loom-browser 0.0.1 → 0.0.3

package/dist/types/src/tracks/ruler/rulerTrackCanvas.d.ts

@@ -1,43 +0,0 @@
-/**
- * Canvas manager for rendering a genomic coordinate ruler.
- *
- * Extends BaseTrackCanvas — canvas lifecycle is handled by the base class.
- * This class only implements ruler-specific rendering.
- *
- * Usage:
- *   const canvas = document.createElement('canvas')
- *   const ruler = new RulerTrackCanvas(canvas, { locus })
- *   ruler.attachTo(containerDiv)
- */
-import type { Locus, RulerRenderConfig, RenderContext, RulerTrackSessionConfig } from '../../types';
-import type { CanvasProvider } from '../../canvasProvider';
-import type { RenderTheme } from '../../themes/renderTheme';
-import type { CumulativeOffsets, ChromSizes } from '../../genome/chromSizes';
-import { BaseTrackCanvas } from '../baseTrackCanvas';
-export interface RulerTrackCanvasOptions {
-    locus: Locus;
-    /** Per-track config overrides. Applied after theme-derived defaults. */
-    config?: Partial<RulerRenderConfig>;
-    /** Unified render theme. Palette drives default colors/fonts. */
-    theme?: Partial<RenderTheme>;
-    /** Canvas provider for environment abstraction. Default: DOMCanvasProvider. */
-    canvasProvider?: CanvasProvider;
-    /** Cumulative offsets for whole genome view. */
-    cumulativeOffsets?: CumulativeOffsets;
-    /** Chromosome sizes for whole genome view. */
-    chromSizes?: ChromSizes;
-}
-export declare class RulerTrackCanvas extends BaseTrackCanvas<RulerRenderConfig> {
-    readonly type = "ruler";
-    private _cumulativeOffsets?;
-    private _chromSizes?;
-    constructor(canvas: HTMLCanvasElement, options: RulerTrackCanvasOptions);
-    /** Set cumulative offsets for whole genome view (called by browser). */
-    setCumulativeOffsets(offsets: CumulativeOffsets): void;
-    /** Set chromosome sizes for whole genome view (called by browser). */
-    setChromSizes(sizes: ChromSizes): void;
-    protected computeHeight(_width: number): number;
-    protected getBackground(): string;
-    protected doRender(ctx: CanvasRenderingContext2D, _width: number, _height: number, rc: RenderContext): void;
-    serializeConfig(theme: RenderTheme): RulerTrackSessionConfig;
-}

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

@@ -1,5 +0,0 @@
-export { renderSequenceTrack } from './sequenceRenderer';
-export type { SequenceFeature } from './sequenceRenderer';
-export { SequenceTrackCanvas } from './sequenceTrackCanvas';
-export type { SequenceTrackCanvasOptions } from './sequenceTrackCanvas';
-export { modernSequenceTheme, darkSequenceTheme } from './sequenceThemes';

package/dist/types/src/tracks/sequence/sequenceRenderer.d.ts

@@ -1,34 +0,0 @@
-/**
- * Pure sequence track renderer — stateless, no DOM, no side effects.
- *
- * Layer 2 (Track Canvas + Themed Renderers): Takes a CanvasRenderingContext2D
- * and draws. All rendering decisions are driven by the config and render context.
- *
- * Port of js/sequenceTrack.ts draw() method with full feature parity:
- * - Base rendering as colored rectangles (zoomed out) or text (zoomed in)
- * - Reverse complement display
- * - Three-frame amino acid translation with START/STOP highlighting
- *
- * The BP_PER_PIXEL_THRESHOLD (1/10 = 0.1) controls text vs block rendering,
- * matching igv.js exactly.
- */
-import type { RenderContext, SequenceRenderConfig } from '../../types';
-/** Sequence data passed from the data lifecycle to the renderer. */
-export interface SequenceFeature {
-    /** Genomic position of the first base in the sequence string. */
-    bpStart: number;
-    /** The nucleotide sequence string. */
-    sequence: string;
-}
-/**
- * Render the sequence track onto a canvas context.
- *
- * Pure function — no state, no side effects, no DOM. Matches igv.js
- * SequenceTrack.draw() (js/sequenceTrack.ts) with exact feature parity.
- *
- * @param ctx - Canvas 2D rendering context (already DPR-scaled by BaseTrackCanvas)
- * @param seqFeature - The sequence data (bpStart + sequence string), or null if no data
- * @param config - Full resolved SequenceRenderConfig
- * @param rc - Render context (bpStart, bpPerPixel, pixelWidth)
- */
-export declare function renderSequenceTrack(ctx: CanvasRenderingContext2D, seqFeature: SequenceFeature | null, config: SequenceRenderConfig, rc: RenderContext): void;

package/dist/types/src/tracks/sequence/sequenceThemes.d.ts

@@ -1,11 +0,0 @@
-/**
- * Preset render themes for sequence tracks.
- *
- * Each theme is a Partial<SequenceRenderConfig> that can be spread over defaults.
- * Usage: resolveSequenceConfig(theme, modernSequenceTheme)
- */
-import type { SequenceRenderConfig } from '../../types';
-/** Modern theme — softer frame colors, solid text, rounded start/stop badges. */
-export declare const modernSequenceTheme: Partial<SequenceRenderConfig>;
-/** Dark theme — muted backgrounds, bright labels, high contrast on dark canvas. */
-export declare const darkSequenceTheme: Partial<SequenceRenderConfig>;

package/dist/types/src/tracks/sequence/sequenceTrackCanvas.d.ts

@@ -1,67 +0,0 @@
-/**
- * Sequence track canvas — extends BaseTrackCanvas for DNA/RNA sequence display.
- *
- * Layer 2 (Track Canvas): Manages canvas lifecycle, DPR scaling, config state,
- * and delegates rendering to the pure sequenceRenderer.
- *
- * Port of js/sequenceTrack.ts with full feature parity:
- * - DNA/RNA/protein sequence rendering
- * - Reverse complement toggle
- * - Three-frame amino acid translation toggle
- * - Dynamic height (25px default, 115px with translation)
- * - Context menu items (strand toggle, translation toggle)
- * - Visibility window enforcement (bpPerPixel threshold of 10)
- * - Session serialization
- *
- * Data is provided via the standard DataSource lifecycle — the browser fetches
- * sequence through a SequenceDataSource and pushes it via setFeatures().
- * Also supports direct setSequence() for standalone usage.
- */
-import { BaseTrackCanvas } from '../baseTrackCanvas';
-import type { Locus, RenderContext, SequenceRenderConfig, TrackSessionConfig, ContextMenuItem } from '../../types';
-import type { RenderTheme } from '../../themes/renderTheme';
-import type { SequenceFeature } from './sequenceRenderer';
-import type { CanvasProvider } from '../../canvasProvider';
-/** Options for constructing a SequenceTrackCanvas. */
-export interface SequenceTrackCanvasOptions {
-    locus: Locus;
-    config?: Partial<SequenceRenderConfig>;
-    theme?: Partial<RenderTheme>;
-    canvasProvider?: CanvasProvider;
-}
-export declare class SequenceTrackCanvas extends BaseTrackCanvas<SequenceRenderConfig> {
-    readonly type = "sequence";
-    private _sequence;
-    private _theme;
-    constructor(canvas: HTMLCanvasElement, options: SequenceTrackCanvasOptions);
-    /**
-     * Whether the current viewport is zoomed in enough to fetch/render sequence.
-     * Matches igv.js bppSequenceThreshold check in getFeatures().
-     */
-    shouldFetchSequence(bpPerPixel: number): boolean;
-    /**
-     * Standard DataSource lifecycle: browser pushes SequenceFeature[] from SequenceDataSource.
-     * Takes the first element (single sequence region) or clears if empty (zoomed out).
-     */
-    setFeatures(features: SequenceFeature[]): void;
-    /** Set the sequence data directly. For standalone usage without a DataSource. */
-    setSequence(feature: SequenceFeature | null): void;
-    /** Get the current sequence data (for context menu operations). */
-    getSequence(): SequenceFeature | null;
-    /** Toggle reverse complement display. */
-    toggleReversed(): void;
-    /** Toggle three-frame translation display. */
-    toggleFrameTranslate(): void;
-    /**
-     * Return context menu items for the sequence track.
-     *
-     * Matches igv.js SequenceTrack.menuItemList() + contextMenuItemList():
-     * - Strand toggle (Forward/Reverse)
-     * - Translation toggle (Three-frame Translate / Close Translation)
-     */
-    getContextMenuItems(_x: number, _y: number): ContextMenuItem[] | undefined;
-    protected computeHeight(_width: number): number;
-    protected getBackground(): string;
-    protected doRender(ctx: CanvasRenderingContext2D, _width: number, _height: number, rc: RenderContext): void;
-    serializeConfig(theme: RenderTheme): TrackSessionConfig;
-}

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

@@ -1,5 +0,0 @@
-export { renderWigTrack } from './wigRenderer';
-export { WigTrackCanvas } from './wigTrackCanvas';
-export type { WigTrackCanvasOptions } from './wigTrackCanvas';
-export { summarizeWigData, computeWigDataRange } from './wigSummary';
-export { modernWigTheme, darkWigTheme, warmWigTheme, lineWigTheme } from './wigThemes';

package/dist/types/src/tracks/wig/wigRenderer.d.ts

@@ -1,15 +0,0 @@
-/**
- * Standalone wig track renderer.
- *
- * Adapted from js/feature/wigTrack.ts draw() method with no `this` context —
- * all configuration is passed as explicit parameters.
- *
- * Supports four graph types: bar, line, points, and dynseq.
- */
-import type { WigFeature, WigRenderConfig, RenderContext } from '../../types';
-/**
- * Render wig features onto a canvas context.
- *
- * The canvas should be sized and cleared before calling this.
- */
-export declare function renderWigTrack(ctx: CanvasRenderingContext2D, features: WigFeature[], config: WigRenderConfig, rc: RenderContext): void;

package/dist/types/src/tracks/wig/wigSummary.d.ts

@@ -1,31 +0,0 @@
-/**
- * Resolution-aware data summarization for wig tracks.
- *
- * When zoomed out, many data points map to the same pixel. This module bins
- * features and applies a window function (mean, min, max) to produce one
- * summary value per pixel-width bin.
- *
- * Ported from js/feature/wigSummary.ts with strict types, no `any`.
- */
-import type { WigFeature, WindowFunction } from '../../types';
-/**
- * Summarize wig features by binning into pixel-width windows and applying
- * a window function.
- *
- * Features must be sorted by position. Wig features cannot overlap.
- *
- * @param features - sorted array of wig features
- * @param startBP - start position in base pairs (left edge of viewport)
- * @param bpPerPixel - base pairs per pixel (bin size)
- * @param windowFunction - aggregation function: mean, min, max, or none
- * @returns summarized features (one per pixel-bin)
- */
-export declare function summarizeWigData(features: WigFeature[], startBP: number, bpPerPixel: number, windowFunction?: WindowFunction): WigFeature[];
-/**
- * Compute the min/max data range from a set of wig features.
- * Useful for autoscaling.
- */
-export declare function computeWigDataRange(features: WigFeature[]): {
-    min: number;
-    max: number;
-};

package/dist/types/src/tracks/wig/wigThemes.d.ts

@@ -1,15 +0,0 @@
-/**
- * Preset render themes for wig tracks.
- *
- * Each theme is a Partial<WigRenderConfig> that can be spread over defaults.
- * Usage: { ...defaultWigRenderConfig(), ...modernWigTheme }
- */
-import type { WigRenderConfig } from '../../types';
-/** Modern theme — blue bars with subtle styling. */
-export declare const modernWigTheme: Partial<WigRenderConfig>;
-/** Dark theme — bright teal on dark background. */
-export declare const darkWigTheme: Partial<WigRenderConfig>;
-/** Warm red theme — for coverage or signal intensity. */
-export declare const warmWigTheme: Partial<WigRenderConfig>;
-/** Line graph variant — modern blue line. */
-export declare const lineWigTheme: Partial<WigRenderConfig>;

package/dist/types/src/tracks/wig/wigTrackCanvas.d.ts

@@ -1,82 +0,0 @@
-/**
- * Canvas manager for rendering wig (wiggle) tracks.
- *
- * Extends BaseTrackCanvas — canvas lifecycle is handled by the base class.
- * This class implements wig-specific logic: value scaling, autoscale,
- * and rendering delegation.
- *
- * Data summarization (pixel-width binning) is handled at the data source
- * layer by BigWigDataSource, not here. This keeps the render layer
- * focused on rendering and lets headless consumers benefit from
- * pre-summarized data.
- *
- * For dynseq mode, an optional `sequenceProvider` can be passed at construction.
- * When in dynseq mode, the track automatically fetches and attaches DNA sequence
- * to features at high zoom (bpPerPixel < 2). This matches the igv.js pattern
- * where sequence is fetched during getFeatures(), not during rendering.
- *
- * Usage:
- *   const canvas = document.createElement('canvas')
- *   const track = new WigTrackCanvas(canvas, { locus, features })
- *   track.attachTo(containerDiv)
- */
-import type { WigFeature, WigRenderConfig, WindowFunction, Locus, RenderContext, WigTrackSessionConfig, HitTestResult, AxisInfo, ContextMenuItem, NumericState, SequenceProvider } from '../../types';
-import type { CanvasProvider } from '../../canvasProvider';
-import type { RenderTheme } from '../../themes/renderTheme';
-import { BaseTrackCanvas } from '../baseTrackCanvas';
-export interface WigTrackCanvasOptions {
-    locus: Locus;
-    features: WigFeature[];
-    /** Per-track config overrides. Applied after theme-derived defaults. */
-    config?: Partial<WigRenderConfig>;
-    /** Unified render theme. Palette drives default colors/fonts. */
-    theme?: Partial<RenderTheme>;
-    /** Fixed pixel height. If not set, uses config.height (default 50). */
-    height?: number;
-    /** Background color. Overrides palette.background if set. */
-    background?: string;
-    /** Canvas provider for environment abstraction. Default: DOMCanvasProvider. */
-    canvasProvider?: CanvasProvider;
-    /** Track name for axis label. */
-    name?: string;
-    /** Sequence provider for dynseq rendering. When set, dynseq appears in the graph type menu. */
-    sequenceProvider?: SequenceProvider;
-}
-export declare class WigTrackCanvas extends BaseTrackCanvas<WigRenderConfig> {
-    private features;
-    private fixedHeight;
-    private _name;
-    private _lastDataRange;
-    private _sequenceProvider;
-    /** Abort controller for in-flight sequence fetch. */
-    private _seqAbort;
-    /** Callback invoked when the user changes the windowing function via context menu. */
-    private _onWindowFunctionChange?;
-    readonly type = "wig";
-    constructor(canvas: HTMLCanvasElement, options: WigTrackCanvasOptions);
-    /** Set a callback invoked when the user changes the windowing function via context menu. */
-    set onWindowFunctionChange(cb: ((wf: WindowFunction) => void) | undefined);
-    /** Update features and re-render. Recomputes autoscale if enabled. */
-    setFeatures(features: WigFeature[]): void;
-    /** Update locus and re-render. Re-fetches sequence in dynseq mode. */
-    setLocus(locus: Locus): void;
-    /** Merge partial config and re-render. Triggers sequence fetch when switching to dynseq. */
-    setConfig(config: Partial<WigRenderConfig>): void;
-    /**
-     * Fetch DNA sequence for current features and re-render.
-     * At low zoom (bpPerPixel >= 2), skips fetch — the renderer falls back to bars.
-     */
-    private augmentWithSequence;
-    protected computeHeight(_width: number): number;
-    protected getBackground(): string;
-    protected doRender(ctx: CanvasRenderingContext2D, _width: number, height: number, rc: RenderContext): void;
-    getAxisInfo(): AxisInfo | undefined;
-    getContextMenuItems(_x: number, _y: number): ContextMenuItem[];
-    /**
-     * Return numeric state for shared menu items (autoscale, log scale, set data range).
-     * The browser calls numericDataMenuItems() with this state when assembling context menus.
-     */
-    getNumericState(): NumericState;
-    hitTest(x: number, _y: number): HitTestResult<WigFeature>[];
-    serializeConfig(theme: RenderTheme): WigTrackSessionConfig;
-}