@jbrowse/bandage-core 9.9.1 → 9.10.0

package/dist/renderer/GeometryBuilder.js

@@ -11,16 +11,16 @@ import {
   endTangent,
   getNodeColor,
   hslToRgb
-} from "../chunks/chunk-F4BKWWLS.js";
+} from "../chunks/chunk-4IYP43W6.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-EDASNMLY.js";
-import "../chunks/chunk-PBENCR5L.js";
 import "../chunks/chunk-WFB5TXRA.js";
-import "../chunks/chunk-3ZZSX5HN.js";
-import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-ES2N6V56.js";
+import "../chunks/chunk-XZ2BLAA6.js";
+import "../chunks/chunk-PBENCR5L.js";
 import "../chunks/chunk-IGJCTPFB.js";
+import "../chunks/chunk-ES2N6V56.js";
 import "../chunks/chunk-BPLIXMH7.js";
+import "../chunks/chunk-3ZZSX5HN.js";
+import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-TAMCZHLW.js";
 import "../chunks/chunk-N6FECAXP.js";
 import "../chunks/chunk-2CVHXFK7.js";

package/dist/tubeMap/bundle.js

@@ -1,14 +1,14 @@
 import {
   bundleRoutes
-} from "../chunks/chunk-WVBYR6Y7.js";
-import "../chunks/chunk-HOZI3FBG.js";
+} from "../chunks/chunk-LZWSZRUY.js";
+import "../chunks/chunk-CXKZYLYS.js";
 import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-C44YRP5F.js";
-import "../chunks/chunk-EDASNMLY.js";
-import "../chunks/chunk-3ZZSX5HN.js";
-import "../chunks/chunk-AB35TJST.js";
+import "../chunks/chunk-XZ2BLAA6.js";
 import "../chunks/chunk-IGJCTPFB.js";
 import "../chunks/chunk-BPLIXMH7.js";
+import "../chunks/chunk-3ZZSX5HN.js";
+import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-TAMCZHLW.js";
 import "../chunks/chunk-N6FECAXP.js";
 import "../chunks/chunk-2CVHXFK7.js";

package/dist/tubeMap/coarsen.js

@@ -1,15 +1,15 @@
 import {
   pathSteps
-} from "../chunks/chunk-HOZI3FBG.js";
+} from "../chunks/chunk-CXKZYLYS.js";
 import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-C44YRP5F.js";
-import "../chunks/chunk-EDASNMLY.js";
-import "../chunks/chunk-3ZZSX5HN.js";
-import "../chunks/chunk-AB35TJST.js";
+import "../chunks/chunk-XZ2BLAA6.js";
 import {
   pathOrigin
 } from "../chunks/chunk-IGJCTPFB.js";
 import "../chunks/chunk-BPLIXMH7.js";
+import "../chunks/chunk-3ZZSX5HN.js";
+import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-TAMCZHLW.js";
 import "../chunks/chunk-N6FECAXP.js";
 import "../chunks/chunk-2CVHXFK7.js";

package/dist/tubeMap/draw.js

@@ -8,8 +8,9 @@ import {
   tubeMapMismatchAt,
   tubeMapPicture,
   tubeMapTrackAt
-} from "../chunks/chunk-2NROXCK3.js";
+} from "../chunks/chunk-PIN7ZMTZ.js";
 import "../chunks/chunk-XXT2JCAC.js";
+import "../chunks/chunk-HK5Y2YWV.js";
 import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-C44YRP5F.js";
 import "../chunks/chunk-IGJCTPFB.js";

package/dist/tubeMap/frame.js

@@ -1,8 +1,8 @@
 import {
   tubeMapFrame,
   tubeMapNodeAt
-} from "../chunks/chunk-JABM3MUS.js";
-import "../chunks/chunk-IJYFJVIT.js";
+} from "../chunks/chunk-2CMYNW3E.js";
+import "../chunks/chunk-HK5Y2YWV.js";
 export {
   tubeMapFrame,
   tubeMapNodeAt

package/dist/tubeMap/nodeColors.js

@@ -1,16 +1,16 @@
 import {
   tubeMapNodeColors
-} from "../chunks/chunk-KJEMKHVB.js";
-import "../chunks/chunk-F4BKWWLS.js";
+} from "../chunks/chunk-TFAFIRZB.js";
+import "../chunks/chunk-4IYP43W6.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-EDASNMLY.js";
-import "../chunks/chunk-PBENCR5L.js";
 import "../chunks/chunk-WFB5TXRA.js";
-import "../chunks/chunk-3ZZSX5HN.js";
-import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-ES2N6V56.js";
+import "../chunks/chunk-XZ2BLAA6.js";
+import "../chunks/chunk-PBENCR5L.js";
 import "../chunks/chunk-IGJCTPFB.js";
+import "../chunks/chunk-ES2N6V56.js";
 import "../chunks/chunk-BPLIXMH7.js";
+import "../chunks/chunk-3ZZSX5HN.js";
+import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-TAMCZHLW.js";
 import "../chunks/chunk-N6FECAXP.js";
 import "../chunks/chunk-2CVHXFK7.js";

package/dist/tubeMap/warp.js

@@ -1,8 +1,10 @@
 import {
+  MAX_GAP_PX,
   referenceKnots,
   warpX
-} from "../chunks/chunk-IJYFJVIT.js";
+} from "../chunks/chunk-HK5Y2YWV.js";
 export {
+  MAX_GAP_PX,
   referenceKnots,
   warpX
 };

package/dist/types/figureData.d.ts

@@ -0,0 +1,146 @@
+import type { BubbleSpread } from './bubbleSpreads.js';
+import type { ColorScheme } from './colorSchemes.js';
+import type { FacetInput } from './facetGrid.js';
+import type { LayoutEngineKind } from './layoutEngines.js';
+import type { LayoutModeValue } from './layoutModes.js';
+import type { NodeWidth } from './nodeWidths.js';
+import type { Graph, LayoutResult } from './types.js';
+import type { WalkLayer } from './walkEncoding.js';
+export interface FigureDataOptions {
+    width?: number;
+    height?: number;
+    walks?: WalkLayer[];
+    facet?: FacetInput;
+    colorScheme?: ColorScheme;
+    nodeWidth?: NodeWidth;
+    showDeletionEdges?: boolean;
+    linearLayout?: boolean;
+    contigThickness?: number;
+    connectorThickness?: number;
+    region?: {
+        refName: string;
+        start: number;
+        end: number;
+    };
+    referenceName?: string;
+    colorDomain?: {
+        start: number;
+        end: number;
+    };
+    fitToDrawing?: boolean;
+}
+type Columns<T> = {
+    [K in keyof T]: T[K][];
+};
+interface NodeRow {
+    panel: string;
+    node: string;
+    stroke: number;
+    x: number;
+    y: number;
+    color: string;
+    alpha: number;
+    width: number;
+}
+interface EdgeRow {
+    panel: string;
+    edge: number;
+    curve: number;
+    x0: number;
+    y0: number;
+    cx0: number;
+    cy0: number;
+    cx1: number;
+    cy1: number;
+    x1: number;
+    y1: number;
+    color: string;
+    alpha: number;
+    width: number;
+    deletion: boolean;
+}
+interface ArrowRow {
+    panel: string;
+    edge: number;
+    x: number;
+    y: number;
+    angle: number;
+    length: number;
+    halfWidth: number;
+    color: string;
+    alpha: number;
+}
+export declare function figureData(graph: Graph, layout: LayoutResult, o?: FigureDataOptions): {
+    meta: {
+        generator: string;
+        width: number;
+        scaleX: number;
+        scaleY: number;
+        pixelRows: boolean;
+        referenceAxis: boolean;
+        colorScheme: import("./colorSchemes.js").ResolvedColorScheme;
+        referenceName: string | null;
+    };
+    panels: {
+        panel: string[];
+        key: string[];
+        range: string[];
+    };
+    nodes: Columns<NodeRow>;
+    edges: Columns<EdgeRow>;
+    arrows: Columns<ArrowRow>;
+    nodeInfo: {
+        node: string[];
+        name: string[];
+        length: number[];
+        depth: number[];
+        backbone: boolean[];
+    };
+    rowLabels: {
+        label: string[];
+        y: number[];
+    };
+};
+export interface GfaFigureSpec extends Omit<FigureDataOptions, 'region' | 'walks'> {
+    region?: string;
+    walks?: (string | WalkLayer)[];
+    layout?: LayoutModeValue;
+    referencePath?: string;
+    quality?: number;
+    bubbleSpread?: BubbleSpread;
+    engine?: LayoutEngineKind;
+    spacing?: number;
+    componentSeparation?: number;
+}
+export declare function gfaFigureData(text: string, name: string, spec?: GfaFigureSpec): Promise<{
+    meta: {
+        generator: string;
+        width: number;
+        scaleX: number;
+        scaleY: number;
+        pixelRows: boolean;
+        referenceAxis: boolean;
+        colorScheme: import("./colorSchemes.js").ResolvedColorScheme;
+        referenceName: string | null;
+    };
+    panels: {
+        panel: string[];
+        key: string[];
+        range: string[];
+    };
+    nodes: Columns<NodeRow>;
+    edges: Columns<EdgeRow>;
+    arrows: Columns<ArrowRow>;
+    nodeInfo: {
+        node: string[];
+        name: string[];
+        length: number[];
+        depth: number[];
+        backbone: boolean[];
+    };
+    rowLabels: {
+        label: string[];
+        y: number[];
+    };
+}>;
+export {};

package/dist/types/index.d.ts

@@ -50,6 +50,8 @@ export type { DeletionDrawing, DeletionEdge } from './deletionEdges.js';
 export { facetLifts, walkHighlight, walkLift } from './walkHighlight.js';
 export { rangeText, walkKey, walkPosition } from './walkKey.js';
 export { figureSvg } from './figure.js';
+export { figureData, gfaFigureData } from './figureData.js';
+export type { FigureDataOptions, GfaFigureSpec } from './figureData.js';
 export { genesFromBed, genesFromGff3Lines, genesFromText, mergeOverlappingByName, } from './genes/geneFiles.js';
 export { HPRC_GBZ, cutGbzRegion, openGbz, parseRegion } from './gbzCut.js';
 export type { GbzSource } from './gbzCut.js';

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

@@ -0,0 +1,2 @@
+import type { NodeSegment } from '../types.js';
+export declare function smoothChain(line: NodeSegment[]): NodeSegment[];

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

@@ -61,7 +61,7 @@ export interface TubeMapPicture {
     mismatches: TubeMapMismatch[];
 }
 export declare function trackColors(layout: TubeMapLayout, pathColors: readonly string[]): ReadonlyMap<number, string>;
-export declare function tubeMapPicture({ layout, pathColors, graph, }: Pick<TubeMapDrawing, 'layout' | 'pathColors'> & Partial<Pick<TubeMapDrawing, 'graph'>>): TubeMapPicture;
+export declare function tubeMapPicture({ layout, pathColors, graph, columns, }: Pick<TubeMapDrawing, 'layout' | 'pathColors'> & Partial<Pick<TubeMapDrawing, 'graph' | 'columns'>>): TubeMapPicture;
 export interface TubeMapFrame extends TubeMapTransform {
     width: number;
     highlightNode?: string | null;

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

@@ -3,5 +3,6 @@ export interface Knot {
     tx: number;
     sx: number;
 }
+export declare const MAX_GAP_PX = 24;
 export declare function referenceKnots(columns: readonly TubeMapColumn[], bpToScreen: (bp: number) => number): Knot[];
 export declare function warpX(knots: readonly Knot[], tx: number): number;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "9.9.1";
+export declare const version = "9.10.0";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-EC4UZHWQ.js";
+} from "./chunks/chunk-2VTM3DHG.js";
 export {
   version
 };

package/dist/viewport.js

@@ -5,18 +5,19 @@ import {
   screenToLayout,
   viewportOf,
   zoomAbout
-} from "./chunks/chunk-ZBLKAWSD.js";
-import "./chunks/chunk-FPTI3WAV.js";
-import "./chunks/chunk-PUG7LXDF.js";
+} from "./chunks/chunk-PT37VS5B.js";
+import "./chunks/chunk-HRAU4VTB.js";
 import "./chunks/chunk-IGVV37VI.js";
+import "./chunks/chunk-OPPVSPEF.js";
+import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-J7YKQ5YW.js";
 import "./chunks/chunk-G45YY72K.js";
 import "./chunks/chunk-OA7RIMZ2.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
 import "./chunks/chunk-JVLURPFW.js";
-import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-IGJCTPFB.js";
+import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-TAMCZHLW.js";
 import "./chunks/chunk-UVBGRJQX.js";

package/dist/walkEncoding.js

@@ -9,17 +9,17 @@ import {
   schemeColor,
   schemeCss,
   schemeRgb
-} from "./chunks/chunk-F5BYHLIN.js";
-import "./chunks/chunk-F4BKWWLS.js";
+} from "./chunks/chunk-KYY5363X.js";
+import "./chunks/chunk-4IYP43W6.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-EDASNMLY.js";
-import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-WFB5TXRA.js";
-import "./chunks/chunk-3ZZSX5HN.js";
-import "./chunks/chunk-AB35TJST.js";
-import "./chunks/chunk-ES2N6V56.js";
+import "./chunks/chunk-XZ2BLAA6.js";
+import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-IGJCTPFB.js";
+import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-BPLIXMH7.js";
+import "./chunks/chunk-3ZZSX5HN.js";
+import "./chunks/chunk-AB35TJST.js";
 import "./chunks/chunk-TAMCZHLW.js";
 import "./chunks/chunk-N6FECAXP.js";
 import "./chunks/chunk-2CVHXFK7.js";

package/dist/walkHighlight.js

@@ -2,18 +2,18 @@ import {
   facetLifts,
   walkHighlight,
   walkLift
-} from "./chunks/chunk-EE37PVQY.js";
-import "./chunks/chunk-F5BYHLIN.js";
-import "./chunks/chunk-F4BKWWLS.js";
+} from "./chunks/chunk-MVMP6AGI.js";
+import "./chunks/chunk-KYY5363X.js";
+import "./chunks/chunk-4IYP43W6.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-EDASNMLY.js";
-import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-WFB5TXRA.js";
-import "./chunks/chunk-3ZZSX5HN.js";
-import "./chunks/chunk-AB35TJST.js";
-import "./chunks/chunk-ES2N6V56.js";
+import "./chunks/chunk-XZ2BLAA6.js";
+import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-IGJCTPFB.js";
+import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-BPLIXMH7.js";
+import "./chunks/chunk-3ZZSX5HN.js";
+import "./chunks/chunk-AB35TJST.js";
 import "./chunks/chunk-TAMCZHLW.js";
 import "./chunks/chunk-N6FECAXP.js";
 import "./chunks/chunk-2CVHXFK7.js";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "9.9.1",
+  "version": "9.10.0",
   "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": {
@@ -37,7 +37,7 @@
   "dependencies": {
     "@gmod/gbz-base": "^7.0.0",
     "@gmod/tabix": "^3.9.1",
-    "@jbrowse/tubemap-core": "^0.2.3"
+    "@jbrowse/tubemap-core": "^0.2.4"
   },
   "devDependencies": {
     "@eslint/js": "^10.0.1",

package/dist/chunks/{chunk-ROQGMTFB.js → chunk-5GZEPPEW.js}

@@ -1,3 +1,8 @@
+import {
+  bubblesFromGraph,
+  walkIndexOf,
+  walkRoutes
+} from "./chunk-CLOP7UVD.js";
 import {
   bubbleSubgraph
 } from "./chunk-A6PSWTLX.js";
@@ -7,11 +12,6 @@ import {
 import {
   bubbleSegmentIds
 } from "./chunk-XKWD2RY3.js";
-import {
-  bubblesFromGraph,
-  walkIndexOf,
-  walkRoutes
-} from "./chunk-CLOP7UVD.js";
 import {
   SATURATED_PATH_COUNT
 } from "./chunk-FX4RDMDN.js";

package/dist/chunks/{chunk-EDASNMLY.js → chunk-XZ2BLAA6.js}

@@ -1,12 +1,12 @@
-import {
-  groupDigits
-} from "./chunk-3ZZSX5HN.js";
 import {
   pathOrigin
 } from "./chunk-IGJCTPFB.js";
 import {
   isGenericSample
 } from "./chunk-BPLIXMH7.js";
+import {
+  groupDigits
+} from "./chunk-3ZZSX5HN.js";
 
 // src/pathColors.ts
 function nameHue(name) {