compressed block range.
-     * Manages the compressed-data cache to minimize HTTP requests.
-     *
-     * Port of js/bam/bgzBlockLoader.ts BGZBlockLoader.getInflatedBlocks().
-     */
-    private getInflatedBlocks;
-    /**
-     * Decompress BGZF blocks, delegating to worker when available.
-     */
-    private inflate;
-    /**
-     * Fetch compressed block data from the remote file.
-     *
-     * Port of js/bam/bgzBlockLoader.ts BGZBlockLoader.loadBLockData().
-     */
-    private loadBlockData;
-}

package/dist/types/tabix/bgzf.d.ts

@@ -1,43 +0,0 @@
-/**
- * BGZF (Block GZipped Format) detection and decompression.
- *
- * BGZF is a variant of gzip that stores data in independently compressed
- * blocks, enabling random access. Each block has a standard gzip header
- * with a BGZF-specific extra field encoding the block size.
- *
- * Uses pako.inflateRaw() for synchronous decompression — matching igv.js
- * which uses the same library via igv-utils. No async overhead, no stream
- * setup per block.
- *
- * Port of js/bam/bgzBlockLoader.ts inflateBlocks() and
- * igv-utils/bgzf.js unbgzf().
- *
- * Layer 1 (Data + Layout): pure data, no DOM.
- */
-/** Check if data starts with BGZF magic (gzip header + BGZF extra field). */
-export declare function isBgzf(data: ArrayBuffer | Uint8Array): boolean;
-/**
- * Read BGZF block size from header bytes 16-17.
- * Returns total block size in bytes (bsize field + 1).
- */
-export declare function bgzBlockSize(data: ArrayBuffer | Uint8Array): number;
-/**
- * Decompress all concatenated BGZF blocks in a buffer.
- *
- * Returns array of decompressed blocks (one Uint8Array per BGZF block).
- * Optionally decompresses only blocks starting between startBlock and endBlock
- * (byte offsets relative to beginning of data buffer).
- *
- * Uses synchronous pako.inflateRaw() per block — no async overhead.
- * Matches igv.js inflateBlocks() which uses the same synchronous approach.
- *
- * Port of js/bam/bgzBlockLoader.ts inflateBlocks().
- */
-export declare function inflateBgzfBlocks(data: ArrayBuffer, startBlock?: number, endBlock?: number): Uint8Array[];
-/**
- * Decompress entire BGZF buffer into a single concatenated Uint8Array.
- * Used for decompressing .tbi index files.
- *
- * Port of igv-utils/bgzf.js unbgzf().
- */
-export declare function unbgzf(data: ArrayBuffer): Uint8Array;

package/dist/types/tabix/tabixIndex.d.ts

@@ -1,85 +0,0 @@
-/**
- * Tabix (.tbi) index parser and range query engine.
- *
- * Parses the binary .tbi format (a BGZF-compressed index for tab-delimited
- * genomic files) and provides efficient range queries via hierarchical binning.
- *
- * Port of js/bam/bamIndex.ts (tabix path) and js/bam/indexUtils.ts.
- * Layer 1 (Data + Layout): pure data, no DOM.
- */
-import type { VirtualOffset, Chunk } from './virtualOffset';
-/** Tabix format codes (from spec). */
-export declare const enum TabixFormat {
-    BED = 0,// 0-based half-open
-    SAM = 1,// 1-based
-    VCF = 2
-}
-/** Parsed tabix header metadata. */
-export interface TabixHeader {
-    /** Number of reference sequences. */
-    nref: number;
-    /** Format code: 0=BED, 1=SAM, 2=VCF/GFF. */
-    format: TabixFormat;
-    /** 1-based column index for sequence name. */
-    colSeq: number;
-    /** 1-based column index for start position. */
-    colBeg: number;
-    /** 1-based column index for end position (0 = compute from start). */
-    colEnd: number;
-    /** ASCII code of meta character (lines starting with this are skipped, e.g. 35='#'). */
-    meta: number;
-    /** Number of header lines to skip before data. */
-    skip: number;
-    /** Sequence names in index order. */
-    sequenceNames: string[];
-}
-interface BinIndex {
-    [binNumber: number]: Chunk[];
-}
-interface RefIndex {
-    binIndex: BinIndex;
-    linearIndex: (VirtualOffset | null)[];
-}
-/** Parsed tabix index with range query support. */
-export interface TabixIndex {
-    header: TabixHeader;
-    /** Map from sequence name to reference index (0-based). */
-    sequenceIndexMap: Record<string, number>;
-    /** Per-reference bin + linear indices. */
-    indices: (RefIndex | undefined)[];
-    /** Byte offset of first data block in the BGZF file. */
-    firstBlockPosition: number;
-    /** Byte offset of last data block in the BGZF file. */
-    lastBlockPosition: number;
-    /** Get chunks overlapping a genomic range. */
-    chunksForRange(refId: number, min: number, max: number): Chunk[];
-}
-/**
- * Parse a decompressed .tbi binary buffer into a TabixIndex.
- *
- * The .tbi file is BGZF-compressed; caller must decompress with unbgzf() first.
- * Binary format mirrors BAI but with an extra header for column metadata and
- * sequence names.
- *
- * Port of js/bam/bamIndex.ts BamIndex.parse() with tabix=true.
- */
-export declare function parseTabixIndex(data: ArrayBuffer): TabixIndex;
-/**
- * Calculate the list of bin ranges that overlap with region [beg, end).
- * Uses the standard 5-level hierarchical binning scheme (same as BAI).
- *
- * Returns array of [startBin, endBin] inclusive ranges.
- *
- * Port of js/bam/bamIndex.ts reg2bins().
- */
-export declare function reg2bins(beg: number, end: number): number[][];
-/**
- * Sort chunks by position, filter by linear index minimum, merge adjacent chunks.
- *
- * Merge criteria (from igv.js): gap between chunks < 65KB and total span < 5MB.
- * This reduces the number of HTTP range requests.
- *
- * Port of js/bam/indexUtils.ts optimizeChunks().
- */
-export declare function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset): Chunk[];
-export {};