@jbrowse/bandage-core 7.2.1 → 7.4.0

package/dist/chunks/{chunk-MH5IA57M.js → chunk-3LXG54PN.js}

@@ -1,7 +1,7 @@
 import {
   encodedColor,
   resolveEncoding
-} from "./chunk-TQ7VCGJR.js";
+} from "./chunk-ZNMHIPUZ.js";
 import {
   pathOrigin
 } from "./chunk-ST2IBUAN.js";

package/dist/chunks/{chunk-Y7UR3MDE.js → chunk-4UBWXZVX.js}

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

package/dist/chunks/{chunk-MQSOTYVF.js → chunk-5XHORHYK.js}

@@ -1,6 +1,6 @@
 import {
-  Canvas2DRenderer
-} from "./chunk-CH3DLBUT.js";
+  layoutGeometryInputs
+} from "./chunk-LOCJN3BZ.js";
 import {
   svgCanvas
 } from "./chunk-47DYCZOK.js";
@@ -8,12 +8,15 @@ import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-OY3CDWFN.js";
+} from "./chunk-PY7EZFL3.js";
 import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-2T3SRIFH.js";
+} from "./chunk-7G7TFATC.js";
+import {
+  Canvas2DRenderer
+} from "./chunk-CH3DLBUT.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
@@ -22,47 +25,47 @@ import {
 import {
   genePins
 } from "./chunk-BUBZ32IC.js";
-import {
-  version
-} from "./chunk-BZKEMAWC.js";
-import {
-  axisScaleOf
-} from "./chunk-Y7UR3MDE.js";
 import {
   facetLifts,
   walkLift
-} from "./chunk-MH5IA57M.js";
+} from "./chunk-3LXG54PN.js";
 import {
   encodingStops
-} from "./chunk-TQ7VCGJR.js";
+} from "./chunk-ZNMHIPUZ.js";
 import {
   rangeText,
   walkKey
 } from "./chunk-2LQ5BWT7.js";
-import {
-  FIT_PADDING,
-  drawingBounds,
-  fitTransform
-} from "./chunk-EPWYRSHH.js";
 import {
   buildGeometry,
   computeReferenceRamp
-} from "./chunk-VST5SR4C.js";
+} from "./chunk-RCWYY6XA.js";
+import {
+  version
+} from "./chunk-LNSAKOXP.js";
+import {
+  axisScaleOf
+} from "./chunk-4UBWXZVX.js";
+import {
+  walkRowLabels,
+  walkRowsExtent
+} from "./chunk-MP7LXLWV.js";
 import {
   nodeInk
 } from "./chunk-PBENCR5L.js";
+import {
+  pathLegend,
+  walkLabelsOf
+} from "./chunk-7GBL7SJY.js";
+import {
+  referenceLabel
+} from "./chunk-RAKOB6IV.js";
 import {
   geneLabelCandidates
 } from "./chunk-GJMC3PGM.js";
 import {
   nodesUnderBox
 } from "./chunk-FP4H7SFT.js";
-import {
-  walkRowsExtent
-} from "./chunk-3JANT2SW.js";
-import {
-  pathLegend
-} from "./chunk-E7FWQQHP.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,
@@ -73,13 +76,6 @@ import {
 import {
   resolveColorScheme
 } from "./chunk-JKJWSY4V.js";
-import {
-  deletionDrawing,
-  deletionEdges
-} from "./chunk-N6FECAXP.js";
-import {
-  ROW_HEIGHT_PX
-} from "./chunk-CPMHA4W5.js";
 import {
   serializeEl
 } from "./chunk-NNODIW4U.js";
@@ -92,8 +88,14 @@ import {
   facetSettingOf
 } from "./chunk-6SBUFFTB.js";
 import {
-  referenceLabel
-} from "./chunk-RAKOB6IV.js";
+  FIT_PADDING,
+  drawingBounds,
+  fitTransform
+} from "./chunk-WZATPZNH.js";
+import {
+  deletionDrawing,
+  deletionEdges
+} from "./chunk-N6FECAXP.js";
 
 // src/figure.ts
 var FONT = 'font-family="Helvetica, Arial, sans-serif" font-size="11"';
@@ -174,11 +176,8 @@ function figureSvg(graph, layout, o = {}) {
   const lift = layers.length > 0 && !layout.tubeMap ? walkLift(graph, layers, walkRamp) : void 0;
   const facet = facetSettingOf(o.facet);
   const panels = facet.field && lift && lift.walks.length > 1 ? facetLifts(graph, lift, layers, walkRamp) : void 0;
-  const labels = new Map(
-    (graph.paths?.length ? pathLegend(graph.paths) : []).map((p) => [
-      p.name,
-      p.label
-    ])
+  const labels = walkLabelsOf(
+    graph.paths?.length ? pathLegend(graph.paths) : []
   );
   const labelOf = (name) => labels.get(name) ?? name;
   const referenceName = o.referenceName ?? referenceLabel(graph, region);
@@ -235,11 +234,7 @@ function figureSvg(graph, layout, o = {}) {
         )
       );
     }
-    const pitch = o.walkRowPitch;
-    const rowLabels = rows ? pitch && !pitch.labelled ? [] : [rows.reference, ...rows.rows].map((r, i) => ({
-      label: r.label,
-      y: i * (pitch?.rowPx ?? ROW_HEIGHT_PX)
-    })) : layout.rowLabels ?? [];
+    const rowLabels = walkRowLabels(rows, layout, o.walkRowPitch);
     for (const { label, y } of rowLabels) {
       const sy = y * t.scaleY + t.translateY;
       if (sy >= 0 && sy <= h) {
@@ -271,7 +266,9 @@ function figureSvg(graph, layout, o = {}) {
     const renderer = new Canvas2DRenderer(canvas);
     renderer.uploadGeometry(
       buildGeometry({
-        nodePositions: rows ? {} : layout.nodePositions,
+        ...layoutGeometryInputs(layout, drawnDeletions, {
+          drawsRows: !!rows
+        }),
         graph,
         nodeById,
         colorScheme,
@@ -279,13 +276,10 @@ function figureSvg(graph, layout, o = {}) {
         connectorThickness: o.connectorThickness ?? 2,
         drawPaths: false,
         nodeWidth,
+        linearLayout: o.linearLayout,
         highlight,
         axis,
-        referenceRamp,
-        deletions: drawnDeletions.bypassed,
-        deletionRoutes: layout.deletionRoutes,
-        stranded: layout.stranded,
-        hiddenEdges: drawnDeletions.hidden
+        referenceRamp
       })
     );
     const t = {

package/dist/chunks/{chunk-2T3SRIFH.js → chunk-7G7TFATC.js}

@@ -3,19 +3,19 @@ import {
   RAMP_GRADIENT_STOPS,
   rampHueCss,
   rampStops
-} from "./chunk-VECR253P.js";
+} from "./chunk-AVJK272H.js";
 import {
   REFERENCE_RAMP_ALT_CSS
-} from "./chunk-VST5SR4C.js";
+} from "./chunk-RCWYY6XA.js";
 import {
   LABEL_CHAR_PX
 } from "./chunk-AB35TJST.js";
-import {
-  ROW_HEIGHT_PX
-} from "./chunk-CPMHA4W5.js";
 import {
   el
 } from "./chunk-NNODIW4U.js";
+import {
+  ROW_HEIGHT_PX
+} from "./chunk-CPMHA4W5.js";
 
 // src/layout/walkRowDraw.ts
 var ON_REFERENCE = "#2f8fd6";

package/dist/chunks/{chunk-E7FWQQHP.js → chunk-7GBL7SJY.js}

@@ -1,9 +1,9 @@
-import {
-  pathOrigin
-} from "./chunk-ST2IBUAN.js";
 import {
   groupDigits
 } from "./chunk-3ZZSX5HN.js";
+import {
+  pathOrigin
+} from "./chunk-ST2IBUAN.js";
 import {
   isGenericSample
 } from "./chunk-BPLIXMH7.js";
@@ -68,6 +68,16 @@ function pathLegend(paths, colors) {
     color: colors?.[i] ?? pathCssColor(i, paths.length)
   }));
 }
+function walkLabelsOf(entries) {
+  const seen = /* @__PURE__ */ new Map();
+  return new Map(
+    [...entries].sort((a, b) => a.label.localeCompare(b.label)).map((e) => {
+      const n = (seen.get(e.label) ?? 0) + 1;
+      seen.set(e.label, n);
+      return [e.name, n > 1 ? `${e.label} (${n})` : e.label];
+    })
+  );
+}
 
 export {
   nameHue,
@@ -78,5 +88,6 @@ export {
   pathColorsLegible,
   pathCssColor,
   pathGreyCssColor,
-  pathLegend
+  pathLegend,
+  walkLabelsOf
 };

package/dist/chunks/{chunk-VECR253P.js → chunk-AVJK272H.js}

@@ -1,6 +1,6 @@
 import {
   REFERENCE_RAMP_MAX_HUE
-} from "./chunk-VST5SR4C.js";
+} from "./chunk-RCWYY6XA.js";
 
 // src/referenceRampCss.ts
 function rampHueCss(hue) {

package/dist/chunks/{chunk-4FQTTG5F.js → chunk-AYOSNXLQ.js}

@@ -7,7 +7,7 @@ import {
 import {
   pathCssColor,
   pathGreyCssColor
-} from "./chunk-E7FWQQHP.js";
+} from "./chunk-7GBL7SJY.js";
 import {
   pathOrigin
 } from "./chunk-ST2IBUAN.js";

package/dist/chunks/chunk-AZFVORTC.js

@@ -0,0 +1,19 @@
+// src/hoverText.ts
+function regionLabel(loc) {
+  return `${loc.refName}:${(loc.start + 1).toLocaleString()}-${loc.end.toLocaleString()}`;
+}
+function edgeHoverText(edge, deletion, nameOf = (id) => id) {
+  return deletion ? {
+    deletion: {
+      bp: `${deletion.bp.toLocaleString()} bp`,
+      where: regionLabel(deletion)
+    }
+  } : {
+    ends: `${nameOf(edge.from)}${edge.fromStrand ?? ""} \u2192 ${nameOf(edge.to)}${edge.toStrand ?? ""}`
+  };
+}
+
+export {
+  regionLabel,
+  edgeHoverText
+};

package/dist/chunks/{chunk-JKXE6CIP.js → chunk-FRR2RGBT.js}

@@ -1,11 +1,11 @@
+import {
+  sampleRowLayout
+} from "./chunk-LOEA5IHZ.js";
 import {
   hasTubeMapPaths,
   tubeMapLayout,
   tubeMapReferenceLayout
-} from "./chunk-4FQTTG5F.js";
-import {
-  sampleRowLayout
-} from "./chunk-LOEA5IHZ.js";
+} from "./chunk-AYOSNXLQ.js";
 import {
   anchoredLayout
 } from "./chunk-L3O7AWLI.js";
@@ -14,7 +14,7 @@ import {
 } from "./chunk-HNQPEMYE.js";
 import {
   walkRowLayout
-} from "./chunk-3JANT2SW.js";
+} from "./chunk-MP7LXLWV.js";
 import {
   isBackbone,
   isOffReference

package/dist/chunks/chunk-H5S2ONCJ.js

@@ -0,0 +1,27 @@
+import {
+  ENGINE_DEFAULTS
+} from "./chunk-WZATPZNH.js";
+
+// src/figureSettings.ts
+var FIGURE_DEFAULTS = {
+  ...ENGINE_DEFAULTS,
+  colorScheme: "auto",
+  nodeWidth: "depth",
+  contigThickness: 6,
+  connectorThickness: 2
+};
+function figureSpecSettings(s) {
+  const defaults = FIGURE_DEFAULTS;
+  const out = {};
+  for (const [k, v] of Object.entries(s)) {
+    if (v !== void 0 && v !== defaults[k]) {
+      out[k] = v;
+    }
+  }
+  return out;
+}
+
+export {
+  FIGURE_DEFAULTS,
+  figureSpecSettings
+};

package/dist/chunks/chunk-K5SIJGAE.js

@@ -0,0 +1,12 @@
+// src/layoutQualities.ts
+var LAYOUT_QUALITIES = [
+  { value: 0, label: "Fastest" },
+  { value: 1, label: "Fast" },
+  { value: 2, label: "Default" },
+  { value: 3, label: "Fine" },
+  { value: 4, label: "Best" }
+];
+
+export {
+  LAYOUT_QUALITIES
+};

package/dist/chunks/{chunk-CNQSHEBS.js → chunk-KEVQ46GG.js}

@@ -1,7 +1,7 @@
 import {
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-VST5SR4C.js";
+} from "./chunk-RCWYY6XA.js";
 import {
   abgrToCssRgba
 } from "./chunk-UMNCCYBN.js";

package/dist/chunks/{chunk-BZKEMAWC.js → chunk-LNSAKOXP.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "7.2.1";
+var version = "7.4.0";
 
 export {
   version

package/dist/chunks/chunk-LOCJN3BZ.js

@@ -0,0 +1,14 @@
+// src/renderer/geometryInputs.ts
+function layoutGeometryInputs(layout, drawing, o = {}) {
+  return {
+    nodePositions: o.drawsRows ? {} : layout.nodePositions,
+    deletions: drawing.bypassed,
+    deletionRoutes: layout.deletionRoutes,
+    stranded: layout.stranded,
+    hiddenEdges: drawing.hidden
+  };
+}
+
+export {
+  layoutGeometryInputs
+};

package/dist/chunks/{chunk-3JANT2SW.js → chunk-MP7LXLWV.js}

@@ -25,6 +25,18 @@ function walkRowsExtent(walks, pitch = {
     maxY: walks.rows.length * pitch.rowPx
   };
 }
+function walkRowLabels(rows, layout, pitch) {
+  if (!rows) {
+    return layout?.rowLabels ?? [];
+  }
+  if (pitch && !pitch.labelled) {
+    return [];
+  }
+  return [rows.reference, ...rows.rows].map((row, i) => ({
+    label: row.label,
+    y: i * (pitch?.rowPx ?? ROW_HEIGHT_PX)
+  }));
+}
 function walkRowLayout(graph, region) {
   const backbone = backboneNodes(graph);
   const walks = walkRows(graph, region);
@@ -53,5 +65,6 @@ function walkRowLayout(graph, region) {
 
 export {
   walkRowsExtent,
+  walkRowLabels,
   walkRowLayout
 };

package/dist/chunks/{chunk-OY3CDWFN.js → chunk-PY7EZFL3.js}

@@ -2,16 +2,16 @@ import {
   alongRow,
   boxesGenes,
   rowPitch
-} from "./chunk-2T3SRIFH.js";
-import {
-  pathOrigin
-} from "./chunk-ST2IBUAN.js";
+} from "./chunk-7G7TFATC.js";
 import {
   LABEL_CHAR_PX
 } from "./chunk-AB35TJST.js";
 import {
   el
 } from "./chunk-NNODIW4U.js";
+import {
+  pathOrigin
+} from "./chunk-ST2IBUAN.js";
 
 // src/layout/walkStrip.ts
 var PAD_PX = 6;

package/dist/chunks/{chunk-VST5SR4C.js → chunk-RCWYY6XA.js}

@@ -7,15 +7,15 @@ import {
   meanDepth,
   nodeWidthPx
 } from "./chunk-PBENCR5L.js";
-import {
-  baseEdgeCurves
-} from "./chunk-WFB5TXRA.js";
 import {
   PATH_LIGHTNESS,
   PATH_SATURATION,
   nameHue,
   pathHueAt
-} from "./chunk-E7FWQQHP.js";
+} from "./chunk-7GBL7SJY.js";
+import {
+  baseEdgeCurves
+} from "./chunk-WFB5TXRA.js";
 import {
   referenceMidpoints
 } from "./chunk-ES2N6V56.js";

package/dist/chunks/{chunk-EXSXBIMH.js → chunk-UJ6GYL6T.js}

@@ -2,7 +2,7 @@ import {
   LIFT_BACKDROP_CSS,
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-VST5SR4C.js";
+} from "./chunk-RCWYY6XA.js";
 import {
   abgrToCssRgba
 } from "./chunk-UMNCCYBN.js";

package/dist/chunks/{chunk-EPWYRSHH.js → chunk-WZATPZNH.js}

@@ -1,20 +1,15 @@
-import {
-  orientToReference
-} from "./chunk-PUG7LXDF.js";
 import {
   seededNodes
 } from "./chunk-IGVV37VI.js";
+import {
+  orientToReference
+} from "./chunk-PUG7LXDF.js";
 import {
   convertGFAToGraph
 } from "./chunk-72N5DJHZ.js";
 import {
   parseGFA
 } from "./chunk-CDLPYR5O.js";
-import {
-  routeNodes,
-  takeRoutes,
-  withDeletionRoutes
-} from "./chunk-JVLURPFW.js";
 import {
   anchorGraph
 } from "./chunk-ST2IBUAN.js";
@@ -22,6 +17,11 @@ import {
   mergeRuns,
   splitRuns
 } from "./chunk-TAMCZHLW.js";
+import {
+  routeNodes,
+  takeRoutes,
+  withDeletionRoutes
+} from "./chunk-JVLURPFW.js";
 import {
   spreadFor
 } from "./chunk-UVBGRJQX.js";
@@ -54,6 +54,26 @@ function loadGraph(text, name, opts = {}) {
   }
   return graph;
 }
+var ENGINE_DEFAULTS = {
+  engine: "fmmm",
+  quality: 2,
+  linearLayout: false,
+  bubbleSpread: "auto",
+  spacing: 1,
+  componentSeparation: 1,
+  showDeletionEdges: true
+};
+function engineSettingsOf(s = {}) {
+  return {
+    engine: s.engine ?? ENGINE_DEFAULTS.engine,
+    quality: s.quality ?? ENGINE_DEFAULTS.quality,
+    linearLayout: s.linearLayout ?? ENGINE_DEFAULTS.linearLayout,
+    bubbleSpread: s.bubbleSpread ?? ENGINE_DEFAULTS.bubbleSpread,
+    spacing: s.spacing ?? ENGINE_DEFAULTS.spacing,
+    componentSeparation: s.componentSeparation ?? ENGINE_DEFAULTS.componentSeparation,
+    showDeletionEdges: s.showDeletionEdges ?? ENGINE_DEFAULTS.showDeletionEdges
+  };
+}
 var COMPONENT_SEPARATION = 15;
 function engineRequest(graph, scaling, settings) {
   const anchored = graph.nodes.some(isBackbone);
@@ -210,6 +230,8 @@ function drawingBounds(layout, opts = {}) {
 
 export {
   loadGraph,
+  ENGINE_DEFAULTS,
+  engineSettingsOf,
   engineRequest,
   engineKey,
   forceLayout,

package/dist/chunks/chunk-XVSBZ4ZW.js

@@ -0,0 +1,54 @@
+import {
+  engineKey,
+  forceLayout
+} from "./chunk-WZATPZNH.js";
+
+// src/layout/forceCache.ts
+var DEFAULT_SIZE = 4;
+function createForceLayoutCache(size = DEFAULT_SIZE) {
+  const caches = /* @__PURE__ */ new WeakMap();
+  const cacheOf = (graph) => {
+    let cache = caches.get(graph);
+    if (!cache) {
+      cache = /* @__PURE__ */ new Map();
+      caches.set(graph, cache);
+    }
+    return cache;
+  };
+  return {
+    layout(graph, settings, engine) {
+      const cache = cacheOf(graph);
+      const key = engineKey(graph, settings);
+      const hit = cache.get(key);
+      if (hit) {
+        return hit.run;
+      }
+      if (cache.size >= size) {
+        cache.delete(cache.keys().next().value);
+      }
+      const started = performance.now();
+      const entry = {
+        run: forceLayout(graph, settings, engine).then((r) => {
+          entry.done = r.result;
+          return { ...r, duration: r.duration || performance.now() - started };
+        })
+      };
+      entry.run.catch(() => cache.delete(key));
+      cache.set(key, entry);
+      return entry.run;
+    },
+    ready(graph, settings) {
+      return caches.get(graph)?.get(engineKey(graph, settings))?.done;
+    },
+    inherit(from, to) {
+      const cache = caches.get(from);
+      if (cache && from !== to) {
+        caches.set(to, cache);
+      }
+    }
+  };
+}
+
+export {
+  createForceLayoutCache
+};

package/dist/chunks/{chunk-TQ7VCGJR.js → chunk-ZNMHIPUZ.js}

@@ -2,7 +2,7 @@ import {
   REFERENCE_RAMP_ALT_COLOR,
   REFERENCE_RAMP_MAX_HUE,
   hslToRgb
-} from "./chunk-VST5SR4C.js";
+} from "./chunk-RCWYY6XA.js";
 import {
   packAbgr
 } from "./chunk-UMNCCYBN.js";