schematex 0.3.4 → 0.4.1

package/dist/chunk-UUBNQV2T.cjs.map

@@ -0,0 +1 @@
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{ parseLegendDirective } from \"../../core/legend-parser\";\nimport { matchQuotedTitle } from \"../../core/quotes\";\n\nexport class SociogramParseError extends Error {\n  constructor(message: string) {\n    super(message);\n    this.name = \"SociogramParseError\";\n  }\n}\n\n// ─── AST Types ──────────────────────────────────────────────\n\nexport type SociogramLayout = \"circular\" | \"force-directed\" | \"concentric\";\nexport type EdgeValence = \"positive\" | \"negative\" | \"neutral\";\nexport type EdgeDirection = \"one-way\" | \"mutual\" | \"undirected\";\nexport type NodeRole = \"star\" | \"isolate\" | \"bridge\" | \"neglectee\" | \"rejected\";\nexport type SizingMode = \"uniform\" | \"in-degree\" | \"betweenness\";\nexport type ColoringMode = \"default\" | \"group\" | \"role\";\n\nexport interface SociogramNode {\n  id: string;\n  label?: string;\n  group?: string;\n  role?: NodeRole;\n  size?: \"small\" | \"medium\" | \"large\";\n  properties?: Record<string, string>;\n}\n\nexport interface SociogramEdge {\n  from: string;\n  to: string;\n  direction: EdgeDirection;\n  valence: EdgeValence;\n  weight: number;\n  label?: string;\n}\n\nexport interface SociogramGroup {\n  id: string;\n  label?: string;\n  color?: string;\n  members: string[];\n}\n\nexport interface SociogramConfig {\n  layout: SociogramLayout;\n  sizing: SizingMode;\n  coloring: ColoringMode;\n  highlight: string[];\n}\n\nexport interface SociogramAST {\n  type: \"sociogram\";\n  title?: string;\n  config: SociogramConfig;\n  nodes: SociogramNode[];\n  edges: SociogramEdge[];\n  groups: SociogramGroup[];\n  legendOverrides?: import(\"../../core/types\").LegendOverrides;\n}\n\n// ─── Edge Operator Parsing ──────────────────────────────────\n\ninterface EdgeOp {\n  direction: EdgeDirection;\n  valence: EdgeValence;\n  weight: number;\n}\n\nconst EDGE_OPS: [string, EdgeOp][] = [\n  [\"<===>\", { direction: \"mutual\", valence: \"positive\", weight: 4 }],\n  [\"===>\" , { direction: \"one-way\", valence: \"positive\", weight: 4 }],\n  [\"<===\", { direction: \"one-way\", valence: \"positive\", weight: 4 }],\n  [\"<==>\", { direction: \"mutual\", valence: \"positive\", weight: 3 }],\n  [\"==>\" , { direction: \"one-way\", valence: \"positive\", weight: 3 }],\n  [\"<==\", { direction: \"one-way\", valence: \"positive\", weight: 3 }],\n  [\"===\", { direction: \"undirected\", valence: \"positive\", weight: 3 }],\n  [\"<x->\", { direction: \"mutual\", valence: \"negative\", weight: 2 }],\n  [\"-x>\", { direction: \"one-way\", valence: \"negative\", weight: 2 }],\n  [\"<x-\", { direction: \"one-way\", valence: \"negative\", weight: 2 }],\n  [\"-x-\", { direction: \"undirected\", valence: \"negative\", weight: 2 }],\n  [\"<.->\", { direction: \"mutual\", valence: \"neutral\", weight: 2 }],\n  [\".->\",  { direction: \"one-way\", valence: \"neutral\", weight: 2 }], // part of -.>\n  [\"-.-\", { direction: \"undirected\", valence: \"neutral\", weight: 2 }],\n  [\"<->\", { direction: \"mutual\", valence: \"positive\", weight: 2 }],\n  [\"->\",  { direction: \"one-way\", valence: \"positive\", weight: 2 }],\n  [\"<-\",  { direction: \"one-way\", valence: \"positive\", weight: 2 }],\n  [\"--\",  { direction: \"undirected\", valence: \"positive\", weight: 2 }],\n];\n\nfunction findEdgeOp(line: string): { leftId: string; rightId: string; op: EdgeOp; rest: string } | null {\n  for (const [opStr, op] of EDGE_OPS) {\n    const idx = line.indexOf(` ${opStr} `);\n    if (idx === -1) continue;\n\n    const leftId = line.slice(0, idx).trim();\n    const afterOp = line.slice(idx + opStr.length + 2).trim();\n\n    if (!leftId || !/^[a-zA-Z][a-zA-Z0-9_-]*$/.test(leftId)) continue;\n\n    // Right side: ID [props]\n    const rightMatch = afterOp.match(/^([a-zA-Z][a-zA-Z0-9_-]*)(.*)/);\n    if (!rightMatch) continue;\n\n    const rightId = rightMatch[1];\n    const rest = rightMatch[2].trim();\n\n    // Handle reverse direction\n    if (opStr === \"<-\" || opStr === \"<==\" || opStr === \"<===\" || opStr === \"<x-\") {\n      return { leftId: rightId, rightId: leftId, op: { ...op, direction: \"one-way\" }, rest };\n    }\n\n    return { leftId, rightId, op, rest };\n  }\n\n  // Try -.> which has the dot embedded\n  const dashDotMatch = line.match(/^([a-zA-Z][a-zA-Z0-9_-]*)\\s+-\\.>\\s+([a-zA-Z][a-zA-Z0-9_-]*)(.*)/);\n  if (dashDotMatch) {\n    return {\n      leftId: dashDotMatch[1],\n      rightId: dashDotMatch[2],\n      op: { direction: \"one-way\", valence: \"neutral\", weight: 2 },\n      rest: dashDotMatch[3].trim(),\n    };\n  }\n\n  return null;\n}\n\n// ─── Property Parsing ───────────────────────────────────────\n\nfunction parseProperties(propsStr: string): Record<string, string> {\n  const result: Record<string, string> = {};\n  // Match key: \"value\" or key: value pairs\n  const regex = /(\\w[\\w-]*):\\s*(?:\"([^\"]*)\"|([^\\s,\\]]+))/g;\n  let match;\n  while ((match = regex.exec(propsStr)) !== null) {\n    result[match[1]] = match[2] ?? match[3];\n  }\n  return result;\n}\n\nfunction extractProps(line: string): { clean: string; props: Record<string, string> } {\n  const bracketMatch = line.match(/\\[([^\\]]*)\\]/);\n  if (!bracketMatch) return { clean: line, props: {} };\n  const clean = line.slice(0, bracketMatch.index).trim();\n  const props = parseProperties(bracketMatch[1]);\n  return { clean, props };\n}\n\n// ─── Main Parser ────────────────────────────────────────────\n\nexport function parseSociogram(text: string): SociogramAST {\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\n  const headerLine = lines[lineIdx]?.trim() ?? \"\";\n  if (!headerLine.toLowerCase().startsWith(\"sociogram\")) {\n    throw new SociogramParseError(\"Sociogram must start with 'sociogram'\");\n  }\n  lineIdx++;\n\n  const titleStr: string | undefined = matchQuotedTitle(headerLine);\n\n  const config: SociogramConfig = {\n    layout: \"circular\",\n    sizing: \"uniform\",\n    coloring: \"default\",\n    highlight: [\"stars\", \"isolates\"],\n  };\n\n  const nodes: SociogramNode[] = [];\n  const edges: SociogramEdge[] = [];\n  const groups: SociogramGroup[] = [];\n  const nodeIds = new Set<string>();\n  const legendOverrides: import(\"../../core/types\").LegendOverrides = {};\n  let hasLegendOverrides = false;\n\n  let currentGroup: SociogramGroup | null = null;\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    // Legend directives (legend.title, legend.position, legend.label, etc.)\n    if (parseLegendDirective(trimmed, legendOverrides)) {\n      hasLegendOverrides = true;\n      continue;\n    }\n\n    // Config line\n    if (trimmed.startsWith(\"config:\")) {\n      const configBody = trimmed.slice(7).trim();\n      const eqIdx = configBody.indexOf(\"=\");\n      if (eqIdx !== -1) {\n        const key = configBody.slice(0, eqIdx).trim();\n        const val = configBody.slice(eqIdx + 1).trim();\n        switch (key) {\n          case \"layout\":\n            if ([\"circular\", \"force-directed\", \"concentric\"].includes(val)) {\n              config.layout = val as SociogramLayout;\n            }\n            break;\n          case \"sizing\":\n            if ([\"uniform\", \"in-degree\", \"betweenness\"].includes(val)) {\n              config.sizing = val as SizingMode;\n            }\n            break;\n          case \"coloring\":\n            if ([\"default\", \"group\", \"role\"].includes(val)) {\n              config.coloring = val as ColoringMode;\n            }\n            break;\n          case \"highlight\":\n            config.highlight = val.split(\",\").map((s) => s.trim());\n            break;\n        }\n      }\n      continue;\n    }\n\n    // 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props.size as \"small\" | \"medium\" | \"large\" | undefined,\n          });\n        }\n        continue;\n      }\n    }\n\n    if (indent < 4) {\n      currentGroup = null;\n    }\n\n    // Try edge parsing\n    const edgeResult = findEdgeOp(trimmed);\n    if (edgeResult) {\n      const { leftId, rightId, op, rest } = edgeResult;\n      const edgeProps = extractProps(rest).props;\n\n      // Auto-register nodes\n      for (const id of [leftId, rightId]) {\n        if (!nodeIds.has(id)) {\n          nodeIds.add(id);\n          nodes.push({ id });\n        }\n      }\n\n      const weight = edgeProps.weight ? Number(edgeProps.weight) : op.weight;\n\n      edges.push({\n        from: leftId,\n        to: rightId,\n        direction: op.direction,\n        valence: op.valence,\n        weight,\n        label: edgeProps.label,\n      });\n      continue;\n    }\n\n    // Node definition: ID [props]\n    const { clean, props } = extractProps(trimmed);\n    const nodeId = clean.split(/\\s/)[0];\n    if (nodeId && /^[a-zA-Z][a-zA-Z0-9_-]*$/.test(nodeId) && !nodeIds.has(nodeId)) {\n      nodeIds.add(nodeId);\n      const node: SociogramNode = {\n        id: nodeId,\n        label: props.label,\n        group: props.group,\n        role: props.role as NodeRole | undefined,\n        size: props.size as \"small\" | \"medium\" | \"large\" | undefined,\n      };\n      nodes.push(node);\n\n      // Auto-add to group by group property\n      if (props.group) {\n        let grp = groups.find((g) => g.id === props.group);\n        if (!grp) {\n          grp = { id: props.group, members: [] };\n          groups.push(grp);\n        }\n        grp.members.push(nodeId);\n      }\n    }\n  }\n\n  return {\n    type: \"sociogram\",\n    title: titleStr,\n    config,\n    nodes,\n    edges,\n    groups,\n    legendOverrides: hasLegendOverrides ? legendOverrides : undefined,\n  };\n}\n","import type {\n  SociogramAST,\n  SociogramNode,\n  SociogramEdge,\n  NodeRole,\n} from \"./parser\";\n\nexport interface SociogramLayoutNode {\n  node: SociogramNode;\n  x: number;\n  y: number;\n  radius: number;\n  computedRole?: NodeRole;\n}\n\nexport interface SociogramLayoutEdge {\n  edge: SociogramEdge;\n  x1: number;\n  y1: number;\n  x2: number;\n  y2: number;\n}\n\nexport interface SociogramLayoutResult {\n  width: number;\n  height: number;\n  nodes: SociogramLayoutNode[];\n  edges: SociogramLayoutEdge[];\n  ast: SociogramAST;\n}\n\n// ─── Metrics ────────────────────────────────────────────────\n\nfunction computeInDegree(nodeId: string, edges: SociogramEdge[]): number {\n  let count = 0;\n  for (const e of edges) {\n    if (e.to === nodeId) count++;\n    if (e.direction === \"mutual\" && e.from === nodeId) count++;\n    if (e.direction === \"undirected\" && e.from === nodeId) count++;\n  }\n  return count;\n}\n\nfunction computeOutDegree(nodeId: string, edges: SociogramEdge[]): number {\n  let count = 0;\n  for (const e of edges) {\n    if (e.from === nodeId) count++;\n    if (e.direction === \"mutual\" && e.to === nodeId) count++;\n    if (e.direction === \"undirected\" && e.to === nodeId) count++;\n  }\n  return count;\n}\n\nfunction autoDetectRole(\n  node: SociogramNode,\n  inDeg: number,\n  outDeg: number,\n  meanIn: number,\n  sdIn: number,\n  rejectionCount: number\n): NodeRole | undefined {\n  if (node.role) return node.role;\n  if (inDeg === 0 && outDeg === 0) return \"isolate\";\n  if (inDeg === 0 && outDeg > 0) return \"neglectee\";\n  if (rejectionCount >= 2) return \"rejected\";\n  if (sdIn > 0 && inDeg >= meanIn + 1.5 * sdIn) return \"star\";\n  return undefined;\n}\n\n// ─── Node Radius ────────────────────────────────────────────\n\nconst BASE_RADIUS = 20;\n\nfunction computeNodeRadius(\n  node: SociogramNode,\n  inDeg: number,\n  sizing: string\n): number {\n  if (node.size === \"small\") return 14;\n  if (node.size === \"large\") return 30;\n  if (sizing === \"in-degree\") {\n    return Math.min(40, Math.max(14, 14 + inDeg * 4));\n  }\n  return BASE_RADIUS;\n}\n\n// ─── Circular Layout ────────────────────────────────────────\n\nfunction layoutCircular(ast: SociogramAST): SociogramLayoutResult {\n  const n = ast.nodes.length;\n  const radius = Math.max(120, n * 22);\n  const canvasSize = radius * 2 + 160;\n  const cx = canvasSize / 2;\n  const cy = canvasSize / 2;\n\n  // Compute metrics\n  const inDegrees = new Map<string, number>();\n  const outDegrees = new Map<string, number>();\n  const rejections = new Map<string, number>();\n\n  for (const node of ast.nodes) {\n    inDegrees.set(node.id, computeInDegree(node.id, ast.edges));\n    outDegrees.set(node.id, computeOutDegree(node.id, ast.edges));\n    rejections.set(node.id, 0);\n  }\n\n  for (const e of ast.edges) {\n    if (e.valence === \"negative\") {\n      rejections.set(e.to, (rejections.get(e.to) ?? 0) + 1);\n    }\n  }\n\n  const inVals = Array.from(inDegrees.values());\n  const meanIn = inVals.reduce((a, b) => a + b, 0) / (inVals.length || 1);\n  const sdIn = Math.sqrt(\n    inVals.reduce((sum, v) => sum + (v - meanIn) ** 2, 0) / (inVals.length || 1)\n  );\n\n  // Sort nodes: group members adjacent, then by id\n  const sortedNodes = [...ast.nodes];\n  if (ast.groups.length > 0) {\n    const groupOrder = new Map<string, number>();\n    ast.groups.forEach((g, i) => {\n      for (const m of g.members) groupOrder.set(m, i);\n    });\n    sortedNodes.sort((a, b) => {\n      const ga = groupOrder.get(a.id) ?? 999;\n      const gb = groupOrder.get(b.id) ?? 999;\n      if (ga !== gb) return ga - gb;\n      return a.id.localeCompare(b.id);\n    });\n  }\n\n  const angleStep = (2 * Math.PI) / n;\n  const startAngle = -Math.PI / 2;\n\n  const layoutNodes: SociogramLayoutNode[] = sortedNodes.map((node, i) => {\n    const angle = startAngle + i * angleStep;\n    const inDeg = inDegrees.get(node.id) ?? 0;\n    const outDeg = outDegrees.get(node.id) ?? 0;\n    const rej = rejections.get(node.id) ?? 0;\n    const nodeRadius = computeNodeRadius(node, inDeg, ast.config.sizing);\n    const computedRole = autoDetectRole(node, inDeg, outDeg, meanIn, sdIn, rej);\n\n    return {\n      node,\n      x: cx + radius * Math.cos(angle),\n      y: cy + radius * Math.sin(angle),\n      radius: nodeRadius,\n      computedRole,\n    };\n  });\n\n  const layoutEdges = computeEdgePositions(layoutNodes, ast.edges);\n\n  return {\n    width: canvasSize,\n    height: canvasSize,\n    nodes: layoutNodes,\n    edges: layoutEdges,\n    ast,\n  };\n}\n\n// ─── Force-Directed Layout ─────────────────────────────────\n\nfunction layoutForceDirected(ast: SociogramAST): SociogramLayoutResult {\n  const n = ast.nodes.length;\n  const canvasSize = n <= 8 ? 400 : n <= 20 ? 600 : n <= 40 ? 800 : 1000;\n  const padding = 60;\n\n  // Compute metrics\n  const inDegrees = new Map<string, number>();\n  const outDegrees = new Map<string, number>();\n  const rejections = new Map<string, number>();\n\n  for (const node of ast.nodes) {\n    inDegrees.set(node.id, computeInDegree(node.id, ast.edges));\n    outDegrees.set(node.id, computeOutDegree(node.id, ast.edges));\n    rejections.set(node.id, 0);\n  }\n\n  for (const e of ast.edges) {\n    if (e.valence === \"negative\") {\n      rejections.set(e.to, (rejections.get(e.to) ?? 0) + 1);\n    }\n  }\n\n  const inVals = Array.from(inDegrees.values());\n  const meanIn = inVals.reduce((a, b) => a + b, 0) / (inVals.length || 1);\n  const sdIn = Math.sqrt(\n    inVals.reduce((sum, v) => sum + (v - meanIn) ** 2, 0) / (inVals.length || 1)\n  );\n\n  // Initialize positions in a circle\n  const initRadius = canvasSize * 0.3;\n  const cx = canvasSize / 2;\n  const cy = canvasSize / 2;\n\n  const positions: { x: number; y: number }[] = ast.nodes.map((_, i) => {\n    const angle = (2 * Math.PI * i) / n - Math.PI / 2;\n    return {\n      x: cx + initRadius * Math.cos(angle),\n      y: cy + initRadius * Math.sin(angle),\n    };\n  });\n\n  // Build adjacency for edges\n  const nodeIdx = new Map<string, number>();\n  ast.nodes.forEach((node, i) => nodeIdx.set(node.id, i));\n\n  // Fruchterman-Reingold\n  const area = (canvasSize - 2 * padding) ** 2;\n  const k = Math.sqrt(area / Math.max(n, 1));\n  const maxIterations = 200;\n  let temperature = canvasSize / 8;\n  const coolingRate = 0.95;\n  const minDist = 60;\n\n  for (let iter = 0; iter < maxIterations; iter++) {\n    const disp: { dx: number; dy: number }[] = positions.map(() => ({ dx: 0, dy: 0 }));\n\n    // Repulsive forces between all pairs\n    for (let i = 0; i < n; i++) {\n      for (let j = i + 1; j < n; j++) {\n        const dx = positions[i].x - positions[j].x;\n        const dy = positions[i].y - positions[j].y;\n        const dist = Math.max(Math.sqrt(dx * dx + dy * dy), 1);\n        const force = (k * k) / dist;\n        const fx = (dx / dist) * force;\n        const fy = (dy / dist) * force;\n        disp[i].dx += fx;\n        disp[i].dy += fy;\n        disp[j].dx -= fx;\n        disp[j].dy -= fy;\n      }\n    }\n\n    // Attractive forces along edges\n    for (const edge of ast.edges) {\n      const i = nodeIdx.get(edge.from);\n      const j = nodeIdx.get(edge.to);\n      if (i === undefined || j === undefined) continue;\n      const dx = positions[i].x - positions[j].x;\n      const dy = positions[i].y - positions[j].y;\n      const dist = Math.max(Math.sqrt(dx * dx + dy * dy), 1);\n      const force = (dist * dist) / k;\n      const fx = (dx / dist) * force;\n      const fy = (dy / dist) * force;\n      disp[i].dx -= fx;\n      disp[i].dy -= fy;\n      disp[j].dx += fx;\n      disp[j].dy += fy;\n    }\n\n    // Apply displacements, clamp to temperature\n    for (let i = 0; i < n; i++) {\n      const mag = Math.sqrt(disp[i].dx ** 2 + disp[i].dy ** 2);\n      if (mag > 0) {\n        const scale = Math.min(mag, temperature) / mag;\n        positions[i].x += disp[i].dx * scale;\n        positions[i].y += disp[i].dy * scale;\n      }\n      // Keep within bounds\n      positions[i].x = Math.max(padding, Math.min(canvasSize - padding, positions[i].x));\n      positions[i].y = Math.max(padding, Math.min(canvasSize - padding, positions[i].y));\n    }\n\n    // Enforce minimum distance\n    for (let i = 0; i < n; i++) {\n      for (let j = i + 1; j < n; j++) {\n        const dx = positions[i].x - positions[j].x;\n        const dy = positions[i].y - positions[j].y;\n        const dist = Math.sqrt(dx * dx + dy * dy);\n        if (dist < minDist && dist > 0) {\n          const push = (minDist - dist) / 2;\n          const nx = dx / dist;\n          const ny = dy / dist;\n          positions[i].x += nx * push;\n          positions[i].y += ny * push;\n          positions[j].x -= nx * push;\n          positions[j].y -= ny * push;\n        }\n      }\n    }\n\n    temperature *= coolingRate;\n  }\n\n  const layoutNodes: SociogramLayoutNode[] = ast.nodes.map((node, i) => {\n    const inDeg = inDegrees.get(node.id) ?? 0;\n    const outDeg = outDegrees.get(node.id) ?? 0;\n    const rej = rejections.get(node.id) ?? 0;\n    const nodeRadius = computeNodeRadius(node, inDeg, ast.config.sizing);\n    const computedRole = autoDetectRole(node, inDeg, outDeg, meanIn, sdIn, rej);\n    return {\n      node,\n      x: positions[i].x,\n      y: positions[i].y,\n      radius: nodeRadius,\n      computedRole,\n    };\n  });\n\n  const layoutEdges = computeEdgePositions(layoutNodes, ast.edges);\n\n  return {\n    width: canvasSize,\n    height: canvasSize,\n    nodes: layoutNodes,\n    edges: layoutEdges,\n    ast,\n  };\n}\n\n// ─── Edge Position Calculation ──────────────────────────────\n\nfunction computeEdgePositions(\n  nodes: SociogramLayoutNode[],\n  edges: SociogramEdge[]\n): SociogramLayoutEdge[] {\n  const nodeMap = new Map<string, SociogramLayoutNode>();\n  for (const n of nodes) nodeMap.set(n.node.id, n);\n\n  return edges.map((edge) => {\n    const fromNode = nodeMap.get(edge.from);\n    const toNode = nodeMap.get(edge.to);\n    if (!fromNode || !toNode) {\n      return { edge, x1: 0, y1: 0, x2: 0, y2: 0 };\n    }\n\n    // Compute edge-to-edge (subtract radius from endpoints)\n    const dx = toNode.x - fromNode.x;\n    const dy = toNode.y - fromNode.y;\n    const dist = Math.sqrt(dx * dx + dy * dy);\n    if (dist === 0) return { edge, x1: fromNode.x, y1: fromNode.y, x2: toNode.x, y2: toNode.y };\n\n    const nx = dx / dist;\n    const ny = dy / dist;\n    const markerGap = 10;\n\n    return {\n      edge,\n      x1: fromNode.x + nx * (fromNode.radius + 2),\n      y1: fromNode.y + ny * (fromNode.radius + 2),\n      x2: toNode.x - nx * (toNode.radius + markerGap),\n      y2: toNode.y - ny * (toNode.radius + markerGap),\n    };\n  });\n}\n\n// ─── Main Layout ────────────────────────────────────────────\n\nexport function layoutSociogram(ast: SociogramAST): SociogramLayoutResult {\n  switch (ast.config.layout) {\n    case \"force-directed\":\n      return layoutForceDirected(ast);\n    case \"circular\":\n    default:\n      return layoutCircular(ast);\n  }\n}\n","/**\n * Auto-derive a LegendSpec from a sociogram AST.\n *\n * Sections (each emitted only when the corresponding encoding is present):\n *   1. Groups   — color swatch per declared group (emits when coloring=\"group\"\n *                 or any group has an explicit color)\n *   2. Roles    — sociometric role markers (star, isolate, neglectee, rejected)\n *                 — only roles actually used in the chart\n *   3. Ties     — edge valence (positive solid, negative dashed red, neutral\n *                 dotted grey) — only valences actually used\n */\n\nimport type { SociogramAST, EdgeValence, NodeRole } from \"./parser\";\nimport type {\n  LegendItem,\n  LegendSection,\n  LegendSpec,\n} from \"../../core/types\";\nimport type { BaseTheme } from \"../../core/theme\";\n\nconst SECTIONS: LegendSection[] = [\n  { id: \"groups\", title: \"Groups\" },\n  { id: \"roles\", title: \"Roles\" },\n  { id: \"ties\", title: \"Ties\" },\n];\n\nexport function buildSociogramLegend(\n  ast: SociogramAST,\n  theme: BaseTheme\n): LegendSpec {\n  const items: LegendItem[] = [];\n\n  // Groups: when coloring=group or groups have explicit colors, list each.\n  const colorByGroup = ast.config.coloring === \"group\" || ast.groups.some(g => g.color);\n  if (colorByGroup) {\n    ast.groups.forEach((g, i) => {\n      const color = g.color ?? theme.palette[i % theme.palette.length];\n      items.push({\n        key: `group.${g.id}`,\n        label: g.label ?? humanize(g.id),\n        kind: \"fill\",\n        color,\n        section: \"groups\",\n      });\n    });\n  }\n\n  // Roles: emit each role actually used (star/isolate/neglectee/rejected).\n  // \"bridge\" is excluded — it's a structural notion (no special visual).\n  const usedRoles = new Set<NodeRole>();\n  for (const n of ast.nodes) {\n    if (n.role) usedRoles.add(n.role);\n  }\n  const roleOrder: NodeRole[] = [\"star\", \"isolate\", \"neglectee\", \"rejected\"];\n  for (const r of roleOrder) {\n    if (!usedRoles.has(r)) continue;\n    items.push(roleItem(r, theme));\n  }\n\n  // Ties: emit each valence used.\n  const usedValences = new Set<EdgeValence>();\n  for (const e of ast.edges) usedValences.add(e.valence);\n  const valOrder: EdgeValence[] = [\"positive\", \"negative\", \"neutral\"];\n  for (const v of valOrder) {\n    if (!usedValences.has(v)) continue;\n    items.push(valenceItem(v, theme));\n  }\n\n  return {\n    mode: \"auto\",\n    title: \"Legend\",\n    position: \"bottom-inline\",\n    columns: 1,\n    sections: SECTIONS,\n    items,\n  };\n}\n\nfunction roleItem(r: NodeRole, theme: BaseTheme): LegendItem {\n  switch (r) {\n    case \"star\":\n      return {\n        key: `role.${r}`,\n        label: \"Star (sociometric center)\",\n        kind: \"shape\",\n        shape: \"circle\",\n        fill: theme.warn,\n        color: theme.warn,\n        section: \"roles\",\n      };\n    case \"isolate\":\n      return {\n        key: `role.${r}`,\n        label: \"Isolate\",\n        kind: \"shape\",\n        shape: \"circle\",\n        fill: theme.fillMuted,\n        color: theme.neutral,\n        section: \"roles\",\n      };\n    case \"neglectee\":\n      return {\n        key: `role.${r}`,\n        label: \"Neglectee\",\n        kind: \"shape\",\n        shape: \"circle\",\n        fill: theme.fillMuted,\n        color: theme.accent,\n        section: \"roles\",\n      };\n    case \"rejected\":\n      return {\n        key: `role.${r}`,\n        label: \"Rejected\",\n        kind: \"shape\",\n        shape: \"circle\",\n        fill: theme.negative,\n        color: theme.negative,\n        section: \"roles\",\n      };\n    default:\n      return {\n        key: `role.${r}`,\n        label: humanize(r),\n        kind: \"shape\",\n        shape: \"circle\",\n        section: \"roles\",\n      };\n  }\n}\n\nfunction valenceItem(v: EdgeValence, theme: BaseTheme): LegendItem {\n  switch (v) {\n    case \"positive\":\n      return {\n        key: `valence.${v}`,\n        label: \"Positive tie\",\n        kind: \"line\",\n        color: theme.positive,\n        pattern: \"solid\",\n        strokeWidth: 2,\n        section: \"ties\",\n      };\n    case \"negative\":\n      return {\n        key: `valence.${v}`,\n        label: \"Negative tie\",\n        kind: \"line\",\n        color: theme.negative,\n        pattern: \"dashed\",\n        strokeWidth: 2,\n        section: \"ties\",\n      };\n    case \"neutral\":\n      return {\n        key: `valence.${v}`,\n        label: \"Neutral tie\",\n        kind: \"line\",\n        color: theme.neutral,\n        pattern: \"dotted\",\n        strokeWidth: 2,\n        section: \"ties\",\n      };\n  }\n}\n\nfunction humanize(s: string): string {\n  return s.replace(/[-_]+/g, \" \").replace(/\\b\\w/g, (c) => c.toUpperCase());\n}\n","import type { SociogramAST, NodeRole } from \"./parser\";\nimport type { SociogramLayoutResult, SociogramLayoutNode } from \"./layout\";\nimport {\n  svgRoot,\n  el,\n  group,\n  circle,\n  line,\n  text,\n  title,\n  desc,\n  polygon,\n} from \"../../core/svg\";\nimport { cssCustomProperties, resolveBaseTheme, FONT_SIZE, STROKE_WIDTH, type BaseTheme } from \"../../core/theme\";\nimport { applyLegendOverrides, renderLegend } from \"../../core/legend\";\nimport { buildSociogramLegend } from \"./legend\";\n\n// ─── Constants ──────────────────────────────────────────────\n\nconst LABEL_GAP = 4;\nconst LABEL_FONT_SIZE = 11;\n\nfunction valenceColors(t: BaseTheme) {\n  return { positive: t.positive, negative: t.negative, neutral: t.neutral };\n}\n\nfunction roleFills(t: BaseTheme) {\n  return { star: t.warn, isolate: t.fillMuted, rejected: t.negative };\n}\n\n// ─── CSS ────────────────────────────────────────────────────\n\nfunction buildCSS(ast: SociogramAST, t: BaseTheme): string {\n  const vc = valenceColors(t);\n  const rf = roleFills(t);\n  const groupColors = ast.groups.map((g, i) => {\n    const color = g.color ?? t.palette[i % t.palette.length];\n    return `.schematex-sociogram-group-${g.id} { fill: ${color}; stroke: ${color}; }`;\n  });\n\n  return `\n.schematex-sociogram {${cssCustomProperties(t)}\n  font-family: system-ui, -apple-system, sans-serif;\n}\n.schematex-sociogram-node { fill: ${t.accent}; stroke: ${t.accent}; stroke-width: ${STROKE_WIDTH.normal}; }\n.schematex-sociogram-node-star { fill: ${rf.star}; stroke: ${t.warn}; stroke-width: ${STROKE_WIDTH.thick}; }\n.schematex-sociogram-node-isolate { fill: ${rf.isolate}; stroke: ${t.neutral}; stroke-width: ${STROKE_WIDTH.normal}; stroke-dasharray: 4 3; }\n.schematex-sociogram-node-neglectee { fill: ${t.fillMuted}; stroke: ${t.accent}; stroke-width: ${STROKE_WIDTH.normal}; stroke-dasharray: 4 3; }\n.schematex-sociogram-node-rejected { fill: ${rf.rejected}; stroke: ${t.negative}; stroke-width: ${STROKE_WIDTH.normal}; stroke-dasharray: 4 3; }\n.schematex-sociogram-edge { stroke-linecap: round; }\n.schematex-sociogram-edge-positive { stroke: ${vc.positive}; }\n.schematex-sociogram-edge-negative { stroke: ${vc.negative}; stroke-dasharray: 6 3; }\n.schematex-sociogram-edge-neutral { stroke: ${vc.neutral}; stroke-dasharray: 2 3; }\n.schematex-sociogram-label { font-size: ${LABEL_FONT_SIZE}px; fill: ${t.text}; text-anchor: middle; }\n.schematex-sociogram-edge-label { font-size: ${FONT_SIZE.small}px; fill: ${t.textMuted}; text-anchor: middle; }\n.schematex-sociogram-title { font-size: ${FONT_SIZE.title}px; font-weight: bold; fill: ${t.text}; text-anchor: middle; }\n.schematex-sociogram-star-badge { font-size: 10px; fill: ${t.warn}; }\n.schematex-sociogram-group-label { font-size: 13px; font-weight: bold; fill-opacity: 0.7; text-anchor: middle; }\n${groupColors.join(\"\\n\")}\n`.trim();\n}\n\n// ─── Defs (Arrow Markers) ───────────────────────────────────\n\nfunction buildDefs(t: BaseTheme): string {\n  const vc = valenceColors(t);\n  const markers = [\n    { id: \"sociogram-arrow\", fill: vc.positive },\n    { id: \"sociogram-arrow-negative\", fill: vc.negative },\n    { id: \"sociogram-arrow-neutral\", fill: vc.neutral },\n  ];\n\n  const markerEls = markers.map((m) =>\n    el(\n      \"marker\",\n      {\n        id: m.id,\n        viewBox: \"0 0 10 10\",\n        refX: \"9\",\n        refY: \"5\",\n        markerWidth: \"8\",\n        markerHeight: \"8\",\n        orient: \"auto\",\n      },\n      el(\"path\", { d: \"M 0 0 L 10 5 L 0 10 z\", fill: m.fill })\n    )\n  );\n\n  return el(\"defs\", {}, markerEls);\n}\n\n// ─── Edge Weight → Stroke Width ─────────────────────────────\n\nfunction edgeStrokeWidth(weight: number): number {\n  if (weight <= 1) return 1;\n  if (weight === 2) return 2;\n  if (weight === 3) return 3.5;\n  return 5;\n}\n\n// ─── Node Rendering ─────────────────────────────────────────\n\nfunction getNodeClass(role?: NodeRole): string {\n  if (!role) return \"schematex-sociogram-node\";\n  switch (role) {\n    case \"star\": return \"schematex-sociogram-node schematex-sociogram-node-star\";\n    case \"isolate\": return \"schematex-sociogram-node schematex-sociogram-node-isolate\";\n    case \"neglectee\": return \"schematex-sociogram-node schematex-sociogram-node-neglectee\";\n    case \"rejected\": return \"schematex-sociogram-node schematex-sociogram-node-rejected\";\n    case \"bridge\": return \"schematex-sociogram-node\";\n    default: return \"schematex-sociogram-node\";\n  }\n}\n\nfunction getNodeFill(\n  node: SociogramLayoutNode,\n  ast: SociogramAST,\n  t: BaseTheme\n): string | undefined {\n  const role = node.computedRole ?? node.node.role;\n  const rf = roleFills(t);\n\n  if (ast.config.coloring === \"role\" && role) {\n    return rf[role as keyof typeof rf];\n  }\n\n  if (ast.config.coloring === \"group\" && node.node.group) {\n    const gIdx = ast.groups.findIndex((g) => g.id === node.node.group);\n    if (gIdx >= 0) {\n      return ast.groups[gIdx].color ?? t.palette[gIdx % t.palette.length];\n    }\n  }\n\n  return undefined;\n}\n\nfunction renderNodes(\n  layout: SociogramLayoutResult,\n  t: BaseTheme\n): { nodeEls: string[]; labelEls: string[] } {\n  const nodeEls: string[] = [];\n  const labelEls: string[] = [];\n  const { ast } = layout;\n\n  for (const layoutNode of layout.nodes) {\n    const { node, x, y, radius, computedRole } = layoutNode;\n    const role = computedRole ?? node.role;\n    const cls = getNodeClass(role);\n    const fill = getNodeFill(layoutNode, ast, t);\n\n    const attrs: Record<string, string | number | undefined> = {\n      cx: x,\n      cy: y,\n      r: radius,\n      class: cls,\n      \"data-node-id\": node.id,\n    };\n    if (fill) attrs.fill = fill;\n\n    nodeEls.push(circle(attrs));\n\n    // Star badge\n    if (role === \"star\") {\n      const badgeX = x + radius * 0.6;\n      const badgeY = y - radius * 0.6;\n      const s = 6;\n      const points = starPoints(badgeX, badgeY, s, s * 0.4, 5);\n      nodeEls.push(\n        polygon({\n          points,\n          fill: t.warn,\n          class: \"schematex-sociogram-star-badge\",\n        })\n      );\n    }\n\n    // Label\n    const label = node.label ?? node.id;\n    labelEls.push(\n      text(\n        {\n          x,\n          y: y + radius + LABEL_GAP + LABEL_FONT_SIZE,\n          class: \"schematex-sociogram-label\",\n          \"data-node-id\": node.id,\n        },\n        label\n      )\n    );\n  }\n\n  return { nodeEls, labelEls };\n}\n\nfunction starPoints(\n  cx: number,\n  cy: number,\n  outerR: number,\n  innerR: number,\n  points: number\n): string {\n  const coords: string[] = [];\n  for (let i = 0; i < points * 2; i++) {\n    const angle = (Math.PI * i) / points - Math.PI / 2;\n    const r = i % 2 === 0 ? outerR : innerR;\n    coords.push(`${cx + r * Math.cos(angle)},${cy + r * Math.sin(angle)}`);\n  }\n  return coords.join(\" \");\n}\n\n// ─── Edge Rendering ─────────────────────────────────────────\n\nfunction getMarkerUrl(valence: string, direction: string): {\n  start?: string;\n  end?: string;\n} {\n  if (direction === \"undirected\") return {};\n\n  const markerId =\n    valence === \"negative\"\n      ? \"sociogram-arrow-negative\"\n      : valence === \"neutral\"\n        ? \"sociogram-arrow-neutral\"\n        : \"sociogram-arrow\";\n\n  if (direction === \"mutual\") {\n    return {\n      start: `url(#${markerId})`,\n      end: `url(#${markerId})`,\n    };\n  }\n\n  return { end: `url(#${markerId})` };\n}\n\nfunction renderEdges(layout: SociogramLayoutResult): {\n  edgeEls: string[];\n  edgeLabelEls: string[];\n} {\n  const edgeEls: string[] = [];\n  const edgeLabelEls: string[] = [];\n\n  for (const layoutEdge of layout.edges) {\n    const { edge, x1, y1, x2, y2 } = layoutEdge;\n    const valenceClass = `schematex-sociogram-edge-${edge.valence}`;\n    const markers = getMarkerUrl(edge.valence, edge.direction);\n    const sw = edgeStrokeWidth(edge.weight);\n\n    const attrs: Record<string, string | number | undefined> = {\n      x1,\n      y1,\n      x2,\n      y2,\n      class: `schematex-sociogram-edge ${valenceClass}`,\n      \"stroke-width\": sw,\n      \"data-from\": edge.from,\n      \"data-to\": edge.to,\n    };\n\n    if (markers.end) attrs[\"marker-end\"] = markers.end;\n    if (markers.start) attrs[\"marker-start\"] = markers.start;\n\n    edgeEls.push(line(attrs));\n\n    // Edge label\n    if (edge.label) {\n      const mx = (x1 + x2) / 2;\n      const my = (y1 + y2) / 2;\n      edgeLabelEls.push(\n        text(\n          { x: mx, y: my - 6, class: \"schematex-sociogram-edge-label\" },\n          edge.label\n        )\n      );\n    }\n  }\n\n  return { edgeEls, edgeLabelEls };\n}\n\n// ─── Group Background Labels ────────────────────────────────\n\nfunction renderGroupLabels(layout: SociogramLayoutResult, t: BaseTheme): string[] {\n  const elements: string[] = [];\n  const { ast } = layout;\n\n  for (let gi = 0; gi < ast.groups.length; gi++) {\n    const grp = ast.groups[gi];\n    const memberNodes = layout.nodes.filter(\n      (n) => n.node.group === grp.id\n    );\n    if (memberNodes.length === 0) continue;\n\n    const color = grp.color ?? t.palette[gi % t.palette.length];\n    const cx = memberNodes.reduce((s, n) => s + n.x, 0) / memberNodes.length;\n    const minY = Math.min(...memberNodes.map((n) => n.y - n.radius));\n\n    elements.push(\n      text(\n        {\n          x: cx,\n          y: minY - 14,\n          class: \"schematex-sociogram-group-label\",\n          fill: color,\n        },\n        grp.label ?? grp.id\n      )\n    );\n  }\n\n  return elements;\n}\n\n// ─── Main Renderer ──────────────────────────────────────────\n\nexport function renderSociogram(\n  layout: SociogramLayoutResult,\n  options: { theme?: string } = {}\n): string {\n  const { ast } = layout;\n  const t = resolveBaseTheme(options.theme ?? \"default\");\n\n  const css = buildCSS(ast, t);\n  const defsStr = buildDefs(t);\n\n  const titleOffset = ast.title ? 30 : 0;\n  const totalWidth = layout.width;\n  const totalHeight = layout.height + titleOffset;\n\n  const { edgeEls, edgeLabelEls } = renderEdges(layout);\n  const { nodeEls, labelEls } = renderNodes(layout, t);\n  const groupLabelEls = renderGroupLabels(layout, t);\n\n  const titleEl = ast.title\n    ? text(\n        { x: totalWidth / 2, y: 20, class: \"schematex-sociogram-title\" },\n        ast.title\n      )\n    : \"\";\n\n  const transformY = titleOffset;\n  const transform = transformY ? `translate(0,${transformY})` : undefined;\n\n  const svgContent: string[] = [\n    title(`Sociogram${ast.title ? `: ${ast.title}` : \"\"}`),\n    desc(\n      `Sociogram with ${ast.nodes.length} members and ${ast.edges.length} connections`\n    ),\n    el(\"style\", {}, css),\n    defsStr,\n  ];\n\n  if (titleEl) svgContent.push(titleEl);\n\n  if (groupLabelEls.length > 0) {\n    svgContent.push(\n      group({ class: \"schematex-sociogram-groups\", transform }, groupLabelEls)\n    );\n  }\n\n  svgContent.push(\n    group({ class: \"schematex-sociogram-edges\", transform }, [\n      ...edgeEls,\n      ...edgeLabelEls,\n    ])\n  );\n\n  svgContent.push(\n    group({ class: \"schematex-sociogram-nodes\", transform }, nodeEls)\n  );\n\n  svgContent.push(\n    group({ class: \"schematex-sociogram-labels\", transform }, labelEls)\n  );\n\n  // Compose legend\n  let finalWidth = totalWidth;\n  let finalHeight = totalHeight;\n  const autoSpec = buildSociogramLegend(ast, t);\n  const finalSpec = applyLegendOverrides(autoSpec, ast.legendOverrides);\n  if (finalSpec.mode === \"on\" && finalSpec.items.length > 0) {\n    const { svg: legendSvg, bbox: lb } = renderLegend(\n      finalSpec,\n      {\n        canvasWidth: totalWidth,\n        canvasHeight: totalHeight,\n        padding: 16,\n        titleHeight: titleOffset,\n      },\n      t,\n      { fontFamily: \"system-ui, sans-serif\", fontSize: 12 }\n    );\n    if (legendSvg) {\n      svgContent.push(legendSvg);\n      const overflowX = lb.x + lb.w + 8;\n      const overflowY = lb.y + lb.h + 8;\n      if (overflowX > finalWidth) finalWidth = overflowX;\n      if (overflowY > finalHeight) finalHeight = overflowY;\n    }\n  }\n\n  return svgRoot(\n    {\n      class: \"schematex-diagram schematex-sociogram\",\n      viewBox: `0 0 ${finalWidth} ${finalHeight}`,\n      width: finalWidth,\n      height: finalHeight,\n    },\n    svgContent\n  );\n}\n","import type { DiagramPlugin } from \"../../core/types\";\nimport { parseSociogram } from \"./parser\";\nimport { layoutSociogram } from \"./layout\";\nimport { renderSociogram } from \"./renderer\";\n\nexport const sociogram: DiagramPlugin = {\n  type: \"sociogram\",\n\n  detect(text: string): boolean {\n    const first = text.trim().split(\"\\n\")[0]?.trim().toLowerCase() ?? \"\";\n    return first.startsWith(\"sociogram\");\n  },\n\n  parse: parseSociogram,\n\n  render(text: string, config): string {\n    const ast = parseSociogram(text);\n    const layout = layoutSociogram(ast);\n    return renderSociogram(layout, { theme: config?.theme });\n  },\n};\n\nexport { parseSociogram } from \"./parser\";\nexport { layoutSociogram } from \"./layout\";\nexport { renderSociogram } from \"./renderer\";\n"]}

package/dist/{chunk-I6VEXSUK.js → chunk-VDSYMSUY.js}

@@ -1,4 +1,5 @@
 import { resolveBiologyTheme, STROKE_WIDTH, FONT_SIZE, cssCustomProperties } from './chunk-2VNMKOUO.js';
+import { matchQuotedTitle } from './chunk-5IKOLUWK.js';
 import { path, circle, text, title, desc, el, group, svgRoot, rect, line } from './chunk-SYYBKDL7.js';
 
 // src/diagrams/phylo/parser.ts
@@ -299,9 +300,7 @@ function parsePhylo(text2) {
     throw new PhyloParseError("Phylo document must start with 'phylo'");
   }
   lineIdx++;
-  let title2;
-  const titleMatch = headerLine.match(/"([^"]+)"/);
-  if (titleMatch) title2 = titleMatch[1];
+  const title2 = matchQuotedTitle(headerLine);
   let headerProps = {
     layout: "rectangular",
     mode: "phylogram",
@@ -885,5 +884,5 @@ var phylo = {
 };
 
 export { PhyloParseError, layoutPhylo, parsePhylo, phylo, renderPhylo };
-//# sourceMappingURL=chunk-I6VEXSUK.js.map
-//# sourceMappingURL=chunk-I6VEXSUK.js.map
+//# sourceMappingURL=chunk-VDSYMSUY.js.map
+//# sourceMappingURL=chunk-VDSYMSUY.js.map

package/dist/chunk-VDSYMSUY.js.map

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type {\n  PhyloTreeAST,\n  PhyloNode,\n  PhyloLayout,\n  PhyloMode,\n  CladeDef,\n  CladeHighlightMode,\n} from \"../../core/types\";\nimport { matchQuotedTitle } from \"../../core/quotes\";\n\nexport class PhyloParseError extends Error {\n  constructor(message: string) {\n    super(message);\n    this.name = \"PhyloParseError\";\n  }\n}\n\n// ─── Newick Parser ──────────────────────────────────────────\n\nlet _pos = 0;\nlet _src = \"\";\nlet _nextId = 0;\n\nfunction genId(): string {\n  return `_n${_nextId++}`;\n}\n\nfunction peek(): string {\n  return _src[_pos] ?? \"\";\n}\n\nfunction advance(): string {\n  return _src[_pos++] ?? \"\";\n}\n\nfunction skipWhitespace(): void {\n  while (_pos < _src.length && /\\s/.test(_src[_pos])) _pos++;\n}\n\nfunction parseNewickName(): string {\n  skipWhitespace();\n  if (peek() === \"'\") {\n    advance();\n    let name = \"\";\n    while (_pos < _src.length) {\n      if (peek() === \"'\") {\n        advance();\n        if (peek() === \"'\") {\n          name += \"'\";\n          advance();\n        } else {\n          break;\n        }\n      } else {\n        name += advance();\n      }\n    }\n    return name;\n  }\n  let name = \"\";\n  while (_pos < _src.length && !/[\\s():,;[\\]']/.test(_src[_pos])) {\n    name += advance();\n  }\n  return name;\n}\n\nfunction parseNewickLength(): number | undefined {\n  skipWhitespace();\n  if (peek() !== \":\") return undefined;\n  advance();\n  skipWhitespace();\n  let numStr = \"\";\n  while (_pos < _src.length && /[0-9eE.+-]/.test(_src[_pos])) {\n    numStr += advance();\n  }\n  if (!numStr) return undefined;\n  const val = Number(numStr);\n  return Number.isNaN(val) ? undefined : val;\n}\n\nfunction parseNHX(): { support?: number; nhx?: Record<string, string> } | undefined {\n  skipWhitespace();\n  if (peek() !== \"[\") return undefined;\n  const start = _pos;\n  advance();\n  let content = \"\";\n  let depth = 1;\n  while (_pos < _src.length && depth > 0) {\n    if (peek() === \"[\") depth++;\n    if (peek() === \"]\") depth--;\n    if (depth > 0) content += advance();\n    else advance();\n  }\n  if (content.startsWith(\"&&NHX:\")) {\n    const pairs = content.slice(6).split(\":\");\n    const nhx: Record<string, string> = {};\n    let support: number | undefined;\n    for (const pair of pairs) {\n      const eq = pair.indexOf(\"=\");\n      if (eq === -1) continue;\n      const key = pair.slice(0, eq);\n      const val = pair.slice(eq + 1);\n      nhx[key] = val;\n      if (key === \"B\") {\n        const num = Number(val);\n        if (!Number.isNaN(num)) support = num;\n      }\n    }\n    return { support, nhx };\n  }\n  // Plain bootstrap value in brackets like [95]\n  const num = Number(content.trim());\n  if (!Number.isNaN(num) && content.trim().length > 0) {\n    return { support: num };\n  }\n  // Unknown bracket content — rewind\n  _pos = start;\n  return undefined;\n}\n\nfunction parseNewickSubtree(): PhyloNode {\n  skipWhitespace();\n  let children: PhyloNode[] = [];\n\n  if (peek() === \"(\") {\n    advance();\n    children = [];\n    children.push(parseNewickSubtree());\n    skipWhitespace();\n    while (peek() === \",\") {\n      advance();\n      children.push(parseNewickSubtree());\n      skipWhitespace();\n    }\n    skipWhitespace();\n    if (peek() === \")\") advance();\n  }\n\n  const name = parseNewickName();\n  const nhxData = parseNHX();\n  const branchLength = parseNewickLength();\n  // NHX can also appear after length\n  const nhxData2 = nhxData ? undefined : parseNHX();\n  const merged = nhxData ?? nhxData2;\n\n  const isLeaf = children.length === 0;\n  const id = name || genId();\n\n  return {\n    id,\n    label: name || undefined,\n    branchLength,\n    support: merged?.support,\n    children,\n    isLeaf,\n    nhx: merged?.nhx,\n  };\n}\n\nexport function parseNewick(newick: string): PhyloNode {\n  _pos = 0;\n  _src = newick.trim();\n  _nextId = 0;\n\n  if (_src.endsWith(\";\")) {\n    _src = _src.slice(0, -1);\n  }\n\n  const root = parseNewickSubtree();\n  return root;\n}\n\n// ─── Indent DSL Parser ──────────────────────────────────────\n\ninterface IndentLine {\n  indent: number;\n  name: string;\n  branchLength?: number;\n  support?: number;\n}\n\nfunction parseIndentTree(lines: string[]): PhyloNode {\n  _nextId = 0;\n  const parsed: IndentLine[] = [];\n\n  for (const raw of lines) {\n    if (!raw.trim() || raw.trim().startsWith(\"#\")) continue;\n    const indent = raw.search(/\\S/);\n    const content = raw.trim();\n\n    let name: string;\n    let branchLength: number | undefined;\n    let support: number | undefined;\n\n    // Check for support value [N]\n    let contentClean = content;\n    const supportMatch = contentClean.match(/\\[(\\d+(?:\\.\\d+)?)\\]\\s*$/);\n    if (supportMatch) {\n      support = Number(supportMatch[1]);\n      contentClean = contentClean.slice(0, supportMatch.index).trim();\n    }\n\n    // \"Name: length\" or \":length\" or \"Name:\" or \"Name\"\n    const colonIdx = contentClean.indexOf(\":\");\n    if (colonIdx === -1) {\n      name = contentClean;\n    } else {\n      name = contentClean.slice(0, colonIdx).trim();\n      const lenStr = contentClean.slice(colonIdx + 1).trim();\n      if (lenStr) {\n        const num = Number(lenStr);\n        if (!Number.isNaN(num)) branchLength = num;\n      }\n    }\n\n    parsed.push({ indent, name, branchLength, support });\n  }\n\n  if (parsed.length === 0) {\n    throw new PhyloParseError(\"Empty indent tree definition\");\n  }\n\n  function buildTree(startIdx: number, parentIndent: number): { node: PhyloNode; nextIdx: number } {\n    const line = parsed[startIdx];\n    const children: PhyloNode[] = [];\n    let idx = startIdx + 1;\n\n    while (idx < parsed.length && parsed[idx].indent > parentIndent) {\n      if (parsed[idx].indent === line.indent + 2 || parsed[idx].indent > line.indent) {\n        const childIndent = parsed[idx].indent;\n        const result = buildTree(idx, childIndent);\n        children.push(result.node);\n        idx = result.nextIdx;\n      } else {\n        break;\n      }\n    }\n\n    const id = line.name || genId();\n    return {\n      node: {\n        id,\n        label: line.name || undefined,\n        branchLength: line.branchLength,\n        support: line.support,\n        children,\n        isLeaf: children.length === 0,\n      },\n      nextIdx: idx,\n    };\n  }\n\n  // Build from the first line\n  const rootLine = parsed[0];\n  const rootIndent = rootLine.indent;\n  const children: PhyloNode[] = [];\n  let idx = 1;\n\n  while (idx < parsed.length) {\n    if (parsed[idx].indent > rootIndent) {\n      const result = buildTree(idx, parsed[idx].indent);\n      children.push(result.node);\n      idx = result.nextIdx;\n    } else {\n      break;\n    }\n  }\n\n  const rootId = rootLine.name || genId();\n  return {\n    id: rootId,\n    label: rootLine.name || undefined,\n    branchLength: rootLine.branchLength,\n    support: rootLine.support,\n    children,\n    isLeaf: children.length === 0,\n  };\n}\n\n// ─── Main Document Parser ───────────────────────────────────\n\nfunction parseHeaderProps(propsStr: string): {\n  layout: PhyloLayout;\n  mode: PhyloMode;\n  unrooted: boolean;\n  branchWidth?: number;\n  openAngle?: number;\n  mrsd?: string;\n} {\n  const result: ReturnType<typeof parseHeaderProps> = {\n    layout: \"rectangular\",\n    mode: \"phylogram\",\n    unrooted: false,\n  };\n\n  const pairs = propsStr.split(\",\").map((s) => s.trim());\n  for (const pair of pairs) {\n    if (pair === \"unrooted\") {\n      result.unrooted = true;\n      continue;\n    }\n    const colonIdx = pair.indexOf(\":\");\n    if (colonIdx === -1) continue;\n    const key = pair.slice(0, colonIdx).trim();\n    const val = pair.slice(colonIdx + 1).trim().replace(/^[\"']|[\"']$/g, \"\");\n\n    switch (key) {\n      case \"layout\":\n        if ([\"rectangular\", \"slanted\", \"circular\", \"unrooted\"].includes(val)) {\n          result.layout = val as PhyloLayout;\n        }\n        break;\n      case \"mode\":\n        if ([\"phylogram\", \"cladogram\", \"chronogram\"].includes(val)) {\n          result.mode = val as PhyloMode;\n        }\n        break;\n      case \"branch-width\":\n        result.branchWidth = Number(val);\n        break;\n      case \"openAngle\":\n        result.openAngle = Number(val);\n        break;\n      case \"mrsd\":\n        result.mrsd = val;\n        break;\n    }\n  }\n\n  if (result.layout === \"unrooted\") {\n    result.unrooted = true;\n  }\n\n  return result;\n}\n\nfunction parseCladeLine(line: string): CladeDef | null {\n  // clade ID = (member1, member2, ...) [color: \"#hex\", label: \"text\", highlight: mode]\n  const match = line.match(\n    /^clade\\s+(\\S+)\\s*=\\s*\\(([^)]+)\\)\\s*(?:\\[([^\\]]*)\\])?\\s*$/\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"]}