@jbrowse/bandage-core 10.2.2 → 10.2.4

package/dist/types/index.d.ts

@@ -102,5 +102,5 @@ export { PathVisits, PathVisitsBuilder } from './pathVisits.js';
 export { engineKey } from './pipeline.js';
 export { axisScaleOf, contains, padded, screenToLayout, viewportOf, zoomAbout, } from './viewport.js';
 export type { PaneTransform } from './viewport.js';
-export { default as loadBandage } from './loadBandage.js';
+export { loadFmmm as loadBandage } from '@jbrowse/graph-fmmm-layout';
 export { panSNContig, panSNHaplotype, panSNSample } from './pansn.js';

package/dist/types/labelLayout.d.ts

@@ -1,4 +1,4 @@
-import type { BubbleHalo, RouteLabel } from './bubbles/bubbleHalos.js';
+import type { BubbleHalo } from './bubbles/bubbleHalos.js';
 import type { DeletionEdge } from './deletionEdges.js';
 import type { GenePin } from './genes/genePins.js';
 import type { GraphLabel } from './graphLabels.js';
@@ -47,10 +47,6 @@ export interface LabelLayout {
     bubbles: PlacedLabel<BubbleHalo>[];
     ticks: BubbleTick[];
     genes: PlacedLabel<GenePin>[];
-    routes: PlacedLabel<{
-        halo: BubbleHalo;
-        route: RouteLabel;
-    }>[];
     sizes: GraphLabel[];
 }
 export declare function geneCoverageNote(pin: GenePin): string | undefined;

package/dist/types/layout/deletionRoutes.d.ts

@@ -2,7 +2,7 @@ import type { BandageScaleOpts } from './drawnScale.js';
 import type { DeletionEdge } from '../deletionEdges.js';
 import type { Graph, GraphEdge, GraphNode, NodeSegment } from '../types.js';
 export type DeletionRoutes = Record<number, NodeSegment[]>;
-export declare function withDeletionRoutes(graph: Graph, deletions: DeletionEdge[], dropped?: Set<number>): {
+export declare function withDeletionRoutes(graph: Graph, deletions: DeletionEdge[], dropped?: ReadonlySet<number>): {
     graph: {
         nodes: {
             id: string;

package/dist/types/layout/orderedLayout.d.ts

@@ -1,9 +1,3 @@
 import type { Graph, LayoutResult } from '../types.js';
 export declare function referenceOrder(graph: Graph): string[];
-export interface LayeredGraph {
-    layers: string[][];
-    layerOf: Map<string, number>;
-    preds: Map<string, string[]>;
-}
-export declare function layerGraph(graph: Graph): LayeredGraph;
 export declare function orderedLayout(graph: Graph): LayoutResult | undefined;

package/dist/types/layout/walkRowLayout.d.ts

@@ -1,6 +1,7 @@
 import type { RowPitch } from './walkRowDraw.js';
 import type { WalkRows } from './walkRows.js';
 import type { Graph, LayoutResult, RowLabel } from '../types.js';
+export declare const READOUT_ROOM = 1.3;
 export declare function walkRowsExtent(walks: WalkRows, pitch?: Pick<RowPitch, 'rowPx' | 'readouts'>): {
     maxX: number;
     maxY: number;

package/dist/types/nodeWidths.d.ts

@@ -10,7 +10,6 @@ export declare const NODE_WIDTHS: readonly [{
     readonly description: "Every node the same thickness.";
 }];
 export type NodeWidth = (typeof NODE_WIDTHS)[number]['value'];
-export declare const NODE_WIDTH_VALUES: ("depth" | "uniform")[];
 export declare function meanDepth(graph: Graph): number;
 export declare function depthWidthFactor(node: GraphNode, mean: number): number;
 export declare function nodeWidthPx(node: GraphNode, contigThickness: number, nodeWidth: NodeWidth, mean: number): number;

package/dist/types/renderer/Canvas2DRenderer.d.ts

@@ -7,6 +7,7 @@ export declare class Canvas2DRenderer implements Renderer {
     private nodeHighlights;
     private highlightedEdge;
     private highlightFactor;
+    private fit;
     constructor(canvas: HTMLCanvasElement);
     setErrorHandler(_handler: (error: Error) => void): void;
     releaseOffscreenTargets(): void;

package/dist/types/renderer/canvas.d.ts

@@ -1,4 +1,4 @@
 export declare const MAX_DPR = 2;
 export declare const MAX_CANVAS_DIM_PX = 8192;
-export declare function getDpr(): number;
-export declare function syncCanvasSize(canvas: HTMLCanvasElement, width: number, height: number): void;
+export declare function getDpr(width?: number, height?: number): number;
+export declare function syncCanvasSize(canvas: HTMLCanvasElement, width: number, height: number): number;

package/dist/types/tubeMap/draw.d.ts

@@ -44,6 +44,7 @@ interface Rect extends Filled {
 }
 interface Shape extends Filled {
     commands: Command[];
+    outline: [number, number][];
 }
 interface Layer {
     rects: Rect[];

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

@@ -41,8 +41,8 @@ export interface AxisScale {
     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): {
+export declare const PATH_RIBBON_SPACING_PX = 3;
+export declare function pathRibbonOffsets(fromSegments: NodeSegment[], toSegments: NodeSegment[], count: number, axis: AxisScale): {
     x: number;
     y: number;
 }[];
@@ -50,6 +50,6 @@ export type SelfLink = boolean | Side;
 export declare function selfLinkOf(edge: GraphEdge): SelfLink;
 export type EdgeJoin = SelfLink | EdgeSides;
 export declare function edgeJoinOf(edge: GraphEdge, stranded?: boolean): EdgeJoin;
-export declare function computeEdgeCurves(fromSegments: NodeSegment[], toSegments: NodeSegment[], join: EdgeJoin, offsetX: number, offsetY: number, axis: AxisScale, bypassed?: NodeSegment[], maxBowIn?: number): BezierCurve[];
+export declare function computeEdgeCurves(fromSegments: NodeSegment[], toSegments: NodeSegment[], join: EdgeJoin, axis: AxisScale, bypassed?: NodeSegment[], maxBowIn?: number): BezierCurve[];
 export declare function routedEdgeCurves(fromSegments: NodeSegment[], toSegments: NodeSegment[], route: NodeSegment[], sides?: EdgeSides): BezierCurve[];
 export {};

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "10.2.2";
+export declare const version = "10.2.4";

package/dist/util/SpatialIndex.js

@@ -1,10 +1,10 @@
 import {
   EdgeSpatialIndex,
   SpatialIndex
-} from "../chunks/chunk-MLSWIMZO.js";
-import "../chunks/chunk-WFB5TXRA.js";
-import "../chunks/chunk-N6FECAXP.js";
-import "../chunks/chunk-2CVHXFK7.js";
+} from "../chunks/chunk-KBEP7VYK.js";
+import "../chunks/chunk-ZY2AFL4Y.js";
+import "../chunks/chunk-24WITXQY.js";
+import "../chunks/chunk-7SRWJLSC.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {

package/dist/util/edgeCurves.js

@@ -1,8 +1,8 @@
 import {
   baseEdgeCurves
-} from "../chunks/chunk-WFB5TXRA.js";
-import "../chunks/chunk-N6FECAXP.js";
-import "../chunks/chunk-2CVHXFK7.js";
+} from "../chunks/chunk-ZY2AFL4Y.js";
+import "../chunks/chunk-24WITXQY.js";
+import "../chunks/chunk-7SRWJLSC.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {

package/dist/util/geometry.js

@@ -1,5 +1,5 @@
 import {
-  PATH_RIBBON_SPACING,
+  PATH_RIBBON_SPACING_PX,
   bowAround,
   computeEdgeCurves,
   curveBounds,
@@ -16,10 +16,10 @@ import {
   svgPath,
   translateCurves,
   yToXOf
-} from "../chunks/chunk-2CVHXFK7.js";
+} from "../chunks/chunk-7SRWJLSC.js";
 import "../chunks/chunk-CPMHA4W5.js";
 export {
-  PATH_RIBBON_SPACING,
+  PATH_RIBBON_SPACING_PX,
   bowAround,
   computeEdgeCurves,
   curveBounds,

package/dist/util/hitDetection.js

@@ -4,11 +4,11 @@ import {
   findHoveredEdge,
   findHoveredNode,
   nodesUnderBox
-} from "../chunks/chunk-FP4H7SFT.js";
-import "../chunks/chunk-MLSWIMZO.js";
-import "../chunks/chunk-WFB5TXRA.js";
-import "../chunks/chunk-N6FECAXP.js";
-import "../chunks/chunk-2CVHXFK7.js";
+} from "../chunks/chunk-4HWM3FNK.js";
+import "../chunks/chunk-KBEP7VYK.js";
+import "../chunks/chunk-ZY2AFL4Y.js";
+import "../chunks/chunk-24WITXQY.js";
+import "../chunks/chunk-7SRWJLSC.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-EYK7DJZV.js";
+} from "./chunks/chunk-2CHS5LMM.js";
 export {
   version
 };

package/dist/viewport.js

@@ -5,26 +5,26 @@ import {
   screenToLayout,
   viewportOf,
   zoomAbout
-} from "./chunks/chunk-L5WF4ZPS.js";
-import "./chunks/chunk-XTCNEKO5.js";
+} from "./chunks/chunk-BS4UZ44I.js";
+import "./chunks/chunk-2QLLQJ72.js";
+import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-OPPVSPEF.js";
 import "./chunks/chunk-VPE4AYP7.js";
-import "./chunks/chunk-PUG7LXDF.js";
-import "./chunks/chunk-IW6CYVX2.js";
+import "./chunks/chunk-AR4BUBMU.js";
 import "./chunks/chunk-QYBZZI5H.js";
+import "./chunks/chunk-5I3K4R2G.js";
 import "./chunks/chunk-PSMKPSO4.js";
-import "./chunks/chunk-CDLPYR5O.js";
 import "./chunks/chunk-M6LK4GII.js";
 import "./chunks/chunk-RAEABQNW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-G45YY72K.js";
 import "./chunks/chunk-BPLIXMH7.js";
-import "./chunks/chunk-TAMCZHLW.js";
+import "./chunks/chunk-N73TI3VG.js";
 import "./chunks/chunk-UVBGRJQX.js";
 import "./chunks/chunk-6JEWNXCQ.js";
-import "./chunks/chunk-N6FECAXP.js";
-import "./chunks/chunk-2CVHXFK7.js";
+import "./chunks/chunk-24WITXQY.js";
+import "./chunks/chunk-7SRWJLSC.js";
 import "./chunks/chunk-CPMHA4W5.js";
 import "./chunks/chunk-FYQWPEEY.js";
 export {

package/dist/walkEncoding.js

@@ -9,21 +9,21 @@ import {
   schemeColor,
   schemeCss,
   schemeRgb
-} from "./chunks/chunk-ALDGONEI.js";
-import "./chunks/chunk-SBMJNRTV.js";
+} from "./chunks/chunk-VQC7KELB.js";
+import "./chunks/chunk-A4PFFC4Q.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-WFB5TXRA.js";
-import "./chunks/chunk-TWRLC3KK.js";
-import "./chunks/chunk-PBENCR5L.js";
+import "./chunks/chunk-ZY2AFL4Y.js";
+import "./chunks/chunk-3XSM4OZU.js";
+import "./chunks/chunk-JBCZIBFC.js";
 import "./chunks/chunk-M6LK4GII.js";
 import "./chunks/chunk-RAEABQNW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-BPLIXMH7.js";
-import "./chunks/chunk-3ZZSX5HN.js";
+import "./chunks/chunk-PTABFYQ7.js";
 import "./chunks/chunk-AB35TJST.js";
-import "./chunks/chunk-TAMCZHLW.js";
-import "./chunks/chunk-N6FECAXP.js";
-import "./chunks/chunk-2CVHXFK7.js";
+import "./chunks/chunk-N73TI3VG.js";
+import "./chunks/chunk-24WITXQY.js";
+import "./chunks/chunk-7SRWJLSC.js";
 import "./chunks/chunk-CPMHA4W5.js";
 import "./chunks/chunk-FYQWPEEY.js";
 export {

package/dist/walkHighlight.js

@@ -2,22 +2,22 @@ import {
   facetLifts,
   walkHighlight,
   walkLift
-} from "./chunks/chunk-R456ME6J.js";
-import "./chunks/chunk-ALDGONEI.js";
-import "./chunks/chunk-SBMJNRTV.js";
+} from "./chunks/chunk-CU6P5RUG.js";
+import "./chunks/chunk-VQC7KELB.js";
+import "./chunks/chunk-A4PFFC4Q.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-WFB5TXRA.js";
-import "./chunks/chunk-TWRLC3KK.js";
-import "./chunks/chunk-PBENCR5L.js";
+import "./chunks/chunk-ZY2AFL4Y.js";
+import "./chunks/chunk-3XSM4OZU.js";
+import "./chunks/chunk-JBCZIBFC.js";
 import "./chunks/chunk-M6LK4GII.js";
 import "./chunks/chunk-RAEABQNW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-BPLIXMH7.js";
-import "./chunks/chunk-3ZZSX5HN.js";
+import "./chunks/chunk-PTABFYQ7.js";
 import "./chunks/chunk-AB35TJST.js";
-import "./chunks/chunk-TAMCZHLW.js";
-import "./chunks/chunk-N6FECAXP.js";
-import "./chunks/chunk-2CVHXFK7.js";
+import "./chunks/chunk-N73TI3VG.js";
+import "./chunks/chunk-24WITXQY.js";
+import "./chunks/chunk-7SRWJLSC.js";
 import "./chunks/chunk-CPMHA4W5.js";
 import "./chunks/chunk-FYQWPEEY.js";
 export {

package/dist/walkKey.js

@@ -2,12 +2,12 @@ import {
   rangeText,
   walkKey,
   walkPosition
-} from "./chunks/chunk-2LQ5BWT7.js";
-import "./chunks/chunk-3ZZSX5HN.js";
+} from "./chunks/chunk-4ETPXDO6.js";
+import "./chunks/chunk-PTABFYQ7.js";
 import "./chunks/chunk-AB35TJST.js";
-import "./chunks/chunk-TAMCZHLW.js";
-import "./chunks/chunk-N6FECAXP.js";
-import "./chunks/chunk-2CVHXFK7.js";
+import "./chunks/chunk-N73TI3VG.js";
+import "./chunks/chunk-24WITXQY.js";
+import "./chunks/chunk-7SRWJLSC.js";
 import "./chunks/chunk-CPMHA4W5.js";
 import "./chunks/chunk-FYQWPEEY.js";
 export {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "10.2.2",
+  "version": "10.2.4",
   "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": {
@@ -37,6 +37,7 @@
   "dependencies": {
     "@gmod/gbz-base": "^7.4.0",
     "@gmod/tabix": "^3.10.1",
+    "@jbrowse/graph-fmmm-layout": "^1.0.2",
     "@jbrowse/graph-stress-layout": "^1.0.0",
     "@jbrowse/tubemap-core": "^1.1.0"
   },
@@ -69,11 +70,7 @@
     "test": "vitest run",
     "test:watch": "vitest",
     "bench": "vitest bench --run",
-    "build:wasm": "./scripts/build-wasm.sh",
-    "test:wasm": "node scripts/smoke-wasm.mjs",
-    "bench:layout": "node scripts/bench-layout.mjs",
-    "layout-digest": "node scripts/layout-digest.mjs",
-    "preversion": "pnpm lint && pnpm format:check && pnpm typecheck && pnpm test && pnpm build && pnpm test:wasm",
+    "preversion": "pnpm lint && pnpm format:check && pnpm typecheck && pnpm test && pnpm build",
     "version": "node scripts/version.mjs",
     "postversion": "git push --follow-tags"
   }