@jbrowse/bandage-core 9.9.2 → 10.0.0

package/README.md

@@ -25,6 +25,9 @@ npm install @jbrowse/bandage-core
   and the `bandage-figure` CLI makes one from a JSON spec with no browser:
   `npx -p @jbrowse/bandage-core bandage-figure spec.json -o figure.svg`. See
   [docs/figures.md](docs/figures.md)
+- Figure data: `figureData` returns what `figureSvg` would paint as columnar
+  tables, for another graphics system to draw;
+  [ggbandage](https://github.com/GMOD/ggbandage) draws them in ggplot2
 
 Nothing here imports React, MobX or a JBrowse host. BandageJS's
 [`src/main.ts`](https://github.com/cmdcolin/BandageJS/blob/main/src/main.ts) is

package/dist/bubbles/popBubble.js

@@ -1,7 +1,8 @@
 import {
   bubbleSubgraph
-} from "../chunks/chunk-A6PSWTLX.js";
-import "../chunks/chunk-IGJCTPFB.js";
+} from "../chunks/chunk-4QTNXTGW.js";
+import "../chunks/chunk-EMUUNWRU.js";
+import "../chunks/chunk-RAEABQNW.js";
 import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {

package/dist/bubbles/superbubbles.js

@@ -1,14 +1,15 @@
 import {
   graphBubbles,
   superbubblesFromGraph
-} from "../chunks/chunk-ROQGMTFB.js";
-import "../chunks/chunk-A6PSWTLX.js";
+} from "../chunks/chunk-BEWLQADP.js";
+import "../chunks/chunk-CLOP7UVD.js";
+import "../chunks/chunk-4QTNXTGW.js";
 import "../chunks/chunk-EHUBJDDB.js";
 import "../chunks/chunk-XKWD2RY3.js";
-import "../chunks/chunk-CLOP7UVD.js";
 import "../chunks/chunk-FX4RDMDN.js";
 import "../chunks/chunk-HNQPEMYE.js";
-import "../chunks/chunk-IGJCTPFB.js";
+import "../chunks/chunk-EMUUNWRU.js";
+import "../chunks/chunk-RAEABQNW.js";
 import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-2CVHXFK7.js";
 import "../chunks/chunk-CPMHA4W5.js";

package/dist/chunks/{chunk-YAN2ZPNV.js → chunk-33T67FPZ.js}

@@ -1,7 +1,7 @@
 import {
   engineKey,
   forceLayout
-} from "./chunk-FPTI3WAV.js";
+} from "./chunk-W4GZCVUK.js";
 
 // src/layout/forceCache.ts
 var DEFAULT_SIZE = 4;

package/dist/chunks/{chunk-TOVOJNT7.js → chunk-3APK25GI.js}

@@ -1,6 +1,6 @@
 import {
   walkRows
-} from "./chunk-6PYZYBBF.js";
+} from "./chunk-KAN2WTG5.js";
 import {
   ROW_HEIGHT_PX
 } from "./chunk-CPMHA4W5.js";

package/dist/chunks/{chunk-A6PSWTLX.js → chunk-4QTNXTGW.js}

@@ -1,6 +1,6 @@
 import {
   trimOrigins
-} from "./chunk-IGJCTPFB.js";
+} from "./chunk-EMUUNWRU.js";
 
 // src/bubbles/popBubble.ts
 function bubbleSubgraph(graph, segmentIds) {

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

@@ -1,17 +1,17 @@
+import {
+  bubblesFromGraph,
+  walkIndexOf,
+  walkRoutes
+} from "./chunk-CLOP7UVD.js";
 import {
   bubbleSubgraph
-} from "./chunk-A6PSWTLX.js";
+} from "./chunk-4QTNXTGW.js";
 import {
   coversGraph
 } from "./chunk-EHUBJDDB.js";
 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-BQ33OOLC.js → chunk-CDPYXHVR.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "9.9.2";
+var version = "10.0.0";
 
 export {
   version

package/dist/chunks/{chunk-YS7VA5SI.js → chunk-DCJC32QW.js}

@@ -1,6 +1,6 @@
 import {
   REFERENCE_RAMP_MAX_HUE
-} from "./chunk-F4BKWWLS.js";
+} from "./chunk-NP356MC2.js";
 
 // src/referenceRampCss.ts
 function rampHueCss(hue) {

package/dist/chunks/{chunk-YGN4KL7W.js → chunk-E5UEYZWK.js}

@@ -1,6 +1,6 @@
 import {
   ENGINE_DEFAULTS
-} from "./chunk-FPTI3WAV.js";
+} from "./chunk-W4GZCVUK.js";
 
 // src/figureSettings.ts
 var FIGURE_DEFAULTS = {

package/dist/chunks/{chunk-IGJCTPFB.js → chunk-EMUUNWRU.js}

@@ -1,3 +1,6 @@
+import {
+  PathVisitsBuilder
+} from "./chunk-RAEABQNW.js";
 import {
   panSNSample
 } from "./chunk-BPLIXMH7.js";
@@ -13,23 +16,13 @@ function pathOrigin(pathName) {
 }
 function surveyPaths(paths, lengthOf) {
   const anchorPaths = [];
-  const pathVisits = /* @__PURE__ */ new Map();
+  const visits = new PathVisitsBuilder();
   for (const path of paths) {
     const sample = panSNSample(path.name);
+    const p = visits.pathOf(path.name, sample);
     let pos = path.start;
     for (const step of path.steps) {
-      const visit = {
-        path: path.name,
-        sample,
-        start: pos,
-        strand: step.strand
-      };
-      const existing = pathVisits.get(step.id);
-      if (existing) {
-        existing.push(visit);
-      } else {
-        pathVisits.set(step.id, [visit]);
-      }
+      visits.addAt(visits.declare(step.id), p, pos, step.strand === "-");
       pos += lengthOf(step.id);
     }
     anchorPaths.push({
@@ -39,7 +32,7 @@ function surveyPaths(paths, lengthOf) {
       length: pos - path.start
     });
   }
-  return { anchorPaths, pathVisits };
+  return { anchorPaths, pathVisits: visits.build() };
 }
 function chooseReferencePath(anchorPaths, preferred) {
   const named = anchorPaths.find(
@@ -49,41 +42,56 @@ function chooseReferencePath(anchorPaths, preferred) {
 }
 var OFF_REFERENCE_RANK = 1;
 function anchorNode(node, visits, reference, samplesOf) {
-  let anchored = node;
-  if (visits && visits.length > 0) {
-    const anchor = visits.find((v) => v.path === reference) ?? visits[0];
-    anchored = {
-      ...node,
-      stable: {
-        refName: anchor.path,
-        start: anchor.start,
-        rank: anchor.path === reference ? REFERENCE_RANK : OFF_REFERENCE_RANK,
-        strand: anchor.strand
-      },
-      samples: samplesOf(visits)
-    };
+  const slot = visits.slot(node.name);
+  if (slot < 0 || visits.offsets[slot] === visits.offsets[slot + 1]) {
+    return node;
   }
-  return anchored;
+  const own = visits.firstBy(slot, reference);
+  const anchor = own >= 0 ? own : visits.offsets[slot];
+  return {
+    ...node,
+    stable: {
+      refName: visits.paths[visits.path[anchor]],
+      start: visits.start[anchor],
+      rank: own >= 0 ? REFERENCE_RANK : OFF_REFERENCE_RANK,
+      strand: visits.strand(anchor)
+    },
+    samples: samplesOf(slot)
+  };
 }
-function sampleSorter(paths) {
-  const sorted = [...new Set(paths.map((p) => p.sample))].sort();
+function sampleSorter(visits) {
+  const sorted = [...new Set(visits.samples)].sort();
   const rank = new Map(sorted.map((sample, i) => [sample, i]));
+  const pathRank = Int32Array.from(visits.samples, (s) => rank.get(s));
   const seen = new Uint8Array(sorted.length);
-  return (visits) => {
-    const ranks = [];
-    for (const { sample } of visits) {
-      const r = rank.get(sample);
-      if (r === void 0) {
-        ranks.forEach((r2) => seen[r2] = 0);
-        return [...new Set(visits.map((v) => v.sample))].sort();
-      }
+  const ranks = new Int32Array(sorted.length);
+  return (slot) => {
+    let n = 0;
+    for (let i = visits.offsets[slot]; i < visits.offsets[slot + 1]; i++) {
+      const r = pathRank[visits.path[i]];
       if (seen[r] === 0) {
         seen[r] = 1;
-        ranks.push(r);
+        ranks[n++] = r;
+      }
+    }
+    let out;
+    if (n === sorted.length) {
+      out = sorted;
+      seen.fill(0);
+    } else if (n * 8 < sorted.length) {
+      const found = ranks.subarray(0, n);
+      found.forEach((r) => seen[r] = 0);
+      out = Array.from(found.sort(), (r) => sorted[r]);
+    } else {
+      out = [];
+      for (let r = 0; r < sorted.length; r++) {
+        if (seen[r] === 1) {
+          seen[r] = 0;
+          out.push(sorted[r]);
+        }
       }
     }
-    ranks.forEach((r) => seen[r] = 0);
-    return Array.from(Int32Array.from(ranks).sort(), (r) => sorted[r]);
+    return out;
   };
 }
 function anchorFromPaths(graph, preferred) {
@@ -92,11 +100,12 @@ function anchorFromPaths(graph, preferred) {
   if (!reference || !anchorPaths || !pathVisits) {
     return graph;
   }
-  const samplesOf = sampleSorter(anchorPaths);
+  const samplesOf = sampleSorter(pathVisits);
+  const referenceIndex = pathVisits.pathIndex(reference.name);
   return {
     ...graph,
     nodes: graph.nodes.map(
-      (node) => anchorNode(node, pathVisits.get(node.name), reference.name, samplesOf)
+      (node) => anchorNode(node, pathVisits, referenceIndex, samplesOf)
     ),
     anchoredBy: "paths",
     referencePath: reference.name

package/dist/chunks/{chunk-PIN7ZMTZ.js → chunk-EU6FBTQF.js}

@@ -1,15 +1,15 @@
-import {
-  tubeMapMismatches
-} from "./chunk-XXT2JCAC.js";
 import {
   MAX_GAP_PX
 } from "./chunk-HK5Y2YWV.js";
+import {
+  tubeMapMismatches
+} from "./chunk-XXT2JCAC.js";
 import {
   readColor
 } from "./chunk-CWFNEKST.js";
 import {
   pathOrigin
-} from "./chunk-IGJCTPFB.js";
+} from "./chunk-EMUUNWRU.js";
 
 // src/tubeMap/draw.ts
 import { curvePaths, nodeOutlinePath } from "@jbrowse/tubemap-core";

package/dist/chunks/{chunk-WVBYR6Y7.js → chunk-FG762CCP.js}

@@ -1,9 +1,9 @@
 import {
   pathSteps
-} from "./chunk-HOZI3FBG.js";
+} from "./chunk-IM4SJUPO.js";
 import {
   pathOrigin
-} from "./chunk-IGJCTPFB.js";
+} from "./chunk-EMUUNWRU.js";
 
 // src/tubeMap/bundle.ts
 function bundleRoutes(graph, groupOf = () => "", merge = true) {
@@ -67,12 +67,7 @@ function bundleRoutes(graph, groupOf = () => "", merge = true) {
     ...graph,
     paths: kept,
     anchorPaths: graph.anchorPaths?.filter((p) => keptWalks.has(p.name)),
-    pathVisits: graph.pathVisits ? new Map(
-      [...graph.pathVisits].map(([segment, visits]) => [
-        segment,
-        visits.filter((v) => keptWalks.has(v.path))
-      ])
-    ) : void 0
+    pathVisits: graph.pathVisits?.filter((path) => keptWalks.has(path))
   };
 }
 

package/dist/chunks/{chunk-73RSLGZT.js → chunk-FLFBYSJO.js}

@@ -5,7 +5,7 @@ import {
   referencePathQuery,
   referenceSamplesOf,
   resolveReferenceSample
-} from "./chunk-LTUWJKHD.js";
+} from "./chunk-Q7LYHGGQ.js";
 
 // src/gbzCut.ts
 import { GBZBase } from "@gmod/gbz-base";

package/dist/chunks/{chunk-IJRNMO4D.js → chunk-ICXMWYOA.js}

@@ -1,12 +1,12 @@
-import {
-  sampleRowLayout
-} from "./chunk-LOEA5IHZ.js";
 import {
   hasTubeMapBackbone,
   hasTubeMapPaths,
   tubeMapLayout,
   tubeMapReferenceLayout
-} from "./chunk-HOZI3FBG.js";
+} from "./chunk-IM4SJUPO.js";
+import {
+  sampleRowLayout
+} from "./chunk-LOEA5IHZ.js";
 import {
   anchoredLayout
 } from "./chunk-L3O7AWLI.js";
@@ -15,7 +15,7 @@ import {
 } from "./chunk-HNQPEMYE.js";
 import {
   walkRowLayout
-} from "./chunk-TOVOJNT7.js";
+} from "./chunk-3APK25GI.js";
 import {
   isBackbone,
   isOffReference

package/dist/chunks/{chunk-HOZI3FBG.js → chunk-IM4SJUPO.js}

@@ -6,10 +6,10 @@ import {
 import {
   pathCssColor,
   pathGreyCssColor
-} from "./chunk-EDASNMLY.js";
+} from "./chunk-REE4GUDM.js";
 import {
   pathOrigin
-} from "./chunk-IGJCTPFB.js";
+} from "./chunk-EMUUNWRU.js";
 import {
   ownStrand,
   strandSides
@@ -22,30 +22,19 @@ import {
 import { forward, isReverse, layoutTubeMap } from "@jbrowse/tubemap-core";
 function pathSteps(graph) {
   const nodeById = new Map(graph.nodes.map((n) => [n.id, n]));
-  const strands = /* @__PURE__ */ new Map();
-  for (const [segment, visits] of graph.pathVisits ?? []) {
-    for (const visit of visits) {
-      const key = `${visit.path}	${segment}`;
-      const list = strands.get(key);
-      if (list) {
-        list.push(visit.strand);
-      } else {
-        strands.set(key, [visit.strand]);
-      }
-    }
-  }
-  const seen = /* @__PURE__ */ new Map();
+  const visits = graph.pathVisits;
+  const next = visits?.replay();
   return (graph.paths ?? []).map((path) => {
-    const walk = pathOrigin(path.name).name;
+    const walk = visits?.pathIndex(pathOrigin(path.name).name) ?? -1;
     return path.nodeIds.flatMap((id) => {
       const node = nodeById.get(id);
       if (!node) {
         return [];
       }
-      const key = `${walk}	${node.name}`;
-      const k = seen.get(key) ?? 0;
-      seen.set(key, k + 1);
-      return [{ node, strand: strands.get(key)?.[k] ?? canonicalStrand(node) }];
+      const at = visits && next ? next(visits.slot(node.name), walk) : -1;
+      return [
+        { node, strand: at >= 0 ? visits.strand(at) : canonicalStrand(node) }
+      ];
     });
   });
 }
@@ -208,8 +197,9 @@ function boxGraph(graph, { members, flipped }) {
       ...path,
       nodeIds: path.nodeIds.filter((id) => !absorbed.has(id))
     })),
-    pathVisits: graph.pathVisits && new Map(
-      [...graph.pathVisits].filter(([name]) => !absorbedNames.has(name))
+    pathVisits: graph.pathVisits?.filter(
+      () => true,
+      (segment) => !absorbedNames.has(segment)
     )
   };
 }

package/dist/chunks/{chunk-6PYZYBBF.js → chunk-KAN2WTG5.js}

@@ -1,6 +1,6 @@
 import {
   pathOrigin
-} from "./chunk-IGJCTPFB.js";
+} from "./chunk-EMUUNWRU.js";
 import {
   panSNContig,
   panSNSample

package/dist/chunks/{chunk-RK3MF4FD.js → chunk-KJYSOHVN.js}

@@ -2,7 +2,7 @@ import {
   LIFT_BACKDROP_CSS,
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-F4BKWWLS.js";
+} from "./chunk-NP356MC2.js";
 import {
   abgrToCssRgba
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-F4BKWWLS.js → chunk-NP356MC2.js}

@@ -3,19 +3,19 @@ import {
   fadeAbgr,
   packAbgr
 } from "./chunk-G2FD7S3C.js";
+import {
+  baseEdgeCurves
+} from "./chunk-WFB5TXRA.js";
 import {
   PATH_LIGHTNESS,
   PATH_SATURATION,
   nameHue,
   pathHueAt
-} from "./chunk-EDASNMLY.js";
+} from "./chunk-REE4GUDM.js";
 import {
   meanDepth,
   nodeWidthPx
 } from "./chunk-PBENCR5L.js";
-import {
-  baseEdgeCurves
-} from "./chunk-WFB5TXRA.js";
 import {
   referenceMidpoints
 } from "./chunk-ES2N6V56.js";

package/dist/chunks/{chunk-KJEMKHVB.js → chunk-OEPCRURR.js}

@@ -1,7 +1,7 @@
 import {
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-F4BKWWLS.js";
+} from "./chunk-NP356MC2.js";
 import {
   abgrToCssRgba
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-ZBLKAWSD.js → chunk-OOLNLCIO.js}

@@ -1,6 +1,6 @@
 import {
   clampZoom
-} from "./chunk-FPTI3WAV.js";
+} from "./chunk-W4GZCVUK.js";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {

package/dist/chunks/chunk-OPPVSPEF.js

@@ -0,0 +1,57 @@
+// src/layout/smoothChains.ts
+var STEP_TURN = Math.PI / 24;
+function turnAt(line, i) {
+  const a = line[i - 1];
+  const b = line[i];
+  const c = line[i + 1];
+  if (!a || !c) {
+    return 0;
+  }
+  const t = Math.abs(
+    Math.atan2(c.y - b.y, c.x - b.x) - Math.atan2(b.y - a.y, b.x - a.x)
+  );
+  return t > Math.PI ? 2 * Math.PI - t : t;
+}
+function centripetal(p0, p1, p2, p3, u) {
+  const knot = (a, b) => Math.max(Math.hypot(b.x - a.x, b.y - a.y) ** 0.5, 1e-9);
+  const t1 = knot(p0, p1);
+  const t2 = t1 + knot(p1, p2);
+  const t3 = t2 + knot(p2, p3);
+  const t = t1 + u * (t2 - t1);
+  const lerp = (a, b, ta, tb) => {
+    const f = (t - ta) / (tb - ta);
+    return { x: a.x + (b.x - a.x) * f, y: a.y + (b.y - a.y) * f };
+  };
+  const a1 = lerp(p0, p1, 0, t1);
+  const a2 = lerp(p1, p2, t1, t2);
+  const a3 = lerp(p2, p3, t2, t3);
+  return lerp(lerp(a1, a2, 0, t2), lerp(a2, a3, t1, t3), t1, t2);
+}
+var reflect = (p, about) => ({
+  x: 2 * about.x - p.x,
+  y: 2 * about.y - p.y
+});
+function smoothChain(line) {
+  if (line.length < 3) {
+    return line;
+  }
+  const out = [line[0]];
+  for (let i = 0; i + 1 < line.length; i++) {
+    const p1 = line[i];
+    const p2 = line[i + 1];
+    const steps = Math.ceil(
+      Math.max(turnAt(line, i), turnAt(line, i + 1)) / STEP_TURN
+    );
+    const p0 = line[i - 1] ?? reflect(p2, p1);
+    const p3 = line[i + 2] ?? reflect(p1, p2);
+    for (let s = 1; s < steps; s++) {
+      out.push(centripetal(p0, p1, p2, p3, s / steps));
+    }
+    out.push(p2);
+  }
+  return out;
+}
+
+export {
+  smoothChain
+};