schematex 0.5.0 → 0.6.0

package/dist/{chunk-S2KJRHDZ.cjs.map → chunk-4UFR2LB6.cjs.map}

@@ -1 +1 @@
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\"unrooted\"].includes(val)) {\n          result.layout = val as PhyloLayout;\n        }\n        break;\n      case \"mode\":\n        if ([\"phylogram\", \"cladogram\", \"chronogram\"].includes(val)) {\n          result.mode = val as PhyloMode;\n        }\n        break;\n      case \"branch-width\":\n        result.branchWidth = Number(val);\n        break;\n      case \"openAngle\":\n        result.openAngle = Number(val);\n        break;\n      case \"mrsd\":\n        result.mrsd = val;\n        break;\n    }\n  }\n\n  if (result.layout === \"unrooted\") {\n    result.unrooted = true;\n  }\n\n  return result;\n}\n\nfunction parseCladeLine(line: string): CladeDef | null {\n  // clade ID = (member1, member2, ...) [color: \"#hex\", label: \"text\", highlight: mode]\n  const match = line.match(\n    /^clade\\s+(\\S+)\\s*=\\s*\\(([^)]+)\\)\\s*(?:\\[([^\\]]*)\\])?\\s*$/\n  );\n  if (!match) return null;\n\n  const id = match[1];\n  const members = match[2].split(\",\").map((s) => s.trim()).filter(Boolean);\n  const propsStr = match[3] ?? \"\";\n\n  let color: string | undefined;\n  let label: string | undefined;\n  let highlight: CladeHighlightMode | undefined;\n\n  if (propsStr) {\n    const colorMatch = propsStr.match(/color:\\s*\"([^\"]+)\"/);\n    if (colorMatch) color = colorMatch[1];\n    const labelMatch = propsStr.match(/label:\\s*\"([^\"]+)\"/);\n    if (labelMatch) label = labelMatch[1];\n    const hlMatch = propsStr.match(/highlight:\\s*(\\w+)/);\n    if (hlMatch && [\"branch\", \"background\", \"both\"].includes(hlMatch[1])) {\n      highlight = hlMatch[1] as CladeHighlightMode;\n    }\n  }\n\n  return { id, members, color, label, highlight };\n}\n\nexport function parsePhylo(text: string): PhyloTreeAST {\n  const lines = text.split(\"\\n\");\n  let lineIdx = 0;\n\n  // Skip empty lines\n  while (lineIdx < lines.length && !lines[lineIdx].trim()) lineIdx++;\n\n  // Parse header: phylo \"title\" [props]\n  const headerLine = lines[lineIdx]?.trim() ?? \"\";\n  if (!headerLine.toLowerCase().startsWith(\"phylo\")) {\n    throw new PhyloParseError(\"Phylo document must start with 'phylo'\");\n  }\n  lineIdx++;\n\n  const title: string | undefined = matchQuotedTitle(headerLine);\n\n  let headerProps: ReturnType<typeof parseHeaderProps> = {\n    layout: \"rectangular\",\n    mode: \"phylogram\",\n    unrooted: false,\n  };\n  const propsMatch = headerLine.match(/\\[([^\\]]+)\\]/);\n  if (propsMatch) {\n    headerProps = parseHeaderProps(propsMatch[1]);\n  }\n\n  // Parse body: newick, indent tree, scale, outgroup, clade definitions\n  let root: PhyloNode | null = null;\n  let scaleLabel: string | undefined;\n  let outgroup: string | undefined;\n  const clades: CladeDef[] = [];\n  const indentLines: string[] = [];\n  let inIndentTree = false;\n\n  while (lineIdx < lines.length) {\n    const raw = lines[lineIdx];\n    const trimmed = raw.trim();\n    lineIdx++;\n\n    if (!trimmed || trimmed.startsWith(\"#\")) continue;\n\n    // Newick definition\n    if (trimmed.startsWith(\"newick:\")) {\n      const newickStr = trimmed.slice(7).trim().replace(/^[\"']|[\"']$/g, \"\");\n      root = parseNewick(newickStr);\n      inIndentTree = false;\n      continue;\n    }\n\n    // Scale definition\n    if (trimmed.startsWith(\"scale\")) {\n      const scaleMatch = trimmed.match(/scale\\s+\"([^\"]+)\"/);\n      if (scaleMatch) {\n        scaleLabel = scaleMatch[1];\n      } else {\n        scaleLabel = trimmed.slice(5).trim().replace(/^[\"']|[\"']$/g, \"\") || \"substitutions/site\";\n      }\n      continue;\n    }\n\n    // Outgroup\n    if (trimmed.startsWith(\"outgroup:\")) {\n      outgroup = trimmed.slice(9).trim();\n      continue;\n    }\n\n    // Clade definition\n    if (trimmed.startsWith(\"clade \")) {\n      const clade = parseCladeLine(trimmed);\n      if (clade) clades.push(clade);\n      continue;\n    }\n\n    // Style line (alternative props)\n    if (trimmed.startsWith(\"style\")) {\n      const styleProps = trimmed.match(/\\[([^\\]]+)\\]/);\n      if (styleProps) {\n        headerProps = { ...headerProps, ...parseHeaderProps(styleProps[1]) };\n      }\n      continue;\n    }\n\n    // Indent tree definition\n    if (trimmed.endsWith(\":\") && (trimmed === \"root:\" || !trimmed.includes(\" \"))) {\n      inIndentTree = true;\n      indentLines.push(raw);\n      continue;\n    }\n\n    if (inIndentTree) {\n      indentLines.push(raw);\n      continue;\n    }\n  }\n\n  // Parse indent tree if present and no Newick was found\n  if (!root && indentLines.length > 0) {\n    root = parseIndentTree(indentLines);\n  }\n\n  if (!root) {\n    throw new PhyloParseError(\"No tree definition found (newick: or indent tree)\");\n  }\n\n  return {\n    type: \"phylo\",\n    title,\n    root,\n    unrooted: headerProps.unrooted,\n    layout: headerProps.layout,\n    mode: headerProps.mode,\n    clades,\n    scaleLabel,\n    mrsd: headerProps.mrsd,\n    outgroup,\n    metadata: {},\n  };\n}\n","import type {\n  PhyloTreeAST,\n  PhyloNode,\n  PhyloLayoutNode,\n} from \"../../core/types\";\n\nexport interface PhyloLayoutResult {\n  width: number;\n  height: number;\n  nodes: PhyloLayoutNode[];\n  /** Branch paths: { path, cladeId?, isConnector } */\n  branches: PhyloBranch[];\n  ast: PhyloTreeAST;\n  scale: number;\n}\n\nexport interface PhyloBranch {\n  path: string;\n  fromId: string;\n  toId: string;\n  /** Clade id if this branch belongs to a highlighted clade */\n  cladeId?: string;\n  /** Is this a vertical/arc connector (no length meaning) vs horizontal branch */\n  isConnector: boolean;\n}\n\n// ─── Tree Utilities ─────────────────────────────────────────\n\nfunction collectLeaves(node: PhyloNode): PhyloNode[] {\n  if (node.isLeaf) return [node];\n  const leaves: PhyloNode[] = [];\n  for (const child of node.children) {\n    leaves.push(...collectLeaves(child));\n  }\n  return leaves;\n}\n\nfunction maxRootToTip(node: PhyloNode, distSoFar: number): number {\n  if (node.isLeaf) return distSoFar;\n  let maxDist = distSoFar;\n  for (const child of node.children) {\n    const childDist = maxRootToTip(child, distSoFar + (child.branchLength ?? 0));\n    if (childDist > maxDist) maxDist = childDist;\n  }\n  return maxDist;\n}\n\nfunction maxDepth(node: PhyloNode): number {\n  if (node.isLeaf) return 0;\n  let max = 0;\n  for (const child of node.children) {\n    const d = maxDepth(child) + 1;\n    if (d > max) max = d;\n  }\n  return max;\n}\n\nfunction estimateLabelWidth(node: PhyloNode): number {\n  const label = node.label ?? node.id;\n  return label.length * 7.2 + 6;\n}\n\n// ─── Clade Membership ───────────────────────────────────────\n\nfunction buildCladeMap(\n  ast: PhyloTreeAST\n): Map<string, string> {\n  const branchToCladeMap = new Map<string, string>();\n\n  for (const clade of ast.clades) {\n    const memberSet = new Set(clade.members);\n    markCladeBranches(ast.root, memberSet, clade.id, branchToCladeMap);\n  }\n\n  return branchToCladeMap;\n}\n\nfunction markCladeBranches(\n  node: PhyloNode,\n  memberSet: Set<string>,\n  cladeId: string,\n  result: Map<string, string>\n): boolean {\n  if (node.isLeaf) {\n    return memberSet.has(node.id);\n  }\n\n  const childResults: boolean[] = [];\n  for (const child of node.children) {\n    childResults.push(markCladeBranches(child, memberSet, cladeId, result));\n  }\n\n  const allIn = childResults.every(Boolean);\n  const anyIn = childResults.some(Boolean);\n\n  if (allIn && anyIn) {\n    for (const child of node.children) {\n      result.set(child.id, cladeId);\n    }\n    return true;\n  }\n\n  // Partial — mark only children that are fully within\n  for (let i = 0; i < node.children.length; i++) {\n    if (childResults[i]) {\n      result.set(node.children[i].id, cladeId);\n    }\n  }\n\n  return false;\n}\n\n// ─── Rectangular Phylogram Layout ───────────────────────────\n\nconst TIP_SPACING = 20;\nconst PADDING_LEFT = 20;\nconst PADDING_RIGHT = 20;\nconst PADDING_TOP = 20;\nconst PADDING_BOTTOM = 40;\n\nexport function layoutPhylo(ast: PhyloTreeAST): PhyloLayoutResult {\n  const leaves = collectLeaves(ast.root);\n  const numLeaves = leaves.length;\n  const tipSpacing = TIP_SPACING;\n\n  // Compute scale\n  const maxLabelWidth = Math.max(...leaves.map(estimateLabelWidth), 60);\n  const maxDist = maxRootToTip(ast.root, 0);\n  const isCladogram = ast.mode === \"cladogram\";\n\n  const availableWidth = Math.max(300, numLeaves * 30 + maxLabelWidth + 100);\n  const plotWidth = availableWidth - PADDING_LEFT - PADDING_RIGHT - maxLabelWidth;\n\n  let scale: number;\n  if (isCladogram || maxDist === 0) {\n    const depth = maxDepth(ast.root);\n    scale = depth > 0 ? plotWidth / depth : plotWidth;\n  } else {\n    scale = plotWidth / maxDist;\n  }\n\n  // Step 1: assign Y to leaves (in-order)\n  const nodeMap = new Map<string, PhyloLayoutNode>();\n  let leafIdx = 0;\n\n  function assignLeafY(node: PhyloNode): void {\n    if (node.isLeaf) {\n      const y = PADDING_TOP + leafIdx * tipSpacing;\n      nodeMap.set(node.id, { node, x: 0, y });\n      leafIdx++;\n      return;\n    }\n    for (const child of node.children) {\n      assignLeafY(child);\n    }\n  }\n  assignLeafY(ast.root);\n\n  // Step 2: assign Y to internal nodes (mean of children)\n  function assignInternalY(node: PhyloNode): number {\n    const existing = nodeMap.get(node.id);\n    if (node.isLeaf && existing) return existing.y;\n    const childYs = node.children.map(assignInternalY);\n    const y = (Math.min(...childYs) + Math.max(...childYs)) / 2;\n    if (!existing) {\n      nodeMap.set(node.id, { node, x: 0, y });\n    } else {\n      existing.y = y;\n    }\n    return y;\n  }\n  assignInternalY(ast.root);\n\n  // Step 3: assign X (distance from root)\n  function assignX(node: PhyloNode, parentX: number, depth: number): void {\n    let x: number;\n    if (node === ast.root) {\n      x = PADDING_LEFT;\n    } else if (isCladogram) {\n      if (node.isLeaf) {\n        x = PADDING_LEFT + plotWidth;\n      } else {\n        x = PADDING_LEFT + depth * (plotWidth / maxDepth(ast.root));\n      }\n    } else {\n      x = parentX + (node.branchLength ?? 0) * scale;\n    }\n\n    const layoutNode = nodeMap.get(node.id);\n    if (layoutNode) layoutNode.x = x;\n\n    for (const child of node.children) {\n      assignX(child, x, depth + 1);\n    }\n  }\n  assignX(ast.root, PADDING_LEFT, 0);\n\n  // For cladogram: recalculate internal node X as parent of children\n  if (isCladogram) {\n    assignCladogramInternalX(ast.root, nodeMap);\n  }\n\n  // Build clade membership map\n  const cladeMap = buildCladeMap(ast);\n\n  // Step 4: generate branch paths\n  const branches: PhyloBranch[] = [];\n\n  function generateBranches(node: PhyloNode): void {\n    const parentLayout = nodeMap.get(node.id);\n    if (!parentLayout) return;\n\n    if (node.children.length === 0) return;\n\n    const childLayouts = node.children\n      .map((c) => nodeMap.get(c.id))\n      .filter((l): l is PhyloLayoutNode => l !== undefined);\n\n    if (childLayouts.length === 0) return;\n\n    // Vertical connector from min child Y to max child Y at parent X\n    const minY = Math.min(...childLayouts.map((c) => c.y));\n    const maxY = Math.max(...childLayouts.map((c) => c.y));\n\n    if (ast.layout === \"slanted\") {\n      // Slanted: diagonal lines from parent to each child\n      for (const child of node.children) {\n        const childLayout = nodeMap.get(child.id);\n        if (!childLayout) continue;\n        const pathStr = `M ${parentLayout.x},${parentLayout.y} L ${childLayout.x},${childLayout.y}`;\n        branches.push({\n          path: pathStr,\n          fromId: node.id,\n          toId: child.id,\n          cladeId: cladeMap.get(child.id),\n          isConnector: false,\n        });\n      }\n    } else {\n      // Rectangular: vertical connector + horizontal branches\n      branches.push({\n        path: `M ${parentLayout.x},${minY} V ${maxY}`,\n        fromId: node.id,\n        toId: node.id,\n        isConnector: true,\n      });\n\n      for (const child of node.children) {\n        const childLayout = nodeMap.get(child.id);\n        if (!childLayout) continue;\n        const pathStr = `M ${parentLayout.x},${childLayout.y} H ${childLayout.x}`;\n        branches.push({\n          path: pathStr,\n          fromId: node.id,\n          toId: child.id,\n          cladeId: cladeMap.get(child.id),\n          isConnector: false,\n        });\n      }\n    }\n\n    for (const child of node.children) {\n      generateBranches(child);\n    }\n  }\n\n  generateBranches(ast.root);\n\n  // Compute final dimensions\n  const allNodes = Array.from(nodeMap.values());\n  let maxX = Math.max(...allNodes.map((n) => n.x + (n.node.isLeaf ? estimateLabelWidth(n.node) : 0)));\n\n  // Add space for clade labels (background/both mode places labels to the right)\n  let maxCladeLabelWidth = 0;\n  for (const clade of ast.clades) {\n    if (clade.label && clade.highlight && clade.highlight !== \"branch\") {\n      const w = clade.label.length * 8 + 30;\n      if (w > maxCladeLabelWidth) maxCladeLabelWidth = w;\n    }\n  }\n  maxX += maxCladeLabelWidth;\n\n  const maxNodeY = Math.max(...allNodes.map((n) => n.y));\n\n  const width = Math.max(maxX + PADDING_RIGHT, availableWidth);\n  const height = maxNodeY + PADDING_TOP + PADDING_BOTTOM;\n\n  return {\n    width,\n    height,\n    nodes: allNodes,\n    branches,\n    ast,\n    scale,\n  };\n}\n\nfunction assignCladogramInternalX(\n  node: PhyloNode,\n  nodeMap: Map<string, PhyloLayoutNode>\n): number {\n  if (node.isLeaf) {\n    return nodeMap.get(node.id)?.x ?? 0;\n  }\n\n  let minChildX = Infinity;\n  for (const child of node.children) {\n    const childX = assignCladogramInternalX(child, nodeMap);\n    if (childX < minChildX) minChildX = childX;\n  }\n\n  const layout = nodeMap.get(node.id);\n  if (layout) {\n    layout.x = minChildX - 40;\n    if (layout.x < PADDING_LEFT) layout.x = PADDING_LEFT;\n  }\n\n  return layout?.x ?? PADDING_LEFT;\n}\n","import type { PhyloTreeAST } from \"../../core/types\";\nimport type { PhyloLayoutResult } from \"./layout\";\nimport {\n  svgRoot,\n  group,\n  path,\n  line,\n  circle,\n  text,\n  title,\n  desc,\n  rect,\n  el,\n} from \"../../core/svg\";\nimport { cssCustomProperties, resolveBiologyTheme, FONT_SIZE, STROKE_WIDTH, type ResolvedTheme, type BiologyTokens } from \"../../core/theme\";\n\n// ─── Constants ──────────────────────────────────────────────\n\nconst TIP_LABEL_GAP = 6;\nconst SUPPORT_THRESHOLD = 50;\n\nfunction getSupportColor(value: number, t: ResolvedTheme<BiologyTokens>): string {\n  if (value >= 95) return t.supportGood;\n  if (value >= 75) return t.supportMedium;\n  if (value >= 50) return t.supportWarn;\n  return t.supportBad;\n}\n\nfunction isSpeciesBinomial(label: string): boolean {\n  const parts = label.trim().split(/\\s+/);\n  if (parts.length !== 2) return false;\n  return /^[A-Z][a-z]+$/.test(parts[0]) && /^[a-z]+$/.test(parts[1]);\n}\n\n// ─── CSS ────────────────────────────────────────────────────\n\nfunction buildCSS(ast: PhyloTreeAST, t: ResolvedTheme<BiologyTokens>): string {\n  const cladeColors = ast.clades.map((c, i) => {\n    const color = c.color ?? t.cladeColors[i % t.cladeColors.length];\n    return `.schematex-phylo-clade-${c.id} { stroke: ${color}; }\n.schematex-phylo-clade-bg-${c.id} { fill: ${color}; fill-opacity: 0.12; }\n.schematex-phylo-clade-label-${c.id} { fill: ${color}; }`;\n  });\n\n  return `\n.schematex-phylo {${cssCustomProperties(t)}\n  font-family: system-ui, -apple-system, sans-serif;\n}\n.schematex-phylo-branch { fill: none; stroke: ${t.text}; stroke-width: ${STROKE_WIDTH.normal}; stroke-linecap: round; }\n.schematex-phylo-branch-connector { fill: none; stroke: ${t.text}; stroke-width: ${STROKE_WIDTH.normal}; }\n.schematex-phylo-tip-label { font-size: ${FONT_SIZE.label}px; fill: ${t.text}; dominant-baseline: central; }\n.schematex-phylo-tip-label-italic { font-style: italic; }\n.schematex-phylo-support-label { font-size: ${FONT_SIZE.small}px; fill: ${t.textMuted}; text-anchor: middle; dominant-baseline: auto; }\n.schematex-phylo-support-dot { stroke: none; }\n.schematex-phylo-scale-bar line { stroke: ${t.text}; stroke-width: ${STROKE_WIDTH.normal}; }\n.schematex-phylo-scale-bar text { font-size: 10px; fill: ${t.text}; text-anchor: middle; }\n.schematex-phylo-scale-tick { stroke: ${t.text}; stroke-width: ${STROKE_WIDTH.thin}; }\n.schematex-phylo-title { font-size: ${FONT_SIZE.title}px; font-weight: bold; fill: ${t.text}; text-anchor: middle; }\n.schematex-phylo-clade-label { font-size: 13px; font-weight: bold; }\n.schematex-phylo-root-marker { fill: none; stroke: ${t.text}; stroke-width: ${STROKE_WIDTH.normal}; }\n${cladeColors.join(\"\\n\")}\n`.trim();\n}\n\n// ─── Scale Bar ──────────────────────────────────────────────\n\nfunction computeScaleBar(\n  scale: number,\n  plotWidth: number\n): { length: number; label: string; pxLength: number } {\n  if (scale <= 0) return { length: 0.1, label: \"0.1\", pxLength: 50 };\n\n  const targetPx = plotWidth * 0.2;\n\n  const magnitudes = [0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1, 2, 5, 10, 20, 50, 100];\n  let best = magnitudes[0];\n  let bestDiff = Infinity;\n\n  for (const m of magnitudes) {\n    const diff = Math.abs(m * scale - targetPx);\n    if (diff < bestDiff) {\n      bestDiff = diff;\n      best = m;\n    }\n  }\n\n  return {\n    length: best,\n    label: best < 0.01 ? best.toExponential() : String(best),\n    pxLength: best * scale,\n  };\n}\n\nfunction renderScaleBar(\n  layout: PhyloLayoutResult,\n  t: ResolvedTheme<BiologyTokens>,\n  scaleLabel?: string\n): string {\n  if (layout.ast.mode === \"cladogram\") return \"\";\n\n  const plotWidth = layout.width - 40;\n  const bar = computeScaleBar(layout.scale, plotWidth);\n  if (bar.pxLength < 5) return \"\";\n\n  const x = 20;\n  const y = layout.height - 20;\n\n  const elements = [\n    line({ x1: x, y1: y, x2: x + bar.pxLength, y2: y, class: \"schematex-phylo-scale-bar\" }),\n    line({ x1: x, y1: y - 4, x2: x, y2: y + 4, class: \"schematex-phylo-scale-tick\" }),\n    line({ x1: x + bar.pxLength, y1: y - 4, x2: x + bar.pxLength, y2: y + 4, class: \"schematex-phylo-scale-tick\" }),\n    text({ x: x + bar.pxLength / 2, y: y + 16, \"text-anchor\": \"middle\", class: \"schematex-phylo-scale-bar\" }, bar.label),\n  ];\n\n  if (scaleLabel) {\n    elements.push(\n      text(\n        { x: x + bar.pxLength / 2, y: y + 28, \"text-anchor\": \"middle\", \"font-size\": \"9\", fill: t.textMuted },\n        scaleLabel\n      )\n    );\n  }\n\n  return group({ class: \"schematex-phylo-scale-bar\" }, elements);\n}\n\n// ─── Clade Backgrounds ──────────────────────────────────────\n\nfunction renderCladeBackgrounds(layout: PhyloLayoutResult, t: ResolvedTheme<BiologyTokens>): string[] {\n  const elements: string[] = [];\n\n  for (let ci = 0; ci < layout.ast.clades.length; ci++) {\n    const clade = layout.ast.clades[ci];\n    const hl = clade.highlight ?? \"branch\";\n    if (hl === \"branch\") continue;\n\n    const memberNodes = layout.nodes.filter(\n      (n) => n.node.isLeaf && clade.members.includes(n.node.id)\n    );\n    if (memberNodes.length === 0) continue;\n\n    const minY = Math.min(...memberNodes.map((n) => n.y)) - 10;\n    const maxY = Math.max(...memberNodes.map((n) => n.y)) + 10;\n    const minX = Math.min(...memberNodes.map((n) => n.x)) - 20;\n    const maxX = Math.max(...memberNodes.map((n) => {\n      const labelW = ((n.node.label ?? n.node.id).length * 7.2) + TIP_LABEL_GAP + 8;\n      return n.x + labelW;\n    }));\n\n    const color = clade.color ?? t.cladeColors[ci % t.cladeColors.length];\n\n    elements.push(\n      rect({\n        x: minX,\n        y: minY,\n        width: maxX - minX,\n        height: maxY - minY,\n        rx: 4,\n        class: `schematex-phylo-clade-bg schematex-phylo-clade-bg-${clade.id}`,\n        fill: color,\n        \"fill-opacity\": 0.12,\n      })\n    );\n\n    if (clade.label) {\n      elements.push(\n        text(\n          {\n            x: maxX + 4,\n            y: (minY + maxY) / 2,\n            class: `schematex-phylo-clade-label schematex-phylo-clade-label-${clade.id}`,\n            fill: color,\n            \"font-weight\": \"bold\",\n            \"font-size\": \"13\",\n            \"dominant-baseline\": \"central\",\n          },\n          clade.label\n        )\n      );\n    }\n  }\n\n  return elements;\n}\n\n// ─── Main Renderer ──────────────────────────────────────────\n\nexport function renderPhylo(layout: PhyloLayoutResult): string {\n  const { ast, nodes, branches } = layout;\n  const t = resolveBiologyTheme(ast.metadata?.theme ?? \"default\");\n\n  const css = buildCSS(ast, t);\n\n  const titleOffset = ast.title ? 30 : 0;\n  const totalHeight = layout.height + titleOffset;\n  const totalWidth = layout.width;\n\n  // Build layers\n  const branchElements: string[] = [];\n  const nodeElements: string[] = [];\n  const labelElements: string[] = [];\n\n  // Branches\n  for (const branch of branches) {\n    const cladeIdx = branch.cladeId\n      ? ast.clades.findIndex((c) => c.id === branch.cladeId)\n      : -1;\n    const cladeColor =\n      cladeIdx >= 0\n        ? ast.clades[cladeIdx].color ?? t.cladeColors[cladeIdx % t.cladeColors.length]\n        : undefined;\n\n    const cls = branch.isConnector\n      ? \"schematex-phylo-branch schematex-phylo-branch-connector\"\n      : `schematex-phylo-branch schematex-phylo-branch-internal${branch.cladeId ? ` schematex-phylo-clade-${branch.cladeId}` : \"\"}`;\n\n    const attrs: Record<string, string | number | undefined> = {\n      d: branch.path,\n      class: cls,\n    };\n    if (cladeColor && !branch.isConnector) {\n      attrs.stroke = cladeColor;\n    }\n\n    branchElements.push(path(attrs));\n  }\n\n  // Nodes (support dots + root marker + tip labels)\n  const rootLayout = nodes.find((n) => n.node === ast.root);\n\n  // Root marker\n  if (rootLayout && !ast.unrooted) {\n    nodeElements.push(\n      circle({\n        cx: rootLayout.x,\n        cy: rootLayout.y,\n        r: 5,\n        class: \"schematex-phylo-root-marker\",\n      })\n    );\n  }\n\n  for (const layoutNode of nodes) {\n    const { node, x, y } = layoutNode;\n\n    // Support dots / labels for internal nodes\n    if (!node.isLeaf && node.support !== undefined) {\n      const support = node.support > 1 ? node.support : node.support * 100;\n      if (support >= SUPPORT_THRESHOLD) {\n        const color = getSupportColor(support, t);\n        nodeElements.push(\n          circle({\n            cx: x,\n            cy: y,\n            r: 4,\n            class: \"schematex-phylo-support-dot\",\n            fill: color,\n          })\n        );\n        labelElements.push(\n          text(\n            { x, y: y - 8, class: \"schematex-phylo-support-label\" },\n            String(Math.round(support))\n          )\n        );\n      }\n    }\n\n    // Tip labels\n    if (node.isLeaf) {\n      const label = node.label ?? node.id;\n      const italic = isSpeciesBinomial(label);\n      const cls = `schematex-phylo-tip-label${italic ? \" schematex-phylo-tip-label-italic\" : \"\"}`;\n\n      labelElements.push(\n        text(\n          {\n            x: x + TIP_LABEL_GAP,\n            y,\n            class: cls,\n            \"font-style\": italic ? \"italic\" : undefined,\n            \"data-taxon-id\": node.id,\n          },\n          label\n        )\n      );\n    }\n  }\n\n  // Clade backgrounds\n  const cladeBgElements = renderCladeBackgrounds(layout, t);\n\n  // Scale bar\n  const scaleBarEl = renderScaleBar(layout, t, ast.scaleLabel);\n\n  // Title\n  const titleEl = ast.title\n    ? text(\n        { x: totalWidth / 2, y: 20, class: \"schematex-phylo-title\" },\n        ast.title\n      )\n    : \"\";\n\n  // Assemble\n  const leafCount = nodes.filter((n) => n.node.isLeaf).length;\n  const svgContent = [\n    title(`Phylogenetic Tree${ast.title ? `: ${ast.title}` : \"\"}`),\n    desc(`Phylogenetic tree with ${leafCount} taxa, ${ast.mode} mode, ${ast.layout} layout`),\n    el(\"style\", {}, css),\n  ];\n\n  if (titleEl) svgContent.push(titleEl);\n\n  const transformY = titleOffset;\n\n  if (cladeBgElements.length > 0) {\n    svgContent.push(\n      group(\n        { class: \"schematex-phylo-clade-highlights\", transform: transformY ? `translate(0,${transformY})` : undefined },\n        cladeBgElements\n      )\n    );\n  }\n\n  svgContent.push(\n    group(\n      { class: \"schematex-phylo-branches\", transform: transformY ? `translate(0,${transformY})` : undefined },\n      branchElements\n    )\n  );\n\n  svgContent.push(\n    group(\n      { class: \"schematex-phylo-nodes\", transform: transformY ? `translate(0,${transformY})` : undefined },\n      nodeElements\n    )\n  );\n\n  svgContent.push(\n    group(\n      { class: \"schematex-phylo-labels\", transform: transformY ? `translate(0,${transformY})` : undefined },\n      labelElements\n    )\n  );\n\n  if (scaleBarEl) {\n    svgContent.push(\n      group(\n        { transform: transformY ? `translate(0,${transformY})` : undefined },\n        [scaleBarEl]\n      )\n    );\n  }\n\n  return svgRoot(\n    {\n      class: \"schematex-diagram schematex-phylo\",\n      viewBox: `0 0 ${totalWidth} ${totalHeight}`,\n      width: totalWidth,\n      height: totalHeight,\n    },\n    svgContent\n  );\n}\n","import type { DiagramPlugin } from \"../../core/types\";\nimport { parsePhylo, PhyloParseError } from \"./parser\";\nimport { layoutPhylo } from \"./layout\";\nimport type { PhyloLayoutResult } from \"./layout\";\nimport { renderPhylo } from \"./renderer\";\n\nexport const phylo: DiagramPlugin = {\n  type: \"phylo\",\n\n  detect(text: string): boolean {\n    const firstLine = text.trim().split(\"\\n\")[0]?.trim().toLowerCase() ?? \"\";\n    return firstLine === \"phylo\" || firstLine.startsWith(\"phylo \");\n  },\n\n  parse: parsePhylo,\n\n  render(text: string): string {\n    const ast = parsePhylo(text);\n    const layout = layoutPhylo(ast);\n    return renderPhylo(layout);\n  },\n};\n\nexport { parsePhylo, PhyloParseError, layoutPhylo, renderPhylo };\nexport type { PhyloLayoutResult };\n"]}
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\"unrooted\"].includes(val)) {\n          result.layout = val as PhyloLayout;\n        }\n        break;\n      case \"mode\":\n        if ([\"phylogram\", \"cladogram\", \"chronogram\"].includes(val)) {\n          result.mode = val as PhyloMode;\n        }\n        break;\n      case \"branch-width\":\n        result.branchWidth = Number(val);\n        break;\n      case \"openAngle\":\n        result.openAngle = Number(val);\n        break;\n      case \"mrsd\":\n        result.mrsd = val;\n        break;\n    }\n  }\n\n  if (result.layout === \"unrooted\") {\n    result.unrooted = true;\n  }\n\n  return result;\n}\n\nfunction parseCladeLine(line: string): CladeDef | null {\n  // clade ID = (member1, member2, ...) [color: \"#hex\", label: \"text\", highlight: mode]\n  const match = line.match(\n    /^clade\\s+(\\S+)\\s*=\\s*\\(([^)]+)\\)\\s*(?:\\[([^\\]]*)\\])?\\s*$/\n  );\n  if (!match) return null;\n\n  const id = match[1];\n  const members = match[2].split(\",\").map((s) => s.trim()).filter(Boolean);\n  const propsStr = match[3] ?? \"\";\n\n  let color: string | undefined;\n  let label: string | undefined;\n  let highlight: CladeHighlightMode | undefined;\n\n  if (propsStr) {\n    const colorMatch = propsStr.match(/color:\\s*\"([^\"]+)\"/);\n    if (colorMatch) color = colorMatch[1];\n    const labelMatch = propsStr.match(/label:\\s*\"([^\"]+)\"/);\n    if (labelMatch) label = labelMatch[1];\n    const hlMatch = propsStr.match(/highlight:\\s*(\\w+)/);\n    if (hlMatch && [\"branch\", \"background\", \"both\"].includes(hlMatch[1])) {\n      highlight = hlMatch[1] as CladeHighlightMode;\n    }\n  }\n\n  return { id, members, color, label, highlight };\n}\n\nexport function parsePhylo(text: string): PhyloTreeAST {\n  const lines = text.split(\"\\n\");\n  let lineIdx = 0;\n\n  // Skip empty lines\n  while (lineIdx < lines.length && !lines[lineIdx].trim()) lineIdx++;\n\n  // Parse header: phylo \"title\" [props]\n  const headerLine = lines[lineIdx]?.trim() ?? \"\";\n  if (!headerLine.toLowerCase().startsWith(\"phylo\")) {\n    throw new PhyloParseError(\"Phylo document must start with 'phylo'\");\n  }\n  lineIdx++;\n\n  const title: string | undefined = matchQuotedTitle(headerLine);\n\n  let headerProps: ReturnType<typeof parseHeaderProps> = {\n    layout: \"rectangular\",\n    mode: \"phylogram\",\n    unrooted: false,\n  };\n  const propsMatch = headerLine.match(/\\[([^\\]]+)\\]/);\n  if (propsMatch) {\n    headerProps = parseHeaderProps(propsMatch[1]);\n  }\n\n  // Parse body: newick, indent tree, scale, outgroup, clade definitions\n  let root: PhyloNode | null = null;\n  let scaleLabel: string | undefined;\n  let outgroup: string | undefined;\n  const clades: CladeDef[] = [];\n  const indentLines: string[] = [];\n  let inIndentTree = false;\n\n  while (lineIdx < lines.length) {\n    const raw = lines[lineIdx];\n    const trimmed = raw.trim();\n    lineIdx++;\n\n    if (!trimmed || trimmed.startsWith(\"#\")) continue;\n\n    // Newick definition\n    if (trimmed.startsWith(\"newick:\")) {\n      const newickStr = trimmed.slice(7).trim().replace(/^[\"']|[\"']$/g, \"\");\n      root = parseNewick(newickStr);\n      inIndentTree = false;\n      continue;\n    }\n\n    // Scale definition\n    if (trimmed.startsWith(\"scale\")) {\n      const scaleMatch = trimmed.match(/scale\\s+\"([^\"]+)\"/);\n      if (scaleMatch) {\n        scaleLabel = scaleMatch[1];\n      } else {\n        scaleLabel = trimmed.slice(5).trim().replace(/^[\"']|[\"']$/g, \"\") || \"substitutions/site\";\n      }\n      continue;\n    }\n\n    // Outgroup\n    if (trimmed.startsWith(\"outgroup:\")) {\n      outgroup = trimmed.slice(9).trim();\n      continue;\n    }\n\n    // Clade definition\n    if (trimmed.startsWith(\"clade \")) {\n      const clade = parseCladeLine(trimmed);\n      if (clade) clades.push(clade);\n      continue;\n    }\n\n    // Style line (alternative props)\n    if (trimmed.startsWith(\"style\")) {\n      const styleProps = trimmed.match(/\\[([^\\]]+)\\]/);\n      if (styleProps) {\n        headerProps = { ...headerProps, ...parseHeaderProps(styleProps[1]) };\n      }\n      continue;\n    }\n\n    // Indent tree definition\n    if (trimmed.endsWith(\":\") && (trimmed === \"root:\" || !trimmed.includes(\" \"))) {\n      inIndentTree = true;\n      indentLines.push(raw);\n      continue;\n    }\n\n    if (inIndentTree) {\n      indentLines.push(raw);\n      continue;\n    }\n  }\n\n  // Parse indent tree if present and no Newick was found\n  if (!root && indentLines.length > 0) {\n    root = parseIndentTree(indentLines);\n  }\n\n  if (!root) {\n    throw new PhyloParseError(\"No tree definition found (newick: or indent tree)\");\n  }\n\n  return {\n    type: \"phylo\",\n    title,\n    root,\n    unrooted: headerProps.unrooted,\n    layout: headerProps.layout,\n    mode: headerProps.mode,\n    clades,\n    scaleLabel,\n    mrsd: headerProps.mrsd,\n    outgroup,\n    metadata: {},\n  };\n}\n","import type {\n  PhyloTreeAST,\n  PhyloNode,\n  PhyloLayoutNode,\n} from \"../../core/types\";\n\nexport interface PhyloLayoutResult {\n  width: number;\n  height: number;\n  nodes: PhyloLayoutNode[];\n  /** Branch paths: { path, cladeId?, isConnector } */\n  branches: PhyloBranch[];\n  ast: PhyloTreeAST;\n  scale: number;\n}\n\nexport interface PhyloBranch {\n  path: string;\n  fromId: string;\n  toId: string;\n  /** Clade id if this branch belongs to a highlighted clade */\n  cladeId?: string;\n  /** Is this a vertical/arc connector (no length meaning) vs horizontal branch */\n  isConnector: boolean;\n}\n\n// ─── Tree Utilities ─────────────────────────────────────────\n\nfunction collectLeaves(node: PhyloNode): PhyloNode[] {\n  if (node.isLeaf) return [node];\n  const leaves: PhyloNode[] = [];\n  for (const child of node.children) {\n    leaves.push(...collectLeaves(child));\n  }\n  return leaves;\n}\n\nfunction maxRootToTip(node: PhyloNode, distSoFar: number): number {\n  if (node.isLeaf) return distSoFar;\n  let maxDist = distSoFar;\n  for (const child of node.children) {\n    const childDist = maxRootToTip(child, distSoFar + (child.branchLength ?? 0));\n    if (childDist > maxDist) maxDist = childDist;\n  }\n  return maxDist;\n}\n\nfunction maxDepth(node: PhyloNode): number {\n  if (node.isLeaf) return 0;\n  let max = 0;\n  for (const child of node.children) {\n    const d = maxDepth(child) + 1;\n    if (d > max) max = d;\n  }\n  return max;\n}\n\nfunction estimateLabelWidth(node: PhyloNode): number {\n  const label = node.label ?? node.id;\n  return label.length * 7.2 + 6;\n}\n\n// ─── Clade Membership ───────────────────────────────────────\n\nfunction buildCladeMap(\n  ast: PhyloTreeAST\n): Map<string, string> {\n  const branchToCladeMap = new Map<string, string>();\n\n  for (const clade of ast.clades) {\n    const memberSet = new Set(clade.members);\n    markCladeBranches(ast.root, memberSet, clade.id, branchToCladeMap);\n  }\n\n  return branchToCladeMap;\n}\n\nfunction markCladeBranches(\n  node: PhyloNode,\n  memberSet: Set<string>,\n  cladeId: string,\n  result: Map<string, string>\n): boolean {\n  if (node.isLeaf) {\n    return memberSet.has(node.id);\n  }\n\n  const childResults: boolean[] = [];\n  for (const child of node.children) {\n    childResults.push(markCladeBranches(child, memberSet, cladeId, result));\n  }\n\n  const allIn = childResults.every(Boolean);\n  const anyIn = childResults.some(Boolean);\n\n  if (allIn && anyIn) {\n    for (const child of node.children) {\n      result.set(child.id, cladeId);\n    }\n    return true;\n  }\n\n  // Partial — mark only children that are fully within\n  for (let i = 0; i < node.children.length; i++) {\n    if (childResults[i]) {\n      result.set(node.children[i].id, cladeId);\n    }\n  }\n\n  return false;\n}\n\n// ─── Rectangular Phylogram Layout ───────────────────────────\n\nconst TIP_SPACING = 20;\nconst PADDING_LEFT = 20;\nconst PADDING_RIGHT = 20;\nconst PADDING_TOP = 20;\nconst PADDING_BOTTOM = 40;\n\nexport function layoutPhylo(ast: PhyloTreeAST): PhyloLayoutResult {\n  const leaves = collectLeaves(ast.root);\n  const numLeaves = leaves.length;\n  const tipSpacing = TIP_SPACING;\n\n  // Compute scale\n  const maxLabelWidth = Math.max(...leaves.map(estimateLabelWidth), 60);\n  const maxDist = maxRootToTip(ast.root, 0);\n  const isCladogram = ast.mode === \"cladogram\";\n\n  const availableWidth = Math.max(300, numLeaves * 30 + maxLabelWidth + 100);\n  const plotWidth = availableWidth - PADDING_LEFT - PADDING_RIGHT - maxLabelWidth;\n\n  let scale: number;\n  if (isCladogram || maxDist === 0) {\n    const depth = maxDepth(ast.root);\n    scale = depth > 0 ? plotWidth / depth : plotWidth;\n  } else {\n    scale = plotWidth / maxDist;\n  }\n\n  // Step 1: assign Y to leaves (in-order)\n  const nodeMap = new Map<string, PhyloLayoutNode>();\n  let leafIdx = 0;\n\n  function assignLeafY(node: PhyloNode): void {\n    if (node.isLeaf) {\n      const y = PADDING_TOP + leafIdx * tipSpacing;\n      nodeMap.set(node.id, { node, x: 0, y });\n      leafIdx++;\n      return;\n    }\n    for (const child of node.children) {\n      assignLeafY(child);\n    }\n  }\n  assignLeafY(ast.root);\n\n  // Step 2: assign Y to internal nodes (mean of children)\n  function assignInternalY(node: PhyloNode): number {\n    const existing = nodeMap.get(node.id);\n    if (node.isLeaf && existing) return existing.y;\n    const childYs = node.children.map(assignInternalY);\n    const y = (Math.min(...childYs) + Math.max(...childYs)) / 2;\n    if (!existing) {\n      nodeMap.set(node.id, { node, x: 0, y });\n    } else {\n      existing.y = y;\n    }\n    return y;\n  }\n  assignInternalY(ast.root);\n\n  // Step 3: assign X (distance from root)\n  function assignX(node: PhyloNode, parentX: number, depth: number): void {\n    let x: number;\n    if (node === ast.root) {\n      x = PADDING_LEFT;\n    } else if (isCladogram) {\n      if (node.isLeaf) {\n        x = PADDING_LEFT + plotWidth;\n      } else {\n        x = PADDING_LEFT + depth * (plotWidth / maxDepth(ast.root));\n      }\n    } else {\n      x = parentX + (node.branchLength ?? 0) * scale;\n    }\n\n    const layoutNode = nodeMap.get(node.id);\n    if (layoutNode) layoutNode.x = x;\n\n    for (const child of node.children) {\n      assignX(child, x, depth + 1);\n    }\n  }\n  assignX(ast.root, PADDING_LEFT, 0);\n\n  // For cladogram: recalculate internal node X as parent of children\n  if (isCladogram) {\n    assignCladogramInternalX(ast.root, nodeMap);\n  }\n\n  // Build clade membership map\n  const cladeMap = buildCladeMap(ast);\n\n  // Step 4: generate branch paths\n  const branches: PhyloBranch[] = [];\n\n  function generateBranches(node: PhyloNode): void {\n    const parentLayout = nodeMap.get(node.id);\n    if (!parentLayout) return;\n\n    if (node.children.length === 0) return;\n\n    const childLayouts = node.children\n      .map((c) => nodeMap.get(c.id))\n      .filter((l): l is PhyloLayoutNode => l !== undefined);\n\n    if (childLayouts.length === 0) return;\n\n    // Vertical connector from min child Y to max child Y at parent X\n    const minY = Math.min(...childLayouts.map((c) => c.y));\n    const maxY = Math.max(...childLayouts.map((c) => c.y));\n\n    if (ast.layout === \"slanted\") {\n      // Slanted: diagonal lines from parent to each child\n      for (const child of node.children) {\n        const childLayout = nodeMap.get(child.id);\n        if (!childLayout) continue;\n        const pathStr = `M ${parentLayout.x},${parentLayout.y} L ${childLayout.x},${childLayout.y}`;\n        branches.push({\n          path: pathStr,\n          fromId: node.id,\n          toId: child.id,\n          cladeId: cladeMap.get(child.id),\n          isConnector: false,\n        });\n      }\n    } else {\n      // Rectangular: vertical connector + horizontal branches\n      branches.push({\n        path: `M ${parentLayout.x},${minY} V ${maxY}`,\n        fromId: node.id,\n        toId: node.id,\n        isConnector: true,\n      });\n\n      for (const child of node.children) {\n        const childLayout = nodeMap.get(child.id);\n        if (!childLayout) continue;\n        const pathStr = `M ${parentLayout.x},${childLayout.y} H ${childLayout.x}`;\n        branches.push({\n          path: pathStr,\n          fromId: node.id,\n          toId: child.id,\n          cladeId: cladeMap.get(child.id),\n          isConnector: false,\n        });\n      }\n    }\n\n    for (const child of node.children) {\n      generateBranches(child);\n    }\n  }\n\n  generateBranches(ast.root);\n\n  // Compute final dimensions\n  const allNodes = Array.from(nodeMap.values());\n  let maxX = Math.max(...allNodes.map((n) => n.x + (n.node.isLeaf ? estimateLabelWidth(n.node) : 0)));\n\n  // Add space for clade labels (background/both mode places labels to the right)\n  let maxCladeLabelWidth = 0;\n  for (const clade of ast.clades) {\n    if (clade.label && clade.highlight && clade.highlight !== \"branch\") {\n      const w = clade.label.length * 8 + 30;\n      if (w > maxCladeLabelWidth) maxCladeLabelWidth = w;\n    }\n  }\n  maxX += maxCladeLabelWidth;\n\n  const maxNodeY = Math.max(...allNodes.map((n) => n.y));\n\n  const width = Math.max(maxX + PADDING_RIGHT, availableWidth);\n  const height = maxNodeY + PADDING_TOP + PADDING_BOTTOM;\n\n  return {\n    width,\n    height,\n    nodes: allNodes,\n    branches,\n    ast,\n    scale,\n  };\n}\n\nfunction assignCladogramInternalX(\n  node: PhyloNode,\n  nodeMap: Map<string, PhyloLayoutNode>\n): number {\n  if (node.isLeaf) {\n    return nodeMap.get(node.id)?.x ?? 0;\n  }\n\n  let minChildX = Infinity;\n  for (const child of node.children) {\n    const childX = assignCladogramInternalX(child, nodeMap);\n    if (childX < minChildX) minChildX = childX;\n  }\n\n  const layout = nodeMap.get(node.id);\n  if (layout) {\n    layout.x = minChildX - 40;\n    if (layout.x < PADDING_LEFT) layout.x = PADDING_LEFT;\n  }\n\n  return layout?.x ?? PADDING_LEFT;\n}\n","import type { PhyloTreeAST } from \"../../core/types\";\nimport type { PhyloLayoutResult } from \"./layout\";\nimport {\n  svgRoot,\n  group,\n  path,\n  line,\n  circle,\n  text,\n  title,\n  desc,\n  rect,\n  el,\n} from \"../../core/svg\";\nimport { cssCustomProperties, resolveBiologyTheme, FONT_SIZE, STROKE_WIDTH, type ResolvedTheme, type BiologyTokens } from \"../../core/theme\";\n\n// ─── Constants ──────────────────────────────────────────────\n\nconst TIP_LABEL_GAP = 6;\nconst SUPPORT_THRESHOLD = 50;\n\nfunction getSupportColor(value: number, t: ResolvedTheme<BiologyTokens>): string {\n  if (value >= 95) return t.supportGood;\n  if (value >= 75) return t.supportMedium;\n  if (value >= 50) return t.supportWarn;\n  return t.supportBad;\n}\n\nfunction isSpeciesBinomial(label: string): boolean {\n  const parts = label.trim().split(/\\s+/);\n  if (parts.length !== 2) return false;\n  return /^[A-Z][a-z]+$/.test(parts[0]) && /^[a-z]+$/.test(parts[1]);\n}\n\n// ─── CSS ────────────────────────────────────────────────────\n\nfunction buildCSS(ast: PhyloTreeAST, t: ResolvedTheme<BiologyTokens>): string {\n  const cladeColors = ast.clades.map((c, i) => {\n    const color = c.color ?? t.cladeColors[i % t.cladeColors.length];\n    return `.schematex-phylo-clade-${c.id} { stroke: ${color}; }\n.schematex-phylo-clade-bg-${c.id} { fill: ${color}; fill-opacity: 0.12; }\n.schematex-phylo-clade-label-${c.id} { fill: ${color}; }`;\n  });\n\n  return `\n.schematex-phylo {${cssCustomProperties(t)}\n  font-family: system-ui, -apple-system, sans-serif;\n}\n.schematex-phylo-branch { fill: none; stroke: ${t.text}; stroke-width: ${STROKE_WIDTH.normal}; stroke-linecap: round; }\n.schematex-phylo-branch-connector { fill: none; stroke: ${t.text}; stroke-width: ${STROKE_WIDTH.normal}; }\n.schematex-phylo-tip-label { font-size: ${FONT_SIZE.label}px; fill: ${t.text}; dominant-baseline: central; }\n.schematex-phylo-tip-label-italic { font-style: italic; }\n.schematex-phylo-support-label { font-size: ${FONT_SIZE.small}px; fill: ${t.textMuted}; text-anchor: middle; dominant-baseline: auto; }\n.schematex-phylo-support-dot { stroke: none; }\n.schematex-phylo-scale-bar line { stroke: ${t.text}; stroke-width: ${STROKE_WIDTH.normal}; }\n.schematex-phylo-scale-bar text { font-size: 10px; fill: ${t.text}; text-anchor: middle; }\n.schematex-phylo-scale-tick { stroke: ${t.text}; stroke-width: ${STROKE_WIDTH.thin}; }\n.schematex-phylo-title { font-size: ${FONT_SIZE.title}px; font-weight: bold; fill: ${t.text}; text-anchor: middle; }\n.schematex-phylo-clade-label { font-size: 13px; font-weight: bold; }\n.schematex-phylo-root-marker { fill: none; stroke: ${t.text}; stroke-width: ${STROKE_WIDTH.normal}; }\n${cladeColors.join(\"\\n\")}\n`.trim();\n}\n\n// ─── Scale Bar ──────────────────────────────────────────────\n\nfunction computeScaleBar(\n  scale: number,\n  plotWidth: number\n): { length: number; label: string; pxLength: number } {\n  if (scale <= 0) return { length: 0.1, label: \"0.1\", pxLength: 50 };\n\n  const targetPx = plotWidth * 0.2;\n\n  const magnitudes = [0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1, 2, 5, 10, 20, 50, 100];\n  let best = magnitudes[0];\n  let bestDiff = Infinity;\n\n  for (const m of magnitudes) {\n    const diff = Math.abs(m * scale - targetPx);\n    if (diff < bestDiff) {\n      bestDiff = diff;\n      best = m;\n    }\n  }\n\n  return {\n    length: best,\n    label: best < 0.01 ? best.toExponential() : String(best),\n    pxLength: best * scale,\n  };\n}\n\nfunction renderScaleBar(\n  layout: PhyloLayoutResult,\n  t: ResolvedTheme<BiologyTokens>,\n  scaleLabel?: string\n): string {\n  if (layout.ast.mode === \"cladogram\") return \"\";\n\n  const plotWidth = layout.width - 40;\n  const bar = computeScaleBar(layout.scale, plotWidth);\n  if (bar.pxLength < 5) return \"\";\n\n  const x = 20;\n  const y = layout.height - 20;\n\n  const elements = [\n    line({ x1: x, y1: y, x2: x + bar.pxLength, y2: y, class: \"schematex-phylo-scale-bar\" }),\n    line({ x1: x, y1: y - 4, x2: x, y2: y + 4, class: \"schematex-phylo-scale-tick\" }),\n    line({ x1: x + bar.pxLength, y1: y - 4, x2: x + bar.pxLength, y2: y + 4, class: \"schematex-phylo-scale-tick\" }),\n    text({ x: x + bar.pxLength / 2, y: y + 16, \"text-anchor\": \"middle\", class: \"schematex-phylo-scale-bar\" }, bar.label),\n  ];\n\n  if (scaleLabel) {\n    elements.push(\n      text(\n        { x: x + bar.pxLength / 2, y: y + 28, \"text-anchor\": \"middle\", \"font-size\": \"9\", fill: t.textMuted },\n        scaleLabel\n      )\n    );\n  }\n\n  return group({ class: \"schematex-phylo-scale-bar\" }, elements);\n}\n\n// ─── Clade Backgrounds ──────────────────────────────────────\n\nfunction renderCladeBackgrounds(layout: PhyloLayoutResult, t: ResolvedTheme<BiologyTokens>): string[] {\n  const elements: string[] = [];\n\n  for (let ci = 0; ci < layout.ast.clades.length; ci++) {\n    const clade = layout.ast.clades[ci];\n    const hl = clade.highlight ?? \"branch\";\n    if (hl === \"branch\") continue;\n\n    const memberNodes = layout.nodes.filter(\n      (n) => n.node.isLeaf && clade.members.includes(n.node.id)\n    );\n    if (memberNodes.length === 0) continue;\n\n    const minY = Math.min(...memberNodes.map((n) => n.y)) - 10;\n    const maxY = Math.max(...memberNodes.map((n) => n.y)) + 10;\n    const minX = Math.min(...memberNodes.map((n) => n.x)) - 20;\n    const maxX = Math.max(...memberNodes.map((n) => {\n      const labelW = ((n.node.label ?? n.node.id).length * 7.2) + TIP_LABEL_GAP + 8;\n      return n.x + labelW;\n    }));\n\n    const color = clade.color ?? t.cladeColors[ci % t.cladeColors.length];\n\n    elements.push(\n      rect({\n        x: minX,\n        y: minY,\n        width: maxX - minX,\n        height: maxY - minY,\n        rx: 4,\n        class: `schematex-phylo-clade-bg schematex-phylo-clade-bg-${clade.id}`,\n        fill: color,\n        \"fill-opacity\": 0.12,\n      })\n    );\n\n    if (clade.label) {\n      elements.push(\n        text(\n          {\n            x: maxX + 4,\n            y: (minY + maxY) / 2,\n            class: `schematex-phylo-clade-label schematex-phylo-clade-label-${clade.id}`,\n            fill: color,\n            \"font-weight\": \"bold\",\n            \"font-size\": \"13\",\n            \"dominant-baseline\": \"central\",\n          },\n          clade.label\n        )\n      );\n    }\n  }\n\n  return elements;\n}\n\n// ─── Main Renderer ──────────────────────────────────────────\n\nexport function renderPhylo(layout: PhyloLayoutResult): string {\n  const { ast, nodes, branches } = layout;\n  const t = resolveBiologyTheme(ast.metadata?.theme ?? \"default\");\n\n  const css = buildCSS(ast, t);\n\n  const titleOffset = ast.title ? 30 : 0;\n  const totalHeight = layout.height + titleOffset;\n  const totalWidth = layout.width;\n\n  // Build layers\n  const branchElements: string[] = [];\n  const nodeElements: string[] = [];\n  const labelElements: string[] = [];\n\n  // Branches\n  for (const branch of branches) {\n    const cladeIdx = branch.cladeId\n      ? ast.clades.findIndex((c) => c.id === branch.cladeId)\n      : -1;\n    const cladeColor =\n      cladeIdx >= 0\n        ? ast.clades[cladeIdx].color ?? t.cladeColors[cladeIdx % t.cladeColors.length]\n        : undefined;\n\n    const cls = branch.isConnector\n      ? \"schematex-phylo-branch schematex-phylo-branch-connector\"\n      : `schematex-phylo-branch schematex-phylo-branch-internal${branch.cladeId ? ` schematex-phylo-clade-${branch.cladeId}` : \"\"}`;\n\n    const attrs: Record<string, string | number | undefined> = {\n      d: branch.path,\n      class: cls,\n    };\n    if (cladeColor && !branch.isConnector) {\n      attrs.stroke = cladeColor;\n    }\n\n    branchElements.push(path(attrs));\n  }\n\n  // Nodes (support dots + root marker + tip labels)\n  const rootLayout = nodes.find((n) => n.node === ast.root);\n\n  // Root marker\n  if (rootLayout && !ast.unrooted) {\n    nodeElements.push(\n      circle({\n        cx: rootLayout.x,\n        cy: rootLayout.y,\n        r: 5,\n        class: \"schematex-phylo-root-marker\",\n      })\n    );\n  }\n\n  for (const layoutNode of nodes) {\n    const { node, x, y } = layoutNode;\n\n    // Support dots / labels for internal nodes\n    if (!node.isLeaf && node.support !== undefined) {\n      const support = node.support > 1 ? node.support : node.support * 100;\n      if (support >= SUPPORT_THRESHOLD) {\n        const color = getSupportColor(support, t);\n        nodeElements.push(\n          circle({\n            cx: x,\n            cy: y,\n            r: 4,\n            class: \"schematex-phylo-support-dot\",\n            fill: color,\n          })\n        );\n        labelElements.push(\n          text(\n            { x, y: y - 8, class: \"schematex-phylo-support-label\" },\n            String(Math.round(support))\n          )\n        );\n      }\n    }\n\n    // Tip labels\n    if (node.isLeaf) {\n      const label = node.label ?? node.id;\n      const italic = isSpeciesBinomial(label);\n      const cls = `schematex-phylo-tip-label${italic ? \" schematex-phylo-tip-label-italic\" : \"\"}`;\n\n      labelElements.push(\n        text(\n          {\n            x: x + TIP_LABEL_GAP,\n            y,\n            class: cls,\n            \"font-style\": italic ? \"italic\" : undefined,\n            \"data-taxon-id\": node.id,\n          },\n          label\n        )\n      );\n    }\n  }\n\n  // Clade backgrounds\n  const cladeBgElements = renderCladeBackgrounds(layout, t);\n\n  // Scale bar\n  const scaleBarEl = renderScaleBar(layout, t, ast.scaleLabel);\n\n  // Title\n  const titleEl = ast.title\n    ? text(\n        { x: totalWidth / 2, y: 20, class: \"schematex-phylo-title\" },\n        ast.title\n      )\n    : \"\";\n\n  // Assemble\n  const leafCount = nodes.filter((n) => n.node.isLeaf).length;\n  const svgContent = [\n    title(`Phylogenetic Tree${ast.title ? `: ${ast.title}` : \"\"}`),\n    desc(`Phylogenetic tree with ${leafCount} taxa, ${ast.mode} mode, ${ast.layout} layout`),\n    el(\"style\", {}, css),\n  ];\n\n  if (titleEl) svgContent.push(titleEl);\n\n  const transformY = titleOffset;\n\n  if (cladeBgElements.length > 0) {\n    svgContent.push(\n      group(\n        { class: \"schematex-phylo-clade-highlights\", transform: transformY ? `translate(0,${transformY})` : undefined },\n        cladeBgElements\n      )\n    );\n  }\n\n  svgContent.push(\n    group(\n      { class: \"schematex-phylo-branches\", transform: transformY ? `translate(0,${transformY})` : undefined },\n      branchElements\n    )\n  );\n\n  svgContent.push(\n    group(\n      { class: \"schematex-phylo-nodes\", transform: transformY ? `translate(0,${transformY})` : undefined },\n      nodeElements\n    )\n  );\n\n  svgContent.push(\n    group(\n      { class: \"schematex-phylo-labels\", transform: transformY ? `translate(0,${transformY})` : undefined },\n      labelElements\n    )\n  );\n\n  if (scaleBarEl) {\n    svgContent.push(\n      group(\n        { transform: transformY ? `translate(0,${transformY})` : undefined },\n        [scaleBarEl]\n      )\n    );\n  }\n\n  return svgRoot(\n    {\n      class: \"schematex-diagram schematex-phylo\",\n      viewBox: `0 0 ${totalWidth} ${totalHeight}`,\n      width: totalWidth,\n      height: totalHeight,\n    },\n    svgContent\n  );\n}\n","import type { DiagramPlugin } from \"../../core/types\";\nimport { parsePhylo, PhyloParseError } from \"./parser\";\nimport { layoutPhylo } from \"./layout\";\nimport type { PhyloLayoutResult } from \"./layout\";\nimport { renderPhylo } from \"./renderer\";\n\nexport const phylo: DiagramPlugin = {\n  type: \"phylo\",\n\n  detect(text: string): boolean {\n    const firstLine = text.trim().split(\"\\n\")[0]?.trim().toLowerCase() ?? \"\";\n    return firstLine === \"phylo\" || firstLine.startsWith(\"phylo \");\n  },\n\n  parse: parsePhylo,\n\n  render(text: string): string {\n    const ast = parsePhylo(text);\n    const layout = layoutPhylo(ast);\n    return renderPhylo(layout);\n  },\n};\n\nexport { parsePhylo, PhyloParseError, layoutPhylo, renderPhylo };\nexport type { PhyloLayoutResult };\n"]}