@jbrowse/bandage-core 7.2.1 → 7.4.0

package/dist/pipeline.js

@@ -1,37 +1,41 @@
 import {
+  ENGINE_DEFAULTS,
   FIT_PADDING,
   clampZoom,
   drawingBounds,
   engineKey,
   engineRequest,
+  engineSettingsOf,
   fitTransform,
   fittedTranslateY,
   forceLayout,
   layoutExtent,
   loadGraph
-} from "./chunks/chunk-EPWYRSHH.js";
-import "./chunks/chunk-PUG7LXDF.js";
+} from "./chunks/chunk-WZATPZNH.js";
 import "./chunks/chunk-IGVV37VI.js";
+import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-72N5DJHZ.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-ST2IBUAN.js";
+import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-TAMCZHLW.js";
+import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-UVBGRJQX.js";
 import "./chunks/chunk-6JEWNXCQ.js";
 import "./chunks/chunk-N6FECAXP.js";
 import "./chunks/chunk-2CVHXFK7.js";
 import "./chunks/chunk-CPMHA4W5.js";
-import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-FYQWPEEY.js";
 export {
+  ENGINE_DEFAULTS,
   FIT_PADDING,
   clampZoom,
   drawingBounds,
   engineKey,
   engineRequest,
+  engineSettingsOf,
   fitTransform,
   fittedTranslateY,
   forceLayout,

package/dist/referenceRampCss.js

@@ -4,21 +4,21 @@ import {
   rampHue,
   rampHueCss,
   rampStops
-} from "./chunks/chunk-VECR253P.js";
-import "./chunks/chunk-VST5SR4C.js";
+} from "./chunks/chunk-AVJK272H.js";
+import "./chunks/chunk-RCWYY6XA.js";
 import "./chunks/chunk-UMNCCYBN.js";
 import "./chunks/chunk-PBENCR5L.js";
+import "./chunks/chunk-7GBL7SJY.js";
 import "./chunks/chunk-WFB5TXRA.js";
-import "./chunks/chunk-E7FWQQHP.js";
-import "./chunks/chunk-ES2N6V56.js";
-import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-3ZZSX5HN.js";
 import "./chunks/chunk-AB35TJST.js";
+import "./chunks/chunk-ES2N6V56.js";
+import "./chunks/chunk-ST2IBUAN.js";
+import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-TAMCZHLW.js";
 import "./chunks/chunk-N6FECAXP.js";
 import "./chunks/chunk-2CVHXFK7.js";
 import "./chunks/chunk-CPMHA4W5.js";
-import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-FYQWPEEY.js";
 export {
   RAMP_GRADIENT_CSS,

package/dist/referenceStrip.js

@@ -7,21 +7,21 @@ import {
   stripBlockAt,
   stripOverhang,
   stripPixels
-} from "./chunks/chunk-EXSXBIMH.js";
-import "./chunks/chunk-VST5SR4C.js";
+} from "./chunks/chunk-UJ6GYL6T.js";
+import "./chunks/chunk-RCWYY6XA.js";
 import "./chunks/chunk-UMNCCYBN.js";
 import "./chunks/chunk-PBENCR5L.js";
+import "./chunks/chunk-7GBL7SJY.js";
 import "./chunks/chunk-WFB5TXRA.js";
-import "./chunks/chunk-E7FWQQHP.js";
-import "./chunks/chunk-ES2N6V56.js";
-import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-3ZZSX5HN.js";
 import "./chunks/chunk-AB35TJST.js";
+import "./chunks/chunk-ES2N6V56.js";
+import "./chunks/chunk-ST2IBUAN.js";
+import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-TAMCZHLW.js";
 import "./chunks/chunk-N6FECAXP.js";
 import "./chunks/chunk-2CVHXFK7.js";
 import "./chunks/chunk-CPMHA4W5.js";
-import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-FYQWPEEY.js";
 export {
   REFERENCE_STRIP_PX,

package/dist/renderer/GeometryBuilder.js

@@ -11,20 +11,20 @@ import {
   endTangent,
   getNodeColor,
   hslToRgb
-} from "../chunks/chunk-VST5SR4C.js";
+} from "../chunks/chunk-RCWYY6XA.js";
 import "../chunks/chunk-UMNCCYBN.js";
 import "../chunks/chunk-PBENCR5L.js";
+import "../chunks/chunk-7GBL7SJY.js";
 import "../chunks/chunk-WFB5TXRA.js";
-import "../chunks/chunk-E7FWQQHP.js";
-import "../chunks/chunk-ES2N6V56.js";
-import "../chunks/chunk-ST2IBUAN.js";
 import "../chunks/chunk-3ZZSX5HN.js";
 import "../chunks/chunk-AB35TJST.js";
+import "../chunks/chunk-ES2N6V56.js";
+import "../chunks/chunk-ST2IBUAN.js";
+import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-TAMCZHLW.js";
 import "../chunks/chunk-N6FECAXP.js";
 import "../chunks/chunk-2CVHXFK7.js";
 import "../chunks/chunk-CPMHA4W5.js";
-import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {
   FADED_ALPHA,

package/dist/renderer/geometryInputs.js

@@ -0,0 +1,6 @@
+import {
+  layoutGeometryInputs
+} from "../chunks/chunk-LOCJN3BZ.js";
+export {
+  layoutGeometryInputs
+};

package/dist/tubeMap/coarsen.js

@@ -1,21 +1,21 @@
 import {
   visitStrands
-} from "../chunks/chunk-4FQTTG5F.js";
+} from "../chunks/chunk-AYOSNXLQ.js";
 import {
   canonicalStrand
 } from "../chunks/chunk-TEDQJPMI.js";
 import "../chunks/chunk-C44YRP5F.js";
-import "../chunks/chunk-E7FWQQHP.js";
+import "../chunks/chunk-7GBL7SJY.js";
+import "../chunks/chunk-3ZZSX5HN.js";
+import "../chunks/chunk-AB35TJST.js";
 import {
   pathOrigin
 } from "../chunks/chunk-ST2IBUAN.js";
-import "../chunks/chunk-3ZZSX5HN.js";
-import "../chunks/chunk-AB35TJST.js";
+import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-TAMCZHLW.js";
 import "../chunks/chunk-N6FECAXP.js";
 import "../chunks/chunk-2CVHXFK7.js";
 import "../chunks/chunk-CPMHA4W5.js";
-import "../chunks/chunk-BPLIXMH7.js";
 import {
   isBackbone
 } from "../chunks/chunk-FYQWPEEY.js";

package/dist/tubeMap/nodeColors.js

@@ -1,20 +1,20 @@
 import {
   tubeMapNodeColors
-} from "../chunks/chunk-CNQSHEBS.js";
-import "../chunks/chunk-VST5SR4C.js";
+} from "../chunks/chunk-KEVQ46GG.js";
+import "../chunks/chunk-RCWYY6XA.js";
 import "../chunks/chunk-UMNCCYBN.js";
 import "../chunks/chunk-PBENCR5L.js";
+import "../chunks/chunk-7GBL7SJY.js";
 import "../chunks/chunk-WFB5TXRA.js";
-import "../chunks/chunk-E7FWQQHP.js";
-import "../chunks/chunk-ES2N6V56.js";
-import "../chunks/chunk-ST2IBUAN.js";
 import "../chunks/chunk-3ZZSX5HN.js";
 import "../chunks/chunk-AB35TJST.js";
+import "../chunks/chunk-ES2N6V56.js";
+import "../chunks/chunk-ST2IBUAN.js";
+import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-TAMCZHLW.js";
 import "../chunks/chunk-N6FECAXP.js";
 import "../chunks/chunk-2CVHXFK7.js";
 import "../chunks/chunk-CPMHA4W5.js";
-import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {
   tubeMapNodeColors

package/dist/types/figure.d.ts

@@ -14,6 +14,7 @@ export interface FigureOptions {
     colorScheme?: ColorScheme;
     nodeWidth?: NodeWidth;
     showDeletionEdges?: boolean;
+    linearLayout?: boolean;
     contigThickness?: number;
     connectorThickness?: number;
     region?: {

package/dist/types/figureSettings.d.ts

@@ -0,0 +1,15 @@
+import type { ColorScheme } from './colorSchemes.js';
+import type { NodeWidth } from './nodeWidths.js';
+import type { EngineSettings } from './pipeline.js';
+export interface FigureSettings extends Partial<EngineSettings> {
+    colorScheme?: ColorScheme;
+    nodeWidth?: NodeWidth;
+    contigThickness?: number;
+    connectorThickness?: number;
+    colorDomain?: {
+        start: number;
+        end: number;
+    };
+}
+export declare const FIGURE_DEFAULTS: Required<Omit<FigureSettings, 'colorDomain'>>;
+export declare function figureSpecSettings(s: FigureSettings): Record<string, unknown>;

package/dist/types/hoverText.d.ts

@@ -0,0 +1,17 @@
+import type { DeletionEdge } from './deletionEdges.js';
+import type { GraphEdge } from './types.js';
+export declare function regionLabel(loc: {
+    refName: string;
+    start: number;
+    end: number;
+}): string;
+export declare function edgeHoverText(edge: GraphEdge, deletion: DeletionEdge | undefined, nameOf?: (id: string) => string): {
+    deletion: {
+        bp: string;
+        where: string;
+    };
+    ends?: undefined;
+} | {
+    ends: string;
+    deletion?: undefined;
+};

package/dist/types/index.d.ts

@@ -1,5 +1,12 @@
 export { FIT_PADDING, clampZoom, drawingBounds, engineRequest, fitTransform, forceLayout, layoutExtent, loadGraph, } from './pipeline.js';
 export type { Bounds, EngineRequest, EngineSettings, LayoutEngine, } from './pipeline.js';
+export { ENGINE_DEFAULTS, engineSettingsOf } from './pipeline.js';
+export { createForceLayoutCache } from './layout/forceCache.js';
+export type { ForceLayoutCache } from './layout/forceCache.js';
+export { edgeHoverText, regionLabel } from './hoverText.js';
+export { layoutGeometryInputs } from './renderer/geometryInputs.js';
+export { FIGURE_DEFAULTS, figureSpecSettings } from './figureSettings.js';
+export type { FigureSettings } from './figureSettings.js';
 export { FORCE_LAYOUT_LABEL, LAYOUT_MODES, layoutModeByValue, modeUsesLayoutEngine, } from './layoutModes.js';
 export type { LayoutModeValue } from './layoutModes.js';
 export { COLOR_SCHEMES, resolveColorScheme } from './colorSchemes.js';
@@ -7,6 +14,8 @@ export type { ColorScheme, ResolvedColorScheme } from './colorSchemes.js';
 export { NODE_WIDTHS, maxNodeWidthPx, meanDepth, nodeInk, nodeWidthPx, } from './nodeWidths.js';
 export type { NodeWidth } from './nodeWidths.js';
 export { BUBBLE_SPREADS } from './bubbleSpreads.js';
+export { LAYOUT_QUALITIES } from './layoutQualities.js';
+export type { LayoutQuality } from './layoutQualities.js';
 export type { BubbleSpread } from './bubbleSpreads.js';
 export { stressLayout } from './layout/stressEngine.js';
 export { LAYOUT_ENGINES, layoutEngine } from './layoutEngines.js';
@@ -50,7 +59,7 @@ export type { FacetBy, FacetGrid, FacetInput, FacetSetting } from './facetGrid.j
 export type { LiftedWalk, WalkLift } from './walkHighlight.js';
 export { WALK_FIELDS, WALK_SCHEMES, encodingStops, encodingSwatchCss, resolveEncoding, schemeCss, } from './walkEncoding.js';
 export type { WalkEncoding, WalkField, WalkLayer, WalkScheme, } from './walkEncoding.js';
-export { pathColorsLegible, pathLegend } from './pathColors.js';
+export { pathColorsLegible, pathLegend, walkLabelsOf } from './pathColors.js';
 export { bubblesFromGraph } from './bubbles/bubblesFromGraph.js';
 export { bubbleHalos } from './bubbles/bubbleHalos.js';
 export type { BubbleHalo } from './bubbles/bubbleHalos.js';
@@ -66,7 +75,7 @@ export type { StripFrame, StripMark } from './layout/walkStrip.js';
 export { el, serializeEl } from './el.js';
 export type { El, ElAttrs } from './el.js';
 export { RAMP_GRADIENT_CSS, rampHue, rampHueCss, rampStops, } from './referenceRampCss.js';
-export { walkRowsExtent } from './layout/walkRowLayout.js';
+export { walkRowLabels, walkRowsExtent } from './layout/walkRowLayout.js';
 export { ROW_HEIGHT_PX } from './layout/rowSpacing.js';
 export { HALO_FACTOR, LEGEND_INSET_PX, geneCoverageNote, layoutLabels, } from './labelLayout.js';
 export type { LabelLayout, LabelLayoutSource } from './labelLayout.js';

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

@@ -0,0 +1,11 @@
+import type { EngineSettings, LayoutEngine } from '../pipeline.js';
+import type { Graph, LayoutResult } from '../types.js';
+export interface ForceLayoutCache {
+    layout(graph: Graph, settings: EngineSettings, engine: LayoutEngine): Promise<{
+        result: LayoutResult;
+        duration: number;
+    }>;
+    ready(graph: Graph, settings: EngineSettings): LayoutResult | undefined;
+    inherit(from: Graph, to: Graph): void;
+}
+export declare function createForceLayoutCache(size?: number): ForceLayoutCache;

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

@@ -1,10 +1,11 @@
 import type { RowPitch } from './walkRowDraw.js';
 import type { WalkRows } from './walkRows.js';
-import type { Graph, LayoutResult } from '../types.js';
+import type { Graph, LayoutResult, RowLabel } from '../types.js';
 export declare function walkRowsExtent(walks: WalkRows, pitch?: Pick<RowPitch, 'rowPx' | 'readouts'>): {
     maxX: number;
     maxY: number;
 };
+export declare function walkRowLabels(rows: WalkRows | undefined, layout?: LayoutResult, pitch?: RowPitch): RowLabel[];
 export declare function walkRowLayout(graph: Graph, region?: {
     start: number;
     end: number;

package/dist/types/layoutQualities.d.ts

@@ -0,0 +1,17 @@
+export declare const LAYOUT_QUALITIES: readonly [{
+    readonly value: 0;
+    readonly label: "Fastest";
+}, {
+    readonly value: 1;
+    readonly label: "Fast";
+}, {
+    readonly value: 2;
+    readonly label: "Default";
+}, {
+    readonly value: 3;
+    readonly label: "Fine";
+}, {
+    readonly value: 4;
+    readonly label: "Best";
+}];
+export type LayoutQuality = (typeof LAYOUT_QUALITIES)[number]['value'];

package/dist/types/pathColors.d.ts

@@ -13,3 +13,7 @@ export interface PathLegendEntry {
     color: string;
 }
 export declare function pathLegend(paths: GraphPath[], colors?: readonly string[]): PathLegendEntry[];
+export declare function walkLabelsOf(entries: {
+    name: string;
+    label: string;
+}[]): Map<string, string>;

package/dist/types/pipeline.d.ts

@@ -33,6 +33,8 @@ export interface EngineSettings {
     showDeletionEdges?: boolean;
     engine?: LayoutEngineKind;
 }
+export declare const ENGINE_DEFAULTS: Required<EngineSettings>;
+export declare function engineSettingsOf(s?: Partial<EngineSettings>): Required<EngineSettings>;
 export declare function engineRequest(graph: Graph, scaling: LayoutScaling, settings: EngineSettings): EngineRequest;
 export declare function engineKey(graph: Graph, settings: EngineSettings): string;
 export declare function forceLayout(graph: Graph, settings: EngineSettings, engine: LayoutEngine): Promise<{

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

@@ -0,0 +1,11 @@
+import type { DeletionDrawing } from '../deletionEdges.js';
+import type { LayoutResult } from '../types.js';
+export declare function layoutGeometryInputs(layout: LayoutResult, drawing: DeletionDrawing, o?: {
+    drawsRows?: boolean;
+}): {
+    nodePositions: Record<string, import("../index.js").NodeSegment[]>;
+    deletions: Map<number, string[]>;
+    deletionRoutes: Record<number, import("../index.js").NodeSegment[]> | undefined;
+    stranded: boolean | undefined;
+    hiddenEdges: ReadonlySet<number>;
+};

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "7.2.1";
+export declare const version = "7.4.0";

package/dist/version.js

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

package/dist/viewport.js

@@ -5,23 +5,23 @@ import {
   screenToLayout,
   viewportOf,
   zoomAbout
-} from "./chunks/chunk-Y7UR3MDE.js";
-import "./chunks/chunk-EPWYRSHH.js";
-import "./chunks/chunk-PUG7LXDF.js";
+} from "./chunks/chunk-4UBWXZVX.js";
+import "./chunks/chunk-WZATPZNH.js";
 import "./chunks/chunk-IGVV37VI.js";
+import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-72N5DJHZ.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-ST2IBUAN.js";
+import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-TAMCZHLW.js";
+import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-UVBGRJQX.js";
 import "./chunks/chunk-6JEWNXCQ.js";
 import "./chunks/chunk-N6FECAXP.js";
 import "./chunks/chunk-2CVHXFK7.js";
 import "./chunks/chunk-CPMHA4W5.js";
-import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-FYQWPEEY.js";
 export {
   axisScaleOf,

package/dist/walkEncoding.js

@@ -9,21 +9,21 @@ import {
   schemeColor,
   schemeCss,
   schemeRgb
-} from "./chunks/chunk-TQ7VCGJR.js";
-import "./chunks/chunk-VST5SR4C.js";
+} from "./chunks/chunk-ZNMHIPUZ.js";
+import "./chunks/chunk-RCWYY6XA.js";
 import "./chunks/chunk-UMNCCYBN.js";
 import "./chunks/chunk-PBENCR5L.js";
+import "./chunks/chunk-7GBL7SJY.js";
 import "./chunks/chunk-WFB5TXRA.js";
-import "./chunks/chunk-E7FWQQHP.js";
-import "./chunks/chunk-ES2N6V56.js";
-import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-3ZZSX5HN.js";
 import "./chunks/chunk-AB35TJST.js";
+import "./chunks/chunk-ES2N6V56.js";
+import "./chunks/chunk-ST2IBUAN.js";
+import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-TAMCZHLW.js";
 import "./chunks/chunk-N6FECAXP.js";
 import "./chunks/chunk-2CVHXFK7.js";
 import "./chunks/chunk-CPMHA4W5.js";
-import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-FYQWPEEY.js";
 export {
   NO_VALUE_COLOR,

package/dist/walkHighlight.js

@@ -2,22 +2,22 @@ import {
   facetLifts,
   walkHighlight,
   walkLift
-} from "./chunks/chunk-MH5IA57M.js";
-import "./chunks/chunk-TQ7VCGJR.js";
-import "./chunks/chunk-VST5SR4C.js";
+} from "./chunks/chunk-3LXG54PN.js";
+import "./chunks/chunk-ZNMHIPUZ.js";
+import "./chunks/chunk-RCWYY6XA.js";
 import "./chunks/chunk-UMNCCYBN.js";
 import "./chunks/chunk-PBENCR5L.js";
+import "./chunks/chunk-7GBL7SJY.js";
 import "./chunks/chunk-WFB5TXRA.js";
-import "./chunks/chunk-E7FWQQHP.js";
-import "./chunks/chunk-ES2N6V56.js";
-import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-3ZZSX5HN.js";
 import "./chunks/chunk-AB35TJST.js";
+import "./chunks/chunk-ES2N6V56.js";
+import "./chunks/chunk-ST2IBUAN.js";
+import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-TAMCZHLW.js";
 import "./chunks/chunk-N6FECAXP.js";
 import "./chunks/chunk-2CVHXFK7.js";
 import "./chunks/chunk-CPMHA4W5.js";
-import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-FYQWPEEY.js";
 export {
   facetLifts,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "7.2.1",
+  "version": "7.4.0",
   "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": {