@jbrowse/bandage-core 11.12.0 → 11.14.0

package/dist/chunks/{chunk-UFF34SGO.js → chunk-ZHCQOC67.js}

@@ -1,7 +1,7 @@
 import {
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-EH5OIV2E.js";
+} from "./chunk-JUYPCLF4.js";
 import {
   abgrToCssRgba
 } from "./chunk-G2FD7S3C.js";

package/dist/cli/figure.js

@@ -9,7 +9,7 @@ import "../chunks/chunk-EQDQ7P4Y.js";
 import {
   laidOutGraph,
   walkLayers
-} from "../chunks/chunk-5UIYXKTA.js";
+} from "../chunks/chunk-JUVIPVXX.js";
 import {
   LAYOUT_ENGINE_VALUES,
   isLayoutEngineKind
@@ -36,28 +36,28 @@ import "../chunks/chunk-ZKSC7QVE.js";
 import "../chunks/chunk-HNWJ4B7S.js";
 import {
   figureSvg
-} from "../chunks/chunk-Q2AMKXAX.js";
+} from "../chunks/chunk-CLY6DKIU.js";
 import "../chunks/chunk-V4YML3GR.js";
-import "../chunks/chunk-T2LYWZ5Q.js";
+import "../chunks/chunk-QL673EK5.js";
 import "../chunks/chunk-4DMSPNYV.js";
 import "../chunks/chunk-RBCE2OQH.js";
 import {
   genesOnRow,
   placeRowGenes
-} from "../chunks/chunk-A6ABMJR5.js";
+} from "../chunks/chunk-OYBYCF2O.js";
 import "../chunks/chunk-JSUCGZ6K.js";
 import "../chunks/chunk-TQ26XEFL.js";
 import "../chunks/chunk-4JDO7ZLN.js";
 import "../chunks/chunk-7YSIP3O2.js";
 import "../chunks/chunk-HEYIAMTC.js";
-import "../chunks/chunk-TOGXPJK7.js";
+import "../chunks/chunk-FXUAVF4A.js";
 import "../chunks/chunk-OKPSS5PG.js";
-import "../chunks/chunk-6ROK45LO.js";
+import "../chunks/chunk-XBX3HSC7.js";
 import "../chunks/chunk-LOCJN3BZ.js";
-import "../chunks/chunk-QOY6SPOS.js";
-import "../chunks/chunk-JQYK6GVJ.js";
-import "../chunks/chunk-EH5OIV2E.js";
-import "../chunks/chunk-4KBZ7WPP.js";
+import "../chunks/chunk-MB4UWYDG.js";
+import "../chunks/chunk-EOB4Y3EM.js";
+import "../chunks/chunk-JUYPCLF4.js";
+import "../chunks/chunk-YUIKEUKY.js";
 import "../chunks/chunk-G2FD7S3C.js";
 import "../chunks/chunk-IZKM4NY7.js";
 import "../chunks/chunk-GQZVR5DW.js";

package/dist/figure.js

@@ -1,24 +1,24 @@
 import {
   figureSvg
-} from "./chunks/chunk-Q2AMKXAX.js";
+} from "./chunks/chunk-CLY6DKIU.js";
 import "./chunks/chunk-V4YML3GR.js";
-import "./chunks/chunk-T2LYWZ5Q.js";
+import "./chunks/chunk-QL673EK5.js";
 import "./chunks/chunk-4DMSPNYV.js";
 import "./chunks/chunk-RBCE2OQH.js";
-import "./chunks/chunk-A6ABMJR5.js";
+import "./chunks/chunk-OYBYCF2O.js";
 import "./chunks/chunk-JSUCGZ6K.js";
 import "./chunks/chunk-TQ26XEFL.js";
 import "./chunks/chunk-4JDO7ZLN.js";
 import "./chunks/chunk-7YSIP3O2.js";
 import "./chunks/chunk-HEYIAMTC.js";
-import "./chunks/chunk-TOGXPJK7.js";
+import "./chunks/chunk-FXUAVF4A.js";
 import "./chunks/chunk-OKPSS5PG.js";
-import "./chunks/chunk-6ROK45LO.js";
+import "./chunks/chunk-XBX3HSC7.js";
 import "./chunks/chunk-LOCJN3BZ.js";
-import "./chunks/chunk-QOY6SPOS.js";
-import "./chunks/chunk-JQYK6GVJ.js";
-import "./chunks/chunk-EH5OIV2E.js";
-import "./chunks/chunk-4KBZ7WPP.js";
+import "./chunks/chunk-MB4UWYDG.js";
+import "./chunks/chunk-EOB4Y3EM.js";
+import "./chunks/chunk-JUYPCLF4.js";
+import "./chunks/chunk-YUIKEUKY.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-IZKM4NY7.js";
 import "./chunks/chunk-GQZVR5DW.js";

package/dist/figureData.js

@@ -3,7 +3,7 @@ import {
   gfaFigureData,
   laidOutGraph,
   walkLayers
-} from "./chunks/chunk-5UIYXKTA.js";
+} from "./chunks/chunk-JUVIPVXX.js";
 import "./chunks/chunk-CO6RGQAD.js";
 import "./chunks/chunk-TEFNVUGD.js";
 import "./chunks/chunk-3JDGPLCL.js";
@@ -18,14 +18,14 @@ import "./chunks/chunk-FNDNSDKW.js";
 import "./chunks/chunk-ZKSC7QVE.js";
 import "./chunks/chunk-HNWJ4B7S.js";
 import "./chunks/chunk-HEYIAMTC.js";
-import "./chunks/chunk-TOGXPJK7.js";
+import "./chunks/chunk-FXUAVF4A.js";
 import "./chunks/chunk-OKPSS5PG.js";
-import "./chunks/chunk-6ROK45LO.js";
+import "./chunks/chunk-XBX3HSC7.js";
 import "./chunks/chunk-LOCJN3BZ.js";
-import "./chunks/chunk-QOY6SPOS.js";
-import "./chunks/chunk-JQYK6GVJ.js";
-import "./chunks/chunk-EH5OIV2E.js";
-import "./chunks/chunk-4KBZ7WPP.js";
+import "./chunks/chunk-MB4UWYDG.js";
+import "./chunks/chunk-EOB4Y3EM.js";
+import "./chunks/chunk-JUYPCLF4.js";
+import "./chunks/chunk-YUIKEUKY.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-IZKM4NY7.js";
 import "./chunks/chunk-GQZVR5DW.js";

package/dist/figureScene.js

@@ -1,11 +1,11 @@
 import {
   figureScene
-} from "./chunks/chunk-6ROK45LO.js";
+} from "./chunks/chunk-XBX3HSC7.js";
 import "./chunks/chunk-LOCJN3BZ.js";
-import "./chunks/chunk-QOY6SPOS.js";
-import "./chunks/chunk-JQYK6GVJ.js";
-import "./chunks/chunk-EH5OIV2E.js";
-import "./chunks/chunk-4KBZ7WPP.js";
+import "./chunks/chunk-MB4UWYDG.js";
+import "./chunks/chunk-EOB4Y3EM.js";
+import "./chunks/chunk-JUYPCLF4.js";
+import "./chunks/chunk-YUIKEUKY.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-IZKM4NY7.js";
 import "./chunks/chunk-GQZVR5DW.js";

package/dist/index.js

@@ -19,7 +19,7 @@ import {
 import "./chunks/chunk-BX4AUMZE.js";
 import {
   tubeMapNodeColors
-} from "./chunks/chunk-UFF34SGO.js";
+} from "./chunks/chunk-ZHCQOC67.js";
 import {
   referenceKnots,
   warpX
@@ -82,7 +82,7 @@ import {
   drawReferenceStrip,
   referenceStripBlocks,
   stripBlockAt
-} from "./chunks/chunk-GGFR4SYO.js";
+} from "./chunks/chunk-K4RGSISK.js";
 import {
   edgeHoverText,
   regionLabel
@@ -97,7 +97,7 @@ import {
 import {
   figureData,
   gfaFigureData
-} from "./chunks/chunk-5UIYXKTA.js";
+} from "./chunks/chunk-JUVIPVXX.js";
 import {
   LAYOUT_ENGINES,
   layoutEngine
@@ -134,7 +134,7 @@ import {
 import "./chunks/chunk-HNWJ4B7S.js";
 import {
   figureSvg
-} from "./chunks/chunk-Q2AMKXAX.js";
+} from "./chunks/chunk-CLY6DKIU.js";
 import {
   svgCanvas
 } from "./chunks/chunk-V4YML3GR.js";
@@ -149,7 +149,7 @@ import {
   walkStripApplies,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunks/chunk-T2LYWZ5Q.js";
+} from "./chunks/chunk-QL673EK5.js";
 import {
   Canvas2DRenderer
 } from "./chunks/chunk-4DMSPNYV.js";
@@ -183,7 +183,7 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunks/chunk-A6ABMJR5.js";
+} from "./chunks/chunk-OYBYCF2O.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
@@ -205,7 +205,7 @@ import {
 } from "./chunks/chunk-HEYIAMTC.js";
 import {
   version
-} from "./chunks/chunk-TOGXPJK7.js";
+} from "./chunks/chunk-FXUAVF4A.js";
 import {
   axisScaleOf,
   contains,
@@ -214,7 +214,7 @@ import {
   viewportOf,
   zoomAbout
 } from "./chunks/chunk-OKPSS5PG.js";
-import "./chunks/chunk-6ROK45LO.js";
+import "./chunks/chunk-XBX3HSC7.js";
 import {
   layoutGeometryInputs
 } from "./chunks/chunk-LOCJN3BZ.js";
@@ -222,7 +222,7 @@ import {
   facetLifts,
   walkHighlight,
   walkLift
-} from "./chunks/chunk-QOY6SPOS.js";
+} from "./chunks/chunk-MB4UWYDG.js";
 import {
   WALK_FIELDS,
   WALK_SCHEMES,
@@ -230,12 +230,12 @@ import {
   encodingSwatchCss,
   resolveEncoding,
   schemeCss
-} from "./chunks/chunk-JQYK6GVJ.js";
+} from "./chunks/chunk-EOB4Y3EM.js";
 import {
   buildGeometry,
   computeReferenceRamp
-} from "./chunks/chunk-EH5OIV2E.js";
-import "./chunks/chunk-4KBZ7WPP.js";
+} from "./chunks/chunk-JUYPCLF4.js";
+import "./chunks/chunk-YUIKEUKY.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import {
   rangeText,

package/dist/layout/walkRowDraw.js

@@ -30,9 +30,9 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "../chunks/chunk-A6ABMJR5.js";
-import "../chunks/chunk-EH5OIV2E.js";
-import "../chunks/chunk-4KBZ7WPP.js";
+} from "../chunks/chunk-OYBYCF2O.js";
+import "../chunks/chunk-JUYPCLF4.js";
+import "../chunks/chunk-YUIKEUKY.js";
 import "../chunks/chunk-G2FD7S3C.js";
 import "../chunks/chunk-GQZVR5DW.js";
 import "../chunks/chunk-P2GJBFNA.js";

package/dist/layout/walkStrip.js

@@ -9,12 +9,12 @@ import {
   walkStripApplies,
   walkStripFrame,
   walkStripLabelsTree
-} from "../chunks/chunk-T2LYWZ5Q.js";
+} from "../chunks/chunk-QL673EK5.js";
 import {
   LABELLED_ROW_PX
-} from "../chunks/chunk-A6ABMJR5.js";
-import "../chunks/chunk-EH5OIV2E.js";
-import "../chunks/chunk-4KBZ7WPP.js";
+} from "../chunks/chunk-OYBYCF2O.js";
+import "../chunks/chunk-JUYPCLF4.js";
+import "../chunks/chunk-YUIKEUKY.js";
 import "../chunks/chunk-G2FD7S3C.js";
 import "../chunks/chunk-GQZVR5DW.js";
 import "../chunks/chunk-P2GJBFNA.js";

package/dist/referenceStrip.js

@@ -7,9 +7,9 @@ import {
   stripBlockAt,
   stripOverhang,
   stripPixels
-} from "./chunks/chunk-GGFR4SYO.js";
-import "./chunks/chunk-EH5OIV2E.js";
-import "./chunks/chunk-4KBZ7WPP.js";
+} from "./chunks/chunk-K4RGSISK.js";
+import "./chunks/chunk-JUYPCLF4.js";
+import "./chunks/chunk-YUIKEUKY.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-GQZVR5DW.js";
 import "./chunks/chunk-P2GJBFNA.js";

package/dist/renderer/GeometryBuilder.js

@@ -11,8 +11,8 @@ import {
   getNodeColor,
   hslToRgb,
   rampFraction
-} from "../chunks/chunk-EH5OIV2E.js";
-import "../chunks/chunk-4KBZ7WPP.js";
+} from "../chunks/chunk-JUYPCLF4.js";
+import "../chunks/chunk-YUIKEUKY.js";
 import "../chunks/chunk-G2FD7S3C.js";
 import {
   REFERENCE_RAMP_MAX_HUE

package/dist/renderer/walkLanes.js

@@ -18,8 +18,9 @@ import {
   passesKey,
   slotCentres,
   threadsPasses,
+  walkSteps,
   walkThreads
-} from "../chunks/chunk-4KBZ7WPP.js";
+} from "../chunks/chunk-YUIKEUKY.js";
 import "../chunks/chunk-JJV2GT2Z.js";
 import "../chunks/chunk-CPMHA4W5.js";
 export {
@@ -42,5 +43,6 @@ export {
   passesKey,
   slotCentres,
   threadsPasses,
+  walkSteps,
   walkThreads
 };

package/dist/tubeMap/nodeColors.js

@@ -1,8 +1,8 @@
 import {
   tubeMapNodeColors
-} from "../chunks/chunk-UFF34SGO.js";
-import "../chunks/chunk-EH5OIV2E.js";
-import "../chunks/chunk-4KBZ7WPP.js";
+} from "../chunks/chunk-ZHCQOC67.js";
+import "../chunks/chunk-JUYPCLF4.js";
+import "../chunks/chunk-YUIKEUKY.js";
 import "../chunks/chunk-G2FD7S3C.js";
 import "../chunks/chunk-GQZVR5DW.js";
 import "../chunks/chunk-P2GJBFNA.js";

package/dist/types/figureData.d.ts

@@ -102,6 +102,7 @@ export declare function figureData(graph: Graph, layout: LayoutResult, o?: Figur
             end: number;
         } | null;
         deletions: number;
+        fadedKey: string | null;
     };
     panels: {
         panel: string[];
@@ -161,6 +162,7 @@ export declare function gfaFigureData(text: string, name: string, spec?: GfaFigu
             end: number;
         } | null;
         deletions: number;
+        fadedKey: string | null;
     };
     panels: {
         panel: string[];

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

@@ -31,6 +31,7 @@ export interface NodeStroke {
         ny: number;
     }[];
     offsetX?: number;
+    offsets?: number[];
 }
 export interface Arrowhead {
     x: number;

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

@@ -28,41 +28,56 @@ export declare const passesKey: (walks: readonly {
     mostPasses: number;
 }[]) => "a thread per pass through a node" | "a thread per pass through a node, thinned to fit";
 export declare function laneSlideAt(start: LaneSlide, end: LaneSlide, along: number): LaneSlide;
-interface LinePoint {
-    x: number;
-    y: number;
+export interface LaneRun {
+    walk: number;
+    ids: string[];
+    visits: number[];
+    forward: boolean[];
+    owned: boolean[];
+    starts: number[];
+    xs: Float64Array;
+    ys: Float64Array;
+    stepOf: Int32Array;
+}
+export interface WalkStep {
     id: string;
-    index: number;
-    middle: boolean;
-    forward: boolean;
+    visit: number;
+    owned: boolean;
+    segments: NodeSegment[] | undefined;
 }
-export interface LaneRuns {
-    runs: LinePoint[][];
-    owned: boolean[][];
+export declare function walkSteps(walkRoutes: readonly (readonly (readonly string[])[])[], nodePositions: Record<string, NodeSegment[]>): WalkStep[][][];
+export declare function laneRuns(steps: readonly (readonly (readonly WalkStep[])[])[], yToX: number, jump: number): LaneRun[];
+export interface VisitFrame {
+    normals: (Normal | undefined)[];
+    shifts: (Shift | undefined)[];
+    offset?: number;
+    offsets?: number[];
 }
-export declare function laneRuns(routes: readonly (readonly string[])[], nodePositions: Record<string, NodeSegment[]>, yToX: number, jump: number): LaneRuns;
-export declare function laneLines(lanes: LaneRuns, nodePositions: Record<string, NodeSegment[]>, yToX: number, reach: number, band: number, smooth?: boolean): {
-    normals: Map<string, (Normal | undefined)[]>;
-    shifts: Map<string, (Shift | undefined)[]>;
+export declare function laneLines(runs: readonly LaneRun[], yToX: number, reach: number, band: number, smooth?: boolean): {
+    frames: Map<string, VisitFrame[][]>;
+    arcs: Float64Array<ArrayBufferLike>[];
+    stepFrames: VisitFrame[][];
 };
 export interface WalkThreads {
     span: ReadonlyMap<string, number>;
     nodeThreads: Map<string, readonly number[]>;
     threadPasses: Map<string, readonly number[]>;
+    threadAt: Map<string, readonly number[]>;
     linkThreads: Map<string, Map<string, [number, number][]>>;
 }
 export declare function walkThreads(route: readonly (readonly string[])[], passes: ReadonlyMap<string, number>, nodePositions: Record<string, NodeSegment[]>, yToX: number, reach: number): WalkThreads;
-export declare function bandSpans(lanes: LaneRuns, spans: readonly ReadonlyMap<string, number>[], { reach, taper }: {
+export declare function bandSpans(runs: readonly LaneRun[], arcs: readonly ArrayLike<number>[], spans: readonly ReadonlyMap<string, number>[], { reach, taper }: {
     reach: number;
     taper: number;
 }): Map<string, {
     slot: number[];
     held: number[];
 }>;
-export declare function liftLanes(walks: readonly LiftedWalk[], nodePositions: Record<string, NodeSegment[]>, yToX: number, worldPerScreenPx: number): {
+export declare function liftLanes(walks: readonly LiftedWalk[], nodePositions: Record<string, NodeSegment[]>, yToX: number, worldPerScreenPx: number, steps?: WalkStep[][][]): {
     lines: {
-        normals: Map<string, (Normal | undefined)[]>;
-        shifts: Map<string, (Shift | undefined)[]>;
+        frames: Map<string, VisitFrame[][]>;
+        arcs: Float64Array<ArrayBufferLike>[];
+        stepFrames: VisitFrame[][];
     };
     threads: WalkThreads[] | undefined;
     spans: Map<string, {
@@ -74,4 +89,3 @@ export declare function liftLanes(walks: readonly LiftedWalk[], nodePositions: R
         dy: number;
     };
 };
-export {};

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "11.12.0";
+export declare const version = "11.14.0";

package/dist/types/walkHighlight.d.ts

@@ -39,6 +39,7 @@ export interface WalkLift {
     edgeIndexes: Set<number>;
     names: Set<string>;
 }
+export declare function fadedKey(graph: Graph, lift: WalkLift, walks: string): string;
 export declare function walkHighlight(graph: Graph, name: string): WalkHighlight | undefined;
 export declare function walkLift(graph: Graph, layers: readonly WalkLayer[], ramp?: ReferenceRamp): WalkLift | undefined;
 export declare function facetLifts(graph: Graph, lift: WalkLift, layers: readonly WalkLayer[], ramp?: ReferenceRamp): WalkLift[];

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-TOGXPJK7.js";
+} from "./chunks/chunk-FXUAVF4A.js";
 export {
   version
 };

package/dist/walkEncoding.js

@@ -10,9 +10,9 @@ import {
   schemeCss,
   schemeRgb,
   splitFamilies
-} from "./chunks/chunk-JQYK6GVJ.js";
-import "./chunks/chunk-EH5OIV2E.js";
-import "./chunks/chunk-4KBZ7WPP.js";
+} from "./chunks/chunk-EOB4Y3EM.js";
+import "./chunks/chunk-JUYPCLF4.js";
+import "./chunks/chunk-YUIKEUKY.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-GQZVR5DW.js";
 import "./chunks/chunk-P2GJBFNA.js";

package/dist/walkHighlight.js

@@ -1,11 +1,12 @@
 import {
   facetLifts,
+  fadedKey,
   walkHighlight,
   walkLift
-} from "./chunks/chunk-QOY6SPOS.js";
-import "./chunks/chunk-JQYK6GVJ.js";
-import "./chunks/chunk-EH5OIV2E.js";
-import "./chunks/chunk-4KBZ7WPP.js";
+} from "./chunks/chunk-MB4UWYDG.js";
+import "./chunks/chunk-EOB4Y3EM.js";
+import "./chunks/chunk-JUYPCLF4.js";
+import "./chunks/chunk-YUIKEUKY.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-GQZVR5DW.js";
 import "./chunks/chunk-P2GJBFNA.js";
@@ -30,6 +31,7 @@ import "./chunks/chunk-DAEEMZ74.js";
 import "./chunks/chunk-2JL2JVZ2.js";
 export {
   facetLifts,
+  fadedKey,
   walkHighlight,
   walkLift
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "11.12.0",
+  "version": "11.14.0",
   "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": {