@jbrowse/bandage-core 10.2.2 → 10.2.4

package/dist/chunks/chunk-JA2HJIYS.js

@@ -0,0 +1,71 @@
+import {
+  bubbleSegmentIds,
+  classifyBubble
+} from "./chunk-URZ3CH2R.js";
+import {
+  svgPath
+} from "./chunk-7SRWJLSC.js";
+import {
+  isBackbone
+} from "./chunk-FYQWPEEY.js";
+
+// src/bubbles/bubbleHalos.ts
+var WHOLE_FRACTION = 0.9;
+function coversGraph(members, nodes) {
+  return members + 2 >= nodes || members >= WHOLE_FRACTION * nodes;
+}
+var SMALL_VARIANT_BP = 50;
+function bubbleHalos(graph, bubbles, positions, repeats = []) {
+  const byName = new Map(graph.nodes.map((n) => [n.name, n]));
+  const halos = [];
+  for (const bubble of bubbles) {
+    const parts = [];
+    let minX = Infinity;
+    let maxX = -Infinity;
+    let minY = Infinity;
+    const nodeIds = [];
+    const names = bubbleSegmentIds(bubble);
+    for (const [i, name] of names.entries()) {
+      const node = byName.get(name);
+      const line = node && positions[node.id];
+      if (!node || !line?.length) {
+        continue;
+      }
+      if (bubble.key ? i === 0 || i === names.length - 1 : isBackbone(node) && (node.stable.start < bubble.start || node.stable.start >= bubble.end)) {
+        continue;
+      }
+      nodeIds.push(node.id);
+      parts.push(svgPath(line.length === 1 ? [line[0], line[0]] : line));
+      for (const p of line) {
+        minX = Math.min(minX, p.x);
+        maxX = Math.max(maxX, p.x);
+        minY = Math.min(minY, p.y);
+      }
+    }
+    if (nodeIds.length === 0) {
+      continue;
+    }
+    const labelAt = { x: (minX + maxX) / 2, y: minY };
+    const whole = bubble.covering === true || coversGraph(nodeIds.length, graph.nodes.length);
+    halos.push({
+      bubble,
+      ...classifyBubble(bubble, repeats),
+      path: parts.join(""),
+      labelAt,
+      members: nodeIds.length,
+      nodeIds,
+      whole,
+      // The drawing's own bubble keeps its name however small. A partial
+      // bubble's lengths are a floor, so it may be no small variant.
+      tick: !whole && !bubble.partial && bubble.longestAlleleLength < SMALL_VARIANT_BP
+    });
+  }
+  return halos;
+}
+
+export {
+  WHOLE_FRACTION,
+  coversGraph,
+  SMALL_VARIANT_BP,
+  bubbleHalos
+};

package/dist/chunks/{chunk-PBENCR5L.js → chunk-JBCZIBFC.js}

@@ -11,7 +11,6 @@ var NODE_WIDTHS = [
     description: "Every node the same thickness."
   }
 ];
-var NODE_WIDTH_VALUES = NODE_WIDTHS.map((w) => w.value);
 var MIN_FACTOR = 0.3;
 var MAX_FACTOR = 3;
 function meanDepth(graph) {
@@ -51,7 +50,6 @@ function nodeInk(graph, nodeById, contigThickness, nodeWidth) {
 
 export {
   NODE_WIDTHS,
-  NODE_WIDTH_VALUES,
   meanDepth,
   depthWidthFactor,
   nodeWidthPx,

package/dist/chunks/{chunk-5BGP5Z64.js → chunk-JLSJMCDJ.js}

@@ -2,7 +2,7 @@ import {
   LIFT_BACKDROP_CSS,
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-SBMJNRTV.js";
+} from "./chunk-A4PFFC4Q.js";
 import {
   abgrToCssRgba
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-DT2GGH4D.js → chunk-JMABOQWL.js}

@@ -1,8 +1,5 @@
-import {
-  loadBandage
-} from "./chunk-7XHHVYG7.js";
-
 // src/layoutEngines.ts
+import { fmmmLayout } from "@jbrowse/graph-fmmm-layout";
 import { stressLayout } from "@jbrowse/graph-stress-layout";
 var LAYOUT_ENGINES = [
   {
@@ -26,9 +23,8 @@ var layoutEngine = async (request) => {
     const result2 = stressLayout(request);
     return { result: result2, duration: performance.now() - start2 };
   }
-  const bandage = await loadBandage();
   const start = performance.now();
-  const result = bandage.computeLayout(request.graph, request.options);
+  const result = await fmmmLayout(request);
   return { result, duration: performance.now() - start };
 };
 

package/dist/chunks/{chunk-3S3YVOJ7.js → chunk-JSUCGZ6K.js}

@@ -1,6 +1,6 @@
 import {
   el
-} from "./chunk-NNODIW4U.js";
+} from "./chunk-H2H4Y3TV.js";
 
 // src/genes/exonOutline.ts
 var EXON_COLOR = "#daa520";

package/dist/chunks/{chunk-MLSWIMZO.js → chunk-KBEP7VYK.js}

@@ -1,10 +1,10 @@
 import {
   baseEdgeCurves
-} from "./chunk-WFB5TXRA.js";
+} from "./chunk-ZY2AFL4Y.js";
 import {
   curveBounds,
   pathRibbonOffsets
-} from "./chunk-2CVHXFK7.js";
+} from "./chunk-7SRWJLSC.js";
 
 // src/util/SpatialIndex.ts
 var FALLBACK_CELL_SIZE = 50;

package/dist/chunks/{chunk-DRG4236Y.js → chunk-KC7T5RWG.js}

@@ -1,12 +1,12 @@
 import {
   nodesUnderBox
-} from "./chunk-FP4H7SFT.js";
+} from "./chunk-4HWM3FNK.js";
 import {
   nodeLabelBudget,
   placeSizeLabels,
   rowLabelBox,
   sizeLabelCandidates
-} from "./chunk-3ZZSX5HN.js";
+} from "./chunk-PTABFYQ7.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,
@@ -18,7 +18,6 @@ import {
 // src/labelLayout.ts
 var HALO_FACTOR = 3.4;
 var LEGEND_INSET_PX = 6;
-var ROUTE_STACK = 8;
 var GENE_PIN_DROP_PX = 18;
 var GENE_STACK = 2;
 var BUBBLE_STACK = 3;
@@ -147,22 +146,6 @@ function layoutLabels(m) {
     version: m.positionsVersion
   }) : { deletions: [], nodes: [] };
   const deletionLabels = placeSizeLabels(sizeCandidates.deletions, take);
-  const routes = placeLabels(
-    byBubble.flatMap(
-      (h) => h.routes.map((route) => {
-        const { x, y } = screen(route.at);
-        return {
-          item: { halo: h, route },
-          x,
-          y: y + 4,
-          text: route.text,
-          stack: ROUTE_STACK
-        };
-      })
-    ),
-    frame,
-    take
-  );
   const nodeLabels = placeSizeLabels(
     sizeCandidates.nodes,
     take,
@@ -172,7 +155,6 @@ function layoutLabels(m) {
     bubbles,
     ticks,
     genes,
-    routes,
     sizes: [...deletionLabels, ...nodeLabels]
   };
 }

package/dist/chunks/{chunk-TAMCZHLW.js → chunk-N73TI3VG.js}

@@ -1,7 +1,7 @@
 import {
   ownStrand,
   strandSides
-} from "./chunk-2CVHXFK7.js";
+} from "./chunk-7SRWJLSC.js";
 import {
   isBackbone
 } from "./chunk-FYQWPEEY.js";
@@ -122,7 +122,7 @@ function splitRuns(positions, runs, weightOf) {
     const arc = arcPrefix(line);
     const total = arc.at(-1);
     const weights = members.map((m) => Math.max(weightOf(m), 0));
-    const weightSum = weights.reduce((a, b) => a + b, 0) || members.length;
+    const weightSum = weights.reduce((a, b) => a + b, 0);
     let from = 0;
     members.forEach((member, k) => {
       const share = weightSum ? weights[k] / weightSum * total : total / members.length;

package/dist/chunks/chunk-O4EGE27I.js

@@ -0,0 +1,10 @@
+// src/cli/decodeText.ts
+import { gunzipSync } from "node:zlib";
+function decodeText(bytes) {
+  const gzipped = bytes[0] === 31 && bytes[1] === 139;
+  return new TextDecoder().decode(gzipped ? gunzipSync(bytes) : bytes);
+}
+
+export {
+  decodeText
+};

package/dist/chunks/{chunk-3ZZSX5HN.js → chunk-PTABFYQ7.js}

@@ -3,14 +3,14 @@ import {
 } from "./chunk-AB35TJST.js";
 import {
   polylineMidpoint
-} from "./chunk-TAMCZHLW.js";
+} from "./chunk-N73TI3VG.js";
 import {
   deletionArcCurves
-} from "./chunk-N6FECAXP.js";
+} from "./chunk-24WITXQY.js";
 import {
   curveBounds,
   curveMidpoint
-} from "./chunk-2CVHXFK7.js";
+} from "./chunk-7SRWJLSC.js";
 
 // src/graphLabels.ts
 var MIN_DELETION_LABEL_PX = 26;
@@ -50,10 +50,11 @@ function groupDigits(n) {
   return String(n).replace(/\B(?=(\d{3})+$)/g, ",");
 }
 function formatBp(bp) {
-  if (bp >= 1e6) {
-    return `${+(bp / 1e6).toFixed(1)} Mb`;
+  const [value, unit] = bp >= 1e6 ? [bp / 1e6, "Mb"] : bp >= 1e3 ? [bp / 1e3, "kb"] : [];
+  if (value === void 0) {
+    return `${bp} bp`;
   }
-  return bp >= 1e3 ? `${+(bp / 1e3).toFixed(1)} kb` : `${bp} bp`;
+  return `${+value.toFixed(value >= 100 ? 0 : 1)} ${unit}`;
 }
 function deletionText(bp) {
   return `${formatBp(bp)} del`;
@@ -181,6 +182,9 @@ function sizeLabelCandidates({
       const box = boxAt(halfW, 0, 0);
       const arcX = apex.x * scaleX + translateX;
       const arcY = apex.y * scaleY + translateY;
+      if (arcX < 0 || arcX > width || arcY < 0 || arcY > height) {
+        continue;
+      }
       const fits = extent >= halfW * 2 / MAX_LABEL_OVERHANG;
       const bow = arcOutward(curves, apex, scaleX, scaleY);
       const offset = boxSupport(box, bow) + LEADER_GAP_PX;

package/dist/chunks/{chunk-WBCOREDZ.js → chunk-QLWI2PZ3.js}

@@ -1,6 +1,7 @@
 import {
+  getDpr,
   syncCanvasSize
-} from "./chunk-4BYTEJGW.js";
+} from "./chunk-RBCE2OQH.js";
 import {
   abgrToCssRgba,
   brightenAbgr,
@@ -15,6 +16,7 @@ var Canvas2DRenderer = class {
     this.nodeHighlights = /* @__PURE__ */ new Map();
     this.highlightedEdge = null;
     this.highlightFactor = 1;
+    this.fit = 1;
     const ctx = canvas.getContext("2d");
     if (!ctx) {
       throw new Error("Canvas 2D context not available");
@@ -26,12 +28,11 @@ var Canvas2DRenderer = class {
   }
   releaseOffscreenTargets() {
   }
-  // Not a local `width * devicePixelRatio`: syncCanvasSize clamps the backing
-  // store at MAX_CANVAS_DIM_PX, reads the ratio through `getDpr()` so this
-  // agrees with the transform the model builds, and writes the css size
-  // independently of the backing size.
+  // A host builds its transform at `getDpr()`. Where syncCanvasSize had to
+  // shrink the ratio to stay under MAX_CANVAS_DIM_PX, `fit` shrinks the
+  // transform to match, so the picture still fills the css box.
   resize(width, height) {
-    syncCanvasSize(this.canvas, width, height);
+    this.fit = syncCanvasSize(this.canvas, width, height) / getDpr();
   }
   uploadGeometry(batch) {
     this.batch = batch;
@@ -45,7 +46,15 @@ var Canvas2DRenderer = class {
     this.highlightFactor = factor;
   }
   updateTransform(transform) {
-    this.transform = transform;
+    const k = this.fit;
+    this.transform = k === 1 ? transform : {
+      ...transform,
+      scaleX: transform.scaleX * k,
+      scaleY: transform.scaleY * k,
+      translateX: transform.translateX * k,
+      translateY: transform.translateY * k,
+      dpr: transform.dpr * k
+    };
   }
   render(clearColor) {
     const t = this.transform;

package/dist/chunks/chunk-RBCE2OQH.js

@@ -0,0 +1,32 @@
+// src/renderer/canvas.ts
+var MAX_DPR = 2;
+var MAX_CANVAS_DIM_PX = 8192;
+function getDpr(width = 0, height = 0) {
+  const dpr = typeof devicePixelRatio === "undefined" ? 1 : Math.min(devicePixelRatio, MAX_DPR);
+  return Math.min(dpr, MAX_CANVAS_DIM_PX / Math.max(width, height, 1));
+}
+function syncCanvasSize(canvas, width, height) {
+  const dpr = getDpr(width, height);
+  const pw = Math.round(width * dpr);
+  const ph = Math.round(height * dpr);
+  if (canvas.width !== pw || canvas.height !== ph) {
+    canvas.width = pw;
+    canvas.height = ph;
+  }
+  const cssWidth = `${width}px`;
+  const cssHeight = `${height}px`;
+  if (canvas.style.width !== cssWidth) {
+    canvas.style.width = cssWidth;
+  }
+  if (canvas.style.height !== cssHeight) {
+    canvas.style.height = cssHeight;
+  }
+  return dpr;
+}
+
+export {
+  MAX_DPR,
+  MAX_CANVAS_DIM_PX,
+  getDpr,
+  syncCanvasSize
+};

package/dist/chunks/{chunk-BUBZ32IC.js → chunk-RPRHR56C.js}

@@ -1,9 +1,9 @@
 import {
   polylineSlice
-} from "./chunk-TAMCZHLW.js";
+} from "./chunk-N73TI3VG.js";
 import {
   svgPath
-} from "./chunk-2CVHXFK7.js";
+} from "./chunk-7SRWJLSC.js";
 import {
   firstNodeAtOrAfter,
   isAnchored
@@ -74,12 +74,8 @@ function genePins(graph, genes, positions) {
       const distance = Math.abs(pinBp - mid);
       if (distance < atDistance) {
         atDistance = distance;
-        const [p] = polylineSlice(
-          line,
-          (pinBp - nodeStart) / node.length,
-          (pinBp - nodeStart) / node.length
-        );
-        at = p;
+        const along = node.length ? (pinBp - nodeStart) / node.length : 0;
+        at = polylineSlice(line, along, along)[0];
       }
     }
     if (at) {

package/dist/chunks/{chunk-47DYCZOK.js → chunk-RUCH6ZFL.js}

@@ -90,6 +90,10 @@ function svgCanvas(width, height) {
         out.push(`<path d="${d}" ${paintAttrs("fill", ctx.fillStyle)}/>`);
       }
     },
+    // the renderer only ever clears the whole canvas
+    clearRect() {
+      out.length = 0;
+    },
     fillRect(x, y, w, h) {
       out.push(
         `<rect x="${n(x)}" y="${n(y)}" width="${n(w)}" height="${n(h)}" ${paintAttrs("fill", ctx.fillStyle)}/>`

package/dist/chunks/{chunk-GNTTI6LA.js → chunk-T2PCSAFY.js}

@@ -1,7 +1,7 @@
 import {
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-SBMJNRTV.js";
+} from "./chunk-A4PFFC4Q.js";
 import {
   abgrToCssRgba
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-XKWD2RY3.js → chunk-URZ3CH2R.js}

@@ -1,6 +1,9 @@
 import {
   SATURATED_PATH_COUNT
 } from "./chunk-FX4RDMDN.js";
+import {
+  formatBp
+} from "./chunk-PTABFYQ7.js";
 
 // src/bubbles/classifyBubble.ts
 var REPEAT_GROWTH = 10;
@@ -12,15 +15,6 @@ function coveringRepeat(b, repeats) {
   );
 }
 var SUPERBUBBLE_SEGMENTS = 40;
-function formatBp(bp) {
-  if (bp >= 1e4) {
-    return `${(bp / 1e3).toFixed(0)} kb`;
-  }
-  if (bp >= 1e3) {
-    return `${(bp / 1e3).toFixed(1)} kb`;
-  }
-  return `${bp} bp`;
-}
 function formatBpRange(shortest, longest) {
   const low = formatBp(shortest);
   const high = formatBp(longest);
@@ -119,7 +113,6 @@ function bubbleSegmentIds(b) {
 }
 
 export {
-  formatBp,
   classifyBubble,
   BUBBLE_KIND_COLORS,
   BUBBLE_KIND_NAMES,

package/dist/chunks/{chunk-ALDGONEI.js → chunk-VQC7KELB.js}

@@ -2,7 +2,7 @@ import {
   REFERENCE_RAMP_ALT_COLOR,
   REFERENCE_RAMP_MAX_HUE,
   hslToRgb
-} from "./chunk-SBMJNRTV.js";
+} from "./chunk-A4PFFC4Q.js";
 import {
   packAbgr
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-FLFBYSJO.js → chunk-VQWHMWLF.js}

@@ -25,7 +25,11 @@ function parseRegion(text) {
     );
   }
   const n = (s) => Number(s.replaceAll(",", ""));
-  return { refName: m[1], start: n(m[2]), end: n(m[3]) };
+  const region = { refName: m[1], start: n(m[2]), end: n(m[3]) };
+  if (region.end <= region.start) {
+    throw new Error(`"${text}" ends at or before it starts`);
+  }
+  return region;
 }
 async function openGbz(db, index) {
   const base = await GBZBase.open({ source: db, haplotypeIndex: index });

package/dist/chunks/{chunk-4R6QNG23.js → chunk-WL6ZKUVC.js}

@@ -6,16 +6,16 @@ import {
   hasTubeMapPaths,
   tubeMapLayout,
   tubeMapReferenceLayout
-} from "./chunk-DK5P2YOL.js";
+} from "./chunk-XI3ZUTWF.js";
 import {
   anchoredLayout
 } from "./chunk-L3O7AWLI.js";
 import {
   orderedLayout
-} from "./chunk-HNQPEMYE.js";
+} from "./chunk-CM6LO6OC.js";
 import {
   walkRowLayout
-} from "./chunk-C7MZJSPT.js";
+} from "./chunk-54POIBVC.js";
 import {
   isBackbone,
   isOffReference

package/dist/chunks/{chunk-CRTD2SBP.js → chunk-WZNPX7Q6.js}

@@ -1,7 +1,7 @@
 import {
   engineKey,
   forceLayout
-} from "./chunk-XTCNEKO5.js";
+} from "./chunk-2QLLQJ72.js";
 
 // src/layout/forceCache.ts
 var DEFAULT_SIZE = 4;
@@ -33,7 +33,11 @@ function createForceLayoutCache(size = DEFAULT_SIZE) {
           return { ...r, duration: r.duration || performance.now() - started };
         })
       };
-      entry.run.catch(() => cache.delete(key));
+      entry.run.catch(() => {
+        if (cache.get(key) === entry) {
+          cache.delete(key);
+        }
+      });
       cache.set(key, entry);
       return entry.run;
     },

package/dist/chunks/{chunk-TICYLD5F.js → chunk-XAWLIU54.js}

@@ -1,32 +1,24 @@
 import {
   layoutEngine
-} from "./chunk-DT2GGH4D.js";
+} from "./chunk-JMABOQWL.js";
 import {
   layoutModeByValue
-} from "./chunk-4R6QNG23.js";
+} from "./chunk-WL6ZKUVC.js";
 import {
   parseRegion
-} from "./chunk-FLFBYSJO.js";
-import {
-  layoutGeometryInputs
-} from "./chunk-LOCJN3BZ.js";
+} from "./chunk-VQWHMWLF.js";
 import {
   version
-} from "./chunk-EYK7DJZV.js";
+} from "./chunk-2CHS5LMM.js";
 import {
   axisScaleOf
-} from "./chunk-L5WF4ZPS.js";
-import {
-  facetLifts,
-  walkLift
-} from "./chunk-R456ME6J.js";
+} from "./chunk-BS4UZ44I.js";
 import {
   walkKey
-} from "./chunk-2LQ5BWT7.js";
+} from "./chunk-4ETPXDO6.js";
 import {
-  buildGeometry,
-  computeReferenceRamp
-} from "./chunk-SBMJNRTV.js";
+  figureScene
+} from "./chunk-D5D36ZF6.js";
 import {
   abgrAlpha,
   abgrBlue,
@@ -34,32 +26,16 @@ import {
   abgrRed
 } from "./chunk-G2FD7S3C.js";
 import {
-  pathLegend,
-  walkLabelsOf
-} from "./chunk-TWRLC3KK.js";
-import {
-  drawingBounds,
   engineSettingsOf,
   fitTransform,
   forceLayout,
   loadGraph
-} from "./chunk-XTCNEKO5.js";
-import {
-  referenceLabel
-} from "./chunk-RAKOB6IV.js";
-import {
-  resolveColorScheme
-} from "./chunk-JKJWSY4V.js";
-import {
-  deletionDrawing,
-  deletionEdges
-} from "./chunk-N6FECAXP.js";
+} from "./chunk-2QLLQJ72.js";
 import {
   isBackbone
 } from "./chunk-FYQWPEEY.js";
 import {
-  facetCells,
-  facetSettingOf
+  facetCells
 } from "./chunk-XV4P5KEQ.js";
 
 // src/figureData.ts
@@ -85,39 +61,24 @@ function figureData(graph, layout, o = {}) {
   }
   const width = o.width ?? 1200;
   const height = o.height ?? 800;
-  const region = o.region;
   const pixelRows = layout.pixelRows ?? false;
-  const bounds = drawingBounds(layout, {
-    region: o.fitToDrawing ? void 0 : region
-  });
+  const {
+    bounds,
+    colorScheme,
+    drawnDeletions,
+    lift,
+    facet,
+    panels: facetted,
+    labelOf,
+    referenceName,
+    reference,
+    geometry
+  } = figureScene(graph, layout, o);
   const fit = fitTransform(bounds, width, height, pixelRows);
   if (!fit) {
     throw new Error("the layout drew nothing to fit");
   }
   const axis = axisScaleOf(fit.scale, pixelRows);
-  const nodeById = new Map(graph.nodes.map((node) => [node.id, node]));
-  const colorScheme = resolveColorScheme(o.colorScheme ?? "auto", graph);
-  const rampDomain = o.colorDomain ?? region;
-  const referenceRamp = colorScheme === "reference-position" ? computeReferenceRamp(graph, rampDomain) : void 0;
-  const drawnDeletions = deletionDrawing(
-    graph,
-    deletionEdges(graph),
-    o.showDeletionEdges
-  );
-  const layers = o.walks ?? [];
-  const walkRamp = layers.some((l) => l.color?.field === "reference") ? referenceRamp ?? computeReferenceRamp(graph, rampDomain) : void 0;
-  const lift = layers.length > 0 ? walkLift(graph, layers, walkRamp) : void 0;
-  const facet = facetSettingOf(o.facet);
-  const facetted = facet.field && lift && lift.walks.length > 1 ? facetLifts(graph, lift, layers, walkRamp) : void 0;
-  const labels = walkLabelsOf(
-    graph.paths?.length ? pathLegend(graph.paths) : []
-  );
-  const labelOf = (name) => labels.get(name) ?? name;
-  const referenceName = o.referenceName ?? referenceLabel(graph, region);
-  const reference = lift?.referenceDomain && {
-    ...lift.referenceDomain,
-    name: referenceName
-  };
   const panels = [];
   if (facetted) {
     const place = facetCells(
@@ -178,20 +139,7 @@ function figureData(graph, layout, o = {}) {
     "alpha"
   ]);
   for (const { highlight, name: panel } of panels) {
-    const batch = buildGeometry({
-      ...layoutGeometryInputs(layout, drawnDeletions),
-      graph,
-      nodeById,
-      colorScheme,
-      contigThickness: o.contigThickness ?? 6,
-      connectorThickness: o.connectorThickness ?? 2,
-      drawPaths: false,
-      nodeWidth: o.nodeWidth ?? "depth",
-      linearLayout: o.linearLayout,
-      highlight,
-      axis,
-      referenceRamp
-    });
+    const batch = geometry(highlight, axis);
     for (const [node, run] of batch.nodeStrokeRuns) {
       for (let i = run.start; i < run.start + run.count; i++) {
         const s = batch.nodeStrokes[i];
@@ -275,18 +223,27 @@ function figureData(graph, layout, o = {}) {
     }
   };
 }
-async function gfaFigureData(text, name, spec = {}) {
-  const region = spec.region ? parseRegion(spec.region) : void 0;
+async function laidOutGraph(text, name, region, spec) {
   const graph = loadGraph(text, name, { referencePath: spec.referencePath });
   const layout = layoutModeByValue(spec.layout ?? "force").run(graph, region) ?? (await forceLayout(graph, engineSettingsOf(spec), layoutEngine)).result;
+  return { graph, layout };
+}
+function walkLayers(walks) {
+  return walks?.map((w) => typeof w === "string" ? { walk: w } : w);
+}
+async function gfaFigureData(text, name, spec = {}) {
+  const region = spec.region ? parseRegion(spec.region) : void 0;
+  const { graph, layout } = await laidOutGraph(text, name, region, spec);
   return figureData(graph, layout, {
     ...spec,
     region,
-    walks: spec.walks?.map((w) => typeof w === "string" ? { walk: w } : w)
+    walks: walkLayers(spec.walks)
   });
 }
 
 export {
   figureData,
+  laidOutGraph,
+  walkLayers,
   gfaFigureData
 };