jbrowse-plugin-graphgenomeviewer 7.1.2 → 7.1.4

package/dist/chunks/chunk-RP3L3Z5W.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/LabelChip.tsx", "../../src/GraphGenomeView/components/LabelLayer.tsx", "../../src/GraphGenomeView/components/GenePins.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 type { GraphPaneModel } from '../model'\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  children,\n}: {\n  model: GraphPaneModel\n  zIndex: number\n  overflow?: 'hidden' | 'visible'\n  testId?: string\n  children: ReactNode\n}) {\n  return (\n    <svg\n      style={paneLayerStyle(zIndex, overflow)}\n      width={model.paneWidth}\n      height={model.canvasHeight}\n      data-testid={testId}\n    >\n      {children}\n    </svg>\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        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 } 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 { scaleX, scaleY, translateX, translateY } = model\n  const halo = model.contigThickness * HALO_FACTOR\n  return (\n    <PaneSvgLayer model={model} zIndex={2} testId=\"graph-bubble-halos\">\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    </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  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\nconst BAR_PX = 48\n\n// getNodeColor's grey for a node the ramp cannot place\nconst 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\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: ${halo?.label ?? 'bubble'}`,\n      swatch: halo\n        ? { kind: 'halo', color: BUBBLE_KIND_COLORS[halo.kind] }\n        : { kind: 'blank' },\n      closesBubble: true,\n    },\n  ]\n}\n\n// Under lifted walks each lane states its own scale, and the rest is grey\nfunction rampRows(model: GraphPaneModel): LegendRow[] {\n  const domain = model.walkLift ? undefined : model.referenceRampDomain\n  if (!domain) {\n    return []\n  }\n  // a measured domain runs between node midpoints, which can fall on a half bp\n  const start = Math.round(domain.start)\n  const end = Math.round(domain.end)\n  const { offReference, unplaced } = model.referenceRampOffKeys\n  return [\n    {\n      key: 'ramp',\n      label: `${start.toLocaleString('en-US')}-${end.toLocaleString('en-US')} (${formatBp(end - start)})`,\n      swatch: { kind: 'fill', stops: RAMP_GRADIENT_STOPS, width: BAR_PX },\n    },\n    ...(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 ${rowPerWalk ? \"that row's walk\" : model.liftedWalksLabel}`\n              : 'reference outside the open bubble',\n          ),\n        ]\n      : []),\n    ...(model.referenceStripOverhangs\n      ? [\n          {\n            key: 'overhang',\n            label: 'graph runs past this edge',\n            swatch: { kind: 'overhang' } as const,\n          },\n        ]\n      : []),\n  ]\n}\n\n// One row per halo colour drawn, naming the kinds it stands for\nfunction haloRows(model: GraphPaneModel): LegendRow[] {\n  const kindsByColor = new Map<string, Set<string>>()\n  for (const h of model.bubbleHalos) {\n    if (!h.whole) {\n      const color = BUBBLE_KIND_COLORS[h.kind]\n      const kinds = kindsByColor.get(color) ?? new Set<string>()\n      kinds.add(BUBBLE_KIND_NAMES[h.kind])\n      kindsByColor.set(color, kinds)\n    }\n  }\n  return [...kindsByColor].map(([color, kinds]) => {\n    const names = [...kinds].join(' or ')\n    return {\n      key: `halo-${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 < ${formatBp(foldBp)}`,\n      swatch: {\n        kind: 'tick',\n        color: deviationInk(),\n        height: TUBE_SWATCH_PX,\n        backing: FOLD_TICK_BACKING,\n      },\n    })\n  }\n  if (logWidths) {\n    rows.push({\n      key: 'log',\n      label: 'width grows with log of length',\n      swatch: { kind: 'bracket' },\n    })\n  }\n  return rows\n}\n\nexport function walkRowSwatch(swatch: KeySwatch): LegendSwatch {\n  return swatch.kind === 'gene'\n    ? {\n        kind: 'outline',\n        color: GENE_INK,\n        stroke: 1.5,\n        radius: 0,\n        height: WALK_ROW_SWATCH_PX,\n      }\n    : {\n        kind: 'fill',\n        stops:\n          swatch.kind === 'bar' && swatch.ramp\n            ? RAMP_GRADIENT_STOPS\n            : flat(swatch.fill),\n        height: swatch.kind === 'gap' ? GAP_PX : WALK_ROW_SWATCH_PX,\n      }\n}\n\n// The walk rows' bar colours, genes and ticks; each tick row appears once\n// the rows hold one, so a catalogue with no genotypes keeps the plain key\nfunction walkRowsRows(model: GraphPaneModel): LegendRow[] {\n  const bars = model.walkRowBars\n  if (!bars) {\n    return []\n  }\n  const calls = [bars.reference, ...bars.rows].flatMap(row => row.call ?? [])\n  const tick = (key: string, color: string, label: string): LegendRow => ({\n    key,\n    label,\n    swatch: { kind: 'tick', color, height: WALK_ROW_SWATCH_PX },\n  })\n  return [\n    ...walkRowsKey(bars, {\n      ramp: model.referenceRampDomain,\n      genes: model.walkRowGeneKey,\n    }).map(entry => ({\n      key: `rows-${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// 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 { 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    >\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 model={model} zIndex={3} testId=\"graph-label-layer\">\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    </PaneSvgLayer>\n  )\n})\n\nexport default LabelLayer\n", "import {\n  exonOutlineTree,\n  exonStretches,\n} from '@jbrowse/bandage-core/genes/exonOutline'\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-${useSvgId()}`\n  const { genePins, walkLift, nodeInk } = model\n  const { scaleX, scaleY, translateX, translateY, paneWidth, canvasHeight } =\n    model\n  // an open bubble rings only its own exons\n  const focus = walkLift ? undefined : model.openBubbleFocus\n  const pins = focus\n    ? genePins.map(pin => ({\n        ...pin,\n        exonsByNode: pin.exonsByNode.filter(e => focus.nodeIds.has(e.nodeId)),\n      }))\n    : genePins\n  const tree = exonOutlineTree(\n    exonStretches(pins, nodeInk.halfWidthPx, walkLift),\n    {\n      id,\n      width: paneWidth,\n      height: canvasHeight,\n      transform: `translate(${translateX} ${translateY}) scale(${scaleX} ${scaleY})`,\n    },\n  )\n  return tree ? (\n    <PaneSvgLayer model={model} zIndex={2} testId=\"graph-gene-pins\">\n      <ElTree el={tree} />\n    </PaneSvgLayer>\n  ) : null\n})\n\nexport default GenePins\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  coalesceRuns,\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  // where each drawn row's spans start in `bars` and `gaps`\n  barRows: Uint32Array\n  gapRows: 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.\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  let longest = 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        longest = Math.max(longest, c.x2[i])\n      }\n    }\n    barRows[row + 1] = bars.count\n    gapRows[row + 1] = gaps.count\n  })\n  return {\n    bars: slice(bars, 0, bars.count),\n    gaps: slice(gaps, 0, gaps.count),\n    barRows,\n    gapRows,\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    ] 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// `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  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 hovered = model.hoveredWalkRowText\n    ? [bars.reference, ...bars.rows].findIndex(\n        r => r.name === model.hoveredWalkRow,\n      )\n    : -1\n  const lit =\n    hovered >= 0\n      ? {\n          row: [bars.reference, ...bars.rows][hovered]!,\n          start: model.toScreen({ x: bars.origin, y: place.rowY(hovered) }),\n        }\n      : undefined\n  const frame = {\n    ...model.screenTransform,\n    width,\n    height: canvasHeight,\n    ...pitch,\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          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={\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        {lit ? (\n          <rect\n            data-testid=\"graph-walk-row-hovered\"\n            x={lit.start.x - 2}\n            y={lit.start.y - pitch.rowPx / 2 - 1}\n            width={lit.row.bp * model.scaleX + 4}\n            height={pitch.rowPx + 2}\n            fill=\"none\"\n            stroke=\"#111\"\n            strokeWidth={1}\n          />\n        ) : null}\n      </PaneSvgLayer>\n    </>\n  )\n})\n\nexport default WalkRowsOverlay\n"],
+  "mappings": 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+  "names": ["paneLayerStyle", "zIndex", "overflow", "PaneSvgLayer", "observer", "model", "testId", "children", "jsx", "PaneOverlayCanvas", "shown", "paint", "ref", "useRef", "useEffect", "autorun", "canvas", "ctx", "width", "height", "dpr", "syncCanvasSize", "BubbleHalos", "observer", "model", "bubbleHalos", "hoveredBubble", "scaleX", "scaleY", "translateX", "translateY", "halo", "HALO_FACTOR", "jsx", "PaneSvgLayer", "h", "sameBubble", "BUBBLE_KIND_COLORS", "bubbleKey", "BubbleHalos_default", "SWATCH_PX", "BAR_PX", "UNPLACED_SWATCH", "FADED_SWATCH", "STRIP_SAMPLES", "TUBE_SWATCH_PX", "FOLD_TICK_BACKING", "WALK_ROW_SWATCH_PX", "swatchWidth", "swatch", "flat", "color", "fillRow", "key", "label", "width", "bandStops", "colors", "i", "openBubbleRows", "model", "open", "halo", "h", "sameBubble", "BUBBLE_KIND_COLORS", "rampRows", "domain", "start", "end", "offReference", "unplaced", "formatBp", "RAMP_GRADIENT_STOPS", "REFERENCE_RAMP_ALT_CSS", "stripBands", "lift", "w", "encodingStops", "b", "c", "all", "n", "LIFT_BACKDROP_CSS", "_", "stripRows", "rowPerWalk", "haloRows", "kindsByColor", "kinds", "BUBBLE_KIND_NAMES", "names", "geneRows", "pin", "EXON_COLOR", "foldRows", "note", "pathRows", "name", "tubeRow", "stops", "tubeMapRows", "roles", "haplotypeTube", "bundled", "values", "logWidths", "foldBp", "forwardReads", "reverseReads", "substitution", "insertion", "deletion", "reads", "rows", "PANEL_REFERENCE_TUBE", "value", "FORWARD_READ_COLORS", "REVERSE_READ_COLORS", "deviationInk", "walkRowSwatch", "GENE_INK", "GAP_PX", "walkRowsRows", "bars", "calls", "row", "tick", "walkRowsKey", "entry", "call", "CALL_TICK", "UNBACKED_TICK", "DISAGREES", "walkKeyRow", "walk", "walkKey", "fadedRows", "faded", "walkReadoutRows", "facetKeyRows", "legendSections", "section", "propName", "name", "_", "c", "toReact", "node", "key", "props", "value", "createElement", "useSvgId", "useId", "ElTree", "el", "Gradient", "id", "x", "y", "stops", "width", "height", "square", "rect", "fill", "jsx", "jsxs", "Fragment", "s", "i", "bandPx", "bands", "swatchHeight", "swatch", "SvgSwatch", "swatchWidth", "band", "top", "SWATCH_PX", "inset", "rulerInk", "LegendSwatchView", "useSvgId", "chipBox", "x", "y", "w", "LABEL_PX", "LABEL_PAD", "inChip", "chip", "px", "py", "box", "LabelChip", "text", "note", "color", "edge", "italic", "dimmed", "title", "testId", "onClick", "onHover", "jsxs", "jsx", "GENE_INK", "TICK_PX", "TICK_WIDTH", "chipReadoutAt", "genes", "px", "py", "pin", "chip", "inChip", "gene", "note", "geneCoverageNote", "LabelLayer", "observer", "model", "bubbles", "ticks", "scaleY", "translateY", "contigThickness", "hoveredBubble", "hoveredTick", "t", "sameBubble", "tickAt", "target", "dimmedBubble", "h", "isOpen", "jsxs", "PaneSvgLayer", "jsx", "e", "tick", "isAlive", "x", "y", "i", "BUBBLE_KIND_COLORS", "bubbleKey", "w", "text", "LABEL_PX", "LabelChip", "EXON_COLOR", "hovered", "labelWidth", "LabelLayer_default", "GenePins", "observer", "model", "id", "useSvgId", "genePins", "walkLift", "nodeInk", "scaleX", "scaleY", "translateX", "translateY", "paneWidth", "canvasHeight", "focus", "pins", "pin", "e", "tree", "exonOutlineTree", "exonStretches", "jsx", "PaneSvgLayer", "ElTree", "GenePins_default", "paintReferenceStrip", "ctx", "model", "lit", "dpr", "frame", "drawReferenceStrip", "ReferenceStripOverlay", "observer", "paint", "useCallback", "jsx", "PaneOverlayCanvas", "ReferenceStripOverlay_default", "PANEL_TICK_ALPHA", "paintTubeMap", "ctx", "model", "highlightNode", "picture", "frame", "width", "panels", "paintPanels", "tubeFrame", "drawTubeMap", "drawn", "drawBundleCounts", "drawSqueezedLengths", "drawDeviationMarks", "drawTubeMapConnectors", "bounds", "drawTubeMapGenes", "boxes", "drawTubeMapRuler", "p", "PANEL_TITLE_FONT", "last", "TubeMapOverlay", "observer", "paint", "useCallback", "jsx", "PaneOverlayCanvas", "TubeMapOverlay_default", "host", "read", "name", "spanMark", "read", "marks_default", "host", "cssRgb", "css", "v", "a", "b", "c", "hslToRgb", "abgr", "r", "g", "packAbgr", "cssAbgr", "packCss", "runPieces", "run", "ramp", "pxPerBp", "end", "paint", "runPaint", "stops", "hues", "hueSpan", "n", "pieces", "k", "t", "i", "f", "j", "channels", "capacity", "slice", "walkRowSpans", "rows", "coalesceRuns", "total", "runs", "bars", "gaps", "barRows", "gapRows", "longest", "row", "x", "x2", "color", "paintWalkRowSpans", "ctx", "spans", "block", "frame", "rowHeight", "first", "count", "rowY", "scrollTop", "top", "starts", "barPx", "GAP_PX", "spanMark", "WalkRowSpansCanvas", "model", "spans", "useMemo", "computed", "bars", "walkRowSpans", "paint", "useCallback", "ctx", "place", "pitch", "painted", "sections", "blocks", "s", "paintWalkRowSpans", "jsx", "PaneOverlayCanvas", "WalkRowsOverlay", "observer", "vector", "idPrefix", "useSvgId", "bare", "r", "width", "canvasHeight", "hovered", "lit", "frame", "jsxs", "Fragment", "PaneSvgLayer", "walkRowTrees", "tree", "i", "ElTree", "header", "SECTION_HEADER_PX", "WalkRowsOverlay_default"]
+}

package/dist/chunks/{chunk-FITPB5X6.js → chunk-VQUMZEGN.js}

@@ -1,2 +1,2 @@
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package/dist/chunks/renderSvg-V4OYQTQZ.js

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+import{c as B,f as C,h as $,i as O,j,k as W,n as X,o as H,p as A,r as z,t as F}from"./chunk-RP3L3Z5W.js";import{K as S,L,Qa as M,Ra as E,Za as R}from"./chunk-LELA7BG7.js";import"./chunk-VQUMZEGN.js";import{k as P}from"./chunk-WAMBI7OX.js";import"./chunk-W6EQLQ6H.js";import"./chunk-N6PQZSAX.js";import"./chunk-TUKJRVBS.js";import"./chunk-ZMOMFU2B.js";import"./chunk-NDRLCGPC.js";import"./chunk-YU7T5WOQ.js";import{a as v,b as e,c as f}from"./chunk-JMBDTNUR.js";var m=JBrowseExports["@jbrowse/display-kit/renderDisplaySvg"],U=t=>m!=null&&t in Object(m)?m[t]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+t+"' from '@jbrowse/display-kit/renderDisplaySvg' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:t});var Y=U("renderDisplaySvg");var ot=m&&m.__esModule?m.default:m;var w=JBrowseExports["@jbrowse/core/util/paintLayer"],Z=t=>w!=null&&t in Object(w)?w[t]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+t+"' from '@jbrowse/core/util/paintLayer' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:t}),G=Z("PaintLayer"),lt=w&&w.__esModule?w.default:w;var k={fontFamily:"sans-serif",fontSize:11},x=16,q=2,J=t=>t;function N({model:t,lift:n,drawPaths:o,width:r,height:a,rasterize:s}){let l=t.buildDrawing(n,o);if(!l)return null;let c=s?q:1,g=s?void 0:M(r,a),h=g?.canvas??document.createElement("canvas");g||(h.width=Math.round(r*c),h.height=Math.round(a*c));let{scaleX:u,scaleY:y,translateX:i,translateY:p}=t.screenTransform,d=new E(h);return d.uploadGeometry(l.batch),d.updateTransform({scaleX:u*c,scaleY:y*c,translateX:i*c,translateY:p*c,dpr:c}),d.render([0,0,0,0]),g?e("svg",{width:r,height:a,overflow:"hidden",children:e("g",{dangerouslySetInnerHTML:{__html:g.markup()}})}):e("image",{width:r,height:a,href:h.toDataURL("image/png")})}function D(t,n){if(!t.swatch)return{key:t.key,width:t.label.length*P,height:x,draw:s=>e("text",{...k,x:s,y:0,fill:"#666",children:t.label},t.key)};let o=t.swatch,r=C(o),a=(t.strong??"")+t.label;return{key:t.key,width:Math.max(r+5+a.length*P,(t.under?.length??0)*P),height:t.under?x*2:x,draw:s=>f("g",{...k,children:[e(W,{swatch:o,x:s,id:n}),f("text",{x:s+r+5,y:0,children:[t.strong?e("tspan",{fontWeight:"bold",children:t.strong}):null,t.label]}),t.under?e("text",{x:s,y:x,children:t.under}):null]},t.key)}}function Q({model:t,idPrefix:n}){let o=j(t).map(({testid:i,rows:p})=>p.map((d,b)=>D(d,`${n}-${i}-${b}`)));if(o.length===0)return null;let r=6,a=o.flat(),s=Math.max(...a.map(i=>i.width))+r*2,l=a.reduce((i,p)=>i+p.height,0)+o.length*r,g=t.paneWidth-R-s+r,h=R+t.referenceStripZonePx,u=[],y=h+12-r/2;for(let i of o){y+=r;for(let p of i)u.push({row:p,y}),y+=p.height}return f("g",{"data-testid":"graph-svg-keys",children:[e("rect",{x:g-r,y:h,width:s,height:l,rx:3,fill:"#fff",fillOpacity:.82}),u.map(({row:i,y:p})=>e("g",{transform:`translate(0 ${p})`,children:i.draw(g)},i.key))]})}function K({x:t,y:n,text:o,fontSize:r,anchor:a,bold:s}){let l=o.length*r*.56+6,c=a==="middle"?t-l/2:t-3;return f(v,{children:[e("rect",{x:c,y:n-r*.65,width:l,height:r*1.3,rx:3,fill:"#fff",fillOpacity:.8}),e("text",{x:t,y:n+r*.35,textAnchor:a,fontSize:r,fontWeight:s?600:void 0,fill:"#18181c",children:o})]})}function tt({model:t}){return e("g",{fontFamily:k.fontFamily,children:t.overlayLabels.sizes.map(({key:n,text:o,x:r,y:a,kind:s,leader:l})=>f("g",{children:[l?e("line",{x1:l.arcX,y1:l.arcY,x2:l.labelX,y2:l.labelY,stroke:"#18181c"}):null,e(K,{x:r,y:a,text:o,fontSize:10,anchor:"middle",bold:s==="deletion"})]},n))})}function et({model:t}){return e("g",{fontFamily:k.fontFamily,children:t.visibleRowLabels.map(({label:n,y:o,top:r})=>e(K,{x:10,y:r,text:n,fontSize:11,anchor:"start"},o))})}function rt({model:t,rasterize:n,idPrefix:o}){let r=t.facetPanels,a=t.facetGrid,s=t.facetPlacement;if(!r||!a||!s)return null;let{columns:l,width:c,height:g}=a,h=a.total+S+14,u=O(t).map((i,p)=>D(i,`${o}-facet-key-${p}`)),y=u.map((i,p)=>u.slice(0,p).reduce((d,b)=>d+b.width+14,6));return f(v,{children:[e("g",{transform:`translate(0 ${h})`,children:u.map((i,p)=>i.draw(y[p]))}),r.map((i,p)=>{let d=s.cells[p],b=d%l*(c+S),I=Math.floor(d/l)*(L+g+S),_=i.walks[0],V=D($(t,_),`${o}-facet-${p}`);return f("g",{transform:`translate(${b} ${I})`,children:[e("g",{transform:`translate(0 ${x-2})`,children:V.draw(6)}),e("g",{transform:`translate(0 ${L})`,children:e(N,{model:t,lift:i,drawPaths:!1,width:c,height:g,rasterize:n})})]},_.name)})]})}function T({model:t,rasterize:n=!1,idPrefix:o}){let r=t.paneWidth,a=t.canvasHeight,s=!!t.layoutResult?.tubeMap,l={rasterizeLayers:n};return f("g",{"data-testid":"graph-pane-svg",children:[t.facetPanels?e(rt,{model:t,rasterize:n,idPrefix:o}):s?e(G,{width:r,height:a,opts:l,paint:c=>{z(J(c),t,{highlightNode:null})}}):e(N,{model:t,lift:t.drawnHighlight,drawPaths:t.effectiveDrawPaths,width:r,height:a,rasterize:n}),t.facetPanels?null:f(v,{children:[e(B,{model:t}),e(H,{model:t}),e(tt,{model:t}),e(X,{model:t}),e(F,{model:t,vector:!0}),e(et,{model:t})]}),t.referenceStripShown?e(G,{width:r,height:a,opts:l,paint:c=>{A(J(c),t,{lit:void 0,dpr:1})}}):null,t.facetPanels?null:e(Q,{model:t,idPrefix:o})]})}function nt({model:t,opts:n}){return e(T,{model:t,rasterize:!!n?.rasterizeLayers,idPrefix:`graph-${t.id}`})}function Gt(t,n){return Y(t,n,nt)}export{Gt as renderGraphTrackSvg};
+//# sourceMappingURL=renderSvg-V4OYQTQZ.js.map

package/dist/chunks/renderSvg-V4OYQTQZ.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["host:@jbrowse/display-kit/renderDisplaySvg", "host:@jbrowse/core/util/paintLayer", "../../src/GraphGenomeView/components/PaneSvg.tsx", "../../src/LinearGraphDisplay/renderSvg.tsx"],
+  "sourcesContent": ["const host = JBrowseExports[\"@jbrowse/display-kit/renderDisplaySvg\"]\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/display-kit/renderDisplaySvg\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const SvgLegend = /* @__PURE__ */ read(\"SvgLegend\")\nexport const SvgPinnedHighlight = /* @__PURE__ */ read(\"SvgPinnedHighlight\")\nexport const SvgYAxis = /* @__PURE__ */ read(\"SvgYAxis\")\nexport const exportsTooLargeNote = /* @__PURE__ */ read(\"exportsTooLargeNote\")\nexport const renderDisplaySvg = /* @__PURE__ */ read(\"renderDisplaySvg\")\nexport const svgSidebarWidthOf = /* @__PURE__ */ read(\"svgSidebarWidthOf\")\nexport default host && host.__esModule ? host.default : host", "const host = JBrowseExports[\"@jbrowse/core/util/paintLayer\"]\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/core/util/paintLayer\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const PaintLayer = /* @__PURE__ */ read(\"PaintLayer\")\nexport default host && host.__esModule ? host.default : host", "import { FACET_GAP_PX, FACET_TITLE_PX } from '@jbrowse/bandage-core/facetGrid'\nimport { LEGEND_INSET_PX } from '@jbrowse/bandage-core/labelLayout'\nimport { LABEL_CHAR_PX } from '@jbrowse/bandage-core/overlayLabels'\nimport { Canvas2DRenderer } from '@jbrowse/bandage-core/renderer/Canvas2DRenderer'\nimport { svgCanvas } from '@jbrowse/bandage-core/renderer/svgCanvas'\nimport { PaintLayer } from '@jbrowse/core/util/paintLayer'\n\nimport BubbleHalos from './BubbleHalos'\nimport GenePins from './GenePins'\nimport LabelLayer from './LabelLayer'\nimport { SvgSwatch } from './LegendSwatch'\nimport { paintReferenceStrip } from './ReferenceStripOverlay'\nimport { paintTubeMap } from './TubeMapOverlay'\nimport WalkRowsOverlay from './WalkRowsOverlay'\nimport {\n  facetKeyRows,\n  legendSections,\n  swatchWidth,\n  walkKeyRow,\n} from '../legendSections'\n\nimport type { LegendRow } from '../legendSections'\nimport type { GraphPaneModel } from '../model'\nimport type { WalkLift } from '@jbrowse/bandage-core/walkHighlight'\nimport type { Ctx2D } from '@jbrowse/core/util/paintLayer'\n\nconst FONT = { fontFamily: 'sans-serif', fontSize: 11 }\nconst ROW_PX = 16\nconst RASTER_SCALE = 2\n\nconst asCanvasCtx = (ctx: Ctx2D) => ctx as CanvasRenderingContext2D\n\n// The drawing's nodes and edges through the pane's own transform, so the\n// export lines up with the linear view's ruler wherever the screen does\nfunction Body({\n  model,\n  lift,\n  drawPaths,\n  width,\n  height,\n  rasterize,\n}: {\n  model: GraphPaneModel\n  lift: WalkLift | undefined\n  drawPaths: boolean\n  width: number\n  height: number\n  rasterize: boolean\n}) {\n  const built = model.buildDrawing(lift, drawPaths)\n  if (!built) {\n    return null\n  }\n  const k = rasterize ? RASTER_SCALE : 1\n  const vector = rasterize ? undefined : svgCanvas(width, height)\n  const canvas = vector?.canvas ?? document.createElement('canvas')\n  if (!vector) {\n    canvas.width = Math.round(width * k)\n    canvas.height = Math.round(height * k)\n  }\n  const { scaleX, scaleY, translateX, translateY } = model.screenTransform\n  const renderer = new Canvas2DRenderer(canvas)\n  renderer.uploadGeometry(built.batch)\n  renderer.updateTransform({\n    scaleX: scaleX * k,\n    scaleY: scaleY * k,\n    translateX: translateX * k,\n    translateY: translateY * k,\n    dpr: k,\n  })\n  renderer.render([0, 0, 0, 0])\n  return vector ? (\n    <svg width={width} height={height} overflow=\"hidden\">\n      <g dangerouslySetInnerHTML={{ __html: vector.markup() }} />\n    </svg>\n  ) : (\n    <image width={width} height={height} href={canvas.toDataURL('image/png')} />\n  )\n}\n\ninterface KeyRow {\n  key: string\n  width: number\n  height: number\n  draw: (left: number) => React.ReactNode\n}\n\n// A legend row as the screen lays it out: its swatch, then its words, the\n// line under it if any; a note is grey words alone\nfunction svgRow(row: LegendRow, id: string): KeyRow {\n  if (!row.swatch) {\n    return {\n      key: row.key,\n      width: row.label.length * LABEL_CHAR_PX,\n      height: ROW_PX,\n      draw: left => (\n        <text key={row.key} {...FONT} x={left} y={0} fill=\"#666\">\n          {row.label}\n        </text>\n      ),\n    }\n  }\n  const swatch = row.swatch\n  const sw = swatchWidth(swatch)\n  const words = (row.strong ?? '') + row.label\n  return {\n    key: row.key,\n    width: Math.max(\n      sw + 5 + words.length * LABEL_CHAR_PX,\n      (row.under?.length ?? 0) * LABEL_CHAR_PX,\n    ),\n    height: row.under ? ROW_PX * 2 : ROW_PX,\n    draw: left => (\n      <g key={row.key} {...FONT}>\n        <SvgSwatch swatch={swatch} x={left} id={id} />\n        <text x={left + sw + 5} y={0}>\n          {row.strong ? <tspan fontWeight=\"bold\">{row.strong}</tspan> : null}\n          {row.label}\n        </text>\n        {row.under ? (\n          <text x={left} y={ROW_PX}>\n            {row.under}\n          </text>\n        ) : null}\n      </g>\n    ),\n  }\n}\n\n// The screen's legend panel, section by section\nfunction Keys({\n  model,\n  idPrefix,\n}: {\n  model: GraphPaneModel\n  idPrefix: string\n}) {\n  const sections = legendSections(model).map(({ testid, rows }) =>\n    rows.map((row, i) => svgRow(row, `${idPrefix}-${testid}-${i}`)),\n  )\n  if (sections.length === 0) {\n    return null\n  }\n  const pad = 6\n  const rows = sections.flat()\n  const boxWidth = Math.max(...rows.map(r => r.width)) + pad * 2\n  const boxHeight =\n    rows.reduce((sum, r) => sum + r.height, 0) + sections.length * pad\n  const right = model.paneWidth - LEGEND_INSET_PX\n  const left = right - boxWidth + pad\n  const top = LEGEND_INSET_PX + model.referenceStripZonePx\n  const placed: { row: KeyRow; y: number }[] = []\n  let y = top + 12 - pad / 2\n  for (const section of sections) {\n    y += pad\n    for (const row of section) {\n      placed.push({ row, y })\n      y += row.height\n    }\n  }\n  return (\n    <g data-testid=\"graph-svg-keys\">\n      <rect\n        x={left - pad}\n        y={top}\n        width={boxWidth}\n        height={boxHeight}\n        rx={3}\n        fill=\"#fff\"\n        fillOpacity={0.82}\n      />\n      {placed.map(({ row, y }) => (\n        <g key={row.key} transform={`translate(0 ${y})`}>\n          {row.draw(left)}\n        </g>\n      ))}\n    </g>\n  )\n}\n\n// Words on a pale rounded backing, as the screen's labels sit\nfunction Chip({\n  x,\n  y,\n  text,\n  fontSize,\n  anchor,\n  bold,\n}: {\n  x: number\n  y: number\n  text: string\n  fontSize: number\n  anchor: 'start' | 'middle'\n  bold?: boolean\n}) {\n  const w = text.length * fontSize * 0.56 + 6\n  const left = anchor === 'middle' ? x - w / 2 : x - 3\n  return (\n    <>\n      <rect\n        x={left}\n        y={y - fontSize * 0.65}\n        width={w}\n        height={fontSize * 1.3}\n        rx={3}\n        fill=\"#fff\"\n        fillOpacity={0.8}\n      />\n      <text\n        x={x}\n        y={y + fontSize * 0.35}\n        textAnchor={anchor}\n        fontSize={fontSize}\n        fontWeight={bold ? 600 : undefined}\n        fill=\"#18181c\"\n      >\n        {text}\n      </text>\n    </>\n  )\n}\n\n// The node and deletion lengths written on the drawing, with their leaders\nfunction SizeLabels({ model }: { model: GraphPaneModel }) {\n  return (\n    <g fontFamily={FONT.fontFamily}>\n      {model.overlayLabels.sizes.map(({ key, text, x, y, kind, leader }) => (\n        <g key={key}>\n          {leader ? (\n            <line\n              x1={leader.arcX}\n              y1={leader.arcY}\n              x2={leader.labelX}\n              y2={leader.labelY}\n              stroke=\"#18181c\"\n            />\n          ) : null}\n          <Chip\n            x={x}\n            y={y}\n            text={text}\n            fontSize={10}\n            anchor=\"middle\"\n            bold={kind === 'deletion'}\n          />\n        </g>\n      ))}\n    </g>\n  )\n}\n\nfunction RowLabels({ model }: { model: GraphPaneModel }) {\n  return (\n    <g fontFamily={FONT.fontFamily}>\n      {model.visibleRowLabels.map(({ label, y, top }) => (\n        <Chip\n          key={y}\n          x={10}\n          y={top}\n          text={label}\n          fontSize={11}\n          anchor=\"start\"\n        />\n      ))}\n    </g>\n  )\n}\n\n// Each lifted walk in a panel of its own, its key as the panel's title\nfunction Facets({\n  model,\n  rasterize,\n  idPrefix,\n}: {\n  model: GraphPaneModel\n  rasterize: boolean\n  idPrefix: string\n}) {\n  const panels = model.facetPanels\n  const grid = model.facetGrid\n  const place = model.facetPlacement\n  if (!panels || !grid || !place) {\n    return null\n  }\n  const { columns, width, height } = grid\n  const keyY = grid.total + FACET_GAP_PX + 14\n  const key = facetKeyRows(model).map((row, i) =>\n    svgRow(row, `${idPrefix}-facet-key-${i}`),\n  )\n  const keyX = key.map((_, i) =>\n    key.slice(0, i).reduce((x, row) => x + row.width + 14, 6),\n  )\n  return (\n    <>\n      <g transform={`translate(0 ${keyY})`}>\n        {key.map((row, i) => row.draw(keyX[i]!))}\n      </g>\n      {panels.map((lift, i) => {\n        const cell = place.cells[i]!\n        const x = (cell % columns) * (width + FACET_GAP_PX)\n        const y =\n          Math.floor(cell / columns) * (FACET_TITLE_PX + height + FACET_GAP_PX)\n        const walk = lift.walks[0]!\n        const title = svgRow(walkKeyRow(model, walk), `${idPrefix}-facet-${i}`)\n        return (\n          <g key={walk.name} transform={`translate(${x} ${y})`}>\n            <g transform={`translate(0 ${ROW_PX - 2})`}>{title.draw(6)}</g>\n            <g transform={`translate(0 ${FACET_TITLE_PX})`}>\n              <Body\n                model={model}\n                lift={lift}\n                drawPaths={false}\n                width={width}\n                height={height}\n                rasterize={rasterize}\n              />\n            </g>\n          </g>\n        )\n      })}\n    </>\n  )\n}\n\n// The pane as the screen draws it, for the linear view's SVG export: the\n// canvas's ink, the tube map and reference strip painters, and the SVG\n// overlays the screen mounts over them. Hover and selection are left out.\nexport default function PaneSvg({\n  model,\n  rasterize = false,\n  idPrefix,\n}: {\n  model: GraphPaneModel\n  rasterize?: boolean\n  idPrefix: string\n}) {\n  const width = model.paneWidth\n  const height = model.canvasHeight\n  const tubeMap = !!model.layoutResult?.tubeMap\n  const opts = { rasterizeLayers: rasterize }\n  return (\n    <g data-testid=\"graph-pane-svg\">\n      {model.facetPanels ? (\n        <Facets model={model} rasterize={rasterize} idPrefix={idPrefix} />\n      ) : tubeMap ? (\n        <PaintLayer\n          width={width}\n          height={height}\n          opts={opts}\n          paint={ctx => {\n            paintTubeMap(asCanvasCtx(ctx), model, { highlightNode: null })\n          }}\n        />\n      ) : (\n        <Body\n          model={model}\n          lift={model.drawnHighlight}\n          drawPaths={model.effectiveDrawPaths}\n          width={width}\n          height={height}\n          rasterize={rasterize}\n        />\n      )}\n      {/* in the screen's stacking order, bottom first */}\n      {model.facetPanels ? null : (\n        <>\n          <BubbleHalos model={model} />\n          <GenePins model={model} />\n          <SizeLabels model={model} />\n          <LabelLayer model={model} />\n          <WalkRowsOverlay model={model} vector />\n          <RowLabels model={model} />\n        </>\n      )}\n      {model.referenceStripShown ? (\n        <PaintLayer\n          width={width}\n          height={height}\n          opts={opts}\n          paint={ctx => {\n            paintReferenceStrip(asCanvasCtx(ctx), model, {\n              lit: undefined,\n              dpr: 1,\n            })\n          }}\n        />\n      ) : null}\n      {model.facetPanels ? null : <Keys model={model} idPrefix={idPrefix} />}\n    </g>\n  )\n}\n", "import { renderDisplaySvg } from '@jbrowse/display-kit/renderDisplaySvg'\n\nimport PaneSvg from '../GraphGenomeView/components/PaneSvg'\n\nimport type { LinearGraphDisplayModel } from './model'\nimport type { LgvSvgBodyProps } from '@jbrowse/display-kit/renderDisplaySvg'\nimport type { ExportSvgDisplayOptions } from '@jbrowse/display-kit/types'\n\nfunction GraphTrackSvgBody({\n  model,\n  opts,\n}: LgvSvgBodyProps<LinearGraphDisplayModel>) {\n  return (\n    <PaneSvg\n      model={model}\n      rasterize={!!opts?.rasterizeLayers}\n      idPrefix={`graph-${model.id}`}\n    />\n  )\n}\n\nexport function renderGraphTrackSvg(\n  model: LinearGraphDisplayModel,\n  opts?: ExportSvgDisplayOptions,\n) {\n  return renderDisplaySvg(model, opts, GraphTrackSvgBody)\n}\n"],
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+}