@jbrowse/bandage-core 6.1.1 → 7.0.0

package/dist/chunks/{chunk-GOY6REMT.js → chunk-2LQ5BWT7.js}

@@ -1,7 +1,7 @@
 import {
   formatBp,
   groupDigits
-} from "./chunk-N62KBLFC.js";
+} from "./chunk-3ZZSX5HN.js";
 
 // src/walkKey.ts
 function rangeText(contig, start, end) {

package/dist/chunks/{chunk-N62KBLFC.js → chunk-3ZZSX5HN.js}

@@ -6,7 +6,7 @@ import {
 } from "./chunk-TAMCZHLW.js";
 import {
   deletionArcCurves
-} from "./chunk-4EMPBO7S.js";
+} from "./chunk-N6FECAXP.js";
 import {
   curveBounds,
   curveMidpoint

package/dist/chunks/{chunk-R6ZUK4Y3.js → chunk-4FQTTG5F.js}

@@ -7,7 +7,7 @@ import {
 import {
   pathCssColor,
   pathGreyCssColor
-} from "./chunk-X5L37W4J.js";
+} from "./chunk-E7FWQQHP.js";
 import {
   pathOrigin
 } from "./chunk-ST2IBUAN.js";

package/dist/chunks/{chunk-7UIMNBJT.js → chunk-6UFS3EWI.js}

@@ -11,11 +11,10 @@ import {
   parseGFA
 } from "./chunk-CDLPYR5O.js";
 import {
-  closableDeletions,
   routeNodes,
   takeRoutes,
   withDeletionRoutes
-} from "./chunk-STNG3Y5X.js";
+} from "./chunk-YZ5CCEDH.js";
 import {
   anchorGraph
 } from "./chunk-ST2IBUAN.js";
@@ -32,8 +31,9 @@ import {
   layoutScaling
 } from "./chunk-6JEWNXCQ.js";
 import {
+  closableDeletions,
   deletionEdges
-} from "./chunk-4EMPBO7S.js";
+} from "./chunk-N6FECAXP.js";
 import {
   isBackbone
 } from "./chunk-FYQWPEEY.js";
@@ -74,13 +74,14 @@ function engineRequest(graph, scaling, settings) {
       linearLayout: settings.linearLayout,
       ...spaced.opts,
       componentSeparation: COMPONENT_SEPARATION * (settings.componentSeparation ?? 1),
-      ...anchored ? { rotateComponents: false } : {}
+      ...anchored ? { rotateComponents: false } : {},
+      engine: settings.engine ?? "fmmm"
     }
   };
 }
 function engineKey(graph, settings) {
   const anchored = graph.nodes.some(isBackbone);
-  return `${settings.quality}|${settings.linearLayout}|${settings.bubbleSpread}|${settings.spacing ?? 1}|${settings.componentSeparation ?? 1}|${settings.showDeletionEdges !== false}|${anchored}|${graph.referencePath ?? ""}`;
+  return `${settings.engine ?? "fmmm"}|${settings.quality}|${settings.linearLayout}|${settings.bubbleSpread}|${settings.spacing ?? 1}|${settings.componentSeparation ?? 1}|${settings.showDeletionEdges !== false}|${anchored}|${graph.referencePath ?? ""}`;
 }
 async function forceLayout(graph, settings, engine) {
   const spread = spreadFor(settings.bubbleSpread);

package/dist/chunks/{chunk-OSDI57GY.js → chunk-7PWMTUAK.js}

@@ -5,61 +5,64 @@ import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-V5BPIOLS.js";
+} from "./chunk-MZ7QQRUJ.js";
 import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-PJESIRDU.js";
+} from "./chunk-JFNPL4UT.js";
 import {
   Canvas2DRenderer
 } from "./chunk-CH3DLBUT.js";
-import {
-  genePins
-} from "./chunk-BUBZ32IC.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
   exonStretches
 } from "./chunk-3S3YVOJ7.js";
+import {
+  genePins
+} from "./chunk-BUBZ32IC.js";
 import {
   version
-} from "./chunk-XH43CLO2.js";
+} from "./chunk-EOSVRILX.js";
 import {
   axisScaleOf
-} from "./chunk-XJWN753L.js";
+} from "./chunk-AWCMVPVP.js";
 import {
   facetLifts,
   walkLift
-} from "./chunk-ZKGM7VLA.js";
+} from "./chunk-MH5IA57M.js";
 import {
   encodingStops
-} from "./chunk-X4VVPLI5.js";
+} from "./chunk-TQ7VCGJR.js";
 import {
   rangeText,
   walkKey
-} from "./chunk-GOY6REMT.js";
+} from "./chunk-2LQ5BWT7.js";
 import {
   FIT_PADDING,
   drawingBounds,
   fitTransform
-} from "./chunk-7UIMNBJT.js";
+} from "./chunk-6UFS3EWI.js";
 import {
   buildGeometry,
   computeReferenceRamp
-} from "./chunk-RX5CSWJW.js";
+} from "./chunk-VST5SR4C.js";
+import {
+  nodeInk
+} from "./chunk-PBENCR5L.js";
 import {
   geneLabelCandidates
-} from "./chunk-DKOB2OPC.js";
+} from "./chunk-GJMC3PGM.js";
 import {
   nodesUnderBox
-} from "./chunk-YMSSF2RK.js";
+} from "./chunk-FP4H7SFT.js";
 import {
   walkRowsExtent
 } from "./chunk-EZPBJPK6.js";
 import {
   pathLegend
-} from "./chunk-X5L37W4J.js";
+} from "./chunk-E7FWQQHP.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,
@@ -67,15 +70,13 @@ import {
   occupancy,
   placeLabels
 } from "./chunk-AB35TJST.js";
-import {
-  nodeInk
-} from "./chunk-PBENCR5L.js";
 import {
   resolveColorScheme
 } from "./chunk-JKJWSY4V.js";
 import {
+  deletionDrawing,
   deletionEdges
-} from "./chunk-4EMPBO7S.js";
+} from "./chunk-N6FECAXP.js";
 import {
   ROW_HEIGHT_PX
 } from "./chunk-CPMHA4W5.js";
@@ -163,7 +164,11 @@ function figureSvg(graph, layout, o = {}) {
     start: referenceRamp.start,
     end: referenceRamp.start + referenceRamp.span
   };
-  const deletions = layout.tubeMap ? [] : deletionEdges(graph);
+  const drawnDeletions = deletionDrawing(
+    graph,
+    layout.tubeMap ? [] : 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 && !layout.tubeMap ? walkLift(graph, layers, walkRamp) : void 0;
@@ -276,12 +281,10 @@ function figureSvg(graph, layout, o = {}) {
         highlight,
         axis,
         referenceRamp,
-        deletions: new Map(deletions.map((d) => [d.edgeIndex, d.bypassed])),
+        deletions: drawnDeletions.bypassed,
         deletionRoutes: layout.deletionRoutes,
         stranded: layout.stranded,
-        hiddenEdges: new Set(
-          o.showDeletionEdges ? [] : deletions.map((d) => d.edgeIndex)
-        )
+        hiddenEdges: drawnDeletions.hidden
       })
     );
     const t = {

package/dist/chunks/{chunk-XJWN753L.js → chunk-AWCMVPVP.js}

@@ -1,6 +1,6 @@
 import {
   clampZoom
-} from "./chunk-7UIMNBJT.js";
+} from "./chunk-6UFS3EWI.js";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {

package/dist/chunks/{chunk-ZZA2AFB4.js → chunk-CNQSHEBS.js}

@@ -1,7 +1,7 @@
 import {
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-RX5CSWJW.js";
+} from "./chunk-VST5SR4C.js";
 import {
   abgrToCssRgba
 } from "./chunk-UMNCCYBN.js";

package/dist/chunks/{chunk-CS3E4ETM.js → chunk-DRA7733Q.js}

@@ -1,6 +1,6 @@
 import {
   formatBp
-} from "./chunk-N62KBLFC.js";
+} from "./chunk-3ZZSX5HN.js";
 import {
   isBackbone
 } from "./chunk-FYQWPEEY.js";

package/dist/chunks/{chunk-X5L37W4J.js → chunk-E7FWQQHP.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-ST2IBUAN.js";
 import {
   groupDigits
-} from "./chunk-N62KBLFC.js";
+} from "./chunk-3ZZSX5HN.js";
 import {
   isGenericSample
 } from "./chunk-BPLIXMH7.js";

package/dist/chunks/{chunk-XH43CLO2.js → chunk-EOSVRILX.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "6.1.1";
+var version = "7.0.0";
 
 export {
   version

package/dist/chunks/{chunk-SMQ545MU.js → chunk-EXSXBIMH.js}

@@ -2,7 +2,7 @@ import {
   LIFT_BACKDROP_CSS,
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-RX5CSWJW.js";
+} from "./chunk-VST5SR4C.js";
 import {
   abgrToCssRgba
 } from "./chunk-UMNCCYBN.js";

package/dist/chunks/{chunk-YMSSF2RK.js → chunk-FP4H7SFT.js}

@@ -1,7 +1,7 @@
 import {
   EdgeSpatialIndex,
   SpatialIndex
-} from "./chunk-MREQ7GIA.js";
+} from "./chunk-MLSWIMZO.js";
 import {
   pathRibbonOffsets,
   translateCurves,

package/dist/chunks/{chunk-DKOB2OPC.js → chunk-GJMC3PGM.js}

@@ -1,12 +1,12 @@
 import {
   nodesUnderBox
-} from "./chunk-YMSSF2RK.js";
+} from "./chunk-FP4H7SFT.js";
 import {
   nodeLabelBudget,
   placeSizeLabels,
   rowLabelBox,
   sizeLabelCandidates
-} from "./chunk-N62KBLFC.js";
+} from "./chunk-3ZZSX5HN.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,
@@ -127,7 +127,7 @@ function layoutLabels(m) {
   const sizeCandidates = m.nodePositions && m.labelsNodeSizes ? sizeLabelCandidates({
     nodePositions: m.nodePositions,
     nodeLengths: m.nodeLengths,
-    deletions: m.showDeletionEdges ? m.deletions : [],
+    deletions: m.deletions,
     deletionRoutes: m.deletionRoutes,
     stranded: m.stranded,
     alleleDeletions: m.alleleDeletions,

package/dist/chunks/{chunk-PJESIRDU.js → chunk-JFNPL4UT.js}

@@ -3,10 +3,10 @@ import {
   RAMP_GRADIENT_STOPS,
   rampHueCss,
   rampStops
-} from "./chunk-ZHCDYSA5.js";
+} from "./chunk-VECR253P.js";
 import {
   REFERENCE_RAMP_ALT_CSS
-} from "./chunk-RX5CSWJW.js";
+} from "./chunk-VST5SR4C.js";
 import {
   LABEL_CHAR_PX
 } from "./chunk-AB35TJST.js";

package/dist/chunks/chunk-L53SXJZI.js

@@ -0,0 +1,22 @@
+import {
+  stressLayout
+} from "./chunk-O4TGF4WS.js";
+import {
+  loadBandage
+} from "./chunk-7XHHVYG7.js";
+
+// src/layoutEngines.ts
+var layoutEngine = async (request) => {
+  const start = performance.now();
+  if (request.options.engine === "stress") {
+    const result2 = stressLayout(request);
+    return { result: result2, duration: performance.now() - start };
+  }
+  const bandage = await loadBandage();
+  const result = bandage.computeLayout(request.graph, request.options);
+  return { result, duration: performance.now() - start };
+};
+
+export {
+  layoutEngine
+};

package/dist/chunks/{chunk-ZKGM7VLA.js → chunk-MH5IA57M.js}

@@ -1,7 +1,7 @@
 import {
   encodedColor,
   resolveEncoding
-} from "./chunk-X4VVPLI5.js";
+} from "./chunk-TQ7VCGJR.js";
 import {
   pathOrigin
 } from "./chunk-ST2IBUAN.js";

package/dist/chunks/{chunk-MREQ7GIA.js → chunk-MLSWIMZO.js}

@@ -1,6 +1,6 @@
 import {
   baseEdgeCurves
-} from "./chunk-Y3IOTZJA.js";
+} from "./chunk-WFB5TXRA.js";
 import {
   curveBounds,
   pathRibbonOffsets

package/dist/chunks/{chunk-V5BPIOLS.js → chunk-MZ7QQRUJ.js}

@@ -1,7 +1,7 @@
 import {
   alongRow,
   boxesGenes
-} from "./chunk-PJESIRDU.js";
+} from "./chunk-JFNPL4UT.js";
 import {
   pathOrigin
 } from "./chunk-ST2IBUAN.js";

package/dist/chunks/{chunk-4EMPBO7S.js → chunk-N6FECAXP.js}

@@ -109,9 +109,59 @@ function deletionEdges(graph) {
   }
   return found;
 }
+function closableDeletions(graph, deletions) {
+  const parent = /* @__PURE__ */ new Map();
+  const root = (id) => {
+    let r = id;
+    while (parent.has(r)) {
+      r = parent.get(r);
+    }
+    if (r !== id) {
+      parent.set(id, r);
+    }
+    return r;
+  };
+  const join = (a, b) => {
+    const [ra, rb] = [root(a), root(b)];
+    if (ra !== rb) {
+      parent.set(ra, rb);
+    }
+    return ra !== rb;
+  };
+  const candidates = new Set(deletions.map((d) => d.edgeIndex));
+  graph.edges.forEach((e, ei) => {
+    if (!candidates.has(ei)) {
+      join(e.from, e.to);
+    }
+  });
+  return new Set(
+    deletions.filter((d) => !join(d.from, d.to)).map((d) => d.edgeIndex)
+  );
+}
+var drawings = /* @__PURE__ */ new WeakMap();
+function deletionDrawing(graph, deletions, show = true) {
+  let byShow = drawings.get(deletions);
+  if (!byShow) {
+    byShow = /* @__PURE__ */ new Map();
+    drawings.set(deletions, byShow);
+  }
+  let drawing = byShow.get(show);
+  if (!drawing) {
+    const hidden = show ? /* @__PURE__ */ new Set() : closableDeletions(graph, deletions);
+    drawing = {
+      shown: deletions.filter((d) => !hidden.has(d.edgeIndex)),
+      bypassed: new Map(deletions.map((d) => [d.edgeIndex, d.bypassed])),
+      hidden
+    };
+    byShow.set(show, drawing);
+  }
+  return drawing;
+}
 
 export {
   bypassedPoints,
   deletionArcCurves,
-  deletionEdges
+  deletionEdges,
+  closableDeletions,
+  deletionDrawing
 };