@jbrowse/bandage-core 7.3.0 → 7.4.0

package/dist/chunks/{chunk-36UKA6RQ.js → chunk-3LXG54PN.js}

@@ -1,7 +1,7 @@
 import {
   encodedColor,
   resolveEncoding
-} from "./chunk-C4IUUTAB.js";
+} from "./chunk-ZNMHIPUZ.js";
 import {
   pathOrigin
 } from "./chunk-ST2IBUAN.js";

package/dist/chunks/{chunk-AGJZ5RDC.js → chunk-4UBWXZVX.js}

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

package/dist/chunks/{chunk-45J7P6YW.js → chunk-5XHORHYK.js}

@@ -1,19 +1,22 @@
 import {
-  stripGeneGaps,
-  walkStripFrame,
-  walkStripLabelsTree
-} from "./chunk-HPIZNWF7.js";
-import {
-  Canvas2DRenderer
-} from "./chunk-CH3DLBUT.js";
+  layoutGeometryInputs
+} from "./chunk-LOCJN3BZ.js";
 import {
   svgCanvas
 } from "./chunk-47DYCZOK.js";
+import {
+  stripGeneGaps,
+  walkStripFrame,
+  walkStripLabelsTree
+} from "./chunk-PY7EZFL3.js";
 import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-RCPGXIWA.js";
+} from "./chunk-7G7TFATC.js";
+import {
+  Canvas2DRenderer
+} from "./chunk-CH3DLBUT.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
@@ -25,27 +28,35 @@ import {
 import {
   facetLifts,
   walkLift
-} from "./chunk-36UKA6RQ.js";
+} from "./chunk-3LXG54PN.js";
+import {
+  encodingStops
+} from "./chunk-ZNMHIPUZ.js";
 import {
   rangeText,
   walkKey
 } from "./chunk-2LQ5BWT7.js";
+import {
+  buildGeometry,
+  computeReferenceRamp
+} from "./chunk-RCWYY6XA.js";
 import {
   version
-} from "./chunk-ERHAGG72.js";
+} from "./chunk-LNSAKOXP.js";
 import {
   axisScaleOf
-} from "./chunk-AGJZ5RDC.js";
+} from "./chunk-4UBWXZVX.js";
 import {
-  encodingStops
-} from "./chunk-C4IUUTAB.js";
-import {
-  buildGeometry,
-  computeReferenceRamp
-} from "./chunk-W7R55CIZ.js";
+  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";
@@ -55,13 +66,6 @@ import {
 import {
   nodesUnderBox
 } from "./chunk-FP4H7SFT.js";
-import {
-  walkRowsExtent
-} from "./chunk-3JANT2SW.js";
-import {
-  pathLegend,
-  walkLabelsOf
-} from "./chunk-7GBL7SJY.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,
@@ -87,14 +91,11 @@ import {
   FIT_PADDING,
   drawingBounds,
   fitTransform
-} from "./chunk-SGAMPIKO.js";
+} from "./chunk-WZATPZNH.js";
 import {
   deletionDrawing,
   deletionEdges
 } from "./chunk-N6FECAXP.js";
-import {
-  ROW_HEIGHT_PX
-} from "./chunk-CPMHA4W5.js";
 
 // src/figure.ts
 var FONT = 'font-family="Helvetica, Arial, sans-serif" font-size="11"';
@@ -233,11 +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) {
@@ -269,7 +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,
@@ -280,11 +279,7 @@ function figureSvg(graph, layout, o = {}) {
         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-RCPGXIWA.js → chunk-7G7TFATC.js}

@@ -3,10 +3,10 @@ import {
   RAMP_GRADIENT_STOPS,
   rampHueCss,
   rampStops
-} from "./chunk-Z3OHBOEA.js";
+} from "./chunk-AVJK272H.js";
 import {
   REFERENCE_RAMP_ALT_CSS
-} from "./chunk-W7R55CIZ.js";
+} from "./chunk-RCWYY6XA.js";
 import {
   LABEL_CHAR_PX
 } from "./chunk-AB35TJST.js";

package/dist/chunks/{chunk-Z3OHBOEA.js → chunk-AVJK272H.js}

@@ -1,6 +1,6 @@
 import {
   REFERENCE_RAMP_MAX_HUE
-} from "./chunk-W7R55CIZ.js";
+} from "./chunk-RCWYY6XA.js";
 
 // src/referenceRampCss.ts
 function rampHueCss(hue) {

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-IW6K4VHZ.js → chunk-FRR2RGBT.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-CBBDB3UC.js → chunk-H5S2ONCJ.js}

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

package/dist/chunks/{chunk-O7QXUXGZ.js → chunk-KEVQ46GG.js}

@@ -1,7 +1,7 @@
 import {
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-W7R55CIZ.js";
+} from "./chunk-RCWYY6XA.js";
 import {
   abgrToCssRgba
 } from "./chunk-UMNCCYBN.js";

package/dist/chunks/{chunk-ERHAGG72.js → chunk-LNSAKOXP.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "7.3.0";
+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-HPIZNWF7.js → chunk-PY7EZFL3.js}

@@ -2,7 +2,7 @@ import {
   alongRow,
   boxesGenes,
   rowPitch
-} from "./chunk-RCPGXIWA.js";
+} from "./chunk-7G7TFATC.js";
 import {
   LABEL_CHAR_PX
 } from "./chunk-AB35TJST.js";

package/dist/chunks/{chunk-5N5YRRFE.js → chunk-UJ6GYL6T.js}

@@ -2,7 +2,7 @@ import {
   LIFT_BACKDROP_CSS,
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-W7R55CIZ.js";
+} from "./chunk-RCWYY6XA.js";
 import {
   abgrToCssRgba
 } from "./chunk-UMNCCYBN.js";

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-C4IUUTAB.js → chunk-ZNMHIPUZ.js}

@@ -2,7 +2,7 @@ import {
   REFERENCE_RAMP_ALT_COLOR,
   REFERENCE_RAMP_MAX_HUE,
   hslToRgb
-} from "./chunk-W7R55CIZ.js";
+} from "./chunk-RCWYY6XA.js";
 import {
   packAbgr
 } from "./chunk-UMNCCYBN.js";

package/dist/cli/figure.js

@@ -4,6 +4,18 @@ import {
   genesFromGff3Lines,
   genesFromText
 } from "../chunks/chunk-BXEPA4KS.js";
+import {
+  LAYOUT_MODES,
+  layoutModeByValue
+} from "../chunks/chunk-FRR2RGBT.js";
+import "../chunks/chunk-LOEA5IHZ.js";
+import "../chunks/chunk-AYOSNXLQ.js";
+import "../chunks/chunk-TEDQJPMI.js";
+import "../chunks/chunk-L3O7AWLI.js";
+import "../chunks/chunk-TZFWUT2C.js";
+import "../chunks/chunk-C44YRP5F.js";
+import "../chunks/chunk-RVS2QCOX.js";
+import "../chunks/chunk-HNQPEMYE.js";
 import {
   HPRC_GBZ,
   cutGbzRegion,
@@ -21,40 +33,35 @@ import {
 import "../chunks/chunk-UNOE2NDN.js";
 import "../chunks/chunk-LYJ4US66.js";
 import "../chunks/chunk-7XHHVYG7.js";
-import {
-  LAYOUT_MODES,
-  layoutModeByValue
-} from "../chunks/chunk-IW6K4VHZ.js";
-import "../chunks/chunk-LOEA5IHZ.js";
-import "../chunks/chunk-AYOSNXLQ.js";
-import "../chunks/chunk-TEDQJPMI.js";
-import "../chunks/chunk-L3O7AWLI.js";
-import "../chunks/chunk-TZFWUT2C.js";
-import "../chunks/chunk-C44YRP5F.js";
-import "../chunks/chunk-RVS2QCOX.js";
-import "../chunks/chunk-HNQPEMYE.js";
 import {
   figureSvg
-} from "../chunks/chunk-45J7P6YW.js";
-import "../chunks/chunk-HPIZNWF7.js";
-import "../chunks/chunk-CH3DLBUT.js";
-import "../chunks/chunk-4BYTEJGW.js";
+} from "../chunks/chunk-5XHORHYK.js";
+import "../chunks/chunk-LOCJN3BZ.js";
 import "../chunks/chunk-47DYCZOK.js";
+import "../chunks/chunk-PY7EZFL3.js";
 import {
   genesOnRow,
   placeRowGenes
-} from "../chunks/chunk-RCPGXIWA.js";
+} from "../chunks/chunk-7G7TFATC.js";
+import "../chunks/chunk-CH3DLBUT.js";
+import "../chunks/chunk-4BYTEJGW.js";
 import "../chunks/chunk-3S3YVOJ7.js";
 import "../chunks/chunk-BUBZ32IC.js";
-import "../chunks/chunk-36UKA6RQ.js";
+import "../chunks/chunk-3LXG54PN.js";
+import "../chunks/chunk-ZNMHIPUZ.js";
 import "../chunks/chunk-2LQ5BWT7.js";
-import "../chunks/chunk-Z3OHBOEA.js";
-import "../chunks/chunk-ERHAGG72.js";
-import "../chunks/chunk-AGJZ5RDC.js";
-import "../chunks/chunk-C4IUUTAB.js";
-import "../chunks/chunk-W7R55CIZ.js";
+import "../chunks/chunk-AVJK272H.js";
+import "../chunks/chunk-RCWYY6XA.js";
 import "../chunks/chunk-UMNCCYBN.js";
+import "../chunks/chunk-LNSAKOXP.js";
+import "../chunks/chunk-4UBWXZVX.js";
+import "../chunks/chunk-MP7LXLWV.js";
+import {
+  filterSamples,
+  walkRows
+} from "../chunks/chunk-SZNZ2T6D.js";
 import "../chunks/chunk-PBENCR5L.js";
+import "../chunks/chunk-7GBL7SJY.js";
 import {
   featuresOnBackbone,
   graphBackbone,
@@ -64,12 +71,6 @@ import "../chunks/chunk-GJMC3PGM.js";
 import "../chunks/chunk-FP4H7SFT.js";
 import "../chunks/chunk-MLSWIMZO.js";
 import "../chunks/chunk-WFB5TXRA.js";
-import "../chunks/chunk-3JANT2SW.js";
-import {
-  filterSamples,
-  walkRows
-} from "../chunks/chunk-SZNZ2T6D.js";
-import "../chunks/chunk-7GBL7SJY.js";
 import "../chunks/chunk-3ZZSX5HN.js";
 import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-JKJWSY4V.js";
@@ -79,17 +80,17 @@ import {
   engineSettingsOf,
   forceLayout,
   loadGraph
-} from "../chunks/chunk-SGAMPIKO.js";
-import "../chunks/chunk-PUG7LXDF.js";
+} from "../chunks/chunk-WZATPZNH.js";
 import "../chunks/chunk-IGVV37VI.js";
+import "../chunks/chunk-PUG7LXDF.js";
 import "../chunks/chunk-72N5DJHZ.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-CDLPYR5O.js";
-import "../chunks/chunk-JVLURPFW.js";
 import "../chunks/chunk-ES2N6V56.js";
 import "../chunks/chunk-ST2IBUAN.js";
 import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-TAMCZHLW.js";
+import "../chunks/chunk-JVLURPFW.js";
 import "../chunks/chunk-UVBGRJQX.js";
 import "../chunks/chunk-6JEWNXCQ.js";
 import "../chunks/chunk-N6FECAXP.js";

package/dist/figure.js

@@ -1,46 +1,47 @@
 import {
   figureSvg
-} from "./chunks/chunk-45J7P6YW.js";
-import "./chunks/chunk-HPIZNWF7.js";
+} from "./chunks/chunk-5XHORHYK.js";
+import "./chunks/chunk-LOCJN3BZ.js";
+import "./chunks/chunk-47DYCZOK.js";
+import "./chunks/chunk-PY7EZFL3.js";
+import "./chunks/chunk-7G7TFATC.js";
 import "./chunks/chunk-CH3DLBUT.js";
 import "./chunks/chunk-4BYTEJGW.js";
-import "./chunks/chunk-47DYCZOK.js";
-import "./chunks/chunk-RCPGXIWA.js";
 import "./chunks/chunk-3S3YVOJ7.js";
 import "./chunks/chunk-BUBZ32IC.js";
-import "./chunks/chunk-36UKA6RQ.js";
+import "./chunks/chunk-3LXG54PN.js";
+import "./chunks/chunk-ZNMHIPUZ.js";
 import "./chunks/chunk-2LQ5BWT7.js";
-import "./chunks/chunk-Z3OHBOEA.js";
-import "./chunks/chunk-ERHAGG72.js";
-import "./chunks/chunk-AGJZ5RDC.js";
-import "./chunks/chunk-C4IUUTAB.js";
-import "./chunks/chunk-W7R55CIZ.js";
+import "./chunks/chunk-AVJK272H.js";
+import "./chunks/chunk-RCWYY6XA.js";
 import "./chunks/chunk-UMNCCYBN.js";
+import "./chunks/chunk-LNSAKOXP.js";
+import "./chunks/chunk-4UBWXZVX.js";
+import "./chunks/chunk-MP7LXLWV.js";
+import "./chunks/chunk-SZNZ2T6D.js";
 import "./chunks/chunk-PBENCR5L.js";
+import "./chunks/chunk-7GBL7SJY.js";
 import "./chunks/chunk-RAKOB6IV.js";
 import "./chunks/chunk-GJMC3PGM.js";
 import "./chunks/chunk-FP4H7SFT.js";
 import "./chunks/chunk-MLSWIMZO.js";
 import "./chunks/chunk-WFB5TXRA.js";
-import "./chunks/chunk-3JANT2SW.js";
-import "./chunks/chunk-SZNZ2T6D.js";
-import "./chunks/chunk-7GBL7SJY.js";
 import "./chunks/chunk-3ZZSX5HN.js";
 import "./chunks/chunk-AB35TJST.js";
 import "./chunks/chunk-JKJWSY4V.js";
 import "./chunks/chunk-NNODIW4U.js";
 import "./chunks/chunk-6SBUFFTB.js";
-import "./chunks/chunk-SGAMPIKO.js";
-import "./chunks/chunk-PUG7LXDF.js";
+import "./chunks/chunk-WZATPZNH.js";
 import "./chunks/chunk-IGVV37VI.js";
+import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-72N5DJHZ.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-TAMCZHLW.js";
+import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-UVBGRJQX.js";
 import "./chunks/chunk-6JEWNXCQ.js";
 import "./chunks/chunk-N6FECAXP.js";

package/dist/figureSettings.js

@@ -1,18 +1,18 @@
 import {
   FIGURE_DEFAULTS,
   figureSpecSettings
-} from "./chunks/chunk-CBBDB3UC.js";
-import "./chunks/chunk-SGAMPIKO.js";
-import "./chunks/chunk-PUG7LXDF.js";
+} from "./chunks/chunk-H5S2ONCJ.js";
+import "./chunks/chunk-WZATPZNH.js";
 import "./chunks/chunk-IGVV37VI.js";
+import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-72N5DJHZ.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-TAMCZHLW.js";
+import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-UVBGRJQX.js";
 import "./chunks/chunk-6JEWNXCQ.js";
 import "./chunks/chunk-N6FECAXP.js";

package/dist/hoverText.js

@@ -0,0 +1,8 @@
+import {
+  edgeHoverText,
+  regionLabel
+} from "./chunks/chunk-AZFVORTC.js";
+export {
+  edgeHoverText,
+  regionLabel
+};