@jbrowse/bandage-core 7.5.1 → 8.0.0

package/dist/chunks/{chunk-7ESIZZO7.js → chunk-5ARDFGLJ.js}

@@ -42,7 +42,7 @@ import {
 } from "./chunk-RCWYY6XA.js";
 import {
   version
-} from "./chunk-CNGKWYUC.js";
+} from "./chunk-XMNHWMGM.js";
 import {
   axisScaleOf
 } from "./chunk-4UBWXZVX.js";

package/dist/chunks/{chunk-EJ5OZTCK.js → chunk-733L2TS6.js}

@@ -1,5 +1,5 @@
 // src/tubeMap/mismatches.ts
-import { forward, getXCoordinateOfBaseWithinNode } from "@gmod/tubemap-core";
+import { forward, getXCoordinateOfBaseWithinNode } from "@jbrowse/tubemap-core";
 function readMismatches(read, layout) {
   const marks = [];
   const entries = read.sequenceNew ?? [];

package/dist/chunks/{chunk-CR7EGAFE.js → chunk-KCRL5JB2.js}

@@ -1,9 +1,12 @@
 import {
   tubeMapMismatches
-} from "./chunk-EJ5OZTCK.js";
+} from "./chunk-733L2TS6.js";
+import {
+  readColor
+} from "./chunk-TEDQJPMI.js";
 
 // src/tubeMap/draw.ts
-import { curvePaths, nodeOutlinePath } from "@gmod/tubemap-core";
+import { curvePaths, nodeOutlinePath } from "@jbrowse/tubemap-core";
 function parsePath(d) {
   const tokens = d.trim().split(/[\s,]+/);
   const commands = [];
@@ -50,29 +53,41 @@ function extentOf(commands) {
   }
   return { x0, x1 };
 }
-function shapeOf(d, color, alpha, track) {
+function shapeOf(d, color, track) {
   const commands = parsePath(d);
-  return { commands, color, track, alpha, ...extentOf(commands) };
+  return { commands, color, track, ...extentOf(commands) };
+}
+function trackColors(layout, pathColors) {
+  return new Map(
+    layout.tracks.map((track) => [
+      track.id,
+      track.type === "read" ? readColor(track) : pathColors[track.id]
+    ])
+  );
 }
-function layerOf(layout, type) {
+function layerOf(layout, type, colors) {
   const { shapes } = layout;
+  const colorOf = (s) => colors.get(s.id);
   const trackOf = (s) => type === "haplotype" ? s.id : void 0;
   const rects = [...shapes.rectangles, ...shapes.verticalRectangles].filter((r) => r.type === type).map((r) => ({
-    color: r.color,
+    color: colorOf(r),
     track: trackOf(r),
-    alpha: r.alpha ?? 1,
     x0: r.xStart,
     x1: r.xEnd + 1,
     y0: r.yStart,
     y1: r.yEnd + 1
   }));
   const curves = curvePaths(shapes.curves, type).map(
-    (c) => shapeOf(c.path, c.color, c.alpha ?? 1, trackOf(c))
+    (c) => shapeOf(c.path, colorOf(c), trackOf(c))
   );
-  const corners = shapes.corners.filter((c) => c.type === type).map((c) => shapeOf(c.path, c.color, 1, trackOf(c)));
+  const corners = shapes.corners.filter((c) => c.type === type).map((c) => shapeOf(c.path, colorOf(c), trackOf(c)));
   return { rects, shapes: [...curves, ...corners] };
 }
-function tubeMapPicture(layout) {
+function tubeMapPicture({
+  layout,
+  pathColors
+}) {
+  const colors = trackColors(layout, pathColors);
   const nodes = [];
   layout.nodes.forEach((node) => {
     if (node.order >= 0) {
@@ -82,7 +97,10 @@ function tubeMapPicture(layout) {
   });
   return {
     bounds: layout.bounds,
-    layers: [layerOf(layout, "haplotype"), layerOf(layout, "read")],
+    layers: [
+      layerOf(layout, "haplotype", colors),
+      layerOf(layout, "read", colors)
+    ],
     nodes,
     mismatches: tubeMapMismatches(layout).filter(
       (m) => m.kind !== "insertion" || !m.softClip
@@ -132,25 +150,23 @@ function fillByColor(ctx, items, visible, colorOf, addTo) {
   const byColor = /* @__PURE__ */ new Map();
   for (const item of items) {
     if (visible(item)) {
-      const key = `${colorOf(item)}|${item.alpha}`;
-      const list = byColor.get(key);
+      const color = colorOf(item);
+      const list = byColor.get(color);
       if (list) {
         list.push(item);
       } else {
-        byColor.set(key, [item]);
+        byColor.set(color, [item]);
       }
     }
   }
   for (const list of byColor.values()) {
     ctx.fillStyle = colorOf(list[0]);
-    ctx.globalAlpha = list[0].alpha;
     ctx.beginPath();
     for (const item of list) {
       addTo(item);
     }
     ctx.fill();
   }
-  ctx.globalAlpha = 1;
 }
 var FULL_OUTLINE_PX = 12;
 var MIN_OUTLINE_ALPHA = 0.15;
@@ -162,6 +178,7 @@ function drawTubeMap(ctx, picture, frame) {
   const { x, y, width } = frame;
   const visible = (item) => x(item.x1) >= 0 && x(item.x0) <= width;
   const colorOf = (item) => item.track !== void 0 && frame.tubeColors?.[item.track] || item.color;
+  ctx.globalAlpha = 1;
   for (const layer of picture.layers) {
     fillByColor(ctx, layer.rects, visible, colorOf, (r) => {
       const left = x(r.x0);
@@ -234,6 +251,7 @@ function drawMismatches(ctx, marks, frame) {
 
 export {
   parsePath,
+  trackColors,
   tubeMapPicture,
   drawTubeMap,
   mismatchesLegible,

package/dist/chunks/{chunk-AYOSNXLQ.js → chunk-W2I4DOL4.js}

@@ -1,6 +1,5 @@
 import {
   canonicalStrand,
-  readColor,
   stepName,
   tubeMapReads
 } from "./chunk-TEDQJPMI.js";
@@ -16,7 +15,7 @@ import {
 } from "./chunk-FYQWPEEY.js";
 
 // src/layout/tubeMapLayout.ts
-import { layoutTubeMap } from "@gmod/tubemap-core";
+import { layoutTubeMap } from "@jbrowse/tubemap-core";
 function visitStrands(graph) {
   const strands = /* @__PURE__ */ new Map();
   for (const [segment, visits] of graph.pathVisits ?? []) {
@@ -93,8 +92,7 @@ function runTubeMap(graph) {
   const pathColors = paths.map((_, i) => tubeColor(i, paths.length));
   const layout = layoutTubeMap(tubeMapNodes(graph), tracks, reads, {
     nodeWidthOption: "compressed",
-    trackWidth: tubeWidth(tracks.length),
-    trackColor: (track) => track.type === "read" ? readColor(track) : pathColors[track.id]
+    trackWidth: tubeWidth(tracks.length)
   });
   return layout ? { layout, pathColors } : void 0;
 }

package/dist/chunks/{chunk-CNGKWYUC.js → chunk-XMNHWMGM.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "7.5.1";
+var version = "8.0.0";
 
 export {
   version

package/dist/chunks/{chunk-FRR2RGBT.js → chunk-ZJQ6H3AR.js}

@@ -5,7 +5,7 @@ import {
   hasTubeMapPaths,
   tubeMapLayout,
   tubeMapReferenceLayout
-} from "./chunk-AYOSNXLQ.js";
+} from "./chunk-W2I4DOL4.js";
 import {
   anchoredLayout
 } from "./chunk-L3O7AWLI.js";

package/dist/cli/figure.js

@@ -7,9 +7,9 @@ import {
 import {
   LAYOUT_MODES,
   layoutModeByValue
-} from "../chunks/chunk-FRR2RGBT.js";
+} from "../chunks/chunk-ZJQ6H3AR.js";
 import "../chunks/chunk-LOEA5IHZ.js";
-import "../chunks/chunk-AYOSNXLQ.js";
+import "../chunks/chunk-W2I4DOL4.js";
 import "../chunks/chunk-TEDQJPMI.js";
 import "../chunks/chunk-L3O7AWLI.js";
 import "../chunks/chunk-TZFWUT2C.js";
@@ -35,7 +35,7 @@ import "../chunks/chunk-LYJ4US66.js";
 import "../chunks/chunk-7XHHVYG7.js";
 import {
   figureSvg
-} from "../chunks/chunk-7ESIZZO7.js";
+} from "../chunks/chunk-5ARDFGLJ.js";
 import "../chunks/chunk-LOCJN3BZ.js";
 import "../chunks/chunk-47DYCZOK.js";
 import "../chunks/chunk-ZYHSUNQO.js";
@@ -53,7 +53,7 @@ import "../chunks/chunk-2LQ5BWT7.js";
 import "../chunks/chunk-AVJK272H.js";
 import "../chunks/chunk-RCWYY6XA.js";
 import "../chunks/chunk-UMNCCYBN.js";
-import "../chunks/chunk-CNGKWYUC.js";
+import "../chunks/chunk-XMNHWMGM.js";
 import "../chunks/chunk-4UBWXZVX.js";
 import "../chunks/chunk-MP7LXLWV.js";
 import {

package/dist/figure.js

@@ -1,6 +1,6 @@
 import {
   figureSvg
-} from "./chunks/chunk-7ESIZZO7.js";
+} from "./chunks/chunk-5ARDFGLJ.js";
 import "./chunks/chunk-LOCJN3BZ.js";
 import "./chunks/chunk-47DYCZOK.js";
 import "./chunks/chunk-ZYHSUNQO.js";
@@ -15,7 +15,7 @@ import "./chunks/chunk-2LQ5BWT7.js";
 import "./chunks/chunk-AVJK272H.js";
 import "./chunks/chunk-RCWYY6XA.js";
 import "./chunks/chunk-UMNCCYBN.js";
-import "./chunks/chunk-CNGKWYUC.js";
+import "./chunks/chunk-XMNHWMGM.js";
 import "./chunks/chunk-4UBWXZVX.js";
 import "./chunks/chunk-MP7LXLWV.js";
 import "./chunks/chunk-SZNZ2T6D.js";

package/dist/index.js

@@ -4,7 +4,7 @@ import {
 import {
   drawTubeMap,
   tubeMapPicture
-} from "./chunks/chunk-CR7EGAFE.js";
+} from "./chunks/chunk-KCRL5JB2.js";
 import {
   tubeMapFrame,
   tubeMapNodeAt
@@ -13,7 +13,7 @@ import {
   drawTubeMapGenes,
   tubeMapGenes
 } from "./chunks/chunk-OWFPAIJI.js";
-import "./chunks/chunk-EJ5OZTCK.js";
+import "./chunks/chunk-733L2TS6.js";
 import {
   tubeMapNodeColors
 } from "./chunks/chunk-KEVQ46GG.js";
@@ -69,9 +69,9 @@ import {
   LAYOUT_MODES,
   layoutModeByValue,
   modeUsesLayoutEngine
-} from "./chunks/chunk-FRR2RGBT.js";
+} from "./chunks/chunk-ZJQ6H3AR.js";
 import "./chunks/chunk-LOEA5IHZ.js";
-import "./chunks/chunk-AYOSNXLQ.js";
+import "./chunks/chunk-W2I4DOL4.js";
 import "./chunks/chunk-TEDQJPMI.js";
 import "./chunks/chunk-L3O7AWLI.js";
 import "./chunks/chunk-TZFWUT2C.js";
@@ -112,7 +112,7 @@ import {
 } from "./chunks/chunk-7XHHVYG7.js";
 import {
   figureSvg
-} from "./chunks/chunk-7ESIZZO7.js";
+} from "./chunks/chunk-5ARDFGLJ.js";
 import {
   layoutGeometryInputs
 } from "./chunks/chunk-LOCJN3BZ.js";
@@ -204,7 +204,7 @@ import {
 import "./chunks/chunk-UMNCCYBN.js";
 import {
   version
-} from "./chunks/chunk-CNGKWYUC.js";
+} from "./chunks/chunk-XMNHWMGM.js";
 import {
   axisScaleOf,
   contains,

package/dist/layout/tubeMapLayout.js

@@ -5,7 +5,7 @@ import {
   tubeMapTracks,
   tubeWidth,
   visitStrands
-} from "../chunks/chunk-AYOSNXLQ.js";
+} from "../chunks/chunk-W2I4DOL4.js";
 import "../chunks/chunk-TEDQJPMI.js";
 import "../chunks/chunk-C44YRP5F.js";
 import "../chunks/chunk-7GBL7SJY.js";

package/dist/layoutModes.js

@@ -4,9 +4,9 @@ import {
   LAYOUT_MODE_VALUES,
   layoutModeByValue,
   modeUsesLayoutEngine
-} from "./chunks/chunk-FRR2RGBT.js";
+} from "./chunks/chunk-ZJQ6H3AR.js";
 import "./chunks/chunk-LOEA5IHZ.js";
-import "./chunks/chunk-AYOSNXLQ.js";
+import "./chunks/chunk-W2I4DOL4.js";
 import "./chunks/chunk-TEDQJPMI.js";
 import "./chunks/chunk-L3O7AWLI.js";
 import "./chunks/chunk-TZFWUT2C.js";

package/dist/tubeMap/coarsen.js

@@ -1,6 +1,6 @@
 import {
   visitStrands
-} from "../chunks/chunk-AYOSNXLQ.js";
+} from "../chunks/chunk-W2I4DOL4.js";
 import {
   canonicalStrand
 } from "../chunks/chunk-TEDQJPMI.js";

package/dist/tubeMap/draw.js

@@ -3,13 +3,17 @@ import {
   mismatchOnScreen,
   mismatchesLegible,
   parsePath,
+  trackColors,
   tubeMapPicture
-} from "../chunks/chunk-CR7EGAFE.js";
-import "../chunks/chunk-EJ5OZTCK.js";
+} from "../chunks/chunk-KCRL5JB2.js";
+import "../chunks/chunk-733L2TS6.js";
+import "../chunks/chunk-TEDQJPMI.js";
+import "../chunks/chunk-C44YRP5F.js";
 export {
   drawTubeMap,
   mismatchOnScreen,
   mismatchesLegible,
   parsePath,
+  trackColors,
   tubeMapPicture
 };

package/dist/tubeMap/mismatches.js

@@ -1,6 +1,6 @@
 import {
   tubeMapMismatches
-} from "../chunks/chunk-EJ5OZTCK.js";
+} from "../chunks/chunk-733L2TS6.js";
 export {
   tubeMapMismatches
 };

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

@@ -1,6 +1,6 @@
 import type { Coarsened } from '../tubeMap/coarsen.js';
 import type { Graph, LayoutResult } from '../types.js';
-import type { InputTrack, TubeMapLayout } from '@gmod/tubemap-core';
+import type { InputTrack, TubeMapLayout } from '@jbrowse/tubemap-core';
 export interface TubeMapColumn {
     order: number;
     x0: number;

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

@@ -1,6 +1,6 @@
 import type { TubeMapFrame } from './draw.js';
 import type { Graph } from '../types.js';
-import type { TubeMapLayout } from '@gmod/tubemap-core';
+import type { TubeMapLayout } from '@jbrowse/tubemap-core';
 export interface Box {
     bp0: number;
     bp1: number;

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

@@ -1,5 +1,5 @@
 import type { Graph } from '../types.js';
-import type { TubeMapLayout } from '@gmod/tubemap-core';
+import type { TubeMapLayout } from '@jbrowse/tubemap-core';
 export interface ReferenceNode {
     node: string;
     bp0: number;

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

@@ -1,7 +1,7 @@
 import type { Deviation } from './coarsen.js';
 import type { TubeMapFrame } from './draw.js';
 import type { Graph } from '../types.js';
-import type { TubeMapLayout } from '@gmod/tubemap-core';
+import type { TubeMapLayout } from '@jbrowse/tubemap-core';
 export interface DeviationMark {
     x0: number;
     x1: number;

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

@@ -1,6 +1,7 @@
 import type { TubeMapTransform } from './frame.js';
 import type { TubeMapMismatch } from './mismatches.js';
-import type { TubeMapLayout } from '@gmod/tubemap-core';
+import type { TubeMapDrawing } from '../layout/tubeMapLayout.js';
+import type { TubeMapLayout } from '@jbrowse/tubemap-core';
 type Command = {
     op: 'M' | 'L';
     x: number;
@@ -32,7 +33,6 @@ export declare function parsePath(d: string): Command[];
 interface Filled {
     color: string;
     track?: number;
-    alpha: number;
     x0: number;
     x1: number;
 }
@@ -58,7 +58,8 @@ export interface TubeMapPicture {
     }[];
     mismatches: TubeMapMismatch[];
 }
-export declare function tubeMapPicture(layout: TubeMapLayout): TubeMapPicture;
+export declare function trackColors(layout: TubeMapLayout, pathColors: readonly string[]): ReadonlyMap<number, string>;
+export declare function tubeMapPicture({ layout, pathColors, }: Pick<TubeMapDrawing, 'layout' | 'pathColors'>): TubeMapPicture;
 export interface TubeMapFrame extends TubeMapTransform {
     width: number;
     highlightNode?: string | null;

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

@@ -1,4 +1,4 @@
-import type { TubeMapLayout } from '@gmod/tubemap-core';
+import type { TubeMapLayout } from '@jbrowse/tubemap-core';
 interface MarkBase {
     readId: number;
     y: number;

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

@@ -1,6 +1,6 @@
 import type { GafRecord } from '../gaf/parseGaf.js';
 import type { Graph, GraphNode } from '../types.js';
-import type { InputTrack } from '@gmod/tubemap-core';
+import type { InputTrack } from '@jbrowse/tubemap-core';
 export declare function canonicalStrand(node: GraphNode): "+" | "-";
 export declare function stepName(node: GraphNode, strand: '+' | '-'): string;
 export declare function tubeMapReads(graph: Graph, records: readonly GafRecord[], firstId: number): InputTrack[];

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "7.5.1";
+export declare const version = "8.0.0";

package/dist/version.js

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

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "7.5.1",
+  "version": "8.0.0",
   "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": {
@@ -36,7 +36,7 @@
   "dependencies": {
     "@gmod/gbz-base": "^7.0.0",
     "@gmod/tabix": "^3.9.1",
-    "@gmod/tubemap-core": "^0.1.0"
+    "@jbrowse/tubemap-core": "^0.2.1"
   },
   "devDependencies": {
     "@eslint/js": "^10.0.1",