jbrowse-plugin-msaview 5.2.0 → 5.4.0

package/dist/chunks/chunk-ASUKJX5J.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["global-externals:mobx", "global-externals:react-dom", "global-externals:react-dom/client", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/renderToSvg.tsx", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/getVisibleLeaves.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/minimap/MinimapSVG.tsx", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/DragHandle.tsx", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/useDragScroll.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/msa/tileColor.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/msa/msaRaster.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/minimap/minimapLayout.ts", "../../node_modules/.pnpm/colord@2.10.0/node_modules/colord/index.mjs", "../../node_modules/.pnpm/colord@2.10.0/node_modules/colord/plugins/a11y.mjs", "../../node_modules/.pnpm/colord@2.10.0/node_modules/colord/plugins/names.mjs", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/util.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/msa/drawFeatureSpans.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/msa/renderBoxFeatureCanvasBlock.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/setFontSize.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/overlayColors.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/msa/renderHighlights.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/msa/domainBandCursor.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/msa/visibleColRange.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/msa/renderMSABlock.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/rowpanels/headerLayout.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/rowpanels/renderFeaturePanel.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/rowpanels/renderStrip.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/rowpanels/renderRowPanel.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/columnCounts.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/sequenceLogo.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/tracks/drawTracks.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/tree/ScaleBarSVG.tsx", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/measureTextCanvas.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/tree/cladeBrackets.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/tree/ellipsize.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/hierarchy.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/tree/renderTreeCanvas.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/tree/renderTreeOverview.ts", "../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/renderToStaticMarkup.ts"],
+  "sourcesContent": ["module.exports = JBrowseExports[\"mobx\"];", "module.exports = JBrowseExports[\"react-dom\"];", "module.exports = JBrowseExports[\"react-dom/client\"];", "/* eslint-disable react-refresh/only-export-components */\nimport React from 'react'\n\nimport { when } from 'mobx'\n\nimport { visibleRowRange } from './components/getVisibleLeaves.ts'\nimport MinimapSVG from './components/minimap/MinimapSVG.tsx'\nimport { legendRows } from './components/msa/legendRows.ts'\nimport { rasterApplies, rasterImageHref } from './components/msa/msaRaster.ts'\nimport { renderBoxFeatureCanvasBlock } from './components/msa/renderBoxFeatureCanvasBlock.ts'\nimport { renderPersistentHighlights } from './components/msa/renderHighlights.ts'\nimport { renderMSABlock } from './components/msa/renderMSABlock.ts'\nimport { visibleColRange } from './components/msa/visibleColRange.ts'\nimport { headerRunsAcross } from './components/rowpanels/headerLayout.ts'\nimport { renderRowPanels } from './components/rowpanels/renderRowPanel.ts'\nimport { renderAllTracks } from './components/tracks/drawTracks.ts'\nimport ScaleBarSVG from './components/tree/ScaleBarSVG.tsx'\nimport { cladeLabelBoxes } from './components/tree/cladeBrackets.ts'\nimport { ellipsize } from './components/tree/ellipsize.ts'\nimport { renderTreeCanvas } from './components/tree/renderTreeCanvas.ts'\nimport { renderTreeOverview } from './components/tree/renderTreeOverview.ts'\nimport { treeScaleBarHeight } from './constants.ts'\nimport {\n  LEGEND_CHAR_W,\n  LEGEND_FONT,\n  LEGEND_PAD,\n  LEGEND_ROW_H,\n  LEGEND_SWATCH,\n  LEGEND_TEXT_X,\n  exportPageSize,\n  getLayout,\n  legendHeight,\n} from './exportLayout.ts'\nimport { measureTextCanvas } from './measureTextCanvas.ts'\nimport { renderToStaticMarkup, svgSafeColors } from './renderToStaticMarkup.ts'\nimport { outlineColor } from './util.ts'\n\nimport type { ExportSvgOptions, Layout } from './exportLayout.ts'\nimport type { MsaViewModel } from './model.ts'\nimport type { Context as ContextType } from '@jbrowse/svgcanvas'\nimport type { Theme } from '@mui/material'\n\nexport type { ExportSvgOptions } from './exportLayout.ts'\n\nexport async function renderToSvg(model: MsaViewModel, opts: ExportSvgOptions) {\n  // dataInitialized stays false while the model holds a load error, so waiting\n  // on it alone would never settle\n  await when(() => model.dataInitialized || !!model.error)\n  if (model.error) {\n    throw model.error\n  }\n  const { Context } = await import('@jbrowse/svgcanvas')\n  // Each svgcanvas layer is already serialized SVG, and React would have to\n  // parse it into a second DOM only for the export to serialize it back out.\n  // The layers register themselves here instead, and their markup is spliced\n  // into the page as strings.\n  const layers = new Map<string, ContextType>()\n  const markup = renderToStaticMarkup(\n    <MsaSvg\n      model={model}\n      theme={opts.theme}\n      Context={Context}\n      layout={getLayout(model, opts)}\n      layers={layers}\n    />,\n  )\n  // innerHTML serializes as HTML, and an XML parser rejects its &nbsp;\n  return svgSafeColors(\n    markup.replaceAll(/<g data-layer=\"([^\"]+)\"><\\/g>/g, (match, id: string) => {\n      const ctx = layers.get(id)\n      return ctx ? `<g id=\"${id}\">${ctx.getSvg().innerHTML}</g>` : match\n    }),\n  ).replaceAll('&nbsp;', '&#160;')\n}\n\nfunction MsaSvg({\n  model,\n  theme,\n  Context,\n  layout,\n  layers,\n}: {\n  model: MsaViewModel\n  theme: Theme\n  Context: typeof ContextType\n  layout: Layout\n  layers: LayerMap\n}) {\n  const { width, trackHeight, includeMinimap, legendWidth, topHeight } = layout\n  const { effectiveTreeAreaWidth, rowPanelsWidth } = model\n  const { width: totalWidth, height } = exportPageSize(model, layout)\n  const legendTop = topHeight\n  const props = { Context, model, theme, layout, layers }\n\n  const body = (\n    <>\n      {trackHeight > 0 ? <TrackRendering {...props} /> : null}\n      <g\n        transform={trackHeight > 0 ? `translate(0 ${trackHeight})` : undefined}\n      >\n        <CoreRendering {...props} />\n      </g>\n    </>\n  )\n\n  return (\n    <svg\n      width={totalWidth}\n      height={height}\n      xmlns=\"http://www.w3.org/2000/svg\"\n      xmlnsXlink=\"http://www.w3.org/1999/xlink\"\n      viewBox={`0 0 ${totalWidth} ${height}`}\n      // the canvas layers name sans-serif on each glyph; the legend, labels\n      // and headers inherit it here instead of an editor's default serif\n      fontFamily=\"sans-serif\"\n    >\n      {/* every layer below draws in the theme's colors, so the page has to be\n          the theme's background too -- a hardcoded white one turns a dark-theme\n          export into white text on white */}\n      <rect\n        width=\"100%\"\n        height=\"100%\"\n        fill={theme.palette.background.default}\n      />\n      {topHeight > 0 ? (\n        <>\n          {includeMinimap ? (\n            <g\n              id=\"minimap-panel\"\n              transform={`translate(${effectiveTreeAreaWidth + rowPanelsWidth} 0)`}\n            >\n              <MinimapSVG model={model} theme={theme} />\n            </g>\n          ) : null}\n          <RowPanelHeadersSVG\n            model={model}\n            theme={theme}\n            bandHeight={topHeight}\n          />\n          {model.showTreeOverview ? (\n            <TreeOverviewSVG\n              model={model}\n              theme={theme}\n              Context={Context}\n              layers={layers}\n            />\n          ) : null}\n          <TreeScaleBarSVG model={model} theme={theme} />\n          <g transform={`translate(0 ${topHeight})`}>{body}</g>\n        </>\n      ) : (\n        body\n      )}\n      {legendWidth > 0 ? (\n        <g id=\"legend-panel\" transform={`translate(${width} ${legendTop})`}>\n          <LegendSVG model={model} theme={theme} width={legendWidth} />\n        </g>\n      ) : null}\n    </svg>\n  )\n}\n\n// The tree overview in the top band, over the tree column, where the live view\n// puts it. It is part of the figure rather than chrome: the inset is what says\n// where the focused clade sits in the whole tree.\nfunction TreeOverviewSVG({\n  model,\n  theme,\n  Context,\n  layers,\n}: {\n  model: MsaViewModel\n  theme: Theme\n  Context: typeof ContextType\n  layers: LayerMap\n}) {\n  const { effectiveTreeAreaWidth, overviewHeight, id } = model\n  const ctx = new Context(effectiveTreeAreaWidth, overviewHeight)\n  renderTreeOverview({\n    model,\n    ctx,\n    theme,\n    width: effectiveTreeAreaWidth,\n    height: overviewHeight,\n  })\n  return (\n    <ClipGroup\n      panelId=\"tree-overview\"\n      clipId={`tree-overview-${id}`}\n      width={effectiveTreeAreaWidth}\n      height={overviewHeight}\n      ctx={ctx}\n      layers={layers}\n    />\n  )\n}\n\n// The branch-length scale bar under the tree overview, where the live view puts\n// it (see TreeRuler). A phylogram whose branch lengths are drawn to a scale\n// nothing states is a figure a reader cannot measure, so the export carries the\n// bar even though it is chrome on screen.\nfunction TreeScaleBarSVG({\n  model,\n  theme,\n}: {\n  model: MsaViewModel\n  theme: Theme\n}) {\n  const { marginLeft, treeScaleBar: bar, treeOverviewHeight } = model\n  if (!bar) {\n    return null\n  }\n  return (\n    <g id=\"tree-scalebar\">\n      <ScaleBarSVG\n        bar={bar}\n        marginLeft={marginLeft}\n        y={treeOverviewHeight + treeScaleBarHeight}\n        color={theme.palette.text.primary}\n      />\n    </g>\n  )\n}\n\n// Each strip's header over the column it names, turned on its side, where the\n// live view puts it (see RowPanelHeaders). The baseline runs up the figure, so\n// the name sits to the left of it, the way TrackLabelsSVG offsets a horizontal\n// baseline by a third of the font size.\nfunction RowPanelHeadersSVG({\n  model,\n  theme,\n  bandHeight,\n}: {\n  model: MsaViewModel\n  theme: Theme\n  bandHeight: number\n}) {\n  const { resolvedRowPanels, effectiveTreeAreaWidth, fontSize } = model\n  const y = bandHeight - 4\n  return resolvedRowPanels.length === 0 ? null : (\n    <g id=\"rowpanel-headers\">\n      {resolvedRowPanels.map(panel => {\n        const across = headerRunsAcross(panel.width)\n        const size = across ? fontSize : Math.min(fontSize, panel.width)\n        const center = effectiveTreeAreaWidth + panel.offsetX + panel.width / 2\n        const x = across ? center : center + size / 3\n        const room = across ? panel.width : y - LEGEND_PAD\n        return size < 5 ? null : (\n          <text\n            key={panel.id}\n            x={x}\n            y={y}\n            {...(across\n              ? { textAnchor: 'middle' }\n              : { transform: `rotate(-90 ${x} ${y})` })}\n            fontSize={size}\n            fill={theme.palette.text.primary}\n          >\n            {\n              ellipsize(t => measureTextCanvas(t, size), panel.header, room)\n                .text\n            }\n          </text>\n        )\n      })}\n    </g>\n  )\n}\n\n// Each bracket's label in the gutter beside its bar, where the live view puts\n// it (see CladeLabels). The canvas layer draws the bar; a label longer than the\n// gutter or the clade is clipped, since text that overruns runs off the figure.\n// cladeGutterWidth sizes the gutter with the same measureTextCanvas, so a label\n// the gutter holds keeps every character.\nfunction CladeLabelsSVG({\n  model,\n  theme,\n  offsetY,\n}: {\n  model: MsaViewModel\n  theme: Theme\n  offsetY: number\n}) {\n  const { fontSize } = model\n  const boxes = cladeLabelBoxes(model)\n  return boxes.length === 0 ? null : (\n    <g id=\"clade-labels\">\n      {boxes.map(box => {\n        const top = box.top - offsetY\n        const x = box.horizontal ? box.left : box.left + fontSize\n        const y = box.horizontal\n          ? top + box.height / 2 + fontSize / 3\n          : top + box.height\n        return (\n          <text\n            key={box.key}\n            x={x}\n            y={y}\n            transform={box.horizontal ? undefined : `rotate(-90 ${x} ${y})`}\n            fontSize={fontSize}\n            fill={box.color ?? theme.palette.text.primary}\n          >\n            {\n              ellipsize(\n                t => measureTextCanvas(t, fontSize),\n                box.label,\n                box.horizontal ? box.width : box.height,\n              ).text\n            }\n          </text>\n        )\n      })}\n    </g>\n  )\n}\n\n// the color keys drawn as a reserved column to the right of the alignment,\n// mirroring the on-screen AnnotationLegend overlay\nfunction LegendSVG({\n  model,\n  theme,\n  width,\n}: {\n  model: MsaViewModel\n  theme: Theme\n  width: number\n}) {\n  const rows = legendRows(model.legends)\n  const boxHeight = legendHeight(rows)\n  // the column is capped at LEGEND_MAX_W, so a name too long for it has to be\n  // clipped here -- text that overruns the reserved width runs off the figure\n  const room = width - LEGEND_TEXT_X - LEGEND_PAD\n  return (\n    <g>\n      <rect\n        x={0}\n        y={0}\n        width={width - 4}\n        height={boxHeight}\n        fill={theme.palette.background.paper}\n        stroke={theme.palette.divider}\n        rx={2}\n      />\n      {rows.map((row, i) => {\n        const y = LEGEND_PAD + i * LEGEND_ROW_H\n        return (\n          <g key={row.key}>\n            {row.color ? (\n              <rect\n                x={LEGEND_PAD}\n                y={y}\n                width={LEGEND_SWATCH}\n                height={LEGEND_SWATCH}\n                fill={row.color}\n                stroke={outlineColor(row.color)}\n              />\n            ) : null}\n            <text\n              x={row.color ? LEGEND_TEXT_X : LEGEND_PAD}\n              y={y + LEGEND_SWATCH - 1}\n              fontSize={LEGEND_FONT}\n              fontWeight={row.color ? undefined : 'bold'}\n              fill={theme.palette.text.primary}\n            >\n              {ellipsize(t => t.length * LEGEND_CHAR_W, row.label, room).text}\n            </text>\n          </g>\n        )\n      })}\n    </g>\n  )\n}\n\ntype LayerMap = Map<string, ContextType>\n\ninterface LayerProps {\n  model: MsaViewModel\n  theme: Theme\n  layout: Layout\n  Context: typeof ContextType\n  layers: LayerMap\n}\n\nfunction CoreRendering({ model, theme, layout, Context, layers }: LayerProps) {\n  const { contentHeight, offsetX, offsetY, msaAreaWidth } = layout\n  const { effectiveTreeAreaWidth, rowPanelsWidth, id } = model\n\n  const treeCtx = new Context(effectiveTreeAreaWidth, contentHeight)\n  renderTreeCanvas({\n    model,\n    theme,\n    ctx: treeCtx,\n    offsetY,\n    blockSizeYOverride: contentHeight,\n    highResScaleFactorOverride: 1,\n  })\n\n  const rowPanelsCtx = rowPanelsWidth\n    ? new Context(rowPanelsWidth, contentHeight)\n    : undefined\n  if (rowPanelsCtx) {\n    renderRowPanels({\n      model,\n      theme,\n      ctx: rowPanelsCtx,\n      offsetY,\n      blockSizeYOverride: contentHeight,\n      highResScaleFactorOverride: 1,\n    })\n  }\n\n  const raster = rasterBackground({ model, theme, layout })\n\n  const msaCtx = new Context(msaAreaWidth, contentHeight)\n  renderBoxFeatureCanvasBlock({\n    model,\n    theme,\n    ctx: msaCtx,\n    offsetX,\n    offsetY,\n    // the overlay culls bands to this width; without it the export falls back\n    // to the on-screen 500px block size and drops every band past it\n    blockSizeXOverride: msaAreaWidth,\n    blockSizeYOverride: contentHeight,\n    highResScaleFactorOverride: 1,\n  })\n  renderMSABlock({\n    model,\n    theme,\n    ctx: msaCtx,\n    offsetX,\n    offsetY,\n    blockSizeXOverride: msaAreaWidth,\n    blockSizeYOverride: contentHeight,\n    highResScaleFactorOverride: 1,\n    rasterTiles: !!raster,\n  })\n  msaCtx.resetTransform()\n  renderPersistentHighlights({\n    ctx: msaCtx,\n    model,\n    theme,\n    offsetX,\n    offsetY,\n    width: msaAreaWidth,\n    height: contentHeight,\n  })\n\n  return (\n    <>\n      <ClipGroup\n        panelId=\"tree-panel\"\n        clipId={`tree-${id}`}\n        width={effectiveTreeAreaWidth}\n        height={contentHeight}\n        ctx={treeCtx}\n        layers={layers}\n      />\n      <CladeLabelsSVG model={model} theme={theme} offsetY={offsetY} />\n      {rowPanelsCtx ? (\n        <ClipGroup\n          panelId=\"rowpanels-panel\"\n          clipId={`rowpanels-${id}`}\n          width={rowPanelsWidth}\n          height={contentHeight}\n          transform={`translate(${effectiveTreeAreaWidth} 0)`}\n          ctx={rowPanelsCtx}\n          layers={layers}\n        />\n      ) : null}\n      <ClipGroup\n        panelId=\"msa-panel\"\n        clipId={`msa-${id}`}\n        width={msaAreaWidth}\n        height={contentHeight}\n        transform={`translate(${effectiveTreeAreaWidth + rowPanelsWidth} 0)`}\n        ctx={msaCtx}\n        layers={layers}\n        underlay={raster}\n      />\n    </>\n  )\n}\n\n/**\n * The alignment background as a single <image>, wherever the live canvas\n * draws the raster.\n *\n * The vector path's <rect> per cell exhausts the heap on a real alignment. The\n * image is one pixel per cell, and image-rendering keeps the upscaled cell\n * edges hard, so it matches the rects pixel for pixel.\n */\nfunction rasterBackground({\n  model,\n  theme,\n  layout,\n}: {\n  model: MsaViewModel\n  theme: Theme\n  layout: Layout\n}) {\n  const { contentHeight, offsetX, offsetY, msaAreaWidth } = layout\n  const { colWidth, rowHeight } = model\n  if (!rasterApplies(model)) {\n    return undefined\n  }\n  const { xStart, xEnd } = visibleColRange({\n    offsetX,\n    blockWidth: msaAreaWidth,\n    colWidth,\n  })\n  const { yStart, yEnd } = visibleRowRange({\n    model,\n    offsetY,\n    blockSizeY: contentHeight,\n  })\n  const numCols = Math.min(xEnd, model.numColumns) - xStart\n  const numRows = Math.min(yEnd, model.numRows) - yStart\n  const href = rasterImageHref({\n    model,\n    theme,\n    col0: xStart,\n    row0: yStart,\n    numCols,\n    numRows,\n  })\n  return href ? (\n    <image\n      href={href}\n      x={xStart * colWidth - offsetX}\n      y={yStart * rowHeight - offsetY}\n      width={numCols * colWidth}\n      height={numRows * rowHeight}\n      imageRendering=\"pixelated\"\n      preserveAspectRatio=\"none\"\n    />\n  ) : undefined\n}\n\nfunction TrackRendering({ model, theme, layout, Context, layers }: LayerProps) {\n  const { trackHeight, offsetX, msaAreaWidth } = layout\n  const { effectiveTreeAreaWidth, rowPanelsWidth, id } = model\n\n  const ctx = new Context(msaAreaWidth, trackHeight)\n  renderAllTracks({\n    model,\n    ctx,\n    theme,\n    offsetX,\n    blockSizeXOverride: msaAreaWidth,\n    highResScaleFactorOverride: 1,\n  })\n\n  return (\n    <>\n      <TrackLabelsSVG model={model} theme={theme} />\n      <g transform={`translate(${effectiveTreeAreaWidth + rowPanelsWidth} 0)`}>\n        <ClipGroup\n          panelId=\"tracks-panel\"\n          clipId={`tracks-${id}`}\n          width={msaAreaWidth}\n          height={trackHeight}\n          ctx={ctx}\n          layers={layers}\n        />\n      </g>\n    </>\n  )\n}\n\n// Each track's name in the tree-width column beside it, where the live view puts\n// it (see TrackLabel). Without these the figure has an unlabeled bar chart and\n// an unlabeled logo, and nothing says which is which.\nfunction TrackLabelsSVG({\n  model,\n  theme,\n}: {\n  model: MsaViewModel\n  theme: Theme\n}) {\n  const { turnedOnTracks, effectiveTreeAreaWidth, fontSize, drawLabels } = model\n  if (!drawLabels) {\n    return null\n  }\n  const labels = turnedOnTracks.map((track, i) => {\n    const { id, name, height } = track.model\n    const size = Math.min(height, fontSize)\n    const top = turnedOnTracks\n      .slice(0, i)\n      .reduce((acc, t) => acc + t.model.height, 0)\n    // pinned to the top of the track, as the live view's flex row pins it\n    return { id, name, size, baseline: top + size * 0.8 }\n  })\n  return (\n    <>\n      {labels.map(({ id, name, size, baseline }) => {\n        return size < 5 ? null : (\n          <text\n            key={id}\n            x={effectiveTreeAreaWidth - 4}\n            y={baseline}\n            fontSize={size}\n            textAnchor=\"end\"\n            fill={theme.palette.text.primary}\n          >\n            {name}\n          </text>\n        )\n      })}\n    </>\n  )\n}\n\n// Clips a svgcanvas Context to its box and leaves a placeholder for renderToSvg\n// to splice the layer's own markup into. `underlay` draws beneath that markup,\n// inside the same clip, for the parts of a layer React emits directly.\n//\n// `panelId` names the spliced group in the output, the same name in every\n// export, so a figure can be taken apart in Illustrator or svgutils. `clipId`\n// carries the model id, which keeps two viewers on one page from colliding.\nfunction ClipGroup({\n  panelId,\n  clipId,\n  width,\n  height,\n  transform,\n  ctx,\n  layers,\n  underlay,\n}: {\n  panelId: string\n  clipId: string\n  width: number\n  height: number\n  transform?: string\n  ctx: ContextType\n  layers: LayerMap\n  underlay?: React.ReactNode\n}) {\n  layers.set(panelId, ctx)\n  return (\n    <>\n      <defs>\n        <clipPath id={clipId}>\n          <rect x={0} y={0} width={width} height={height} />\n        </clipPath>\n      </defs>\n      <g clipPath={`url(#${clipId})`} transform={transform}>\n        {underlay}\n        <g data-layer={panelId} />\n      </g>\n    </>\n  )\n}\n", "import type { MsaViewModel } from '../model.ts'\n\n// The half-open range of rows [yStart, yEnd) whose leaves intersect a block of\n// height blockSizeY at vertical offset offsetY, padded by one row on each side.\n// Y-axis counterpart to visibleColRange.\nexport function visibleRowRange({\n  model,\n  offsetY,\n  blockSizeY,\n}: {\n  model: MsaViewModel\n  offsetY: number\n  blockSizeY: number\n}) {\n  const { rowHeight } = model\n  return {\n    yStart: Math.max(0, Math.floor((offsetY - rowHeight) / rowHeight)),\n    yEnd: Math.max(\n      0,\n      Math.ceil((offsetY + blockSizeY + rowHeight) / rowHeight),\n    ),\n  }\n}\n\n// The leaves in that range.\nexport function getVisibleLeaves({\n  model,\n  offsetY,\n  blockSizeY,\n}: {\n  model: MsaViewModel\n  offsetY: number\n  blockSizeY: number\n}) {\n  const { yStart, yEnd } = visibleRowRange({ model, offsetY, blockSizeY })\n  return model.leaves.slice(yStart, yEnd)\n}\n", "import React from 'react'\n\nimport { scrollbarThumbFill } from '../DragHandle.tsx'\nimport { canvasHref, msaThumbnail } from '../msa/msaRaster.ts'\nimport { MINIMAP_BAR_HEIGHT, getMinimapLayout } from './minimapLayout.ts'\n\nimport type { MsaViewModel } from '../../model.ts'\nimport type { Theme } from '@mui/material'\n\n// The static counterpart to Minimap, for the SVG export. renderToSvg drives it\n// through renderToStaticMarkup, so it reads the model once and never re-renders\n// -- no observer wrapper.\nexport default function MinimapSVG({\n  model,\n  theme,\n}: {\n  model: MsaViewModel\n  theme: Theme\n}) {\n  const { msaCanvasWidth } = model\n  const { s, w, polygonPoints } = getMinimapLayout(model)\n  // the same downsampled alignment the live minimap draws behind its thumb;\n  // undefined wherever a canvas cannot be read back, leaving a bare outline\n  const href = canvasHref(\n    msaThumbnail({ model, theme, height: MINIMAP_BAR_HEIGHT }),\n  )\n\n  return (\n    <>\n      {href ? (\n        <image\n          href={href}\n          x={0}\n          y={0}\n          width={msaCanvasWidth}\n          height={MINIMAP_BAR_HEIGHT}\n          preserveAspectRatio=\"none\"\n        />\n      ) : null}\n      <rect\n        x={0}\n        y={0}\n        width={msaCanvasWidth}\n        height={MINIMAP_BAR_HEIGHT}\n        stroke={theme.palette.text.secondary}\n        fill=\"none\"\n      />\n      <rect\n        x={Math.max(0, s)}\n        y={0}\n        width={w}\n        height={MINIMAP_BAR_HEIGHT}\n        fill={scrollbarThumbFill}\n        stroke={theme.palette.text.secondary}\n      />\n      <g transform={`translate(0 ${MINIMAP_BAR_HEIGHT})`}>\n        <polygon fill={scrollbarThumbFill} points={polygonPoints} />\n      </g>\n    </>\n  )\n}\n", "import React, { useState } from 'react'\n\nimport { useTheme } from '@mui/material'\n\nimport { useDragScroll } from '../useDragScroll.ts'\n\nimport type { Theme } from '@mui/material'\n\nexport const scrollbarThumbFill = 'rgba(66,119,127,0.3)'\n\n// the model's resizeHandleWidth feeds the layout, so a divider keeps its drawn\n// width and widens its target with this much invisible margin each side\nconst hitSlop = 4\n\n// The scroll thumbs (minimap, vertical scrollbar) and the resize dividers are\n// one widget -- press, drag along an axis, report the pixel delta -- differing\n// only in the affordance they present, so the variant carries the whole\n// difference rather than a second copy of the drag wiring.\nconst variants: Record<\n  'thumb' | 'resizer',\n  {\n    fill: (theme: Theme) => string\n    fillHovered: (theme: Theme) => string\n    cursor: (axis: 'x' | 'y') => string\n    position: React.CSSProperties['position']\n    zIndex?: number\n  }\n> = {\n  thumb: {\n    fill: () => scrollbarThumbFill,\n    fillHovered: () => 'rgba(66,119,127,0.6)',\n    cursor: () => 'pointer',\n    position: 'absolute',\n    zIndex: 100,\n  },\n  resizer: {\n    fill: theme =>\n      theme.palette.mode === 'dark'\n        ? theme.palette.grey[800]\n        : 'rgba(200,200,200)',\n    fillHovered: theme =>\n      theme.palette.mode === 'dark'\n        ? theme.palette.grey[600]\n        : 'rgba(150,150,150)',\n    cursor: axis => (axis === 'x' ? 'ew-resize' : 'ns-resize'),\n    position: 'relative',\n  },\n}\n\n/**\n * A handle dragged along a single axis. `getStart` is read at mousedown and\n * handed back to `onDrag` alongside the pixel delta since, so a caller only\n * supplies the dimension it drives and where the handle sits.\n *\n * Memoize `onDrag` (useCallback) so the document listeners are not re-attached\n * on every render.\n */\nexport default function DragHandle({\n  axis,\n  variant,\n  getStart,\n  onDrag,\n  style,\n}: {\n  axis: 'x' | 'y'\n  variant: keyof typeof variants\n  getStart: () => number\n  onDrag: (delta: number, startValue: number) => void\n  style: React.CSSProperties\n}) {\n  const theme = useTheme()\n  const [hovered, setHovered] = useState(false)\n  const { startDrag } = useDragScroll(axis, onDrag)\n  const { fill, fillHovered, cursor, position, zIndex } = variants[variant]\n\n  return (\n    <div\n      {...(variant === 'resizer' && {\n        role: 'separator',\n        'aria-orientation': axis === 'x' ? 'vertical' : 'horizontal',\n      })}\n      onMouseEnter={() => {\n        setHovered(true)\n      }}\n      onMouseLeave={() => {\n        setHovered(false)\n      }}\n      onMouseDown={event => {\n        startDrag(event, getStart())\n      }}\n      style={{\n        position,\n        zIndex,\n        cursor: cursor(axis),\n        background: hovered ? fillHovered(theme) : fill(theme),\n        ...style,\n      }}\n    >\n      {variant === 'resizer' ? (\n        <div\n          style={{\n            position: 'absolute',\n            zIndex: 101,\n            ...(axis === 'x'\n              ? { top: 0, bottom: 0, left: -hitSlop, right: -hitSlop }\n              : { left: 0, right: 0, top: -hitSlop, bottom: -hitSlop }),\n          }}\n        />\n      ) : null}\n    </div>\n  )\n}\n", "import { useEffect, useRef, useState } from 'react'\n\n/**\n * Tracks a mouse drag along a single axis and reports the scroll delta on each\n * animation frame. Shared by the horizontal Minimap and the VerticalScrollbar.\n *\n * `onScroll` is invoked with the pixel delta since drag start and the scroll\n * offset captured when the drag began. Memoize it (useCallback) so the document\n * listeners are not re-attached on every render.\n */\nexport function useDragScroll(\n  axis: 'x' | 'y',\n  onScroll: (delta: number, startScroll: number) => void,\n) {\n  const scheduled = useRef(false)\n  const [mouseDown, setMouseDown] = useState<{\n    client: number\n    startScroll: number\n  }>()\n\n  useEffect(() => {\n    if (mouseDown !== undefined) {\n      const { client: startClient, startScroll } = mouseDown\n      function onMove(event: MouseEvent) {\n        if (!scheduled.current) {\n          scheduled.current = true\n          requestAnimationFrame(() => {\n            const client = axis === 'x' ? event.clientX : event.clientY\n            onScroll(client - startClient, startScroll)\n            scheduled.current = false\n          })\n        }\n      }\n      function onUp() {\n        setMouseDown(undefined)\n      }\n      document.addEventListener('mousemove', onMove)\n      document.addEventListener('mouseup', onUp)\n      return () => {\n        document.removeEventListener('mousemove', onMove)\n        document.removeEventListener('mouseup', onUp)\n      }\n    }\n  }, [axis, onScroll, mouseDown])\n\n  return {\n    dragging: mouseDown !== undefined,\n    startDrag: (event: React.MouseEvent, startScroll: number) => {\n      setMouseDown({\n        client: axis === 'x' ? event.clientX : event.clientY,\n        startScroll,\n      })\n    },\n  }\n}\n", "import type { MsaViewModel } from '../../model.ts'\n\n// Per-cell tile color for the active scheme, resolved once per block. Reading\n// only the active scheme's column table leaves the other per-column table\n// uncomputed.\nexport function tileColorFn(model: MsaViewModel) {\n  const { dynamicColorSchemeName } = model\n  if (dynamicColorSchemeName === 'clustalx_protein_dynamic') {\n    const { colClustalX } = model\n    return (col: number, letter: string) => colClustalX[col]![letter]\n  }\n  if (dynamicColorSchemeName === 'percent_identity_dynamic') {\n    const { colConsensus } = model\n    return (col: number, letter: string) => {\n      const consensus = colConsensus[col]!\n      return letter === consensus.letter ? consensus.color : undefined\n    }\n  }\n  const { colorScheme } = model\n  return (_col: number, letter: string) => colorScheme[letter]\n}\n\n// The table the active scheme colors from: a dynamic scheme's per-column table,\n// or the letter table of a static scheme or a `customColorScheme` map. A cache\n// of rendered colors keys on its identity plus the scheme name.\nexport function tileColorTable(model: MsaViewModel) {\n  const { dynamicColorSchemeName } = model\n  if (dynamicColorSchemeName === 'clustalx_protein_dynamic') {\n    return model.colClustalX\n  }\n  if (dynamicColorSchemeName === 'percent_identity_dynamic') {\n    return model.colConsensus\n  }\n  return model.colorScheme\n}\n", "import { tileColorFn, tileColorTable } from './tileColor.ts'\n\nimport type { MsaViewModel } from '../../model.ts'\nimport type { Theme } from '@mui/material'\n\n// One raster tile holds this many cells on a side. A tile costs ~10ms to build\n// and ~1MB to hold, and is then drawn at any zoom for ~1ms, so the cache only\n// has to be large enough to cover a screen without thrashing.\nexport const rasterTileSize = 512\nconst maxCachedTiles = 64\nconst maxThumbnailColumns = 2000\nconst maxColorCacheEntries = 4096\n\nexport type RasterCanvas = HTMLCanvasElement | OffscreenCanvas\ntype RasterCtx = CanvasRenderingContext2D | OffscreenCanvasRenderingContext2D\n\nexport interface RasterSpec {\n  rowNames: string[]\n  columns: Map<string, string>\n  relativeTo: string | undefined\n  colorAt: (col: number, letter: string) => string | undefined\n  bg: string\n  hover: string\n}\n\nconst littleEndian = new Uint8Array(new Uint32Array([1]).buffer)[0] === 1\n\nfunction packRgba(r: number, g: number, b: number, a: number) {\n  return littleEndian\n    ? ((a << 24) | (b << 16) | (g << 8) | r) >>> 0\n    : ((r << 24) | (g << 16) | (b << 8) | a) >>> 0\n}\n\nlet scratch: RasterCtx | null | undefined\nconst colorCache = new Map<string, number>()\n\n/**\n * CSS color string -> the packed pixel an ImageData holds for it. Painting a 1x1\n * canvas and reading it back parses hex, rgb(), hsl() and named colors; the\n * cache resolves each distinct color once per session.\n */\nexport function cssColorToPixel(css: string) {\n  const hit = colorCache.get(css)\n  if (hit !== undefined) {\n    return hit\n  }\n  if (scratch === undefined) {\n    scratch = makeRasterCanvas(1, 1)?.ctx ?? null\n  }\n  let packed = 0\n  if (scratch) {\n    scratch.clearRect(0, 0, 1, 1)\n    scratch.fillStyle = css\n    scratch.fillRect(0, 0, 1, 1)\n    const [r = 0, g = 0, b = 0, a = 0] = scratch.getImageData(0, 0, 1, 1).data\n    packed = packRgba(r, g, b, a)\n  }\n  if (colorCache.size >= maxColorCacheEntries) {\n    colorCache.clear()\n  }\n  colorCache.set(css, packed)\n  return packed\n}\n\nfunction cellPixelFn(spec: RasterSpec, toPixel: (css: string) => number) {\n  const { columns, relativeTo, colorAt, bg, hover } = spec\n  const bgPixel = toPixel(bg)\n  const hoverPixel = toPixel(hover)\n  const reference = relativeTo ? columns.get(relativeTo) : undefined\n  return (name: string, col: number, letter: string) => {\n    if (reference && name !== relativeTo && letter === reference[col]) {\n      return hoverPixel\n    }\n    const color = colorAt(col, letter)\n    return color === undefined ? bgPixel : toPixel(color)\n  }\n}\n\n/**\n * Packs a rectangle of the alignment into one pixel per cell, in `rowNames`\n * order, ready to hand to putImageData. Cells past the end of a row, and rows\n * with no sequence, stay transparent, as in the per-cell painter.\n *\n * `colStep`/`rowStep` sample every nth cell, which fits a whole alignment into\n * the minimap's 12px bar. `colSpan`/`rowSpan` average each block of that many\n * cells into one pixel, so a zoom below a device pixel per column still shows\n * every column's color without blending neighbouring rows.\n */\nexport function rasterPixels({\n  spec,\n  col0,\n  row0,\n  width,\n  height,\n  colStep = 1,\n  rowStep = 1,\n  colSpan = 1,\n  rowSpan = 1,\n  toPixel = cssColorToPixel,\n  out = new Uint32Array(width * height),\n}: {\n  spec: RasterSpec\n  col0: number\n  row0: number\n  width: number\n  height: number\n  colStep?: number\n  rowStep?: number\n  colSpan?: number\n  rowSpan?: number\n  toPixel?: (css: string) => number\n  out?: Uint32Array\n}) {\n  if (colSpan > 1 || rowSpan > 1) {\n    averagePixels({\n      spec,\n      col0,\n      row0,\n      width,\n      height,\n      colSpan,\n      rowSpan,\n      toPixel,\n      out,\n    })\n    return out\n  }\n  const { rowNames, columns } = spec\n  const cellPixel = cellPixelFn(spec, toPixel)\n\n  for (let r = 0; r < height; r++) {\n    const name = rowNames[row0 + r * rowStep]\n    if (name === undefined) {\n      break\n    }\n    const str = columns.get(name)\n    if (!str) {\n      continue\n    }\n    const base = r * width\n    for (let c = 0; c < width; c++) {\n      const col = col0 + c * colStep\n      const letter = str[col]\n      if (letter === undefined) {\n        break\n      }\n      out[base + c] = cellPixel(name, col, letter)\n    }\n  }\n  return out\n}\n\nfunction averagePixels({\n  spec,\n  col0,\n  row0,\n  width,\n  height,\n  colSpan,\n  rowSpan,\n  toPixel,\n  out,\n}: {\n  spec: RasterSpec\n  col0: number\n  row0: number\n  width: number\n  height: number\n  colSpan: number\n  rowSpan: number\n  toPixel: (css: string) => number\n  out: Uint32Array\n}) {\n  const { rowNames, columns } = spec\n  const cellPixel = cellPixelFn(spec, toPixel)\n  const cells = colSpan * rowSpan\n  const rShift = littleEndian ? 0 : 24\n  const gShift = littleEndian ? 8 : 16\n  const bShift = littleEndian ? 16 : 8\n  const aShift = littleEndian ? 24 : 0\n  const names: string[] = []\n  const strs: string[] = []\n\n  for (let r = 0; r < height; r++) {\n    names.length = 0\n    strs.length = 0\n    for (let dr = 0; dr < rowSpan; dr++) {\n      const name = rowNames[row0 + r * rowSpan + dr]\n      const str = name === undefined ? undefined : columns.get(name)\n      if (name !== undefined && str) {\n        names.push(name)\n        strs.push(str)\n      }\n    }\n    const base = r * width\n    for (let c = 0; c < width; c++) {\n      // premultiplied, so a cell past the end of a row dilutes the alpha of its\n      // pixel rather than darkening its color\n      let sumR = 0\n      let sumG = 0\n      let sumB = 0\n      let sumA = 0\n      for (let i = 0; i < strs.length; i++) {\n        const str = strs[i]!\n        const name = names[i]!\n        for (let dc = 0; dc < colSpan; dc++) {\n          const col = col0 + c * colSpan + dc\n          const letter = str[col]\n          if (letter === undefined) {\n            break\n          }\n          const p = cellPixel(name, col, letter)\n          const a = (p >>> aShift) & 255\n          sumR += ((p >>> rShift) & 255) * a\n          sumG += ((p >>> gShift) & 255) * a\n          sumB += ((p >>> bShift) & 255) * a\n          sumA += a\n        }\n      }\n      out[base + c] =\n        sumA === 0\n          ? 0\n          : packRgba(\n              Math.round(sumR / sumA),\n              Math.round(sumG / sumA),\n              Math.round(sumB / sumA),\n              Math.round(sumA / cells),\n            )\n    }\n  }\n}\n\nfunction usableRasterCtx(ctx: unknown): ctx is RasterCtx {\n  const c = ctx as Record<string, unknown> | null\n  return (\n    !!c &&\n    typeof c.createImageData === 'function' &&\n    typeof c.putImageData === 'function' &&\n    typeof c.getImageData === 'function' &&\n    typeof c.clearRect === 'function' &&\n    typeof c.fillRect === 'function'\n  )\n}\n\n/**\n * A canvas off the page, an OffscreenCanvas where there is one, with its 2d\n * context, or undefined where the context fails `usable` (jsdom has none).\n */\nexport function makeOffscreenCanvas<Ctx>(\n  width: number,\n  height: number,\n  usable: (ctx: unknown) => ctx is Ctx,\n  settings?: CanvasRenderingContext2DSettings,\n) {\n  const canvas =\n    typeof OffscreenCanvas !== 'undefined'\n      ? new OffscreenCanvas(width, height)\n      : typeof document !== 'undefined'\n        ? Object.assign(document.createElement('canvas'), { width, height })\n        : undefined\n  const ctx = canvas?.getContext('2d', settings)\n  return usable(ctx) ? { canvas: canvas as RasterCanvas, ctx } : undefined\n}\n\nfunction makeRasterCanvas(width: number, height: number) {\n  return makeOffscreenCanvas(width, height, usableRasterCtx, {\n    willReadFrequently: true,\n  })\n}\n\nfunction paint(\n  width: number,\n  height: number,\n  fill: (out: Uint32Array) => void,\n) {\n  const made = makeRasterCanvas(width, height)\n  if (!made) {\n    return undefined\n  }\n  const image = made.ctx.createImageData(width, height)\n  fill(new Uint32Array(image.data.buffer))\n  made.ctx.putImageData(image, 0, 0)\n  return made.canvas\n}\n\nlet supported: boolean | undefined\n\n/**\n * Whether the alignment background comes from the raster: true with\n * background coloring on, the domain overlay off, and a 2d context that reads\n * back, which jsdom lacks. renderMSABlock paints each cell otherwise.\n */\nexport function rasterApplies(\n  model: Pick<MsaViewModel, 'actuallyShowDomains' | 'bgColor'>,\n) {\n  supported ??= !!makeRasterCanvas(1, 1)\n  return !model.actuallyShowDomains && model.bgColor && supported\n}\n\ninterface RasterCache {\n  keys: unknown[]\n  spec: RasterSpec\n  numColumns: number\n  numRows: number\n  tiles: Map<string, RasterCanvas>\n  thumbnail?: { height: number; canvas: RasterCanvas | undefined }\n}\n\nconst caches = new WeakMap<object, RasterCache>()\n\n// Everything a cell's color depends on; a change to any of them starts a fresh\n// cache.\nfunction rasterKeys(model: MsaViewModel, theme: Theme) {\n  return [\n    model.columns,\n    model.leaves,\n    model.colorSchemeName,\n    model.customColorScheme,\n    tileColorTable(model),\n    model.relativeTo,\n    theme.palette.action.hover,\n    theme.palette.background.default,\n  ]\n}\n\nfunction getCache(model: MsaViewModel, theme: Theme) {\n  const keys = rasterKeys(model, theme)\n  const prev = caches.get(model)\n  if (prev && keys.every((key, i) => key === prev.keys[i])) {\n    return prev\n  }\n  const next: RasterCache = {\n    keys,\n    spec: {\n      rowNames: model.leaves.map(node => node.data.name),\n      columns: model.columns,\n      relativeTo: model.relativeTo,\n      colorAt: tileColorFn(model),\n      bg: theme.palette.background.default,\n      hover: theme.palette.action.hover,\n    },\n    numColumns: model.numColumns,\n    numRows: model.numRows,\n    tiles: new Map(),\n  }\n  caches.set(model, next)\n  return next\n}\n\n// Cells averaged into one tile pixel along an axis: the smallest power of two\n// that brings a pixel back to at least one device pixel. Powers of two keep the\n// number of distinct tile sets a zoom sweep builds to a handful.\nfunction cellsPerPixel(devicePixelsPerCell: number) {\n  return devicePixelsPerCell >= 1\n    ? 1\n    : 2 ** Math.ceil(Math.log2(1 / devicePixelsPerCell))\n}\n\nfunction getTile({\n  cache,\n  tileRow,\n  tileCol,\n  colSpan,\n  rowSpan,\n}: {\n  cache: RasterCache\n  tileRow: number\n  tileCol: number\n  colSpan: number\n  rowSpan: number\n}) {\n  const key = `${colSpan}_${rowSpan}_${tileRow}_${tileCol}`\n  const hit = cache.tiles.get(key)\n  if (hit) {\n    // re-inserting makes this the newest entry: a Map iterates in insertion\n    // order, so its first key is the least recently used one\n    cache.tiles.delete(key)\n    cache.tiles.set(key, hit)\n    return hit\n  }\n  const col0 = tileCol * rasterTileSize * colSpan\n  const row0 = tileRow * rasterTileSize * rowSpan\n  const width = Math.min(\n    rasterTileSize,\n    Math.ceil((cache.numColumns - col0) / colSpan),\n  )\n  const height = Math.min(\n    rasterTileSize,\n    Math.ceil((cache.numRows - row0) / rowSpan),\n  )\n  if (width <= 0 || height <= 0) {\n    return undefined\n  }\n  const canvas = paint(width, height, out => {\n    rasterPixels({\n      spec: cache.spec,\n      col0,\n      row0,\n      width,\n      height,\n      colSpan,\n      rowSpan,\n      out,\n    })\n  })\n  if (!canvas) {\n    return undefined\n  }\n  cache.tiles.set(key, canvas)\n  for (const stale of cache.tiles.keys()) {\n    if (cache.tiles.size <= maxCachedTiles) {\n      break\n    }\n    cache.tiles.delete(stale)\n  }\n  return canvas\n}\n\n/**\n * Paints the alignment background of one MSA block from cached\n * one-pixel-per-cell tiles. The tiles do not depend on the zoom level, so a zoom\n * frame costs a handful of drawImage calls. A fillRect per visible cell measured\n * 885ms per block at the minimum column width.\n *\n * Below a device pixel per cell the tiles average cells together, per axis.\n * The browser's image smoothing blurs both axes, which turns every row\n * boundary into a gradient at fit-to-width, where only the columns are narrow.\n */\nexport function drawMsaRaster({\n  ctx,\n  model,\n  theme,\n  offsetX,\n  offsetY,\n}: {\n  ctx: CanvasRenderingContext2D\n  model: MsaViewModel\n  theme: Theme\n  offsetX: number\n  offsetY: number\n}) {\n  const { colWidth, rowHeight, blockSize, highResScaleFactor } = model\n  const cache = getCache(model, theme)\n  const colSpan = cellsPerPixel(colWidth * highResScaleFactor)\n  const rowSpan = cellsPerPixel(rowHeight * highResScaleFactor)\n\n  ctx.resetTransform()\n  ctx.scale(highResScaleFactor, highResScaleFactor)\n  ctx.translate(-offsetX, -offsetY)\n  ctx.imageSmoothingEnabled = false\n\n  const pixelWidth = colWidth * colSpan\n  const pixelHeight = rowHeight * rowSpan\n  const tileWidth = rasterTileSize * pixelWidth\n  const tileHeight = rasterTileSize * pixelHeight\n  const firstCol = Math.max(0, Math.floor(offsetX / tileWidth))\n  const lastCol = Math.floor((offsetX + blockSize) / tileWidth)\n  const firstRow = Math.max(0, Math.floor(offsetY / tileHeight))\n  const lastRow = Math.floor((offsetY + blockSize) / tileHeight)\n\n  for (let tileRow = firstRow; tileRow <= lastRow; tileRow++) {\n    for (let tileCol = firstCol; tileCol <= lastCol; tileCol++) {\n      const tile = getTile({ cache, tileRow, tileCol, colSpan, rowSpan })\n      if (tile) {\n        ctx.drawImage(\n          tile,\n          0,\n          0,\n          tile.width,\n          tile.height,\n          tileCol * tileWidth,\n          tileRow * tileHeight,\n          tile.width * pixelWidth,\n          tile.height * pixelHeight,\n        )\n      }\n    }\n  }\n  ctx.resetTransform()\n  ctx.imageSmoothingEnabled = true\n}\n\n/**\n * A raster canvas as a PNG data URI, for embedding in the SVG export.\n *\n * toDataURL is the synchronous read-back. The DOM canvas and a headless node\n * canvas have it; a browser OffscreenCanvas, which the tile and thumbnail\n * caches hold where it exists, is copied onto a DOM canvas first. Returns\n * undefined where read-back is unavailable (jsdom), and the caller then draws\n * in vector.\n */\nexport function canvasHref(canvas: RasterCanvas | undefined) {\n  if (!canvas) {\n    return undefined\n  }\n  try {\n    if ('toDataURL' in canvas && typeof canvas.toDataURL === 'function') {\n      return canvas.toDataURL('image/png')\n    }\n    if (typeof document === 'undefined') {\n      return undefined\n    }\n    const out = document.createElement('canvas')\n    out.width = canvas.width\n    out.height = canvas.height\n    const ctx = out.getContext('2d')\n    if (typeof ctx?.drawImage !== 'function') {\n      return undefined\n    }\n    ctx.drawImage(canvas, 0, 0)\n    return out.toDataURL('image/png')\n  } catch {\n    return undefined\n  }\n}\n\n// A canvas much past this many pixels fails to allocate, and the browser's\n// per-side limit is lower still, so a larger raster averages down per axis and\n// is drawn across the same rectangle. An alignment that hits the limit on\n// columns alone keeps every row.\nconst maxImagePixels = 64e6\nconst maxImageSide = 16384\n\n/**\n * The alignment rectangle [col0, col0+numCols) x [row0, row0+numRows) as a PNG\n * data URI, for the SVG export.\n *\n * SVG has no blit, so the export draws the whole background as one <image>. The\n * vector path emits a <rect> per cell, and a 200x500 alignment exhausts the\n * heap building them.\n *\n * Returns undefined where a canvas cannot be read back (jsdom), and the caller\n * then keeps the per-cell path.\n */\nexport function rasterImageHref({\n  model,\n  theme,\n  col0,\n  row0,\n  numCols,\n  numRows,\n}: {\n  model: MsaViewModel\n  theme: Theme\n  col0: number\n  row0: number\n  numCols: number\n  numRows: number\n}) {\n  if (numCols <= 0 || numRows <= 0 || typeof document === 'undefined') {\n    return undefined\n  }\n  const cache = getCache(model, theme)\n  let colSpan = 1\n  let rowSpan = 1\n  while (Math.ceil(numCols / colSpan) > maxImageSide) {\n    colSpan *= 2\n  }\n  while (Math.ceil(numRows / rowSpan) > maxImageSide) {\n    rowSpan *= 2\n  }\n  while (\n    Math.ceil(numCols / colSpan) * Math.ceil(numRows / rowSpan) >\n    maxImagePixels\n  ) {\n    if (numCols / colSpan >= numRows / rowSpan) {\n      colSpan *= 2\n    } else {\n      rowSpan *= 2\n    }\n  }\n  const width = Math.ceil(numCols / colSpan)\n  const height = Math.ceil(numRows / rowSpan)\n\n  return canvasHref(\n    paint(width, height, out => {\n      rasterPixels({\n        spec: cache.spec,\n        col0,\n        row0,\n        width,\n        height,\n        colSpan,\n        rowSpan,\n        out,\n      })\n    }),\n  )\n}\n\n/**\n * The whole alignment sampled down to a strip behind the minimap thumb, cached\n * with the block tiles since the same keys invalidate both.\n */\nexport function msaThumbnail({\n  model,\n  theme,\n  height,\n}: {\n  model: MsaViewModel\n  theme: Theme\n  height: number\n}) {\n  const cache = getCache(model, theme)\n  const { numColumns, numRows } = cache\n  if (numColumns <= 0 || numRows <= 0) {\n    return undefined\n  }\n  // keyed on the requested height as well as the cache: rowStep is derived from\n  // it, so a thumbnail built for a different bar height is the wrong sampling\n  if (cache.thumbnail?.height !== height) {\n    const colStep = Math.max(1, Math.ceil(numColumns / maxThumbnailColumns))\n    const rowStep = Math.max(1, Math.ceil(numRows / height))\n    const w = Math.ceil(numColumns / colStep)\n    const h = Math.ceil(numRows / rowStep)\n    cache.thumbnail = {\n      height,\n      canvas: paint(w, h, out => {\n        rasterPixels({\n          spec: cache.spec,\n          col0: 0,\n          row0: 0,\n          width: w,\n          height: h,\n          colStep,\n          rowStep,\n          out,\n        })\n      }),\n    }\n  }\n  return cache.thumbnail.canvas\n}\n", "import type { MsaViewModel } from '../../model.ts'\n\nexport const MINIMAP_BAR_HEIGHT = 12\n\n/**\n * Viewport-rectangle and trapezoid geometry for the minimap, shared by the\n * interactive Minimap and the static MinimapSVG. Both span the alignment canvas\n * exactly -- a minimap drawn a different width than the columns it maps puts\n * its viewport rectangle over the wrong ones.\n */\nexport function getMinimapLayout(model: MsaViewModel) {\n  const { scrollX, minimapHeight, totalWidth, msaCanvasWidth } = model\n  const unit = totalWidth > 0 ? msaCanvasWidth / totalWidth : 0\n  const s = -scrollX * unit\n  // the rectangle marks the visible slice of the alignment, so it can never be\n  // wider than the bar itself\n  const w = Math.min(msaCanvasWidth, Math.max(msaCanvasWidth * unit, 20))\n  const polygonHeight = minimapHeight - MINIMAP_BAR_HEIGHT\n  const polygonPoints = `${s + w},0 ${s},0 0,${polygonHeight} ${msaCanvasWidth},${polygonHeight}`\n  return { unit, s, w, polygonHeight, polygonPoints }\n}\n", "for(var r={grad:.9,turn:360,rad:360/(2*Math.PI)},t=function(r){return\"string\"==typeof r?r.length>0:\"number\"==typeof r},n=function(r,t,n){return void 0===t&&(t=0),void 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A(k(this.rgba,-1))},r.prototype.lighten=function(r){return void 0===r&&(r=.1),A(R(this.rgba,r))},r.prototype.darken=function(r){return void 0===r&&(r=.1),A(R(this.rgba,-r))},r.prototype.rotate=function(r){return void 0===r&&(r=15),this.hue(y(this.rgba).h+r)},r.prototype.alpha=function(r){return\"number\"==typeof r?A({r:(t=this.rgba).r,g:t.g,b:t.b,a:r}):n(this.rgba.a,3);var t},r.prototype.hue=function(r){var t=y(this.rgba);return\"number\"==typeof r?A({h:r,s:t.s,l:t.l,a:t.a}):o(t.h)},r.prototype.isEqual=function(r){return this.toHex()===A(r).toHex()},r}(),A=function(r){return r instanceof q?r:new q(r)},C=[],D=function(r){r.forEach(function(r){C.indexOf(r)<0&&(r(q,$),C.push(r))})},F=function(){return new q({r:255*Math.random(),g:255*Math.random(),b:255*Math.random()})};export{q as Colord,A as colord,D as extend,S as getFormat,F as random};\n", "var o=function(o){var t=o/255;return t<.04045?t/12.92:Math.pow((t+.055)/1.055,2.4)},t=function(t){return.2126*o(t.r)+.7152*o(t.g)+.0722*o(t.b)},r=function(o){o.prototype.luminance=function(){return o=t(this.rgba),void 0===(r=2)&&(r=0),void 0===n&&(n=Math.pow(10,r)),Math.round(n*o)/n+0;var o,r,n},o.prototype.contrast=function(r){void 0===r&&(r=\"#FFF\");var n,a,i,e,v,u,d,c=r instanceof o?r:new o(r);return e=this.rgba,v=c.toRgb(),u=t(e),d=t(v),n=u>d?(u+.05)/(d+.05):(d+.05)/(u+.05),void 0===(a=2)&&(a=0),void 0===i&&(i=Math.pow(10,a)),Math.floor(i*n)/i+0},o.prototype.isReadable=function(o,t){return void 0===o&&(o=\"#FFF\"),void 0===t&&(t={}),this.contrast(o)>=(e=void 0===(i=(r=t).size)?\"normal\":i,\"AAA\"===(a=void 0===(n=r.level)?\"AA\":n)&&\"normal\"===e?7:\"AA\"===a&&\"large\"===e?3:4.5);var r,n,a,i,e}};export{r as default};\n", "var e=function(e,f){var a={white:\"#ffffff\",bisque:\"#ffe4c4\",blue:\"#0000ff\",cadetblue:\"#5f9ea0\",chartreuse:\"#7fff00\",chocolate:\"#d2691e\",coral:\"#ff7f50\",antiquewhite:\"#faebd7\",aqua:\"#00ffff\",azure:\"#f0ffff\",whitesmoke:\"#f5f5f5\",papayawhip:\"#ffefd5\",plum:\"#dda0dd\",blanchedalmond:\"#ffebcd\",black:\"#000000\",gold:\"#ffd700\",goldenrod:\"#daa520\",gainsboro:\"#dcdcdc\",cornsilk:\"#fff8dc\",cornflowerblue:\"#6495ed\",burlywood:\"#deb887\",aquamarine:\"#7fffd4\",beige:\"#f5f5dc\",crimson:\"#dc143c\",cyan:\"#00ffff\",darkblue:\"#00008b\",darkcyan:\"#008b8b\",darkgoldenrod:\"#b8860b\",darkkhaki:\"#bdb76b\",darkgray:\"#a9a9a9\",darkgreen:\"#006400\",darkgrey:\"#a9a9a9\",peachpuff:\"#ffdab9\",darkmagenta:\"#8b008b\",darkred:\"#8b0000\",darkorchid:\"#9932cc\",darkorange:\"#ff8c00\",darkslateblue:\"#483d8b\",gray:\"#808080\",darkslategray:\"#2f4f4f\",darkslategrey:\"#2f4f4f\",deeppink:\"#ff1493\",deepskyblue:\"#00bfff\",wheat:\"#f5deb3\",firebrick:\"#b22222\",floralwhite:\"#fffaf0\",ghostwhite:\"#f8f8ff\",darkviolet:\"#9400d3\",magenta:\"#ff00ff\",green:\"#008000\",dodgerblue:\"#1e90ff\",grey:\"#808080\",honeydew:\"#f0fff0\",hotpink:\"#ff69b4\",blueviolet:\"#8a2be2\",forestgreen:\"#228b22\",lawngreen:\"#7cfc00\",indianred:\"#cd5c5c\",indigo:\"#4b0082\",fuchsia:\"#ff00ff\",brown:\"#a52a2a\",maroon:\"#800000\",mediumblue:\"#0000cd\",lightcoral:\"#f08080\",darkturquoise:\"#00ced1\",lightcyan:\"#e0ffff\",ivory:\"#fffff0\",lightyellow:\"#ffffe0\",lightsalmon:\"#ffa07a\",lightseagreen:\"#20b2aa\",linen:\"#faf0e6\",mediumaquamarine:\"#66cdaa\",lemonchiffon:\"#fffacd\",lime:\"#00ff00\",khaki:\"#f0e68c\",mediumseagreen:\"#3cb371\",limegreen:\"#32cd32\",mediumspringgreen:\"#00fa9a\",lightskyblue:\"#87cefa\",lightblue:\"#add8e6\",midnightblue:\"#191970\",lightpink:\"#ffb6c1\",mistyrose:\"#ffe4e1\",moccasin:\"#ffe4b5\",mintcream:\"#f5fffa\",lightslategray:\"#778899\",lightslategrey:\"#778899\",navajowhite:\"#ffdead\",navy:\"#000080\",mediumvioletred:\"#c71585\",powderblue:\"#b0e0e6\",palegoldenrod:\"#eee8aa\",oldlace:\"#fdf5e6\",paleturquoise:\"#afeeee\",mediumturquoise:\"#48d1cc\",mediumorchid:\"#ba55d3\",rebeccapurple:\"#663399\",lightsteelblue:\"#b0c4de\",mediumslateblue:\"#7b68ee\",thistle:\"#d8bfd8\",tan:\"#d2b48c\",orchid:\"#da70d6\",mediumpurple:\"#9370db\",purple:\"#800080\",pink:\"#ffc0cb\",skyblue:\"#87ceeb\",springgreen:\"#00ff7f\",palegreen:\"#98fb98\",red:\"#ff0000\",yellow:\"#ffff00\",slateblue:\"#6a5acd\",lavenderblush:\"#fff0f5\",peru:\"#cd853f\",palevioletred:\"#db7093\",violet:\"#ee82ee\",teal:\"#008080\",slategray:\"#708090\",slategrey:\"#708090\",aliceblue:\"#f0f8ff\",darkseagreen:\"#8fbc8f\",darkolivegreen:\"#556b2f\",greenyellow:\"#adff2f\",seagreen:\"#2e8b57\",seashell:\"#fff5ee\",tomato:\"#ff6347\",silver:\"#c0c0c0\",sienna:\"#a0522d\",lavender:\"#e6e6fa\",lightgreen:\"#90ee90\",orange:\"#ffa500\",orangered:\"#ff4500\",steelblue:\"#4682b4\",royalblue:\"#4169e1\",turquoise:\"#40e0d0\",yellowgreen:\"#9acd32\",salmon:\"#fa8072\",saddlebrown:\"#8b4513\",sandybrown:\"#f4a460\",rosybrown:\"#bc8f8f\",darksalmon:\"#e9967a\",lightgoldenrodyellow:\"#fafad2\",snow:\"#fffafa\",lightgrey:\"#d3d3d3\",lightgray:\"#d3d3d3\",dimgray:\"#696969\",dimgrey:\"#696969\",olivedrab:\"#6b8e23\",olive:\"#808000\"},r={};for(var d in a)r[a[d]]=d;var l={};e.prototype.toName=function(f){if(!(this.rgba.a||this.rgba.r||this.rgba.g||this.rgba.b))return\"transparent\";var d,i,n=r[this.toHex()];if(n)return n;if(null==f?void 0:f.closest){var o=this.toRgb(),t=1/0,b=\"black\";if(!l.length)for(var c in a)l[c]=new e(a[c]).toRgb();for(var g in a){var u=(d=o,i=l[g],Math.pow(d.r-i.r,2)+Math.pow(d.g-i.g,2)+Math.pow(d.b-i.b,2));u<t&&(t=u,b=g)}return b}};f.string.push([function(f){var r=f.toLowerCase(),d=\"transparent\"===r?\"#0000\":a[r];return d?new e(d).toRgb():null},\"name\"])};export{e as default};\n", "import { colord, extend } from 'colord'\nimport a11yPlugin from 'colord/plugins/a11y'\nimport namesPlugin from 'colord/plugins/names'\n\nimport type { Theme } from '@mui/material'\n\nextend([namesPlugin, a11yPlugin])\n\nconst contrastAdjustCache = new Map<string, string>()\n\n// Adjusts a background-tile color until it meets WCAG AA (4.5:1) contrast\n// against `bg`, so it can be used as letter text in letter-color mode.\n// Darkens on light backgrounds, lightens on dark backgrounds.\nexport function adjustColorForContrast(color: string, bg: string): string {\n  const cacheKey = `${color}|${bg}`\n  const cached = contrastAdjustCache.get(cacheKey)\n  if (cached !== undefined) {\n    return cached\n  }\n  let c = colord(color)\n  if (!c.isReadable(bg)) {\n    const bgIsDark = colord(bg).luminance() < 0.5\n    for (let i = 0; i < 40 && !c.isReadable(bg); i++) {\n      c = bgIsDark ? c.lighten(0.05) : c.darken(0.05)\n    }\n  }\n  const result = c.toHex()\n  contrastAdjustCache.set(cacheKey, result)\n  return result\n}\n\n// a wash over the alignment or the tree: a color carrying its own alpha draws\n// at that alpha, and one with none takes `alpha` so the marks under it stay\n// readable\nexport function withAlpha(color: string, alpha: number) {\n  const parsed = colord(color)\n  return parsed.alpha() === 1 ? parsed.alpha(alpha).toRgbString() : color\n}\n\nexport function outlineColor(fill: string) {\n  return colord(fill).darken(0.1).toHex()\n}\n\nexport function transform<T>(\n  obj: Record<string, T>,\n  cb: (arg0: [string, T]) => [string, T],\n) {\n  return Object.fromEntries(Object.entries(obj).map(cb))\n}\n\nconst contrastTextCaches = new WeakMap<Theme, Map<string, string>>()\n\n/**\n * Readable letter color over a given cell color, memoized per theme.\n *\n * Keyed by cell color, since a dynamic scheme has no letter->color table; this\n * covers static schemes and a track's own `colors` too. An uncolored cell gets\n * the theme's text color, which stays readable in the dark theme.\n */\nexport function contrastTextFn(theme: Theme) {\n  let cache = contrastTextCaches.get(theme)\n  if (!cache) {\n    cache = new Map()\n    contrastTextCaches.set(theme, cache)\n  }\n  const fallback = theme.palette.text.primary\n  return (color: string | undefined) => {\n    if (!color) {\n      return fallback\n    }\n    const hit = cache.get(color)\n    if (hit !== undefined) {\n      return hit\n    }\n    const out = theme.palette.getContrastText(colord(color).toHex())\n    cache.set(color, out)\n    return out\n  }\n}\n\nexport function dropBlanks<T>(blanks: number[], arr: T[]) {\n  if (blanks.length === 0) {\n    return arr\n  }\n  const set = new Set(blanks)\n  return arr.filter((_, i) => !set.has(i))\n}\n\nexport function skipBlanks(blanks: number[], str: string) {\n  if (blanks.length === 0) {\n    return str\n  }\n  const chunks = []\n  let lastEnd = 0\n  for (const blankIdx of blanks) {\n    if (blankIdx > lastEnd) {\n      chunks.push(str.slice(lastEnd, blankIdx))\n    }\n    lastEnd = blankIdx + 1\n  }\n  if (lastEnd < str.length) {\n    chunks.push(str.slice(lastEnd))\n  }\n  return chunks.join('')\n}\n\nexport function computeRowInsertions(blanks: number[], seq: string) {\n  const insertions: { pos: number; letters: string }[] = []\n  const blanksLen = blanks.length\n  let displayPos = 0\n  let blankIdx = 0\n  let currentInsertPos = -1\n  let letterChars: string[] = []\n  for (let i = 0; i < seq.length; i++) {\n    if (blankIdx < blanksLen && blanks[blankIdx] === i) {\n      // bit trick: (code - 45) >>> 0 <= 1 checks for '-' (45) or '.' (46)\n      if (!((seq.charCodeAt(i) - 45) >>> 0 <= 1)) {\n        if (currentInsertPos === displayPos) {\n          letterChars.push(seq[i]!)\n        } else {\n          if (letterChars.length > 0) {\n            insertions.push({\n              pos: currentInsertPos,\n              letters: letterChars.join(''),\n            })\n          }\n          currentInsertPos = displayPos\n          letterChars = [seq[i]!]\n        }\n      }\n      blankIdx++\n    } else {\n      displayPos++\n    }\n  }\n  if (letterChars.length > 0) {\n    insertions.push({ pos: currentInsertPos, letters: letterChars.join('') })\n  }\n  return insertions\n}\n\nexport function len(a: { end: number; start: number }) {\n  return a.end - a.start\n}\n", "import { minFeatureLabelHeight } from '../../constants.ts'\n\nimport type { HierarchyNode } from '../../hierarchy.ts'\nimport type { Annotation, NodeWithIdsAndLength } from '../../types.ts'\nimport type { RenderCtx } from '../renderCtx.ts'\n\n/** one drawn span: a feature, the lane it sits in, and its row's depth */\nexport interface SpanBand {\n  annotation: Annotation\n  lane: number\n  laneCount: number\n}\n\n/** one row's spans, at the row baseline `y` the tree layout gives it */\nexport interface SpanRow<T extends SpanBand> {\n  y: number\n  bands: T[]\n}\n\n/**\n * Where a band lands inside its row. The alignment overlay fills the row, bars\n * it along the bottom, or stacks thin sub-rows; a `features` row panel divides\n * the row between its lanes.\n */\nexport interface SpanLayout {\n  /** the band height in a row needing `laneCount` lanes */\n  height: (laneCount: number) => number\n  /** the band's top edge, from its row baseline, its lane and its height */\n  top: (y: number, lane: number, height: number) => number\n  /** how far back from the feature's end the head starts */\n  headLength: (height: number) => number\n  /**\n   * how far the head rises above the band. A bar too thin to taper reads its\n   * direction off a head taller than itself, and the bar sits on the row's\n   * bottom edge, so the room is above.\n   */\n  headRise?: (height: number) => number\n}\n\n/**\n * What a renderer hands the span mark: its rows, where a band lands in them,\n * its x mapping, the colors and the label each feature takes.\n */\nexport interface SpanSource<T extends SpanBand> {\n  rows: SpanRow<T>[]\n  layout: SpanLayout\n  xOf: (band: T) => [number, number]\n  colors: Map<Annotation, { fill: string; stroke: string }>\n  labelOf?: (band: T) => string | undefined\n  labelDrawn?: (band: T) => void\n}\n\n/** a span as drawn: a box, or an arrow's outline where it carries a strand */\nexport interface SpanShape<T extends SpanBand> {\n  band: T\n  fill: string\n  stroke: string\n  box?: { x: number; y: number; w: number; h: number }\n  outline?: [number, number][]\n}\n\nexport interface SpanLabel {\n  text: string\n  x: number\n  y: number\n  fill: string\n}\n\n/** one row's shapes, then the labels drawn over them at `fontSize` */\nexport interface SpanMarkRow<T extends SpanBand> {\n  shapes: SpanShape<T>[]\n  labels: SpanLabel[]\n  fontSize: number\n}\n\n/** the rows of `bandsByRow` that `leaves` covers, in display order */\nexport function spanRows<T extends SpanBand>(\n  leaves: HierarchyNode<NodeWithIdsAndLength>[],\n  bandsByRow: Map<string, T[]>,\n): SpanRow<T>[] {\n  const rows: SpanRow<T>[] = []\n  for (const leaf of leaves) {\n    const bands = bandsByRow.get(leaf.data.name)\n    if (bands && bands.length > 0) {\n      rows.push({ y: leaf.x!, bands })\n    }\n  }\n  return rows\n}\n\n/**\n * The span mark as geometry, in whatever x space `xOf` maps its bands into:\n * alignment columns for the domain overlay, panel pixels for a `features` row\n * panel. A feature with a strand is an arrow, one without a box, and a label\n * lands inside the span wherever `measureText` says the text fits.\n *\n * `y - rowHeight` is the row's top edge in the coordinates `rows` gives.\n */\nexport function featureSpanMarks<T extends SpanBand>({\n  rows,\n  layout,\n  xOf,\n  colors,\n  labelOf,\n  labelDrawn,\n  measureText,\n  xMin,\n  xMax,\n}: SpanSource<T> & {\n  measureText: (text: string, fontSize: number) => number\n  xMin: number\n  xMax: number\n}): SpanMarkRow<T>[] {\n  const out: SpanMarkRow<T>[] = []\n  for (const { y, bands } of rows) {\n    const h = layout.height(bands[0]!.laneCount)\n    const headLen = layout.headLength(h)\n    const rise = layout.headRise?.(h) ?? 0\n    const labelled = labelOf !== undefined && h >= minFeatureLabelHeight\n    const fontSize = Math.min(h - 2, 11)\n    const shapes: SpanShape<T>[] = []\n    const labels: SpanLabel[] = []\n    // one row's spans are drawn before any of its labels. Bands are ordered\n    // longest-first so a nested one lands on top, and drawing each label with\n    // its own span put the child's box over the parent's text: `S` covered\n    // `RBD`, and `RBD` read as `RB`.\n    const placed: {\n      band: T\n      xStart: number\n      w: number\n      t: number\n      head: number\n      fill: string\n    }[] = []\n\n    for (const band of bands) {\n      const [xStart, xEnd] = xOf(band)\n      const w = xEnd - xStart\n      if (xEnd < xMin || xStart > xMax) {\n        continue\n      }\n      const t = layout.top(y, band.lane, h)\n      const { fill, stroke } = colors.get(band.annotation)!\n      const { strand } = band.annotation\n      const head = strand === undefined ? 0 : Math.min(headLen, w)\n      shapes.push(\n        strand === undefined\n          ? { band, fill, stroke, box: { x: xStart, y: t, w, h } }\n          : {\n              band,\n              fill,\n              stroke,\n              outline: geneArrow({ x: xStart, t, w, h, head, rise, strand }),\n            },\n      )\n      if (labelled) {\n        placed.push({ band, xStart, w, t, head, fill })\n      }\n    }\n\n    for (const { band, xStart, w, t, head, fill } of placed) {\n      // asking for the label here rather than in the pass above keeps the\n      // once-per-block segment numbering in drawing order\n      const text = labelOf!(band)\n      // the head narrows to a point, so only about half of it holds text\n      if (\n        text !== undefined &&\n        measureText(text, fontSize) + 2 <= w - head / 2\n      ) {\n        labelDrawn?.(band)\n        labels.push({ text, x: xStart + w / 2, y: t + h / 2, fill })\n      }\n    }\n    out.push({ shapes, labels, fontSize })\n  }\n  return out\n}\n\n/**\n * The span mark, drawn into `ctx` from `featureSpanMarks`, with the context\n * translated so that `y - rowHeight` is the row's top edge.\n */\nexport function drawFeatureSpans<T extends SpanBand>({\n  ctx,\n  contrastText,\n  ...source\n}: SpanSource<T> & {\n  ctx: RenderCtx\n  contrastText: (color: string) => string\n  xMin: number\n  xMax: number\n}) {\n  let font = ''\n  const setFont = (fontSize: number) => {\n    const next = `${fontSize}px sans-serif`\n    if (next !== font) {\n      ctx.font = next\n      font = next\n    }\n  }\n  const rows = featureSpanMarks({\n    ...source,\n    measureText: (text, fontSize) => {\n      setFont(fontSize)\n      return ctx.measureText(text).width\n    },\n  })\n  for (const { shapes, labels, fontSize } of rows) {\n    for (const { fill, stroke, box, outline } of shapes) {\n      ctx.fillStyle = fill\n      ctx.strokeStyle = stroke\n      if (box) {\n        ctx.fillRect(box.x, box.y, box.w, box.h)\n        ctx.strokeRect(box.x, box.y, box.w, box.h)\n      } else if (outline) {\n        ctx.beginPath()\n        ctx.moveTo(...outline[0]!)\n        for (let i = 1; i < outline.length; i++) {\n          ctx.lineTo(...outline[i]!)\n        }\n        ctx.closePath()\n        ctx.fill()\n        ctx.stroke()\n      }\n    }\n    if (labels.length > 0) {\n      setFont(fontSize)\n      ctx.textAlign = 'center'\n      ctx.textBaseline = 'middle'\n      for (const { text, x, y, fill } of labels) {\n        ctx.fillStyle = contrastText(fill)\n        ctx.fillText(text, x, y)\n      }\n    }\n  }\n}\n\n/**\n * A gene arrow's outline, the way gggenes and gggenomes draw one: the head is\n * the last `head` pixels *of* the feature, tapering to a point at its end, and\n * a feature shorter than the head is all head. The glyph therefore covers its\n * start..end span and nothing else, so adjacent genes butt together instead of\n * biting triangles out of each other, a neighbour never draws over a label, and\n * a gene 20 columns wide reads as 20 columns wide.\n *\n * `rise` lifts the head above the band, for a bar too thin to taper.\n */\nfunction geneArrow({\n  x,\n  t,\n  w,\n  h,\n  head,\n  rise,\n  strand,\n}: {\n  x: number\n  t: number\n  w: number\n  h: number\n  head: number\n  rise: number\n  strand: number\n}): [number, number][] {\n  const tip = strand > 0 ? x + w : x\n  const tail = strand > 0 ? x : x + w\n  const flange = strand > 0 ? tip - head : tip + head\n  const bottom = t + h\n  const crown = t - rise\n  const point = (crown + bottom) / 2\n  if (head >= w) {\n    return [\n      [tail, crown],\n      [tip, point],\n      [tail, bottom],\n    ]\n  }\n  return [\n    [tail, t],\n    [flange, t],\n    ...(rise > 0 ? [[flange, crown] as [number, number]] : []),\n    [tip, point],\n    [flange, bottom],\n    [tail, bottom],\n  ]\n}\n", "import { domainUnderlineHeight, subFeatureRowHeight } from '../../constants.ts'\nimport { contrastTextFn } from '../../util.ts'\nimport { getVisibleLeaves } from '../getVisibleLeaves.ts'\nimport { drawFeatureSpans, spanRows } from './drawFeatureSpans.ts'\n\nimport type { HierarchyNode } from '../../hierarchy.ts'\nimport type { MsaViewModel } from '../../model.ts'\nimport type { DomainBand, NodeWithIdsAndLength } from '../../types.ts'\nimport type { RenderCtx } from '../renderCtx.ts'\nimport type { SpanSource } from './drawFeatureSpans.ts'\nimport type { Theme } from '@mui/material'\n\nexport function renderBoxFeatureCanvasBlock({\n  model,\n  theme,\n  offsetX,\n  offsetY,\n  ctx,\n  highResScaleFactorOverride,\n  blockSizeXOverride,\n  blockSizeYOverride,\n}: {\n  offsetX: number\n  offsetY: number\n  model: MsaViewModel\n  theme: Theme\n  ctx: RenderCtx\n  highResScaleFactorOverride?: number\n  blockSizeXOverride?: number\n  blockSizeYOverride?: number\n}) {\n  const { blockSize, rowHeight, highResScaleFactor, actuallyShowDomains } =\n    model\n  if (!actuallyShowDomains) {\n    return\n  }\n  const k = highResScaleFactorOverride ?? highResScaleFactor\n  const bx = blockSizeXOverride ?? blockSize\n  const by = blockSizeYOverride ?? blockSize\n  ctx.resetTransform()\n  ctx.scale(k, k)\n  ctx.translate(-offsetX, rowHeight / 2 - offsetY)\n\n  drawFeatureSpans<DomainBand>({\n    ctx,\n    ...domainOverlaySource(\n      model,\n      getVisibleLeaves({ model, offsetY, blockSizeY: by }),\n    ),\n    contrastText: contrastTextFn(theme),\n    xMin: offsetX,\n    xMax: offsetX + bx,\n  })\n}\n\n/**\n * The domain overlay's spans over `leaves`, in alignment pixels: filled rows,\n * an underline bar, or thin sub-rows, as `domainUnderline` and\n * `subFeatureRows` decide.\n */\nexport function domainOverlaySource(\n  model: MsaViewModel,\n  leaves: HierarchyNode<NodeWithIdsAndLength>[],\n): SpanSource<DomainBand> {\n  const {\n    rowHeight,\n    subFeatureRows,\n    colWidth,\n    featureColors,\n    featureLabels,\n    segmentLabels,\n    showMsaLetters,\n    domainUnderline,\n    domainBands,\n  } = model\n  // the plain and underline modes give every band the same height; a sub-row\n  // band is thinner, and how thin depends on how many lanes its row needs\n  const barHeight = domainUnderline\n    ? Math.min(domainUnderlineHeight, rowHeight)\n    : rowHeight\n  // exon numbers label the bands only when residue letters aren't drawn (zoomed\n  // out); when letters show, the alternating shades alone mark the boundaries\n  // and a number would collide with the sequence. A featureLabel encoding names\n  // what every span carries instead\n  const drawSegmentLabels = !featureLabels && !showMsaLetters && !subFeatureRows\n  // a segment (exon) number labels its band once per block, on the topmost\n  // visible row carrying that segment, so it reads as a column header for the\n  // whole band. Keyed by accession rather than drawn on row 0, because the rows\n  // carrying the gene model are often not the first ones in the alignment\n  const labelled = drawSegmentLabels ? new Set<string>() : undefined\n\n  return {\n    rows: spanRows(leaves, domainBands),\n    layout: {\n      // sub-rows are thin, but a row whose lanes would spill onto the row below\n      // shares out the row height between them instead\n      height: laneCount =>\n        subFeatureRows\n          ? Math.min(subFeatureRowHeight, rowHeight / laneCount)\n          : barHeight,\n      top: (y, lane, h) =>\n        y -\n        rowHeight +\n        (subFeatureRows ? lane * h : domainUnderline ? rowHeight - h : 0),\n      headLength: h => (domainUnderline ? rowHeight / 2 : h),\n      // a head only as tall as an underline bar tapers over ten pixels of\n      // three, which reads as nothing; it takes the lower two fifths of the\n      // row instead, leaving the letters above it\n      headRise: h => (domainUnderline ? Math.max(0, rowHeight * 0.4 - h) : 0),\n    },\n    xOf: band => [band.startCol * colWidth, band.endCol * colWidth],\n    colors: featureColors,\n    labelOf: band =>\n      featureLabels?.get(band.annotation) ??\n      (labelled && !labelled.has(band.annotation.accession)\n        ? segmentLabels.get(band.annotation.accession)\n        : undefined),\n    labelDrawn: band => labelled?.add(band.annotation.accession),\n  }\n}\n", "// Replace just the px size token in a canvas font string, preserving the\n// family (and optionally toggling bold). Accepts anything with a `font` field,\n// so it works for both a real CanvasRenderingContext2D and the svgcanvas\n// export context.\n//\n// [\\d.]+ is load-bearing: it matches fractional sizes produced by smooth zoom.\n// \\d+ alone matches only the fraction (\"8604\" in \"14.8604px\"), splicing the new\n// size into the middle to make an invalid string like \"14 0.18px sans-serif\" \u2014\n// which canvas silently rejects, freezing the font and making fillText draw\n// nothing while fillRect still works.\nexport function setFontSize(\n  ctx: { font: string },\n  fontSize: number,\n  bold = false,\n) {\n  ctx.font = ctx.font.replace(\n    /(?:bold )?[\\d.]+px/,\n    `${bold ? 'bold ' : ''}${fontSize}px`,\n  )\n}\n", "// Shared highlight colors for the MSA/tree hover and selection overlay canvases.\n// Kept in one place so the reference-row color (drawn identically over both the\n// tree and the alignment) can't drift between the two surfaces.\n\n// reference (relativeTo) row, drawn over both the tree and the alignment\nexport const referenceColor = 'rgba(0,128,255,0.3)'\n\n// tree-node descendant rows highlighted on hover. The alpha differs by surface\n// intentionally: the tree background is plain so it can take a stronger wash,\n// while the alignment cells are already colored so a lighter wash reads better.\nexport const treeHoverColor = 'rgba(255,165,0,0.2)'\nexport const multiRowHoverColor = 'rgba(255,165,0,0.15)'\n\n// the hovered column/row, and the one pinned by a click. Drawn on the alignment\n// overlay canvas and again as plain divs over the track area, which have to\n// match or the crosshair appears to change color as it crosses the tracks.\nexport const hoverColor = 'rgba(0,0,0,0.15)'\nexport const clickColor = 'rgba(128,128,0,0.2)'\n\n// the selected block, a blue that reads apart from the orange highlights\nexport const selectionFill = 'rgba(25,118,210,0.22)'\nexport const selectionBorder = 'rgba(25,118,210,0.95)'\n", "import { setFontSize } from '../../setFontSize.ts'\nimport {\n  referenceColor,\n  selectionBorder,\n  selectionFill,\n} from '../overlayColors.ts'\n\nimport type { MsaViewModel } from '../../model.ts'\nimport type { RenderCtx } from '../renderCtx.ts'\nimport type { Theme } from '@mui/material'\n\n// a fill plus a solid border; the hover wash alone is invisible over clustalx\n// coloring\nexport const highlightFill = 'rgba(255,140,0,0.28)'\nexport const highlightBorder = 'rgba(210,90,0,0.95)'\nexport const highlightRowFill = 'rgba(255,140,0,0.18)'\n\nexport const labelFontSize = 11\nconst labelPad = 3\n// the label box above a highlight band; tree blocks also check rows this far\n// outside themselves\nexport const highlightLabelHeight = labelFontSize + labelPad * 2\n\nexport interface LabelBox {\n  left: number\n  right: number\n  top: number\n  bottom: number\n}\n\n/**\n * A highlight's label, over its band where it fits and beside it where it does\n * not, kept inside `bounds` and out of the way of the labels already placed.\n *\n * `bounds` keeps the label of a band scrolled partly off the left edge visible.\n * With `placed`, a label that would overlap an earlier one, as two\n * single-residue highlights a column apart do, steps down a row.\n */\nexport function drawHighlightLabel({\n  ctx,\n  theme,\n  label,\n  x,\n  y,\n  spanWidth,\n  bounds,\n  placed,\n}: {\n  ctx: RenderCtx\n  theme: Theme\n  label: string\n  x: number\n  y: number\n  spanWidth: number\n  bounds?: { min: number; max: number }\n  placed?: LabelBox[]\n}) {\n  setFontSize(ctx, labelFontSize)\n  ctx.textAlign = 'start'\n  const boxWidth = ctx.measureText(label).width + labelPad * 2\n  const boxHeight = highlightLabelHeight\n  let left = boxWidth <= spanWidth ? x : x + spanWidth + 2\n  if (bounds) {\n    left = Math.max(bounds.min, Math.min(left, bounds.max - boxWidth))\n  }\n  let top = y\n  if (placed) {\n    const overlaps = (box: LabelBox) =>\n      box.left < left + boxWidth &&\n      box.right > left &&\n      box.top < top + boxHeight &&\n      box.bottom > top\n    while (placed.some(overlaps)) {\n      top += boxHeight\n    }\n    placed.push({ left, right: left + boxWidth, top, bottom: top + boxHeight })\n  }\n  ctx.fillStyle = theme.palette.background.paper\n  ctx.fillRect(left, top, boxWidth, boxHeight)\n  ctx.fillStyle = theme.palette.text.primary\n  ctx.fillText(label, left + labelPad, top + labelPad + labelFontSize - 2)\n}\n\n/**\n * The persistent overlay on the alignment: the band behind each clade of\n * `clades`, the `rowTint` encoding's wash, the row tints and bordered column\n * bands of `highlights`, and a label above each band. `offsetX`/`offsetY` are\n * the content coordinates at the canvas origin, the convention renderMSABlock\n * uses, so the live overlay passes -scrollX/-scrollY and the export passes its\n * layout offsets.\n *\n * Rows are culled to the ones this block covers. A tint over every row of a\n * large alignment would otherwise draw the whole column of rects in each block,\n * and again on every pointer move through renderMouseover.\n */\nexport function renderHighlights({\n  ctx,\n  model,\n  theme,\n  offsetX,\n  offsetY,\n  width,\n  height,\n}: {\n  ctx: RenderCtx\n  model: MsaViewModel\n  theme: Theme\n  offsetX: number\n  offsetY: number\n  width: number\n  height: number\n}) {\n  const { resolvedClades, resolvedHighlights, rowTints, colWidth, rowHeight } =\n    model\n  const placed: LabelBox[] = []\n  ctx.lineWidth = 2\n  const firstRow = Math.max(0, Math.floor(offsetY / rowHeight))\n  const lastRow = Math.ceil((offsetY + height) / rowHeight)\n  const fillRow = (index: number) => {\n    ctx.fillRect(0, index * rowHeight - offsetY, width, rowHeight)\n  }\n  for (const { rows, color, mark } of resolvedClades) {\n    if (mark === 'highlight' && rows[1] >= firstRow && rows[0] <= lastRow) {\n      ctx.fillStyle = color\n      ctx.fillRect(\n        0,\n        rows[0] * rowHeight - offsetY,\n        width,\n        (rows[1] - rows[0] + 1) * rowHeight,\n      )\n    }\n  }\n  if (rowTints) {\n    for (\n      let index = firstRow;\n      index <= Math.min(lastRow, rowTints.length - 1);\n      index++\n    ) {\n      const color = rowTints[index]\n      if (color) {\n        ctx.fillStyle = color\n        fillRow(index)\n      }\n    }\n  }\n  for (const { rowIndices, color } of resolvedHighlights) {\n    ctx.fillStyle = color ?? highlightRowFill\n    for (const index of rowIndices) {\n      if (index >= firstRow && index <= lastRow) {\n        fillRow(index)\n      }\n    }\n  }\n  for (const { startCol, endCol, label, color } of resolvedHighlights) {\n    if (startCol === undefined || endCol === undefined) {\n      continue\n    }\n    const x = startCol * colWidth - offsetX\n    const spanWidth = (endCol - startCol + 1) * colWidth\n    ctx.fillStyle = color ?? highlightFill\n    ctx.fillRect(x, 0, spanWidth, height)\n    ctx.strokeStyle = color ?? highlightBorder\n    ctx.strokeRect(x, 0, spanWidth, height)\n    if (label) {\n      drawHighlightLabel({\n        ctx,\n        theme,\n        label,\n        x,\n        y: 0,\n        spanWidth,\n        bounds: { min: 0, max: width },\n        placed,\n      })\n    }\n  }\n}\n\n/**\n * The selected block, a bordered band per run of consecutive selected rows,\n * culled to the rows this block covers\n */\nexport function renderSelection({\n  ctx,\n  model,\n  offsetX,\n  offsetY,\n  height,\n}: {\n  ctx: RenderCtx\n  model: MsaViewModel\n  offsetX: number\n  offsetY: number\n  height: number\n}) {\n  const { resolvedSelection, colWidth, rowHeight } = model\n  if (!resolvedSelection) {\n    return\n  }\n  const { startCol, endCol, rowRuns } = resolvedSelection\n  const x = startCol * colWidth - offsetX\n  const w = (endCol - startCol + 1) * colWidth\n  ctx.lineWidth = 1\n  for (const [first, last] of rowRuns) {\n    const y = first * rowHeight - offsetY\n    const h = (last - first + 1) * rowHeight\n    if (y < height && y + h > 0) {\n      ctx.fillStyle = selectionFill\n      ctx.fillRect(x, y, w, h)\n      ctx.strokeStyle = selectionBorder\n      ctx.strokeRect(x, y, w, h)\n    }\n  }\n}\n\n/**\n * The overlay parts that come from the snapshot: the reference row's tint, a\n * bordered band per run of highlighted columns and the `highlights` layer. The\n * live overlay draws these under the selected block and its hover and click\n * bands; the SVG export draws only these.\n */\nexport function renderPersistentHighlights({\n  ctx,\n  model,\n  theme,\n  offsetX,\n  offsetY,\n  width,\n  height,\n}: {\n  ctx: RenderCtx\n  model: MsaViewModel\n  theme: Theme\n  offsetX: number\n  offsetY: number\n  width: number\n  height: number\n}) {\n  const { colWidth, rowHeight, referenceRowIndex, highlightedColumnRuns } =\n    model\n\n  if (referenceRowIndex !== undefined) {\n    ctx.fillStyle = referenceColor\n    ctx.fillRect(0, referenceRowIndex * rowHeight - offsetY, width, rowHeight)\n  }\n\n  ctx.lineWidth = 2\n  for (const { start, end } of highlightedColumnRuns) {\n    const x = start * colWidth - offsetX\n    const w = (end - start + 1) * colWidth\n    ctx.fillStyle = highlightFill\n    ctx.fillRect(x, 0, w, height)\n    ctx.strokeStyle = highlightBorder\n    ctx.strokeRect(x, 0, w, height)\n  }\n\n  renderHighlights({ ctx, model, theme, offsetX, offsetY, width, height })\n}\n", "import type { DomainBand } from '../../types.ts'\n\n/**\n * Left-to-right cursor over one row's domain bands that returns the band drawn\n * on top at a column, for a letter's contrast color.\n *\n * The overlay paints in `domainBands` order, largest first, so where signatures\n * nest (InterProScan often emits a family enclosing a domain) the visible band\n * is the last one painted. `stackIndex` is that paint order.\n *\n * `bands` must be sorted by start column (`domainBandsByStart`) and columns\n * visited in increasing order, which keeps this to one pass per row.\n */\nexport function domainBandCursor(bands: DomainBand[] | undefined) {\n  let next = 0\n  let active: DomainBand[] = []\n\n  return (col: number) => {\n    if (!bands) {\n      return undefined\n    }\n    while (next < bands.length && bands[next]!.startCol <= col) {\n      active.push(bands[next]!)\n      next++\n    }\n    if (active.some(band => band.endCol <= col)) {\n      active = active.filter(band => band.endCol > col)\n    }\n    let top: DomainBand | undefined\n    for (const band of active) {\n      if (!top || band.stackIndex > top.stackIndex) {\n        top = band\n      }\n    }\n    return top\n  }\n}\n", "// The half-open range of alignment columns [xStart, xEnd) intersecting a block\n// of width blockWidth at horizontal offset offsetX. X-axis counterpart to\n// getVisibleLeaves.\nexport function visibleColRange({\n  offsetX,\n  blockWidth,\n  colWidth,\n}: {\n  offsetX: number\n  blockWidth: number\n  colWidth: number\n}) {\n  return {\n    xStart: Math.max(0, Math.floor(offsetX / colWidth)),\n    xEnd: Math.max(0, Math.ceil((offsetX + blockWidth) / colWidth)),\n  }\n}\n", "import { setFontSize } from '../../setFontSize.ts'\nimport { adjustColorForContrast, contrastTextFn } from '../../util.ts'\nimport { getVisibleLeaves } from '../getVisibleLeaves.ts'\nimport { domainBandCursor } from './domainBandCursor.ts'\nimport { tileColorFn } from './tileColor.ts'\nimport { visibleColRange } from './visibleColRange.ts'\n\nimport type { HierarchyNode } from '../../hierarchy.ts'\nimport type { MsaViewModel } from '../../model.ts'\nimport type { NodeWithIdsAndLength } from '../../types.ts'\nimport type { RenderCtx } from '../renderCtx.ts'\nimport type { Theme } from '@mui/material'\n\nexport function renderMSABlock({\n  model,\n  offsetX,\n  offsetY,\n  ctx,\n  theme,\n  highResScaleFactorOverride,\n  blockSizeXOverride,\n  blockSizeYOverride,\n  rasterTiles,\n}: {\n  offsetX: number\n  offsetY: number\n  theme: Theme\n  model: MsaViewModel\n  ctx: RenderCtx\n  highResScaleFactorOverride?: number\n  blockSizeXOverride?: number\n  blockSizeYOverride?: number\n  rasterTiles?: boolean\n}) {\n  const {\n    colWidth,\n    blockSize,\n    rowHeight,\n    fontSize,\n    highResScaleFactor,\n    actuallyShowDomains,\n    bgColor,\n  } = model\n  const k = highResScaleFactorOverride ?? highResScaleFactor\n  const bx = blockSizeXOverride ?? blockSize\n  const by = blockSizeYOverride ?? blockSize\n  ctx.resetTransform()\n  ctx.scale(k, k)\n  ctx.translate(-offsetX, rowHeight / 2 - offsetY)\n  ctx.textAlign = 'center'\n  ctx.textBaseline = 'alphabetic'\n  setFontSize(ctx, fontSize, !bgColor)\n\n  const { xStart, xEnd } = visibleColRange({\n    offsetX,\n    blockWidth: bx,\n    colWidth,\n  })\n  const visibleLeaves = getVisibleLeaves({ model, offsetY, blockSizeY: by })\n  const { relativeTo, columns } = model\n  const referenceSeq = relativeTo\n    ? columns.get(relativeTo)?.slice(xStart, xEnd)\n    : null\n\n  drawTilesAndText({\n    model,\n    ctx,\n    theme,\n    xStart,\n    xEnd,\n    visibleLeaves,\n    referenceSeq,\n    // when domains are shown the background tiles come from\n    // renderBoxFeatureCanvasBlock, so only the letters are drawn here\n    drawTiles: !actuallyShowDomains,\n    // ...and when the caller has already laid the raster down, the tiles are\n    // there but nothing here has to paint them\n    rasterTiles,\n  })\n  drawInsertionIndicators({\n    model,\n    ctx,\n    xStart,\n    xEnd,\n    visibleLeaves,\n  })\n  ctx.resetTransform()\n}\n\nfunction drawTilesAndText({\n  model,\n  ctx,\n  theme,\n  visibleLeaves,\n  xStart,\n  xEnd,\n  referenceSeq,\n  drawTiles,\n  rasterTiles,\n}: {\n  model: MsaViewModel\n  theme: Theme\n  ctx: RenderCtx\n  visibleLeaves: HierarchyNode<NodeWithIdsAndLength>[]\n  xStart: number\n  xEnd: number\n  referenceSeq: string | null | undefined\n  drawTiles: boolean\n  rasterTiles?: boolean\n}) {\n  const {\n    bgColor,\n    columns,\n    colWidth,\n    rowHeight,\n    fontSize,\n    relativeTo,\n    showMsaLetters,\n    subFeatureRows,\n    domainUnderline,\n    domainBandsByStart,\n    featureColors,\n  } = model\n\n  const tiles = drawTiles && bgColor\n  const paintTiles = tiles && !rasterTiles\n  if (paintTiles || showMsaLetters) {\n    const tileColor = tileColorFn(model)\n    // Domain fills come from a categorical palette with no fixed lightness, and\n    // a dynamic scheme colors a cell from its column, so a readable letter color\n    // is a question about the cell's own color rather than about its letter.\n    const contrastText = contrastTextFn(theme)\n    const offsetXAligned = xStart * colWidth\n    const halfColWidth = colWidth / 2\n    // the context is translated by rowHeight/2, so `y` is the row's bottom\n    // edge and the baseline lands fontSize/4 below the row center, where the\n    // tree puts its tip labels\n    const baselineOffset = rowHeight / 2 - fontSize / 4\n    // with the tiles coming from the domain overlay instead, letters sit either\n    // on a domain box or on the plain background; sub-row layout stacks the boxes\n    // above the letters and letter-color mode shrinks them to a bar under the\n    // row, so neither leaves anything behind a letter\n    const overDomains = !drawTiles && !subFeatureRows && !domainUnderline\n\n    for (let i = 0, l1 = visibleLeaves.length; i < l1; i++) {\n      const node = visibleLeaves[i]!\n      const { name } = node.data\n      const y = node.x!\n      const str = columns.get(name)?.slice(xStart, xEnd)\n      if (str) {\n        const tileY = y - rowHeight\n        const textY = y - baselineOffset\n        const bandAt = domainBandCursor(\n          overDomains ? domainBandsByStart.get(name) : undefined,\n        )\n\n        for (let j = 0, l2 = str.length; j < l2; j++) {\n          const col = xStart + j\n          const letter = str[j]!\n          const x = j * colWidth + offsetXAligned\n          const isMatchingReference =\n            referenceSeq && name !== relativeTo && letter === referenceSeq[j]\n          const color = tileColor(col, letter)\n\n          if (paintTiles) {\n            ctx.fillStyle = isMatchingReference\n              ? theme.palette.action.hover\n              : color || theme.palette.background.default\n            ctx.fillRect(x, tileY, colWidth, rowHeight)\n          }\n\n          if (showMsaLetters) {\n            const covering = bandAt(col)\n            ctx.fillStyle = covering\n              ? // on top of a domain box: contrast against the box fill\n                contrastText(featureColors.get(covering.annotation)?.fill)\n              : isMatchingReference\n                ? // the dot sits on the faint reference-match wash, which is\n                  // the theme's background with a little of its text color in it\n                  theme.palette.text.primary\n                : tiles\n                  ? // on top of a colored tile, or on the background where the\n                    // scheme gives that cell no color\n                    contrastText(color)\n                  : bgColor || !color\n                    ? // plain background, uncolored letters\n                      theme.palette.text.primary\n                    : // letter-color mode: darken/lighten to stay readable\n                      adjustColorForContrast(\n                        color,\n                        theme.palette.background.default,\n                      )\n            ctx.fillText(\n              isMatchingReference ? '.' : letter,\n              x + halfColWidth,\n              textY,\n            )\n          }\n        }\n      }\n    }\n  }\n}\n\nfunction drawInsertionIndicators({\n  model,\n  ctx,\n  visibleLeaves,\n  xStart,\n  xEnd,\n}: {\n  model: MsaViewModel\n  ctx: RenderCtx\n  visibleLeaves: HierarchyNode<NodeWithIdsAndLength>[]\n  xStart: number\n  xEnd: number\n}) {\n  const { bgColor, hideGapsEffective } = model\n  if (!hideGapsEffective) {\n    return\n  }\n\n  ctx.lineWidth = 1\n  ctx.strokeStyle = '#f0f'\n  drawZigZag({ visibleLeaves, xStart, ctx, model, xEnd, offset: 0 })\n  ctx.strokeStyle = !bgColor ? '#000' : '#fff'\n  drawZigZag({ visibleLeaves, xStart, ctx, model, xEnd, offset: -1 })\n}\n\nfunction drawZigZag({\n  model,\n  ctx,\n  visibleLeaves,\n  xStart,\n  xEnd,\n  offset,\n}: {\n  model: MsaViewModel\n  ctx: RenderCtx\n  visibleLeaves: HierarchyNode<NodeWithIdsAndLength>[]\n  xStart: number\n  xEnd: number\n  offset: number\n}) {\n  const zigSize = 1\n  const { colWidth, rowHeight, insertionPositions } = model\n  for (const node of visibleLeaves) {\n    const { name } = node.data\n    const insertions = insertionPositions.get(name)\n    if (insertions) {\n      const y = node.x!\n      for (const { pos } of insertions) {\n        if (pos >= xStart && pos < xEnd) {\n          const x = pos * colWidth\n          const top = y - rowHeight\n          const bottom = y\n          ctx.beginPath()\n          ctx.moveTo(x + offset, top + offset)\n          let currentY = top\n          let goRight = true\n          while (currentY < bottom) {\n            const nextY = Math.min(currentY + zigSize * 2, bottom)\n            const nextX = goRight ? x + zigSize : x - zigSize\n            ctx.lineTo(nextX + offset, nextY + offset)\n            currentY = nextY\n            goRight = !goRight\n          }\n          ctx.stroke()\n        }\n      }\n    }\n  }\n}\n", "import { rowPanelHeaderHeight } from '../../constants.ts'\n\nexport function headerRunsAcross(panelWidth: number) {\n  return panelWidth > rowPanelHeaderHeight\n}\n", "import { contrastTextFn } from '../../util.ts'\nimport { getVisibleLeaves } from '../getVisibleLeaves.ts'\nimport { drawFeatureSpans, spanRows } from '../msa/drawFeatureSpans.ts'\n\nimport type { HierarchyNode } from '../../hierarchy.ts'\nimport type { MsaViewModel } from '../../model.ts'\nimport type {\n  NodeWithIdsAndLength,\n  ResolvedFeaturePanel,\n  RowPanelSpan,\n} from '../../types.ts'\nimport type { SpanSource } from '../msa/drawFeatureSpans.ts'\nimport type { RenderCtx } from '../renderCtx.ts'\nimport type { Theme } from '@mui/material'\n\n// a span keeps a pixel clear above and below it, so stacked lanes and adjacent\n// rows read apart\nconst rowPadding = 2\n\n/**\n * The spans of a `features` panel, drawn with the mark the alignment overlay\n * draws: an arrow where the feature carries a strand, a box otherwise, labeled\n * where the text fits. The x mapping is the panel's own, resolved in\n * `resolvedRowPanels`; a row needing several lanes divides its height between\n * them.\n */\nexport function renderFeaturePanel({\n  ctx,\n  model,\n  theme,\n  panel,\n  x,\n  offsetY,\n  blockSizeYOverride,\n  highResScaleFactorOverride,\n}: {\n  ctx: RenderCtx\n  model: MsaViewModel\n  theme: Theme\n  panel: ResolvedFeaturePanel\n  x: number\n  offsetY: number\n  blockSizeYOverride?: number\n  highResScaleFactorOverride?: number\n}) {\n  const { rowHeight, blockSize, highResScaleFactor } = model\n  const by = blockSizeYOverride ?? blockSize\n  const k = highResScaleFactorOverride ?? highResScaleFactor\n  ctx.resetTransform()\n  ctx.scale(k, k)\n  ctx.translate(x, rowHeight / 2 - offsetY)\n\n  drawFeatureSpans<RowPanelSpan>({\n    ctx,\n    ...featurePanelSource(\n      model,\n      panel,\n      getVisibleLeaves({ model, offsetY, blockSizeY: by }),\n    ),\n    contrastText: contrastTextFn(theme),\n    xMin: 0,\n    xMax: panel.width,\n  })\n}\n\n/** a features panel's spans over `leaves`, in panel pixels, a lane apiece */\nexport function featurePanelSource(\n  model: MsaViewModel,\n  panel: ResolvedFeaturePanel,\n  leaves: HierarchyNode<NodeWithIdsAndLength>[],\n): SpanSource<RowPanelSpan> {\n  const { rowHeight } = model\n  return {\n    rows: spanRows(leaves, panel.spans),\n    layout: {\n      height: laneCount => Math.max(1, rowHeight / laneCount - rowPadding),\n      top: (y, lane, h) =>\n        y - rowHeight + lane * (h + rowPadding) + rowPadding / 2,\n      headLength: h => h,\n    },\n    xOf: span => [span.xStart, span.xEnd],\n    colors: panel.colors,\n    labelOf: span => panel.labels?.get(span.annotation),\n  }\n}\n", "import { getVisibleLeaves } from '../getVisibleLeaves.ts'\n\nimport type { MsaViewModel } from '../../model.ts'\nimport type { ResolvedStripPanel } from '../../types.ts'\nimport type { RenderCtx } from '../renderCtx.ts'\n\n/**\n * One cell per row of a `strip` panel, in the color its field takes through\n * the panel's scale. A row the table has no value for leaves the cell empty.\n *\n * `x` is the panel's left edge in the context: the live view gives each panel\n * a canvas of its own and passes 0, and the export packs every panel into one\n * context and passes the panel's own offset.\n */\nexport function renderStrip({\n  ctx,\n  model,\n  panel,\n  x,\n  offsetY,\n  blockSizeYOverride,\n  highResScaleFactorOverride,\n}: {\n  ctx: RenderCtx\n  model: MsaViewModel\n  panel: ResolvedStripPanel\n  x: number\n  offsetY: number\n  blockSizeYOverride?: number\n  highResScaleFactorOverride?: number\n}) {\n  const { rowHeight, blockSize, highResScaleFactor } = model\n  const by = blockSizeYOverride ?? blockSize\n  ctx.resetTransform()\n  const k = highResScaleFactorOverride ?? highResScaleFactor\n  ctx.scale(k, k)\n  ctx.translate(x, -offsetY)\n  for (const leaf of getVisibleLeaves({ model, offsetY, blockSizeY: by })) {\n    const color = panel.colors.get(leaf.data.name)\n    if (color) {\n      ctx.fillStyle = color\n      // leaf.x is the row's center, at rowHeight*(index+0.5)\n      ctx.fillRect(0, leaf.x! - rowHeight / 2, panel.width, rowHeight)\n    }\n  }\n}\n", "import { renderFeaturePanel } from './renderFeaturePanel.ts'\nimport { renderStrip } from './renderStrip.ts'\n\nimport type { MsaViewModel } from '../../model.ts'\nimport type { ResolvedRowPanel } from '../../types.ts'\nimport type { RenderCtx } from '../renderCtx.ts'\nimport type { Theme } from '@mui/material'\n\ninterface PanelArgs {\n  ctx: RenderCtx\n  model: MsaViewModel\n  theme: Theme\n  panel: ResolvedRowPanel\n  x: number\n  offsetY: number\n  blockSizeYOverride?: number\n  highResScaleFactorOverride?: number\n}\n\n/**\n * One row panel, by kind. `x` is the panel's left edge in the context: the\n * live view gives each panel a canvas of its own and passes 0, and the export\n * packs every panel into one context and passes the panel's own offset.\n */\nexport function renderRowPanel({ panel, ...rest }: PanelArgs) {\n  if (panel.kind === 'features') {\n    renderFeaturePanel({ panel, ...rest })\n  } else {\n    renderStrip({ panel, ...rest })\n  }\n}\n\n/** every row panel side by side in one context, for the SVG export */\nexport function renderRowPanels({\n  model,\n  ...rest\n}: Omit<PanelArgs, 'panel' | 'x'>) {\n  for (const panel of model.resolvedRowPanels) {\n    renderRowPanel({ model, panel, x: panel.offsetX, ...rest })\n  }\n}\n", "// Per-column residue counts for an alignment, stored as a flat typed array\n// instead of one `Record<string, number>` per column. Column statistics are the\n// hottest computation in the viewer (they feed conservation, ClustalX coloring,\n// consensus and the hover tooltip), and the object-per-column form spent all of\n// its time on megamorphic string-keyed property increments: 1000x5000 residues\n// took ~1.6s to tally that way versus ~35ms here.\n//\n// Each column owns a fixed stride of counter slots. Slots 1-26 are A-Z (case\n// folded), plus a slot each for the two gap characters, '*', and anything else.\n\nconst SLOTS = 32\nconst DASH = 27\nconst DOT = 28\nconst STAR = 29\nconst OTHER = 30\n\nconst A = 'A'.charCodeAt(0)\nconst Z = 'Z'.charCodeAt(0)\nconst a = 'a'.charCodeAt(0)\nconst z = 'z'.charCodeAt(0)\n\n// charCode -> slot. A plain `code & 31` would fold digits and punctuation onto\n// letter slots ('0' onto 'P'), so the mapping is an explicit table.\nconst slotOfCode = new Uint8Array(128).fill(OTHER)\nfor (let c = A; c <= Z; c++) {\n  slotOfCode[c] = c - A + 1\n}\nfor (let c = a; c <= z; c++) {\n  slotOfCode[c] = c - a + 1\n}\nslotOfCode['-'.charCodeAt(0)] = DASH\nslotOfCode['.'.charCodeAt(0)] = DOT\nslotOfCode['*'.charCodeAt(0)] = STAR\n\nconst letterOfSlot = Array.from({ length: SLOTS }, (_, slot) =>\n  slot >= 1 && slot <= 26 ? String.fromCharCode(A + slot - 1) : '',\n)\nletterOfSlot[DASH] = '-'\nletterOfSlot[DOT] = '.'\nletterOfSlot[STAR] = '*'\nletterOfSlot[OTHER] = '?'\n\nfunction slotOf(code: number) {\n  return code < 128 ? slotOfCode[code]! : OTHER\n}\n\nfunction isGapSlot(slot: number) {\n  return slot === DASH || slot === DOT\n}\n\nexport class ColumnCounts {\n  readonly numColumns: number\n  private readonly counts: Uint32Array\n  // per-column residue+gap totals\n  readonly totals: Uint32Array\n  // whole-alignment totals per slot, so \"which letters appear anywhere\" is a\n  // 32-slot scan rather than a walk over every column\n  private readonly slotTotals = new Uint32Array(SLOTS)\n\n  constructor(numColumns: number) {\n    this.numColumns = numColumns\n    this.counts = new Uint32Array(numColumns * SLOTS)\n    this.totals = new Uint32Array(numColumns)\n  }\n\n  /** tallies a row, counting the columns past a short row's end as gaps */\n  addRow(row: string) {\n    const { counts, totals, slotTotals, numColumns } = this\n    const n = Math.min(row.length, numColumns)\n    for (let col = 0; col < n; col++) {\n      const slot = slotOf(row.charCodeAt(col))\n      counts[col * SLOTS + slot]!++\n      totals[col]!++\n      slotTotals[slot]!++\n    }\n    for (let col = n; col < numColumns; col++) {\n      counts[col * SLOTS + DASH]!++\n      totals[col]!++\n    }\n    slotTotals[DASH]! += numColumns - n\n  }\n\n  add(col: number, letter: string) {\n    const slot = slotOf(letter.charCodeAt(0))\n    this.counts[col * SLOTS + slot]!++\n    this.totals[col]!++\n    this.slotTotals[slot]!++\n  }\n\n  total(col: number) {\n    return this.totals[col] ?? 0\n  }\n\n  count(col: number, letter: string) {\n    return this.counts[col * SLOTS + slotOf(letter.charCodeAt(0))] ?? 0\n  }\n\n  gapCount(col: number) {\n    const base = col * SLOTS\n    return (this.counts[base + DASH] ?? 0) + (this.counts[base + DOT] ?? 0)\n  }\n\n  /**\n   * Visits every non-gap residue present in a column. Slots with a zero count\n   * are skipped, so this is ~the number of distinct residues, not 32.\n   */\n  forEachResidue(col: number, cb: (slot: number, count: number) => void) {\n    const { counts } = this\n    const base = col * SLOTS\n    for (let slot = 1; slot < SLOTS; slot++) {\n      const count = counts[base + slot]!\n      if (count > 0 && !isGapSlot(slot)) {\n        cb(slot, count)\n      }\n    }\n  }\n\n  /**\n   * Shannon entropy of a column in bits, taken over its non-gap residues only:\n   * a column of two residues and eight gaps is a two-way choice, not a ten-way\n   * one, and gap occupancy is accounted for separately by every caller. 0 for\n   * an all-gap column.\n   */\n  entropy(col: number) {\n    const nonGapTotal = this.total(col) - this.gapCount(col)\n    if (nonGapTotal === 0) {\n      return 0\n    }\n    let entropy = 0\n    this.forEachResidue(col, (_slot, count) => {\n      const freq = count / nonGapTotal\n      entropy -= freq * Math.log2(freq)\n    })\n    return entropy\n  }\n\n  /** non-gap [letter, count] pairs for one column, for display */\n  residueEntries(col: number) {\n    const entries: [string, number][] = []\n    this.forEachResidue(col, (slot, count) => {\n      entries.push([letterOfSlot[slot]!, count])\n    })\n    return entries\n  }\n\n  /** the distinct non-gap letters appearing anywhere in the alignment */\n  get lettersPresent() {\n    const letters = new Set<string>()\n    for (let slot = 1; slot < SLOTS; slot++) {\n      if (this.slotTotals[slot]! > 0 && !isGapSlot(slot)) {\n        letters.add(letterOfSlot[slot]!)\n      }\n    }\n    return letters\n  }\n}\n\nexport function letterOfResidueSlot(slot: number) {\n  return letterOfSlot[slot]!\n}\n\nexport function residueSlotOfLetter(letter: string) {\n  return slotOf(letter.charCodeAt(0))\n}\n\nexport const numResidueSlots = SLOTS\n\n/**\n * Tally counts from alignment rows (gapped sequence strings, one per row). The\n * column count defaults to the longest row, and a shorter row counts as gapped\n * to the end.\n */\nexport function columnCountsFromRows(\n  rows: string[],\n  numColumns = rows.reduce((max, row) => Math.max(max, row.length), 0),\n) {\n  const counts = new ColumnCounts(numColumns)\n  for (const row of rows) {\n    counts.addRow(row)\n  }\n  return counts\n}\n\n/**\n * Tally counts from column strings (one string per column, listing that\n * column's residues top to bottom). Convenient for tests and for callers that\n * already think column-wise.\n */\nexport function columnCountsFromColumns(columns: string[]) {\n  const counts = new ColumnCounts(columns.length)\n  for (const [col, column] of columns.entries()) {\n    for (const letter of column) {\n      counts.add(col, letter)\n    }\n  }\n  return counts\n}\n", "import { letterOfResidueSlot } from './columnCounts.ts'\n\nimport type { ColumnCounts } from './columnCounts.ts'\n\nexport interface LogoLetter {\n  letter: string\n  /** height of this letter's slice of the stack, in bits */\n  bits: number\n}\n\n/** the y-axis ceiling of a logo: the information content of a fully conserved\n * column, log2 of the alphabet size */\nexport function maxBitsFor(sequenceType: 'dna' | 'rna' | 'amino') {\n  return Math.log2(sequenceType === 'amino' ? 20 : 4)\n}\n\n/**\n * One column of a sequence logo, tallest letter last so a caller can draw the\n * stack bottom-up in array order.\n *\n * Heights follow Schneider & Stephens: the column's information content is\n * `log2(alphabet) - H` bits, split among residues by frequency. Frequencies\n * count non-gap residues only, so two residues and eight gaps form a two-way\n * choice.\n *\n * Unlike plain WebLogo, the stack is then scaled by the non-gap fraction, so a\n * 90%-gap column with one conserved pair does not draw a full-height stack, and\n * stack height matches the conservation track.\n */\nexport function columnLogoStack(\n  colStats: ColumnCounts,\n  col: number,\n  maxBits: number,\n): LogoLetter[] {\n  const total = colStats.total(col)\n  const nonGapTotal = total - colStats.gapCount(col)\n  if (nonGapTotal === 0) {\n    return []\n  }\n\n  const informationContent =\n    Math.max(0, maxBits - colStats.entropy(col)) * (nonGapTotal / total)\n  if (informationContent === 0) {\n    return []\n  }\n\n  const stack: LogoLetter[] = []\n  colStats.forEachResidue(col, (slot, count) => {\n    stack.push({\n      letter: letterOfResidueSlot(slot),\n      bits: (count / nonGapTotal) * informationContent,\n    })\n  })\n  // ascending, so drawing in order stacks the tallest letter on top. Ties break\n  // on letter to keep the stack order stable between redraws.\n  stack.sort((a, b) => a.bits - b.bits || a.letter.localeCompare(b.letter))\n  return stack\n}\n", "import { columnLogoStack } from '../../sequenceLogo.ts'\nimport { setFontSize } from '../../setFontSize.ts'\nimport { contrastTextFn } from '../../util.ts'\nimport { visibleColRange } from '../msa/visibleColRange.ts'\n\nimport type { ColumnCounts } from '../../columnCounts.ts'\nimport type { MsaViewModel } from '../../model.ts'\nimport type { Arc, BasicTrack } from '../../types.ts'\nimport type { RenderCtx } from '../renderCtx.ts'\nimport type { Theme } from '@mui/material'\n\nfunction drawConservationBars({\n  ctx,\n  values,\n  color,\n  colWidth,\n  trackHeight,\n  offsetX,\n  blockSize,\n}: {\n  ctx: RenderCtx\n  values: number[]\n  color: string\n  colWidth: number\n  trackHeight: number\n  offsetX: number\n  blockSize: number\n}) {\n  const { xStart, xEnd } = visibleColRange({\n    offsetX,\n    blockWidth: blockSize,\n    colWidth,\n  })\n\n  ctx.fillStyle = color\n  for (let i = xStart; i < xEnd && i < values.length; i++) {\n    const value = values[i]!\n    const barHeight = value * trackHeight\n    const x = i * colWidth\n    ctx.fillRect(x, trackHeight - barHeight, colWidth, barHeight)\n  }\n}\n\n// bar-track values are model getters, off the plain track object, so the canvas\n// autorun stays reactive\nexport function barTrackValues(model: MsaViewModel, trackId: string) {\n  const supplied = model.columnTrackContent.get(trackId)?.values\n  if (supplied) {\n    return supplied\n  }\n  return trackId === 'property-conservation'\n    ? model.propertyConservation\n    : model.conservation\n}\n\n// An arc's apex scales with the square root of its span. Contact-map spans skew\n// short, and a linear scale flattens them along the baseline.\nfunction drawArcs({\n  ctx,\n  arcs,\n  color,\n  colWidth,\n  trackHeight,\n  offsetX,\n  blockSize,\n}: {\n  ctx: RenderCtx\n  arcs: Arc[] | undefined\n  color: string\n  colWidth: number\n  trackHeight: number\n  offsetX: number\n  blockSize: number\n}) {\n  if (!arcs?.length) {\n    return\n  }\n  const { xStart, xEnd } = visibleColRange({\n    offsetX,\n    blockWidth: blockSize,\n    colWidth,\n  })\n  let maxSpan = 1\n  for (const arc of arcs) {\n    maxSpan = Math.max(maxSpan, arc.end - arc.start)\n  }\n  // a full-height apex would put the stroke half outside the track\n  const apexRoom = trackHeight - 1\n  ctx.lineWidth = 1\n  for (const arc of arcs) {\n    // an arc that spans the block draws even though neither foot is inside it\n    if (arc.end < xStart || arc.start > xEnd) {\n      continue\n    }\n    const x1 = (arc.start + 0.5) * colWidth\n    const x2 = (arc.end + 0.5) * colWidth\n    const apex = apexRoom * Math.sqrt((arc.end - arc.start) / maxSpan)\n    ctx.strokeStyle = arc.color ?? color\n    ctx.beginPath()\n    ctx.moveTo(x1, trackHeight)\n    ctx.quadraticCurveTo((x1 + x2) / 2, trackHeight - 2 * apex, x2, trackHeight)\n    ctx.stroke()\n  }\n}\n\nfunction drawTextTrackContent({\n  ctx,\n  data,\n  colorScheme,\n  contrastText,\n  bgColor,\n  drawLetters,\n  colWidth,\n  rowHeight,\n  offsetX,\n  blockSize,\n}: {\n  ctx: RenderCtx\n  data: string | undefined\n  colorScheme: Record<string, string>\n  contrastText: (color: string | undefined) => string\n  bgColor: boolean\n  drawLetters: boolean\n  colWidth: number\n  rowHeight: number\n  offsetX: number\n  blockSize: number\n}) {\n  const { xStart, xEnd } = visibleColRange({\n    offsetX,\n    blockWidth: blockSize,\n    colWidth,\n  })\n  const str = data?.slice(xStart, xEnd)\n\n  for (let i = 0; str && i < str.length; i++) {\n    const letter = str[i]!\n    const upper = letter.toUpperCase()\n    const fill = bgColor ? colorScheme[upper] : undefined\n    const x = (xStart + i) * colWidth\n    if (fill) {\n      ctx.fillStyle = fill\n      ctx.fillRect(x, 0, colWidth, rowHeight)\n    }\n    if (drawLetters) {\n      ctx.fillStyle = contrastText(fill)\n      ctx.fillText(letter, x + colWidth / 2, rowHeight / 2)\n    }\n  }\n}\n\n// the smallest 1/2/5 x 10^n column step that leaves room for a label\nexport function rulerStep(colWidth: number, minPixels = 55) {\n  let step = 1\n  const mantissas = [1, 2, 5]\n  for (let i = 0; step * colWidth < minPixels; i++) {\n    step = mantissas[i % 3]! * 10 ** Math.floor(i / 3)\n  }\n  return step\n}\n\n// The 0-based columns in [xStart, end) to label: column 1, then each column\n// whose 1-based number is a multiple of the step. A step of 2 or more puts the\n// first multiple at least half a step's width past column 1, which clears the\n// two labels.\nexport function rulerCols(xStart: number, end: number, colWidth: number) {\n  const step = rulerStep(colWidth)\n  const cols = step > 1 && xStart <= 0 && end > 0 ? [0] : []\n  const first = Math.max(1, Math.ceil((xStart + 1) / step)) * step\n  for (let n = first; n <= end; n += step) {\n    cols.push(n - 1)\n  }\n  return cols\n}\n\nconst RULER_FONT_SIZE = 10\nconst TICK_HEIGHT = 4\n\nfunction drawColumnRuler({\n  ctx,\n  numColumns,\n  label,\n  textColor,\n  colWidth,\n  trackHeight,\n  offsetX,\n  blockSize,\n}: {\n  ctx: RenderCtx\n  numColumns: number\n  label: (col: number) => string | undefined\n  textColor: string\n  colWidth: number\n  trackHeight: number\n  offsetX: number\n  blockSize: number\n}) {\n  const { xStart, xEnd } = visibleColRange({\n    offsetX,\n    blockWidth: blockSize,\n    colWidth,\n  })\n  const end = Math.min(xEnd, numColumns)\n  setFontSize(ctx, RULER_FONT_SIZE)\n  ctx.textAlign = 'center'\n  ctx.textBaseline = 'alphabetic'\n  ctx.fillStyle = textColor\n  ctx.strokeStyle = textColor\n  ctx.lineWidth = 1\n\n  for (const col of rulerCols(xStart, end, colWidth)) {\n    const text = label(col)\n    if (text === undefined) {\n      continue\n    }\n    const x = (col + 0.5) * colWidth\n    ctx.fillText(text, x, trackHeight - TICK_HEIGHT - 2)\n    ctx.beginPath()\n    ctx.moveTo(x, trackHeight - TICK_HEIGHT)\n    ctx.lineTo(x, trackHeight)\n    ctx.stroke()\n  }\n}\n\n// Cap height as a fraction of the font size, within a percent or two for the\n// sans-serif faces both backends use. `measureText` reports no vertical box in\n// the SVG export backend, so one constant ratio scales every logo letter, and\n// the slices sum to the stack height.\nconst CAP_HEIGHT_RATIO = 0.72\nconst MIN_LETTER_PX = 3\n\nfunction drawSequenceLogo({\n  ctx,\n  colStats,\n  colorScheme,\n  maxBits,\n  textColor,\n  colWidth,\n  trackHeight,\n  offsetX,\n  blockSize,\n}: {\n  ctx: RenderCtx\n  colStats: ColumnCounts\n  colorScheme: Record<string, string>\n  maxBits: number\n  textColor: string\n  colWidth: number\n  trackHeight: number\n  offsetX: number\n  blockSize: number\n}) {\n  const { xStart, xEnd } = visibleColRange({\n    offsetX,\n    blockWidth: blockSize,\n    colWidth,\n  })\n  const end = Math.min(xEnd, colStats.numColumns)\n\n  // one reference font size for the block; each letter's transform scales it to\n  // a height proportional to its frequency\n  const referenceFontSize = trackHeight\n  setFontSize(ctx, referenceFontSize)\n  ctx.textAlign = 'left'\n  ctx.textBaseline = 'alphabetic'\n  const capHeight = referenceFontSize * CAP_HEIGHT_RATIO\n\n  for (let col = xStart; col < end; col++) {\n    const stack = columnLogoStack(colStats, col, maxBits)\n    if (stack.length === 0) {\n      continue\n    }\n    const x = col * colWidth\n    // the stack is ascending, so the tallest letter lands on top\n    let bottom = trackHeight\n    for (const { letter, bits } of stack) {\n      const h = (bits / maxBits) * trackHeight\n      if (h < MIN_LETTER_PX) {\n        bottom -= h\n        continue\n      }\n      const width = ctx.measureText(letter).width\n      if (width === 0) {\n        bottom -= h\n        continue\n      }\n      ctx.fillStyle = colorScheme[letter] ?? textColor\n      ctx.save()\n      // land the glyph's baseline on the bottom of its slice, then stretch it to\n      // fill the slice vertically and the column horizontally\n      ctx.translate(x, bottom)\n      ctx.scale(colWidth / width, h / capHeight)\n      ctx.fillText(letter, 0, 0)\n      ctx.restore()\n      bottom -= h\n    }\n  }\n}\n\n/**\n * Draw one track's content into a block of the alignment's column space, at\n * `offsetY` within the ctx. Owns the transform, so the live canvas blocks and\n * the SVG export draw into the same coordinate space. A new track kind needs a\n * `kind`, a draw function above, and a case here.\n */\nexport function drawTrackBlock({\n  model,\n  ctx,\n  track,\n  offsetX,\n  offsetY = 0,\n  theme,\n  blockSizeXOverride,\n  highResScaleFactorOverride,\n}: {\n  model: MsaViewModel\n  ctx: RenderCtx\n  track: BasicTrack\n  offsetX: number\n  offsetY?: number\n  theme: Theme\n  blockSizeXOverride?: number\n  highResScaleFactorOverride?: number\n}) {\n  // an autorun tracks every model read here, so each kind reads only what it\n  // draws and a vertical zoom leaves the bar and arc canvases alone\n  const { blockSize, colWidth, highResScaleFactor } = model\n  const {\n    id,\n    kind,\n    height: trackHeight,\n    barColor,\n    arcColor,\n    arcs,\n    customColorScheme,\n    data,\n  } = track.model\n  const blockSizeX = blockSizeXOverride ?? blockSize\n  const k = highResScaleFactorOverride ?? highResScaleFactor\n  const textColor = theme.palette.text.primary\n\n  ctx.resetTransform()\n  ctx.scale(k, k)\n  ctx.translate(-offsetX, offsetY)\n\n  switch (kind) {\n    case 'bar': {\n      drawConservationBars({\n        ctx,\n        values: barTrackValues(model, id),\n        color: barColor ?? 'gray',\n        colWidth,\n        trackHeight,\n        offsetX,\n        blockSize: blockSizeX,\n      })\n      break\n    }\n    case 'arc': {\n      drawArcs({\n        ctx,\n        arcs,\n        color: arcColor ?? theme.palette.text.primary,\n        colWidth,\n        trackHeight,\n        offsetX,\n        blockSize: blockSizeX,\n      })\n      break\n    }\n    case 'logo': {\n      drawSequenceLogo({\n        ctx,\n        colStats: model.colStats,\n        colorScheme: model.colorScheme,\n        maxBits: model.alphabetMaxBits,\n        textColor,\n        colWidth,\n        trackHeight,\n        offsetX,\n        blockSize: blockSizeX,\n      })\n      break\n    }\n    case 'ruler': {\n      const { relativeTo, numColumns } = model\n      drawColumnRuler({\n        ctx,\n        numColumns,\n        // with relativeTo set, number by the reference row's residues\n        label: relativeTo\n          ? col => {\n              const pos = model.visibleColToSeqPosOneBased(relativeTo, col)\n              return pos === undefined ? undefined : `${pos}`\n            }\n          : col => `${col + 1}`,\n        textColor,\n        colWidth,\n        trackHeight,\n        offsetX,\n        blockSize: blockSizeX,\n      })\n      break\n    }\n    case 'text': {\n      const { bgColor, fontSize, rowHeight, showMsaLetters } = model\n      ctx.textAlign = 'center'\n      ctx.textBaseline = 'middle'\n      setFontSize(ctx, fontSize)\n      drawTextTrackContent({\n        ctx,\n        data,\n        colorScheme: customColorScheme ?? model.colorScheme,\n        contrastText: contrastTextFn(theme),\n        bgColor,\n        drawLetters: showMsaLetters,\n        colWidth,\n        rowHeight,\n        offsetX,\n        blockSize: blockSizeX,\n      })\n      break\n    }\n  }\n\n  ctx.resetTransform()\n}\n\n/**\n * Every turned-on track stacked top to bottom, for the SVG export. The live\n * view draws the same content one canvas block at a time in TrackBlocks.\n */\nexport function renderAllTracks({\n  model,\n  ctx,\n  offsetX,\n  theme,\n  blockSizeXOverride,\n  highResScaleFactorOverride,\n}: {\n  model: MsaViewModel\n  ctx: RenderCtx\n  offsetX: number\n  theme: Theme\n  blockSizeXOverride?: number\n  highResScaleFactorOverride?: number\n}) {\n  let currentY = 0\n  for (const track of model.turnedOnTracks) {\n    drawTrackBlock({\n      model,\n      ctx,\n      track,\n      offsetX,\n      offsetY: currentY,\n      theme,\n      blockSizeXOverride,\n      highResScaleFactorOverride,\n    })\n    currentY += track.model.height\n  }\n}\n", "import React from 'react'\n\n/**\n * The branch-length scale bar: its label over a bracket `bar.px` wide, both\n * resting on `y`.\n */\nexport default function ScaleBarSVG({\n  bar,\n  marginLeft,\n  y,\n  color,\n}: {\n  bar: { label: string; px: number }\n  marginLeft: number\n  y: number\n  color: string\n}) {\n  return (\n    <>\n      <text x={marginLeft} y={y - 9} fontSize={10} fill={color}>\n        {bar.label}\n      </text>\n      <path\n        d={`M${marginLeft} ${y - 7} v6 h${bar.px} v-6`}\n        fill=\"none\"\n        stroke={color}\n      />\n    </>\n  )\n}\n", "import { setFontSize } from './setFontSize.ts'\n\n// Cached across calls, since both createElement and getContext are far more\n// expensive than measureText.\n// `null` records that this environment has no 2d context, so the lookup is not\n// retried on every label.\nlet ctxHandle: CanvasRenderingContext2D | null | undefined\n\nfunction getCtx() {\n  if (ctxHandle === undefined) {\n    ctxHandle =\n      typeof document === 'undefined'\n        ? null\n        : document.createElement('canvas').getContext('2d')\n  }\n  return ctxHandle\n}\n\n/**\n * Rough average glyph width as a fraction of the font size for the sans-serif\n * stack the labels use. measureTextCanvas falls back on it where there is no\n * canvas to measure with (jsdom, SSR), and the headless render environment's\n * `measureText` reports it.\n */\nexport const CHAR_WIDTH_RATIO = 0.6\n\nexport function measureTextCanvas(text: string, fontSize: number) {\n  const ctx = getCtx()\n  if (!ctx) {\n    return text.length * fontSize * CHAR_WIDTH_RATIO\n  }\n  setFontSize(ctx, fontSize)\n  return ctx.measureText(text).width\n}\n", "import { labelFitFontSize } from '../../constants.ts'\nimport { measureTextCanvas } from '../../measureTextCanvas.ts'\n\nimport type { MsaViewModel } from '../../model.ts'\nimport type { Clade, ResolvedClade } from '../../types.ts'\n\n// The bar of the bracket mark and the space around it, in px.\nexport const bracketBarWidth = 3\nexport const bracketGap = 4\n\n// The widest gutter the bracket mark takes. A longer label is clipped, so one\n// long name cannot squeeze the tree it annotates.\nexport const maxCladeGutterWidth = 140\n\n/** whether a clade draws in the gutter: a bracket, or a highlight with a label */\nexport function cladeInGutter(clade: Pick<Clade, 'mark' | 'label'>) {\n  return (\n    clade.mark === 'bracket' || (clade.mark === 'highlight' && !!clade.label)\n  )\n}\n\n/** the pixel height of the rows a clade covers */\nfunction cladeHeight(clade: ResolvedClade, rowHeight: number) {\n  return (clade.rows[1] - clade.rows[0] + 1) * rowHeight\n}\n\n/**\n * Whether a label reads across the rows. It does where they are taller than the\n * font, and runs up the bar where they are not.\n */\nfunction cladeLabelHorizontal(\n  clade: ResolvedClade,\n  rowHeight: number,\n  fontSize: number,\n) {\n  return cladeHeight(clade, rowHeight) >= fontSize\n}\n\n/** the px between the left edge of the gutter and the label's own column */\nfunction cladeLabelOffset(clade: Pick<Clade, 'mark'>) {\n  return clade.mark === 'bracket'\n    ? bracketGap + bracketBarWidth + bracketGap\n    : bracketGap\n}\n\n/**\n * The gutter the bracket mark needs at the right of the tree area: the bar plus\n * the widest label read across at labelFitFontSize, zero where no clade draws\n * there, and at most maxCladeGutterWidth. The records size it, so a zoom, a\n * collapse or a focus leaves it as it is, and a renderer clips a label that\n * outgrows it.\n */\nexport function cladeGutterWidth(clades: Pick<Clade, 'mark' | 'label'>[]) {\n  let widest = 0\n  for (const clade of clades) {\n    if (!cladeInGutter(clade)) {\n      continue\n    }\n    const text = clade.label\n      ? measureTextCanvas(clade.label, labelFitFontSize)\n      : 0\n    widest = Math.max(widest, cladeLabelOffset(clade) + text + bracketGap)\n  }\n  // a whole pixel, so the room the renderers measure against covers the label\n  // the measurement here sized the gutter for\n  return Math.min(maxCladeGutterWidth, Math.ceil(widest))\n}\n\n/**\n * The box each gutter label takes, in unscrolled tree-area px: from the\n * label's column to the right edge of the gutter, across the clade's rows. The\n * live view sets DOM text in it, and the SVG export a `<text>`.\n */\nexport function cladeLabelBoxes(\n  model: Pick<\n    MsaViewModel,\n    | 'resolvedClades'\n    | 'cladeGutterWidth'\n    | 'rowHeight'\n    | 'effectiveTreeAreaWidth'\n    | 'fontSize'\n  >,\n) {\n  const {\n    resolvedClades,\n    cladeGutterWidth,\n    rowHeight,\n    effectiveTreeAreaWidth,\n    fontSize,\n  } = model\n  const gutterLeft = effectiveTreeAreaWidth - cladeGutterWidth\n  return cladeGutterWidth === 0\n    ? []\n    : resolvedClades.flatMap((clade, index) => {\n        const { label, markColor, rows } = clade\n        if (!label || !cladeInGutter(clade)) {\n          return []\n        }\n        const left = gutterLeft + cladeLabelOffset(clade)\n        return [\n          {\n            key: `${rows[0]}-${rows[1]}-${index}`,\n            label,\n            color: markColor,\n            left,\n            top: rows[0] * rowHeight,\n            width: effectiveTreeAreaWidth - left - bracketGap,\n            height: cladeHeight(clade, rowHeight),\n            horizontal: cladeLabelHorizontal(clade, rowHeight, fontSize),\n          },\n        ]\n      })\n}\n", "const ellipsis = '\u2026'\n\n/**\n * the longest prefix of `text`, plus an ellipsis, that measures at most\n * `room` px\n */\nexport function ellipsize(\n  measure: (text: string) => number,\n  text: string,\n  room: number,\n) {\n  const width = measure(text)\n  if (width <= room) {\n    return { text, width }\n  }\n  for (let n = Math.floor((text.length * room) / width); n > 0; n--) {\n    const truncated = text.slice(0, n).trimEnd() + ellipsis\n    const truncatedWidth = measure(truncated)\n    if (truncatedWidth <= room) {\n      return { text: truncated, width: truncatedWidth }\n    }\n  }\n  return { text: '', width: 0 }\n}\n", "import {\n  descendants,\n  find,\n  forEachDescendant,\n  forEachLink,\n  hierarchy as coreHierarchy,\n  leaves,\n  links,\n  sort,\n  sum,\n} from '@gmod/newick'\n\nimport type { NodeWithIds } from './types.ts'\nimport type { HierarchyNode as CoreHierarchyNode } from '@gmod/newick'\n\n/**\n * A hierarchy node plus the fields this viewer hangs off it during layout.\n *\n * The traversals in `@gmod/newick` are generic over the node type rather than\n * over its data, so they take and return this extended node rather than the base\n * one, and no call site has to cast.\n */\nexport interface HierarchyNode<T = NodeWithIds> extends CoreHierarchyNode<T> {\n  children: HierarchyNode<T>[] | null\n  parent: HierarchyNode<T> | null\n  x?: number\n  y?: number\n  // the span of `x` over this node's subtree. Leaves are laid out in order, so\n  // a subtree occupies one contiguous run of rows and a renderer can skip the\n  // whole thing when the run misses its block.\n  xMin?: number\n  xMax?: number\n  len?: number\n  depthToLeaf?: number\n  _children?: HierarchyNode<T>[] | null\n  // pixel x-position of the farthest tip of a collapsed subtree, where the base\n  // of the collapsed-clade triangle goes\n  collapsedTipXFar?: number\n}\n\n// The @gmod/newick traversals are iterative: a caterpillar tree's depth equals\n// its leaf count, and recursion overflows the stack past about 5000 tips.\nexport {\n  descendants,\n  find,\n  forEachDescendant,\n  forEachLink,\n  leaves,\n  links,\n  sort,\n  sum,\n}\nexport type { HierarchyLink } from '@gmod/newick'\n\n// declares the wider return type so the layout code can assign the optional\n// fields above onto coreHierarchy's nodes\nexport function hierarchy<T>(\n  data: T,\n  childrenAccessor: (d: T) => T[] | undefined,\n): HierarchyNode<T> {\n  return coreHierarchy(data, childrenAccessor)\n}\n\nexport interface TreeScale {\n  readonly rowHeight: number\n  readonly treeWidth: number\n}\n\ninterface LayoutFrame {\n  scale: TreeScale\n  rootToTipLength: number\n}\n\n/**\n * A node of `layoutTree`: its source node's fields plus its place in unit\n * space, rows down and branch length across. The pixel getters multiply by the\n * scale on every read, so a zoom leaves the nodes valid, and an observer\n * reading `x` observes whatever the scale reads.\n */\nexport class LaidOutNode<T> implements HierarchyNode<T> {\n  data: T\n  depth: number\n  height: number\n  value?: number\n  children: LaidOutNode<T>[] | null\n  depthToLeaf = 0\n  row = 0\n  rowMin = 0\n  rowMax = 0\n  depthFraction = 0\n  branchLength = 0\n  collapsedBranchLength?: number\n\n  constructor(\n    source: HierarchyNode<T>,\n    readonly parent: LaidOutNode<T> | null,\n    private readonly frame: LayoutFrame,\n  ) {\n    this.data = source.data\n    this.depth = source.depth\n    this.height = source.height\n    this.value = source.value\n    this.children = source.children ? [] : null\n  }\n\n  private get pxPerBranchLength() {\n    const { scale, rootToTipLength } = this.frame\n    return rootToTipLength ? scale.treeWidth / rootToTipLength : 0\n  }\n\n  get x() {\n    return this.row * this.frame.scale.rowHeight\n  }\n\n  get xMin() {\n    return this.rowMin * this.frame.scale.rowHeight\n  }\n\n  get xMax() {\n    return this.rowMax * this.frame.scale.rowHeight\n  }\n\n  get y() {\n    return this.depthFraction * this.frame.scale.treeWidth\n  }\n\n  get len() {\n    return this.branchLength * this.pxPerBranchLength\n  }\n\n  get collapsedTipXFar() {\n    return this.collapsedBranchLength === undefined\n      ? undefined\n      : this.collapsedBranchLength * this.pxPerBranchLength\n  }\n}\n\n/**\n * The tree laid out on new nodes: tips one row apart, a parent at the mean of\n * its children, and branch length measured from the root, whose own branch is\n * not drawn. A collapsed node records the farthest tip of its hidden subtree,\n * where the base of its triangle goes.\n */\nexport function layoutTree<T extends { length?: number }>(\n  root: HierarchyNode<T>,\n  scale: TreeScale,\n) {\n  const frame: LayoutFrame = { scale, rootToTipLength: 0 }\n  const nodes: LaidOutNode<T>[] = []\n  const leafNodes: LaidOutNode<T>[] = []\n  const rootHeight = root.height\n  const stack: { source: HierarchyNode<T>; parent: LaidOutNode<T> | null }[] = [\n    { source: root, parent: null },\n  ]\n  while (stack.length > 0) {\n    const { source, parent } = stack.pop()!\n    const node = new LaidOutNode(source, parent, frame)\n    nodes.push(node)\n    node.depthFraction =\n      rootHeight === 0 ? 1 : (source.depth - root.depth) / rootHeight\n    if (parent) {\n      parent.children!.push(node)\n      node.branchLength =\n        parent.branchLength + Math.max(source.data.length || 0, 0)\n      frame.rootToTipLength = Math.max(frame.rootToTipLength, node.branchLength)\n    }\n    if (source._children) {\n      node.collapsedBranchLength =\n        node.branchLength + collapsedSubtreeMaxLength(source)\n    }\n    if (source.children) {\n      for (let i = source.children.length - 1; i >= 0; i--) {\n        stack.push({ source: source.children[i]!, parent: node })\n      }\n    } else {\n      node.row = leafNodes.length + 0.5\n      node.depthToLeaf = source.depthToLeaf ?? 0\n      leafNodes.push(node)\n    }\n  }\n\n  for (let i = nodes.length - 1; i >= 0; i--) {\n    const node = nodes[i]!\n    if (node.children) {\n      let sum = 0\n      let min = Infinity\n      let max = -Infinity\n      let depthToLeaf = 0\n      for (const child of node.children) {\n        sum += child.row\n        min = Math.min(min, child.rowMin)\n        max = Math.max(max, child.rowMax)\n        depthToLeaf = Math.max(depthToLeaf, 1 + child.depthToLeaf)\n      }\n      node.row = sum / node.children.length\n      node.rowMin = min\n      node.rowMax = max\n      node.depthToLeaf = depthToLeaf\n    } else {\n      node.rowMin = node.row\n      node.rowMax = node.row\n    }\n  }\n  return {\n    root: nodes[0]!,\n    leaves: leafNodes,\n    rootToTipLength: frame.rootToTipLength,\n  }\n}\n\nexport function collapse<T>(node: HierarchyNode<T>) {\n  if (node.children) {\n    // memoize the real subtree depth onto the node before detaching its\n    // children, so cladogram positioning keeps the node (now the apex of a\n    // collapsed-clade triangle) at its true branch point rather than snapping\n    // it to the tip-alignment line. This also keeps the rest of the tree's\n    // horizontal layout stable when a clade is collapsed.\n    calcDepthToLeaf(node)\n    node._children = node.children\n    node.children = null\n  }\n}\n\n// Cumulative raw branch length from a collapsed node down to the farthest tip of\n// its detached subtree (excludes the node's own branch). Sizes the base of the\n// collapsed-clade triangle in phylogram mode.\nexport function collapsedSubtreeMaxLength<T extends { length?: number }>(\n  node: HierarchyNode<T>,\n) {\n  const roots = node._children ?? node.children\n  let max = 0\n  if (roots) {\n    const stack = roots.map(child => ({\n      node: child,\n      acc: Math.max(child.data.length ?? 0, 0),\n    }))\n    while (stack.length > 0) {\n      const { node: n, acc } = stack.pop()!\n      const kids = n.children ?? n._children\n      if (kids?.length) {\n        for (const child of kids) {\n          stack.push({\n            node: child,\n            acc: acc + Math.max(child.data.length ?? 0, 0),\n          })\n        }\n      } else {\n        max = Math.max(max, acc)\n      }\n    }\n  }\n  return max\n}\n\n// Cladogram positioning based on ape's plot.phylo: uses topological depth (max\n// steps to a tip) instead of branch length so all leaves align at the rightmost\n// x. Memoizes onto node.depthToLeaf since the layout walks the tree repeatedly.\n// See https://github.com/emmanuelparadis/ape/blob/master/R/plot.phylo.R\nexport function calcDepthToLeaf<T>(node: HierarchyNode<T>): number {\n  // the memo check has to guard the traversal, not just the arithmetic: the tree\n  // renderer asks for the depth of every node on every pass, and re-walking each\n  // subtree makes that quadratic (a 5000-tip caterpillar tree spent >1s per draw\n  // here). Once a node is memoized so are all of its descendants.\n  if (node.depthToLeaf === undefined) {\n    const nodes = descendants(node)\n    for (let i = nodes.length - 1; i >= 0; i--) {\n      const n = nodes[i]!\n      if (n.depthToLeaf === undefined) {\n        let maxDepth = 0\n        if (n.children) {\n          for (const child of n.children) {\n            maxDepth = Math.max(maxDepth, 1 + child.depthToLeaf!)\n          }\n        }\n        n.depthToLeaf = maxDepth\n      }\n    }\n  }\n  return node.depthToLeaf!\n}\n\n/**\n * Every leaf by name, with a name two leaves share mapping to undefined: a tip\n * set naming it cannot say which tip it means.\n */\nexport function leafIndex<T extends { name: string }>(root: HierarchyNode<T>) {\n  const index = new Map<string, HierarchyNode<T> | undefined>()\n  for (const leaf of leaves(root)) {\n    const { name } = leaf.data\n    index.set(name, index.has(name) ? undefined : leaf)\n  }\n  return index\n}\n\n/**\n * The most recent common ancestor of a set of tip names, or undefined when a\n * name is not a tip of this tree or names two of them.\n *\n * Each name lifts through `parent` to the ancestor the names before it share,\n * so the walk holds two nodes. Recording a root-to-tip path per name instead\n * costs the depth in memory per name, and a caterpillar tree's depth is its tip\n * count. `index` is `leafIndex(root)`, which a caller resolving several tip\n * sets against one tree builds once.\n */\nexport function mrca<T extends { name: string }>(\n  root: HierarchyNode<T>,\n  names: string[],\n  index = leafIndex(root),\n) {\n  let node: HierarchyNode<T> | undefined\n  for (const name of names) {\n    let other = index.get(name)\n    if (!other) {\n      return undefined\n    }\n    if (!node) {\n      node = other\n      continue\n    }\n    while (node.depth > other.depth) {\n      node = node.parent!\n    }\n    while (other.depth > node.depth) {\n      other = other.parent!\n    }\n    while (node !== other) {\n      node = node.parent!\n      other = other.parent!\n    }\n  }\n  return node\n}\n\n/**\n * The deepest node whose subtree covers a run of rows, given in the row-space\n * coordinates layoutTree writes to xMin/xMax. A subtree's leaves are one\n * contiguous run, so at most one child per level covers the run and the descent\n * visits the tree's depth rather than its nodes.\n */\nexport function nodeCoveringRows<T>(\n  root: HierarchyNode<T>,\n  top: number,\n  bottom: number,\n) {\n  let node = root\n  for (;;) {\n    const child = node.children?.find(c => c.xMin! <= top && c.xMax! >= bottom)\n    if (!child) {\n      return node\n    }\n    node = child\n  }\n}\n", "import { calcDepthToLeaf, nodeCoveringRows } from '../../hierarchy.ts'\nimport { setFontSize } from '../../setFontSize.ts'\nimport { getVisibleLeaves } from '../getVisibleLeaves.ts'\nimport {\n  drawHighlightLabel,\n  highlightLabelHeight,\n  highlightRowFill,\n} from '../msa/renderHighlights.ts'\nimport { referenceColor } from '../overlayColors.ts'\nimport { bracketBarWidth, bracketGap } from './cladeBrackets.ts'\nimport { ellipsize } from './ellipsize.ts'\n\nimport type { HierarchyNode } from '../../hierarchy.ts'\nimport type { MsaViewModel } from '../../model.ts'\nimport type { LabelBox } from '../msa/renderHighlights.ts'\nimport type { RenderCtx } from '../renderCtx.ts'\nimport type { ClickMapIndex } from './clickMap.ts'\nimport type { Theme } from '@mui/material'\n\nconst radius = 2.5\nconst d = radius * 2\n\n// How far outside a block a node's row-center can sit and still draw into it: a\n// collapsed triangle reaches 0.42 rows each way, a tip label an em, and a\n// highlight label its whole box. Five pixels clipped all three at block edges.\nfunction blockPad(model: MsaViewModel) {\n  return Math.max(model.rowHeight, highlightLabelHeight)\n}\n\n// whether a node's row-center y falls within the block being drawn, padded so\n// bubbles/labels/triangles straddling the edge still render\nfunction inYBlock(y: number, offsetY: number, by: number, pad: number) {\n  return y > offsetY - pad && y < offsetY + by + pad\n}\n\n/**\n * Every node whose subtree reaches into the block, skipping the subtrees that\n * do not. A subtree's leaves are one contiguous run of rows, recorded by\n * layoutTree as xMin/xMax, so a block of a 200k-tip tree visits a few dozen\n * nodes.\n *\n * A link out of a visited node is drawn even when its child is pruned, so a\n * branch crossing the block stays visible.\n */\nfunction forEachNodeInBlock(\n  root: HierarchyNode,\n  offsetY: number,\n  by: number,\n  pad: number,\n  cb: (node: HierarchyNode) => void,\n) {\n  const top = offsetY - pad\n  const bottom = offsetY + by + pad\n  const stack = [root]\n  while (stack.length > 0) {\n    const node = stack.pop()!\n    if (node.xMax! < top || node.xMin! > bottom) {\n      continue\n    }\n    cb(node)\n    if (node.children) {\n      for (const child of node.children) {\n        stack.push(child)\n      }\n    }\n  }\n}\n\n// withId gives an unnamed node its path, node-0-1-1, as its name\nfunction cladeName(node: HierarchyNode, unnamed: string) {\n  const { id, name } = node.data\n  const label = name === id ? unnamed : name\n  return node.value === undefined ? label : `${label} (${node.value} tips)`\n}\n\n// Calculate node x-coordinate for both phylogram (with branch lengths) and\n// cladogram (topology only) modes. tipX is the pixel x the tips sit at.\n// For cladograms: x = (maxDepthToLeaf - nodeDepthToLeaf) / maxDepthToLeaf * tipX\n// This positions: leaves at tipX (rightmost), root at 0 (leftmost), internal nodes proportionally in between\n// Matches ape's: xx <- max(xx) - xx (where xx is depth from each node to tips)\nexport function getNodeX(\n  node: HierarchyNode,\n  showBranchLen: boolean,\n  tipX: number,\n  maxDepthToLeaf: number,\n): number | undefined {\n  if (showBranchLen) {\n    return node.len\n  }\n  if (maxDepthToLeaf === 0) {\n    return 0\n  }\n  const depthToLeaf = calcDepthToLeaf(node)\n  return ((maxDepthToLeaf - depthToLeaf) / maxDepthToLeaf) * tipX\n}\n\nfunction renderTree({\n  offsetY,\n  ctx,\n  model,\n  theme,\n  tipX,\n  maxDepthToLeaf,\n  blockSizeYOverride,\n}: {\n  offsetY: number\n  ctx: RenderCtx\n  model: MsaViewModel\n  theme: Theme\n  tipX: number\n  maxDepthToLeaf: number\n  blockSizeYOverride?: number\n}) {\n  const {\n    hierarchy,\n    showBranchLenEffective: showBranchLen,\n    blockSize,\n    branchColors,\n  } = model\n  const by = blockSizeYOverride ?? blockSize\n  const defaultStroke = theme.palette.text.primary\n  ctx.strokeStyle = defaultStroke\n  forEachNodeInBlock(hierarchy, offsetY, by, blockPad(model), source => {\n    const sy = source.x!\n    const sx = getNodeX(source, showBranchLen, tipX, maxDepthToLeaf)\n    if (sx === undefined || !source.children) {\n      return\n    }\n    for (const target of source.children) {\n      const ty = target.x!\n      const tx = getNodeX(target, showBranchLen, tipX, maxDepthToLeaf)\n      if (tx === undefined) {\n        continue\n      }\n      const y1 = Math.min(sy, ty)\n      const y2 = Math.max(sy, ty)\n      // 1d line intersection to check if line crosses block at all, this is an\n      // optimization that allows us to skip drawing most tree links outside the\n      // block\n      if (offsetY + by >= y1 && y2 >= offsetY) {\n        // the edge belongs to the child, whose id the branch channel colors\n        if (branchColors) {\n          ctx.strokeStyle = branchColors.get(target.data.id) ?? defaultStroke\n        }\n        ctx.beginPath()\n        ctx.moveTo(sx, sy)\n        ctx.lineTo(sx, ty)\n        ctx.lineTo(tx, ty)\n        ctx.stroke()\n      }\n    }\n  })\n  ctx.strokeStyle = defaultStroke\n}\n\nfunction renderCollapsedTriangles({\n  ctx,\n  clickMap,\n  offsetY,\n  model,\n  theme,\n  tipX,\n  maxDepthToLeaf,\n  blockSizeYOverride,\n  collapsedSet,\n}: {\n  ctx: RenderCtx\n  clickMap?: ClickMapIndex\n  offsetY: number\n  model: MsaViewModel\n  theme: Theme\n  tipX: number\n  maxDepthToLeaf: number\n  blockSizeYOverride?: number\n  collapsedSet: Set<string>\n}) {\n  const {\n    hierarchy,\n    showBranchLenEffective: showBranchLen,\n    blockSize,\n    rowHeight,\n    fontSize,\n    marginLeft: ml,\n    branchColors,\n  } = model\n  // nothing collapsed is the common case, and the traversal below visits every\n  // node in the tree on every block of every redraw\n  if (collapsedSet.size === 0) {\n    return\n  }\n  const by = blockSizeYOverride ?? blockSize\n  const halfHeight = Math.max(2, rowHeight * 0.42)\n  forEachNodeInBlock(hierarchy, offsetY, by, blockPad(model), node => {\n    const { id } = node.data\n    if (collapsedSet.has(id)) {\n      const apexX = getNodeX(node, showBranchLen, tipX, maxDepthToLeaf)\n      const y = node.x!\n      const inBlock = inYBlock(y, offsetY, by, blockPad(model))\n      // in cladogram mode the hidden tips align at the right edge, otherwise use\n      // the branch-length extent recorded in the model's hierarchy getter\n      const baseX = showBranchLen ? (node.collapsedTipXFar ?? tipX) : tipX\n      if (apexX !== undefined && inBlock && baseX > apexX) {\n        ctx.beginPath()\n        ctx.moveTo(apexX, y)\n        ctx.lineTo(baseX, y - halfHeight)\n        ctx.lineTo(baseX, y + halfHeight)\n        ctx.closePath()\n        ctx.fillStyle = branchColors?.get(id) ?? theme.palette.action.disabled\n        ctx.fill()\n        ctx.strokeStyle = theme.palette.text.primary\n        ctx.stroke()\n\n        // node.value carries the leaf count from the pre-collapse sum() pass\n        const count = node.value\n        if (count !== undefined && rowHeight >= 8) {\n          ctx.fillStyle = theme.palette.text.primary\n          ctx.textAlign = 'left'\n          ctx.fillText(`${count}`, baseX + 3, y + fontSize / 4)\n        }\n\n        // the whole triangle is a click/hover target that opens the\n        // branch menu (Expand this node); the apex bubble's own click entry is\n        // skipped for collapsed nodes so this descriptive label wins\n        clickMap?.insert({\n          minX: apexX + ml,\n          maxX: baseX + ml,\n          minY: y - halfHeight,\n          maxY: y + halfHeight,\n          branch: true,\n          id,\n          name: cladeName(node, 'Collapsed clade'),\n        })\n      }\n    }\n  })\n}\n\n// the bubbles are click targets whether or not they are painted, so this pass\n// always runs and `draw` only decides whether it also strokes the circles\nfunction renderNodeBubbles({\n  ctx,\n  theme,\n  clickMap,\n  offsetY,\n  model,\n  tipX,\n  maxDepthToLeaf,\n  blockSizeYOverride,\n  collapsedSet,\n  draw,\n}: {\n  ctx: RenderCtx\n  clickMap?: ClickMapIndex\n  offsetY: number\n  model: MsaViewModel\n  tipX: number\n  maxDepthToLeaf: number\n  blockSizeYOverride?: number\n  collapsedSet: Set<string>\n  draw: boolean\n  theme: Theme\n}) {\n  const {\n    hierarchy,\n    showBranchLenEffective: showBranchLen,\n    blockSize,\n    marginLeft: ml,\n  } = model\n  const by = blockSizeYOverride ?? blockSize\n  forEachNodeInBlock(hierarchy, offsetY, by, blockPad(model), node => {\n    const x = getNodeX(node, showBranchLen, tipX, maxDepthToLeaf)\n    if (x === undefined) {\n      return\n    }\n    const { data } = node\n    const y = node.x!\n    const { id } = data\n    if (node.height >= 1 && inYBlock(y, offsetY, by, blockPad(model))) {\n      const isCollapsed = collapsedSet.has(id)\n      if (draw) {\n        ctx.strokeStyle = theme.palette.text.primary\n        ctx.fillStyle = isCollapsed\n          ? theme.palette.text.primary\n          : theme.palette.background.default\n        ctx.beginPath()\n        ctx.arc(x, y, radius, 0, 2 * Math.PI)\n        ctx.fill()\n        ctx.stroke()\n      }\n\n      // collapsed nodes get their click/hover target from the triangle pass,\n      // which covers the apex bubble and carries a descriptive label\n      if (!isCollapsed) {\n        clickMap?.insert({\n          minX: x - radius + ml,\n          maxX: x - radius + d + ml,\n          minY: y - radius,\n          maxY: y - radius + d,\n          branch: true,\n          id,\n          name: cladeName(node, 'Clade'),\n        })\n      }\n    }\n  })\n}\n\n// The label a newick file puts on an internal node, which is where a bootstrap\n// or posterior support value lands: ((A,B)95,(C,D)80);. withId falls back to the\n// path-derived id for an unnamed node, so a node whose name is its id has no\n// label of its own and an ungated pass prints node-0-1-1 across the tree.\nfunction renderNodeLabels({\n  ctx,\n  theme,\n  offsetY,\n  model,\n  tipX,\n  maxDepthToLeaf,\n  blockSizeYOverride,\n}: {\n  ctx: RenderCtx\n  theme: Theme\n  offsetY: number\n  model: MsaViewModel\n  tipX: number\n  maxDepthToLeaf: number\n  blockSizeYOverride?: number\n}) {\n  const {\n    hierarchy,\n    showBranchLenEffective: showBranchLen,\n    blockSize,\n    fontSize,\n  } = model\n  const by = blockSizeYOverride ?? blockSize\n  const pad = blockPad(model)\n  setFontSize(ctx, Math.max(6, fontSize - 3))\n  ctx.fillStyle = theme.palette.text.primary\n  ctx.textAlign = 'right'\n  forEachNodeInBlock(hierarchy, offsetY, by, pad, node => {\n    const { id, name } = node.data\n    if (node.height < 1 || name === id) {\n      return\n    }\n    const x = getNodeX(node, showBranchLen, tipX, maxDepthToLeaf)\n    const y = node.x!\n    if (x !== undefined && inYBlock(y, offsetY, by, pad)) {\n      ctx.fillText(name, x - radius - 1, y - radius - 1)\n    }\n  })\n  ctx.textAlign = 'start'\n  setFontSize(ctx, fontSize)\n}\n\nfunction renderTreeLabels({\n  theme,\n  model,\n  offsetY,\n  ctx,\n  clickMap,\n  tipX,\n  maxDepthToLeaf,\n  blockSizeYOverride,\n  collapsedSet,\n}: {\n  model: MsaViewModel\n  offsetY: number\n  ctx: RenderCtx\n  clickMap?: ClickMapIndex\n  theme: Theme\n  tipX: number\n  maxDepthToLeaf: number\n  blockSizeYOverride?: number\n  collapsedSet: Set<string>\n}) {\n  const {\n    fontSize,\n    showBranchLenEffective: showBranchLen,\n    tipLabelColors,\n    blockSize,\n    labelsAlignRight,\n    drawTree,\n    treeAreaWidthMinusMargin,\n    marginLeft,\n    noTree,\n  } = model\n  const treeDrawn = drawTree && !noTree\n  const by = blockSizeYOverride ?? blockSize\n  // labels only exist for leaves, which are laid out top to bottom, so take the\n  // same slice the MSA renderer uses instead of walking every tip per block\n  const visibleLeaves = getVisibleLeaves({ model, offsetY, blockSizeY: by })\n  const pad = blockPad(model)\n  const emHeight = ctx.measureText('M').width\n  if (labelsAlignRight) {\n    ctx.textAlign = 'right'\n    ctx.setLineDash([1, 3])\n    ctx.strokeStyle = theme.palette.text.primary\n  } else {\n    ctx.textAlign = 'start'\n  }\n  for (const node of visibleLeaves) {\n    const {\n      data: { name, id },\n    } = node\n    const y = node.x!\n\n    const displayName = model.rowDataOf(name)?.genome || name\n    // a collapsed clade is drawn as a triangle + tip count; suppress its leaf\n    // label when the \"name\" is just the auto-generated internal-node id\n    const isAnonymousCollapsed = collapsedSet.has(id) && name === id\n    if (!isAnonymousCollapsed && inYBlock(y, offsetY, by, pad)) {\n      // fontSize/4 below the row center, the baseline the alignment letters\n      // share\n      const yp = y + fontSize / 4\n      const xp = treeDrawn\n        ? (getNodeX(node, showBranchLen, tipX, maxDepthToLeaf) ?? 0)\n        : 0\n      const fit = (room: number) =>\n        ellipsize(text => ctx.measureText(text).width, displayName, room)\n      // a label cut to nothing still gets a click box the font size wide\n      const boxWidth = (width: number) => Math.max(width, fontSize)\n\n      ctx.fillStyle = tipLabelColors?.get(name) ?? theme.palette.text.primary\n      if (labelsAlignRight) {\n        const smallPadding = 2\n        const offset = treeAreaWidthMinusMargin - smallPadding\n        const { text, width } = fit(\n          offset - (treeDrawn ? xp + radius + 2 + smallPadding : 0),\n        )\n        if (treeDrawn) {\n          // beginPath is load-bearing: without it every leader line re-strokes\n          // all the ones before it, which is quadratic in the label count\n          ctx.beginPath()\n          ctx.moveTo(xp + radius + 2, y)\n          ctx.lineTo(offset - smallPadding - width, y)\n          ctx.stroke()\n        }\n        ctx.fillText(text, offset, yp)\n        // everything here is drawn under translate(marginLeft), so the click box\n        // has to be the text's own right edge in that same space -- taking\n        // the tree area width instead put the target smallPadding off the label\n        const labelRight = offset + marginLeft\n        clickMap?.insert({\n          minX: labelRight - boxWidth(width),\n          maxX: labelRight,\n          minY: yp - emHeight,\n          maxY: yp,\n          name,\n          label: displayName,\n          id,\n        })\n      } else {\n        const labelX = treeDrawn ? xp + d : 2\n        const { text, width } = fit(treeAreaWidthMinusMargin - labelX)\n        ctx.fillText(text, labelX, yp)\n        clickMap?.insert({\n          minX: labelX + marginLeft,\n          maxX: labelX + boxWidth(width) + marginLeft,\n          minY: yp - emHeight,\n          maxY: yp,\n          name,\n          label: displayName,\n          id,\n        })\n      }\n    }\n  }\n  ctx.setLineDash([])\n}\n\n// the first row of a set, as a loop: spreading into Math.min passes one\n// argument per row, and the ~125k argument limit throws RangeError on a set\n// covering the 230k-tip COVID tree\nfunction firstRow(rowIndices: number[]) {\n  let min = Infinity\n  for (const index of rowIndices) {\n    if (index < min) {\n      min = index\n    }\n  }\n  return min\n}\n\n// the highlight mark of the `clades` layer: a translucent rectangle from the\n// clade's common ancestor to the right edge of the tree area, under the\n// branches. A clade spanning hundreds of rows crosses several blocks, so each\n// block draws the whole rectangle and the canvas takes the part that is its.\nfunction renderCladeHighlights({\n  ctx,\n  model,\n  offsetY,\n  tipX,\n  maxDepthToLeaf,\n  blockSizeYOverride,\n}: {\n  ctx: RenderCtx\n  model: MsaViewModel\n  offsetY: number\n  tipX: number\n  maxDepthToLeaf: number\n  blockSizeYOverride?: number\n}) {\n  const {\n    resolvedClades,\n    hierarchy,\n    showBranchLenEffective: showBranchLen,\n    rowHeight,\n    effectiveTreeAreaWidth,\n    marginLeft,\n    blockSize,\n  } = model\n  const by = blockSizeYOverride ?? blockSize\n  const right = effectiveTreeAreaWidth - marginLeft\n  for (const { rows, color, mark } of resolvedClades) {\n    if (mark !== 'highlight') {\n      continue\n    }\n    const top = rows[0] * rowHeight\n    const bottom = (rows[1] + 1) * rowHeight\n    if (bottom < offsetY || top > offsetY + by) {\n      continue\n    }\n    const node = nodeCoveringRows(\n      hierarchy,\n      top + rowHeight / 2,\n      bottom - rowHeight / 2,\n    )\n    const x = getNodeX(node, showBranchLen, tipX, maxDepthToLeaf) ?? 0\n    ctx.fillStyle = color\n    ctx.fillRect(x, top, right - x, bottom - top)\n  }\n}\n\n// the bar of the bracket mark, in the gutter `cladeGutterWidth` reserves at the\n// right of the tree area. The label beside it is DOM text on screen and a\n// <text> in the export, since the canvas layer has no rotation.\nfunction renderCladeBrackets({\n  ctx,\n  model,\n  theme,\n  offsetY,\n  blockSizeYOverride,\n}: {\n  ctx: RenderCtx\n  model: MsaViewModel\n  theme: Theme\n  offsetY: number\n  blockSizeYOverride?: number\n}) {\n  const {\n    resolvedClades,\n    cladeGutterWidth,\n    rowHeight,\n    effectiveTreeAreaWidth,\n    marginLeft,\n    blockSize,\n  } = model\n  if (cladeGutterWidth === 0) {\n    return\n  }\n  const by = blockSizeYOverride ?? blockSize\n  const x =\n    effectiveTreeAreaWidth -\n    marginLeft -\n    cladeGutterWidth +\n    bracketGap +\n    bracketBarWidth / 2\n  ctx.lineWidth = bracketBarWidth\n  for (const { rows, mark, markColor } of resolvedClades) {\n    const top = rows[0] * rowHeight + 1\n    const bottom = (rows[1] + 1) * rowHeight - 1\n    if (mark !== 'bracket' || bottom < offsetY || top > offsetY + by) {\n      continue\n    }\n    ctx.strokeStyle = markColor ?? theme.palette.text.primary\n    ctx.beginPath()\n    ctx.moveTo(x, top)\n    ctx.lineTo(x, bottom)\n    ctx.stroke()\n  }\n  ctx.lineWidth = 1\n  ctx.strokeStyle = theme.palette.text.primary\n}\n\n// the `rowTint` encoding, the reference row and the row sets of `highlights`,\n// washed across the tree area under the labels, with each set's label in the\n// gutter at its first row\nfunction renderRowHighlights({\n  ctx,\n  model,\n  theme,\n  offsetY,\n  blockSizeYOverride,\n}: {\n  ctx: RenderCtx\n  model: MsaViewModel\n  theme: Theme\n  offsetY: number\n  blockSizeYOverride?: number\n}) {\n  const {\n    resolvedHighlights,\n    rowTints,\n    referenceRowIndex,\n    rowHeight,\n    effectiveTreeAreaWidth,\n    marginLeft,\n    blockSize,\n  } = model\n  const by = blockSizeYOverride ?? blockSize\n  const pad = blockPad(model)\n  const placed: LabelBox[] = []\n  const fillRow = (index: number) => {\n    ctx.fillRect(\n      -marginLeft,\n      index * rowHeight,\n      effectiveTreeAreaWidth,\n      rowHeight,\n    )\n  }\n  if (rowTints) {\n    const top = Math.max(0, Math.floor((offsetY - pad) / rowHeight))\n    const bottom = Math.min(\n      rowTints.length - 1,\n      Math.ceil((offsetY + by + pad) / rowHeight),\n    )\n    for (let index = top; index <= bottom; index++) {\n      const color = rowTints[index]\n      if (color) {\n        ctx.fillStyle = color\n        fillRow(index)\n      }\n    }\n  }\n  if (referenceRowIndex !== undefined) {\n    ctx.fillStyle = referenceColor\n    fillRow(referenceRowIndex)\n  }\n  for (const { rowIndices, label, color } of resolvedHighlights) {\n    ctx.fillStyle = color ?? highlightRowFill\n    for (const index of rowIndices) {\n      if (inYBlock(index * rowHeight + rowHeight / 2, offsetY, by, pad)) {\n        fillRow(index)\n      }\n    }\n    const first = firstRow(rowIndices)\n    if (\n      label &&\n      rowIndices.length &&\n      inYBlock(first * rowHeight, offsetY, by, pad)\n    ) {\n      drawHighlightLabel({\n        ctx,\n        theme,\n        label,\n        x: -marginLeft + 2,\n        y: first * rowHeight,\n        spanWidth: effectiveTreeAreaWidth,\n        bounds: { min: -marginLeft, max: effectiveTreeAreaWidth - marginLeft },\n        placed,\n      })\n    }\n  }\n}\n\nexport function renderTreeCanvas({\n  model,\n  clickMap,\n  ctx,\n  offsetY,\n  theme,\n  highResScaleFactorOverride,\n  blockSizeYOverride,\n}: {\n  model: MsaViewModel\n  offsetY: number\n  ctx: RenderCtx\n  clickMap?: ClickMapIndex\n  theme: Theme\n  highResScaleFactorOverride?: number\n  blockSizeYOverride?: number\n}) {\n  clickMap?.clear()\n\n  // Defer the finish call until after all inserts are done\n  const {\n    noTree,\n    drawTree,\n    drawNodeBubbles,\n    drawNodeLabels,\n    highResScaleFactor,\n    fontSize,\n    showTreeText,\n    marginLeft,\n    // eslint-disable-next-line  @typescript-eslint/no-unused-vars\n    rowHeight: _rowHeight, // read so the draw autorun re-fires after a zoom change\n  } = model\n\n  ctx.resetTransform()\n\n  const k = highResScaleFactorOverride ?? highResScaleFactor\n  ctx.scale(k, k)\n  ctx.translate(marginLeft, -offsetY)\n\n  setFontSize(ctx, fontSize)\n\n  // memoized on the model and shared across the tree/bubble/label passes (and\n  // across all tree blocks) rather than re-traversing the hierarchy in each\n  const { maxDepthToLeaf, effectiveTreeWidth: tipX } = model\n  // built once for all three passes: each of them asks about a different node on\n  // every block of every redraw, and `collapsed` is a list\n  const collapsedSet = new Set(model.collapsed)\n\n  renderCladeHighlights({\n    ctx,\n    model,\n    offsetY,\n    tipX,\n    maxDepthToLeaf,\n    blockSizeYOverride,\n  })\n  renderRowHighlights({ ctx, model, theme, offsetY, blockSizeYOverride })\n  setFontSize(ctx, fontSize)\n\n  if (!noTree && drawTree) {\n    renderTree({\n      ctx,\n      offsetY,\n      model,\n      theme,\n      tipX,\n      maxDepthToLeaf,\n      blockSizeYOverride,\n    })\n\n    renderCollapsedTriangles({\n      ctx,\n      clickMap,\n      offsetY,\n      model,\n      theme,\n      tipX,\n      maxDepthToLeaf,\n      blockSizeYOverride,\n      collapsedSet,\n    })\n\n    renderNodeBubbles({\n      ctx,\n      theme,\n      offsetY,\n      clickMap,\n      model,\n      tipX,\n      maxDepthToLeaf,\n      blockSizeYOverride,\n      collapsedSet,\n      draw: drawNodeBubbles,\n    })\n\n    if (drawNodeLabels) {\n      renderNodeLabels({\n        ctx,\n        theme,\n        offsetY,\n        model,\n        tipX,\n        maxDepthToLeaf,\n        blockSizeYOverride,\n      })\n    }\n  }\n\n  if (showTreeText) {\n    renderTreeLabels({\n      ctx,\n      offsetY,\n      model,\n      clickMap,\n      theme,\n      tipX,\n      maxDepthToLeaf,\n      blockSizeYOverride,\n      collapsedSet,\n    })\n  }\n\n  renderCladeBrackets({ ctx, model, theme, offsetY, blockSizeYOverride })\n\n  // Finish the index so it's ready for queries\n  clickMap?.finish()\n}\n", "import { descendants } from '../../hierarchy.ts'\nimport { makeOffscreenCanvas } from '../msa/msaRaster.ts'\nimport { getNodeX } from './renderTreeCanvas.ts'\n\nimport type { HierarchyNode } from '../../hierarchy.ts'\nimport type { MsaViewModel } from '../../model.ts'\nimport type { RasterCanvas } from '../msa/msaRaster.ts'\nimport type { RenderCtx } from '../renderCtx.ts'\nimport type { Theme } from '@mui/material'\n\n// the tree draws this far inside the band, so a box around the first or the\n// last row keeps both of its edges\nconst pad = 1\n\ninterface OverviewArgs {\n  model: MsaViewModel\n  ctx: RenderCtx\n  theme: Theme\n  width: number\n  height: number\n}\n\nfunction rowScale(numTips: number, height: number) {\n  const inner = height - pad * 2\n  return (row: number) => pad + (row / numTips) * inner\n}\n\n/**\n * The whole tree at the size of the overview band, with the clade highlights\n * under it.\n *\n * A branch that moves less than a pixel on both axes is dropped. The 230k-tip\n * COVID tree has 460k of them over a 120px band, and the ones landing on the\n * pixel their parent already covers cost a path segment each and change no\n * pixel; the test in renderTreeOverview.test.ts measures a 200k-tip tree.\n */\nexport function drawTreeOverview({\n  model,\n  ctx,\n  theme,\n  width,\n  height,\n}: OverviewArgs) {\n  const layout = model.treeOverviewLayout\n  if (!layout) {\n    return\n  }\n  const { root, numTips, maxDepthToLeaf, showBranchLen } = layout\n  const innerWidth = width - pad * 2\n  const rowY = rowScale(numTips, height)\n  const nodeX = (node: HierarchyNode) =>\n    pad + (getNodeX(node, showBranchLen, 1, maxDepthToLeaf) ?? 0) * innerWidth\n\n  for (const { rows, color } of model.treeOverviewClades) {\n    ctx.fillStyle = color\n    ctx.fillRect(0, rowY(rows[0]), width, rowY(rows[1] + 1) - rowY(rows[0]))\n  }\n\n  ctx.strokeStyle = theme.palette.text.primary\n  ctx.beginPath()\n  for (const source of descendants(root)) {\n    if (!source.children) {\n      continue\n    }\n    const sx = nodeX(source)\n    const sy = rowY(source.x)\n    for (const target of source.children) {\n      const tx = nodeX(target)\n      const ty = rowY(target.x)\n      if (Math.abs(tx - sx) < 1 && Math.abs(ty - sy) < 1) {\n        continue\n      }\n      ctx.moveTo(sx, sy)\n      ctx.lineTo(sx, ty)\n      ctx.lineTo(tx, ty)\n    }\n  }\n  ctx.stroke()\n}\n\n/**\n * A box across the overview around a run of tip rows: the focused subtree's\n * extent, or the one a hovered pixel would focus.\n */\nexport function drawTreeOverviewBox({\n  model,\n  ctx,\n  color,\n  rows,\n  width,\n  height,\n}: Omit<OverviewArgs, 'theme'> & {\n  color: string\n  rows: [number, number]\n}) {\n  const layout = model.treeOverviewLayout\n  if (!layout) {\n    return\n  }\n  const rowY = rowScale(layout.numTips, height)\n  const top = rowY(rows[0])\n  ctx.strokeStyle = color\n  ctx.strokeRect(0.5, top, width - 1, Math.max(2, rowY(rows[1] + 1) - top))\n}\n\n/**\n * The overview as the figure carries it: the tree, the clade highlights and\n * the focus box. The SVG export draws it straight onto a svgcanvas Context,\n * and the live canvas blits `treeOverviewImage` in place of the first two.\n */\nexport function renderTreeOverview(args: OverviewArgs) {\n  drawTreeOverview(args)\n  const rows = args.model.treeOverviewFocusRows\n  if (rows) {\n    drawTreeOverviewBox({\n      ...args,\n      rows,\n      color: args.theme.palette.text.primary,\n    })\n  }\n}\n\ninterface OverviewCache {\n  keys: unknown[]\n  canvas: RasterCanvas | undefined\n}\n\nconst caches = new WeakMap<object, OverviewCache>()\n\n/**\n * Everything the drawn tree depends on. `treeOverviewLayout` and\n * `treeOverviewClades` are computed views, which recompute on every read\n * outside a reaction, so the key holds the values behind them instead.\n */\nfunction overviewKeys({\n  model,\n  theme,\n  width,\n  height,\n  scale,\n}: {\n  model: MsaViewModel\n  theme: Theme\n  width: number\n  height: number\n  scale: number\n}) {\n  return [\n    model.data.tree,\n    model.data.msa,\n    model.currentAlignment,\n    model.collapsed.join(','),\n    JSON.stringify(model.clades),\n    model.showBranchLen,\n    width,\n    height,\n    scale,\n    theme.palette.text.primary,\n  ]\n}\n\nfunction canStroke(ctx: unknown): ctx is CanvasRenderingContext2D {\n  return typeof (ctx as CanvasRenderingContext2D | null)?.stroke === 'function'\n}\n\n/**\n * The tree and its clade highlights on an offscreen canvas, drawn once per\n * change of anything they depend on and blitted every frame after that. A\n * 230k-branch tree takes hundreds of milliseconds to walk and cannot be redrawn\n * as the focus box follows the pointer.\n *\n * Returns undefined where a canvas has no 2d context (jsdom), and the caller\n * then draws the tree itself.\n */\nexport function treeOverviewImage({\n  model,\n  theme,\n  width,\n  height,\n  scale,\n}: {\n  model: MsaViewModel\n  theme: Theme\n  width: number\n  height: number\n  scale: number\n}) {\n  const keys = overviewKeys({ model, theme, width, height, scale })\n  const prev = caches.get(model)\n  if (prev && keys.every((key, i) => key === prev.keys[i])) {\n    return prev.canvas\n  }\n  const made = makeOffscreenCanvas(\n    Math.max(1, Math.round(width * scale)),\n    Math.max(1, Math.round(height * scale)),\n    canStroke,\n  )\n  if (made) {\n    made.ctx.scale(scale, scale)\n    drawTreeOverview({ model, ctx: made.ctx, theme, width, height })\n  }\n  const next = { keys, canvas: made?.canvas }\n  caches.set(model, next)\n  return next.canvas\n}\n", "import { colord } from 'colord'\nimport { flushSync } from 'react-dom'\nimport { createRoot } from 'react-dom/client'\n\nimport type React from 'react'\n\n/**\n * Render a React element to a static markup string, for the SVG export.\n *\n * Inlined because core removed `renderToStaticMarkup` from the\n * `@jbrowse/core/util` barrel in jbrowse-components 0d034e2bd8; see the\n * `@jbrowse/core` note in CLAUDE.md. `react-dom` and `react-dom/client` are\n * host externals, so this adds a few hundred bytes to the plugin bundle and no\n * duplicate react.\n */\nexport function renderToStaticMarkup(node: React.ReactElement) {\n  const div = document.createElement('div')\n  const root = createRoot(div)\n  let html: string\n  try {\n    flushSync(() => {\n      root.render(node)\n    })\n    html = div.innerHTML\n  } finally {\n    // effects run in a client root, so every `observer` holds a MobX reaction;\n    // a mounted export of a large alignment would keep tens of thousands of\n    // detached nodes re-rendering on every pan and zoom\n    root.unmount()\n  }\n  return html\n}\n\nconst tag = /<[a-zA-Z][^>]*>/g\nconst colorAttr = /\\b(fill|stroke|stop-color)=\"([^\"]+)\"/g\n\n/**\n * Rewrites every color an SVG 1.1 presentation attribute cannot hold.\n *\n * `fill`, `stroke` and `stop-color` take a keyword, a hex triplet or rgb(). MUI\n * palette values use rgba() and the percent-identity scheme uses hsl(), and\n * Illustrator and older Inkscape drop an element whose fill they cannot parse.\n * Alpha moves to the matching -opacity attribute unless the element already\n * carries one.\n */\nexport function svgSafeColors(html: string) {\n  return html.replaceAll(tag, el =>\n    el.replaceAll(colorAttr, (match, attr: string, value: string) => {\n      if (!/^(rgba|hsl)/i.test(value)) {\n        return match\n      }\n      const color = colord(value)\n      if (!color.isValid()) {\n        return match\n      }\n      const alpha = color.alpha()\n      const hex = color.alpha(1).toHex()\n      return alpha === 1 || el.includes(`${attr}-opacity=`)\n        ? `${attr}=\"${hex}\"`\n        : `${attr}=\"${hex}\" ${attr}-opacity=\"${alpha}\"`\n    }),\n  )\n}\n"],
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+  "names": ["require_mobx", "__commonJSMin", "exports", "module", "require_react_dom", "__commonJSMin", "exports", "module", "require_client", "__commonJSMin", "exports", "module", "import_react", "import_mobx", "visibleRowRange", "model", "offsetY", "blockSizeY", "rowHeight", "getVisibleLeaves", "yStart", "yEnd", "import_react", "import_react", "import_material", "import_react", "useDragScroll", "axis", "onScroll", "scheduled", "mouseDown", "setMouseDown", "onMove", "event", "client", "startClient", "startScroll", "onUp", "scrollbarThumbFill", "hitSlop", "variants", "theme", "axis", "DragHandle", "variant", "getStart", "onDrag", "style", "hovered", "setHovered", "startDrag", "useDragScroll", "fill", "fillHovered", "cursor", "position", "zIndex", "React", "event", "tileColorFn", "model", "dynamicColorSchemeName", "colClustalX", "col", "letter", "colConsensus", "consensus", "colorScheme", "_col", "tileColorTable", "rasterTileSize", "maxCachedTiles", "maxThumbnailColumns", "maxColorCacheEntries", "littleEndian", "packRgba", "r", "g", "b", "a", "scratch", "colorCache", "cssColorToPixel", "css", "hit", "makeRasterCanvas", "packed", "cellPixelFn", "spec", "toPixel", "columns", "relativeTo", "colorAt", "bg", "hover", "bgPixel", "hoverPixel", "reference", "name", "col", "letter", "color", "rasterPixels", "col0", "row0", "width", "height", "colStep", "rowStep", "colSpan", "rowSpan", "out", "averagePixels", "rowNames", "cellPixel", "str", "base", "c", "cells", "rShift", "gShift", "bShift", "aShift", "names", "strs", "dr", "sumR", "sumG", "sumB", "sumA", "i", "dc", "p", "usableRasterCtx", "ctx", "makeOffscreenCanvas", "usable", "settings", "canvas", "paint", "fill", "made", "image", "supported", "rasterApplies", "model", "caches", "rasterKeys", "theme", "tileColorTable", "getCache", "keys", "prev", "key", "next", "node", "tileColorFn", "cellsPerPixel", "devicePixelsPerCell", "getTile", "cache", "tileRow", "tileCol", "stale", "drawMsaRaster", "offsetX", "offsetY", "colWidth", "rowHeight", "blockSize", "highResScaleFactor", "pixelWidth", "pixelHeight", "tileWidth", "tileHeight", "firstCol", "lastCol", "firstRow", "lastRow", "tile", "canvasHref", "maxImagePixels", "maxImageSide", "rasterImageHref", "numCols", "numRows", "msaThumbnail", "numColumns", "w", "h", "getMinimapLayout", "model", "scrollX", "minimapHeight", "totalWidth", "msaCanvasWidth", "unit", "s", "w", "polygonHeight", "polygonPoints", "MinimapSVG", "model", "theme", "msaCanvasWidth", "s", "w", "polygonPoints", "getMinimapLayout", "href", "canvasHref", "msaThumbnail", "React", "scrollbarThumbFill", "r", "t", "n", "u", "e", "o", "a", "i", "s", "d", "h", "b", "f", "g", "c", "v", "l", "p", "m", "y", "N", "x", "M", "H", "$", "j", "w", "k", "r", "y", "u", "E", "R", "q", "w", "n", "i", "t", "e", "o", "g", "p", "c", "A", "C", "D", "$", "o", "t", "r", "n", "a", "i", "e", "v", "u", "d", "e", "f", "a", "d", "l", "i", "n", "o", "t", "b", "c", "g", "u", "r", "D", "e", "r", "contrastAdjustCache", "adjustColorForContrast", "color", "bg", "cacheKey", "cached", "c", "A", "bgIsDark", "i", "result", "withAlpha", "alpha", "parsed", "outlineColor", "fill", "transform", "obj", "cb", "contrastTextCaches", "contrastTextFn", "theme", "cache", "fallback", "hit", "out", "dropBlanks", "blanks", "arr", "set", "_", "skipBlanks", "str", "chunks", "lastEnd", "blankIdx", "computeRowInsertions", "seq", "insertions", "blanksLen", "displayPos", "currentInsertPos", "letterChars", "len", "a", "spanRows", "leaves", "bandsByRow", "rows", "leaf", "bands", "featureSpanMarks", "layout", "xOf", "colors", "labelOf", "labelDrawn", "measureText", "xMin", "xMax", "out", "y", "headLen", "rise", "labelled", "minFeatureLabelHeight", "fontSize", "shapes", "labels", "placed", "band", "xStart", "xEnd", "w", "t", "fill", "stroke", "strand", "head", "geneArrow", "text", "drawFeatureSpans", "ctx", "contrastText", "source", "font", "setFont", "next", "box", "outline", "i", "x", "h", "tip", "tail", "flange", "bottom", "crown", "point", "renderBoxFeatureCanvasBlock", "model", "theme", "offsetX", "offsetY", "ctx", "highResScaleFactorOverride", "blockSizeXOverride", "blockSizeYOverride", "blockSize", "rowHeight", "highResScaleFactor", "actuallyShowDomains", "k", "bx", "by", "drawFeatureSpans", "domainOverlaySource", "getVisibleLeaves", "contrastTextFn", "leaves", "subFeatureRows", "colWidth", "featureColors", "featureLabels", "segmentLabels", "showMsaLetters", "domainUnderline", "domainBands", "barHeight", "labelled", "spanRows", "laneCount", "y", "lane", "h", "band", "setFontSize", "ctx", "fontSize", "bold", "referenceColor", "treeHoverColor", "multiRowHoverColor", "hoverColor", "clickColor", "selectionFill", "selectionBorder", "highlightFill", "highlightBorder", "highlightRowFill", "labelFontSize", "labelPad", "highlightLabelHeight", "drawHighlightLabel", "ctx", "theme", "label", "x", "y", "spanWidth", "bounds", "placed", "setFontSize", "boxWidth", "boxHeight", "left", "top", "overlaps", "box", "renderHighlights", "model", "offsetX", "offsetY", "width", "height", "resolvedClades", "resolvedHighlights", "rowTints", "colWidth", "rowHeight", "firstRow", "lastRow", "fillRow", "index", "rows", "color", "mark", "rowIndices", "startCol", "endCol", "renderSelection", "resolvedSelection", "rowRuns", "w", "first", "last", "h", "selectionFill", "selectionBorder", "renderPersistentHighlights", "referenceRowIndex", "highlightedColumnRuns", "referenceColor", "start", "end", "domainBandCursor", "bands", "next", "active", "col", "band", "top", "visibleColRange", "offsetX", "blockWidth", "colWidth", "renderMSABlock", "model", "offsetX", "offsetY", "ctx", "theme", "highResScaleFactorOverride", "blockSizeXOverride", "blockSizeYOverride", "rasterTiles", "colWidth", "blockSize", "rowHeight", "fontSize", "highResScaleFactor", "actuallyShowDomains", "bgColor", "k", "bx", "by", "setFontSize", "xStart", "xEnd", "visibleColRange", "visibleLeaves", "getVisibleLeaves", "relativeTo", "columns", "referenceSeq", "drawTilesAndText", "drawInsertionIndicators", "drawTiles", "showMsaLetters", "subFeatureRows", "domainUnderline", "domainBandsByStart", "featureColors", "tiles", "paintTiles", "tileColor", "tileColorFn", "contrastText", "contrastTextFn", "offsetXAligned", "halfColWidth", "baselineOffset", "overDomains", "i", "l1", "node", "name", "y", "str", "tileY", "textY", "bandAt", "domainBandCursor", "j", "l2", "col", "letter", "x", "isMatchingReference", "color", "covering", "adjustColorForContrast", "hideGapsEffective", "drawZigZag", "offset", "insertionPositions", "insertions", "pos", "top", "bottom", "currentY", "goRight", "nextY", "nextX", "headerRunsAcross", "panelWidth", "rowPanelHeaderHeight", "rowPadding", "renderFeaturePanel", "ctx", "model", "theme", "panel", "x", "offsetY", "blockSizeYOverride", "highResScaleFactorOverride", "rowHeight", "blockSize", "highResScaleFactor", "by", "k", "drawFeatureSpans", "featurePanelSource", "getVisibleLeaves", "contrastTextFn", "leaves", "spanRows", "laneCount", "y", "lane", "h", "span", "renderStrip", "ctx", "model", "panel", "x", "offsetY", "blockSizeYOverride", "highResScaleFactorOverride", "rowHeight", "blockSize", "highResScaleFactor", "by", "k", "leaf", "getVisibleLeaves", "color", "renderRowPanel", "panel", "rest", "renderFeaturePanel", "renderStrip", "renderRowPanels", "model", "slotOfCode", "c", "letterOfSlot", "_", "slot", "slotOf", "code", "isGapSlot", "ColumnCounts", "numColumns", "row", "counts", "totals", "slotTotals", "n", "col", "letter", "base", "cb", "count", "nonGapTotal", "entropy", "_slot", "freq", "entries", "letters", "letterOfResidueSlot", "residueSlotOfLetter", "numResidueSlots", "columnCountsFromRows", "rows", "max", "maxBitsFor", "sequenceType", "columnLogoStack", "colStats", "col", "maxBits", "total", "nonGapTotal", "informationContent", "stack", "slot", "count", "letterOfResidueSlot", "a", "b", "drawConservationBars", "ctx", "values", "color", "colWidth", "trackHeight", "offsetX", "blockSize", "xStart", "xEnd", "visibleColRange", "i", "barHeight", "x", "barTrackValues", "model", "trackId", "supplied", "drawArcs", "arcs", "maxSpan", "arc", "apexRoom", "x1", "x2", "apex", "drawTextTrackContent", "data", "colorScheme", "contrastText", "bgColor", "drawLetters", "rowHeight", "str", "letter", "upper", "fill", "rulerStep", "minPixels", "step", "mantissas", "rulerCols", "end", "cols", "first", "n", "RULER_FONT_SIZE", "TICK_HEIGHT", "drawColumnRuler", "numColumns", "label", "textColor", "setFontSize", "col", "text", "CAP_HEIGHT_RATIO", "MIN_LETTER_PX", "drawSequenceLogo", "colStats", "maxBits", "referenceFontSize", "capHeight", "stack", "columnLogoStack", "bottom", "bits", "h", "width", "drawTrackBlock", "track", "offsetY", "theme", "blockSizeXOverride", "highResScaleFactorOverride", "highResScaleFactor", "id", "kind", "barColor", "arcColor", "customColorScheme", "blockSizeX", "k", "relativeTo", "pos", "fontSize", "showMsaLetters", "contrastTextFn", "renderAllTracks", "currentY", "import_react", "ScaleBarSVG", "bar", "marginLeft", "y", "color", "React", "ctxHandle", "getCtx", "CHAR_WIDTH_RATIO", "measureTextCanvas", "text", "fontSize", "ctx", "setFontSize", "bracketBarWidth", "bracketGap", "maxCladeGutterWidth", "cladeInGutter", "clade", "cladeHeight", "rowHeight", "cladeLabelHorizontal", "fontSize", "cladeLabelOffset", "cladeGutterWidth", "clades", "widest", "text", "measureTextCanvas", "labelFitFontSize", "cladeLabelBoxes", "model", "resolvedClades", "effectiveTreeAreaWidth", "gutterLeft", "index", "label", "markColor", "rows", "left", "ellipsize", "measure", "text", "room", "width", "n", "truncated", "truncatedWidth", "hierarchy", "data", "childrenAccessor", "LaidOutNode", "source", "parent", "frame", "scale", "rootToTipLength", "layoutTree", "root", "nodes", "leafNodes", "rootHeight", "stack", "node", "collapsedSubtreeMaxLength", "i", "sum", "min", "max", "depthToLeaf", "child", "collapse", "calcDepthToLeaf", "roots", "n", "acc", "kids", "descendants", "maxDepth", "leafIndex", "index", "leaf", "leaves", "name", "mrca", "names", "other", "nodeCoveringRows", "top", "bottom", "c", "radius", "d", "blockPad", "model", "highlightLabelHeight", "inYBlock", "y", "offsetY", "by", "pad", "forEachNodeInBlock", "root", "cb", "top", "bottom", "stack", "node", "child", "cladeName", "unnamed", "id", "name", "label", "getNodeX", "showBranchLen", "tipX", "maxDepthToLeaf", "depthToLeaf", "calcDepthToLeaf", "renderTree", "ctx", "theme", "blockSizeYOverride", "hierarchy", "blockSize", "branchColors", "defaultStroke", "source", "sy", "sx", "target", "ty", "tx", "y1", "y2", "renderCollapsedTriangles", "clickMap", "collapsedSet", "rowHeight", "fontSize", "ml", "halfHeight", "apexX", "inBlock", "baseX", "count", "renderNodeBubbles", "draw", "x", "data", "isCollapsed", "renderNodeLabels", "setFontSize", "renderTreeLabels", "tipLabelColors", "labelsAlignRight", "drawTree", "treeAreaWidthMinusMargin", "marginLeft", "noTree", "treeDrawn", "visibleLeaves", "getVisibleLeaves", "emHeight", "displayName", "yp", "xp", "fit", "room", "ellipsize", "text", "boxWidth", "width", "offset", "labelRight", "labelX", "firstRow", "rowIndices", "min", "index", "renderCladeHighlights", "resolvedClades", "effectiveTreeAreaWidth", "right", "rows", "color", "mark", "nodeCoveringRows", "renderCladeBrackets", "cladeGutterWidth", "bracketGap", "bracketBarWidth", "markColor", "renderRowHighlights", "resolvedHighlights", "rowTints", "referenceRowIndex", "placed", "fillRow", "referenceColor", "highlightRowFill", "first", "drawHighlightLabel", "renderTreeCanvas", "highResScaleFactorOverride", "drawNodeBubbles", "drawNodeLabels", "highResScaleFactor", "showTreeText", "_rowHeight", "k", "pad", "rowScale", "numTips", "height", "inner", "row", "drawTreeOverview", "model", "ctx", "theme", "width", "layout", "root", "maxDepthToLeaf", "showBranchLen", "innerWidth", "rowY", "nodeX", "node", "getNodeX", "rows", "color", "source", "descendants", "sx", "sy", "target", "tx", "ty", "drawTreeOverviewBox", "top", "renderTreeOverview", "args", "caches", "overviewKeys", "scale", "canStroke", "treeOverviewImage", "keys", "prev", "key", "i", "made", "makeOffscreenCanvas", "next", "import_react_dom", "import_client", "renderToStaticMarkup", "node", "div", "root", "html", "tag", "colorAttr", "svgSafeColors", "el", "match", "attr", "value", "color", "A", "alpha", "hex", "renderToSvg", "model", "opts", "Context", "layers", "markup", "renderToStaticMarkup", "React", "MsaSvg", "getLayout", "svgSafeColors", "match", "id", "ctx", "theme", "layout", "width", "trackHeight", "includeMinimap", "legendWidth", "topHeight", "effectiveTreeAreaWidth", "rowPanelsWidth", "totalWidth", "height", "exportPageSize", "legendTop", "props", "body", "TrackRendering", "CoreRendering", "MinimapSVG", "RowPanelHeadersSVG", "TreeOverviewSVG", "TreeScaleBarSVG", "LegendSVG", "overviewHeight", "renderTreeOverview", "ClipGroup", "marginLeft", "bar", "treeOverviewHeight", "ScaleBarSVG", "treeScaleBarHeight", "bandHeight", "resolvedRowPanels", "fontSize", "y", "panel", "across", "headerRunsAcross", "size", "center", "x", "room", "LEGEND_PAD", "ellipsize", "t", "measureTextCanvas", "CladeLabelsSVG", "offsetY", "boxes", "cladeLabelBoxes", "box", "top", "rows", "legendRows", "boxHeight", "legendHeight", "LEGEND_TEXT_X", "row", "i", "LEGEND_ROW_H", "LEGEND_SWATCH", "outlineColor", "LEGEND_FONT", "LEGEND_CHAR_W", "contentHeight", "offsetX", "msaAreaWidth", "treeCtx", "renderTreeCanvas", "rowPanelsCtx", "renderRowPanels", "raster", "rasterBackground", "msaCtx", "renderBoxFeatureCanvasBlock", "renderMSABlock", "renderPersistentHighlights", "colWidth", "rowHeight", "rasterApplies", "xStart", "xEnd", "visibleColRange", "yStart", "yEnd", "visibleRowRange", "numCols", "numRows", "href", "rasterImageHref", "renderAllTracks", "TrackLabelsSVG", "turnedOnTracks", "drawLabels", "labels", "track", "name", "acc", "baseline", "panelId", "clipId", "transform", "underlay"]
+}