@jbrowse/bandage-core 0.1.1

package/dist/types/types.d.ts

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+import type { GafRecord } from './gaf/parseGaf';
+import type { StableCoordinate } from './gfa-core/index';
+import type { TubeMapDrawing } from './layout/tubeMapLayout';
+export interface GraphNode {
+    id: string;
+    name: string;
+    length: number;
+    depth: number;
+    stable?: StableCoordinate;
+    samples?: string[];
+}
+export interface GraphEdge {
+    from: string;
+    to: string;
+    fromStrand?: '+' | '-';
+    toStrand?: '+' | '-';
+    pathIds?: string[];
+}
+export interface GraphPath {
+    name: string;
+    nodeIds: string[];
+    sample?: string;
+    haplotype?: number;
+    contig?: string;
+}
+export interface PathOrigin {
+    name: string;
+    sample: string;
+    start: number;
+    length: number;
+}
+export interface PathVisit {
+    path: string;
+    sample: string;
+    start: number;
+    strand: '+' | '-';
+}
+export interface Graph {
+    name: string;
+    nodes: GraphNode[];
+    edges: GraphEdge[];
+    paths?: GraphPath[];
+    anchorPaths?: PathOrigin[];
+    pathVisits?: Map<string, PathVisit[]>;
+    anchoredBy?: 'tags' | 'paths';
+    referencePath?: string;
+    reads?: GafRecord[];
+}
+export interface NodeSegment {
+    x: number;
+    y: number;
+}
+export interface RowLabel {
+    label: string;
+    y: number;
+}
+export interface AlleleDeletion {
+    nodeIds: string[];
+    bp: number;
+}
+export interface LayoutResult {
+    nodePositions: Record<string, NodeSegment[]>;
+    rowLabels?: RowLabel[];
+    sampleRows?: string[];
+    alleleDeletions?: AlleleDeletion[];
+    referenceAxis?: boolean;
+    pixelRows?: boolean;
+    extent?: {
+        minX?: number;
+        minY?: number;
+        maxX?: number;
+        maxY?: number;
+    };
+    tubeMap?: TubeMapDrawing;
+}

package/dist/types/util/SpatialIndex.d.ts

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+import type { Graph, NodeSegment } from '../types';
+import type { AxisScale } from './geometry';
+interface CellEntry {
+    nodeId: string;
+    segmentIdx: number;
+}
+export interface CellSize {
+    x: number;
+    y: number;
+}
+export declare class SpatialIndex {
+    private cellSize;
+    private cells;
+    constructor(nodePositions: Record<string, NodeSegment[]>, cellSize?: number | CellSize);
+    query(x: number, y: number, radiusX: number, radiusY?: number): CellEntry[];
+}
+export declare class EdgeSpatialIndex {
+    private cellSize;
+    private cells;
+    private edgeCurves;
+    constructor(nodePositions: Record<string, NodeSegment[]>, graph: Graph, drawPaths: boolean, axis: AxisScale, cellSize?: number | CellSize, deletions?: Map<number, string[]>, version?: number);
+    getCurves(ei: number): import("./geometry").BezierCurve[] | undefined;
+    query(x: number, y: number, radiusX: number, radiusY?: number): number[];
+}
+export {};

package/dist/types/util/edgeCurves.d.ts

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+import type { Graph, NodeSegment } from '../types';
+import type { AxisScale, BezierCurve } from './geometry';
+export type EdgeCurves = Map<number, BezierCurve[]>;
+export declare function baseEdgeCurves(nodePositions: Record<string, NodeSegment[]>, graph: Graph, axis: AxisScale, deletions: Map<number, string[]> | undefined, version: number): EdgeCurves;

package/dist/types/util/geometry.d.ts

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+import type { GraphEdge, NodeSegment } from '../types';
+export declare function svgPath(points: NodeSegment[]): string;
+export declare function projectLine(x1: number, y1: number, x2: number, y2: number, distance: number): [number, number];
+export interface BezierCurve {
+    x0: number;
+    y0: number;
+    cx0: number;
+    cy0: number;
+    cx1: number;
+    cy1: number;
+    x1: number;
+    y1: number;
+}
+export declare function curvePointAt(c: BezierCurve, t: number): {
+    x: number;
+    y: number;
+};
+export declare function curveMidpoint(curves: BezierCurve[]): {
+    x: number;
+    y: number;
+} | undefined;
+export declare function curveBounds(curves: BezierCurve[]): {
+    minX: number;
+    minY: number;
+    maxX: number;
+    maxY: number;
+};
+export declare function dashCurves(curves: BezierCurve[], dashWorld: number): BezierCurve[][];
+export declare function translateCurves(curves: BezierCurve[], dx: number, dy: number): BezierCurve[];
+type Side = 'start' | 'end';
+export declare function bowAround(p1x: number, p1y: number, p2x: number, p2y: number, toward: NodeSegment[], maxBow?: number): number;
+export interface AxisScale {
+    scaleX: number;
+    scaleY: number;
+    pixelRows?: boolean;
+}
+export declare function yToXOf({ scaleX, scaleY }: AxisScale): number;
+export declare const PATH_RIBBON_SPACING = 3;
+export declare function pathRibbonOffsets(fromSegments: NodeSegment[], toSegments: NodeSegment[], count: number, axis: AxisScale, spacing?: number): {
+    x: number;
+    y: number;
+}[];
+export type SelfLink = boolean | Side;
+export declare function selfLinkOf(edge: GraphEdge): SelfLink;
+export declare function computeEdgeCurves(fromSegments: NodeSegment[], toSegments: NodeSegment[], selfLink: SelfLink, offsetX: number, offsetY: number, axis: AxisScale, bypassed?: NodeSegment[], maxBowIn?: number): BezierCurve[];
+export {};

package/dist/types/util/hitDetection.d.ts

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+import type { Graph, NodeSegment } from '../types';
+import type { AxisScale } from './geometry';
+export declare function distanceToSegment(px: number, py: number, x1: number, y1: number, x2: number, y2: number): number;
+export declare function distanceToCubicBezier(px: number, py: number, x1: number, y1: number, cx1: number, cy1: number, cx2: number, cy2: number, x2: number, y2: number): number;
+export interface NodeInk {
+    halfWidthPx: (nodeId: string) => number;
+    maxHalfWidthPx: number;
+}
+export declare function findHoveredNode(nodePositions: Record<string, NodeSegment[]>, graphX: number, graphY: number, axis: AxisScale, version?: number, ink?: NodeInk): string | null;
+export declare function findHoveredEdge(nodePositions: Record<string, NodeSegment[]>, graph: Graph, graphX: number, graphY: number, axis: AxisScale, drawPaths: boolean, version?: number, deletions?: Map<number, string[]>, hiddenEdges?: ReadonlySet<number>): number | null;

package/dist/types/util/wheelZoom.d.ts

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+export declare function wheelZoomFactor(e: {
+    deltaY: number;
+    deltaMode: number;
+    ctrlKey: boolean;
+}): number;

package/dist/types/viewport.d.ts

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+import type { Bounds } from './pipeline';
+import type { AxisScale } from './util/geometry';
+export interface PaneTransform {
+    scale: number;
+    translateX: number;
+    translateY: number;
+}
+export declare function axisScaleOf(scale: number, pixelRows: boolean): AxisScale;
+export declare function viewportOf(t: {
+    translateX: number;
+    translateY: number;
+}, axis: AxisScale, width: number, height: number): Bounds;
+export declare function padded(v: Bounds, panes: number): Bounds;
+export declare function contains(outer: Bounds, inner: Bounds): boolean;
+export declare function zoomAbout(t: PaneTransform, factor: number, centerX: number, centerY: number, pixelRows: boolean): PaneTransform;
+export declare function screenToLayout(x: number, y: number, t: {
+    translateX: number;
+    translateY: number;
+}, axis: AxisScale): {
+    x: number;
+    y: number;
+};

package/dist/types/walkHighlight.d.ts

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+import type { Graph } from './types';
+export interface WalkHighlight {
+    name: string;
+    nodeIds: Set<string>;
+    edgeIndexes: Set<number>;
+    steps: number;
+    bp: number;
+    referenceBp?: number;
+}
+export declare function walkHighlight(graph: Graph, name: string): WalkHighlight | undefined;

package/package.json

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+{
+  "name": "@jbrowse/bandage-core",
+  "version": "0.1.1",
+  "description": "Pangenome graph layout and drawing with no host: GFA in, the Bandage force-directed engine and reference-anchored layouts, a Canvas2D renderer, hit testing and labels out",
+  "license": "GPL-3.0-or-later",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/GMOD/jbrowse-plugin-graphgenomeviewer.git",
+    "directory": "packages/core"
+  },
+  "keywords": [
+    "pangenome",
+    "graph",
+    "gfa",
+    "bandage"
+  ],
+  "type": "module",
+  "exports": {
+    ".": {
+      "types": "./dist/types/index.d.ts",
+      "default": "./dist/index.js"
+    }
+  },
+  "publishConfig": {
+    "access": "public"
+  },
+  "files": [
+    "dist"
+  ],
+  "dependencies": {
+    "@gmod/gbz-base": "^2.8.0",
+    "@gmod/tubemap-core": "^0.1.0",
+    "@jbrowse/core": "5.0.0-beta.9",
+    "@jbrowse/render-core": "5.0.0-beta.9"
+  },
+  "devDependencies": {
+    "esbuild": "^0.28.2",
+    "typescript": "^6.0.3"
+  },
+  "scripts": {
+    "build": "node build.mjs"
+  }
+}