@jbrowse/bandage-core 6.0.2 → 6.0.4

package/dist/bubbles/bubbleHalos.js

@@ -1,9 +1,9 @@
 import {
   bubbleHalos
-} from "../chunks/chunk-3C2LGJKY.js";
+} from "../chunks/chunk-ISEI2FH3.js";
 import "../chunks/chunk-WOO7QYKB.js";
 import "../chunks/chunk-MFKORG3F.js";
-import "../chunks/chunk-3PLYZLYV.js";
+import "../chunks/chunk-2CVHXFK7.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {

package/dist/chunks/{chunk-3PLYZLYV.js → chunk-2CVHXFK7.js}

@@ -159,6 +159,20 @@ function facingSides(fromSegments, toSegments) {
     to: facingSide(toSegments, spanOf(fromSegments), "start")
   };
 }
+var laidSides = /* @__PURE__ */ new WeakMap();
+function heldFacingSides(fromSegments, toSegments) {
+  let byTo = laidSides.get(fromSegments);
+  if (!byTo) {
+    byTo = /* @__PURE__ */ new WeakMap();
+    laidSides.set(fromSegments, byTo);
+  }
+  let sides = byTo.get(toSegments);
+  if (!sides) {
+    sides = facingSides(fromSegments, toSegments);
+    byTo.set(toSegments, sides);
+  }
+  return sides;
+}
 var APEX_FRACTION = 0.75;
 var BOW_CLEARANCE = 1.15;
 var ALONG_FRACTION = 0.35;
@@ -298,6 +312,9 @@ function computeEdgeCurves(fromSegments, toSegments, join, offsetX, offsetY, axi
   const scale = axis.scaleX;
   const yToX = yToXOf(axis);
   const maxBow = maxBowIn ?? (axis.pixelRows ? MAX_ROW_BOW_PX : void 0);
+  if (join === false) {
+    join = heldFacingSides(fromSegments, toSegments);
+  }
   if (yToX !== 1) {
     return unscaleYOf(
       computeEdgeCurves(
@@ -324,7 +341,7 @@ function computeEdgeCurves(fromSegments, toSegments, join, offsetX, offsetY, axi
     );
   }
   const loop = join === true;
-  const sides = loop ? { from: "end", to: "start" } : join || facingSides(fromSegments, toSegments);
+  const sides = join === true ? { from: "end", to: "start" } : join;
   const fromAttach = attachment(fromSegments, sides.from);
   const toAttach = attachment(toSegments, sides.to);
   const fromEnd = fromAttach.at;

package/dist/chunks/chunk-4BYTEJGW.js

@@ -0,0 +1,44 @@
+// src/renderer/canvas.ts
+var MAX_DPR = 2;
+var MAX_CANVAS_DIM_PX = 8192;
+function getDpr() {
+  return typeof devicePixelRatio === "undefined" ? 1 : Math.min(devicePixelRatio, MAX_DPR);
+}
+var warnedCanvasClamp = false;
+function backingPx(cssSize, dpr, axis) {
+  const value = Math.round(cssSize * dpr);
+  if (value > MAX_CANVAS_DIM_PX) {
+    if (!warnedCanvasClamp) {
+      warnedCanvasClamp = true;
+      console.warn(
+        `Canvas ${axis} ${value}px exceeds the safe limit ${MAX_CANVAS_DIM_PX}px and was clamped`
+      );
+    }
+    return MAX_CANVAS_DIM_PX;
+  }
+  return value;
+}
+function syncCanvasSize(canvas, width, height) {
+  const dpr = getDpr();
+  const pw = backingPx(width, dpr, "width");
+  const ph = backingPx(height, dpr, "height");
+  if (canvas.width !== pw || canvas.height !== ph) {
+    canvas.width = pw;
+    canvas.height = ph;
+  }
+  const cssWidth = `${width}px`;
+  const cssHeight = `${height}px`;
+  if (canvas.style.width !== cssWidth) {
+    canvas.style.width = cssWidth;
+  }
+  if (canvas.style.height !== cssHeight) {
+    canvas.style.height = cssHeight;
+  }
+}
+
+export {
+  MAX_DPR,
+  MAX_CANVAS_DIM_PX,
+  getDpr,
+  syncCanvasSize
+};

package/dist/chunks/{chunk-X32PABB7.js → chunk-4EMPBO7S.js}

@@ -3,7 +3,7 @@ import {
   edgeJoinOf,
   routedEdgeCurves,
   strandSides
-} from "./chunk-3PLYZLYV.js";
+} from "./chunk-2CVHXFK7.js";
 import {
   firstNodeAtOrAfter,
   isBackbone

package/dist/chunks/{chunk-SV27AJCC.js → chunk-BUBZ32IC.js}

@@ -1,9 +1,9 @@
 import {
   polylineSlice
-} from "./chunk-SDGM243E.js";
+} from "./chunk-TAMCZHLW.js";
 import {
   svgPath
-} from "./chunk-3PLYZLYV.js";
+} from "./chunk-2CVHXFK7.js";
 import {
   firstNodeAtOrAfter,
   isAnchored

package/dist/chunks/{chunk-D3M7SBKL.js → chunk-CH3DLBUT.js}

@@ -1,29 +1,37 @@
 import {
-  brightenAbgr
-} from "./chunk-MNUSQCLG.js";
-
-// src/renderer/Canvas2DRenderer.ts
+  syncCanvasSize
+} from "./chunk-4BYTEJGW.js";
 import {
   abgrToCssRgba,
+  brightenAbgr,
   normalizedRgbToCssRgba
-} from "@jbrowse/core/util/colorBits";
-import { syncCanvasSize } from "@jbrowse/render-core/canvas2dUtils";
-import { Canvas2DRenderingBackendBase } from "@jbrowse/render-core/renderingBackendBase";
-var Canvas2DRenderer = class extends Canvas2DRenderingBackendBase {
-  constructor() {
-    super(...arguments);
+} from "./chunk-UMNCCYBN.js";
+
+// src/renderer/Canvas2DRenderer.ts
+var Canvas2DRenderer = class {
+  constructor(canvas) {
     this.transform = null;
     this.batch = null;
     this.nodeHighlights = /* @__PURE__ */ new Map();
     this.highlightedEdge = null;
     this.highlightFactor = 1;
+    const ctx = canvas.getContext("2d");
+    if (!ctx) {
+      throw new Error("Canvas 2D context not available");
+    }
+    this.canvas = canvas;
+    this.ctx = ctx;
+  }
+  setErrorHandler(_handler) {
+  }
+  releaseOffscreenTargets() {
   }
-  // render-core's, not a local `width * devicePixelRatio`: it 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
+  // 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.
   resize(width, height) {
-    syncCanvasSize(this.ctx.canvas, width, height);
+    syncCanvasSize(this.canvas, width, height);
   }
   uploadGeometry(batch) {
     this.batch = batch;
@@ -159,7 +167,6 @@ var Canvas2DRenderer = class extends Canvas2DRenderingBackendBase {
     }
   }
   dispose() {
-    super.dispose();
     this.batch = null;
     this.nodeHighlights = /* @__PURE__ */ new Map();
     this.highlightedEdge = null;

package/dist/chunks/{chunk-Q3KCTA4N.js → chunk-CS3E4ETM.js}

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

package/dist/chunks/{chunk-57ZIXHZA.js → chunk-CTSBC2O6.js}

@@ -1,6 +1,6 @@
 import {
   tubeSpan
-} from "./chunk-Q3KCTA4N.js";
+} from "./chunk-CS3E4ETM.js";
 
 // src/tubeMap/genes.ts
 function tubeMapGenes(byRefName, genes) {

package/dist/chunks/{chunk-HB6PDCOU.js → chunk-DKOB2OPC.js}

@@ -1,12 +1,12 @@
 import {
   nodesUnderBox
-} from "./chunk-BJV2W4KZ.js";
+} from "./chunk-YMSSF2RK.js";
 import {
   nodeLabelBudget,
   placeSizeLabels,
   rowLabelBox,
   sizeLabelCandidates
-} from "./chunk-HCANBJDD.js";
+} from "./chunk-N62KBLFC.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,

package/dist/chunks/{chunk-CZ54VG2H.js → chunk-FZCOVJAL.js}

@@ -5,18 +5,18 @@ import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-MHGHYHTL.js";
+} from "./chunk-V5BPIOLS.js";
 import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-QCYM44UL.js";
+} from "./chunk-PJESIRDU.js";
 import {
   Canvas2DRenderer
-} from "./chunk-D3M7SBKL.js";
+} from "./chunk-CH3DLBUT.js";
 import {
   genePins
-} from "./chunk-SV27AJCC.js";
+} from "./chunk-BUBZ32IC.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
@@ -24,42 +24,42 @@ import {
 } from "./chunk-3S3YVOJ7.js";
 import {
   version
-} from "./chunk-KCW7L3NV.js";
+} from "./chunk-QFBZQJFK.js";
 import {
   axisScaleOf
-} from "./chunk-L5RYUPZI.js";
+} from "./chunk-MQJUG2D2.js";
 import {
   facetLifts,
   walkLift
-} from "./chunk-6Q6HFBJT.js";
+} from "./chunk-ZKGM7VLA.js";
 import {
   encodingStops
-} from "./chunk-IMW3AK27.js";
+} from "./chunk-X4VVPLI5.js";
 import {
   rangeText,
   walkKey
-} from "./chunk-AE3UQZY3.js";
+} from "./chunk-GOY6REMT.js";
 import {
   FIT_PADDING,
   drawingBounds,
   fitTransform
-} from "./chunk-VKB57ZYE.js";
+} from "./chunk-IO2PCPZI.js";
 import {
   buildGeometry,
   computeReferenceRamp
-} from "./chunk-3WHKR5TY.js";
+} from "./chunk-RX5CSWJW.js";
 import {
   geneLabelCandidates
-} from "./chunk-HB6PDCOU.js";
+} from "./chunk-DKOB2OPC.js";
 import {
   nodesUnderBox
-} from "./chunk-BJV2W4KZ.js";
+} from "./chunk-YMSSF2RK.js";
 import {
   walkRowsExtent
 } from "./chunk-EZPBJPK6.js";
 import {
   pathLegend
-} from "./chunk-7CHJKABZ.js";
+} from "./chunk-X5L37W4J.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,
@@ -75,7 +75,7 @@ import {
 } from "./chunk-JKJWSY4V.js";
 import {
   deletionEdges
-} from "./chunk-X32PABB7.js";
+} from "./chunk-4EMPBO7S.js";
 import {
   ROW_HEIGHT_PX
 } from "./chunk-CPMHA4W5.js";

package/dist/chunks/{chunk-AE3UQZY3.js → chunk-GOY6REMT.js}

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

package/dist/chunks/{chunk-VKB57ZYE.js → chunk-IO2PCPZI.js}

@@ -21,7 +21,7 @@ import {
 import {
   mergeRuns,
   splitRuns
-} from "./chunk-SDGM243E.js";
+} from "./chunk-TAMCZHLW.js";
 import {
   spreadFor
 } from "./chunk-UVBGRJQX.js";
@@ -32,7 +32,7 @@ import {
 } from "./chunk-6JEWNXCQ.js";
 import {
   deletionEdges
-} from "./chunk-X32PABB7.js";
+} from "./chunk-4EMPBO7S.js";
 import {
   isBackbone
 } from "./chunk-FYQWPEEY.js";

package/dist/chunks/{chunk-3C2LGJKY.js → chunk-ISEI2FH3.js}

@@ -5,7 +5,7 @@ import {
 } from "./chunk-WOO7QYKB.js";
 import {
   svgPath
-} from "./chunk-3PLYZLYV.js";
+} from "./chunk-2CVHXFK7.js";
 import {
   isBackbone
 } from "./chunk-FYQWPEEY.js";

package/dist/chunks/{chunk-L5RYUPZI.js → chunk-MQJUG2D2.js}

@@ -1,6 +1,6 @@
 import {
   clampZoom
-} from "./chunk-VKB57ZYE.js";
+} from "./chunk-IO2PCPZI.js";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {

package/dist/chunks/{chunk-LVZZH2NI.js → chunk-MREQ7GIA.js}

@@ -1,10 +1,10 @@
 import {
   baseEdgeCurves
-} from "./chunk-6YRRNX2P.js";
+} from "./chunk-Y3IOTZJA.js";
 import {
   curveBounds,
   pathRibbonOffsets
-} from "./chunk-3PLYZLYV.js";
+} from "./chunk-2CVHXFK7.js";
 
 // src/util/SpatialIndex.ts
 var FALLBACK_CELL_SIZE = 50;

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

@@ -3,14 +3,14 @@ import {
 } from "./chunk-AB35TJST.js";
 import {
   polylineMidpoint
-} from "./chunk-SDGM243E.js";
+} from "./chunk-TAMCZHLW.js";
 import {
   deletionArcCurves
-} from "./chunk-X32PABB7.js";
+} from "./chunk-4EMPBO7S.js";
 import {
   curveBounds,
   curveMidpoint
-} from "./chunk-3PLYZLYV.js";
+} from "./chunk-2CVHXFK7.js";
 
 // src/graphLabels.ts
 var MIN_DELETION_LABEL_PX = 26;

package/dist/chunks/{chunk-QCYM44UL.js → chunk-PJESIRDU.js}

@@ -3,10 +3,10 @@ import {
   RAMP_GRADIENT_STOPS,
   rampHueCss,
   rampStops
-} from "./chunk-5QT6NPSO.js";
+} from "./chunk-ZHCDYSA5.js";
 import {
   REFERENCE_RAMP_ALT_CSS
-} from "./chunk-3WHKR5TY.js";
+} from "./chunk-RX5CSWJW.js";
 import {
   LABEL_CHAR_PX
 } from "./chunk-AB35TJST.js";

package/dist/chunks/{chunk-KCW7L3NV.js → chunk-QFBZQJFK.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "6.0.2";
+var version = "6.0.4";
 
 export {
   version

package/dist/chunks/{chunk-P7B3GDAY.js → chunk-R6ZUK4Y3.js}

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

package/dist/chunks/{chunk-3WHKR5TY.js → chunk-RX5CSWJW.js}

@@ -1,15 +1,17 @@
 import {
-  fadeAbgr
-} from "./chunk-MNUSQCLG.js";
+  abgrToCssRgba,
+  fadeAbgr,
+  packAbgr
+} from "./chunk-UMNCCYBN.js";
 import {
   baseEdgeCurves
-} from "./chunk-6YRRNX2P.js";
+} from "./chunk-Y3IOTZJA.js";
 import {
   PATH_LIGHTNESS,
   PATH_SATURATION,
   nameHue,
   pathHueAt
-} from "./chunk-7CHJKABZ.js";
+} from "./chunk-X5L37W4J.js";
 import {
   referenceMidpoints
 } from "./chunk-ES2N6V56.js";
@@ -23,10 +25,9 @@ import {
   strandSides,
   translateCurves,
   yToXOf
-} from "./chunk-3PLYZLYV.js";
+} from "./chunk-2CVHXFK7.js";
 
 // src/renderer/GeometryBuilder.ts
-import { abgrToCssRgba, packAbgr } from "@jbrowse/core/util/colorBits";
 var EDGE_DEFAULT_COLOR = packAbgr(119, 119, 119, 217);
 var EDGE_PATH_FALLBACK_COLOR = packAbgr(136, 136, 136, 217);
 var EDGE_DELETION_COLOR = packAbgr(24, 24, 28, 240);

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

@@ -2,13 +2,15 @@ import {
   LIFT_BACKDROP_CSS,
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-3WHKR5TY.js";
+} from "./chunk-RX5CSWJW.js";
+import {
+  abgrToCssRgba
+} from "./chunk-UMNCCYBN.js";
 import {
   isBackbone
 } from "./chunk-FYQWPEEY.js";
 
 // src/referenceStrip.ts
-import { abgrToCssRgba } from "@jbrowse/core/util/colorBits";
 var REFERENCE_STRIP_PX = 12;
 var REFERENCE_STRIP_ZONE_PX = REFERENCE_STRIP_PX + 8;
 var OVERHANG_PX = 8;

package/dist/chunks/{chunk-527AI7CP.js → chunk-T43W7NKK.js}

@@ -2,7 +2,7 @@ import {
   hasTubeMapPaths,
   tubeMapLayout,
   tubeMapReferenceLayout
-} from "./chunk-P7B3GDAY.js";
+} from "./chunk-R6ZUK4Y3.js";
 import {
   sampleRowLayout
 } from "./chunk-LOEA5IHZ.js";

package/dist/chunks/{chunk-SDGM243E.js → chunk-TAMCZHLW.js}

@@ -1,7 +1,7 @@
 import {
   ownStrand,
   strandSides
-} from "./chunk-3PLYZLYV.js";
+} from "./chunk-2CVHXFK7.js";
 import {
   isBackbone
 } from "./chunk-FYQWPEEY.js";

package/dist/chunks/chunk-UMNCCYBN.js

@@ -0,0 +1,50 @@
+// src/renderer/colorBits.ts
+function packAbgr(r, g, b, a) {
+  return (a << 24 | b << 16 | g << 8 | r) >>> 0;
+}
+function abgrRed(c) {
+  return c & 255;
+}
+function abgrGreen(c) {
+  return c >>> 8 & 255;
+}
+function abgrBlue(c) {
+  return c >>> 16 & 255;
+}
+function abgrAlpha(c) {
+  return c >>> 24 & 255;
+}
+function abgrToCssRgba(c) {
+  return `rgba(${abgrRed(c)},${abgrGreen(c)},${abgrBlue(c)},${abgrAlpha(c) / 255})`;
+}
+function normalizedRgbToCssRgba(c, alpha) {
+  return `rgba(${Math.round(c[0] * 255)},${Math.round(c[1] * 255)},${Math.round(c[2] * 255)},${alpha})`;
+}
+function fadeAbgr(c, alpha) {
+  return packAbgr(
+    abgrRed(c),
+    abgrGreen(c),
+    abgrBlue(c),
+    Math.round(abgrAlpha(c) * alpha)
+  );
+}
+function brightenAbgr(c, factor) {
+  return packAbgr(
+    Math.min(255, Math.round(abgrRed(c) * factor)),
+    Math.min(255, Math.round(abgrGreen(c) * factor)),
+    Math.min(255, Math.round(abgrBlue(c) * factor)),
+    abgrAlpha(c)
+  );
+}
+
+export {
+  packAbgr,
+  abgrRed,
+  abgrGreen,
+  abgrBlue,
+  abgrAlpha,
+  abgrToCssRgba,
+  normalizedRgbToCssRgba,
+  fadeAbgr,
+  brightenAbgr
+};

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

@@ -1,7 +1,7 @@
 import {
   alongRow,
   boxesGenes
-} from "./chunk-QCYM44UL.js";
+} from "./chunk-PJESIRDU.js";
 import {
   pathOrigin
 } from "./chunk-ST2IBUAN.js";

package/dist/chunks/{chunk-IMW3AK27.js → chunk-X4VVPLI5.js}

@@ -2,10 +2,12 @@ import {
   REFERENCE_RAMP_ALT_COLOR,
   REFERENCE_RAMP_MAX_HUE,
   hslToRgb
-} from "./chunk-3WHKR5TY.js";
+} from "./chunk-RX5CSWJW.js";
+import {
+  packAbgr
+} from "./chunk-UMNCCYBN.js";
 
 // src/walkEncoding.ts
-import { packAbgr } from "@jbrowse/core/util/colorBits";
 var WALK_FIELDS = [
   { value: "progress", label: "Progress along the walk" },
   { value: "walk", label: "One colour for the walk" },

package/dist/chunks/{chunk-7CHJKABZ.js → chunk-X5L37W4J.js}

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

package/dist/chunks/{chunk-6YRRNX2P.js → chunk-Y3IOTZJA.js}

@@ -1,12 +1,12 @@
 import {
   bypassedPoints
-} from "./chunk-X32PABB7.js";
+} from "./chunk-4EMPBO7S.js";
 import {
   computeEdgeCurves,
   edgeJoinOf,
   routedEdgeCurves,
   strandSides
-} from "./chunk-3PLYZLYV.js";
+} from "./chunk-2CVHXFK7.js";
 
 // src/util/edgeCurves.ts
 var cache = /* @__PURE__ */ new WeakMap();

package/dist/chunks/{chunk-BJV2W4KZ.js → chunk-YMSSF2RK.js}

@@ -1,12 +1,12 @@
 import {
   EdgeSpatialIndex,
   SpatialIndex
-} from "./chunk-LVZZH2NI.js";
+} from "./chunk-MREQ7GIA.js";
 import {
   pathRibbonOffsets,
   translateCurves,
   yToXOf
-} from "./chunk-3PLYZLYV.js";
+} from "./chunk-2CVHXFK7.js";
 
 // src/util/hitDetection.ts
 function distanceToSegment(px, py, x1, y1, x2, y2) {

package/dist/chunks/{chunk-5QT6NPSO.js → chunk-ZHCDYSA5.js}

@@ -1,6 +1,6 @@
 import {
   REFERENCE_RAMP_MAX_HUE
-} from "./chunk-3WHKR5TY.js";
+} from "./chunk-RX5CSWJW.js";
 
 // src/referenceRampCss.ts
 function rampHueCss(hue) {

package/dist/chunks/{chunk-6Q6HFBJT.js → chunk-ZKGM7VLA.js}

@@ -1,7 +1,7 @@
 import {
   encodedColor,
   resolveEncoding
-} from "./chunk-IMW3AK27.js";
+} from "./chunk-X4VVPLI5.js";
 import {
   pathOrigin
 } from "./chunk-ST2IBUAN.js";

package/dist/chunks/{chunk-YJQ7CT7F.js → chunk-ZZA2AFB4.js}

@@ -1,10 +1,12 @@
 import {
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-3WHKR5TY.js";
+} from "./chunk-RX5CSWJW.js";
+import {
+  abgrToCssRgba
+} from "./chunk-UMNCCYBN.js";
 
 // src/tubeMap/nodeColors.ts
-import { abgrToCssRgba } from "@jbrowse/core/util/colorBits";
 function tubeMapNodeColors(graph, colorScheme, referenceRamp) {
   if (colorScheme === "uniform" || colorScheme === "grey") {
     return void 0;