@jbrowse/bandage-core 7.1.0 → 7.2.0

package/dist/index.js

@@ -62,12 +62,13 @@ import {
   stripBlockAt
 } from "./chunks/chunk-EXSXBIMH.js";
 import {
+  LAYOUT_ENGINES,
   layoutEngine
-} from "./chunks/chunk-L53SXJZI.js";
+} from "./chunks/chunk-6EJIU6IA.js";
 import {
-  LAYOUT_ENGINES,
   stressLayout
-} from "./chunks/chunk-O4TGF4WS.js";
+} from "./chunks/chunk-UNOE2NDN.js";
+import "./chunks/chunk-LYJ4US66.js";
 import {
   FORCE_LAYOUT_LABEL,
   LAYOUT_MODES,
@@ -87,7 +88,13 @@ import {
 } from "./chunks/chunk-7XHHVYG7.js";
 import {
   figureSvg
-} from "./chunks/chunk-2WA4EY25.js";
+} from "./chunks/chunk-QMJ4J5PT.js";
+import {
+  Canvas2DRenderer
+} from "./chunks/chunk-CH3DLBUT.js";
+import {
+  getDpr
+} from "./chunks/chunk-4BYTEJGW.js";
 import {
   svgCanvas
 } from "./chunks/chunk-47DYCZOK.js";
@@ -128,12 +135,6 @@ import {
   walkRowsKeyTree,
   walkRowsTree
 } from "./chunks/chunk-UGD6ZMOF.js";
-import {
-  Canvas2DRenderer
-} from "./chunks/chunk-CH3DLBUT.js";
-import {
-  getDpr
-} from "./chunks/chunk-4BYTEJGW.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
@@ -144,7 +145,7 @@ import {
 } from "./chunks/chunk-BUBZ32IC.js";
 import {
   version
-} from "./chunks/chunk-MAPRJ2H2.js";
+} from "./chunks/chunk-S73EYTZA.js";
 import {
   axisScaleOf,
   contains,
@@ -152,7 +153,7 @@ import {
   screenToLayout,
   viewportOf,
   zoomAbout
-} from "./chunks/chunk-AWCMVPVP.js";
+} from "./chunks/chunk-Y7UR3MDE.js";
 import {
   facetLifts,
   walkHighlight,
@@ -181,13 +182,12 @@ import {
   forceLayout,
   layoutExtent,
   loadGraph
-} from "./chunks/chunk-6UFS3EWI.js";
+} from "./chunks/chunk-EPWYRSHH.js";
 import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-72N5DJHZ.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-YZ5CCEDH.js";
 import {
   RAMP_GRADIENT_CSS,
   rampHue,
@@ -219,6 +219,7 @@ import {
 } from "./chunks/chunk-FP4H7SFT.js";
 import "./chunks/chunk-MLSWIMZO.js";
 import "./chunks/chunk-WFB5TXRA.js";
+import "./chunks/chunk-JVLURPFW.js";
 import {
   walkRowsExtent
 } from "./chunks/chunk-3JANT2SW.js";

package/dist/layout/deletionRoutes.js

@@ -1,9 +1,11 @@
 import {
+  ROUTE_ID,
   routeNodes,
   takeRoutes,
   withDeletionRoutes
-} from "../chunks/chunk-YZ5CCEDH.js";
+} from "../chunks/chunk-JVLURPFW.js";
 export {
+  ROUTE_ID,
   routeNodes,
   takeRoutes,
   withDeletionRoutes

package/dist/layout/stressEngine.js

@@ -1,11 +1,11 @@
 import {
-  LAYOUT_ENGINES,
-  LAYOUT_ENGINE_VALUES,
+  chains,
   stressLayout
-} from "../chunks/chunk-O4TGF4WS.js";
+} from "../chunks/chunk-UNOE2NDN.js";
+import "../chunks/chunk-LYJ4US66.js";
+import "../chunks/chunk-JVLURPFW.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {
-  LAYOUT_ENGINES,
-  LAYOUT_ENGINE_VALUES,
+  chains,
   stressLayout
 };

package/dist/layout/stressPlacement.js

@@ -0,0 +1,7 @@
+import {
+  stressPlacement
+} from "../chunks/chunk-LYJ4US66.js";
+import "../chunks/chunk-JVLURPFW.js";
+export {
+  stressPlacement
+};

package/dist/layoutEngines.js

@@ -1,9 +1,17 @@
 import {
+  LAYOUT_ENGINES,
+  LAYOUT_ENGINE_VALUES,
+  isLayoutEngineKind,
   layoutEngine
-} from "./chunks/chunk-L53SXJZI.js";
-import "./chunks/chunk-O4TGF4WS.js";
+} from "./chunks/chunk-6EJIU6IA.js";
+import "./chunks/chunk-UNOE2NDN.js";
+import "./chunks/chunk-LYJ4US66.js";
 import "./chunks/chunk-7XHHVYG7.js";
+import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-FYQWPEEY.js";
 export {
+  LAYOUT_ENGINES,
+  LAYOUT_ENGINE_VALUES,
+  isLayoutEngineKind,
   layoutEngine
 };

package/dist/pipeline.js

@@ -9,13 +9,13 @@ import {
   forceLayout,
   layoutExtent,
   loadGraph
-} from "./chunks/chunk-6UFS3EWI.js";
+} from "./chunks/chunk-EPWYRSHH.js";
 import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-72N5DJHZ.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-YZ5CCEDH.js";
+import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-TAMCZHLW.js";

package/dist/types/cli/figure.d.ts

@@ -1,7 +1,7 @@
 import type { BubbleSpread } from '../bubbleSpreads.js';
 import type { FigureOptions } from '../figure.js';
 import type { GbzSource } from '../gbzCut.js';
-import type { LayoutEngineKind } from '../layout/stressEngine.js';
+import type { LayoutEngineKind } from '../layoutEngines.js';
 import type { LayoutModeValue } from '../layoutModes.js';
 import type { WalkLayer } from '../walkEncoding.js';
 export interface FigureSpec extends Omit<FigureOptions, 'walks' | 'region' | 'genes' | 'spec' | 'walkStrip'> {

package/dist/types/index.d.ts

@@ -8,9 +8,9 @@ export { NODE_WIDTHS, maxNodeWidthPx, meanDepth, nodeInk, nodeWidthPx, } from '.
 export type { NodeWidth } from './nodeWidths.js';
 export { BUBBLE_SPREADS } from './bubbleSpreads.js';
 export type { BubbleSpread } from './bubbleSpreads.js';
-export { LAYOUT_ENGINES, stressLayout } from './layout/stressEngine.js';
-export type { LayoutEngineKind } from './layout/stressEngine.js';
-export { layoutEngine } from './layoutEngines.js';
+export { stressLayout } from './layout/stressEngine.js';
+export { LAYOUT_ENGINES, layoutEngine } from './layoutEngines.js';
+export type { LayoutEngineKind } from './layoutEngines.js';
 export { REFERENCE_RAMP_MAX_HUE, buildGeometry, computeReferenceRamp, } from './renderer/GeometryBuilder.js';
 export { Canvas2DRenderer } from './renderer/Canvas2DRenderer.js';
 export { getDpr } from './renderer/canvas.js';

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

@@ -1,6 +1,7 @@
 import type { BandageScaleOpts } from './drawnScale.js';
 import type { DeletionEdge } from '../deletionEdges.js';
 import type { Graph, GraphEdge, GraphNode, NodeSegment } from '../types.js';
+export declare const ROUTE_ID = "\0deletion:";
 export type DeletionRoutes = Record<number, NodeSegment[]>;
 export declare function withDeletionRoutes(graph: Graph, deletions: DeletionEdge[], dropped?: Set<number>): {
     graph: {

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

@@ -1,16 +1,24 @@
 import type { EngineRequest } from '../pipeline.js';
 import type { LayoutResult } from '../types.js';
-export declare const LAYOUT_ENGINES: readonly [{
-    readonly value: "fmmm";
-    readonly label: "Bandage (FMMM)";
-    readonly description: "Bandage's force-directed layout: OGDF's fast multipole multilevel method, compiled to wasm.";
-}, {
-    readonly value: "stress";
-    readonly label: "Stress (experimental)";
-    readonly description: "Stress layout by stochastic gradient descent in plain JS: distances along the graph become distances on the page, so the reference reads straight and a repeat loop reads as a ring.";
-}];
-export type LayoutEngineKind = (typeof LAYOUT_ENGINES)[number]['value'];
-export declare const LAYOUT_ENGINE_VALUES: ("fmmm" | "stress")[];
+export type Side = 0 | 1;
+export interface Chains {
+    ids: string[];
+    first: Int32Array;
+    count: Int32Array;
+    per: Float64Array;
+    links: [number, Side][][][];
+    chainOf: Int32Array;
+    indexOf: Int32Array;
+    seedX: Float64Array;
+    seedY: Float64Array;
+    backbone: Uint8Array;
+    off: Int32Array;
+    nb: Int32Array;
+    wt: Float64Array;
+    n: number;
+    link: number;
+}
+export declare function chains(request: EngineRequest): Chains;
 export interface StressOptions {
     quality?: number;
     seed?: number;

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

@@ -0,0 +1,5 @@
+import type { Chains } from './stressEngine.js';
+export declare function stressPlacement(c: Chains): {
+    X: Float64Array<ArrayBuffer>;
+    Y: Float64Array<ArrayBuffer>;
+};

package/dist/types/layoutEngines.d.ts

@@ -1,2 +1,14 @@
 import type { LayoutEngine } from './pipeline.js';
+export declare const LAYOUT_ENGINES: readonly [{
+    readonly value: "fmmm";
+    readonly label: "Bandage (FMMM)";
+    readonly description: "Bandage's force-directed layout: OGDF's fast multipole multilevel method, compiled to wasm.";
+}, {
+    readonly value: "stress";
+    readonly label: "Stress (experimental)";
+    readonly description: "Stress layout by stochastic gradient descent in plain JS: distances along the graph become distances on the page, so the reference reads straight and a repeat loop reads as a ring.";
+}];
+export type LayoutEngineKind = (typeof LAYOUT_ENGINES)[number]['value'];
+export declare const LAYOUT_ENGINE_VALUES: ("fmmm" | "stress")[];
+export declare function isLayoutEngineKind(value: unknown): value is LayoutEngineKind;
 export declare const layoutEngine: LayoutEngine;

package/dist/types/pipeline.d.ts

@@ -1,7 +1,7 @@
 import type { BubbleSpread } from './bubbleSpreads.js';
 import type { LayoutScaling } from './layout/drawnScale.js';
 import type { LayoutNode } from './layout/referenceSeeds.js';
-import type { LayoutEngineKind } from './layout/stressEngine.js';
+import type { LayoutEngineKind } from './layoutEngines.js';
 import type { Graph, LayoutResult, NodeSegment } from './types.js';
 export interface Bounds {
     minX: number;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "7.1.0";
+export declare const version = "7.2.0";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-MAPRJ2H2.js";
+} from "./chunks/chunk-S73EYTZA.js";
 export {
   version
 };

package/dist/viewport.js

@@ -5,14 +5,14 @@ import {
   screenToLayout,
   viewportOf,
   zoomAbout
-} from "./chunks/chunk-AWCMVPVP.js";
-import "./chunks/chunk-6UFS3EWI.js";
+} from "./chunks/chunk-Y7UR3MDE.js";
+import "./chunks/chunk-EPWYRSHH.js";
 import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-72N5DJHZ.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-YZ5CCEDH.js";
+import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-TAMCZHLW.js";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "7.1.0",
+  "version": "7.2.0",
   "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": {

package/dist/chunks/chunk-L53SXJZI.js

@@ -1,22 +0,0 @@
-import {
-  stressLayout
-} from "./chunk-O4TGF4WS.js";
-import {
-  loadBandage
-} from "./chunk-7XHHVYG7.js";
-
-// src/layoutEngines.ts
-var layoutEngine = async (request) => {
-  const start = performance.now();
-  if (request.options.engine === "stress") {
-    const result2 = stressLayout(request);
-    return { result: result2, duration: performance.now() - start };
-  }
-  const bandage = await loadBandage();
-  const result = bandage.computeLayout(request.graph, request.options);
-  return { result, duration: performance.now() - start };
-};
-
-export {
-  layoutEngine
-};