npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 7.1.0 → 7.1.2 - Mend

jbrowse-plugin-graphgenomeviewer 7.1.0 → 7.1.2

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package/dist/chunks/chunk-GOFS7BXK.js.map DELETED Viewed

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../src/GraphGenomeView/components/BubbleHalos.tsx", "../../src/GraphGenomeView/legendSections.ts", "../../src/GraphGenomeView/components/ElTree.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 { 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 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 svgStyle = {\n  position: 'absolute' as const,\n  left: 0,\n  top: 0,\n  pointerEvents: 'none' as const,\n  overflow: 'hidden' as const,\n  zIndex: 2,\n}\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 {\n    scaleX,\n    scaleY,\n    translateX,\n    translateY,\n    paneWidth: width,\n    canvasHeight,\n  } = model\n  const halo = model.contigThickness * HALO_FACTOR\n  return (\n    <svg\n      style={svgStyle}\n      width={width}\n      height={canvasHeight}\n      data-testid=\"graph-bubble-halos\"\n    >\n      <g\n        transform={`translate(${translateX} ${translateY}) scale(${scaleX} ${scaleY})`}\n      >\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      </g>\n    </svg>\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  GAP_PX,\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\nexport const BAR_PX = 48\n\n// getNodeColor's grey for a node the ramp cannot place\nexport const UNPLACED_SWATCH = 'rgb(160, 160, 160)'\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\nexport interface 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\n// One key entry per halo colour drawn, naming the kinds it stands for\nexport function haloKeyEntries(model: GraphPaneModel) {\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      color,\n      label:\n        names === BUBBLE_KIND_NAMES.superbubble ? names : `${names} bubble`,\n    }\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: ${halo?.label ?? 'bubble'}`,\n      swatch: halo\n        ? { kind: 'halo', color: BUBBLE_KIND_COLORS[halo.kind] }\n        : { kind: 'blank' },\n      closesBubble: true,\n    },\n  ]\n}\n\n// Under lifted walks each lane states its own scale, and the rest is grey\nfunction rampRows(model: GraphPaneModel): LegendRow[] {\n  const domain = model.walkLift ? undefined : model.referenceRampDomain\n  if (!domain) {\n    return []\n  }\n  // a measured domain runs between node midpoints, which can fall on a half bp\n  const start = Math.round(domain.start)\n  const end = Math.round(domain.end)\n  const { offReference, unplaced } = model.referenceRampOffKeys\n  return [\n    {\n      key: 'ramp',\n      label: `${start.toLocaleString()}-${end.toLocaleString()} (${formatBp(end - start)})`,\n      swatch: { kind: 'fill', stops: RAMP_GRADIENT_STOPS, width: BAR_PX },\n    },\n    ...(offReference\n      ? [fillRow('off', REFERENCE_RAMP_ALT_CSS, 'off the reference', BAR_PX)]\n      : []),\n    ...(unplaced\n      ? [fillRow('unplaced', UNPLACED_SWATCH, 'no reference position', 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 ${rowPerWalk ? \"that row's walk\" : model.liftedWalksLabel}`\n              : 'reference outside the open bubble',\n          ),\n        ]\n      : []),\n    ...(model.referenceStripOverhangs\n      ? [\n          {\n            key: 'overhang',\n            label: 'graph runs past this edge',\n            swatch: { kind: 'overhang' } as const,\n          },\n        ]\n      : []),\n  ]\n}\n\nfunction haloRows(model: GraphPaneModel): LegendRow[] {\n  return haloKeyEntries(model).map(({ color, label }) => ({\n    key: `halo-${color}`,\n    label,\n    swatch: { kind: 'halo', color },\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-${name}`,\n    label,\n    swatch: { kind: 'line', color },\n  }))\n}\n\nfunction tubeRow(key: string, color: string, label: string): LegendRow {\n  return {\n    key,\n    label,\n    swatch: {\n      kind: 'fill',\n      stops: flat(color),\n      height: TUBE_SWATCH_PX,\n      square: true,\n    },\n  }\n}\n\n// What a tube map draws that nothing else on screen explains, each listed\n// only while it applies\nexport function tubeMapRows(model: GraphPaneModel): LegendRow[] {\n  const {\n    roles,\n    haplotypeTube,\n    bundled,\n    values,\n    logWidths,\n    foldBp,\n    forwardReads,\n    reverseReads,\n    substitution,\n    insertion,\n    deletion,\n  } = model.tubeMapKeys\n  const reads = model.readsShown\n  const rows: LegendRow[] = []\n  if (values) {\n    rows.push(\n      tubeRow('value-reference', PANEL_REFERENCE_TUBE, 'reference'),\n      ...values.map(({ value, color }) =>\n        tubeRow(`value-${value}`, color, value),\n      ),\n    )\n  }\n  if (roles) {\n    rows.push(\n      tubeRow('ref', PANEL_REFERENCE_TUBE, 'reference'),\n      tubeRow(\n        'hap',\n        haplotypeTube,\n        bundled ? 'shared route, \u00D7n haplotypes' : 'haplotype',\n      ),\n    )\n  }\n  const readRow = (key: string, colors: readonly string[], label: string) => ({\n    key,\n    label,\n    swatch: {\n      kind: 'fill',\n      stops: bandStops(colors),\n      height: TUBE_SWATCH_PX,\n      square: true,\n    } as const,\n  })\n  if (forwardReads) {\n    rows.push(readRow('fwd', FORWARD_READ_COLORS, 'read on the forward strand'))\n  }\n  if (reverseReads) {\n    rows.push(readRow('rev', REVERSE_READ_COLORS, 'read on the reverse strand'))\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', 'grey', 'read deletion'))\n  }\n  if (foldBp !== undefined) {\n    rows.push({\n      key: 'tube-fold',\n      label: `haplotype variant < ${formatBp(foldBp)}`,\n      swatch: {\n        kind: 'tick',\n        color: deviationInk(),\n        height: TUBE_SWATCH_PX,\n        backing: FOLD_TICK_BACKING,\n      },\n    })\n  }\n  if (logWidths) {\n    rows.push({\n      key: 'log',\n      label: 'width grows with log of length',\n      swatch: { kind: 'bracket' },\n    })\n  }\n  return rows\n}\n\nexport function walkRowSwatch(swatch: KeySwatch): LegendSwatch {\n  return swatch.kind === 'gene'\n    ? {\n        kind: 'outline',\n        color: GENE_INK,\n        stroke: 1.5,\n        radius: 0,\n        height: WALK_ROW_SWATCH_PX,\n      }\n    : {\n        kind: 'fill',\n        stops:\n          swatch.kind === 'bar' && swatch.ramp\n            ? RAMP_GRADIENT_STOPS\n            : flat(swatch.fill),\n        height: swatch.kind === 'gap' ? GAP_PX : WALK_ROW_SWATCH_PX,\n      }\n}\n\n// The walk rows' bar colours, genes and ticks; each tick row appears once\n// the rows hold one, so a catalogue with no genotypes keeps the plain key\nfunction walkRowsRows(model: GraphPaneModel): LegendRow[] {\n  const bars = model.walkRowBars\n  if (!bars) {\n    return []\n  }\n  const calls = [bars.reference, ...bars.rows].flatMap(row => row.call ?? [])\n  const tick = (key: string, color: string, label: string): LegendRow => ({\n    key,\n    label,\n    swatch: { kind: 'tick', color, height: WALK_ROW_SWATCH_PX },\n  })\n  return [\n    ...walkRowsKey(bars, {\n      ramp: model.referenceRampDomain,\n      genes: model.walkRowGeneKey,\n    }).map(entry => ({\n      key: `rows-${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.outside + 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// 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    // the ramp's own key, which names this, is off while walks are lifted\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, `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\n    ? [\n        ...(model.liftPaintsOffReference\n          ? [fillRow('lift-off', REFERENCE_RAMP_ALT_CSS, 'off the reference')]\n          : []),\n        fillRow('faded', FADED_SWATCH, \"not on the panel's walk\"),\n      ]\n    : []\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 } 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 core element tree as React elements\nexport default function ElTree({ el }: { el: El }) {\n  return toReact(el, 0)\n}\n", "import { useId } from 'react'\n\nimport {\n  exonOutlineTree,\n  exonStretches,\n} from '@jbrowse/bandage-core/genes/exonOutline'\nimport { observer } from 'mobx-react'\n\nimport ElTree from './ElTree'\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 svgStyle = {\n  position: 'absolute' as const,\n  left: 0,\n  top: 0,\n  pointerEvents: 'none' as const,\n  overflow: 'hidden' as const,\n  zIndex: 2,\n}\n\nexport { EXON_COLOR } from '@jbrowse/bandage-core/genes/exonOutline'\n\nconst GenePins = observer(function GenePins({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const id = `exon-outline-${useId().replaceAll(/[^\\w-]/g, '')}`\n  const { genePins, walkLift, nodeInk } = model\n  const { scaleX, scaleY, translateX, translateY, paneWidth, canvasHeight } =\n    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 => focus.nodeIds.has(e.nodeId)),\n      }))\n    : genePins\n  const tree = exonOutlineTree(\n    exonStretches(pins, nodeInk.halfWidthPx, walkLift),\n    {\n      id,\n      width: paneWidth,\n      height: canvasHeight,\n      transform: `translate(${translateX} ${translateY}) scale(${scaleX} ${scaleY})`,\n    },\n  )\n  return tree ? (\n    <svg\n      style={svgStyle}\n      width={paneWidth}\n      height={canvasHeight}\n      data-testid=\"graph-gene-pins\"\n    >\n      <ElTree el={tree} />\n    </svg>\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\nexport function 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  small,\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  small?: 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    >\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={small ? 0.6 : 1}\n      />\n      <text\n        x={x}\n        y={y}\n        fontSize={small ? LABEL_PX - 1 : 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 { 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 { EXON_COLOR } from './GenePins'\nimport LabelChip, { inChip } from './LabelChip'\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 svgStyle = {\n  position: 'absolute' as const,\n  left: 0,\n  top: 0,\n  pointerEvents: 'none' as const,\n  overflow: 'hidden' as const,\n  zIndex: 3,\n}\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    <svg\n      style={svgStyle}\n      width={model.paneWidth}\n      height={model.canvasHeight}\n      data-testid=\"graph-label-layer\"\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      >\n        {ticks.map(({ item: h, x, y }, i) => (\n          <rect\n            key={bubbleKey(h.bubble)}\n            data-tick={i}\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    </svg>\n  )\n})\n\nexport default LabelLayer\n", "import { useEffect, useRef } from 'react'\n\nimport { drawReferenceStrip } from '@jbrowse/bandage-core/referenceStrip'\nimport { getDpr } from '@jbrowse/bandage-core/renderer/canvas'\nimport { autorun } from 'mobx'\nimport { observer } from 'mobx-react'\n\nimport type { GraphPaneModel } from '../model'\n\nconst canvasStyle = {\n  position: 'absolute' as const,\n  left: 0,\n  top: 0,\n  pointerEvents: 'none' as const,\n  zIndex: 5,\n}\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      darkMode: model.darkMode,\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 ref = useRef<HTMLCanvasElement>(null)\n  const { referenceStripShown, paneWidth, canvasHeight } = model\n  useEffect(\n    () =>\n      autorun(() => {\n        const canvas = ref.current\n        const ctx = canvas?.getContext('2d')\n        if (canvas && ctx && model.referenceStripShown) {\n          const dpr = getDpr()\n          const width = model.paneWidth\n          const height = model.canvasHeight\n          canvas.width = Math.round(width * dpr)\n          canvas.height = Math.round(height * dpr)\n          ctx.setTransform(dpr, 0, 0, dpr, 0, 0)\n          ctx.clearRect(0, 0, width, height)\n          paintReferenceStrip(ctx, model, {\n            lit: model.referenceStripLit,\n            dpr,\n          })\n        }\n      }),\n    [model],\n  )\n  return (\n    <canvas\n      ref={ref}\n      data-testid={referenceStripShown ? 'graph-reference-strip' : undefined}\n      style={{\n        ...canvasStyle,\n        width: paneWidth,\n        height: canvasHeight,\n        display: referenceStripShown ? 'block' : 'none',\n      }}\n    />\n  )\n})\n\nexport default ReferenceStripOverlay\n", "import { useEffect, useRef } from 'react'\n\nimport { getDpr } from '@jbrowse/bandage-core/renderer/canvas'\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 { autorun } from 'mobx'\nimport { observer } from 'mobx-react'\n\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\nconst canvasStyle = {\n  position: 'absolute' as const,\n  left: 0,\n  top: 0,\n  pointerEvents: 'none' as const,\n  zIndex: 1,\n}\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    darkMode: model.darkMode,\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  const ink = model.darkMode ? '255,255,255' : '0,0,0'\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      darkMode: model.darkMode,\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(${ink},0.15)`\n    ctx.lineWidth = 1\n    ctx.beginPath()\n    ctx.moveTo(0, Math.round(p.titleTop) + 0.5)\n    ctx.lineTo(width, Math.round(p.titleTop) + 0.5)\n    ctx.stroke()\n    ctx.font = PANEL_TITLE_FONT\n    ctx.textAlign = 'left'\n    ctx.textBaseline = 'top'\n    ctx.fillStyle = `rgba(${ink},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, darkMode: model.darkMode },\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 ref = useRef<HTMLCanvasElement>(null)\n  const { tubeMapPicture, paneWidth, canvasHeight } = model\n  useEffect(\n    () =>\n      autorun(() => {\n        const canvas = ref.current\n        const ctx = canvas?.getContext('2d')\n        if (canvas && ctx && model.tubeMapPicture && model.tubeMapFrame) {\n          const dpr = getDpr()\n          const width = model.paneWidth\n          const height = model.canvasHeight\n          canvas.width = Math.round(width * dpr)\n          canvas.height = Math.round(height * dpr)\n          ctx.setTransform(dpr, 0, 0, dpr, 0, 0)\n          ctx.clearRect(0, 0, width, height)\n          paintTubeMap(ctx, model, { highlightNode: model.selectedNode })\n        }\n      }),\n    [model],\n  )\n  // Mounted whether or not there is a tube map, so the autorun above has its\n  // canvas the moment a layout brings one.\n  return (\n    <canvas\n      ref={ref}\n      data-testid={tubeMapPicture ? 'graph-tube-map' : undefined}\n      style={{\n        ...canvasStyle,\n        width: paneWidth,\n        height: canvasHeight,\n        display: tubeMapPicture ? 'block' : 'none',\n      }}\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  coalesceRuns,\n  runPaint,\n} from '@jbrowse/bandage-core/layout/walkRowDraw'\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\nfunction hslRgb(h: number, s: number, l: number): Rgb {\n  const a = s * Math.min(l, 1 - l)\n  const f = (n: number) => {\n    const k = (n + h / 30) % 12\n    return 255 * (l - a * Math.max(-1, Math.min(k - 3, 9 - k, 1)))\n  }\n  return [f(0), f(8), f(4)]\n}\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') ? hslRgb(a, b / 100, c / 100) : [a, b, c]\n}\n\nconst abgr = ([r, g, b]: Rgb) =>\n  ((0xff << 24) |\n    (Math.round(b) << 16) |\n    (Math.round(g) << 8) |\n    Math.round(r)) >>>\n  0\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  // where each drawn row's spans start in `bars` and `gaps`\n  barRows: Uint32Array\n  gapRows: Uint32Array\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 trim(c: ReturnType<typeof channels>) {\n  const n = c.count\n  return {\n    x: c.x.subarray(0, n),\n    x2: c.x2.subarray(0, n),\n    row: c.row.subarray(0, n),\n    color: c.color.subarray(0, n),\n    count: n,\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.\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      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 barRows = new Uint32Array(rows.length + 1)\n  const gapRows = new Uint32Array(rows.length + 1)\n  pieces.forEach((runs, row) => {\n    for (const run of runs) {\n      const c = 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      }\n    }\n    barRows[row + 1] = bars.count\n    gapRows[row + 1] = gaps.count\n  })\n  return { bars: trim(bars), gaps: trim(gaps), barRows, gapRows }\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\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  let longest = 1\n  for (const c of [spans.bars, spans.gaps]) {\n    for (const x2 of c.x2) {\n      longest = Math.max(longest, x2)\n    }\n  }\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    ] 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 { useEffect, useId, useMemo, useRef } from 'react'\n\nimport { walkRowsTree } from '@jbrowse/bandage-core/layout/walkRowDraw'\nimport { getDpr } from '@jbrowse/bandage-core/renderer/canvas'\nimport { autorun, computed } from 'mobx'\nimport { observer } from 'mobx-react'\n\nimport ElTree from './ElTree'\nimport { SECTION_HEADER_PX } from '../walkRowGroups'\nimport { paintWalkRowSpans, walkRowSpans } from '../walkRowSpans'\n\nimport type { GraphPaneModel } from '../model'\nimport type { WalkRowSection } from '../walkRowGroups'\nimport type { El } from '@jbrowse/bandage-core/el'\nimport type {\n  WalkRowsFrame,\n  WalkRowsWithCalls,\n} from '@jbrowse/bandage-core/layout/walkRowDraw'\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\nconst svgStyle = {\n  position: 'absolute' as const,\n  left: 0,\n  top: 0,\n  pointerEvents: 'none' as const,\n  overflow: 'visible' as const,\n  zIndex: 3,\n}\n\n// The rows' trees, a section at a time while grouped. walkRowsTree puts its\n// i-th row at i * rowPx below its reference row and draws that row too, so\n// each section is drawn shifted down to its place with its reference row\n// dropped.\nexport function walkRowTrees(\n  bars: WalkRowsWithCalls,\n  sections: WalkRowSection[],\n  rowY: (i: number) => number,\n  frame: WalkRowsFrame & { rowPx: number },\n  o: Parameters<typeof walkRowsTree>[2] & { idPrefix: string },\n): El[] {\n  if (sections.length === 0) {\n    return [walkRowsTree(bars, frame, o)]\n  }\n  return [\n    walkRowsTree({ ...bars, rows: [] }, frame, o),\n    ...sections.flatMap((section, k) => {\n      const tree = walkRowsTree(\n        {\n          ...bars,\n          rows: bars.rows.slice(\n            section.first - 1,\n            section.first - 1 + section.count,\n          ),\n        },\n        {\n          ...frame,\n          translateY:\n            frame.translateY +\n            (rowY(section.first) - frame.rowPx) * frame.scaleY,\n        },\n        { ...o, idPrefix: `${o.idPrefix}-s${k}` },\n      )\n      return tree.children.filter(\n        (c): c is El =>\n          typeof c !== 'string' &&\n          c.attrs['data-testid'] !== 'graph-walk-reference',\n      )\n    }),\n  ]\n}\n\nconst canvasStyle = { ...svgStyle, overflow: undefined }\n\n// Repainted by an autorun, as the other overlay canvases are, so a pan moves\n// the bars in the same frame as the drawing. The spans are recut only when\n// the rows, the zoom or the ramp change.\nconst WalkRowSpansCanvas = observer(function WalkRowSpansCanvas({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const ref = useRef<HTMLCanvasElement>(null)\n  useEffect(() => {\n    const spans = 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    return autorun(() => {\n      const canvas = ref.current\n      const ctx = canvas?.getContext('2d')\n      const bars = model.walkRowBars\n      const place = model.walkRowPlacement\n      const pitch = model.walkRowPitch\n      const painted = spans.get()\n      if (!canvas || !ctx || !bars || !place || !pitch || !painted) {\n        return\n      }\n      const width = model.paneWidth\n      const height = model.canvasHeight\n      const dpr = getDpr()\n      canvas.width = Math.round(width * dpr)\n      canvas.height = Math.round(height * dpr)\n      ctx.setTransform(dpr, 0, 0, dpr, 0, 0)\n      ctx.clearRect(0, 0, width, height)\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        scaleX: model.scaleX,\n        scaleY: model.scaleY,\n        translateX: model.translateX,\n        translateY: model.translateY,\n        width,\n        height,\n        rowPx: pitch.rowPx,\n        barPx: pitch.barPx,\n        origin: bars.origin,\n        blocks,\n      })\n    })\n  }, [model])\n  return (\n    <canvas\n      ref={ref}\n      data-testid=\"graph-walk-rows-spans\"\n      style={{\n        ...canvasStyle,\n        width: model.paneWidth,\n        height: model.canvasHeight,\n      }}\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 = useId().replace(/[^\\w-]/g, '')\n  const bars = model.walkRowBars\n  const place = model.walkRowPlacement\n  const pitch = model.walkRowPitch\n  const bare = useMemo(\n    () =>\n      bars && {\n        ...bars,\n        reference: { ...bars.reference, runs: [] },\n        rows: bars.rows.map(r => ({ ...r, runs: [] })),\n      },\n    [bars],\n  )\n  if (!bars || !bare || !place || !pitch) {\n    return null\n  }\n  const { paneWidth: width, canvasHeight } = model\n  const Y = (y: number) => y * model.scaleY + model.translateY\n  const hovered = model.hoveredWalkRowText\n    ? [bars.reference, ...bars.rows].findIndex(\n        r => r.name === model.hoveredWalkRow,\n      )\n    : -1\n  const row =\n    hovered >= 0 ? [bars.reference, ...bars.rows][hovered]! : undefined\n  const frame = {\n    scaleX: model.scaleX,\n    scaleY: model.scaleY,\n    translateX: model.translateX,\n    translateY: model.translateY,\n    width,\n    height: canvasHeight,\n    ...pitch,\n  }\n  return (\n    <>\n      {vector ? null : <WalkRowSpansCanvas model={model} />}\n      <svg\n        style={svgStyle}\n        width={width}\n        height={canvasHeight}\n        data-testid=\"graph-walk-rows\"\n      >\n        {walkRowTrees(\n          vector ? bars : bare,\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={Y(header.top) + SECTION_HEADER_PX - 4}\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        {row ? (\n          <rect\n            data-testid=\"graph-walk-row-hovered\"\n            x={bars.origin * model.scaleX + model.translateX - 2}\n            y={Y(place.rowY(hovered)) - 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        ) : null}\n      </svg>\n    </>\n  )\n})\n\nexport default WalkRowsOverlay\n"],
-  "mappings": 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e.layoutResult?.tubeMap&&(this.tubeMapReads||e.chosenColorScheme==="auto")?"uniform":ct(e.chosenColorScheme,e.graph)},get tubeMapReads(){return(e.layoutResult?.tubeMap?.layout.reads.length??0)>0},get colorSchemeLock(){return this.walkLift?{value:"By walk",why:"Each highlighted haplotype colours its own lane: set it under Haplotypes, Color highlighted..."}:this.tubeMapReads?{value:"By strand",why:"Reads take the reds and blues, so the tube map leaves its nodes clear"}:void 0},get nodePositions(){return e.layoutResult?.nodePositions},get labelsNodeSizes(){return!e.layoutResult?.tubeMap&&!this.walkLift},get rowLabels(){return e.layoutResult?.rowLabels??[]},get alleleDeletions(){return e.layoutResult?.alleleDeletions??[]},get deletionRoutes(){return e.layoutResult?.deletionRoutes},get stranded(){return e.layoutResult?.stranded},get pixelRows(){return e.layoutResult?.pixelRows??!1},get zoomPercent(){return`${(e.scale*100).toFixed(1)}%`},get isDefaultViewport(){return e.scale===1&&e.translateX===0&&e.translateY===0}})).views(e=>({get derivedBubbles(){return e.graph?tn(e.graph):[]},get openBubbleInsides(){let{graph:t}=e;return t?e.openBubbles.map(n=>tn(mt(t,we(n)),n).filter(o=>!o.covering)):[]},get openBubble(){return e.openBubbles.at(-1)},get openBubbleFocus(){let t=this.openBubble,{graph:n}=e;if(!t||!n)return;let o=new Set(we(t)),s=new Set(n.nodes.filter(a=>o.has(a.name)).map(a=>a.id)),r=new Set;return n.edges.forEach((a,i)=>{s.has(a.from)&&s.has(a.to)&&r.add(i)}),{walks:[],nodeIds:s,edgeIndexes:r,names:new Set}},bubbleIsOpen(t){return e.openBubbles.some(n=>Bt(n,t))},bubbleFaded({bubble:t,nodeIds:n}){let o=e.walkLift,s=this.openBubbleFocus;return o?!n.some(r=>o.nodeIds.has(r)):!!s&&!this.bubbleIsOpen(t)&&!n.every(r=>s.nodeIds.has(r))}})).views(e=>({get bubbles(){let t=e.indexBubbles?.length?e.indexBubbles:e.derivedBubbles,n=new Set(t.map(Ot));return[...t,...e.openBubbleInsides.flat().filter(o=>!n.has(Ot(o))&&n.add(Ot(o)))]},get foldNote(){let t=e.foldedBelowBp;return t===void 0?void 0:`variants under ${Ue(t)} folded into the reference`}})).views(e=>({get cutHaplotypes(){},get sourceGfaLocation(){},get sourceAdapter(){let t=e.sourceTrack;return t?Kr(e,t):void 0},get sourceTrackId(){let t=e.sourceTrack;return t?H(t,"trackId"):void 0},get assemblyTrackChoices(){let t=e.graphRegion;return t?J(e).tracks.filter(n=>H(n,"assemblyNames").includes(t.assemblyName)).map(n=>({trackId:n.trackId,name:H(n,"name"),adapterType:H(n,"adapter").type})):[]}})).views(e=>({get geneTrackChoices(){return e.assemblyTrackChoices.filter(t=>ht.has(t.adapterType))},get repeatTrackChoices(){return e.assemblyTrackChoices.filter(t=>go.has(t.adapterType))},get repeatChoices(){return e.repeatArrays??[]}})).views(e=>({get repeatTrack(){return pa(e.repeatTrackChoices,e.repeatTrackId)},get geneTrack(){return rn(e.geneTrackChoices,e.geneTrackId)},get selectedRepeat(){return e.repeatChoices.find(t=>t.key===e.repeatKey)},get backbone(){return e.graph?mn(e.graph):void 0},get cutWalkRows(){let t=e.walkCut?.walkRowRuns;return t?wn(t):e.graph?Ce(e.graph,e.graphRegion):void 0},assemblySpellings(t){let{assemblyManager:n}=J(e),o=n.has(t)?n.get(t):void 0,s=e.sourceAdapter?.assemblyNameToPanSN??{},r=[t,...o?[o.name,...o.aliases]:[]];return{name:t,aliases:[...r,...r.flatMap(a=>s[a]??[])]}},get drawsLoadedReference(){let t=e.graph;return t?.anchoredBy==="tags"||t?.referencePath!==void 0&&t.referencePath===e.loadedReferencePath}})).views(e=>({get geneAssembly(){let t=e.graphRegion;return t?e.assemblySpellings(t.assemblyName):void 0},get geneLaneFilter(){let t;try{t=We(e)}catch{return}let n=ha(t,e.geneTrack?.trackId);return n.length?new ua({filters:n,jexl:Lo(e).pluginManager.jexl}):void 0},get geneFeatures(){let t=e.geneTrackFeatures,n=this.geneLaneFilter;return t?ba(n?t.filter(o=>n.passes(o)):t):void 0}})).views(e=>({get backboneGenes(){let{backbone:t,geneAssembly:n,geneFeatures:o}=e,s=e.drawsLoadedReference||n!==void 0&&hn(t,[n])!==void 0;return t&&o&&s?gn(o,t):void 0}})).views(e=>({get nodeNeighbors(){return e.drawnGraph?ce(e.drawnGraph):void 0},get nodeInk(){return Mt(e.drawnGraph,e.nodeById,e.contigThickness,e.nodeWidth)},get allDeletions(){return e.graph&&this.drawsNodes?he(e.graph):[]},get cohortWalkRows(){if(e.chosenLayoutMode!=="walkrows"||!e.graph)return;let t=e.selectedRepeat,n=e.walkCut,o=t?n?Tc(n,t,t.unit):Ce(e.graph,t,t.unit):e.cutWalkRows;if(!o)return;let[s,...r]=zr([o.reference,...o.rows],t?.calls);return{...o,reference:s,rows:r}},get walkRowSampleChoices(){let t=this.cohortWalkRows?.rows??[];return{samples:[...new Set(t.map(n=>n.sample))].sort(),disagreeing:[...new Set(t.filter(n=>n.call?.agrees===!1).map(n=>n.sample))]}},get walkRowSamplesTsv(){let t=e.sourceAdapter?.samplesTsvLocation;return t&&To(t)?t:void 0},get walkRowGroupFields(){return Dr(e.walkRowSampleTable)},get tubeMapColoring(){let t=e.tubeMapColorBy,n=e.walkRowSampleTable;if(!t||!n||!this.walkRowGroupFields.includes(t))return;let o=Or(t,n),s=(e.graph?.paths??[]).map(r=>W(r.name).name).filter(r=>r!==e.graph?.referencePath);return{field:t,valueOf:o,palette:Br(s.map(o)),unvalued:s.some(r=>o(r)==="")}},get tubeMapPanelSplit(){let{field:t,domain:n}=e.facetSetting,o=e.walkRowGroupBy,s=e.walkRowSampleTable;return t!==""?{by:t,domain:n}:o&&s&&this.walkRowGroupFields.includes(o.field)?{by:"column",...o,table:s}:void 0},get walkRowGroups(){let t=this.cohortWalkRows,n=e.walkRowSampleTable,o=e.walkRowGroupBy;return t&&n&&o&&this.walkRowGroupFields.includes(o.field)?Wr(Oe(t.rows,e.walkRowSamples),n,o):void 0},get walkRowBars(){let t=this.cohortWalkRows;return t?{...t,rows:this.walkRowGroups?.rows??Oe(t.rows,e.walkRowSamples)}:void 0},get drawsNodes(){return Q(e.drawnLayoutMode??e.chosenLayoutMode).drawsNodes},get genePins(){pt(e.positionsVersion);let t=e.layoutResult?.nodePositions;return e.showGenes&&this.drawsNodes&&e.graph&&e.backboneGenes&&t?tt(e.graph,e.backboneGenes,t):[]},get bubbleHalos(){pt(e.positionsVersion);let t=e.layoutResult?.nodePositions;return!e.showBubbles||!this.drawsNodes||!e.graph||!t?[]:so(e.graph,e.bubbles,t,e.repeatArrays)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"&&e.drawnGraph?Ee(e.drawnGraph,e.rampDomain):void 0},get assemblyNames(){let t=e.graphRegion;return t?[t.assemblyName]:[]},get scaleX(){return ke(e.scale,e.pixelRows).scaleX},get scaleY(){return ke(e.scale,e.pixelRows).scaleY},get axisScale(){return ke(e.scale,e.pixelRows)}})).views(e=>({get deletionDrawing(){return e.graph?ge(e.graph,e.allDeletions,e.showDeletionEdges):void 0},get deletions(){return this.deletionDrawing?.shown??[]},get deletionEdgeIndexes(){return this.deletionDrawing?.bypassed},get hiddenEdgeIndexes(){return this.deletionDrawing?.hidden},get referenceRampDomain(){let t=e.referenceRamp;return t?{start:t.start,end:t.start+t.span}:void 0},get referenceRampOffKeys(){let t=e.referenceRamp,n=e.layoutResult,o=n?.tubeMap?n.nodePositions:void 0,s=!1,r=!1;if(t&&e.drawnGraph)for(let a of e.drawnGraph.nodes)o&&!o[a.id]||(t.midpoints.has(a.id)?a.stable&&a.stable.rank>0&&(s=!0):r=!0);return{offReference:s,unplaced:r}},get tubeMapNodeColors(){let t=e.drawnGraph;return e.layoutResult?.tubeMap&&t?ut(t,e.effectiveColorScheme,e.referenceRamp):void 0},get tubeMapTubeColors(){let t=e.layoutResult?.tubeMap,n=t?.pathColors,o=e.drawnGraph?.paths,s=e.tubeMapColoring,r=n&&o&&s&&t.layout.reads.length===0?Ft(o,e.drawnGraph.referencePath,s.valueOf,s.palette):n&&o&&this.tubeMapNodeColors?Ze(o,e.drawnGraph.referencePath,$t):n&&o&&t.layout.reads.length===0&&(!Ae(o.length)||o.some(i=>i.members))?Ze(o,e.drawnGraph.referencePath):n,a=new Set(e.hoveredRowWalks);return r&&o&&a.size>0?r.map((i,c)=>a.has(o[c]?.name??"")?i:Te):r},nodeSpan(t){let{nodeById:n,nodeNeighbors:o}=e;return n&&o?St({nodeId:t,nodeById:n,neighbors:o}):void 0},get hoverDrawing(){let t=e.hoveredPanel;return(t===null?void 0:e.layoutResult?.tubeMapPanels?.[t]?.result.tubeMap)??e.layoutResult?.tubeMap}})).views(e=>({get hoverGraph(){return e.hoverDrawing?.graph??e.drawnGraph}})).views(e=>({get hoverNodeById(){let t=e.hoverGraph;return t===e.drawnGraph?e.nodeById:t&&new Map(t.nodes.map(n=>[n.id,n]))},get hoverNeighbors(){let t=e.hoverGraph;return t===e.drawnGraph?e.nodeNeighbors:t&&ce(t)}})).views(e=>({get pathLegend(){let t=e.drawnGraph?.paths,n=e.layoutResult?.tubeMap;return(e.drawPaths||n)&&t&&Ae(t.length)&&!e.layoutResult?.tubeMapPanels&&!e.tubeMapNodeColors&&!t.some(s=>s.members)&&!e.tubeMapColoring?ze(t,e.tubeMapTubeColors):[]},get hoveredSpan(){let t=e.hoveredNode,n=e.hoveredBubble,o=e.hoverNodeById,s=e.hoverNeighbors;return t!==null?o&&s?St({nodeId:t,nodeById:o,neighbors:s}):void 0:n&&!n.offReference?{start:n.start,end:n.end}:void 0}})).views(e=>({get hoverHighlight(){let t=e.graphRegion,n=e.hoveredSpan;return 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fitPadLeft(){return Math.max(G,...this.drawnRowLabels.map(t=>Wo(t.label,0).x1+6))},get layoutBounds(){let t=e.layoutResult,n=e.walkRowBars,o=n&&t?.extent?Ge(n,this.walkRowPitch):void 0;return t?rt(t,{region:e.graphRegion,extent:o&&{...o,maxY:o.maxY+(this.walkRowPlacement?.headersPx??0)}}):void 0},get hoveredWalkRowText(){let t=e.walkRowBars,n=e.hoveredWalkRow;if(!t||n===null||this.walkRowPitch?.readouts!==!1)return;let o=t.reference.name===n,s=o?t.reference:t.rows.find(r=>r.name===n);return s?{label:s.label,readout:Uo(s,o?void 0:t.reference,t.unit,s.call)}:void 0},walkRowAt(t,n){let o=e.walkRowBars,s=this.walkRowPitch,r=this.walkRowPlacement;if(!o||!s||!r)return;let a=r.rowAt((n-e.translateY)/e.scaleY,o.rows.length+1),i=[o.reference,...o.rows][a],c=r.rowY(a)*e.scaleY+e.translateY,d=(t-e.translateX)/e.scaleX-o.origin;return i&&Math.abs(n-c)<=s.barPx/2+2&&d>=0&&d<=i.bp?a:void 0},get fitPadTopBase(){let t=Tr(e.tubeMapGenes);return G+Math.max(0,t-1)*Ar+e.referenceStripZonePx},get legendRoom(){let t=this.layoutBounds,{width:n,height:o}=e.legendSize;if(!t||t.w<=0||n===0||e.facetPanels||e.tubeMapReads)return;if(e.hostPlacesX)return"top";let s=this.fitPadTopBase,r=this.fitRoom,a=l=>(e.paneWidth-this.fitPadLeft-l)/t.w,i=l=>e.pixelRows?t.h+l+G<=r?1/0:0:(r-l-G)/t.h,c=Math.min(a(n+2*ue),i(s));return Math.min(a(G),i(s+o+ue))>=c?"top":"right"},get fitPadTop(){return this.fitPadTopBase+(this.legendRoom==="top"?e.legendSize.height+ue:0)},get fitPadRight(){return this.legendRoom==="right"?Math.max(G,e.legendSize.width+2*ue):G},get minFitScale(){let t=this.layoutBounds,n=e.layoutResult,o=n?.tubeMap?.layout.tracks[0]?.width;return t&&t.h>0&&o&&!n.referenceAxis?Math.min(Js/o,(this.paneCeiling-this.fitPadTop-G)/t.h):0},get facetSpec(){let{field:t,domain:n,columns:o}=e.facetSetting;return t===""?void 0:n.length===0&&o===void 0?t:{field:t,domain:[...n],...o===void 0?{}:{columns:o}}},get facetPlacement(){let t=e.facetPanels,{field:n,domain:o}=e.facetSetting;return t?Et(t.map(s=>s.walks[0].name),e.hostPlacesX||n===""?"walk":n,o):void 0},facetGridIn(t){let n=this.facetPlacement,o=this.layoutBounds;return n&&o&&o.w>0?At({count:n.count,bounds:o,pixelRows:e.pixelRows,width:e.paneWidth,room:t,columns:e.hostPlacesX?1:n.columns??e.facetSetting.columns}):void 0},get facetGrid(){return this.facetGridIn(this.fitRoom-Ba)},get tooltipRightPx(){let{width:t,height:n}=e.legendSize,o=ue+e.referenceStripZonePx+n;return!e.facetPanels&&t>0&&o>this.canvasHeight-Wc?t+2*ue:Dc},get canvasHeight(){let t=this.layoutBounds,n=e.paneWidth-G-this.fitPadRight,o=this.paneCeiling;if(!t)return o;let s=this.facetGrid;if(s)return Math.max(Zt,s.total+Ba);let r=Math.max(Zt,e.legendSize.height+2*ue+e.referenceStripZonePx);return e.pixelRows?Math.min(o,Math.max(r,t.h+this.fitPadTop+G)):t.w>0&&n>0?Math.min(o,Math.max(r,t.h*Math.max(n/t.w,this.minFitScale)+this.fitPadTop+G)):o},get viewBox(){let t=this.facetGrid;return t?{width:t.width,height:t.height}:{width:e.paneWidth,height:this.canvasHeight}},get fittedTransform(){let t=this.layoutBounds,n=this.facetGrid;return t?n?$e(t,n.width,n.height,e.pixelRows,{padLeft:oe,padTop:oe,padRight:oe,padBottom:oe}):$e(t,e.paneWidth,this.canvasHeight,e.pixelRows,{minScale:this.minFitScale,padLeft:this.fitPadLeft,padTop:this.fitPadTop,padRight:this.fitPadRight}):void 0}})).views(e=>({viewportToBuild(){return Yn(na(e),ea)},applySelection(t){let n=e.selectedNode;t.setNodeHighlights(n===null?new Map:new Map([[n,Qs]]))},get hoverLayerNode(){let{litNode:t,selectedNode:n}=e;return t===n?null:t},get paintTransform(){let t=In();return{scaleX:e.scaleX*t,scaleY:e.scaleY*t,translateX:e.translateX*t,translateY:e.translateY*t,dpr:t}}})).views(e=>({paint(t){t.updateTransform(e.paintTransform),t.render(e.referenceStripShown?[0,0,0,0]:e.darkMode?en:Qt)}})).views(e=>({buildDrawing(t,n){let{graph:o,nodeById:s,layoutResult:r,deletionDrawing:a}=e;if(!o||!s||!r||!a)return;pt(e.viewportDirty,e.positionsVersion);let i=yn(()=>e.viewportToBuild()),c=vt({...st(r,a,{drawsRows:!!e.walkRowBars}),graph:o,nodeById:s,colorScheme:e.effectiveColorScheme,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,drawPaths:n,nodeWidth:e.nodeWidth,highlight:t,axis:yn(()=>e.axisScale),linearLayout:e.linearLayout,viewportBounds:i,referenceRamp:e.referenceRamp,version:e.positionsVersion}),d=e.morphEntering;return d?.layout===r&&Ea(c,o.edges,d),{batch:c,viewportBounds:i}},get overlayLabels(){return fr(e)},hoveredOn(t){let n=e.hoveredNode,o=n?e.nodeById?.get(n):void 0;return o?br(t,o.id,o.length)??"not on this walk":void 0},figureSpec(){let t=e.graphRegion,n=e.sourceAdapter,o=n?.assemblyNameToPanSN,s=t&&`${t.refName}:${t.start}-${t.end}`,r=De(e.sourceGfaLocation),a=n?.type==="GbzBaseSyntenyAdapter"?De(n.gbzDbLocation):void 0,i=r?{gfa:r,region:s}:a&&t&&s?{gbz:{db:a,index:De(n.haplotypeIndexLocation),region:s,haplotypes:e.cutHaplotypes?.map(u=>o?.[u]??u),referenceSample:n.referenceSample||o?.[t.assemblyName]||t.assemblyName,context:n.context,snarls:e.cutsWholeWalks?"overlapping":n.subgraphSnarls}}:void 0;if(!i)return;let c=e.showGenes?e.geneTrack:void 0,d=c?J(e).tracks.find(u=>u.trackId===c.trackId):void 0,l=d?Ao(H(d,"adapter"),"gffGzLocation"):void 0,p=l?.type==="Gff3TabixAdapter"?{file:De(l.gffGzLocation),index:De(l.index?.location),format:"gff3"}:void 0;return JSON.parse(JSON.stringify({...i,genes:p?.file&&p.index?p:void 0,referencePath:e.referencePath||void 0,layout:e.chosenLayoutMode,...Un({engine:e.layoutEngine,quality:e.layoutQuality,linearLayout:e.linearLayout,bubbleSpread:e.bubbleSpread,showDeletionEdges:e.showDeletionEdges,colorScheme:e.chosenColorScheme,nodeWidth:e.nodeWidth,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,colorDomain:e.statedColorDomain}),walks:e.walkLayers.length?e.walkLayers.map(u=>u.color?u:u.walk):void 0,facet:e.walkLayers.length>1?e.facetSpec:void 0,walkStrip:e.walkStripShown||void 0,walkRowSamples:e.walkStripShown?e.walkRowSamples:void 0,width:e.paneWidth,height:e.paneCeiling}))},get figureUnavailable(){return e.layoutResult?e.walkRowGroups?"The SVG export cannot group walk rows yet: set Group by... to None first":e.drawsNodes||e.walkRowBars?void 0:`${Q(e.chosenLayoutMode).label} draws a picture of its own, which the SVG export does not`:"Nothing is drawn yet"},get figureSpecUnavailable(){return e.drawsNodes?this.figureSpec()?void 0:"bandage-figure reads a graph cut from a gbz-base 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t?qt(t,{scaleX:e.scaleX,translateX:e.translateX,scaleY:e.scaleY,translateY:e.translateY,usableHeight:e.canvasHeight-e.fitPadTop-G}):void 0}})).views(e=>({get tubeMapRulerBoxes(){let t=e.tubeMapReference;return t&&!e.hostPlacesX&&!e.layoutResult?.tubeMapPanels?On(t):void 0},get tubeMapPanelRulerBoxes(){let{layoutResult:t}=e,n=t?.tubeMapPanels?.at(-1);return n&&t?.referenceAxis&&!e.hostPlacesX?On(Ct(n.result.tubeMap)):void 0},get connectorZoneBottom(){let t=e.tubeMapPicture,n=e.tubeMapFrame;return t&&n?n.y(t.bounds.minY)-2:0},get tubeMapConnectors(){let t=e.tubeMapConnectedBoxes,n=e.tubeMapFrame,o=t&&n?e.hostBpFrame:void 0;return t&&n&&o?wr(t,s=>s*o.scale+o.translateX,n.x,e.paneWidth):[]},get tubeMapPanelPictures(){let t=e.layoutResult?.tubeMapPanels;if(!t)return;let n=new Set(e.hoveredRowWalks),o=e.tubeMapColoring,s=a=>{let i=a.paths??[];return(o?Ft(i,a.referencePath,o.valueOf,o.palette):Ze(i,a.referencePath)).map((d,l)=>{let p=i[l].name;return n.size>0&&!n.has(p)&&W(p).name!==a.referencePath?Te:d})},{field:r}=e.facetSetting;return t.map(a=>{let i=a.result.tubeMap,{graph:c,coarse:d}=i;return{panel:a,label:a.label??(r==="walk"?e.walkLabel(a.paths[0]):a.key),picture:_t(i),tubeColors:s(c),nodeColors:e.tubeMapNodeColors?ut(c,e.effectiveColorScheme,e.referenceRamp):void 0,deviations:d?Gt(i,d.deviations):[]}})}})).views(e=>({get hoveredMember(){let t=e.hoveredNode,n=t===null?void 0:e.hoverDrawing?.members.get(t);if(!n)return t;let o=e.hoveredAt,s=e.hoveredPanel,r=s===null?void 0:this.tubeMapPanelViews?.[s],a;return r?.panel.result.tubeMap.layout.nodes.forEach(c=>{c.name===t&&(a=c)}),(o&&r&&a?Gr(n,c=>e.nodeSpan(c),r.frame.x(a.x),r.frame.x(a.x+a.pixelWidth),o.x):void 0)??n[0]},get tubeMapPanelHover(){let t=e.hoveredNode,n=e.tubeMapPanelPictures;if(t===null||!n)return;let o=this.hoveredMember??t;return n.map(({panel:s})=>{let r=s.result.tubeMap,a=Cr(r,o);return a?{box:a,..._r(r.graph,a)}:void 0})},get tubeMapPanelViews(){let t=e.tubeMapPanelPictures,n=e.layoutResult;if(!t||!n)return;let o=t.length*Cn,s=t.reduce((c,d)=>c+d.panel.height,0),r=e.canvasHeight-e.fitPadTop-G-o,a=e.scaleY*(n.referenceAxis&&s>0?Math.max(Xc,Math.min(1,r/s)):1),i=e.translateY;return t.map(c=>{let{panel:d}=c,l=d.result.extent?.minY??0,p=i,u=p+Cn;return i=u+d.height*a,{...c,frame:qt(d.result.tubeMap,{scaleX:e.scaleX,translateX:e.translateX,scaleY:a,translateY:u-l*a,usableHeight:1/0}),titleTop:p,top:u,bottom:i}})}})).views(e=>({tubeMapPanelAt(t){let n=e.tubeMapPanelViews?.findIndex(o=>o.titleTop<=t&&t<=o.bottom)??-1;return n<0?null:n}})).views(e=>({paintHover(t,n){let o=e.tubeMapPicture,s=e.tubeMapFrame,r=e.hoverLayerNode;if(o&&s){let{ctx:a,canvas:i}=t,c=In();a.setTransform(1,0,0,1,0,0),a.clearRect(0,0,i.width,i.height),a.setTransform(c,0,0,c,0,0);let 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