jbrowse-plugin-graphgenomeviewer 8.3.0 → 8.3.2

package/dist/chunks/chunk-D6NFDQQI.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/GraphGenomeView/components/PaneLayer.tsx", "../../src/GraphGenomeView/components/BubbleHalos.tsx", "../../src/GraphGenomeView/walkRowBlocks.ts", "../../src/GraphGenomeView/legendSections.ts", "../../src/GraphGenomeView/components/ElTree.tsx", "../../src/GraphGenomeView/components/LegendSwatch.tsx", "../../src/GraphGenomeView/components/legendStyles.ts", "../../src/GraphGenomeView/components/GenePins.tsx", "../../src/GraphGenomeView/components/LabelChip.tsx", "../../src/GraphGenomeView/components/LabelLayer.tsx", "../../src/GraphGenomeView/components/ReferenceStripOverlay.tsx", "../../src/GraphGenomeView/components/TubeMapOverlay.tsx", "host:@jbrowse/render-core/marks", "../../src/GraphGenomeView/walkRowSpans.ts", "../../src/GraphGenomeView/components/WalkRowsOverlay.tsx"],
+  "sourcesContent": ["import { useEffect, useRef } from 'react'\nimport type { ReactNode } from 'react'\n\nimport { syncCanvasSize } from '@jbrowse/bandage-core/renderer/canvas'\nimport { autorun } from 'mobx'\nimport { observer } from 'mobx-react'\n\nimport { dependOn } from '../pane/paneBase'\nimport { trackedDpr } from '../trackedDpr'\n\nimport type { GraphPaneModel } from '../model'\n\n// marks an overlay whose labels move with the drawing, so a press on one pans\nexport const PANS_WITH_DRAWING = 'data-pans-with-drawing'\n\n// A layer over the pane's canvas that leaves the pointer to it\nexport function paneLayerStyle(\n  zIndex: number,\n  overflow?: 'hidden' | 'visible',\n) {\n  return {\n    position: 'absolute' as const,\n    left: 0,\n    top: 0,\n    pointerEvents: 'none' as const,\n    overflow,\n    zIndex,\n  }\n}\n\n// An SVG the pane's size, over the canvas or inside PaneSvg's export\nexport const PaneSvgLayer = observer(function PaneSvgLayer({\n  model,\n  zIndex,\n  overflow = 'hidden',\n  testId,\n  pansWithDrawing,\n  children,\n}: {\n  model: GraphPaneModel\n  zIndex: number\n  overflow?: 'hidden' | 'visible'\n  testId?: string\n  pansWithDrawing?: boolean\n  children: ReactNode\n}) {\n  return (\n    <svg\n      style={{\n        ...paneLayerStyle(zIndex, overflow),\n        userSelect: pansWithDrawing ? 'none' : undefined,\n      }}\n      width={model.paneWidth}\n      height={model.canvasHeight}\n      data-testid={testId}\n      {...(pansWithDrawing ? { [PANS_WITH_DRAWING]: '' } : {})}\n    >\n      {children}\n    </svg>\n  )\n})\n\n// Layout units onto the screen. Its own observer, so a pan frame re-renders\n// this group's transform and not the children a parent built.\nexport const PaneTransformGroup = observer(function PaneTransformGroup({\n  model,\n  children,\n}: {\n  model: GraphPaneModel\n  children: ReactNode\n}) {\n  const { scaleX, scaleY, translateX, translateY } = model\n  return (\n    <g\n      transform={`translate(${translateX} ${translateY}) scale(${scaleX} ${scaleY})`}\n    >\n      {children}\n    </g>\n  )\n})\n\n// A canvas the pane's size that an autorun repaints, so a pan moves its ink in\n// the same frame as the drawing. `paint` draws in css px.\nexport function PaneOverlayCanvas({\n  model,\n  zIndex,\n  shown = true,\n  testId,\n  paint,\n}: {\n  model: GraphPaneModel\n  zIndex: number\n  shown?: boolean\n  testId: string\n  paint: (ctx: CanvasRenderingContext2D, dpr: number) => void\n}) {\n  const ref = useRef<HTMLCanvasElement>(null)\n  useEffect(() => {\n    if (!shown) {\n      return undefined\n    }\n    return autorun(() => {\n      const canvas = ref.current\n      const ctx = canvas?.getContext('2d')\n      if (canvas && ctx) {\n        const width = model.paneWidth\n        const height = model.canvasHeight\n        dependOn(trackedDpr())\n        const dpr = syncCanvasSize(canvas, width, height)\n        ctx.setTransform(dpr, 0, 0, dpr, 0, 0)\n        ctx.clearRect(0, 0, width, height)\n        paint(ctx, dpr)\n      }\n    })\n  }, [model, shown, paint])\n  return (\n    <canvas\n      ref={ref}\n      data-testid={shown ? testId : undefined}\n      style={{ ...paneLayerStyle(zIndex), display: shown ? 'block' : 'none' }}\n    />\n  )\n}\n", "import { bubbleKey, sameBubble } from '@jbrowse/bandage-core/bubbles/bubbleLine'\nimport { BUBBLE_KIND_COLORS } from '@jbrowse/bandage-core/bubbles/classifyBubble'\nimport { HALO_FACTOR } from '@jbrowse/bandage-core/labelLayout'\nimport { observer } from 'mobx-react'\n\nimport { PaneSvgLayer, PaneTransformGroup } from './PaneLayer'\n\nimport type { GraphPaneModel } from '../model'\n\n// The bubbles over a node drawing: each a translucent halo along its nodes,\n// drawn once in layout units and moved with the canvas by one transform. The\n// halo takes no pointer events, so the nodes under it still hover and drag;\n// its name and its routes' chips are LabelLayer's. A small variant is\n// LabelLayer's tick, and shows its halo only while hovered.\n\nconst BubbleHalos = observer(function BubbleHalos({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const { bubbleHalos, hoveredBubble } = model\n  if (bubbleHalos.length === 0) {\n    return null\n  }\n  const halo = model.contigThickness * HALO_FACTOR\n  return (\n    <PaneSvgLayer model={model} zIndex={2} testId=\"graph-bubble-halos\">\n      <PaneTransformGroup model={model}>\n        {bubbleHalos\n          .filter(\n            h =>\n              !h.whole &&\n              (!h.tick ||\n                (hoveredBubble && sameBubble(h.bubble, hoveredBubble))),\n          )\n          .map(h => (\n            <path\n              key={bubbleKey(h.bubble)}\n              d={h.path}\n              fill=\"none\"\n              stroke={BUBBLE_KIND_COLORS[h.kind]}\n              strokeOpacity={\n                hoveredBubble && sameBubble(h.bubble, hoveredBubble)\n                  ? 0.45\n                  : model.bubbleFaded(h)\n                    ? 0.06\n                    : 0.22\n              }\n              strokeWidth={halo}\n              strokeLinecap=\"round\"\n              strokeLinejoin=\"round\"\n              vectorEffect=\"non-scaling-stroke\"\n            />\n          ))}\n      </PaneTransformGroup>\n    </PaneSvgLayer>\n  )\n})\n\nexport default BubbleHalos\n", "import type { WalkRowBlock } from '@jbrowse/bandage-core/layout/walkRowLinks'\n\n// ggbandage's: the three biggest blocks in colour, the rest a pale grey that\n// still carries its letter\nconst BLOCK_COLORS = ['#d4735e', '#d8a94a', '#c98aa4']\nconst OTHER_BLOCK = '#e6e6e6'\nconst BLOCK_EDGE = '#555'\nconst LETTER_FONT = 'bold 11px sans-serif'\nconst MIN_LETTER_PX = 12\nconst MIN_LETTER_BAR_PX = 9\n\nexport const blockFill = (block: number) => BLOCK_COLORS[block] ?? OTHER_BLOCK\n\n// A, B, ... Z, then AA, AB, ...\nexport function blockLetter(block: number): string {\n  const letter = String.fromCharCode(65 + (block % 26))\n  return block < 26 ? letter : blockLetter(Math.floor(block / 26) - 1) + letter\n}\n\n// How many blocks get a colour of their own, for the key\nexport const COLORED_BLOCKS = BLOCK_COLORS.length\n\n// Each stretch as a box over its row's bar, lettered where it is wide enough\nexport function paintWalkRowBlocks(\n  ctx: CanvasRenderingContext2D,\n  blocks: WalkRowBlock[],\n  f: {\n    x: (offset: number) => number\n    rowCentre: (row: number) => number\n    barPx: number\n  },\n) {\n  ctx.font = LETTER_FONT\n  ctx.textAlign = 'center'\n  ctx.textBaseline = 'middle'\n  for (const { row, start, bp, block } of blocks) {\n    const left = f.x(start)\n    const width = f.x(start + bp) - left\n    const top = f.rowCentre(row) - f.barPx / 2\n    ctx.fillStyle = blockFill(block)\n    ctx.fillRect(left, top, width, f.barPx)\n    ctx.strokeStyle = BLOCK_EDGE\n    ctx.lineWidth = 1\n    ctx.strokeRect(left + 0.5, top + 0.5, width - 1, f.barPx - 1)\n    if (width >= MIN_LETTER_PX && f.barPx >= MIN_LETTER_BAR_PX) {\n      ctx.fillStyle = '#111'\n      ctx.fillText(blockLetter(block), left + width / 2, f.rowCentre(row))\n    }\n  }\n}\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 {\n  dashedDeletions,\n  deletionKey,\n} from '@jbrowse/bandage-core/deletionEdges'\nimport { edgeWidthFactor } from '@jbrowse/bandage-core/edgeWidths'\nimport { EXON_COLOR } from '@jbrowse/bandage-core/genes/exonOutline'\nimport { formatBp } from '@jbrowse/bandage-core/graphLabels'\nimport {\n  BAR_PX as WALK_ROW_BAR_PX,\n  CALL_TICK,\n  DISAGREES,\n  GENE_INK,\n  UNBACKED_TICK,\n  walkRowsKey,\n} from '@jbrowse/bandage-core/layout/walkRowDraw'\nimport { frequencyKey, nodeWidthPx } from '@jbrowse/bandage-core/nodeWidths'\nimport { referenceLabel } from '@jbrowse/bandage-core/reference'\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 { fadedKey } from '@jbrowse/bandage-core/walkHighlight'\nimport { walkKey } from '@jbrowse/bandage-core/walkKey'\n\nimport { CALL_TOLERANCE } from './repeats/walkCalls'\nimport { PANEL_REFERENCE_TUBE } from './tubeMapPanels'\nimport { COLORED_BLOCKS, blockFill, blockLetter } from './walkRowBlocks'\n\nimport type { GraphPaneModel } from './model'\nimport type { KeySwatch } from '@jbrowse/bandage-core/layout/walkRowDraw'\nimport type { GraphNode } from '@jbrowse/bandage-core/types'\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 = 32\n\n// LIFT_BACKDROP_CSS reads paler alone than faded strokes do where they\n// overlap, so the key samples it darker\nconst FADED_SWATCH = 'rgba(160, 160, 160, 0.45)'\nconst DELETION_INK = '#18181c'\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\nconst LINK_INK = 'rgba(119, 119, 119, 0.85)'\nconst LINE_PX = 15\nconst CHIP_PX = 10\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      // a hairline edge, so a pale colour still shows on the white key\n      edged?: true\n    }\n  // the reference strip, a band per lifted walk\n  | { kind: 'bands'; bands: Stop[][] }\n  | { kind: 'line'; color: string; dashed?: true }\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  group?: string\n  // the group's name, over the first of its sections\n  heading?: string\n  // set apart from the group above by a heading's gap, though it has none\n  spaced?: true\n}\n\nexport function swatchWidth(swatch: LegendSwatch) {\n  return swatch.kind === 'fill' ? (swatch.width ?? SWATCH_PX) : SWATCH_PX\n}\n\nexport const bandPx = (bands: readonly unknown[]) => (bands.length > 1 ? 3 : 4)\n\nexport function 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// One column every swatch of a key sits in, so the words after them line up\nexport function swatchColumn(rows: readonly LegendRow[]) {\n  return rows.reduce(\n    (px, row) => (row.swatch ? Math.max(px, swatchWidth(row.swatch)) : px),\n    0,\n  )\n}\n\n// One pitch for every line of a key, roomy enough for its tallest swatch, so\n// rows sit evenly however their swatches differ\nexport function rowPitch(rows: readonly LegendRow[]) {\n  return rows.reduce(\n    (px, row) =>\n      row.swatch ? Math.max(px, Math.ceil(swatchHeight(row.swatch)) + 3) : px,\n    LINE_PX,\n  )\n}\n\nconst flat = (color: string): Stop[] => [{ offset: 0, color }]\n\n// A colour's key is a square chip, so it never reads as a thickness bar\nfunction fillRow(key: string, color: string, label: string): LegendRow {\n  return {\n    key,\n    label,\n    swatch: {\n      kind: 'fill',\n      stops: flat(color),\n      width: CHIP_PX,\n      height: CHIP_PX,\n      edged: true,\n    },\n  }\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 reference = model.graph ? referenceLabel(model.graph) : 'reference'\n  return [\n    {\n      key: 'ramp',\n      label: `position on ${reference}`,\n      swatch: { kind: 'fill', stops: RAMP_GRADIENT_STOPS, width: BAR_PX },\n      under: `${start.toLocaleString('en-US')}-${end.toLocaleString('en-US')} (${formatBp(end - start)})`,\n    },\n    ...(model.referenceRampDrawsOffReference\n      ? [fillRow('off', REFERENCE_RAMP_ALT_CSS, 'off the reference')]\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: `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 : `${names} bubble`,\n      swatch: { kind: 'halo', color },\n    }\n  })\n}\n\nfunction deletionRows(model: GraphPaneModel): LegendRow[] {\n  const { graph } = model\n  return graph && dashedDeletions(model.deletions, model.walkLift).length > 0\n    ? [\n        {\n          key: 'deletion',\n          label: deletionKey(referenceLabel(graph)),\n          swatch: {\n            kind: 'line',\n            color: model.walkLift ? FADED_SWATCH : DELETION_INK,\n            dashed: true,\n          },\n        },\n      ]\n    : []\n}\n\nfunction thicknessRow(\n  key: string,\n  label: string,\n  px: number,\n  color: string,\n): LegendRow {\n  return {\n    key,\n    label,\n    swatch: { kind: 'fill', stops: flat(color), width: BAR_PX, height: px },\n  }\n}\n\nconst roundDepth = (depth: number) =>\n  depth >= 10 ? Math.round(depth) : Math.round(depth * 10) / 10\n\n// What a node's thickness counts, with bars as thick as the drawing makes\n// the thinnest, the mean and the thickest node\nfunction nodeWidthRows(model: GraphPaneModel): LegendRow[] {\n  const { graph, contigThickness: px, depthRange: range } = model\n  if (!graph || !model.drawsNodes || model.walkRowBars) {\n    return []\n  }\n  if (model.nodeWidth === 'frequency') {\n    const tagged = graph.nodes.some(n => n.frequency !== undefined)\n    return frequencyKey(px).map(({ label, widthPx }) =>\n      thicknessRow(\n        `width-${label}`,\n        tagged ? `AF ${label}` : `${label} of haplotypes`,\n        widthPx,\n        REFERENCE_RAMP_ALT_CSS,\n      ),\n    )\n  }\n  if (model.nodeWidth !== 'depth' || !range || range.min === range.max) {\n    return []\n  }\n  const walkCount = graph.paths?.length ?? 0\n  const walks = walkCount > 0\n  const depths = [\n    ...new Set(\n      [range.max, range.mean, range.min].map(walks ? Math.round : roundDepth),\n    ),\n  ]\n  // a walk looping through a repeat passes its nodes more than once, and\n  // each pass counts\n  const passes = depths[0]! > walkCount\n  const counted = (n: number) =>\n    passes\n      ? `${n.toLocaleString('en-US')} walk pass${n === 1 ? '' : 'es'}`\n      : `${n.toLocaleString('en-US')} walk${n === 1 ? '' : 's'}`\n  return depths.map(depth =>\n    thicknessRow(\n      `width-${depth}`,\n      walks ? counted(depth) : `depth ${depth.toLocaleString('en-US')}`,\n      nodeWidthPx({ depth } as GraphNode, px, 'depth', range.mean),\n      REFERENCE_RAMP_ALT_CSS,\n    ),\n  )\n}\n\nfunction linkWidthRows(model: GraphPaneModel): LegendRow[] {\n  const busiest = model.busiestLink\n  if (\n    !model.drawsNodes ||\n    model.walkRowBars ||\n    model.linkWidth !== 'walks' ||\n    busiest === 0\n  ) {\n    return []\n  }\n  const counts = busiest > 1 ? [busiest, 1] : [1]\n  return counts.map(n =>\n    thicknessRow(\n      `link-width-${n}`,\n      `${n.toLocaleString('en-US')} walk${n === 1 ? '' : 's'}`,\n      model.connectorThickness * edgeWidthFactor(n, busiest, 'walks'),\n      LINK_INK,\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-${name}`,\n    label,\n    swatch: { kind: 'line', color },\n  }))\n}\n\nfunction tubeRow(key: string, stops: Stop[], label: string): LegendRow {\n  return {\n    key,\n    label,\n    swatch: { kind: 'fill', stops, height: TUBE_SWATCH_PX, square: true },\n  }\n}\n\n// What a tube map draws that nothing else on screen explains, each listed\n// only while it applies\nexport function tubeMapRows(model: GraphPaneModel): LegendRow[] {\n  const {\n    roles,\n    haplotypeTube,\n    bundled,\n    values,\n    logWidths,\n    foldBp,\n    forwardReads,\n    reverseReads,\n    substitution,\n    insertion,\n    deletion,\n  } = model.tubeMapKeys\n  const reads = model.readsShown\n  const rows: LegendRow[] = []\n  if (values) {\n    rows.push(\n      tubeRow('value-reference', flat(PANEL_REFERENCE_TUBE), 'reference'),\n    )\n    for (const { value, color } of values) {\n      rows.push(tubeRow(`value-${value}`, flat(color), value))\n    }\n  }\n  if (roles) {\n    rows.push(\n      tubeRow('ref', flat(PANEL_REFERENCE_TUBE), 'reference'),\n      tubeRow(\n        'hap',\n        flat(haplotypeTube),\n        bundled ? 'shared route, \u00D7n haplotypes' : 'haplotype',\n      ),\n    )\n  }\n  if (forwardReads) {\n    rows.push(\n      tubeRow(\n        'fwd',\n        bandStops(FORWARD_READ_COLORS),\n        'read on the forward strand',\n      ),\n    )\n  }\n  if (reverseReads) {\n    rows.push(\n      tubeRow(\n        'rev',\n        bandStops(REVERSE_READ_COLORS),\n        'read on the reverse strand',\n      ),\n    )\n  }\n  if (reads && reads.shown < reads.total) {\n    rows.push({\n      key: 'sampled',\n      label: `${reads.shown.toLocaleString('en-US')} of ${reads.total.toLocaleString('en-US')} reads shown`,\n      swatch: { kind: 'blank' },\n    })\n  }\n  if (substitution) {\n    rows.push({\n      key: 'sub',\n      label: 'read mismatch',\n      swatch: { kind: 'glyph', char: 'A' },\n    })\n  }\n  if (insertion) {\n    rows.push({\n      key: 'ins',\n      label: 'read insertion',\n      swatch: { kind: 'glyph', char: '*' },\n    })\n  }\n  if (deletion) {\n    rows.push(tubeRow('del', flat('grey'), 'read deletion'))\n  }\n  if (foldBp !== undefined) {\n    rows.push({\n      key: 'tube-fold',\n      label: `haplotype variant < ${formatBp(foldBp)}`,\n      swatch: {\n        kind: 'tick',\n        color: deviationInk(),\n        height: TUBE_SWATCH_PX,\n        backing: FOLD_TICK_BACKING,\n      },\n    })\n  }\n  if (logWidths) {\n    rows.push({\n      key: 'log',\n      label: 'width grows with log of length',\n      swatch: { kind: 'bracket' },\n    })\n  }\n  return rows\n}\n\nexport function walkRowSwatch(swatch: KeySwatch): LegendSwatch {\n  return swatch.kind === 'gene'\n    ? {\n        kind: 'outline',\n        color: GENE_INK,\n        stroke: 1.5,\n        radius: 0,\n        height: WALK_ROW_SWATCH_PX,\n      }\n    : {\n        kind: 'fill',\n        stops:\n          swatch.kind === 'bar' && swatch.ramp\n            ? RAMP_GRADIENT_STOPS\n            : flat(swatch.fill),\n        height: swatch.kind === 'gap' ? swatch.px : WALK_ROW_SWATCH_PX,\n      }\n}\n\n// The shared blocks the rows draw: each coloured one by its letter, then one\n// row for the grey rest\nfunction blockRows(model: GraphPaneModel): LegendRow[] {\n  const present = new Set(model.sharedBlocks?.map(b => b.block))\n  const swatch = (block: number) => ({\n    kind: 'fill' as const,\n    stops: flat(blockFill(block)),\n    height: WALK_ROW_SWATCH_PX,\n  })\n  return [\n    ...[...present]\n      .filter(block => block < COLORED_BLOCKS)\n      .sort((a, b) => a - b)\n      .map(block => ({\n        key: `block-${block}`,\n        label: `${blockLetter(block)}: off the reference, walked by several rows`,\n        swatch: swatch(block),\n      })),\n    ...([...present].some(block => block >= COLORED_BLOCKS)\n      ? [\n          {\n            key: 'block-more',\n            label: 'more shared blocks',\n            swatch: swatch(COLORED_BLOCKS),\n          },\n        ]\n      : []),\n  ]\n}\n\n// The walk rows' bar colours, genes and ticks; each tick row appears once\n// the rows hold one, so a catalogue with no genotypes keeps the plain key\nfunction walkRowsRows(model: GraphPaneModel): LegendRow[] {\n  const bars = model.walkRowBars\n  if (!bars) {\n    return []\n  }\n  const calls = [bars.reference, ...bars.rows].flatMap(row => row.call ?? [])\n  const tick = (key: string, color: string, label: string): LegendRow => ({\n    key,\n    label,\n    swatch: { kind: 'tick', color, height: WALK_ROW_SWATCH_PX },\n  })\n  return [\n    ...walkRowsKey(bars, {\n      ramp: model.referenceRampDomain,\n      genes: model.walkRowGeneKey,\n      annotation: model.walkRowAnnotation,\n    }).map(entry => ({\n      key: `rows-${entry.label}`,\n      label: entry.label,\n      swatch: entry.note ? undefined : walkRowSwatch(entry.swatch),\n    })),\n    ...blockRows(model),\n    ...(calls.some(call => call.spanningReads !== 0)\n      ? [tick('call', CALL_TICK, 'allele length called for this walk')]\n      : []),\n    ...(calls.some(call => call.spanningReads === 0)\n      ? [tick('unbacked', UNBACKED_TICK, 'called with no read spanning it')]\n      : []),\n    ...(calls.some(call => call.agrees === false)\n      ? [\n          tick(\n            'disagrees',\n            DISAGREES,\n            `walk and call over ${Math.round(CALL_TOLERANCE * 100)}% apart`,\n          ),\n        ]\n      : []),\n  ]\n}\n\n// One lifted walk's key: a swatch, or a short bar of the scale its lane\n// shades by, then its name, with the scale's stretch under it\nexport function walkKeyRow(model: GraphPaneModel, walk: LiftedWalk): LegendRow {\n  const key = walkKey(walk, model.walkReference)\n  return {\n    key: `walk-${walk.name}`,\n    strong: model.walkLabel(walk.name),\n    label: key.delta + key.gaps + key.reversed,\n    swatch: {\n      kind: 'fill',\n      stops: encodingStops(walk.encoding),\n      width: key.shades ? BAR_PX : SWATCH_PX,\n    },\n    under: key.scale,\n    title: key.hover,\n    walk,\n  }\n}\n\n// The off-reference colour, where the lift paints it, and the faded rest.\n// rampRows draws no key while walks are lifted, so these rows name both.\nfunction fadedRows(model: GraphPaneModel, faded: string): LegendRow[] {\n  return [\n    ...(model.liftPaintsOffReference\n      ? [fillRow('lift-off', REFERENCE_RAMP_ALT_CSS, 'off the reference')]\n      : []),\n    fillRow('faded', FADED_SWATCH, faded),\n  ]\n}\n\n// Each lifted walk's key, then what the faded rest is\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 faded = model.graph\n    ? fadedKey(model.graph, lift, model.liftedWalksLabel)\n    : `not on ${model.liftedWalksLabel}`\n  return [...rows, ...fadedRows(model, faded)]\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  const { graph, facetPanels } = model\n  if (!graph || !facetPanels) {\n    return []\n  }\n  const keys = new Set(\n    facetPanels.map(panel => fadedKey(graph, panel, \"the panel's walk\")),\n  )\n  return [\n    ...fadedRows(\n      model,\n      keys.size === 1 ? [...keys][0]! : \"not on the panel's walk\",\n    ),\n    ...deletionRows(model),\n  ]\n}\n\n// The keys in the order the panel stacks them, top first, each under its\n// group's heading once the key holds more than one group\nexport function legendSections(model: GraphPaneModel): LegendSection[] {\n  const sections: LegendSection[] = [\n    { testid: 'graph-open-bubble-legend', rows: openBubbleRows(model) },\n    { testid: 'graph-ramp-legend', rows: rampRows(model), group: 'Color' },\n    {\n      testid: 'graph-walk-readout',\n      rows: walkReadoutRows(model),\n      group: 'Walks',\n    },\n    {\n      testid: 'graph-width-legend',\n      rows: nodeWidthRows(model),\n      group: 'Node thickness',\n    },\n    {\n      testid: 'graph-link-width-legend',\n      rows: linkWidthRows(model),\n      group: 'Link thickness',\n    },\n    { testid: 'graph-halo-legend', rows: haloRows(model), group: 'Marks' },\n    {\n      testid: 'graph-deletion-legend',\n      rows: deletionRows(model),\n      group: 'Marks',\n    },\n    { testid: 'graph-gene-legend', rows: geneRows(model), group: 'Marks' },\n    { testid: 'graph-path-legend', rows: pathRows(model), group: 'Paths' },\n    {\n      testid: 'graph-tube-map-legend',\n      rows: tubeMapRows(model),\n      group: 'Tube map',\n    },\n    {\n      testid: 'graph-walk-rows-legend',\n      rows: walkRowsRows(model),\n      group: 'Walk rows',\n    },\n    {\n      testid: 'graph-reference-strip-legend',\n      rows: stripRows(model),\n      group: 'Top strip',\n    },\n    { testid: 'graph-fold-legend', rows: foldRows(model) },\n  ].filter(section => section.rows.length > 0)\n  const groups = new Set(sections.flatMap(section => section.group ?? []))\n  if (groups.size < 2) {\n    return sections\n  }\n  const headed = new Set<string>()\n  return sections.map((section, i) => {\n    const { group } = section\n    if (!group) {\n      return i === 0 ? section : { ...section, spaced: true as const }\n    }\n    if (headed.has(group)) {\n      return section\n    }\n    headed.add(group)\n    return { ...section, heading: group }\n  })\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, bandPx, swatchHeight, swatchWidth } from '../legendSections'\n\nimport type { LegendSwatch, Stop } from '../legendSections'\n\nconst EDGE_INK = 'rgba(0, 0, 0, 0.28)'\n\nfunction Gradient({\n  id,\n  x,\n  y,\n  stops,\n  width,\n  height,\n  square,\n  edged,\n}: {\n  id: string\n  x: number\n  y: number\n  stops: readonly Stop[]\n  width: number\n  height: number\n  square?: boolean\n  edged?: boolean\n}) {\n  // an edge's stroke sits half inside, so the chip keeps its size\n  const inset = edged ? 0.5 : 0\n  const rect = (fill: string) => (\n    <rect\n      x={x + inset}\n      y={y + inset}\n      width={width - inset * 2}\n      height={height - inset * 2}\n      rx={square ? 0 : 2}\n      fill={fill}\n      stroke={edged ? EDGE_INK : undefined}\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\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          edged={swatch.edged}\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 swatch.dashed ? (\n        <line\n          x1={x + 1}\n          x2={x + SWATCH_PX}\n          y1={mid}\n          y2={mid}\n          stroke={swatch.color}\n          strokeWidth={3}\n          strokeDasharray=\"4 3\"\n        />\n      ) : (\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 ${height / 2 + 5})`}>\n        <SvgSwatch swatch={swatch} x={0} id={id} />\n      </g>\n    </svg>\n  )\n}\n", "// A key's section of the legend panel, and one row in it: a swatch beside its\n// words\nexport const legendBoxStyle = {\n  background: '#fff',\n  padding: '3px 6px',\n  fontSize: 11,\n  lineHeight: '15px',\n  whiteSpace: 'nowrap' as const,\n}\n\nexport const legendRowStyle = { display: 'flex', alignItems: 'center', gap: 5 }\n\n// A line with no swatch, such as what the drawing folded away\nexport const legendNoteStyle = { color: '#666' }\n\nexport const HEADING_INK = '#6b7479'\nexport const HEADING_GAP_PX = 4\n\n// A group's name over its rows, set apart by a gap unless it opens the key\nexport const legendHeadingStyle = {\n  color: HEADING_INK,\n  fontSize: 9.5,\n  fontWeight: 600,\n  letterSpacing: '0.06em',\n  textTransform: 'uppercase' as const,\n}\n", "import { useMemo } from 'react'\n\nimport {\n  exonOutlineTree,\n  exonStretches,\n} from '@jbrowse/bandage-core/genes/exonOutline'\nimport { computed } from 'mobx'\nimport { observer } from 'mobx-react'\n\nimport ElTree, { useSvgId } from './ElTree'\nimport { PaneSvgLayer } from './PaneLayer'\n\nimport type { GraphPaneModel } from '../model'\n\n// The session's genes drawn onto the graph: each exon outlined round its\n// stretch of node, as core's exonOutlineTree draws it for every host, moved by\n// the same transform the halos use. Their names are LabelLayer's.\n\nconst GenePins = observer(function GenePins({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const id = `exon-outline-${useSvgId()}`\n  // in layout units, so a pan frame reuses them and only moves the transform\n  const stretches = useMemo(\n    () =>\n      computed(() => {\n        const { genePins, walkLift } = model\n        // an open bubble rings only its own exons\n        const focus = walkLift ? undefined : model.openBubbleFocus\n        const pins = focus\n          ? genePins.map(pin => ({\n              ...pin,\n              exonsByNode: pin.exonsByNode.filter(e =>\n                focus.nodeIds.has(e.nodeId),\n              ),\n            }))\n          : genePins\n        return exonStretches(pins, model.nodeInk.halfWidthPx, walkLift)\n      }),\n    [model],\n  )\n  const { scaleX, scaleY, translateX, translateY, paneWidth, canvasHeight } =\n    model\n  const tree = exonOutlineTree(stretches.get(), {\n    id,\n    width: paneWidth,\n    height: canvasHeight,\n    transform: `translate(${translateX} ${translateY}) scale(${scaleX} ${scaleY})`,\n  })\n  return tree ? (\n    <PaneSvgLayer model={model} zIndex={2} testId=\"graph-gene-pins\">\n      <ElTree el={tree} />\n    </PaneSvgLayer>\n  ) : null\n})\n\nexport default GenePins\n", "import { LABEL_PAD, LABEL_PX } from '@jbrowse/bandage-core/overlayLabels'\n\n// A chip's box, its text's baseline at y and centred on x\nfunction chipBox(x: number, y: number, w: number) {\n  return {\n    x: x - w / 2,\n    y: y - LABEL_PX - LABEL_PAD + 2,\n    width: w,\n    height: LABEL_PX + LABEL_PAD * 2 - 2,\n  }\n}\n\nexport function inChip(\n  chip: { x: number; y: number; w: number },\n  px: number,\n  py: number,\n) {\n  const box = chipBox(chip.x, chip.y, chip.w)\n  return (\n    px >= box.x &&\n    px <= box.x + box.width &&\n    py >= box.y &&\n    py <= box.y + box.height\n  )\n}\n\n// One label on an overlay: a white chip with a coloured edge and text. A note\n// follows the text in plain type. A chip takes the pointer only with a\n// handler, so its title shows only then.\nexport default function LabelChip({\n  x,\n  y,\n  w,\n  text,\n  note,\n  color,\n  edge = color,\n  italic,\n  dimmed,\n  title,\n  testId,\n  onClick,\n  onHover,\n}: {\n  x: number\n  y: number\n  w: number\n  text: string\n  note?: string\n  color: string\n  edge?: string\n  italic?: boolean\n  dimmed?: boolean\n  title?: string\n  testId?: string\n  onClick?: () => void\n  onHover?: (hovered: boolean) => void\n}) {\n  return (\n    <g\n      style={{\n        pointerEvents: onClick || onHover ? 'auto' : 'none',\n        cursor: onClick ? 'pointer' : undefined,\n        opacity: dimmed ? 0.35 : 1,\n      }}\n      data-testid={testId}\n      onClick={onClick}\n      onMouseEnter={() => {\n        onHover?.(true)\n      }}\n      onMouseLeave={() => {\n        onHover?.(false)\n      }}\n      // a clickable chip is a button to the keyboard too\n      {...(onClick && {\n        role: 'button',\n        tabIndex: 0,\n        'aria-label': (title ?? text).replaceAll('\\n', ', '),\n        onKeyDown: (e: React.KeyboardEvent) => {\n          if (e.key === 'Enter' || e.key === ' ') {\n            e.preventDefault()\n            onClick()\n          }\n        },\n        onFocus: () => {\n          onHover?.(true)\n        },\n        onBlur: () => {\n          onHover?.(false)\n        },\n      })}\n    >\n      {title ? <title>{title}</title> : null}\n      <rect\n        {...chipBox(x, y, w)}\n        rx={3}\n        fill=\"rgba(255,255,255,0.85)\"\n        stroke={edge}\n        strokeWidth={1}\n      />\n      <text\n        x={x}\n        y={y}\n        fontSize={LABEL_PX}\n        fontFamily=\"sans-serif\"\n        fontStyle={italic ? 'italic' : undefined}\n        fontWeight={italic ? 600 : undefined}\n        fill={color}\n        textAnchor=\"middle\"\n      >\n        {text}\n        {note ? (\n          <tspan fontStyle=\"normal\" fontWeight=\"normal\">\n            {note}\n          </tspan>\n        ) : null}\n      </text>\n    </g>\n  )\n}\n", "import { bubbleKey, sameBubble } from '@jbrowse/bandage-core/bubbles/bubbleLine'\nimport { BUBBLE_KIND_COLORS } from '@jbrowse/bandage-core/bubbles/classifyBubble'\nimport { EXON_COLOR } from '@jbrowse/bandage-core/genes/exonOutline'\nimport { geneCoverageNote } from '@jbrowse/bandage-core/labelLayout'\nimport { LABEL_PX, labelWidth } from '@jbrowse/bandage-core/overlayLabels'\nimport { isAlive } from '@jbrowse/mobx-state-tree'\nimport { observer } from 'mobx-react'\n\nimport LabelChip, { inChip } from './LabelChip'\nimport { PaneSvgLayer } from './PaneLayer'\n\nimport type { GraphPaneModel } from '../model'\nimport type { BubbleHalo } from '@jbrowse/bandage-core/bubbles/bubbleHalos'\nimport type { LabelLayout } from '@jbrowse/bandage-core/labelLayout'\n\n// Every chip drawn over the graph, above all of its ink: bubble names and gene\n// names on their pins. `overlayLabels` has placed\n// them against each other and against the row labels already.\n\nconst GENE_INK = '#1c1c22'\nconst TICK_PX = 9\nconst TICK_WIDTH = 3\n\n// What the gene chip under a point reads out, for the hover tooltip: those\n// chips leave the pointer to the canvas, so a drag can start on one\nexport function chipReadoutAt(\n  { genes }: Pick<LabelLayout, 'genes'>,\n  px: number,\n  py: number,\n) {\n  const pin = genes.find(chip => inChip(chip, px, py))?.item\n  if (!pin) {\n    return undefined\n  }\n  const { gene } = pin\n  const note = geneCoverageNote(pin)\n  return {\n    label: gene.name,\n    readout: `${gene.refName}:${gene.start.toLocaleString()}-${gene.end.toLocaleString()}${note ? `, ${note} in the cut` : ''}`,\n  }\n}\n\nconst LabelLayer = observer(function LabelLayer({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const { bubbles, genes, ticks } = model.overlayLabels\n  if (bubbles.length + genes.length + ticks.length === 0) {\n    return null\n  }\n  const { scaleY, translateY, contigThickness, hoveredBubble } = model\n  const hoveredTick = hoveredBubble\n    ? ticks.find(t => sameBubble(t.item.bubble, hoveredBubble))\n    : undefined\n  const tickAt = (target: EventTarget) =>\n    ticks[Number((target as Element).getAttribute('data-tick'))]\n  const dimmedBubble = (h: BubbleHalo) => model.bubbleFaded(h)\n  const isOpen = (h: BubbleHalo) => model.bubbleIsOpen(h.bubble)\n\n  return (\n    <PaneSvgLayer\n      model={model}\n      zIndex={3}\n      testId=\"graph-label-layer\"\n      pansWithDrawing\n    >\n      <g\n        data-testid=\"graph-bubble-ticks\"\n        onClick={e => {\n          const tick = tickAt(e.target)\n          if (tick) {\n            model.toggleBubble(tick.item.bubble)\n          }\n        }}\n        onMouseOver={e => {\n          const tick = tickAt(e.target)\n          if (tick) {\n            model.setHoveredBubble(tick.item.bubble)\n          }\n        }}\n        // a leave also fires as the view closing it unmounts the tick\n        onMouseOut={() => {\n          if (isAlive(model)) {\n            model.setHoveredBubble(null)\n          }\n        }}\n        onFocus={e => {\n          const tick = tickAt(e.target)\n          if (tick) {\n            model.setHoveredBubble(tick.item.bubble)\n          }\n        }}\n        onBlur={() => {\n          if (isAlive(model)) {\n            model.setHoveredBubble(null)\n          }\n        }}\n        onKeyDown={e => {\n          const tick = tickAt(e.target)\n          if (tick && (e.key === 'Enter' || e.key === ' ')) {\n            e.preventDefault()\n            model.toggleBubble(tick.item.bubble)\n          }\n        }}\n      >\n        {ticks.map(({ item: h, x, y }, i) => (\n          <rect\n            key={bubbleKey(h.bubble)}\n            data-tick={i}\n            role=\"button\"\n            tabIndex={0}\n            aria-label={`${h.label}, ${isOpen(h) ? 'close' : 'open'} bubble`}\n            x={x - TICK_WIDTH / 2}\n            y={y - TICK_PX}\n            width={TICK_WIDTH}\n            height={TICK_PX}\n            rx={TICK_WIDTH / 2}\n            fill={BUBBLE_KIND_COLORS[h.kind]}\n            opacity={dimmedBubble(h) ? 0.35 : 1}\n            style={{ pointerEvents: 'all', cursor: 'pointer' }}\n          />\n        ))}\n      </g>\n      {genes.map(({ item: pin, x, y, w, text }) => {\n        const { gene } = pin\n        return (\n          <g key={`${gene.name}-${gene.start}`}>\n            <line\n              x1={x}\n              x2={x}\n              y1={y - LABEL_PX - 2}\n              y2={pin.at.y * scaleY + translateY + contigThickness / 2}\n              stroke={GENE_INK}\n              strokeWidth={0.8}\n              strokeOpacity={0.6}\n            />\n            <LabelChip\n              x={x}\n              y={y}\n              w={w}\n              text={gene.name}\n              note={text.slice(gene.name.length) || undefined}\n              color={GENE_INK}\n              edge={EXON_COLOR}\n              italic\n              testId=\"graph-gene-pin-label\"\n            />\n          </g>\n        )\n      })}\n      {bubbles.map(({ item: h, x, y, w, text }) => (\n        <LabelChip\n          key={bubbleKey(h.bubble)}\n          x={x}\n          y={y}\n          w={w}\n          text={text}\n          color={BUBBLE_KIND_COLORS[h.kind]}\n          dimmed={dimmedBubble(h)}\n          title={`${h.label}\\n${h.bubble.segmentCount} segments${h.bubble.covering ? '' : isOpen(h) ? ' \u00B7 click to close' : ' \u00B7 click to open'}`}\n          testId=\"graph-bubble-halo-label\"\n          // the bubble the drawing is would open into this same drawing\n          onClick={\n            h.bubble.covering\n              ? undefined\n              : () => {\n                  model.toggleBubble(h.bubble)\n                }\n          }\n          // a leave also fires as the view closing it unmounts the chip\n          onHover={hovered => {\n            if (isAlive(model)) {\n              model.setHoveredBubble(hovered ? h.bubble : null)\n            }\n          }}\n        />\n      ))}\n      {hoveredTick ? (\n        <LabelChip\n          x={hoveredTick.x}\n          y={hoveredTick.y - TICK_PX - 4}\n          w={labelWidth(hoveredTick.item.label)}\n          text={hoveredTick.item.label}\n          color={BUBBLE_KIND_COLORS[hoveredTick.item.kind]}\n          testId=\"graph-bubble-tick-label\"\n        />\n      ) : null}\n    </PaneSvgLayer>\n  )\n})\n\nexport default LabelLayer\n", "import { useCallback } from 'react'\n\nimport { drawReferenceStrip } from '@jbrowse/bandage-core/referenceStrip'\nimport { observer } from 'mobx-react'\n\nimport { PaneOverlayCanvas } from './PaneLayer'\n\nimport type { GraphPaneModel } from '../model'\n\n// Each reference segment at its bp in the linear view, onto the pane's\n// canvas or the linear view's SVG export\nexport function paintReferenceStrip(\n  ctx: CanvasRenderingContext2D,\n  model: GraphPaneModel,\n  {\n    lit,\n    dpr,\n  }: { lit: GraphPaneModel['referenceStripLit'] | undefined; dpr: number },\n) {\n  const frame = model.hostBpFrame\n  if (frame) {\n    drawReferenceStrip(ctx, model.referenceStripBlocks, frame, {\n      width: model.paneWidth,\n      lit,\n      dpr,\n    })\n  }\n}\n\n// Each reference segment at its bp in the linear view, over a drawing that\n// has no bp axis of its own. Repainted by an autorun, so a pan in the linear\n// view moves the strip in the same frame as its other tracks.\nconst ReferenceStripOverlay = observer(function ReferenceStripOverlay({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const paint = useCallback(\n    (ctx: CanvasRenderingContext2D, dpr: number) => {\n      paintReferenceStrip(ctx, model, { lit: model.referenceStripLit, dpr })\n    },\n    [model],\n  )\n  return (\n    <PaneOverlayCanvas\n      model={model}\n      zIndex={5}\n      shown={model.referenceStripShown}\n      testId=\"graph-reference-strip\"\n      paint={paint}\n    />\n  )\n})\n\nexport default ReferenceStripOverlay\n", "import { useCallback } from 'react'\n\nimport { drawTubeMapRuler } from '@jbrowse/bandage-core/tubeMap/axis'\nimport { drawTubeMapConnectors } from '@jbrowse/bandage-core/tubeMap/connectors'\nimport { drawDeviationMarks } from '@jbrowse/bandage-core/tubeMap/deviations'\nimport { drawTubeMap } from '@jbrowse/bandage-core/tubeMap/draw'\nimport { drawTubeMapGenes } from '@jbrowse/bandage-core/tubeMap/genes'\nimport { observer } from 'mobx-react'\n\nimport { PaneOverlayCanvas } from './PaneLayer'\nimport {\n  PANEL_TITLE_FONT,\n  drawBundleCounts,\n  drawSqueezedLengths,\n} from '../tubeMapPanels'\n\n// variants folded into a box mark texture under a panel's routes\nconst PANEL_TICK_ALPHA = 0.45\n\nimport type { GraphPaneModel } from '../model'\n\n// The tubes, their connectors, genes and ruler, onto a canvas sized to the\n// pane or onto the linear view's SVG export\nexport function paintTubeMap(\n  ctx: CanvasRenderingContext2D,\n  model: GraphPaneModel,\n  { highlightNode }: { highlightNode: string | null },\n) {\n  const picture = model.tubeMapPicture\n  const frame = model.tubeMapFrame\n  if (!picture || !frame) {\n    return\n  }\n  const width = model.paneWidth\n  const panels = model.tubeMapPanelViews\n  if (panels) {\n    paintPanels(ctx, model, panels, highlightNode)\n    return\n  }\n  const tubeFrame = {\n    ...frame,\n    width,\n    highlightNode,\n    tubeColors: model.tubeMapTubeColors,\n    nodeColors: model.tubeMapNodeColors,\n  }\n  drawTubeMap(ctx, picture, tubeFrame)\n  const drawn = model.layoutResult?.tubeMap\n  if (drawn) {\n    drawBundleCounts(ctx, picture, drawn.graph, tubeFrame)\n    drawSqueezedLengths(ctx, drawn, tubeFrame)\n  }\n  drawDeviationMarks(ctx, model.tubeMapDeviations, tubeFrame)\n  drawTubeMapConnectors(\n    ctx,\n    model.tubeMapConnectors,\n    model.connectorZoneBottom,\n    tubeFrame,\n  )\n  const { bounds } = picture\n  drawTubeMapGenes(ctx, model.tubeMapGenes, tubeFrame, frame.y(bounds.minY) - 2)\n  const boxes = model.tubeMapRulerBoxes\n  if (boxes) {\n    drawTubeMapRuler(\n      ctx,\n      boxes,\n      tubeFrame,\n      frame.y(bounds.maxY) + 4,\n      model.layoutResult?.referenceAxis,\n    )\n  }\n}\n\n// Each panel of a split tube map under a rule and its title, which the canvas\n// draws so a figure's SVG carries them\nfunction paintPanels(\n  ctx: CanvasRenderingContext2D,\n  model: GraphPaneModel,\n  panels: NonNullable<GraphPaneModel['tubeMapPanelViews']>,\n  highlightNode: string | null,\n) {\n  const width = model.paneWidth\n  for (const p of panels) {\n    if (p.bottom < 0 || p.titleTop > model.canvasHeight) {\n      continue\n    }\n    const tubeFrame = {\n      ...p.frame,\n      width,\n      highlightNode,\n      tubeColors: p.tubeColors,\n      nodeColors: p.nodeColors,\n    }\n    drawTubeMap(ctx, p.picture, tubeFrame)\n    drawBundleCounts(ctx, p.picture, p.panel.result.tubeMap.graph, tubeFrame)\n    drawSqueezedLengths(ctx, p.panel.result.tubeMap, tubeFrame)\n    ctx.globalAlpha = PANEL_TICK_ALPHA\n    drawDeviationMarks(ctx, p.deviations, tubeFrame)\n    ctx.globalAlpha = 1\n    ctx.strokeStyle = 'rgba(0,0,0,0.15)'\n    ctx.lineWidth = 1\n    ctx.beginPath()\n    ctx.moveTo(0, Math.round(p.titleTop) + 0.5)\n    ctx.lineTo(width, Math.round(p.titleTop) + 0.5)\n    ctx.stroke()\n    ctx.font = PANEL_TITLE_FONT\n    ctx.textAlign = 'left'\n    ctx.textBaseline = 'top'\n    ctx.fillStyle = 'rgba(0,0,0,0.85)'\n    ctx.fillText(p.label, 6, p.titleTop + 4)\n  }\n  const last = panels.at(-1)\n  const boxes = model.tubeMapPanelRulerBoxes\n  if (last && boxes) {\n    drawTubeMapRuler(\n      ctx,\n      boxes,\n      { ...last.frame, width },\n      last.bottom + 4,\n      true,\n    )\n  }\n}\n\n// The tube map's ink, over the canvas, which draws nothing under a tube map\n// layout. Above the tubes go the session's genes in a view of its own, or in\n// a linear view the bands tying each reference box to its bp there; under\n// them a reference ruler, unless the linear view's is already the axis.\n// Repainted by an autorun on every change of transform, so a pan in the linear\n// view above moves the tubes in the same frame as its other tracks.\nconst TubeMapOverlay = observer(function TubeMapOverlay({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const paint = useCallback(\n    (ctx: CanvasRenderingContext2D) => {\n      paintTubeMap(ctx, model, { highlightNode: model.selectedNode })\n    },\n    [model],\n  )\n  return (\n    <PaneOverlayCanvas\n      model={model}\n      zIndex={1}\n      shown={!!model.tubeMapPicture}\n      testId=\"graph-tube-map\"\n      paint={paint}\n    />\n  )\n})\n\nexport default TubeMapOverlay\n", "const host = JBrowseExports[\"@jbrowse/render-core/marks\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/render-core/marks\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const BandPen = /* @__PURE__ */ read(\"BandPen\")\nexport const CONNECTOR_ARROW = /* @__PURE__ */ read(\"CONNECTOR_ARROW\")\nexport const CONNECTOR_BOW = /* @__PURE__ */ read(\"CONNECTOR_BOW\")\nexport const CONNECTOR_DASHED = /* @__PURE__ */ read(\"CONNECTOR_DASHED\")\nexport const CONNECTOR_LEADING_2 = /* @__PURE__ */ read(\"CONNECTOR_LEADING_2\")\nexport const CONNECTOR_MAX_REACH_PX = /* @__PURE__ */ read(\"CONNECTOR_MAX_REACH_PX\")\nexport const CONNECTOR_MINUS_1 = /* @__PURE__ */ read(\"CONNECTOR_MINUS_1\")\nexport const CONNECTOR_MINUS_2 = /* @__PURE__ */ read(\"CONNECTOR_MINUS_2\")\nexport const CONNECTOR_STRAIGHT = /* @__PURE__ */ read(\"CONNECTOR_STRAIGHT\")\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_LINE_BANDS = /* @__PURE__ */ read(\"RAMP_LINE_BANDS\")\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 connectorEnds = /* @__PURE__ */ read(\"connectorEnds\")\nexport const connectorMark = /* @__PURE__ */ read(\"connectorMark\")\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 linkApex = /* @__PURE__ */ read(\"linkApex\")\nexport const linkFeet = /* @__PURE__ */ read(\"linkFeet\")\nexport const linkInstance = /* @__PURE__ */ read(\"linkInstance\")\nexport const linkLabelAnchor = /* @__PURE__ */ read(\"linkLabelAnchor\")\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 pointInstance = /* @__PURE__ */ read(\"pointInstance\")\nexport const pointMark = /* @__PURE__ */ read(\"pointMark\")\nexport const rampAsThreshold = /* @__PURE__ */ read(\"rampAsThreshold\")\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 rowTableKeys = /* @__PURE__ */ read(\"rowTableKeys\")\nexport const rowTableTextures = /* @__PURE__ */ read(\"rowTableTextures\")\nexport const ruleMark = /* @__PURE__ */ read(\"ruleMark\")\nexport const shiftInk = /* @__PURE__ */ read(\"shiftInk\")\nexport const spanMark = /* @__PURE__ */ read(\"spanMark\")\nexport const spansInRow = /* @__PURE__ */ read(\"spansInRow\")\nexport const thresholdBandOf = /* @__PURE__ */ read(\"thresholdBandOf\")\nexport const valueWindow = /* @__PURE__ */ read(\"valueWindow\")\nexport const withPassId = /* @__PURE__ */ read(\"withPassId\")\nexport default host && host.__esModule ? host.default : host", "import {\n  GAP_PX,\n  MISSING_PX,\n  coalesceRuns,\n  gapStyle,\n  runPaint,\n} from '@jbrowse/bandage-core/layout/walkRowDraw'\nimport { hslToRgb } from '@jbrowse/bandage-core/renderer/GeometryBuilder'\nimport { packAbgr } from '@jbrowse/bandage-core/renderer/colorBits'\nimport { spanMark } from '@jbrowse/render-core/marks'\n\nimport type { WalkRow, WalkRun } from '@jbrowse/bandage-core/layout/walkRows'\nimport type { MarkContext2D, SpanChannels } from '@jbrowse/render-core/marks'\n\ntype Rgb = [number, number, number]\n\n// The colours runPaint writes: `#rrggbb`, `rgb(r, g, b)` and\n// `hsl(h, s%, l%)`\nexport function cssRgb(css: string): Rgb {\n  if (css.startsWith('#')) {\n    const v = Number.parseInt(css.slice(1), 16)\n    return [(v >> 16) & 0xff, (v >> 8) & 0xff, v & 0xff]\n  }\n  const [a = 0, b = 0, c = 0] = css.match(/[\\d.]+/g)!.map(Number)\n  return css.startsWith('hsl')\n    ? (hslToRgb(a, b / 100, c / 100).map(v => v * 255) as Rgb)\n    : [a, b, c]\n}\n\nconst abgr = ([r, g, b]: Rgb) =>\n  packAbgr(Math.round(r), Math.round(g), Math.round(b), 255)\n\nconst cssAbgr = new Map<string, number>()\nfunction packCss(css: string) {\n  let v = cssAbgr.get(css)\n  if (v === undefined) {\n    v = abgr(cssRgb(css))\n    cssAbgr.set(css, v)\n  }\n  return v\n}\n\n/**\n * A run as the pieces it paints in, each `[start, end, abgr]` in bp along\n * the row: one for a solid fill, and for a gradient one per pixel or per\n * degree of hue, whichever is fewer, coloured as the SVG gradient through\n * the same stops colours its middle\n */\nexport function runPieces(\n  run: WalkRun,\n  ramp: { start: number; end: number } | undefined,\n  pxPerBp: number,\n): [number, number, number][] {\n  const end = run.start + run.bp\n  const paint = runPaint(run, ramp)\n  if ('fill' in paint) {\n    return [[run.start, end, packCss(paint.fill)]]\n  }\n  const stops = paint.stops.map(cssRgb)\n  const hues = paint.stops.map(css => Number(/[\\d.]+/.exec(css)![0]))\n  const hueSpan = Math.abs(hues.at(-1)! - hues[0]!)\n  const n = Math.max(\n    1,\n    Math.min(Math.ceil(run.bp * pxPerBp), Math.ceil(hueSpan), run.bp),\n  )\n  const pieces: [number, number, number][] = []\n  for (let k = 0; k < n; k++) {\n    const t = ((k + 0.5) / n) * (stops.length - 1)\n    const i = Math.min(Math.floor(t), stops.length - 2)\n    const a = stops[i]!\n    const b = stops[i + 1]!\n    const f = t - i\n    pieces.push([\n      Math.round(run.start + (run.bp * k) / n),\n      Math.round(run.start + (run.bp * (k + 1)) / n),\n      abgr([0, 1, 2].map(j => a[j]! + (b[j]! - a[j]!) * f) as Rgb),\n    ])\n  }\n  return pieces\n}\n\nexport interface WalkRowSpans {\n  bars: SpanChannels & { color: Uint32Array }\n  gaps: SpanChannels & { color: Uint32Array }\n  // gaps of bases the graph lacks, which draw as a hairline\n  hairlines: SpanChannels & { color: Uint32Array }\n  // where each drawn row's spans start in `bars`, `gaps` and `hairlines`\n  barRows: Uint32Array\n  gapRows: Uint32Array\n  hairlineRows: Uint32Array\n  // the furthest any span reaches along its row, in bp, and at least 1\n  longest: number\n}\n\nfunction channels(capacity: number) {\n  return {\n    x: new Uint32Array(capacity),\n    x2: new Uint32Array(capacity),\n    row: new Uint32Array(capacity),\n    color: new Uint32Array(capacity),\n    count: 0,\n  }\n}\n\nfunction slice<T extends SpanChannels & { color: Uint32Array }>(\n  c: T,\n  a: number,\n  b: number,\n) {\n  return {\n    x: c.x.subarray(a, b),\n    x2: c.x2.subarray(a, b),\n    row: c.row.subarray(a, b),\n    color: c.color.subarray(a, b),\n    count: b - a,\n  }\n}\n\n/**\n * Each row's runs as `walkRowsTree` coalesces and colours them at\n * `pxPerBp`, as span channels: `x`/`x2` in bp along the row, `row` its index\n * among `rows`. Gaps go apart, since they draw thinner, and gaps of bases the\n * graph lacks apart again, as a hairline.\n */\nexport function walkRowSpans(\n  rows: WalkRow[],\n  pxPerBp: number,\n  ramp?: { start: number; end: number },\n): WalkRowSpans {\n  const pieces = rows.map(r =>\n    coalesceRuns(r.runs, pxPerBp).map(run => ({\n      gap: run.gap,\n      hairline: run.gap && gapStyle(run.cause).px === MISSING_PX,\n      pieces: runPieces(run, ramp, pxPerBp),\n    })),\n  )\n  let total = 0\n  for (const runs of pieces) {\n    for (const run of runs) {\n      total += run.pieces.length\n    }\n  }\n  const bars = channels(total)\n  const gaps = channels(total)\n  const hairlines = channels(total)\n  const barRows = new Uint32Array(rows.length + 1)\n  const gapRows = new Uint32Array(rows.length + 1)\n  const hairlineRows = new Uint32Array(rows.length + 1)\n  let longest = 1\n  pieces.forEach((runs, row) => {\n    for (const run of runs) {\n      const c = run.hairline ? hairlines : run.gap ? gaps : bars\n      for (const [x, x2, color] of run.pieces) {\n        const i = c.count++\n        c.x[i] = x\n        c.x2[i] = x2\n        c.row[i] = row\n        c.color[i] = color\n        longest = Math.max(longest, c.x2[i])\n      }\n    }\n    barRows[row + 1] = bars.count\n    gapRows[row + 1] = gaps.count\n    hairlineRows[row + 1] = hairlines.count\n  })\n  return {\n    bars: slice(bars, 0, bars.count),\n    gaps: slice(gaps, 0, gaps.count),\n    hairlines: slice(hairlines, 0, hairlines.count),\n    barRows,\n    gapRows,\n    hairlineRows,\n    longest,\n  }\n}\n\nexport interface WalkRowSpanFrame {\n  scaleX: number\n  scaleY: number\n  translateX: number\n  translateY: number\n  width: number\n  height: number\n  rowPx: number\n  barPx: number\n  origin: number\n  // runs of rows whose y is `rowY(first)` plus a row pitch each, as the\n  // reference row and each grouped section are\n  blocks: { first: number; count: number; rowY: number }[]\n}\n\n/**\n * Paints the spans through render-core's span mark, a block of rows at a\n * time: row i's bar centred where `walkRowsTree` centres it, `barPx` tall,\n * its x at `origin + bp` through the pane's transform.\n */\nexport function paintWalkRowSpans(\n  ctx: MarkContext2D,\n  spans: WalkRowSpans,\n  f: WalkRowSpanFrame,\n) {\n  const { longest } = spans\n  const block = {\n    start: 0,\n    end: longest,\n    screenStartPx: f.origin * f.scaleX + f.translateX,\n    screenEndPx: (f.origin + longest) * f.scaleX + f.translateX,\n    reversed: false,\n    displayedRegionIndex: 0,\n  }\n  const frame = { canvasWidth: f.width, canvasHeight: f.height }\n  const rowHeight = f.rowPx * f.scaleY\n  for (const { first, count, rowY } of f.blocks) {\n    // slot `row` centres at (rowY + (row - first) * rowPx) * scaleY + translateY\n    const scrollTop =\n      rowHeight / 2 - f.translateY - (rowY - first * f.rowPx) * f.scaleY\n    const top = (rowY - f.rowPx / 2) * f.scaleY + f.translateY\n    if (top > f.height || top + count * rowHeight < 0) {\n      continue\n    }\n    for (const [c, starts, barPx] of [\n      [spans.bars, spans.barRows, f.barPx],\n      [spans.gaps, spans.gapRows, Math.min(GAP_PX, f.barPx)],\n      [spans.hairlines, spans.hairlineRows, Math.min(MISSING_PX, f.barPx)],\n    ] as const) {\n      spanMark.paintBlock(\n        ctx,\n        slice(c, starts[first]!, starts[first + count]!),\n        block,\n        frame,\n        {\n          rowHeight,\n          rowProportion: barPx / rowHeight,\n          minWidthPx: 1,\n          seamPx: 0,\n          scrollTop,\n        },\n      )\n    }\n  }\n}\n", "import { useCallback, useMemo } from 'react'\n\nimport { computed } from 'mobx'\nimport { observer } from 'mobx-react'\n\nimport ElTree, { useSvgId } from './ElTree'\nimport { PaneOverlayCanvas, PaneSvgLayer } from './PaneLayer'\nimport { paintWalkRowBlocks } from '../walkRowBlocks'\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\nconst RIBBON_FORWARD = 'rgba(160, 196, 232, 0.55)'\nconst RIBBON_REVERSED = 'rgba(160, 140, 220, 0.55)'\n\n// Under the bars, a ribbon from each stretch of a row to where the row below\n// walks the same nodes, lavender where it walks them backwards, as ggbandage\n// draws them: neighbours that share a copy, an inversion or a duplication\n// read off the ribbons' shape\nfunction WalkRowRibbonsCanvas({ model }: { model: GraphPaneModel }) {\n  const paint = useCallback(\n    (ctx: CanvasRenderingContext2D) => {\n      const links = model.walkRowRibbons\n      const bars = model.walkRowBars\n      const place = model.walkRowPlacement\n      const pitch = model.walkRowPitch\n      if (!links || !bars || !place || !pitch) {\n        return\n      }\n      const { scaleX, scaleY, translateX, translateY } = model.screenTransform\n      const x = (offset: number) => (bars.origin + offset) * scaleX + translateX\n      const half = pitch.barPx / 2\n      for (const { row, a0, a1, b0, b1 } of links) {\n        const top = place.rowY(row) * scaleY + translateY + half\n        const bottom = place.rowY(row + 1) * scaleY + translateY - half\n        ctx.fillStyle = b0 > b1 ? RIBBON_REVERSED : RIBBON_FORWARD\n        ctx.beginPath()\n        ctx.moveTo(x(a0), top)\n        ctx.lineTo(x(a1), top)\n        ctx.lineTo(x(b1), bottom)\n        ctx.lineTo(x(b0), bottom)\n        ctx.closePath()\n        ctx.fill()\n      }\n    },\n    [model],\n  )\n  return (\n    <PaneOverlayCanvas\n      model={model}\n      zIndex={2}\n      testId=\"graph-walk-rows-ribbons\"\n      paint={paint}\n    />\n  )\n}\n\n// Over the bars, the lettered blocks: copy A on two rows, and C where another\n// row has A, read at a glance\nfunction WalkRowBlocksCanvas({ model }: { model: GraphPaneModel }) {\n  const paint = useCallback(\n    (ctx: CanvasRenderingContext2D) => {\n      const blocks = model.sharedBlocks\n      const bars = model.walkRowBars\n      const place = model.walkRowPlacement\n      const pitch = model.walkRowPitch\n      if (!blocks || !bars || !place || !pitch) {\n        return\n      }\n      const { scaleX, scaleY, translateX, translateY } = model.screenTransform\n      paintWalkRowBlocks(ctx, blocks, {\n        x: offset => (bars.origin + offset) * scaleX + translateX,\n        rowCentre: row => place.rowY(row) * scaleY + translateY,\n        barPx: pitch.barPx,\n      })\n    },\n    [model],\n  )\n  return (\n    <PaneOverlayCanvas\n      model={model}\n      zIndex={3}\n      testId=\"graph-walk-rows-blocks\"\n      paint={paint}\n    />\n  )\n}\n\n// Its own observer, so moving between rows redraws this rect and not every row\nconst HoveredWalkRow = observer(function HoveredWalkRow({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const bars = model.walkRowBars\n  const place = model.walkRowPlacement\n  const pitch = model.walkRowPitch\n  if (!bars || !place || !pitch || !model.hoveredWalkRowText) {\n    return null\n  }\n  const rows = [bars.reference, ...bars.rows]\n  const index = rows.findIndex(r => r.name === model.hoveredWalkRow)\n  const row = rows[index]\n  if (!row) {\n    return null\n  }\n  const start = model.toScreen({ x: bars.origin, y: place.rowY(index) })\n  return (\n    <rect\n      data-testid=\"graph-walk-row-hovered\"\n      x={start.x - 2}\n      y={start.y - pitch.rowPx / 2 - 1}\n      width={row.bp * model.scaleX + 4}\n      height={pitch.rowPx + 2}\n      fill=\"none\"\n      stroke=\"#111\"\n      strokeWidth={1}\n    />\n  )\n})\n\n// `vector` for an SVG export, which draws the bars as walkRowsTree's rects\nconst WalkRowsOverlay = observer(function WalkRowsOverlay({\n  model,\n  vector = false,\n}: {\n  model: GraphPaneModel\n  vector?: boolean\n}) {\n  const idPrefix = useSvgId()\n  const bars = model.walkRowBars\n  const place = model.walkRowPlacement\n  const pitch = model.walkRowPitch\n  if (!bars || !place || !pitch) {\n    return null\n  }\n  const { paneWidth: width, canvasHeight } = model\n  // the canvas paints the bars, except in a vector export\n  const frame = {\n    ...model.screenTransform,\n    width,\n    height: canvasHeight,\n    ...pitch,\n    bars: vector,\n  }\n  return (\n    <>\n      {vector || !model.walkRowRibbons ? null : (\n        <WalkRowRibbonsCanvas model={model} />\n      )}\n      {vector ? null : <WalkRowSpansCanvas model={model} />}\n      {vector || !model.sharedBlocks ? null : (\n        <WalkRowBlocksCanvas model={model} />\n      )}\n      <PaneSvgLayer\n        model={model}\n        zIndex={3}\n        overflow=\"visible\"\n        testId=\"graph-walk-rows\"\n      >\n        {walkRowTrees(\n          bars,\n          model.walkRowGroups?.sections ?? [],\n          place.rowY,\n          frame,\n          {\n            ramp: model.referenceRampDomain,\n            rowGenes: model.walkRowGenes,\n            idPrefix,\n          },\n        ).map((tree, i) => (\n          <ElTree key={i} el={tree} />\n        ))}\n        {place.headers.map(header => (\n          <text\n            key={header.key}\n            x={10}\n            y={\n              model.toScreen({ x: 0, y: header.top }).y + SECTION_HEADER_PX - 4\n            }\n            fontFamily=\"sans-serif\"\n            fontSize={11}\n            fontWeight=\"bold\"\n            fill=\"#333\"\n            data-testid=\"graph-walk-section\"\n          >\n            {header.title}\n          </text>\n        ))}\n        <HoveredWalkRow model={model} />\n      </PaneSvgLayer>\n    </>\n  )\n})\n\nexport default WalkRowsOverlay\n"],
+  "mappings": 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"a1", "b0", "b1", "top", "bottom", "WalkRowBlocksCanvas", "paintWalkRowBlocks", "HoveredWalkRow", "observer", "rows", "index", "r", "start", "WalkRowsOverlay", "vector", "idPrefix", "useSvgId", "width", "canvasHeight", "frame", "jsxs", "Fragment", "PaneSvgLayer", "walkRowTrees", "tree", "i", "ElTree", "header", "SECTION_HEADER_PX", "WalkRowsOverlay_default"]
+}

package/dist/chunks/chunk-D7MOOK6H.js

@@ -0,0 +1,4 @@
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t&&n?Tt({nodeId:e,nodeById:t,neighbors:n}):void 0}var Yr=uo.views(e=>({sessionTrack(t){return Y(e).tracks.find(n=>n.trackId===t)},get grammar(){return{}},get hasPendingSource(){return!1},get canRetryLoad(){return!1},get sourceTrack(){return Vr(()=>Rn(e).configuration)},get containingView(){return Vr(()=>Rt(e))}})).views(e=>{let t=a=>Bn(a,{equals:(s,i)=>JSON.stringify(s)===JSON.stringify(i)}),n=t(()=>Hr(e.grammar.encoding?.color)),o=t(()=>Ue(e.grammar.facet)),r=t(()=>{let a=vo(e.grammar.facet);return a&&a.field!=="walk"&&a.field!=="sample"?a:void 0});return{get chosenLayoutMode(){return e.grammar.layoutMode??"force"},get chosenColorScheme(){return Wr(e.grammar.encoding?.color)},get statedColorDomain(){return n.get()},get chosenHover(){return e.grammar.hover??"nodes"},get nodeWidth(){return kt(e.grammar.size).width},get contigThickness(){return kt(e.grammar.size).px},get linkWidth(){return kt(e.grammar.size).links},get layerSet(){return _r(e.grammar.layers)},get drawPaths(){return this.layerSet.has("paths")},get showBubbles(){return this.layerSet.has("bubbles")},get showDeletionEdges(){return this.layerSet.has("deletions")},get showGenes(){return this.layerSet.has("genes")},get showReferenceStrip(){return this.layerSet.has("referenceStrip")},get walkStrip(){return this.layerSet.has("walkStrip")},get walkRibbons(){return this.layerSet.has("walkRibbons")},get facetSetting(){return o.get()},get walkRowGroupBy(){return r.get()},get walkRowSamples(){let a=e.grammar.rows?.kept;return Array.isArray(a)?a:void 0},get walkRowOrder(){return e.grammar.rows?.order==="shared"?"shared":void 0},get hoverLightsEverything(){return this.chosenHover==="everything"},get litNode(){return this.chosenHover==="off"?null:e.hoveredNode}}}).views(e=>({get paneWidth(){return Rt(e).width},get paneMeasured(){return!0},get drawnGraph(){return e.layoutResult?.tubeMap?.graph??e.graph}})).views(e=>({get nodeById(){return e.drawnGraph&&Xr(e.drawnGraph)},get nodeLengths(){let t=new Map;for(let n of e.drawnGraph?.nodes??[])t.set(n.id,n.length);return t},get nodeCount(){return e.graph?.nodes.length??0},get edgeCount(){return e.graph?.edges.length??0},get pathCount(){return e.graph?.paths?.length??0},get legendAtRest(){return e.hoveredNode===null&&e.hoveredRowWalks.length===0},get hasGraph(){return e.graph!==void 0},get geometryPainted(){return lo(e)},get paintSuperseded(){return!this.geometryPainted},get showLoading(){return e.error===void 0&&(e.isLoading||e.hasPendingSource||e.graph!==void 0&&!this.geometryPainted)},get canCancelLoad(){return e.isLoading&&!e.layoutResult},get usesLayoutEngine(){return e.graph?Yt(e.chosenLayoutMode,e.graph):!1},get anchorPaths(){return e.graph?.anchorPaths??[]},get walkChoices(){let t=e.graph?.paths;return t?.length?Se(t):[]},get effectiveDrawPaths(){return e.drawPaths&&Ve(e.graph?.paths?.length??0)},get activeReferencePath(){return e.graph?.referencePath},get rampDomain(){let t=e.openBubbles.at(-1);return t&&!t.offReference&&t.end>t.start?{start:t.start,end:t.end}:e.statedColorDomain??e.graphRegion},get drawnReferenceRamp(){let t=e.drawnGraph;return t?Pe(t,this.rampDomain):void 0},get walkRamp(){return e.walkLayers.some(t=>t.color?.field==="reference")?this.drawnReferenceRamp:void 0},get modeDrawsNodes(){return j(e.chosenLayoutMode).drawsNodes},get liftedWalkLayers(){return e.walkLayers.length>0||!this.modeDrawsNodes?e.walkLayers:e.hoveredRowWalks.map(t=>({walk:t}))},get walkLift(){let{graph:t}=e,n=this.liftedWalkLayers;return t&&!e.walkCut&&n.length>0&&!e.layoutResult?.tubeMap?it(t,n,this.walkRamp):void 0},get facetPanels(){let{graph:t}=e,n=this.walkLift;return e.facetSetting.field!==""&&this.modeDrawsNodes&&t&&n&&e.walkLayers.length>1&&n.walks.length>1?ct(t,n,e.walkLayers,this.walkRamp):void 0},get drawnWalks(){return this.facetPanels?.map(t=>t.walks[0])??this.walkLift?.walks??[]},get liftsWalks(){return!so.has(e.chosenLayoutMode)},get walkReference(){let t=this.walkLift?.referenceDomain;return t&&{...t,name:e.graphRegion?.refName}},get walkLabels(){return Xe(this.walkChoices)},walkLabel(t){return this.walkLabels.get(t)??t},get liftPaintsOffReference(){return!!this.walkLift?.walks.some(t=>t.encoding.field!=="walk"&&[...t.colors.values()].includes(no))},get liftedWalksLabel(){let t=this.walkLift?.walks??[];return t.length===1?this.walkLabel(t[0].name):"these walks"},get effectiveColorScheme(){return e.layoutResult?.tubeMap&&(this.tubeMapReads||e.chosenColorScheme==="auto")?"uniform":Oe(e.chosenColorScheme,e.graph)},get tubeMapReads(){let t=e.layoutResult;return!t?.tubeMapPanels&&(t?.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 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?bt(e.graph):[]},get openBubbleInsides(){let{graph:t}=e;return t?e.openBubbles.map(n=>bt(He(t,de(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(de(t)),r=new Set(n.nodes.filter(s=>o.has(s.name)).map(s=>s.id)),a=new Set;return n.edges.forEach((s,i)=>{r.has(s.from)&&r.has(s.to)&&a.add(i)}),{walks:[],nodeIds:r,edgeIndexes:a,names:new Set}},get drawnHighlight(){return e.walkLift??this.openBubbleFocus},bubbleIsOpen(t){return e.openBubbles.some(n=>tt(n,t))},bubbleFaded({bubble:t,nodeIds:n}){let o=e.walkLift,r=this.openBubbleFocus;return o?!n.some(a=>o.nodeIds.has(a)):!!r&&!this.bubbleIsOpen(t)&&!n.every(a=>r.nodeIds.has(a))}})).views(e=>({get bubbles(){let t=e.indexBubbles?.length?e.indexBubbles:e.derivedBubbles,n=new Set(t.map(nt));return[...t,...e.openBubbleInsides.flat().filter(o=>!n.has(nt(o))&&n.add(nt(o)))]},get foldNote(){let t=e.foldedBelowBp;return t===void 0?void 0:`variants under ${Dn(t)} folded into the reference`}})).views(e=>({get cutHaplotypes(){},get sourceAdapter(){let t=e.sourceTrack;return t?rr(e,t):void 0},get sourceTrackId(){return e.sourceTrack?.trackId},get sessionTracks(){let t=Y(e);return t.tracks.map(n=>({trackId:n.trackId,name:Cn(n,t),adapterType:je(n).type,assemblies:Jt(t,n)}))}})).views(e=>({get assemblyTrackChoices(){let t=e.graphRegion,n=t&&Kt(Y(e),t.assemblyName);return n?e.sessionTracks.filter(o=>o.assemblies.includes(n)):[]}})).views(e=>({get geneTrackChoices(){return e.assemblyTrackChoices.filter(t=>pt.has(t.adapterType))},get repeatTrackChoices(){return e.assemblyTrackChoices.filter(t=>Ko.has(t.adapterType))},get repeatChoices(){return e.repeatArrays??[]}})).views(e=>({get repeatTrack(){return Jo(e.repeatTrackChoices,e.repeatTrackId)},get geneTrack(){return lt(e.geneTrackChoices,e.geneTrackId)},get walkRowAnnotation(){return mt(this.geneTrack)},get repeatOptions(){return[{value:"",label:"Whole window"},...e.repeatChoices.map(({key:t,name:n,unit:o})=>({value:t,label:`${n} \xB7 ${o.toLocaleString()} bp unit`}))]},get selectedRepeat(){return e.repeatChoices.find(t=>t.key===e.repeatKey)},get backbone(){return e.graph?Nn(e.graph):void 0},get cutWalkRows(){let t=e.walkCut,n=t?.walkRowRuns,o=this.rowVisitsNeeded;return t&&n&&o&&e.graphRegion?Dr(t,e.graphRegion,void 0,!0):n?Pt(n):e.graph?ue(e.graph,e.graphRegion,void 0,{visits:o}):void 0},get rowVisitsNeeded(){return e.chosenLayoutMode==="walkrows"&&(e.walkRibbons||e.layerSet.has("walkBlocks")||e.walkRowOrder==="shared")},assemblySpellings(t){let{assemblyManager:n}=Y(e),o=n.has(t)?n.get(t):void 0,r=e.sourceAdapter?.assemblyNameToPanSN??{},a=[t,...o?[o.name,...o.aliases]:[]];return{name:t,aliases:[...a,...a.flatMap(s=>r[s]??[])]}},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=e.containingView;if(!t)return;let n=qo(t,e.geneTrack?.trackId);return n.length?new Or({filters:n,jexl:xn(e).pluginManager.jexl}):void 0},get geneFeatures(){let t=e.geneTrackFeatures,n=this.geneLaneFilter;return t?Zo(n?t.filter(o=>n.passes(o)):t):void 0},get backboneGenes(){let{backbone:t}=e,{geneAssembly:n,geneFeatures:o}=this,r=e.drawsLoadedReference||n!==void 0&&Pn(t,[n])!==void 0;return t&&o&&r?An(o,t):void 0}})).views(e=>({get nodeNeighbors(){return e.drawnGraph?Q(e.drawnGraph):void 0},get nodeInk(){return qe(e.drawnGraph,e.nodeById,e.contigThickness,e.nodeWidth)},get depthRange(){let t=e.graph?.nodes;if(!t?.length)return;let n=1/0,o=-1/0;for(let{depth:r}of t)n=Math.min(n,r),o=Math.max(o,r);return{min:n,max:o,mean:Zn(e.graph)}},get busiestLink(){return e.graph?Qn(e.graph):0},get allDeletions(){return e.graph&&this.drawsNodes?Fe(e.graph):[]},get cohortWalkRows(){if(e.chosenLayoutMode!=="walkrows"||!e.graph)return;let t=e.selectedRepeat,n=e.walkCut,o=e.rowVisitsNeeded,r=t?n?Dr(n,t,t.unit,o):ue(e.graph,t,t.unit,{visits:o}):e.cutWalkRows;if(!r)return;let[a,...s]=Qo([r.reference,...r.rows],t?.calls);return{...r,reference:a,rows:s}},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&&Tn(t)?t:void 0},get walkRowGroupFields(){return So(e.walkRowSampleTable)},get tubeMapColoring(){let t=e.tubeMapColorBy,n=e.walkRowSampleTable;if(!t||!n||!this.walkRowGroupFields.includes(t))return;let o=To(t,n),r=(e.graph?.paths??[]).map(a=>ce(a.name).name).filter(a=>a!==e.graph?.referencePath);return{field:t,valueOf:o,palette:Po(r.map(o)),unvalued:r.some(a=>o(a)==="")}},get tableGroupBy(){let t=e.walkRowGroupBy,n=e.walkRowSampleTable;return t&&n&&this.walkRowGroupFields.includes(t.field)?{groupBy:t,table:n}:void 0},get tubeMapPanelSplit(){let{field:t,sort:n}=e.facetSetting,o=this.tableGroupBy;return t!==""?{by:t,sort:n}:o?{by:"column",...o.groupBy,table:o.table}:void 0},get keptCohortRows(){let t=this.cohortWalkRows,n=t&&ve(t.rows,e.walkRowSamples);if(!t||!n||e.walkRowOrder!=="shared")return n;let o=[t.reference,...n];return hn(o).filter(r=>r>0).map(r=>o[r])},get walkRowGroups(){let t=this.keptCohortRows,n=this.tableGroupBy;return t&&n?Mo(t,n.table,n.groupBy):void 0},get walkRowBars(){let t=this.cohortWalkRows,n=this.keptCohortRows;return t&&n?{...t,rows:this.walkRowGroups?.rows??n}:void 0},get walkRowRibbons(){let t=this.walkRowBars;if(!e.walkRibbons||!e.rowVisitsNeeded||!t)return;let n=[t.reference,...t.rows];return fn(n,we(n))},get sharedBlocks(){let t=this.walkRowBars;if(!e.layerSet.has("walkBlocks")||!e.rowVisitsNeeded||!t)return;let n=[t.reference,...t.rows];return gn(n,we(n))},get drawsNodes(){return j(e.drawnLayoutMode??e.chosenLayoutMode).drawsNodes},get genePins(){Ae(e.positionsVersion);let t=e.layoutResult?.nodePositions,n=[...e.backboneGenes??[],...e.ownGeneFeatures??[]];return e.showGenes&&this.drawsNodes&&e.graph&&n.length>0&&t?Ce(e.graph,n,t):[]},get bubbleHalos(){Ae(e.positionsVersion);let t=e.layoutResult?.nodePositions,n=e.showBubbles?e.bubbles:e.hoveredBubble?[e.hoveredBubble]:[];return n.length===0||!this.drawsNodes||!e.graph||!t?[]:an(e.graph,n,t,e.repeatArrays)},get referenceRamp(){return e.effectiveColorScheme==="reference-position"?e.drawnReferenceRamp:void 0},get assemblyNames(){let t=e.graphRegion;return t?[t.assemblyName]:[]},get axisScale(){return Je(e.scale,e.pixelRows)},get scaleX(){return this.axisScale.scaleX},get scaleY(){return this.axisScale.scaleY}})).views(e=>({get screenTransform(){return{scaleX:e.scaleX,scaleY:e.scaleY,translateX:e.translateX,translateY:e.translateY}},toScreen(t){return{x:t.x*e.scaleX+e.translateX,y:t.y*e.scaleY+e.translateY}},get deletionDrawing(){return e.graph?De(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 paintsNodeColors(){return e.drawsNodes||!!e.layoutResult?.tubeMap},get referenceRampDrawsOffReference(){return!!e.referenceRamp&&this.paintsNodeColors&&!!e.drawnGraph?.nodes.some(t=>!T(t))},get tubeMapNodeColors(){let t=e.drawnGraph;return e.layoutResult?.tubeMap&&t?wn(t,e.effectiveColorScheme,e.referenceRamp):void 0},get tubeColorKind(){let t=e.layoutResult,n=e.drawnGraph?.paths??[],o=e.tubeMapReads;return t?.tubeMap?e.tubeMapColoring&&!o?"value":t.tubeMapPanels?"role":this.tubeMapNodeColors?"tinted":!o&&(!Ve(n.length)||n.some(r=>r.members))?"role":"path":void 0},tubeColorsOf(t,n){let o=t.paths??[],r=this.tubeColorKind,a=e.tubeMapColoring;return r==="value"&&a?Ao(o,t.referencePath,a.valueOf,a.palette):r==="tinted"?Ft(o,t.referencePath,Lo):r==="role"?Ft(o,t.referencePath):n},fadeUnhovered(t,n,o){let r=new Set(e.hoveredRowWalks);return r.size>0?t.map((a,s)=>{let i=n[s]?.name??"";return r.has(i)||o!==void 0&&ce(i).name===o?a:Ze}):t},get tubeMapTubeColors(){let t=e.layoutResult?.tubeMap,n=e.drawnGraph;return t&&n?this.fadeUnhovered(this.tubeColorsOf(n,t.pathColors),n.paths??[]):void 0},nodeSpan(t){return jr(t,e.nodeById,e.nodeNeighbors)},get hoverDrawing(){let t=e.hoveredPanel;return(t===null?void 0:e.layoutResult?.tubeMapPanels?.[t]?.result.tubeMap)??e.layoutResult?.tubeMap},get hoverGraph(){return this.hoverDrawing?.graph??e.drawnGraph},get hoverNodeById(){let t=this.hoverGraph;return t===e.drawnGraph?e.nodeById:t&&Xr(t)},get hoverNeighbors(){let t=this.hoverGraph;return t===e.drawnGraph?e.nodeNeighbors:t&&Q(t)}})).views(e=>({get pathLegend(){let t=e.drawnGraph?.paths;return(e.layoutResult?.tubeMap?e.tubeColorKind==="path":e.drawPaths)&&t&&Ve(t.length)&&!t.some(o=>o.members)?Se(t,e.tubeMapTubeColors):[]},get hoveredSpan(){let t=e.hoveredNode,n=e.hoveredBubble;return t!==null?jr(t,e.hoverNodeById,e.hoverNeighbors):n&&!n.offReference?{start:n.start,end:n.end}:void 0},get hoverHighlight(){let t=e.graphRegion,n=this.hoveredSpan;return t&&n&&e.chosenHover!=="off"?{refName:t.refName,assemblyName:t.assemblyName,...n}:void 0}}));var zr=Yr.views(e=>({get host(){let t=e.containingView;return tr(t)?t:void 0}})).views(e=>({get pairedViewId(){return e.host?.id??e.connectedViewId}})).views(e=>({get contributingAssemblies(){let t=e.graph,n=t?J(t):[];return t?wr(t,{maxGap:n.length>0?vt(n):1/0}):[]}})).views(e=>({get assemblyResolver(){let{assemblyManager:t}=Y(e),n=e.sourceAdapter?.assemblyNameToPanSN,o=new Map(Object.entries(n??{}).map(([a,s])=>[s,a])),r=a=>a!==void 0&&t.has(a)?t.get(a)?.name??a:void 0;return a=>r(o.get(a))??r(a)},get geneTracksByAssembly(){let t=new Map;for(let n of e.sessionTracks)if(pt.has(n.adapterType)&&mt(n)===e.walkRowAnnotation)for(let o of n.assemblies)t.set(o,[...t.get(o)??[],n]);return new Map([...t].flatMap(([n,o])=>{let r=lt(o,"");return r?[[n,r]]:[]}))}})).views(e=>({get launchableAssemblies(){return br(Rr(e.contributingAssemblies,e.graphRegion),e.assemblyResolver)},get canHighlightInLinearView(){let t=e.graphRegion;return t!==void 0&&Ge({views:[...Y(e).views],connectedViewId:e.pairedViewId,assemblyName:t.assemblyName})!==void 0},nodeLaunchTargets(t){let n=e.nodeById?.get(t),o=n?zt(n):void 0,r=o?me(e.assemblyResolver,o):void 0,a=e.graphRegion,s=a?e.nodeSpan(t):void 0,i=a&&s?{sample:a.assemblyName,haplotype:void 0,refName:a.refName,...s}:void 0;return{own:o&&r?{location:qt(o),assembly:r}:void 0,reference:a&&i?{location:qt(i),assembly:a.assemblyName}:void 0,highlight:a&&i?{location:i,assembly:a.assemblyName}:void 0}},get ownGeneReads(){let{graph:t}=e;return!t||!e.showGenes||!e.modeDrawsNodes?[]:gr(t,e.assemblyResolver,e.graphRegion?.assemblyName).flatMap(({stableRefName:n,assemblyName:o,refName:r,start:a,end:s})=>{let i=e.geneTracksByAssembly.get(o);return i?[{stableRefName:n,trackId:i.trackId,region:{assemblyName:o,refName:r,start:a,end:s}}]:[]}).slice(0,po)},get assemblyHoverHighlights(){let t=e.hoveredNode,n=t===null?void 0:e.nodeById?.get(t);return n&&e.graph&&e.chosenHover!=="off"?fr(e.graph,n,e.assemblyResolver,e.graphRegion?.assemblyName):[]}}));var Ur=zr.views(e=>({get walkStripShown(){return Zt({walkStrip:e.walkStrip,mode:{drawsNodes:e.modeDrawsNodes},drawsPicture:!!e.layoutResult?.tubeMap||!!e.walkRowBars,walks:e.graph?.paths?.length??0,host:!!e.host})},get walkStripRows(){let t=this.walkStripShown?e.cutWalkRows:void 0;return t?{...t,rows:ve(t.rows,e.walkRowSamples)}:void 0},get walkStripFrame(){let t=this.walkStripRows;if(t)return Ie(t,{width:e.paneWidth})},cutsWholeWalksIn(t,n=e.walkStrip){let o=j(t);return e.sourceAdapter?.type==="GbzBaseSyntenyAdapter"&&Qt(o,{walkStrip:n&&o.drawsNodes,host:!!e.host})},get cutsWholeWalks(){return this.cutsWholeWalksIn(e.chosenLayoutMode)},get walkStripMarks(){let t=this.walkStripRows,n=e.hoveredNode??e.selectedNode,o=n===null?void 0:e.nodeById?.get(n);return t&&o&&e.graph?en(e.graph,[t.reference,...t.rows],o):[]},rowLocation(t,n){let o={sample:t.sample,haplotype:t.haplotype===void 0?void 0:`${t.sample}#${t.haplotype}`};return{...o,assembly:me(e.assemblyResolver,o),span:{refName:n.contig,...ot(n,t.bp)}}},get walkStripLocator(){let t=e.stripHover?e.hoveredNode:null;return t===null?void 0:dt(e.nodePositions?.[t],e.toScreen)}})).views(e=>({get walkGeneReads(){let t=e.walkRowBars??e.walkStripRows;if(!t||!e.showGenes)return;let n=[],o=0,r=0;for(let a of t.rows){if(!a.axis){r++;continue}let{assembly:s,span:i}=e.rowLocation(a,a.axis),c=s?e.geneTracksByAssembly.get(s):void 0;if(!s||!c){o++;continue}n.push({row:a.name,trackId:c.trackId,region:{assemblyName:s,...i}})}return{reads:n.slice(0,_t),gaps:{untracked:o,unplaced:r,unread:Math.max(0,n.length-_t)}}},get walkRowGeneGaps(){return this.walkGeneReads?.gaps},walkRowLaunchTarget(t,n=e.walkRowBars){let o=n?[n.reference,...n.rows][t]:void 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n&&o&&o.w>0?ze({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-Zr)},get tooltipRightPx(){let{width:t,height:n}=e.legendSize,o=st+e.referenceStripZonePx+n;return!e.facetPanels&&t>0&&o>this.canvasHeight-hs?t+2*st:ms},get canvasHeight(){let t=this.layoutBounds,n=this.paneCeiling;if(!t)return n;let o=this.facetGrid;if(o)return Math.max(et,o.total+Zr);let r=Math.max(et,e.legendSize.height+2*st+e.referenceStripZonePx),a=this.fitPads,s=a.top+a.bottom;if(e.pixelRows)return Math.min(n,Math.max(r,t.h+s));let i=e.paneWidth-a.left-a.right;return t.w>0&&i>0?Math.min(n,Math.max(r,t.h*Math.max(i/t.w,this.minFitScale)+s)):n},get viewBox(){let t=this.facetGrid;return t?{width:t.width,height:t.height}:{width:e.paneWidth,height:this.canvasHeight}},get fitPads(){return this.facetGrid?{left:z,top:z,right:z,bottom:z}:{left:this.fitPadLeft,top:this.fitPadTop,right:X,bottom:X}},get usableHeight(){let{top:t,bottom:n}=this.fitPads;return this.viewBox.height-t-n},get fittedTransform(){let t=this.layoutBounds,{width:n,height:o}=this.viewBox,r=this.fitPads;return t?Ne(t,n,o,e.pixelRows,{minScale:this.facetGrid?0:this.minFitScale,padLeft:r.left,padTop:r.top,padRight:r.right,padBottom:r.bottom}):void 0}})).views(e=>({viewportToBuild(){return Yn(mo(e),co)},applySelection(t){let n=e.selectedNode;t.setNodeHighlights(n===null?new Map:new Map([[n,io]]))},get hoverLayerNode(){let{litNode:t,selectedNode:n}=e;return t===n?null:t},get paintTransform(){let t=er();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]:ro)}})).views(e=>({buildDrawing(t,n){let{graph:o,nodeById:r,layoutResult:a,deletionDrawing:s}=e;if(!o||!r||!a||!s)return;Ae(e.viewportDirty,e.positionsVersion);let i=At(()=>e.viewportToBuild()),c=Qe({...Be(a,s,{drawsRows:!!e.walkRowBars}),graph:o,nodeById:r,colorScheme:e.effectiveColorScheme,contigThickness:e.contigThickness,connectorThickness:e.connectorThickness,drawPaths:n,nodeWidth:e.nodeWidth,edgeWidth:e.linkWidth,highlight:t,axis:At(()=>e.axisScale),linearLayout:e.linearLayout,viewportBounds:i,referenceRamp:e.referenceRamp,version:e.positionsVersion}),d=e.morphEntering;return d?.layout===a&&qr(c,o.edges,d),{batch:c,viewportBounds:i}},get overlayLabels(){return _o(e)},hoveredOn(t){let n=e.hoveredNode,o=n?e.nodeById?.get(n):void 0;return o?Fo(t,o.id,o.length)??"not on this 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gs="Linear genome view",ws="Linear synteny view",bs="No synteny track in this session aligns these assemblies";function ta({label:e,icon:t,entries:n,entryLabel:o,onSelect:r,disabledHelpText:a,nameTheOnlyEntry:s=!0}){let[i]=n,c=a?[{label:e,icon:t,disabled:!0,disabledHelpText:a,onClick:()=>{}}]:[];return n.length===0?c:n.length===1&&i?[{label:s?`${e} \u2014 ${o(i)}`:e,icon:t,onClick:r(i)}]:[{label:e,icon:t,type:"subMenu",subMenu:n.map(d=>({label:o(d),onClick:r(d)}))}]}function Xg({contributors:e,linearContributors:t=e,syntenyTracks:n,onShowLinear:o,onShowSynteny:r}){let a=n[0]?.coverage??e.length;return[...ta({label:gs,icon:kn,entries:t,entryLabel:s=>`${s.sample} ${oe(s)}`,onSelect:s=>()=>{o({location:s,assembly:s.sample})}}),...e.length>=2?ta({label:`${ws} (${a} assemblies)`,icon:Qr,entries:n,entryLabel:s=>s.coverage<a?`${s.name} (${s.coverage} of ${a})`:s.name,nameTheOnlyEntry:!1,disabledHelpText:bs,onSelect:s=>()=>{r(s.trackId)}}):[]]}function jg({own:e,reference:t,highlight:n,onShowLinear:o,onHighlight:r}){let a=[e?{label:`Open in ${e.assembly} \u2014 ${oe(e.location)}`,target:e}:void 0,t&&t.assembly!==e?.assembly?{label:`Open in ${t.assembly} \u2014 around this node`,target:t}:void 0].filter(s=>s!==void 0);return[...r&&n?[{label:`Highlight in ${n.assembly}`,icon:ea,onClick:()=>{r(n)}}]:[],...a.map(({label:s,target:i})=>({label:s,icon:kn,onClick:()=>{o(i)}}))]}var Kg=$(F("path",{d:"M19 15.18V7c0-2.21-1.79-4-4-4s-4 1.79-4 4v10c0 1.1-.9 2-2 2s-2-.9-2-2V8.82C8.16 8.4 9 7.3 9 6c0-1.66-1.34-3-3-3S3 4.34 3 6c0 1.3.84 2.4 2 2.82V17c0 2.21 1.79 4 4 4s4-1.79 4-4V7c0-1.1.9-2 2-2s2 .9 2 2v8.18c-1.16.41-2 1.51-2 2.82 0 1.66 1.34 3 3 3s3-1.34 3-3c0-1.3-.84-2.4-2-2.82"}),"Route");var Qg=$(F("path",{d:"M19.14 12.94c.04-.3.06-.61.06-.94 0-.32-.02-.64-.07-.94l2.03-1.58c.18-.14.23-.41.12-.61l-1.92-3.32c-.12-.22-.37-.29-.59-.22l-2.39.96c-.5-.38-1.03-.7-1.62-.94l-.36-2.54c-.04-.24-.24-.41-.48-.41h-3.84c-.24 0-.43.17-.47.41l-.36 2.54c-.59.24-1.13.57-1.62.94l-2.39-.96c-.22-.08-.47 0-.59.22L2.74 8.87c-.12.21-.08.47.12.61l2.03 1.58c-.05.3-.09.63-.09.94s.02.64.07.94l-2.03 1.58c-.18.14-.23.41-.12.61l1.92 3.32c.12.22.37.29.59.22l2.39-.96c.5.38 1.03.7 1.62.94l.36 2.54c.05.24.24.41.48.41h3.84c.24 0 .44-.17.47-.41l.36-2.54c.59-.24 1.13-.56 1.62-.94l2.39.96c.22.08.47 0 .59-.22l1.92-3.32c.12-.22.07-.47-.12-.61zM12 15.6c-1.98 0-3.6-1.62-3.6-3.6s1.62-3.6 3.6-3.6 3.6 1.62 3.6 3.6-1.62 3.6-3.6 3.6"}),"Settings");var ow=$(F("path",{d:"M12 4.5C7 4.5 2.73 7.61 1 12c1.73 4.39 6 7.5 11 7.5s9.27-3.11 11-7.5c-1.73-4.39-6-7.5-11-7.5M12 17c-2.76 0-5-2.24-5-5s2.24-5 5-5 5 2.24 5 5-2.24 5-5 5m0-8c-1.66 0-3 1.34-3 3s1.34 3 3 3 3-1.34 3-3-1.34-3-3-3"}),"Visibility");export{$ as a,lr as b,gt as c,Ra as d,j as e,oe as f,xa as g,zt as h,W as i,Na as j,Kt as k,qi as l,Jt as m,Zi as n,Qi as o,ec as p,Nr as q,ow as r,Ea as s,Ia as t,Ca as u,tn as v,nn as w,og as x,rg as y,ag as z,sg as A,ig as B,cg as C,wn as D,tr as E,Ss as F,ia as G,vs as H,la as I,rr as J,rh as K,ih as L,ph as M,ms as N,us as O,Zr as P,Ag as Q,kn as R,Xg as S,jg as T,Kg as U,Qg as V};
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