jbrowse-plugin-graphgenomeviewer 7.1.13 → 7.2.1

package/dist/chunks/chunk-RFDSEB2X.js

@@ -0,0 +1,4 @@
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s=n.at(-1),l=t.tubeMapPanelRulerBoxes;s&&l&&re(e,l,{...s.frame,width:r},s.bottom+4,!0)}var Gt=m(function({model:t}){let n=E(o=>{Nt(o,t,{highlightNode:t.selectedNode})},[t]);return p(A,{model:t,zIndex:1,shown:!!t.tubeMapPicture,testId:"graph-tube-map",paint:n})}),Jr=Gt;var _=JBrowseExports["@jbrowse/render-core/marks"],Dt=e=>_!=null&&e in Object(_)?_[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/render-core/marks' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var ot=Dt("spanMark");var eo=_&&_.__esModule?_.default:_;function st(e){if(e.startsWith("#")){let r=Number.parseInt(e.slice(1),16);return[r>>16&255,r>>8&255,r&255]}let[t=0,n=0,o=0]=e.match(/[\d.]+/g).map(Number);return e.startsWith("hsl")?xe(t,n/100,o/100).map(r=>r*255):[t,n,o]}var it=([e,t,n])=>ye(Math.round(e),Math.round(t),Math.round(n),255),at=new Map;function Ht(e){let t=at.get(e);return 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Uint32Array(e.length+1),d=new Uint32Array(e.length+1),u=new Uint32Array(e.length+1),h=1;return o.forEach((f,a)=>{for(let b of f){let g=b.hairline?i:b.gap?l:s;for(let[k,I,x]of b.pieces){let B=g.count++;g.x[B]=k,g.x2[B]=I,g.row[B]=a,g.color[B]=x,h=Math.max(h,g.x2[B])}}c[a+1]=s.count,d[a+1]=l.count,u[a+1]=i.count}),{bars:V(s,0,s.count),gaps:V(l,0,l.count),hairlines:V(i,0,i.count),barRows:c,gapRows:d,hairlineRows:u,longest:h}}function pt(e,t,n){let{longest:o}=t,r={start:0,end:o,screenStartPx:n.origin*n.scaleX+n.translateX,screenEndPx:(n.origin+o)*n.scaleX+n.translateX,reversed:!1,displayedRegionIndex:0},s={canvasWidth:n.width,canvasHeight:n.height},l=n.rowPx*n.scaleY;for(let{first:i,count:c,rowY:d}of n.blocks){let u=l/2-n.translateY-(d-i*n.rowPx)*n.scaleY,h=(d-n.rowPx/2)*n.scaleY+n.translateY;if(!(h>n.height||h+c*l<0))for(let[f,a,b]of[[t.bars,t.barRows,n.barPx],[t.gaps,t.gapRows,Math.min(Pe,n.barPx)],[t.hairlines,t.hairlineRows,Math.min(ee,n.barPx)]])ot.paintBlock(e,V(f,a[i],a[i+c]),r,s,{rowHeight:l,rowProportion:b/l,minWidthPx:1,seamPx:0,scrollTop:u})}}function Kt({model:e}){let t=U(()=>K(()=>{let o=e.walkRowBars;return o?lt([o.reference,...o.rows],e.scaleX,e.referenceRampDomain):void 0}),[e]),n=E(o=>{let r=e.walkRowBars,s=e.walkRowPlacement,l=e.walkRowPitch,i=t.get();if(!r||!s||!l||!i)return;let c=e.walkRowGroups?.sections,d=c?.length?[{first:0,count:1,rowY:s.rowY(0)},...c.map(u=>({first:u.first,count:u.count,rowY:s.rowY(u.first)}))]:[{first:0,count:r.rows.length+1,rowY:s.rowY(0)}];pt(o,i,{...e.screenTransform,width:e.paneWidth,height:e.canvasHeight,rowPx:l.rowPx,barPx:l.barPx,origin:r.origin,blocks:d})},[e,t]);return p(A,{model:e,zIndex:3,testId:"graph-walk-rows-spans",paint:n})}var Ut=m(function({model:t}){let n=t.walkRowBars,o=t.walkRowPlacement,r=t.walkRowPitch;if(!n||!o||!r||!t.hoveredWalkRowText)return null;let s=[n.reference,...n.rows],l=s.findIndex(d=>d.name===t.hoveredWalkRow),i=s[l];if(!i)return null;let c=t.toScreen({x:n.origin,y:o.rowY(l)});return p("rect",{"data-testid":"graph-walk-row-hovered",x:c.x-2,y:c.y-r.rowPx/2-1,width:i.bp*t.scaleX+4,height:r.rowPx+2,fill:"none",stroke:"#111",strokeWidth:1})}),Ft=m(function({model:t,vector:n=!1}){let o=O(),r=t.walkRowBars,s=t.walkRowPlacement,l=t.walkRowPitch;if(!r||!s||!l)return null;let{paneWidth:i,canvasHeight:c}=t,d={...t.screenTransform,width:i,height:c,...l,bars:n};return R(C,{children:[n?null:p(Kt,{model:t}),R(S,{model:t,zIndex:3,overflow:"visible",testId:"graph-walk-rows",children:[Ge(r,t.walkRowGroups?.sections??[],s.rowY,d,{ramp:t.referenceRampDomain,rowGenes:t.walkRowGenes,idPrefix:o}).map((u,h)=>p(D,{el:u},h)),s.headers.map(u=>p("text",{x:10,y:t.toScreen({x:0,y:u.top}).y+We-4,fontFamily:"sans-serif",fontSize:11,fontWeight:"bold",fill:"#333","data-testid":"graph-walk-section",children:u.title},u.key)),p(Ut,{model:t})]})]})}),ho=Ft;export{ct as a,Ve as b,S as c,on as d,O as e,D as f,Y as g,Pt as h,vt as i,Vn as j,zn as k,Et as l,tr as m,cr as n,Ar as o,Or as p,It as q,Dr as r,Nt as s,Jr as t,ho as u};
+//# sourceMappingURL=chunk-RFDSEB2X.js.map

package/dist/chunks/chunk-RFDSEB2X.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/GraphGenomeView/components/PaneLayer.tsx", "../../src/GraphGenomeView/components/BubbleHalos.tsx", "../../src/GraphGenomeView/legendSections.ts", "../../src/GraphGenomeView/components/ElTree.tsx", "../../src/GraphGenomeView/components/LegendSwatch.tsx", "../../src/GraphGenomeView/components/GenePins.tsx", "../../src/GraphGenomeView/components/LabelChip.tsx", "../../src/GraphGenomeView/components/LabelLayer.tsx", "../../src/GraphGenomeView/components/ReferenceStripOverlay.tsx", "../../src/GraphGenomeView/components/TubeMapOverlay.tsx", "host:@jbrowse/render-core/marks", "../../src/GraphGenomeView/walkRowSpans.ts", "../../src/GraphGenomeView/components/WalkRowsOverlay.tsx"],
+  "sourcesContent": ["import { useEffect, useRef } from 'react'\nimport type { ReactNode } from 'react'\n\nimport { syncCanvasSize } from '@jbrowse/bandage-core/renderer/canvas'\nimport { autorun } from 'mobx'\nimport { observer } from 'mobx-react'\n\nimport { dependOn } from '../pane/paneBase'\nimport { trackedDpr } from '../trackedDpr'\n\nimport type { GraphPaneModel } from '../model'\n\n// marks an overlay whose labels move with the drawing, so a press on one pans\nexport const PANS_WITH_DRAWING = 'data-pans-with-drawing'\n\n// A layer over the pane's canvas that leaves the pointer to it\nexport function paneLayerStyle(\n  zIndex: number,\n  overflow?: 'hidden' | 'visible',\n) {\n  return {\n    position: 'absolute' as const,\n    left: 0,\n    top: 0,\n    pointerEvents: 'none' as const,\n    overflow,\n    zIndex,\n  }\n}\n\n// An SVG the pane's size, over the canvas or inside PaneSvg's export\nexport const PaneSvgLayer = observer(function PaneSvgLayer({\n  model,\n  zIndex,\n  overflow = 'hidden',\n  testId,\n  pansWithDrawing,\n  children,\n}: {\n  model: GraphPaneModel\n  zIndex: number\n  overflow?: 'hidden' | 'visible'\n  testId?: string\n  pansWithDrawing?: boolean\n  children: ReactNode\n}) {\n  return (\n    <svg\n      style={{\n        ...paneLayerStyle(zIndex, overflow),\n        userSelect: pansWithDrawing ? 'none' : undefined,\n      }}\n      width={model.paneWidth}\n      height={model.canvasHeight}\n      data-testid={testId}\n      {...(pansWithDrawing ? { [PANS_WITH_DRAWING]: '' } : {})}\n    >\n      {children}\n    </svg>\n  )\n})\n\n// Layout units onto the screen. Its own observer, so a pan frame re-renders\n// this group's transform and not the children a parent built.\nexport const PaneTransformGroup = observer(function PaneTransformGroup({\n  model,\n  children,\n}: {\n  model: GraphPaneModel\n  children: ReactNode\n}) {\n  const { scaleX, scaleY, translateX, translateY } = model\n  return (\n    <g\n      transform={`translate(${translateX} ${translateY}) scale(${scaleX} ${scaleY})`}\n    >\n      {children}\n    </g>\n  )\n})\n\n// A canvas the pane's size that an autorun repaints, so a pan moves its ink in\n// the same frame as the drawing. `paint` draws in css px.\nexport function PaneOverlayCanvas({\n  model,\n  zIndex,\n  shown = true,\n  testId,\n  paint,\n}: {\n  model: GraphPaneModel\n  zIndex: number\n  shown?: boolean\n  testId: string\n  paint: (ctx: CanvasRenderingContext2D, dpr: number) => void\n}) {\n  const ref = useRef<HTMLCanvasElement>(null)\n  useEffect(() => {\n    if (!shown) {\n      return undefined\n    }\n    return autorun(() => {\n      const canvas = ref.current\n      const ctx = canvas?.getContext('2d')\n      if (canvas && ctx) {\n        const width = model.paneWidth\n        const height = model.canvasHeight\n        dependOn(trackedDpr())\n        const dpr = syncCanvasSize(canvas, width, height)\n        ctx.setTransform(dpr, 0, 0, dpr, 0, 0)\n        ctx.clearRect(0, 0, width, height)\n        paint(ctx, dpr)\n      }\n    })\n  }, [model, shown, paint])\n  return (\n    <canvas\n      ref={ref}\n      data-testid={shown ? testId : undefined}\n      style={{ ...paneLayerStyle(zIndex), display: shown ? 'block' : 'none' }}\n    />\n  )\n}\n", "import { bubbleKey, sameBubble } from '@jbrowse/bandage-core/bubbles/bubbleLine'\nimport { BUBBLE_KIND_COLORS } from '@jbrowse/bandage-core/bubbles/classifyBubble'\nimport { HALO_FACTOR } from '@jbrowse/bandage-core/labelLayout'\nimport { observer } from 'mobx-react'\n\nimport { PaneSvgLayer, PaneTransformGroup } from './PaneLayer'\n\nimport type { GraphPaneModel } from '../model'\n\n// The bubbles over a node drawing: each a translucent halo along its nodes,\n// drawn once in layout units and moved with the canvas by one transform. The\n// halo takes no pointer events, so the nodes under it still hover and drag;\n// its name and its routes' chips are LabelLayer's. A small variant is\n// LabelLayer's tick, and shows its halo only while hovered.\n\nconst BubbleHalos = observer(function BubbleHalos({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const { bubbleHalos, hoveredBubble } = model\n  if (bubbleHalos.length === 0) {\n    return null\n  }\n  const halo = model.contigThickness * HALO_FACTOR\n  return (\n    <PaneSvgLayer model={model} zIndex={2} testId=\"graph-bubble-halos\">\n      <PaneTransformGroup model={model}>\n        {bubbleHalos\n          .filter(\n            h =>\n              !h.whole &&\n              (!h.tick ||\n                (hoveredBubble && sameBubble(h.bubble, hoveredBubble))),\n          )\n          .map(h => (\n            <path\n              key={bubbleKey(h.bubble)}\n              d={h.path}\n              fill=\"none\"\n              stroke={BUBBLE_KIND_COLORS[h.kind]}\n              strokeOpacity={\n                hoveredBubble && sameBubble(h.bubble, hoveredBubble)\n                  ? 0.45\n                  : model.bubbleFaded(h)\n                    ? 0.06\n                    : 0.22\n              }\n              strokeWidth={halo}\n              strokeLinecap=\"round\"\n              strokeLinejoin=\"round\"\n              vectorEffect=\"non-scaling-stroke\"\n            />\n          ))}\n      </PaneTransformGroup>\n    </PaneSvgLayer>\n  )\n})\n\nexport default BubbleHalos\n", "import { sameBubble } from '@jbrowse/bandage-core/bubbles/bubbleLine'\nimport {\n  BUBBLE_KIND_COLORS,\n  BUBBLE_KIND_NAMES,\n} from '@jbrowse/bandage-core/bubbles/classifyBubble'\nimport { EXON_COLOR } from '@jbrowse/bandage-core/genes/exonOutline'\nimport { formatBp } from '@jbrowse/bandage-core/graphLabels'\nimport {\n  BAR_PX as WALK_ROW_BAR_PX,\n  CALL_TICK,\n  DISAGREES,\n  GENE_INK,\n  UNBACKED_TICK,\n  walkRowsKey,\n} from '@jbrowse/bandage-core/layout/walkRowDraw'\nimport { RAMP_GRADIENT_STOPS } from '@jbrowse/bandage-core/referenceRampCss'\nimport {\n  LIFT_BACKDROP_CSS,\n  REFERENCE_RAMP_ALT_CSS,\n} from '@jbrowse/bandage-core/renderer/GeometryBuilder'\nimport { deviationInk } from '@jbrowse/bandage-core/tubeMap/deviations'\nimport {\n  FORWARD_READ_COLORS,\n  REVERSE_READ_COLORS,\n} from '@jbrowse/bandage-core/tubeMap/reads'\nimport { encodingStops } from '@jbrowse/bandage-core/walkEncoding'\nimport { walkKey } from '@jbrowse/bandage-core/walkKey'\n\nimport { CALL_TOLERANCE } from './repeats/walkCalls'\nimport { PANEL_REFERENCE_TUBE } from './tubeMapPanels'\n\nimport type { GraphPaneModel } from './model'\nimport type { KeySwatch } from '@jbrowse/bandage-core/layout/walkRowDraw'\nimport type { LiftedWalk } from '@jbrowse/bandage-core/walkHighlight'\n\n// The legend as data, so the screen's panel and the exported figure's key\n// draw the same rows from one place\n\nexport const SWATCH_PX = 18\nconst BAR_PX = 48\n\n// LIFT_BACKDROP_CSS reads paler alone than faded strokes do where they\n// overlap, so the key samples it darker\nconst FADED_SWATCH = 'rgba(160, 160, 160, 0.45)'\n\nconst STRIP_SAMPLES = 6\nconst TUBE_SWATCH_PX = 7\nconst FOLD_TICK_BACKING = '#b8b8c0'\nconst WALK_ROW_SWATCH_PX = WALK_ROW_BAR_PX - 4\n\nexport interface Stop {\n  offset: number\n  color: string\n}\n\nexport type LegendSwatch =\n  | {\n      kind: 'fill'\n      stops: Stop[]\n      width?: number\n      height?: number\n      square?: boolean\n    }\n  // the reference strip, a band per lifted walk\n  | { kind: 'bands'; bands: Stop[][] }\n  | { kind: 'line'; color: string }\n  | { kind: 'halo'; color: string }\n  | {\n      kind: 'outline'\n      color: string\n      stroke: number\n      radius: number\n      height: number\n    }\n  | { kind: 'overhang' }\n  | { kind: 'glyph'; char: string }\n  | { kind: 'tick'; color: string; height: number; backing?: string }\n  | { kind: 'bracket' }\n  | { kind: 'blank' }\n\n// A row with no swatch is a note on the drawing\nexport interface LegendRow {\n  key: string\n  label: string\n  swatch?: LegendSwatch\n  strong?: string\n  under?: string\n  title?: string\n  walk?: LiftedWalk\n  closesBubble?: true\n}\n\ninterface LegendSection {\n  testid: string\n  rows: LegendRow[]\n}\n\nexport function swatchWidth(swatch: LegendSwatch) {\n  return swatch.kind === 'fill' ? (swatch.width ?? SWATCH_PX) : SWATCH_PX\n}\n\nconst flat = (color: string): Stop[] => [{ offset: 0, color }]\n\nfunction fillRow(\n  key: string,\n  color: string,\n  label: string,\n  width = SWATCH_PX,\n): LegendRow {\n  return { key, label, swatch: { kind: 'fill', stops: flat(color), width } }\n}\n\n// hard-edged bands, a read taking one shade of its strand's palette\nfunction bandStops(colors: readonly string[]) {\n  return colors.flatMap((color, i) => [\n    { offset: i / colors.length, color },\n    { offset: (i + 1) / colors.length, color },\n  ])\n}\n\nfunction openBubbleRows(model: GraphPaneModel): LegendRow[] {\n  const open = model.openBubble\n  if (!open) {\n    return []\n  }\n  const halo = model.bubbleHalos.find(h => sameBubble(h.bubble, open))\n  return [\n    {\n      key: 'open',\n      label: `open: ${halo?.label ?? 'bubble'}`,\n      swatch: halo\n        ? { kind: 'halo', color: BUBBLE_KIND_COLORS[halo.kind] }\n        : { kind: 'blank' },\n      closesBubble: true,\n    },\n  ]\n}\n\n// Under lifted walks each lane states its own scale, and the rest is grey\nfunction rampRows(model: GraphPaneModel): LegendRow[] {\n  const domain = model.walkLift ? undefined : model.referenceRampDomain\n  if (!domain) {\n    return []\n  }\n  // a measured domain runs between node midpoints, which can fall on a half bp\n  const start = Math.round(domain.start)\n  const end = Math.round(domain.end)\n  return [\n    {\n      key: 'ramp',\n      label: `${start.toLocaleString('en-US')}-${end.toLocaleString('en-US')} (${formatBp(end - start)})`,\n      swatch: { kind: 'fill', stops: RAMP_GRADIENT_STOPS, width: BAR_PX },\n    },\n    ...(model.referenceRampDrawsOffReference\n      ? [fillRow('off', REFERENCE_RAMP_ALT_CSS, 'off the reference', BAR_PX)]\n      : []),\n  ]\n}\n\n// The strip's own colours: a band per lifted walk in its lane's, else the\n// node scheme's, a few of its blocks in bp order rather than a rainbow it\n// does not draw\nfunction stripBands(model: GraphPaneModel): Stop[][] {\n  const lift = model.walkLift\n  if (lift) {\n    return lift.walks.map(w => encodingStops(w.encoding))\n  }\n  if (model.effectiveColorScheme === 'reference-position') {\n    return [RAMP_GRADIENT_STOPS]\n  }\n  const colors = model.referenceStripBlocks\n    .map(b => b.colors[0]!)\n    .filter((c, i, all) => c !== all[i - 1])\n  const n = Math.min(STRIP_SAMPLES, colors.length)\n  return [\n    n === 0\n      ? flat(LIFT_BACKDROP_CSS)\n      : Array.from({ length: n }, (_, i) => ({\n          offset: n > 1 ? i / (n - 1) : 0,\n          color:\n            colors[\n              n > 1 ? Math.round((i * (colors.length - 1)) / (n - 1)) : 0\n            ]!,\n        })),\n  ]\n}\n\nfunction stripRows(model: GraphPaneModel): LegendRow[] {\n  if (!model.referenceStripShown) {\n    return []\n  }\n  const rowPerWalk = (model.walkLift?.walks.length ?? 0) > 1\n  return [\n    {\n      key: 'strip',\n      label: `top strip: reference${rowPerWalk ? ', a row per walk' : ''}`,\n      swatch: { kind: 'bands', bands: stripBands(model) },\n    },\n    ...(model.referenceStripFaded\n      ? [\n          fillRow(\n            'strip-faded',\n            LIFT_BACKDROP_CSS,\n            model.walkLift\n              ? `reference not on ${rowPerWalk ? \"that row's walk\" : model.liftedWalksLabel}`\n              : 'reference outside the open bubble',\n          ),\n        ]\n      : []),\n    ...(model.referenceStripOverhangs\n      ? [\n          {\n            key: 'overhang',\n            label: 'graph runs past this edge',\n            swatch: { kind: 'overhang' } as const,\n          },\n        ]\n      : []),\n  ]\n}\n\n// One row per halo colour drawn, naming the kinds it stands for\nfunction haloRows(model: GraphPaneModel): LegendRow[] {\n  const kindsByColor = new Map<string, Set<string>>()\n  for (const h of model.bubbleHalos) {\n    if (!h.whole) {\n      const color = BUBBLE_KIND_COLORS[h.kind]\n      const kinds = kindsByColor.get(color) ?? new Set<string>()\n      kinds.add(BUBBLE_KIND_NAMES[h.kind])\n      kindsByColor.set(color, kinds)\n    }\n  }\n  return [...kindsByColor].map(([color, kinds]) => {\n    const names = [...kinds].join(' or ')\n    return {\n      key: `halo-${color}`,\n      label:\n        names === BUBBLE_KIND_NAMES.superbubble ? names : `${names} bubble`,\n      swatch: { kind: 'halo', color },\n    }\n  })\n}\n\nfunction geneRows(model: GraphPaneModel): LegendRow[] {\n  return model.genePins.some(pin => pin.exonsByNode.length > 0)\n    ? [\n        {\n          key: 'exon',\n          label: 'exon',\n          swatch: {\n            kind: 'outline',\n            color: EXON_COLOR,\n            stroke: 2,\n            radius: 5,\n            height: 8,\n          },\n        },\n      ]\n    : []\n}\n\nfunction foldRows(model: GraphPaneModel): LegendRow[] {\n  const note = model.foldNote\n  return note ? [{ key: 'fold', label: note }] : []\n}\n\nfunction pathRows(model: GraphPaneModel): LegendRow[] {\n  return model.pathLegend.map(({ name, label, color }) => ({\n    key: `path-${name}`,\n    label,\n    swatch: { kind: 'line', color },\n  }))\n}\n\nfunction tubeRow(key: string, stops: Stop[], label: string): LegendRow {\n  return {\n    key,\n    label,\n    swatch: { kind: 'fill', stops, height: TUBE_SWATCH_PX, square: true },\n  }\n}\n\n// What a tube map draws that nothing else on screen explains, each listed\n// only while it applies\nexport function tubeMapRows(model: GraphPaneModel): LegendRow[] {\n  const {\n    roles,\n    haplotypeTube,\n    bundled,\n    values,\n    logWidths,\n    foldBp,\n    forwardReads,\n    reverseReads,\n    substitution,\n    insertion,\n    deletion,\n  } = model.tubeMapKeys\n  const reads = model.readsShown\n  const rows: LegendRow[] = []\n  if (values) {\n    rows.push(\n      tubeRow('value-reference', flat(PANEL_REFERENCE_TUBE), 'reference'),\n      ...values.map(({ value, color }) =>\n        tubeRow(`value-${value}`, flat(color), value),\n      ),\n    )\n  }\n  if (roles) {\n    rows.push(\n      tubeRow('ref', flat(PANEL_REFERENCE_TUBE), 'reference'),\n      tubeRow(\n        'hap',\n        flat(haplotypeTube),\n        bundled ? 'shared route, \u00D7n haplotypes' : 'haplotype',\n      ),\n    )\n  }\n  if (forwardReads) {\n    rows.push(\n      tubeRow(\n        'fwd',\n        bandStops(FORWARD_READ_COLORS),\n        'read on the forward strand',\n      ),\n    )\n  }\n  if (reverseReads) {\n    rows.push(\n      tubeRow(\n        'rev',\n        bandStops(REVERSE_READ_COLORS),\n        'read on the reverse strand',\n      ),\n    )\n  }\n  if (reads && reads.shown < reads.total) {\n    rows.push({\n      key: 'sampled',\n      label: `${reads.shown.toLocaleString('en-US')} of ${reads.total.toLocaleString('en-US')} reads shown`,\n      swatch: { kind: 'blank' },\n    })\n  }\n  if (substitution) {\n    rows.push({\n      key: 'sub',\n      label: 'read mismatch',\n      swatch: { kind: 'glyph', char: 'A' },\n    })\n  }\n  if (insertion) {\n    rows.push({\n      key: 'ins',\n      label: 'read insertion',\n      swatch: { kind: 'glyph', char: '*' },\n    })\n  }\n  if (deletion) {\n    rows.push(tubeRow('del', flat('grey'), 'read deletion'))\n  }\n  if (foldBp !== undefined) {\n    rows.push({\n      key: 'tube-fold',\n      label: `haplotype variant < ${formatBp(foldBp)}`,\n      swatch: {\n        kind: 'tick',\n        color: deviationInk(),\n        height: TUBE_SWATCH_PX,\n        backing: FOLD_TICK_BACKING,\n      },\n    })\n  }\n  if (logWidths) {\n    rows.push({\n      key: 'log',\n      label: 'width grows with log of length',\n      swatch: { kind: 'bracket' },\n    })\n  }\n  return rows\n}\n\nexport function walkRowSwatch(swatch: KeySwatch): LegendSwatch {\n  return swatch.kind === 'gene'\n    ? {\n        kind: 'outline',\n        color: GENE_INK,\n        stroke: 1.5,\n        radius: 0,\n        height: WALK_ROW_SWATCH_PX,\n      }\n    : {\n        kind: 'fill',\n        stops:\n          swatch.kind === 'bar' && swatch.ramp\n            ? RAMP_GRADIENT_STOPS\n            : flat(swatch.fill),\n        height: swatch.kind === 'gap' ? swatch.px : WALK_ROW_SWATCH_PX,\n      }\n}\n\n// The walk rows' bar colours, genes and ticks; each tick row appears once\n// the rows hold one, so a catalogue with no genotypes keeps the plain key\nfunction walkRowsRows(model: GraphPaneModel): LegendRow[] {\n  const bars = model.walkRowBars\n  if (!bars) {\n    return []\n  }\n  const calls = [bars.reference, ...bars.rows].flatMap(row => row.call ?? [])\n  const tick = (key: string, color: string, label: string): LegendRow => ({\n    key,\n    label,\n    swatch: { kind: 'tick', color, height: WALK_ROW_SWATCH_PX },\n  })\n  return [\n    ...walkRowsKey(bars, {\n      ramp: model.referenceRampDomain,\n      genes: model.walkRowGeneKey,\n    }).map(entry => ({\n      key: `rows-${entry.label}`,\n      label: entry.label,\n      swatch: entry.note ? undefined : walkRowSwatch(entry.swatch),\n    })),\n    ...(calls.some(call => call.spanningReads !== 0)\n      ? [tick('call', CALL_TICK, 'allele length called for this walk')]\n      : []),\n    ...(calls.some(call => call.spanningReads === 0)\n      ? [tick('unbacked', UNBACKED_TICK, 'called with no read spanning it')]\n      : []),\n    ...(calls.some(call => call.agrees === false)\n      ? [\n          tick(\n            'disagrees',\n            DISAGREES,\n            `walk and call over ${Math.round(CALL_TOLERANCE * 100)}% apart`,\n          ),\n        ]\n      : []),\n  ]\n}\n\n// One lifted walk's key: a swatch, or a short bar of the scale its lane\n// shades by, then its name, with the scale's stretch under it\nexport function walkKeyRow(model: GraphPaneModel, walk: LiftedWalk): LegendRow {\n  const key = walkKey(walk, model.walkReference)\n  return {\n    key: `walk-${walk.name}`,\n    strong: model.walkLabel(walk.name),\n    label: key.delta + key.gaps + key.reversed,\n    swatch: {\n      kind: 'fill',\n      stops: encodingStops(walk.encoding),\n      width: key.shades ? BAR_PX : SWATCH_PX,\n    },\n    under: key.scale,\n    title: key.hover,\n    walk,\n  }\n}\n\n// The off-reference colour, where the lift paints it, and the faded rest.\n// rampRows draws no key while walks are lifted, so these rows name both.\nfunction fadedRows(\n  model: GraphPaneModel,\n  faded: string,\n  width = SWATCH_PX,\n): LegendRow[] {\n  return [\n    ...(model.liftPaintsOffReference\n      ? [\n          fillRow(\n            'lift-off',\n            REFERENCE_RAMP_ALT_CSS,\n            'off the reference',\n            width,\n          ),\n        ]\n      : []),\n    fillRow('faded', FADED_SWATCH, faded, width),\n  ]\n}\n\n// Each lifted walk's key, then what the faded rest is; the colours under a\n// shaded walk's bar are bars of its width\nfunction walkReadoutRows(model: GraphPaneModel): LegendRow[] {\n  const lift = model.walkLift\n  if (!lift || model.facetPanels) {\n    return []\n  }\n  const rows = lift.walks.map(w => walkKeyRow(model, w))\n  const width = rows.some(r => swatchWidth(r.swatch!) === BAR_PX)\n    ? BAR_PX\n    : SWATCH_PX\n  return [\n    ...rows,\n    ...fadedRows(model, `not on ${model.liftedWalksLabel}`, width),\n  ]\n}\n\n// The faceted pane's one key line under its panels: each panel's title keys\n// its walk, so this keys only what every panel greys\nexport function facetKeyRows(model: GraphPaneModel): LegendRow[] {\n  return model.facetPanels ? fadedRows(model, \"not on the panel's walk\") : []\n}\n\n// The keys in the order the panel stacks them, top first\nexport function legendSections(model: GraphPaneModel): LegendSection[] {\n  return [\n    { testid: 'graph-open-bubble-legend', rows: openBubbleRows(model) },\n    { testid: 'graph-ramp-legend', rows: rampRows(model) },\n    { testid: 'graph-reference-strip-legend', rows: stripRows(model) },\n    { testid: 'graph-halo-legend', rows: haloRows(model) },\n    { testid: 'graph-gene-legend', rows: geneRows(model) },\n    { testid: 'graph-fold-legend', rows: foldRows(model) },\n    { testid: 'graph-path-legend', rows: pathRows(model) },\n    { testid: 'graph-tube-map-legend', rows: tubeMapRows(model) },\n    { testid: 'graph-walk-rows-legend', rows: walkRowsRows(model) },\n    { testid: 'graph-walk-readout', rows: walkReadoutRows(model) },\n  ].filter(section => section.rows.length > 0)\n}\n", "import { createElement, useId } from 'react'\nimport type { ReactNode } from 'react'\n\nimport type { El } from '@jbrowse/bandage-core/el'\n\n// SVG's attribute names as React's props: `class` is className, `data-` and\n// `aria-` keep their dashes, the rest are camel-cased (`stroke-width` is\n// strokeWidth)\nfunction propName(name: string) {\n  return name === 'class'\n    ? 'className'\n    : /^(data|aria)-/.test(name)\n      ? name\n      : name.replace(/-([a-z])/g, (_, c: string) => c.toUpperCase())\n}\n\nfunction toReact(node: El | string, key: number): ReactNode {\n  if (typeof node === 'string') {\n    return node\n  }\n  const props: Record<string, unknown> = { key }\n  for (const [name, value] of Object.entries(node.attrs)) {\n    if (value !== undefined) {\n      props[propName(name)] = value\n    }\n  }\n  return createElement(node.tag, props, ...node.children.map(toReact))\n}\n\n// A useId fit for an SVG id and for url(#\u2026)\nexport function useSvgId() {\n  return useId().replaceAll(/[^\\w-]/g, '')\n}\n\n// A core element tree as React elements\nexport default function ElTree({ el }: { el: El }) {\n  return toReact(el, 0)\n}\n", "import { rulerInk } from '@jbrowse/bandage-core/tubeMap/axis'\n\nimport { useSvgId } from './ElTree'\nimport { SWATCH_PX, swatchWidth } from '../legendSections'\n\nimport type { LegendSwatch, Stop } from '../legendSections'\n\nfunction Gradient({\n  id,\n  x,\n  y,\n  stops,\n  width,\n  height,\n  square,\n}: {\n  id: string\n  x: number\n  y: number\n  stops: readonly Stop[]\n  width: number\n  height: number\n  square?: boolean\n}) {\n  const rect = (fill: string) => (\n    <rect\n      x={x}\n      y={y}\n      width={width}\n      height={height}\n      rx={square ? 0 : 2}\n      fill={fill}\n    />\n  )\n  return stops.length > 1 ? (\n    <>\n      <defs>\n        <linearGradient id={id}>\n          {stops.map((s, i) => (\n            <stop key={i} offset={s.offset} stopColor={s.color} />\n          ))}\n        </linearGradient>\n      </defs>\n      {rect(`url(#${id})`)}\n    </>\n  ) : (\n    rect(stops[0]!.color)\n  )\n}\n\nconst bandPx = (bands: readonly unknown[]) => (bands.length > 1 ? 3 : 4)\n\nfunction swatchHeight(swatch: LegendSwatch) {\n  switch (swatch.kind) {\n    case 'fill':\n      return swatch.height ?? 8\n    case 'bands':\n      return bandPx(swatch.bands) * swatch.bands.length\n    case 'line':\n      return 3\n    case 'halo':\n    case 'overhang':\n      return 10\n    case 'outline':\n    case 'tick':\n      return swatch.height\n    case 'glyph':\n      return 15\n    case 'bracket':\n      return 7\n    case 'blank':\n      return 0\n  }\n}\n\n// A row's swatch with its left edge at x, centred on the row's text 5 px\n// above the baseline\nexport function SvgSwatch({\n  swatch,\n  x,\n  id,\n}: {\n  swatch: LegendSwatch\n  x: number\n  id: string\n}) {\n  const mid = -5\n  switch (swatch.kind) {\n    case 'fill': {\n      const height = swatchHeight(swatch)\n      return (\n        <Gradient\n          id={id}\n          x={x}\n          y={mid - height / 2}\n          stops={swatch.stops}\n          width={swatchWidth(swatch)}\n          height={height}\n          square={swatch.square}\n        />\n      )\n    }\n    case 'bands': {\n      const band = bandPx(swatch.bands)\n      const top = mid - swatchHeight(swatch) / 2\n      return (\n        <>\n          {swatch.bands.map((stops, i) => (\n            <Gradient\n              key={i}\n              id={`${id}-${i}`}\n              x={x}\n              y={top + i * band}\n              stops={stops}\n              width={SWATCH_PX}\n              height={band}\n              square\n            />\n          ))}\n        </>\n      )\n    }\n    case 'line':\n      return (\n        <rect\n          x={x}\n          y={mid - 1.5}\n          width={SWATCH_PX}\n          height={3}\n          rx={2}\n          fill={swatch.color}\n        />\n      )\n    case 'halo':\n      return (\n        <line\n          x1={x + 5}\n          x2={x + 13}\n          y1={mid}\n          y2={mid}\n          stroke={swatch.color}\n          strokeOpacity={0.35}\n          strokeWidth={8}\n          strokeLinecap=\"round\"\n        />\n      )\n    case 'outline': {\n      const inset = swatch.stroke / 2\n      return (\n        <rect\n          x={x + inset}\n          y={mid - swatch.height / 2 + inset}\n          width={SWATCH_PX - swatch.stroke}\n          height={swatch.height - swatch.stroke}\n          rx={Math.max(0, swatch.radius - inset)}\n          fill=\"none\"\n          stroke={swatch.color}\n          strokeWidth={swatch.stroke}\n        />\n      )\n    }\n    case 'overhang':\n      return (\n        <path\n          transform={`translate(${x} ${mid - 5})`}\n          d=\"M0,5 L8,0 L8,10 Z M18,5 L10,0 L10,10 Z\"\n          fill=\"#18181c\"\n        />\n      )\n    case 'glyph':\n      return (\n        <text\n          x={x + SWATCH_PX / 2}\n          y={mid + 4}\n          textAnchor=\"middle\"\n          fontFamily=\"monospace\"\n          fontSize={12}\n          fill=\"currentColor\"\n        >\n          {swatch.char}\n        </text>\n      )\n    case 'tick': {\n      const y = mid - swatch.height / 2\n      return (\n        <>\n          {swatch.backing ? (\n            <rect\n              x={x}\n              y={y}\n              width={SWATCH_PX}\n              height={swatch.height}\n              fill={swatch.backing}\n            />\n          ) : null}\n          <rect\n            x={x + SWATCH_PX / 2 - 1}\n            y={y}\n            width={2}\n            height={swatch.height}\n            fill={swatch.color}\n          />\n        </>\n      )\n    }\n    case 'bracket':\n      return (\n        <path\n          transform={`translate(${x} ${mid - 3.5})`}\n          d={`M0.5,6 V1.5 H5.5 V6 M8.5,6 V1.5 H${SWATCH_PX - 0.5} V6`}\n          fill=\"none\"\n          stroke={rulerInk()}\n        />\n      )\n    case 'blank':\n      return null\n  }\n}\n\n// The same swatch on screen, in a box as tall as the swatch so the row\n// centres it on its words\nexport function LegendSwatchView({ swatch }: { swatch: LegendSwatch }) {\n  const id = useSvgId()\n  const height = swatchHeight(swatch)\n  return (\n    <svg\n      width={swatchWidth(swatch)}\n      height={height}\n      overflow=\"visible\"\n      style={{ flex: 'none' }}\n    >\n      <g transform={`translate(0 ${height / 2 + 5})`}>\n        <SvgSwatch swatch={swatch} x={0} id={id} />\n      </g>\n    </svg>\n  )\n}\n", "import { useMemo } from 'react'\n\nimport {\n  exonOutlineTree,\n  exonStretches,\n} from '@jbrowse/bandage-core/genes/exonOutline'\nimport { computed } from 'mobx'\nimport { observer } from 'mobx-react'\n\nimport ElTree, { useSvgId } from './ElTree'\nimport { PaneSvgLayer } from './PaneLayer'\n\nimport type { GraphPaneModel } from '../model'\n\n// The session's genes drawn onto the graph: each exon outlined round its\n// stretch of node, as core's exonOutlineTree draws it for every host, moved by\n// the same transform the halos use. Their names are LabelLayer's.\n\nconst GenePins = observer(function GenePins({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const id = `exon-outline-${useSvgId()}`\n  // in layout units, so a pan frame reuses them and only moves the transform\n  const stretches = useMemo(\n    () =>\n      computed(() => {\n        const { genePins, walkLift } = model\n        // an open bubble rings only its own exons\n        const focus = walkLift ? undefined : model.openBubbleFocus\n        const pins = focus\n          ? genePins.map(pin => ({\n              ...pin,\n              exonsByNode: pin.exonsByNode.filter(e =>\n                focus.nodeIds.has(e.nodeId),\n              ),\n            }))\n          : genePins\n        return exonStretches(pins, model.nodeInk.halfWidthPx, walkLift)\n      }),\n    [model],\n  )\n  const { scaleX, scaleY, translateX, translateY, paneWidth, canvasHeight } =\n    model\n  const tree = exonOutlineTree(stretches.get(), {\n    id,\n    width: paneWidth,\n    height: canvasHeight,\n    transform: `translate(${translateX} ${translateY}) scale(${scaleX} ${scaleY})`,\n  })\n  return tree ? (\n    <PaneSvgLayer model={model} zIndex={2} testId=\"graph-gene-pins\">\n      <ElTree el={tree} />\n    </PaneSvgLayer>\n  ) : null\n})\n\nexport default GenePins\n", "import { LABEL_PAD, LABEL_PX } from '@jbrowse/bandage-core/overlayLabels'\n\n// A chip's box, its text's baseline at y and centred on x\nfunction chipBox(x: number, y: number, w: number) {\n  return {\n    x: x - w / 2,\n    y: y - LABEL_PX - LABEL_PAD + 2,\n    width: w,\n    height: LABEL_PX + LABEL_PAD * 2 - 2,\n  }\n}\n\nexport function inChip(\n  chip: { x: number; y: number; w: number },\n  px: number,\n  py: number,\n) {\n  const box = chipBox(chip.x, chip.y, chip.w)\n  return (\n    px >= box.x &&\n    px <= box.x + box.width &&\n    py >= box.y &&\n    py <= box.y + box.height\n  )\n}\n\n// One label on an overlay: a white chip with a coloured edge and text. A note\n// follows the text in plain type. A chip takes the pointer only with a\n// handler, so its title shows only then.\nexport default function LabelChip({\n  x,\n  y,\n  w,\n  text,\n  note,\n  color,\n  edge = color,\n  italic,\n  dimmed,\n  title,\n  testId,\n  onClick,\n  onHover,\n}: {\n  x: number\n  y: number\n  w: number\n  text: string\n  note?: string\n  color: string\n  edge?: string\n  italic?: boolean\n  dimmed?: boolean\n  title?: string\n  testId?: string\n  onClick?: () => void\n  onHover?: (hovered: boolean) => void\n}) {\n  return (\n    <g\n      style={{\n        pointerEvents: onClick || onHover ? 'auto' : 'none',\n        cursor: onClick ? 'pointer' : undefined,\n        opacity: dimmed ? 0.35 : 1,\n      }}\n      data-testid={testId}\n      onClick={onClick}\n      onMouseEnter={() => {\n        onHover?.(true)\n      }}\n      onMouseLeave={() => {\n        onHover?.(false)\n      }}\n      // a clickable chip is a button to the keyboard too\n      {...(onClick && {\n        role: 'button',\n        tabIndex: 0,\n        'aria-label': (title ?? text).replaceAll('\\n', ', '),\n        onKeyDown: (e: React.KeyboardEvent) => {\n          if (e.key === 'Enter' || e.key === ' ') {\n            e.preventDefault()\n            onClick()\n          }\n        },\n        onFocus: () => {\n          onHover?.(true)\n        },\n        onBlur: () => {\n          onHover?.(false)\n        },\n      })}\n    >\n      {title ? <title>{title}</title> : null}\n      <rect\n        {...chipBox(x, y, w)}\n        rx={3}\n        fill=\"rgba(255,255,255,0.85)\"\n        stroke={edge}\n        strokeWidth={1}\n      />\n      <text\n        x={x}\n        y={y}\n        fontSize={LABEL_PX}\n        fontFamily=\"sans-serif\"\n        fontStyle={italic ? 'italic' : undefined}\n        fontWeight={italic ? 600 : undefined}\n        fill={color}\n        textAnchor=\"middle\"\n      >\n        {text}\n        {note ? (\n          <tspan fontStyle=\"normal\" fontWeight=\"normal\">\n            {note}\n          </tspan>\n        ) : null}\n      </text>\n    </g>\n  )\n}\n", "import { bubbleKey, sameBubble } from '@jbrowse/bandage-core/bubbles/bubbleLine'\nimport { BUBBLE_KIND_COLORS } from '@jbrowse/bandage-core/bubbles/classifyBubble'\nimport { EXON_COLOR } from '@jbrowse/bandage-core/genes/exonOutline'\nimport { geneCoverageNote } from '@jbrowse/bandage-core/labelLayout'\nimport { LABEL_PX, labelWidth } from '@jbrowse/bandage-core/overlayLabels'\nimport { isAlive } from '@jbrowse/mobx-state-tree'\nimport { observer } from 'mobx-react'\n\nimport LabelChip, { inChip } from './LabelChip'\nimport { PaneSvgLayer } from './PaneLayer'\n\nimport type { GraphPaneModel } from '../model'\nimport type { BubbleHalo } from '@jbrowse/bandage-core/bubbles/bubbleHalos'\nimport type { LabelLayout } from '@jbrowse/bandage-core/labelLayout'\n\n// Every chip drawn over the graph, above all of its ink: bubble names and gene\n// names on their pins. `overlayLabels` has placed\n// them against each other and against the row labels already.\n\nconst GENE_INK = '#1c1c22'\nconst TICK_PX = 9\nconst TICK_WIDTH = 3\n\n// What the gene chip under a point reads out, for the hover tooltip: those\n// chips leave the pointer to the canvas, so a drag can start on one\nexport function chipReadoutAt(\n  { genes }: Pick<LabelLayout, 'genes'>,\n  px: number,\n  py: number,\n) {\n  const pin = genes.find(chip => inChip(chip, px, py))?.item\n  if (!pin) {\n    return undefined\n  }\n  const { gene } = pin\n  const note = geneCoverageNote(pin)\n  return {\n    label: gene.name,\n    readout: `${gene.refName}:${gene.start.toLocaleString()}-${gene.end.toLocaleString()}${note ? `, ${note} in the cut` : ''}`,\n  }\n}\n\nconst LabelLayer = observer(function LabelLayer({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const { bubbles, genes, ticks } = model.overlayLabels\n  if (bubbles.length + genes.length + ticks.length === 0) {\n    return null\n  }\n  const { scaleY, translateY, contigThickness, hoveredBubble } = model\n  const hoveredTick = hoveredBubble\n    ? ticks.find(t => sameBubble(t.item.bubble, hoveredBubble))\n    : undefined\n  const tickAt = (target: EventTarget) =>\n    ticks[Number((target as Element).getAttribute('data-tick'))]\n  const dimmedBubble = (h: BubbleHalo) => model.bubbleFaded(h)\n  const isOpen = (h: BubbleHalo) => model.bubbleIsOpen(h.bubble)\n\n  return (\n    <PaneSvgLayer\n      model={model}\n      zIndex={3}\n      testId=\"graph-label-layer\"\n      pansWithDrawing\n    >\n      <g\n        data-testid=\"graph-bubble-ticks\"\n        onClick={e => {\n          const tick = tickAt(e.target)\n          if (tick) {\n            model.toggleBubble(tick.item.bubble)\n          }\n        }}\n        onMouseOver={e => {\n          const tick = tickAt(e.target)\n          if (tick) {\n            model.setHoveredBubble(tick.item.bubble)\n          }\n        }}\n        // a leave also fires as the view closing it unmounts the tick\n        onMouseOut={() => {\n          if (isAlive(model)) {\n            model.setHoveredBubble(null)\n          }\n        }}\n        onFocus={e => {\n          const tick = tickAt(e.target)\n          if (tick) {\n            model.setHoveredBubble(tick.item.bubble)\n          }\n        }}\n        onBlur={() => {\n          if (isAlive(model)) {\n            model.setHoveredBubble(null)\n          }\n        }}\n        onKeyDown={e => {\n          const tick = tickAt(e.target)\n          if (tick && (e.key === 'Enter' || e.key === ' ')) {\n            e.preventDefault()\n            model.toggleBubble(tick.item.bubble)\n          }\n        }}\n      >\n        {ticks.map(({ item: h, x, y }, i) => (\n          <rect\n            key={bubbleKey(h.bubble)}\n            data-tick={i}\n            role=\"button\"\n            tabIndex={0}\n            aria-label={`${h.label}, ${isOpen(h) ? 'close' : 'open'} bubble`}\n            x={x - TICK_WIDTH / 2}\n            y={y - TICK_PX}\n            width={TICK_WIDTH}\n            height={TICK_PX}\n            rx={TICK_WIDTH / 2}\n            fill={BUBBLE_KIND_COLORS[h.kind]}\n            opacity={dimmedBubble(h) ? 0.35 : 1}\n            style={{ pointerEvents: 'all', cursor: 'pointer' }}\n          />\n        ))}\n      </g>\n      {genes.map(({ item: pin, x, y, w, text }) => {\n        const { gene } = pin\n        return (\n          <g key={`${gene.name}-${gene.start}`}>\n            <line\n              x1={x}\n              x2={x}\n              y1={y - LABEL_PX - 2}\n              y2={pin.at.y * scaleY + translateY + contigThickness / 2}\n              stroke={GENE_INK}\n              strokeWidth={0.8}\n              strokeOpacity={0.6}\n            />\n            <LabelChip\n              x={x}\n              y={y}\n              w={w}\n              text={gene.name}\n              note={text.slice(gene.name.length) || undefined}\n              color={GENE_INK}\n              edge={EXON_COLOR}\n              italic\n              testId=\"graph-gene-pin-label\"\n            />\n          </g>\n        )\n      })}\n      {bubbles.map(({ item: h, x, y, w, text }) => (\n        <LabelChip\n          key={bubbleKey(h.bubble)}\n          x={x}\n          y={y}\n          w={w}\n          text={text}\n          color={BUBBLE_KIND_COLORS[h.kind]}\n          dimmed={dimmedBubble(h)}\n          title={`${h.label}\\n${h.bubble.segmentCount} segments${h.bubble.covering ? '' : isOpen(h) ? ' \u00B7 click to close' : ' \u00B7 click to open'}`}\n          testId=\"graph-bubble-halo-label\"\n          // the bubble the drawing is would open into this same drawing\n          onClick={\n            h.bubble.covering\n              ? undefined\n              : () => {\n                  model.toggleBubble(h.bubble)\n                }\n          }\n          // a leave also fires as the view closing it unmounts the chip\n          onHover={hovered => {\n            if (isAlive(model)) {\n              model.setHoveredBubble(hovered ? h.bubble : null)\n            }\n          }}\n        />\n      ))}\n      {hoveredTick ? (\n        <LabelChip\n          x={hoveredTick.x}\n          y={hoveredTick.y - TICK_PX - 4}\n          w={labelWidth(hoveredTick.item.label)}\n          text={hoveredTick.item.label}\n          color={BUBBLE_KIND_COLORS[hoveredTick.item.kind]}\n          testId=\"graph-bubble-tick-label\"\n        />\n      ) : null}\n    </PaneSvgLayer>\n  )\n})\n\nexport default LabelLayer\n", "import { useCallback } from 'react'\n\nimport { drawReferenceStrip } from '@jbrowse/bandage-core/referenceStrip'\nimport { observer } from 'mobx-react'\n\nimport { PaneOverlayCanvas } from './PaneLayer'\n\nimport type { GraphPaneModel } from '../model'\n\n// Each reference segment at its bp in the linear view, onto the pane's\n// canvas or the linear view's SVG export\nexport function paintReferenceStrip(\n  ctx: CanvasRenderingContext2D,\n  model: GraphPaneModel,\n  {\n    lit,\n    dpr,\n  }: { lit: GraphPaneModel['referenceStripLit'] | undefined; dpr: number },\n) {\n  const frame = model.hostBpFrame\n  if (frame) {\n    drawReferenceStrip(ctx, model.referenceStripBlocks, frame, {\n      width: model.paneWidth,\n      lit,\n      dpr,\n    })\n  }\n}\n\n// Each reference segment at its bp in the linear view, over a drawing that\n// has no bp axis of its own. Repainted by an autorun, so a pan in the linear\n// view moves the strip in the same frame as its other tracks.\nconst ReferenceStripOverlay = observer(function ReferenceStripOverlay({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const paint = useCallback(\n    (ctx: CanvasRenderingContext2D, dpr: number) => {\n      paintReferenceStrip(ctx, model, { lit: model.referenceStripLit, dpr })\n    },\n    [model],\n  )\n  return (\n    <PaneOverlayCanvas\n      model={model}\n      zIndex={5}\n      shown={model.referenceStripShown}\n      testId=\"graph-reference-strip\"\n      paint={paint}\n    />\n  )\n})\n\nexport default ReferenceStripOverlay\n", "import { useCallback } from 'react'\n\nimport { drawTubeMapRuler } from '@jbrowse/bandage-core/tubeMap/axis'\nimport { drawTubeMapConnectors } from '@jbrowse/bandage-core/tubeMap/connectors'\nimport { drawDeviationMarks } from '@jbrowse/bandage-core/tubeMap/deviations'\nimport { drawTubeMap } from '@jbrowse/bandage-core/tubeMap/draw'\nimport { drawTubeMapGenes } from '@jbrowse/bandage-core/tubeMap/genes'\nimport { observer } from 'mobx-react'\n\nimport { PaneOverlayCanvas } from './PaneLayer'\nimport {\n  PANEL_TITLE_FONT,\n  drawBundleCounts,\n  drawSqueezedLengths,\n} from '../tubeMapPanels'\n\n// variants folded into a box mark texture under a panel's routes\nconst PANEL_TICK_ALPHA = 0.45\n\nimport type { GraphPaneModel } from '../model'\n\n// The tubes, their connectors, genes and ruler, onto a canvas sized to the\n// pane or onto the linear view's SVG export\nexport function paintTubeMap(\n  ctx: CanvasRenderingContext2D,\n  model: GraphPaneModel,\n  { highlightNode }: { highlightNode: string | null },\n) {\n  const picture = model.tubeMapPicture\n  const frame = model.tubeMapFrame\n  if (!picture || !frame) {\n    return\n  }\n  const width = model.paneWidth\n  const panels = model.tubeMapPanelViews\n  if (panels) {\n    paintPanels(ctx, model, panels, highlightNode)\n    return\n  }\n  const tubeFrame = {\n    ...frame,\n    width,\n    highlightNode,\n    tubeColors: model.tubeMapTubeColors,\n    nodeColors: model.tubeMapNodeColors,\n  }\n  drawTubeMap(ctx, picture, tubeFrame)\n  const drawn = model.layoutResult?.tubeMap\n  if (drawn) {\n    drawBundleCounts(ctx, picture, drawn.graph, tubeFrame)\n    drawSqueezedLengths(ctx, drawn, tubeFrame)\n  }\n  drawDeviationMarks(ctx, model.tubeMapDeviations, tubeFrame)\n  drawTubeMapConnectors(\n    ctx,\n    model.tubeMapConnectors,\n    model.connectorZoneBottom,\n    tubeFrame,\n  )\n  const { bounds } = picture\n  drawTubeMapGenes(ctx, model.tubeMapGenes, tubeFrame, frame.y(bounds.minY) - 2)\n  const boxes = model.tubeMapRulerBoxes\n  if (boxes) {\n    drawTubeMapRuler(\n      ctx,\n      boxes,\n      tubeFrame,\n      frame.y(bounds.maxY) + 4,\n      model.layoutResult?.referenceAxis,\n    )\n  }\n}\n\n// Each panel of a split tube map under a rule and its title, which the canvas\n// draws so a figure's SVG carries them\nfunction paintPanels(\n  ctx: CanvasRenderingContext2D,\n  model: GraphPaneModel,\n  panels: NonNullable<GraphPaneModel['tubeMapPanelViews']>,\n  highlightNode: string | null,\n) {\n  const width = model.paneWidth\n  for (const p of panels) {\n    if (p.bottom < 0 || p.titleTop > model.canvasHeight) {\n      continue\n    }\n    const tubeFrame = {\n      ...p.frame,\n      width,\n      highlightNode,\n      tubeColors: p.tubeColors,\n      nodeColors: p.nodeColors,\n    }\n    drawTubeMap(ctx, p.picture, tubeFrame)\n    drawBundleCounts(ctx, p.picture, p.panel.result.tubeMap.graph, tubeFrame)\n    drawSqueezedLengths(ctx, p.panel.result.tubeMap, tubeFrame)\n    ctx.globalAlpha = PANEL_TICK_ALPHA\n    drawDeviationMarks(ctx, p.deviations, tubeFrame)\n    ctx.globalAlpha = 1\n    ctx.strokeStyle = 'rgba(0,0,0,0.15)'\n    ctx.lineWidth = 1\n    ctx.beginPath()\n    ctx.moveTo(0, Math.round(p.titleTop) + 0.5)\n    ctx.lineTo(width, Math.round(p.titleTop) + 0.5)\n    ctx.stroke()\n    ctx.font = PANEL_TITLE_FONT\n    ctx.textAlign = 'left'\n    ctx.textBaseline = 'top'\n    ctx.fillStyle = 'rgba(0,0,0,0.85)'\n    ctx.fillText(p.label, 6, p.titleTop + 4)\n  }\n  const last = panels.at(-1)\n  const boxes = model.tubeMapPanelRulerBoxes\n  if (last && boxes) {\n    drawTubeMapRuler(\n      ctx,\n      boxes,\n      { ...last.frame, width },\n      last.bottom + 4,\n      true,\n    )\n  }\n}\n\n// The tube map's ink, over the canvas, which draws nothing under a tube map\n// layout. Above the tubes go the session's genes in a view of its own, or in\n// a linear view the bands tying each reference box to its bp there; under\n// them a reference ruler, unless the linear view's is already the axis.\n// Repainted by an autorun on every change of transform, so a pan in the linear\n// view above moves the tubes in the same frame as its other tracks.\nconst TubeMapOverlay = observer(function TubeMapOverlay({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const paint = useCallback(\n    (ctx: CanvasRenderingContext2D) => {\n      paintTubeMap(ctx, model, { highlightNode: model.selectedNode })\n    },\n    [model],\n  )\n  return (\n    <PaneOverlayCanvas\n      model={model}\n      zIndex={1}\n      shown={!!model.tubeMapPicture}\n      testId=\"graph-tube-map\"\n      paint={paint}\n    />\n  )\n})\n\nexport default TubeMapOverlay\n", "const host = JBrowseExports[\"@jbrowse/render-core/marks\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/render-core/marks\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const HIDDEN_ROW = /* @__PURE__ */ read(\"HIDDEN_ROW\")\nexport const LINK_ELSEWHERE = /* @__PURE__ */ read(\"LINK_ELSEWHERE\")\nexport const LINK_NO_REGION = /* @__PURE__ */ read(\"LINK_NO_REGION\")\nexport const NO_ROW_COLOR = /* @__PURE__ */ read(\"NO_ROW_COLOR\")\nexport const RAMP_NOT_A_NUMBER_COLOR = /* @__PURE__ */ read(\"RAMP_NOT_A_NUMBER_COLOR\")\nexport const RAMP_NO_VALUE_BITS = /* @__PURE__ */ read(\"RAMP_NO_VALUE_BITS\")\nexport const RAMP_NO_VALUE_COLOR = /* @__PURE__ */ read(\"RAMP_NO_VALUE_COLOR\")\nexport const RowKeys = /* @__PURE__ */ read(\"RowKeys\")\nexport const abgrToCssRgba = /* @__PURE__ */ read(\"abgrToCssRgba\")\nexport const appendGlyph = /* @__PURE__ */ read(\"appendGlyph\")\nexport const backToFront = /* @__PURE__ */ read(\"backToFront\")\nexport const barMark = /* @__PURE__ */ read(\"barMark\")\nexport const buildRowTable = /* @__PURE__ */ read(\"buildRowTable\")\nexport const defineMark = /* @__PURE__ */ read(\"defineMark\")\nexport const ellipseDistance = /* @__PURE__ */ read(\"ellipseDistance\")\nexport const ellipseNearest = /* @__PURE__ */ read(\"ellipseNearest\")\nexport const inkOfInstances = /* @__PURE__ */ read(\"inkOfInstances\")\nexport const instanceColor = /* @__PURE__ */ read(\"instanceColor\")\nexport const isThreshold = /* @__PURE__ */ read(\"isThreshold\")\nexport const keepRampValues = /* @__PURE__ */ read(\"keepRampValues\")\nexport const keySlot = /* @__PURE__ */ read(\"keySlot\")\nexport const lineCenterMark = /* @__PURE__ */ read(\"lineCenterMark\")\nexport const lineMarkOf = /* @__PURE__ */ read(\"lineMarkOf\")\nexport const lineStepMark = /* @__PURE__ */ read(\"lineStepMark\")\nexport const linkFeet = /* @__PURE__ */ read(\"linkFeet\")\nexport const linkMark = /* @__PURE__ */ read(\"linkMark\")\nexport const makeAbgrFill = /* @__PURE__ */ read(\"makeAbgrFill\")\nexport const nearestMarkHit = /* @__PURE__ */ read(\"nearestMarkHit\")\nexport const paintColors = /* @__PURE__ */ read(\"paintColors\")\nexport const paintMarkBlocks = /* @__PURE__ */ read(\"paintMarkBlocks\")\nexport const planMarks = /* @__PURE__ */ read(\"planMarks\")\nexport const pointInsetPx = /* @__PURE__ */ read(\"pointInsetPx\")\nexport const pointMark = /* @__PURE__ */ read(\"pointMark\")\nexport const rampUniforms = /* @__PURE__ */ read(\"rampUniforms\")\nexport const rampValueBits = /* @__PURE__ */ read(\"rampValueBits\")\nexport const recordPath = /* @__PURE__ */ read(\"recordPath\")\nexport const rowColor = /* @__PURE__ */ read(\"rowColor\")\nexport const rowSlot = /* @__PURE__ */ read(\"rowSlot\")\nexport const rowSpanIndex = /* @__PURE__ */ read(\"rowSpanIndex\")\nexport const ruleMark = /* @__PURE__ */ read(\"ruleMark\")\nexport const shiftInk = /* @__PURE__ */ read(\"shiftInk\")\nexport const spanMark = /* @__PURE__ */ read(\"spanMark\")\nexport const spansInRow = /* @__PURE__ */ read(\"spansInRow\")\nexport const thresholdBandOf = /* @__PURE__ */ read(\"thresholdBandOf\")\nexport const valueWindow = /* @__PURE__ */ read(\"valueWindow\")\nexport const withPassId = /* @__PURE__ */ read(\"withPassId\")\nexport default host && host.__esModule ? host.default : host", "import {\n  GAP_PX,\n  MISSING_PX,\n  coalesceRuns,\n  gapStyle,\n  runPaint,\n} from '@jbrowse/bandage-core/layout/walkRowDraw'\nimport { hslToRgb } from '@jbrowse/bandage-core/renderer/GeometryBuilder'\nimport { packAbgr } from '@jbrowse/bandage-core/renderer/colorBits'\nimport { spanMark } from '@jbrowse/render-core/marks'\n\nimport type { WalkRow, WalkRun } from '@jbrowse/bandage-core/layout/walkRows'\nimport type { MarkContext2D, SpanChannels } from '@jbrowse/render-core/marks'\n\ntype Rgb = [number, number, number]\n\n// The colours runPaint writes: `#rrggbb`, `rgb(r, g, b)` and\n// `hsl(h, s%, l%)`\nexport function cssRgb(css: string): Rgb {\n  if (css.startsWith('#')) {\n    const v = Number.parseInt(css.slice(1), 16)\n    return [(v >> 16) & 0xff, (v >> 8) & 0xff, v & 0xff]\n  }\n  const [a = 0, b = 0, c = 0] = css.match(/[\\d.]+/g)!.map(Number)\n  return css.startsWith('hsl')\n    ? (hslToRgb(a, b / 100, c / 100).map(v => v * 255) as Rgb)\n    : [a, b, c]\n}\n\nconst abgr = ([r, g, b]: Rgb) =>\n  packAbgr(Math.round(r), Math.round(g), Math.round(b), 255)\n\nconst cssAbgr = new Map<string, number>()\nfunction packCss(css: string) {\n  let v = cssAbgr.get(css)\n  if (v === undefined) {\n    v = abgr(cssRgb(css))\n    cssAbgr.set(css, v)\n  }\n  return v\n}\n\n/**\n * A run as the pieces it paints in, each `[start, end, abgr]` in bp along\n * the row: one for a solid fill, and for a gradient one per pixel or per\n * degree of hue, whichever is fewer, coloured as the SVG gradient through\n * the same stops colours its middle\n */\nexport function runPieces(\n  run: WalkRun,\n  ramp: { start: number; end: number } | undefined,\n  pxPerBp: number,\n): [number, number, number][] {\n  const end = run.start + run.bp\n  const paint = runPaint(run, ramp)\n  if ('fill' in paint) {\n    return [[run.start, end, packCss(paint.fill)]]\n  }\n  const stops = paint.stops.map(cssRgb)\n  const hues = paint.stops.map(css => Number(/[\\d.]+/.exec(css)![0]))\n  const hueSpan = Math.abs(hues.at(-1)! - hues[0]!)\n  const n = Math.max(\n    1,\n    Math.min(Math.ceil(run.bp * pxPerBp), Math.ceil(hueSpan), run.bp),\n  )\n  const pieces: [number, number, number][] = []\n  for (let k = 0; k < n; k++) {\n    const t = ((k + 0.5) / n) * (stops.length - 1)\n    const i = Math.min(Math.floor(t), stops.length - 2)\n    const a = stops[i]!\n    const b = stops[i + 1]!\n    const f = t - i\n    pieces.push([\n      Math.round(run.start + (run.bp * k) / n),\n      Math.round(run.start + (run.bp * (k + 1)) / n),\n      abgr([0, 1, 2].map(j => a[j]! + (b[j]! - a[j]!) * f) as Rgb),\n    ])\n  }\n  return pieces\n}\n\nexport interface WalkRowSpans {\n  bars: SpanChannels & { color: Uint32Array }\n  gaps: SpanChannels & { color: Uint32Array }\n  // gaps of bases the graph lacks, which draw as a hairline\n  hairlines: SpanChannels & { color: Uint32Array }\n  // where each drawn row's spans start in `bars`, `gaps` and `hairlines`\n  barRows: Uint32Array\n  gapRows: Uint32Array\n  hairlineRows: Uint32Array\n  // the furthest any span reaches along its row, in bp, and at least 1\n  longest: number\n}\n\nfunction channels(capacity: number) {\n  return {\n    x: new Uint32Array(capacity),\n    x2: new Uint32Array(capacity),\n    row: new Uint32Array(capacity),\n    color: new Uint32Array(capacity),\n    count: 0,\n  }\n}\n\nfunction slice<T extends SpanChannels & { color: Uint32Array }>(\n  c: T,\n  a: number,\n  b: number,\n) {\n  return {\n    x: c.x.subarray(a, b),\n    x2: c.x2.subarray(a, b),\n    row: c.row.subarray(a, b),\n    color: c.color.subarray(a, b),\n    count: b - a,\n  }\n}\n\n/**\n * Each row's runs as `walkRowsTree` coalesces and colours them at\n * `pxPerBp`, as span channels: `x`/`x2` in bp along the row, `row` its index\n * among `rows`. Gaps go apart, since they draw thinner, and gaps of bases the\n * graph lacks apart again, as a hairline.\n */\nexport function walkRowSpans(\n  rows: WalkRow[],\n  pxPerBp: number,\n  ramp?: { start: number; end: number },\n): WalkRowSpans {\n  const pieces = rows.map(r =>\n    coalesceRuns(r.runs, pxPerBp).map(run => ({\n      gap: run.gap,\n      hairline: run.gap && gapStyle(run.cause).px === MISSING_PX,\n      pieces: runPieces(run, ramp, pxPerBp),\n    })),\n  )\n  let total = 0\n  for (const runs of pieces) {\n    for (const run of runs) {\n      total += run.pieces.length\n    }\n  }\n  const bars = channels(total)\n  const gaps = channels(total)\n  const hairlines = channels(total)\n  const barRows = new Uint32Array(rows.length + 1)\n  const gapRows = new Uint32Array(rows.length + 1)\n  const hairlineRows = new Uint32Array(rows.length + 1)\n  let longest = 1\n  pieces.forEach((runs, row) => {\n    for (const run of runs) {\n      const c = run.hairline ? hairlines : run.gap ? gaps : bars\n      for (const [x, x2, color] of run.pieces) {\n        const i = c.count++\n        c.x[i] = x\n        c.x2[i] = x2\n        c.row[i] = row\n        c.color[i] = color\n        longest = Math.max(longest, c.x2[i])\n      }\n    }\n    barRows[row + 1] = bars.count\n    gapRows[row + 1] = gaps.count\n    hairlineRows[row + 1] = hairlines.count\n  })\n  return {\n    bars: slice(bars, 0, bars.count),\n    gaps: slice(gaps, 0, gaps.count),\n    hairlines: slice(hairlines, 0, hairlines.count),\n    barRows,\n    gapRows,\n    hairlineRows,\n    longest,\n  }\n}\n\nexport interface WalkRowSpanFrame {\n  scaleX: number\n  scaleY: number\n  translateX: number\n  translateY: number\n  width: number\n  height: number\n  rowPx: number\n  barPx: number\n  origin: number\n  // runs of rows whose y is `rowY(first)` plus a row pitch each, as the\n  // reference row and each grouped section are\n  blocks: { first: number; count: number; rowY: number }[]\n}\n\n/**\n * Paints the spans through render-core's span mark, a block of rows at a\n * time: row i's bar centred where `walkRowsTree` centres it, `barPx` tall,\n * its x at `origin + bp` through the pane's transform.\n */\nexport function paintWalkRowSpans(\n  ctx: MarkContext2D,\n  spans: WalkRowSpans,\n  f: WalkRowSpanFrame,\n) {\n  const { longest } = spans\n  const block = {\n    start: 0,\n    end: longest,\n    screenStartPx: f.origin * f.scaleX + f.translateX,\n    screenEndPx: (f.origin + longest) * f.scaleX + f.translateX,\n    reversed: false,\n    displayedRegionIndex: 0,\n  }\n  const frame = { canvasWidth: f.width, canvasHeight: f.height }\n  const rowHeight = f.rowPx * f.scaleY\n  for (const { first, count, rowY } of f.blocks) {\n    // slot `row` centres at (rowY + (row - first) * rowPx) * scaleY + translateY\n    const scrollTop =\n      rowHeight / 2 - f.translateY - (rowY - first * f.rowPx) * f.scaleY\n    const top = (rowY - f.rowPx / 2) * f.scaleY + f.translateY\n    if (top > f.height || top + count * rowHeight < 0) {\n      continue\n    }\n    for (const [c, starts, barPx] of [\n      [spans.bars, spans.barRows, f.barPx],\n      [spans.gaps, spans.gapRows, Math.min(GAP_PX, f.barPx)],\n      [spans.hairlines, spans.hairlineRows, Math.min(MISSING_PX, f.barPx)],\n    ] as const) {\n      spanMark.paintBlock(\n        ctx,\n        slice(c, starts[first]!, starts[first + count]!),\n        block,\n        frame,\n        {\n          rowHeight,\n          rowProportion: barPx / rowHeight,\n          minWidthPx: 1,\n          seamPx: 0,\n          scrollTop,\n        },\n      )\n    }\n  }\n}\n", "import { useCallback, useMemo } from 'react'\n\nimport { computed } from 'mobx'\nimport { observer } from 'mobx-react'\n\nimport ElTree, { useSvgId } from './ElTree'\nimport { PaneOverlayCanvas, PaneSvgLayer } from './PaneLayer'\nimport { SECTION_HEADER_PX, walkRowTrees } from '../walkRowGroups'\nimport { paintWalkRowSpans, walkRowSpans } from '../walkRowSpans'\n\nimport type { GraphPaneModel } from '../model'\n\n// The walk-rows layout's bars: one per haplotype walk under the reference\n// row, each on its own bp axis from the window's left edge. The runs paint as\n// spans on a canvas, coloured by whether they are on the reference walk's\n// path, and core's walkRowsTree draws the rest: unit separators, each row's\n// genes from its own assembly's annotation, the allele a repeat genotype\n// called and a readout. Under the\n// reference-position ramp an aligned run takes the hue of the reference it is\n// threaded through. In a tandem array that is the aligner's pick among\n// near-identical copies, so the hue says which reference copy the graph used,\n// not which one a copy resembles.\n//\n// The walk rows pair a repeat record's allele with each walk \u2014 see\n// repeats/walkCalls.ts, which also holds the threshold a red readout is read\n// off. Colouring each copy by its unit is jbrowse-plugin-tandem-repeat's.\n\n// The spans are recut only when the rows, the zoom or the ramp change\nfunction WalkRowSpansCanvas({ model }: { model: GraphPaneModel }) {\n  const spans = useMemo(\n    () =>\n      computed(() => {\n        const bars = model.walkRowBars\n        return bars\n          ? walkRowSpans(\n              [bars.reference, ...bars.rows],\n              model.scaleX,\n              model.referenceRampDomain,\n            )\n          : undefined\n      }),\n    [model],\n  )\n  const paint = useCallback(\n    (ctx: CanvasRenderingContext2D) => {\n      const bars = model.walkRowBars\n      const place = model.walkRowPlacement\n      const pitch = model.walkRowPitch\n      const painted = spans.get()\n      if (!bars || !place || !pitch || !painted) {\n        return\n      }\n      const sections = model.walkRowGroups?.sections\n      const blocks = sections?.length\n        ? [\n            { first: 0, count: 1, rowY: place.rowY(0) },\n            ...sections.map(s => ({\n              first: s.first,\n              count: s.count,\n              rowY: place.rowY(s.first),\n            })),\n          ]\n        : [{ first: 0, count: bars.rows.length + 1, rowY: place.rowY(0) }]\n      paintWalkRowSpans(ctx, painted, {\n        ...model.screenTransform,\n        width: model.paneWidth,\n        height: model.canvasHeight,\n        rowPx: pitch.rowPx,\n        barPx: pitch.barPx,\n        origin: bars.origin,\n        blocks,\n      })\n    },\n    [model, spans],\n  )\n  return (\n    <PaneOverlayCanvas\n      model={model}\n      zIndex={3}\n      testId=\"graph-walk-rows-spans\"\n      paint={paint}\n    />\n  )\n}\n\n// Its own observer, so moving between rows redraws this rect and not every row\nconst HoveredWalkRow = observer(function HoveredWalkRow({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const bars = model.walkRowBars\n  const place = model.walkRowPlacement\n  const pitch = model.walkRowPitch\n  if (!bars || !place || !pitch || !model.hoveredWalkRowText) {\n    return null\n  }\n  const rows = [bars.reference, ...bars.rows]\n  const index = rows.findIndex(r => r.name === model.hoveredWalkRow)\n  const row = rows[index]\n  if (!row) {\n    return null\n  }\n  const start = model.toScreen({ x: bars.origin, y: place.rowY(index) })\n  return (\n    <rect\n      data-testid=\"graph-walk-row-hovered\"\n      x={start.x - 2}\n      y={start.y - pitch.rowPx / 2 - 1}\n      width={row.bp * model.scaleX + 4}\n      height={pitch.rowPx + 2}\n      fill=\"none\"\n      stroke=\"#111\"\n      strokeWidth={1}\n    />\n  )\n})\n\n// `vector` for an SVG export, which draws the bars as walkRowsTree's rects\nconst WalkRowsOverlay = observer(function WalkRowsOverlay({\n  model,\n  vector = false,\n}: {\n  model: GraphPaneModel\n  vector?: boolean\n}) {\n  const idPrefix = useSvgId()\n  const bars = model.walkRowBars\n  const place = model.walkRowPlacement\n  const pitch = model.walkRowPitch\n  if (!bars || !place || !pitch) {\n    return null\n  }\n  const { paneWidth: width, canvasHeight } = model\n  // the canvas paints the bars, except in a vector export\n  const frame = {\n    ...model.screenTransform,\n    width,\n    height: canvasHeight,\n    ...pitch,\n    bars: vector,\n  }\n  return (\n    <>\n      {vector ? null : <WalkRowSpansCanvas model={model} />}\n      <PaneSvgLayer\n        model={model}\n        zIndex={3}\n        overflow=\"visible\"\n        testId=\"graph-walk-rows\"\n      >\n        {walkRowTrees(\n          bars,\n          model.walkRowGroups?.sections ?? [],\n          place.rowY,\n          frame,\n          {\n            ramp: model.referenceRampDomain,\n            rowGenes: model.walkRowGenes,\n            idPrefix,\n          },\n        ).map((tree, i) => (\n          <ElTree key={i} el={tree} />\n        ))}\n        {place.headers.map(header => (\n          <text\n            key={header.key}\n            x={10}\n            y={\n              model.toScreen({ x: 0, y: header.top }).y + SECTION_HEADER_PX - 4\n            }\n            fontFamily=\"sans-serif\"\n            fontSize={11}\n            fontWeight=\"bold\"\n            fill=\"#333\"\n            data-testid=\"graph-walk-section\"\n          >\n            {header.title}\n          </text>\n        ))}\n        <HoveredWalkRow model={model} />\n      </PaneSvgLayer>\n    </>\n  )\n})\n\nexport default WalkRowsOverlay\n"],
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+}

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package/dist/chunks/{chunk-N4WBX2OS.js → chunk-VQ77X5QU.js}

@@ -1,4 +1,4 @@
-import{p as T}from"./chunk-BWP3XYKD.js";import{a as I,b as L,g as S,j as w}from"./chunk-VDHDEEMF.js";var O=62,Z=60,G=9,k=48,z=57,_=/^(?:LN:i|SN:Z|SO:i|SR:i):/,q=/^[PEOUFG]\t/,C=s=>s.endsWith("\r")?s.slice(0,-1):s;function P(){return{nodes:new T(new Int32Array(65536)),reversed:new T(new Uint8Array(65536))}}var R=class{constructor(){this.names=[],this.byName=new Map,this.byNumber=new Map}has(s){return this.byName.has(s)}add(s){let e=this.names.length;this.byName.set(s,e),this.names.push(s);let t=+s;return Number.isSafeInteger(t)&&String(t)===s&&this.byNumber.set(t,e),e}of(s){return this.byName.get(s)??this.add(s)}ofNumber(s){return this.byNumber.get(s)}};function U(s){let[,e,t="*",...r]=s.split("	");if(!e||/^\d+$/.test(t))return;let i=t==="*"?0:t.length,n,a,l;for(let c of r){if(!_.test(c))return;let o=c.slice(5),p=c.slice(0,2);p==="LN"?i=+o:p==="SN"?n=o:p==="SO"?a=+o:l=+o}return{name:e,length:i,stable:n!==void 0&&a!==void 0&&l!==void 0?{refName:n,start:a,rank:l}:void 0}}function $(s,e,t,r){let i=0,n=-1,a=0,l=!0,d=o=>{if(n>=0&&o>n){let p=l&&o-n<16&&(o-n===1||s.charCodeAt(n)!==k)?t.ofNumber(a):void 0;r.nodes.push(p??t.of(s.slice(n,o))),r.reversed.push(i)}},c=e;for(;c<s.length;c++){let o=s.charCodeAt(c);if(o===O||o===Z)d(c),i=o===Z?1:0,n=c+1,a=0,l=!0;else{if(o===G)break;l&&o>=k&&o<=z?a=a*10+o-k:l=!1}}return d(c),c}function x(s){let e=[],t=0;for(;e.length<6;){let d=s.indexOf("	",t);if(d===-1)return;e.push(s.slice(t,d)),t=d+1}let[,r,i,n,a,l]=e;return r&&i&&n&&a&&l&&t<s.length?{sample:r,haplotype:i,contig:n,start:a,end:l,body:t}:void 0}function K(s){let e=s.split(`
+import{a as I,b as L,f as S,h as w}from"./chunk-6KUHGRHU.js";import{p as T}from"./chunk-6MUBJVBG.js";var O=62,Z=60,G=9,k=48,z=57,_=/^(?:LN:i|SN:Z|SO:i|SR:i):/,q=/^[PEOUFG]\t/,C=s=>s.endsWith("\r")?s.slice(0,-1):s;function P(){return{nodes:new T(new Int32Array(65536)),reversed:new T(new Uint8Array(65536))}}var R=class{constructor(){this.names=[],this.byName=new Map,this.byNumber=new Map}has(s){return this.byName.has(s)}add(s){let e=this.names.length;this.byName.set(s,e),this.names.push(s);let t=+s;return Number.isSafeInteger(t)&&String(t)===s&&this.byNumber.set(t,e),e}of(s){return this.byName.get(s)??this.add(s)}ofNumber(s){return this.byNumber.get(s)}};function U(s){let[,e,t="*",...r]=s.split("	");if(!e||/^\d+$/.test(t))return;let i=t==="*"?0:t.length,n,a,l;for(let c of r){if(!_.test(c))return;let o=c.slice(5),p=c.slice(0,2);p==="LN"?i=+o:p==="SN"?n=o:p==="SO"?a=+o:l=+o}return{name:e,length:i,stable:n!==void 0&&a!==void 0&&l!==void 0?{refName:n,start:a,rank:l}:void 0}}function $(s,e,t,r){let i=0,n=-1,a=0,l=!0,d=o=>{if(n>=0&&o>n){let p=l&&o-n<16&&(o-n===1||s.charCodeAt(n)!==k)?t.ofNumber(a):void 0;r.nodes.push(p??t.of(s.slice(n,o))),r.reversed.push(i)}},c=e;for(;c<s.length;c++){let o=s.charCodeAt(c);if(o===O||o===Z)d(c),i=o===Z?1:0,n=c+1,a=0,l=!0;else{if(o===G)break;l&&o>=k&&o<=z?a=a*10+o-k:l=!1}}return d(c),c}function x(s){let e=[],t=0;for(;e.length<6;){let d=s.indexOf("	",t);if(d===-1)return;e.push(s.slice(t,d)),t=d+1}let[,r,i,n,a,l]=e;return r&&i&&n&&a&&l&&t<s.length?{sample:r,haplotype:i,contig:n,start:a,end:l,body:t}:void 0}function K(s){let e=s.split(`
 `),t=new R,r=[],i=[],n=[],a=[],l=[],d=new Map;for(let u of e){if(q.test(u))return;if(u.startsWith("S	")){let f=U(C(u));if(!f||t.has(f.name))return;t.add(f.name),r.push(f.length);let h=-1;f.stable&&(h=d.get(f.stable.refName)??l.length,h===l.length&&(l.push(f.stable.refName),d.set(f.stable.refName,h))),i.push(h),n.push(f.stable?.start??0),a.push(f.stable?.rank??0)}}let c=[],o=[],p=[],v=[],E=[],W=[],y=[0],g=P(),A=new w,N=new w;for(let u of e)if(u.startsWith("L	")){let[,f,h,b,m]=C(u).split("	");f&&b&&m&&(c.push(t.of(f)),o.push(t.of(b)),p.push((h==="-"?1:0)|(m==="-"?2:0)))}else if(u.startsWith("W	")){let f=C(u),h=x(f);if(h){v.push(`${h.sample}#${h.haplotype}#${h.contig}`),E.push(h.start==="*"?0:+h.start),W.push(h.end==="*"?-1:+h.end);let b=$(f,h.body,t,g),m=F(f,b);if(m===void 0||(m.before&&A.push(m.before),m.after&&N.push(m.after),g.nodes.length===y.at(-1)))return;y.push(g.nodes.length)}}if(![A.kinds.length,N.kinds.length].some(u=>u>0&&u<v.length))return{nodes:{names:t.names,lengths:Int32Array.from(r),refs:Int32Array.from(i),starts:Float64Array.from(n),ranks:Int32Array.from(a),refNames:l},links:{from:Int32Array.from(c),to:Int32Array.from(o),strands:Uint8Array.from(p)},walks:{names:v,starts:Float64Array.from(E),ends:Float64Array.from(W),offsets:Int32Array.from(y),steps:g.nodes.data.slice(0,g.nodes.length),reversed:g.reversed.data.slice(0,g.reversed.length),...B(v.length,A,N)}}}function F(s,e){let t={};for(let r of e<s.length?s.slice(e+1).split("	"):[]){let i=r.slice(5);if(r.startsWith(`${I}:Z:`)){if(t.before=S(i),!t.before)return}else if(r.startsWith(`${L}:Z:`)&&(t.after=S(i),!t.after))return}return t}function B(s,e,t){return{...e.kinds.length===s&&s>0?{before:e.table()}:{},...t.kinds.length===s&&s>0?{after:t.table()}:{}}}var D=/([><])([^><]+)/g;function M(s){if(!s.startsWith(">")&&!s.startsWith("<"))return;let e=[];for(let[,t,r]of s.matchAll(D))e.push({name:r,strand:t===">"?"+":"-"});return e}function Q(s){let e=s.split("	");if(e.length<12||s.startsWith("#"))return;let t=M(e[5]);if(!t)return;let r,i=!1;for(let n=12;n<e.length;n++){let a=e[n];a.startsWith("cs:Z:")?r=a.slice(5):a==="tp:A:S"&&(i=!0)}return{name:e[0],queryLength:+e[1],queryStart:+e[2],queryEnd:+e[3],strand:e[4]==="-"?"-":"+",path:t,pathLength:+e[6],pathStart:+e[7],pathEnd:+e[8],matches:+e[9],blockLength:+e[10],mappingQuality:+e[11],secondary:i,...r===void 0?{}:{cs:r}}}function Y(s){let e=[];for(let t of s.split(`
 `)){let r=Q(t.trimEnd());r&&e.push(r)}return e}var j=/:(\d+)|=([A-Za-z]+)|\*[a-zA-Z]([a-zA-Z])|\+([A-Za-z]+)|-([A-Za-z]+)|~[a-z]{2}(\d+)[a-z]{2}/g;function tt(s){let e=[];for(let t of s.matchAll(j))t[1]!==void 0?e.push({op:"match",length:+t[1]}):t[2]!==void 0?e.push({op:"match",length:t[2].length}):t[3]!==void 0?e.push({op:"substitution",seq:t[3].toUpperCase()}):t[4]!==void 0?e.push({op:"insertion",seq:t[4].toUpperCase()}):t[5]!==void 0?e.push({op:"deletion",length:t[5].length}):t[6]!==void 0&&e.push({op:"match",length:+t[6]});return e}export{K as a,Q as b,Y as c,tt as d};
-//# sourceMappingURL=chunk-N4WBX2OS.js.map
+//# sourceMappingURL=chunk-VQ77X5QU.js.map

package/dist/chunks/{chunk-N4WBX2OS.js.map → chunk-VQ77X5QU.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.0.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-DZR37KXT.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.0.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-C44YRP5F.js"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-DZR37KXT.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-C44YRP5F.js"],
   "sourcesContent": ["import {\n  END_STOP_TAG,\n  START_STOP_TAG,\n  StopColumns,\n  parseStopTag\n} from \"./chunk-EIY2SKD3.js\";\nimport {\n  Column\n} from \"./chunk-ZPZ7GNBT.js\";\n\n// src/gfa/gfaTables.ts\nvar GT = 62;\nvar LT = 60;\nvar TAB = 9;\nvar ZERO = 48;\nvar NINE = 57;\nvar TABLE_TAG = /^(?:LN:i|SN:Z|SO:i|SR:i):/;\nvar UNTABLED_RECORD = /^[PEOUFG]\\t/;\nvar trimCR = (line) => line.endsWith(\"\\r\") ? line.slice(0, -1) : line;\nfunction stepColumns() {\n  return {\n    nodes: new Column(new Int32Array(1 << 16)),\n    reversed: new Column(new Uint8Array(1 << 16))\n  };\n}\nvar SegmentIndex = class {\n  constructor() {\n    this.names = [];\n    this.byName = /* @__PURE__ */ new Map();\n    // ids that are plain decimal, so a walk step finds its segment without\n    // slicing a string out of the body\n    this.byNumber = /* @__PURE__ */ new Map();\n  }\n  has(name) {\n    return this.byName.has(name);\n  }\n  add(name) {\n    const i = this.names.length;\n    this.byName.set(name, i);\n    this.names.push(name);\n    const n = +name;\n    if (Number.isSafeInteger(n) && String(n) === name) {\n      this.byNumber.set(n, i);\n    }\n    return i;\n  }\n  of(name) {\n    return this.byName.get(name) ?? this.add(name);\n  }\n  ofNumber(n) {\n    return this.byNumber.get(n);\n  }\n};\nfunction readSegment(line) {\n  const [, name, sequence = \"*\", ...tags] = line.split(\"\t\");\n  if (!name || /^\\d+$/.test(sequence)) {\n    return void 0;\n  }\n  let length = sequence === \"*\" ? 0 : sequence.length;\n  let refName;\n  let start;\n  let rank;\n  for (const tag of tags) {\n    if (!TABLE_TAG.test(tag)) {\n      return void 0;\n    }\n    const value = tag.slice(5);\n    const key = tag.slice(0, 2);\n    if (key === \"LN\") {\n      length = +value;\n    } else if (key === \"SN\") {\n      refName = value;\n    } else if (key === \"SO\") {\n      start = +value;\n    } else {\n      rank = +value;\n    }\n  }\n  const stable = refName !== void 0 && start !== void 0 && rank !== void 0 ? { refName, start, rank } : void 0;\n  return { name, length, stable };\n}\nfunction readWalkBody(line, from, segments, steps) {\n  let reversed = 0;\n  let start = -1;\n  let value = 0;\n  let decimal = true;\n  const finish = (end) => {\n    if (start >= 0 && end > start) {\n      const node = decimal && end - start < 16 && (end - start === 1 || line.charCodeAt(start) !== ZERO) ? segments.ofNumber(value) : void 0;\n      steps.nodes.push(node ?? segments.of(line.slice(start, end)));\n      steps.reversed.push(reversed);\n    }\n  };\n  let i = from;\n  for (; i < line.length; i++) {\n    const ch = line.charCodeAt(i);\n    if (ch === GT || ch === LT) {\n      finish(i);\n      reversed = ch === LT ? 1 : 0;\n      start = i + 1;\n      value = 0;\n      decimal = true;\n    } else if (ch === TAB) {\n      break;\n    } else if (decimal && ch >= ZERO && ch <= NINE) {\n      value = value * 10 + ch - ZERO;\n    } else {\n      decimal = false;\n    }\n  }\n  finish(i);\n  return i;\n}\nfunction walkFields(line) {\n  const fields = [];\n  let at = 0;\n  while (fields.length < 6) {\n    const tab = line.indexOf(\"\t\", at);\n    if (tab === -1) {\n      return void 0;\n    }\n    fields.push(line.slice(at, tab));\n    at = tab + 1;\n  }\n  const [, sample, haplotype, contig, start, end] = fields;\n  return sample && haplotype && contig && start && end && at < line.length ? { sample, haplotype, contig, start, end, body: at } : void 0;\n}\nfunction gfaTables(text) {\n  const lines = text.split(\"\\n\");\n  const segments = new SegmentIndex();\n  const lengths = [];\n  const refs = [];\n  const starts = [];\n  const ranks = [];\n  const refNames = [];\n  const refIndex = /* @__PURE__ */ new Map();\n  for (const raw of lines) {\n    if (UNTABLED_RECORD.test(raw)) {\n      return void 0;\n    }\n    if (raw.startsWith(\"S\t\")) {\n      const s = readSegment(trimCR(raw));\n      if (!s || segments.has(s.name)) {\n        return void 0;\n      }\n      segments.add(s.name);\n      lengths.push(s.length);\n      let ref = -1;\n      if (s.stable) {\n        ref = refIndex.get(s.stable.refName) ?? refNames.length;\n        if (ref === refNames.length) {\n          refNames.push(s.stable.refName);\n          refIndex.set(s.stable.refName, ref);\n        }\n      }\n      refs.push(ref);\n      starts.push(s.stable?.start ?? 0);\n      ranks.push(s.stable?.rank ?? 0);\n    }\n  }\n  const from = [];\n  const to = [];\n  const strands = [];\n  const names = [];\n  const walkStarts = [];\n  const walkEnds = [];\n  const offsets = [0];\n  const steps = stepColumns();\n  const before = new StopColumns();\n  const after = new StopColumns();\n  for (const raw of lines) {\n    if (raw.startsWith(\"L\t\")) {\n      const [, source, strand1, target, strand2] = trimCR(raw).split(\"\t\");\n      if (source && target && strand2) {\n        from.push(segments.of(source));\n        to.push(segments.of(target));\n        strands.push((strand1 === \"-\" ? 1 : 0) | (strand2 === \"-\" ? 2 : 0));\n      }\n    } else if (raw.startsWith(\"W\t\")) {\n      const line = trimCR(raw);\n      const w = walkFields(line);\n      if (w) {\n        names.push(`${w.sample}#${w.haplotype}#${w.contig}`);\n        walkStarts.push(w.start === \"*\" ? 0 : +w.start);\n        walkEnds.push(w.end === \"*\" ? -1 : +w.end);\n        const end = readWalkBody(line, w.body, segments, steps);\n        const tags = walkTags(line, end);\n        if (tags === void 0) {\n          return void 0;\n        }\n        if (tags.before) {\n          before.push(tags.before);\n        }\n        if (tags.after) {\n          after.push(tags.after);\n        }\n        if (steps.nodes.length === offsets.at(-1)) {\n          return void 0;\n        }\n        offsets.push(steps.nodes.length);\n      }\n    }\n  }\n  if ([before.kinds.length, after.kinds.length].some(\n    (n) => n > 0 && n < names.length\n  )) {\n    return void 0;\n  }\n  return {\n    nodes: {\n      names: segments.names,\n      lengths: Int32Array.from(lengths),\n      refs: Int32Array.from(refs),\n      starts: Float64Array.from(starts),\n      ranks: Int32Array.from(ranks),\n      refNames\n    },\n    links: {\n      from: Int32Array.from(from),\n      to: Int32Array.from(to),\n      strands: Uint8Array.from(strands)\n    },\n    walks: {\n      names,\n      starts: Float64Array.from(walkStarts),\n      ends: Float64Array.from(walkEnds),\n      offsets: Int32Array.from(offsets),\n      steps: steps.nodes.data.slice(0, steps.nodes.length),\n      reversed: steps.reversed.data.slice(0, steps.reversed.length),\n      ...stopColumns(names.length, before, after)\n    }\n  };\n}\nfunction walkTags(line, from) {\n  const out = {};\n  for (const tag of from < line.length ? line.slice(from + 1).split(\"\t\") : []) {\n    const value = tag.slice(5);\n    if (tag.startsWith(`${START_STOP_TAG}:Z:`)) {\n      out.before = parseStopTag(value);\n      if (!out.before) {\n        return void 0;\n      }\n    } else if (tag.startsWith(`${END_STOP_TAG}:Z:`)) {\n      out.after = parseStopTag(value);\n      if (!out.after) {\n        return void 0;\n      }\n    }\n  }\n  return out;\n}\nfunction stopColumns(walks, before, after) {\n  return {\n    ...before.kinds.length === walks && walks > 0 ? { before: before.table() } : {},\n    ...after.kinds.length === walks && walks > 0 ? { after: after.table() } : {}\n  };\n}\n\nexport {\n  gfaTables\n};\n", "// src/gaf/parseGaf.ts\nvar STEP = /([><])([^><]+)/g;\nfunction parseGafPath(column) {\n  if (!column.startsWith(\">\") && !column.startsWith(\"<\")) {\n    return void 0;\n  }\n  const steps = [];\n  for (const [, arrow, name] of column.matchAll(STEP)) {\n    steps.push({ name, strand: arrow === \">\" ? \"+\" : \"-\" });\n  }\n  return steps;\n}\nfunction parseGafLine(line) {\n  const columns = line.split(\"\t\");\n  if (columns.length < 12 || line.startsWith(\"#\")) {\n    return void 0;\n  }\n  const path = parseGafPath(columns[5]);\n  if (!path) {\n    return void 0;\n  }\n  let cs;\n  let secondary = false;\n  for (let i = 12; i < columns.length; i++) {\n    const tag = columns[i];\n    if (tag.startsWith(\"cs:Z:\")) {\n      cs = tag.slice(5);\n    } else if (tag === \"tp:A:S\") {\n      secondary = true;\n    }\n  }\n  return {\n    name: columns[0],\n    queryLength: +columns[1],\n    queryStart: +columns[2],\n    queryEnd: +columns[3],\n    strand: columns[4] === \"-\" ? \"-\" : \"+\",\n    path,\n    pathLength: +columns[6],\n    pathStart: +columns[7],\n    pathEnd: +columns[8],\n    matches: +columns[9],\n    blockLength: +columns[10],\n    mappingQuality: +columns[11],\n    secondary,\n    ...cs === void 0 ? {} : { cs }\n  };\n}\nfunction parseGaf(text) {\n  const records = [];\n  for (const line of text.split(\"\\n\")) {\n    const record = parseGafLine(line.trimEnd());\n    if (record) {\n      records.push(record);\n    }\n  }\n  return records;\n}\nvar CS_OP = /:(\\d+)|=([A-Za-z]+)|\\*[a-zA-Z]([a-zA-Z])|\\+([A-Za-z]+)|-([A-Za-z]+)|~[a-z]{2}(\\d+)[a-z]{2}/g;\nfunction parseCs(cs) {\n  const ops = [];\n  for (const m of cs.matchAll(CS_OP)) {\n    if (m[1] !== void 0) {\n      ops.push({ op: \"match\", length: +m[1] });\n    } else if (m[2] !== void 0) {\n      ops.push({ op: \"match\", length: m[2].length });\n    } else if (m[3] !== void 0) {\n      ops.push({ op: \"substitution\", seq: m[3].toUpperCase() });\n    } else if (m[4] !== void 0) {\n      ops.push({ op: \"insertion\", seq: m[4].toUpperCase() });\n    } else if (m[5] !== void 0) {\n      ops.push({ op: \"deletion\", length: m[5].length });\n    } else if (m[6] !== void 0) {\n      ops.push({ op: \"match\", length: +m[6] });\n    }\n  }\n  return ops;\n}\n\nexport {\n  parseGafPath,\n  parseGafLine,\n  parseGaf,\n  parseCs\n};\n"],
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