loom-browser 0.0.4 → 0.0.6

package/dist/types/dataSources/memoryDataSource.d.ts

@@ -0,0 +1,32 @@
+/**
+ * DataSource backed by an in-memory feature array.
+ *
+ * Wraps a pre-loaded feature array in a FeatureCache for spatial queries,
+ * enabling inline features to flow through the same data lifecycle as
+ * URL-based data sources.
+ *
+ * Layer 1 (Data + Layout): no DOM, no canvas.
+ */
+import type { DataSource, Locus } from '../types';
+import type { CacheableFeature } from '../featureCache';
+import type { CumulativeOffsets } from '../genome/chromSizes';
+/**
+ * DataSource that serves features from an in-memory array.
+ *
+ * Features are indexed in a FeatureCache on construction for efficient
+ * spatial queries. Calling `setFeatures()` replaces the cache entirely.
+ */
+export declare class MemoryDataSource<F extends CacheableFeature = CacheableFeature> implements DataSource<F> {
+    private cache;
+    private _resolveChromName?;
+    private _cumulativeOffsets?;
+    constructor(features: F[]);
+    /** Replace the in-memory features and rebuild the spatial index. */
+    setFeatures(features: F[]): void;
+    /** Set a chromosome name resolver for alias resolution. */
+    setChromNameResolver(resolver: (chr: string) => string): void;
+    /** Set cumulative offsets for whole genome view coordinate transformation. */
+    setCumulativeOffsets(offsets: CumulativeOffsets): void;
+    fetch(locus: Locus, _bpPerPixel: number, _signal: AbortSignal): Promise<F[]>;
+    private fetchWG;
+}

package/dist/types/headlessGenomeBrowser.d.ts

@@ -16,7 +16,7 @@
  *   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 type { Locus, Track, DataSource, FeatureCacheEntry, SessionConfig, TrackSessionConfig, DataSourceConfig, TrackInteractionEvent, TrackContextMenuEvent, WindowFunction, WigFeature, AnnotationFeature, 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';
@@ -231,6 +231,32 @@ export interface AddAnnotationTrackOptions {
     /** Arbitrary key-value metadata (e.g., assay, biosample, tissue). */
     metadata?: Record<string, string>;
 }
+export interface AddWigTrackWithFeaturesOptions {
+    config?: Partial<WigRenderConfig>;
+    /** Fixed pixel height (overrides config.height). */
+    height?: number;
+    /** Background color. */
+    background?: string;
+    /** 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 AddBedTrackWithFeaturesOptions {
+    config?: Partial<AnnotationRenderConfig>;
+    /** Fixed pixel height. */
+    height?: number;
+    /** Background color. */
+    background?: string;
+    /** 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 declare class HeadlessGenomeBrowser {
     protected _locus: Locus;
     protected _viewportWidth: number;
@@ -434,6 +460,12 @@ export declare class HeadlessGenomeBrowser {
     addBedTrack(url: string, options?: AddBedTrackOptions): AnnotationTrackCanvas;
     /** Add an interaction (arc/BEDPE) track from a URL. */
     addInteractionTrack(url: string, options?: AddInteractionTrackOptions): InteractionTrackCanvas;
+    /** Add a BigWig-style signal track backed by in-memory features (no URL required). */
+    addWigTrackWithFeatures(features: WigFeature[], options?: AddWigTrackWithFeaturesOptions): WigTrackCanvas;
+    /** Add a BED/annotation track backed by in-memory features (no URL required). Features must include `chr`. */
+    addBedTrackWithFeatures(features: (AnnotationFeature & {
+        chr: string;
+    })[], options?: AddBedTrackWithFeaturesOptions): AnnotationTrackCanvas;
     /** Add a DNA/RNA sequence track. Data fetching is handled automatically via the genome's sequence provider. */
     addSequenceTrack(options?: AddSequenceTrackOptions): SequenceTrackCanvas;
     /** Apply a new render theme to the browser and all existing tracks. */

package/dist/types/index.d.ts

@@ -19,7 +19,7 @@ export type { InteractionFeature, InteractionRenderConfig, ArcOrientation, ArcDi
 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 type { SessionConfig, TrackSessionConfig, WigTrackSessionConfig, AnnotationTrackSessionConfig, RulerTrackSessionConfig, WigSessionOverrides, AnnotationSessionOverrides, RulerSessionOverrides, DataSourceConfig, BigWigDataSourceConfig, GtxDataSourceConfig, UCSCDataSourceConfig, TextDataSourceConfig, MemoryDataSourceConfig, 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';
@@ -36,7 +36,7 @@ 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 type { HeadlessGenomeBrowserOptions, ManagedTrack, AddRulerOptions, AddWigTrackOptions, AddGtxTrackOptions, AddBedTrackOptions, AddAnnotationTrackOptions, AddInteractionTrackOptions, AddSequenceTrackOptions, AddWigTrackWithFeaturesOptions, AddBedTrackWithFeaturesOptions } from './headlessGenomeBrowser';
 export { GenomeBrowser } from './genomeBrowser';
 export type { GenomeBrowserOptions, BrowserEvents } from './genomeBrowser';
 export type { ChromSizes, CumulativeOffsets } from './genome/chromSizes';
@@ -92,6 +92,7 @@ export { GeneDataSource } from './dataSources/geneDataSource';
 export { TextFeatureSource } from './dataSources/textFeatureSource';
 export type { TextFeatureSourceConfig } from './dataSources/textFeatureSource';
 export { SequenceDataSource } from './dataSources/sequenceDataSource';
+export { MemoryDataSource } from './dataSources/memoryDataSource';
 export { createFeatureSource } from './dataSources/featureSourceFactory';
 export type { FeatureSourceConfig, FeatureSourceResult } from './dataSources/featureSourceFactory';
 export { dataSourceCacheKey } from './dataSources/dataSourceCacheKey';

package/dist/types/react/GenomeBrowserContext.d.ts

@@ -1,6 +1,9 @@
 import type { GenomeBrowser } from '../genomeBrowser';
+import type { ShellTheme } from '../ui/themes';
 export interface GenomeBrowserContextValue {
     /** The underlying GenomeBrowser instance. null before initialization or during SSR. */
     browser: GenomeBrowser | null;
+    /** Inferred shell theme for UI components. */
+    shellTheme: ShellTheme;
 }
 export declare const GenomeBrowserContext: import("react").Context<GenomeBrowserContextValue | null>;

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

@@ -3,5 +3,7 @@ export type { LoomBrowserProps, LoomBrowserHandle } from './LoomBrowser';
 export { useGenomeBrowser, useBrowserEvent, useLocus } from './hooks';
 export { RulerTrack, WigTrack, GeneTrack, BedTrack, SequenceTrack, InteractionTrack, GtxTrack, } from './tracks';
 export type { RulerTrackProps, WigTrackProps, GeneTrackProps, BedTrackProps, SequenceTrackProps, InteractionTrackProps, GtxTrackProps, } from './tracks';
+export { ChromosomeSelect, LocusInput, ZoomControls, WindowSize, ExportControls, Navbar, } from './ui';
+export type { ChromosomeSelectProps, LocusInputProps, ZoomControlsProps, WindowSizeProps, ExportControlsProps, NavbarProps, } from './ui';
 export { GenomeBrowserContext } from './GenomeBrowserContext';
 export type { GenomeBrowserContextValue } from './GenomeBrowserContext';

package/dist/types/react/tracks/BedTrack.d.ts

@@ -1,6 +1,11 @@
-import type { AnnotationRenderConfig, TextFileFormat } from '../../types';
+import type { AnnotationFeature, AnnotationRenderConfig, TextFileFormat } from '../../types';
 export interface BedTrackProps {
-    url: string;
+    /** URL to a BED/peak file. Mutually exclusive with `features`. */
+    url?: string;
+    /** In-memory annotation features. Mutually exclusive with `url`. Features must include `chr`. */
+    features?: (AnnotationFeature & {
+        chr: string;
+    })[];
     config?: Partial<AnnotationRenderConfig>;
     height?: number;
     background?: string;
@@ -11,4 +16,4 @@ export interface BedTrackProps {
     name?: string;
     metadata?: Record<string, string>;
 }
-export declare function BedTrack({ url, config, height, background, format, indexURL, indexed, maxTrackHeight, name, metadata }: BedTrackProps): null;
+export declare function BedTrack({ url, features, config, height, background, format, indexURL, indexed, maxTrackHeight, name, metadata }: BedTrackProps): null;

package/dist/types/react/tracks/WigTrack.d.ts

@@ -1,6 +1,9 @@
-import type { WigRenderConfig, WindowFunction } from '../../types';
+import type { WigFeature, WigRenderConfig, WindowFunction } from '../../types';
 export interface WigTrackProps {
-    url: string;
+    /** URL to a BigWig file. Mutually exclusive with `features`. */
+    url?: string;
+    /** In-memory wig features. Mutually exclusive with `url`. */
+    features?: WigFeature[];
     config?: Partial<WigRenderConfig>;
     height?: number;
     background?: string;
@@ -9,4 +12,4 @@ export interface WigTrackProps {
     name?: string;
     metadata?: Record<string, string>;
 }
-export declare function WigTrack({ url, config, height, background, windowFunction, maxTrackHeight, name, metadata }: WigTrackProps): null;
+export declare function WigTrack({ url, features, config, height, background, windowFunction, maxTrackHeight, name, metadata }: WigTrackProps): null;

package/dist/types/react/ui/ChromosomeSelect.d.ts

@@ -0,0 +1,7 @@
+import type { GenomeBrowser } from '../../genomeBrowser';
+import './types';
+export interface ChromosomeSelectProps {
+    /** Override the browser from context. */
+    browser?: GenomeBrowser | null;
+}
+export declare function ChromosomeSelect({ browser: browserProp }: ChromosomeSelectProps): import("react/jsx-runtime").JSX.Element;

package/dist/types/react/ui/ExportControls.d.ts

@@ -0,0 +1,7 @@
+import type { GenomeBrowser } from '../../genomeBrowser';
+import './types';
+export interface ExportControlsProps {
+    /** Override the browser from context. */
+    browser?: GenomeBrowser | null;
+}
+export declare function ExportControls({ browser: browserProp }: ExportControlsProps): import("react/jsx-runtime").JSX.Element;

package/dist/types/react/ui/LocusInput.d.ts

@@ -0,0 +1,7 @@
+import type { GenomeBrowser } from '../../genomeBrowser';
+import './types';
+export interface LocusInputProps {
+    /** Override the browser from context. */
+    browser?: GenomeBrowser | null;
+}
+export declare function LocusInput({ browser: browserProp }: LocusInputProps): import("react/jsx-runtime").JSX.Element;

package/dist/types/react/ui/Navbar.d.ts

@@ -0,0 +1,10 @@
+import type { GenomeBrowser } from '../../genomeBrowser';
+import type { ShellTheme } from '../../ui/themes';
+import './types';
+export interface NavbarProps {
+    /** Override the browser from context. */
+    browser?: GenomeBrowser | null;
+    /** Override the shell theme. By default, inferred from the parent LoomBrowser's render theme. */
+    theme?: ShellTheme;
+}
+export declare function Navbar({ browser: browserProp, theme: themeProp }: NavbarProps): import("react/jsx-runtime").JSX.Element;

package/dist/types/react/ui/WindowSize.d.ts

@@ -0,0 +1,7 @@
+import type { GenomeBrowser } from '../../genomeBrowser';
+import './types';
+export interface WindowSizeProps {
+    /** Override the browser from context. */
+    browser?: GenomeBrowser | null;
+}
+export declare function WindowSize({ browser: browserProp }: WindowSizeProps): import("react/jsx-runtime").JSX.Element;

package/dist/types/react/ui/ZoomControls.d.ts

@@ -0,0 +1,7 @@
+import type { GenomeBrowser } from '../../genomeBrowser';
+import './types';
+export interface ZoomControlsProps {
+    /** Override the browser from context. */
+    browser?: GenomeBrowser | null;
+}
+export declare function ZoomControls({ browser: browserProp }: ZoomControlsProps): import("react/jsx-runtime").JSX.Element;

package/dist/types/react/ui/ensureRegistered.d.ts

@@ -0,0 +1,5 @@
+/**
+ * Ensures all Loom UI web components are registered as custom elements.
+ * Safe to call multiple times — each element is only registered once.
+ */
+export declare function ensureRegistered(): void;

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

@@ -0,0 +1,12 @@
+export { ChromosomeSelect } from './ChromosomeSelect';
+export type { ChromosomeSelectProps } from './ChromosomeSelect';
+export { LocusInput } from './LocusInput';
+export type { LocusInputProps } from './LocusInput';
+export { ZoomControls } from './ZoomControls';
+export type { ZoomControlsProps } from './ZoomControls';
+export { WindowSize } from './WindowSize';
+export type { WindowSizeProps } from './WindowSize';
+export { ExportControls } from './ExportControls';
+export type { ExportControlsProps } from './ExportControls';
+export { Navbar } from './Navbar';
+export type { NavbarProps } from './Navbar';

package/dist/types/react/ui/types.d.ts

@@ -0,0 +1,24 @@
+/**
+ * JSX IntrinsicElements augmentation for Loom web components.
+ * This lets TypeScript accept <loom-*> elements in JSX without errors.
+ */
+import type { LoomChromosomeSelect } from '../../ui/components/LoomChromosomeSelect';
+import type { LoomLocusInput } from '../../ui/components/LoomLocusInput';
+import type { LoomZoomControls } from '../../ui/components/LoomZoomControls';
+import type { LoomWindowSize } from '../../ui/components/LoomWindowSize';
+import type { LoomExportControls } from '../../ui/components/LoomExportControls';
+import type { LoomNavbar } from '../../ui/components/LoomNavbar';
+type WebComponentProps<T> = React.DetailedHTMLProps<React.HTMLAttributes<T>, T>;
+declare module 'react' {
+    namespace JSX {
+        interface IntrinsicElements {
+            'loom-chromosome-select': WebComponentProps<LoomChromosomeSelect>;
+            'loom-locus-input': WebComponentProps<LoomLocusInput>;
+            'loom-zoom-controls': WebComponentProps<LoomZoomControls>;
+            'loom-window-size': WebComponentProps<LoomWindowSize>;
+            'loom-export-controls': WebComponentProps<LoomExportControls>;
+            'loom-navbar': WebComponentProps<LoomNavbar>;
+        }
+    }
+}
+export {};

package/dist/types/types.d.ts

@@ -736,7 +736,7 @@ export type SequenceSessionOverrides = Partial<SequenceRenderConfig>;
 /** Serializable subset of InteractionRenderConfig (all fields are already serializable). */
 export type InteractionSessionOverrides = Partial<InteractionRenderConfig>;
 /** Discriminated union for data source reconstruction. */
-export type DataSourceConfig = BigWigDataSourceConfig | GtxDataSourceConfig | UCSCDataSourceConfig | TextDataSourceConfig;
+export type DataSourceConfig = BigWigDataSourceConfig | GtxDataSourceConfig | UCSCDataSourceConfig | TextDataSourceConfig | MemoryDataSourceConfig;
 export interface BigWigDataSourceConfig {
     type: 'bigwig';
     url: string;
@@ -763,6 +763,9 @@ export interface TextDataSourceConfig {
     /** 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. */

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "loom-browser",
-  "version": "0.0.4",
+  "version": "0.0.6",
   "main": "dist/loom.esm.js",
   "module": "dist/loom.esm.js",
   "types": "dist/types/index.d.ts",