schematex 0.3.3 → 0.3.4

package/dist/chunk-6XGSEG3K.js.map

@@ -0,0 +1 @@
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type {\n  DiagramAST,\n  Individual,\n  LegendOverrides,\n  Relationship,\n  RelationshipType,\n  GeneticStatus,\n  IndividualMarker,\n  LegendEntry,\n  ConditionFill,\n} from \"../../core/types\";\nimport { parseLegendDirective } from \"../../core/legend-parser\";\n\n// ─── ParseError ─────────────────────────────────────────────\n\nexport class PedigreeParseError extends Error {\n  constructor(message: string, public line: number) {\n    super(`Line ${line}: ${message}`);\n    this.name = \"PedigreeParseError\";\n  }\n}\n\n// ─── Couple operators ───────────────────────────────────────\n\nconst COUPLE_OPS: Array<{ token: string; type: RelationshipType }> = [\n  { token: \"-/-\", type: \"separated\" },\n  { token: \"==\", type: \"consanguineous\" },\n  { token: \"--\", type: \"married\" },\n  { token: \"~\", type: \"cohabiting\" },\n];\n\nconst VALID_SEX = new Set([\"male\", \"female\", \"unknown\", \"amab\", \"afab\", \"uaab\"]);\nconst GENETIC_STATUSES = new Set([\n  \"affected\",\n  \"carrier\",\n  \"carrier-x\",\n  \"obligate-carrier\",\n  \"presymptomatic\",\n  \"unaffected\",\n]);\nconst MARKERS = new Set([\"proband\", \"consultand\", \"evaluated\"]);\nconst VALID_STATUS = new Set([\"deceased\", \"stillborn\", \"pregnancy\", \"sab\", \"tab\", \"ectopic\"]);\n\n// ─── Public API ────────────────────────────────────────────\n\nexport function parsePedigree(text: string): DiagramAST {\n  const rawLines = text.split(\"\\n\");\n  let i = 0;\n\n  while (i < rawLines.length && rawLines[i].trim() === \"\") i++;\n  if (i >= rawLines.length) throw new PedigreeParseError(\"Empty input\", 1);\n\n  const headerLine = rawLines[i].trim();\n  const headerMatch = headerLine.match(/^pedigree\\s*(?:\"([^\"]*)\")?$/i);\n  if (!headerMatch) throw new PedigreeParseError(\"Expected 'pedigree' header\", i + 1);\n\n  const metadata: Record<string, string> = {};\n  if (headerMatch[1]) metadata.title = headerMatch[1];\n  i++;\n\n  const legend: LegendEntry[] = [];\n  const legendOverrides: LegendOverrides = {};\n  let hasLegendOverrides = false;\n  const individualsMap = new Map<string, Individual>();\n  const relationships: Relationship[] = [];\n\n  while (i < rawLines.length) {\n    const raw = rawLines[i];\n    const trimmed = raw.trim();\n\n    if (trimmed === \"\" || trimmed.startsWith(\"#\") || trimmed.startsWith(\"//\")) {\n      i++;\n      continue;\n    }\n\n    // Unified legend directives (legend.title / .position / .label / .hide /\n    // .section / .item / `legend: on|off|<position>`). Legacy `legend: id =\n    // \"...\"` falls through to the regex below — applyMaster() returns false\n    // for the trait-id form, so parseLegendDirective hands it back to us.\n    if (parseLegendDirective(trimmed, legendOverrides)) {\n      hasLegendOverrides = true;\n      i++;\n      continue;\n    }\n\n    // Legend definition (legacy trait-fill DSL).\n    const legendMatch = trimmed.match(\n      /^legend:\\s*([a-zA-Z][a-zA-Z0-9_-]*)\\s*=\\s*\"([^\"]*)\"\\s*(?:\\(\\s*fill:\\s*([a-zA-Z-]+)\\s*\\))?$/\n    );\n    if (legendMatch) {\n      legend.push({\n        id: legendMatch[1],\n        label: legendMatch[2],\n        fill: (legendMatch[3] as ConditionFill) ?? \"full\",\n      });\n      i++;\n      continue;\n    }\n\n    // Couple line\n    const coupleMatch = detectCoupleOp(trimmed);\n    if (coupleMatch) {\n      const { leftId, op, rightRaw } = coupleMatch;\n      const lineNum = i + 1;\n\n      const { id: rightId, propsStr: rightProps } = parseIdWithProps(rightRaw);\n      const leftKey = leftId.toLowerCase();\n      const rightKey = rightId.toLowerCase();\n\n      if (!individualsMap.has(leftKey)) {\n        throw new PedigreeParseError(`Unknown individual '${leftId}'`, lineNum);\n      }\n\n      if (rightProps) {\n        individualsMap.set(rightKey, buildIndividual(rightId, rightProps, lineNum));\n      } else if (!individualsMap.has(rightKey)) {\n        throw new PedigreeParseError(`Unknown individual '${rightId}'`, lineNum);\n      }\n\n      relationships.push({ type: op.type, from: leftKey, to: rightKey });\n\n      const coupleIndent = leadingSpaces(raw);\n      i++;\n\n      // Children (indented under couple)\n      while (i < rawLines.length) {\n        const childLine = rawLines[i];\n        const childTrimmed = childLine.trim();\n\n        if (childTrimmed === \"\" || childTrimmed.startsWith(\"#\")) {\n          i++;\n          continue;\n        }\n\n        if (leadingSpaces(childLine) <= coupleIndent) break;\n\n        const childLineNum = i + 1;\n        const { id: childId, propsStr } = parseIdWithProps(childTrimmed);\n        const childKey = childId.toLowerCase();\n\n        individualsMap.set(childKey, buildIndividual(childId, propsStr, childLineNum));\n\n        const coupleKey = `${leftKey}+${rightKey}`;\n        relationships.push({ type: \"parent-child\", from: coupleKey, to: childKey });\n\n        i++;\n      }\n      continue;\n    }\n\n    // Individual definition\n    const { id, propsStr } = parseIdWithProps(trimmed);\n    const key = id.toLowerCase();\n    const ind = buildIndividual(id, propsStr, i + 1);\n    const existing = individualsMap.get(key);\n    if (existing) {\n      individualsMap.set(key, mergeIndividual(existing, ind));\n    } else {\n      individualsMap.set(key, ind);\n    }\n    i++;\n  }\n\n  return {\n    type: \"pedigree\",\n    individuals: Array.from(individualsMap.values()),\n    relationships,\n    metadata: Object.keys(metadata).length > 0 ? metadata : undefined,\n    legend: legend.length > 0 ? legend : undefined,\n    legendOverrides: hasLegendOverrides ? legendOverrides : undefined,\n  };\n}\n\n// ─── Helpers ────────────────────────────────────────────────\n\nfunction leadingSpaces(line: string): number {\n  const m = line.match(/^(\\s*)/);\n  return m ? m[1].length : 0;\n}\n\nfunction detectCoupleOp(trimmed: string): { leftId: string; op: typeof COUPLE_OPS[0]; rightRaw: string } | null {\n  for (const op of COUPLE_OPS) {\n    let bracketDepth = 0;\n    for (let j = 0; j < trimmed.length; j++) {\n      if (trimmed[j] === \"[\") bracketDepth++;\n      if (trimmed[j] === \"]\") bracketDepth--;\n      if (bracketDepth > 0) continue;\n\n      if (trimmed.substring(j, j + op.token.length) === op.token) {\n        const left = trimmed.substring(0, j).trim();\n        const right = trimmed.substring(j + op.token.length).trim();\n        if (left && right && /^[a-zA-Z][a-zA-Z0-9_-]*$/.test(left)) {\n          return { leftId: left, op, rightRaw: right };\n        }\n      }\n    }\n  }\n  return null;\n}\n\nfunction parseIdWithProps(raw: string): { id: string; propsStr: string | null } {\n  const bracketIdx = raw.indexOf(\"[\");\n  if (bracketIdx === -1) return { id: raw.trim(), propsStr: null };\n  const id = raw.substring(0, bracketIdx).trim();\n  const endBracket = raw.lastIndexOf(\"]\");\n  const propsStr = raw.substring(bracketIdx + 1, endBracket === -1 ? raw.length : endBracket);\n  return { id, propsStr };\n}\n\nfunction splitProps(propsStr: string): string[] {\n  const result: string[] = [];\n  let current = \"\";\n  let parenDepth = 0;\n  for (const ch of propsStr) {\n    if (ch === \"(\") parenDepth++;\n    if (ch === \")\") parenDepth--;\n    if (ch === \",\" && parenDepth === 0) {\n      result.push(current);\n      current = \"\";\n    } else {\n      current += ch;\n    }\n  }\n  if (current.trim()) result.push(current);\n  return result;\n}\n\nfunction buildIndividual(id: string, propsStr: string | null, _lineNum: number): Individual {\n  const ind: Individual = {\n    id: id.toLowerCase(),\n    label: id,\n    sex: \"unknown\",\n    status: \"alive\",\n  };\n\n  if (!propsStr) return ind;\n\n  const tokens = splitProps(propsStr);\n  for (const rawToken of tokens) {\n    const token = rawToken.trim();\n    const lower = token.toLowerCase();\n\n    if (VALID_SEX.has(lower)) {\n      ind.sex = lower === \"amab\" ? \"male\" : lower === \"afab\" ? \"female\" : lower === \"uaab\" ? \"unknown\" : lower as Individual[\"sex\"];\n    } else if (VALID_STATUS.has(lower)) {\n      ind.status = lower as Individual[\"status\"];\n    } else if (GENETIC_STATUSES.has(lower)) {\n      ind.geneticStatus = lower as GeneticStatus;\n    } else if (MARKERS.has(lower)) {\n      if (!ind.markers) ind.markers = [];\n      ind.markers.push(lower as IndividualMarker);\n    } else if (/^\\d{4}$/.test(lower)) {\n      ind.birthYear = parseInt(token, 10);\n    } else if (lower.startsWith(\"affected:\")) {\n      ind.geneticStatus = \"affected\";\n      const traits = token.substring(\"affected:\".length).trim().split(\"+\").map(t => t.trim());\n      ind.conditions = traits.map(t => ({ label: t, fill: \"full\" as ConditionFill }));\n    } else if (token.includes(\":\")) {\n      const colonIdx = token.indexOf(\":\");\n      const key = token.substring(0, colonIdx).trim().toLowerCase();\n      const value = token.substring(colonIdx + 1).trim().replace(/^\"|\"$/g, \"\");\n      if (key === \"label\") {\n        ind.label = value;\n      } else {\n        if (!ind.properties) ind.properties = {};\n        ind.properties[key] = value;\n      }\n    }\n  }\n\n  return ind;\n}\n\nfunction mergeIndividual(existing: Individual, incoming: Individual): Individual {\n  return {\n    ...existing,\n    sex: incoming.sex !== \"unknown\" ? incoming.sex : existing.sex,\n    status: incoming.status !== \"alive\" ? incoming.status : existing.status,\n    birthYear: incoming.birthYear ?? existing.birthYear,\n    geneticStatus: incoming.geneticStatus ?? existing.geneticStatus,\n    markers: incoming.markers ?? existing.markers,\n    conditions: incoming.conditions ?? existing.conditions,\n    properties: { ...existing.properties, ...incoming.properties },\n  };\n}\n","import type {\n  DiagramAST,\n  Individual,\n  Relationship,\n  RelationshipType,\n  LayoutConfig,\n  LayoutResult,\n  LayoutNode,\n  LayoutEdge,\n} from \"../../core/types\";\n\n// ─── Internal types ─────────────────────────────────────────\n\ninterface FamilyUnit {\n  id: string;\n  partners: [string, string];\n  relationship: RelationshipType;\n  children: string[];\n}\n\ninterface LayoutGraph {\n  individuals: Map<string, Individual>;\n  familyUnits: FamilyUnit[];\n  generations: Map<string, number>;\n  childOf: Map<string, string>;\n}\n\n// ─── Constants ─────────────────────────────────────────────\n\nconst LABEL_HEIGHT = 20;\nconst LABEL_GAP = 6;\nconst GEN_LABEL_MARGIN = 50;\n\n// ─── Public API ─────────────────────────────────────────────\n\nexport function layoutPedigree(\n  ast: DiagramAST,\n  config: LayoutConfig\n): LayoutResult {\n  const graph = buildGraph(ast);\n  assignGenerations(graph);\n  const ordered = orderNodesInGenerations(graph);\n  const positions = assignPositions(ordered, graph, config);\n  const edges = computeEdges(graph, positions, config);\n  return packageResult(positions, edges, graph, config);\n}\n\n// ─── Step 1: Build graph ────────────────────────────────────\n\nfunction buildGraph(ast: DiagramAST): LayoutGraph {\n  const individuals = new Map<string, Individual>();\n  for (const ind of ast.individuals) individuals.set(ind.id, ind);\n\n  const familyUnits: FamilyUnit[] = [];\n  const childOf = new Map<string, string>();\n\n  const coupleRels = ast.relationships.filter(\n    (r) => r.type === \"married\" || r.type === \"separated\" ||\n           r.type === \"consanguineous\" || r.type === \"cohabiting\"\n  );\n\n  for (const rel of coupleRels) {\n    const fuId = `${rel.from}+${rel.to}`;\n    const indA = individuals.get(rel.from);\n    const indB = individuals.get(rel.to);\n\n    let partners: [string, string];\n    if (indA && indB) {\n      if (indA.sex === \"male\" && indB.sex === \"female\") {\n        partners = [rel.from, rel.to];\n      } else if (indA.sex === \"female\" && indB.sex === \"male\") {\n        partners = [rel.to, rel.from];\n      } else {\n        partners = [rel.from, rel.to];\n      }\n    } else {\n      partners = [rel.from, rel.to];\n    }\n\n    const children: string[] = [];\n    for (const r of ast.relationships) {\n      if (r.type === \"parent-child\" && r.from === fuId) {\n        children.push(r.to);\n        childOf.set(r.to, fuId);\n      }\n    }\n\n    children.sort((a, b) => {\n      const ia = individuals.get(a);\n      const ib = individuals.get(b);\n      return (ia?.birthYear ?? 9999) - (ib?.birthYear ?? 9999);\n    });\n\n    familyUnits.push({ id: fuId, partners, relationship: rel.type, children });\n  }\n\n  return { individuals, familyUnits, generations: new Map(), childOf };\n}\n\n// ─── Step 2: Assign generations ─────────────────────────────\n\nfunction assignGenerations(graph: LayoutGraph): void {\n  const { individuals, familyUnits, childOf, generations } = graph;\n  const allIds = Array.from(individuals.keys());\n  const roots = allIds.filter((id) => !childOf.has(id));\n\n  if (roots.length === 0 && allIds.length > 0) {\n    for (const id of allIds) generations.set(id, 0);\n    return;\n  }\n\n  for (const root of roots) {\n    if (!generations.has(root)) generations.set(root, 0);\n  }\n\n  let changed = true;\n  while (changed) {\n    changed = false;\n    for (const fu of familyUnits) {\n      const gen0 = generations.get(fu.partners[0]);\n      const gen1 = generations.get(fu.partners[1]);\n\n      let partnerGen: number;\n      if (gen0 !== undefined && gen1 !== undefined) {\n        partnerGen = Math.max(gen0, gen1);\n        if (gen0 !== partnerGen) { generations.set(fu.partners[0], partnerGen); changed = true; }\n        if (gen1 !== partnerGen) { generations.set(fu.partners[1], partnerGen); changed = true; }\n      } else if (gen0 !== undefined) {\n        partnerGen = gen0;\n        generations.set(fu.partners[1], partnerGen); changed = true;\n      } else if (gen1 !== undefined) {\n        partnerGen = gen1;\n        generations.set(fu.partners[0], partnerGen); changed = true;\n      } else {\n        continue;\n      }\n\n      for (const childId of fu.children) {\n        const childGen = partnerGen + 1;\n        const existing = generations.get(childId);\n        if (existing === undefined || existing < childGen) {\n          generations.set(childId, childGen);\n          changed = true;\n        }\n      }\n    }\n  }\n\n  for (const id of allIds) {\n    if (!generations.has(id)) generations.set(id, 0);\n  }\n}\n\n// ─── Step 3: Order nodes ───────────────────────────────────\n\ninterface OrderedGeneration {\n  index: number;\n  nodeIds: string[];\n}\n\nfunction orderNodesInGenerations(graph: LayoutGraph): OrderedGeneration[] {\n  const genGroups = new Map<number, string[]>();\n  for (const [id, gen] of graph.generations) {\n    const grp = genGroups.get(gen) ?? [];\n    grp.push(id);\n    genGroups.set(gen, grp);\n  }\n\n  const genIndices = Array.from(genGroups.keys()).sort((a, b) => a - b);\n  const result: OrderedGeneration[] = [];\n\n  for (const genIdx of genIndices) {\n    const nodeIds = genGroups.get(genIdx) ?? [];\n    result.push({ index: genIdx, nodeIds: orderGeneration(nodeIds, graph) });\n  }\n\n  return result;\n}\n\nfunction orderGeneration(nodeIds: string[], graph: LayoutGraph): string[] {\n  if (nodeIds.length <= 1) return [...nodeIds];\n\n  const nodeSet = new Set(nodeIds);\n  const placed = new Set<string>();\n  const ordered: string[] = [];\n\n  const fuInGen = graph.familyUnits.filter(\n    (fu) => nodeSet.has(fu.partners[0]) || nodeSet.has(fu.partners[1])\n  );\n\n  for (const fu of fuInGen) {\n    for (const p of fu.partners) {\n      if (nodeSet.has(p) && !placed.has(p)) {\n        ordered.push(p);\n        placed.add(p);\n      }\n    }\n  }\n\n  for (const id of nodeIds) {\n    if (!placed.has(id)) {\n      ordered.push(id);\n      placed.add(id);\n    }\n  }\n\n  return ordered;\n}\n\n// ─── Step 4: Assign positions ──────────────────────────────\n\ninterface NodePosition {\n  id: string;\n  x: number;\n  y: number;\n  generation: number;\n}\n\nfunction assignPositions(\n  orderedGens: OrderedGeneration[],\n  graph: LayoutGraph,\n  config: LayoutConfig\n): Map<string, NodePosition> {\n  const positions = new Map<string, NodePosition>();\n  const { nodeWidth, nodeSpacingX } = config;\n  const half = nodeWidth / 2;\n  const coupleGap = nodeWidth + nodeSpacingX * 0.6;\n  const familyGap = nodeWidth + nodeSpacingX * 1.5;\n  const genStepY = config.nodeHeight + LABEL_HEIGHT + LABEL_GAP + config.nodeSpacingY;\n\n  for (const gen of orderedGens) {\n    const y = gen.index * genStepY + half;\n    const segments = buildSegments(gen.nodeIds, graph);\n\n    let xCursor = GEN_LABEL_MARGIN + half;\n    for (let s = 0; s < segments.length; s++) {\n      const seg = segments[s];\n      if (s > 0) xCursor += familyGap;\n\n      if (seg.type === \"couple\") {\n        positions.set(seg.ids[0], { id: seg.ids[0], x: xCursor, y, generation: gen.index });\n        xCursor += coupleGap;\n        positions.set(seg.ids[1], { id: seg.ids[1], x: xCursor, y, generation: gen.index });\n      } else {\n        positions.set(seg.ids[0], { id: seg.ids[0], x: xCursor, y, generation: gen.index });\n      }\n    }\n  }\n\n  resolveOverlaps(positions, orderedGens, config);\n  centerChildrenUnderParents(positions, graph, config);\n  resolveOverlaps(positions, orderedGens, config);\n\n  return positions;\n}\n\ninterface Segment {\n  type: \"couple\" | \"single\";\n  ids: string[];\n}\n\nfunction buildSegments(nodeIds: string[], graph: LayoutGraph): Segment[] {\n  const nodeSet = new Set(nodeIds);\n  const segments: Segment[] = [];\n  const placed = new Set<string>();\n\n  for (const id of nodeIds) {\n    if (placed.has(id)) continue;\n\n    const fu = graph.familyUnits.find(\n      (f) =>\n        (f.partners[0] === id || f.partners[1] === id) &&\n        !placed.has(f.partners[0]) &&\n        !placed.has(f.partners[1]) &&\n        nodeSet.has(f.partners[0]) &&\n        nodeSet.has(f.partners[1])\n    );\n\n    if (fu) {\n      segments.push({ type: \"couple\", ids: [fu.partners[0], fu.partners[1]] });\n      placed.add(fu.partners[0]);\n      placed.add(fu.partners[1]);\n    } else {\n      segments.push({ type: \"single\", ids: [id] });\n      placed.add(id);\n    }\n  }\n\n  return segments;\n}\n\nfunction centerChildrenUnderParents(\n  positions: Map<string, NodePosition>,\n  graph: LayoutGraph,\n  config: LayoutConfig\n): void {\n  const coupleGap = config.nodeSpacingX + config.nodeWidth;\n\n  const personToFUs = new Map<string, FamilyUnit[]>();\n  for (const fu of graph.familyUnits) {\n    for (const p of fu.partners) {\n      const arr = personToFUs.get(p) ?? [];\n      arr.push(fu);\n      personToFUs.set(p, arr);\n    }\n  }\n\n  for (let pass = 0; pass < 3; pass++) {\n    for (const fu of graph.familyUnits) {\n      if (fu.children.length === 0) continue;\n\n      const posA = positions.get(fu.partners[0]);\n      const posB = positions.get(fu.partners[1]);\n      if (!posA || !posB) continue;\n\n      const parentMidX = (posA.x + posB.x) / 2;\n      const childSpacing = config.nodeSpacingX + config.nodeWidth;\n\n      const sortedChildren = [...fu.children].sort((a, b) => {\n        const ia = graph.individuals.get(a);\n        const ib = graph.individuals.get(b);\n        return (ia?.birthYear ?? 9999) - (ib?.birthYear ?? 9999);\n      });\n\n      if (sortedChildren.length > 1) {\n        // Calculate per-gap spacing: add room for married-in spouses\n        const gaps: number[] = [];\n        for (let j = 0; j < sortedChildren.length - 1; j++) {\n          let gap = childSpacing;\n\n          // If the RIGHT child has a spouse placed to their LEFT\n          const nextChild = sortedChildren[j + 1];\n          const nextFUs = personToFUs.get(nextChild) ?? [];\n          for (const cfu of nextFUs) {\n            const pid = cfu.partners[0] === nextChild ? cfu.partners[1] : cfu.partners[0];\n            const cInd = graph.individuals.get(nextChild);\n            const pInd = graph.individuals.get(pid);\n            if (!(cInd?.sex === \"male\" || (cInd?.sex !== \"female\" && pInd?.sex === \"female\"))) {\n              gap += coupleGap;\n            }\n          }\n\n          // If the LEFT child has a spouse placed to their RIGHT\n          const currChild = sortedChildren[j];\n          const currFUs = personToFUs.get(currChild) ?? [];\n          for (const cfu of currFUs) {\n            const pid = cfu.partners[0] === currChild ? cfu.partners[1] : cfu.partners[0];\n            const cInd = graph.individuals.get(currChild);\n            const pInd = graph.individuals.get(pid);\n            if (cInd?.sex === \"male\" || (cInd?.sex !== \"female\" && pInd?.sex === \"female\")) {\n              gap += coupleGap;\n            }\n          }\n\n          gaps.push(gap);\n        }\n\n        const totalWidth = gaps.reduce((s, g) => s + g, 0);\n        const startX = parentMidX - totalWidth / 2;\n        let cx = startX;\n        for (let j = 0; j < sortedChildren.length; j++) {\n          const pos = positions.get(sortedChildren[j]);\n          if (pos) pos.x = cx;\n          if (j < gaps.length) cx += gaps[j];\n        }\n      } else {\n        const pos = positions.get(sortedChildren[0]);\n        if (pos) pos.x = parentMidX;\n      }\n\n      for (const childId of fu.children) {\n        const childPos = positions.get(childId);\n        if (!childPos) continue;\n        const childFUs = personToFUs.get(childId) ?? [];\n        for (const childFU of childFUs) {\n          const partnerId = childFU.partners[0] === childId ? childFU.partners[1] : childFU.partners[0];\n          const partnerPos = positions.get(partnerId);\n          if (!partnerPos) continue;\n          const childInd = graph.individuals.get(childId);\n          const partnerInd = graph.individuals.get(partnerId);\n          if (childInd?.sex === \"male\" || (childInd?.sex !== \"female\" && partnerInd?.sex === \"female\")) {\n            partnerPos.x = childPos.x + coupleGap;\n          } else {\n            partnerPos.x = childPos.x - coupleGap;\n          }\n        }\n      }\n    }\n  }\n}\n\nfunction resolveOverlaps(\n  positions: Map<string, NodePosition>,\n  orderedGens: OrderedGeneration[],\n  config: LayoutConfig\n): void {\n  const minGap = config.nodeWidth + config.nodeSpacingX;\n\n  for (const gen of orderedGens) {\n    const genNodes = gen.nodeIds\n      .map((id) => positions.get(id))\n      .filter((p): p is NodePosition => p !== undefined);\n    genNodes.sort((a, b) => a.x - b.x);\n\n    for (let j = 1; j < genNodes.length; j++) {\n      const gap = genNodes[j].x - genNodes[j - 1].x;\n      if (gap < minGap) {\n        const shift = minGap - gap;\n        for (let k = j; k < genNodes.length; k++) genNodes[k].x += shift;\n      }\n    }\n  }\n\n  let minX = Infinity;\n  for (const pos of positions.values()) {\n    if (pos.x < minX) minX = pos.x;\n  }\n  const minAllowed = GEN_LABEL_MARGIN + config.nodeWidth / 2;\n  if (minX < minAllowed) {\n    const shift = minAllowed - minX;\n    for (const pos of positions.values()) pos.x += shift;\n  }\n}\n\n// ─── Step 5: Compute edges ─────────────────────────────────\n\nfunction computeEdges(\n  graph: LayoutGraph,\n  positions: Map<string, NodePosition>,\n  config: LayoutConfig\n): LayoutEdge[] {\n  const edges: LayoutEdge[] = [];\n  const half = config.nodeWidth / 2;\n  const dropY_offset = config.nodeHeight / 2 + LABEL_HEIGHT + LABEL_GAP + config.nodeSpacingY * 0.35;\n\n  for (const fu of graph.familyUnits) {\n    const posA = positions.get(fu.partners[0]);\n    const posB = positions.get(fu.partners[1]);\n    if (!posA || !posB) continue;\n\n    const leftPos = posA.x < posB.x ? posA : posB;\n    const rightPos = posA.x < posB.x ? posB : posA;\n    const leftId = posA.x < posB.x ? fu.partners[0] : fu.partners[1];\n    const rightId = posA.x < posB.x ? fu.partners[1] : fu.partners[0];\n\n    const coupleRel: Relationship = { type: fu.relationship, from: leftId, to: rightId };\n    const couplePath = `M ${leftPos.x + half} ${leftPos.y} L ${rightPos.x - half} ${rightPos.y}`;\n    edges.push({ from: leftId, to: rightId, relationship: coupleRel, path: couplePath });\n\n    // Consanguinity: add second parallel line\n    if (fu.relationship === \"consanguineous\") {\n      const offset = 3;\n      const consPath = `M ${leftPos.x + half} ${leftPos.y + offset} L ${rightPos.x - half} ${rightPos.y + offset}`;\n      edges.push({\n        from: leftId, to: rightId,\n        relationship: { type: \"consanguineous\", from: leftId, to: rightId, label: \"_double\" },\n        path: consPath,\n      });\n    }\n\n    if (fu.children.length > 0) {\n      const midX = (posA.x + posB.x) / 2;\n      const coupleY = posA.y;\n      const dropY = coupleY + dropY_offset;\n\n      const childPositions = fu.children\n        .map((cid) => ({ id: cid, pos: positions.get(cid) }))\n        .filter((c): c is { id: string; pos: NodePosition } => c.pos !== undefined);\n\n      if (childPositions.length === 0) continue;\n      childPositions.sort((a, b) => a.pos.x - b.pos.x);\n\n      const leftX = childPositions[0].pos.x;\n      const rightX = childPositions[childPositions.length - 1].pos.x;\n\n      edges.push({\n        from: fu.partners[0], to: fu.partners[1],\n        relationship: { type: \"parent-child\", from: fu.id, to: \"_drop\" },\n        path: `M ${midX} ${coupleY} L ${midX} ${dropY}`,\n      });\n\n      if (childPositions.length > 1) {\n        edges.push({\n          from: fu.partners[0], to: fu.partners[1],\n          relationship: { type: \"parent-child\", from: fu.id, to: \"_sibship\" },\n          path: `M ${leftX} ${dropY} L ${rightX} ${dropY}`,\n        });\n      }\n\n      for (const child of childPositions) {\n        const childTop = child.pos.y - config.nodeHeight / 2;\n        const childPath = childPositions.length === 1\n          ? `M ${midX} ${coupleY} L ${midX} ${childTop}`\n          : `M ${child.pos.x} ${dropY} L ${child.pos.x} ${childTop}`;\n\n        edges.push({\n          from: fu.id, to: child.id,\n          relationship: { type: \"parent-child\", from: fu.id, to: child.id },\n          path: childPath,\n        });\n      }\n    }\n  }\n\n  return edges;\n}\n\n// ─── Step 6: Package result ─────────────────────────────────\n\nfunction packageResult(\n  positions: Map<string, NodePosition>,\n  edges: LayoutEdge[],\n  graph: LayoutGraph,\n  config: LayoutConfig\n): LayoutResult {\n  const padding = 40;\n  const nodes: LayoutNode[] = [];\n\n  for (const [id, pos] of positions) {\n    const ind = graph.individuals.get(id);\n    if (!ind) continue;\n    nodes.push({\n      id,\n      x: pos.x - config.nodeWidth / 2 + padding,\n      y: pos.y - config.nodeHeight / 2 + padding,\n      width: config.nodeWidth,\n      height: config.nodeHeight,\n      generation: pos.generation,\n      individual: ind,\n    });\n  }\n\n  const shiftedEdges = edges.map((e) => ({\n    ...e,\n    path: shiftPath(e.path, padding, padding),\n  }));\n\n  let maxX = 0;\n  let maxY = 0;\n  let minX = Infinity;\n  for (const node of nodes) {\n    const cx = node.x + node.width / 2;\n    const labelText = node.individual.label || node.individual.id;\n    const labelHalfWidth = labelText.length * 3.8;\n    const right = Math.max(node.x + node.width, cx + labelHalfWidth);\n    const left = Math.min(node.x, cx - labelHalfWidth);\n    const bottom = node.y + node.height;\n    if (right > maxX) maxX = right;\n    if (bottom > maxY) maxY = bottom;\n    if (left < minX) minX = left;\n  }\n\n  if (minX < 0) {\n    const shift = -minX;\n    for (const node of nodes) {\n      node.x += shift;\n    }\n    for (const edge of shiftedEdges) {\n      edge.path = shiftPath(edge.path, shift, 0);\n    }\n    maxX += shift;\n  }\n\n  return {\n    width: maxX + padding,\n    height: maxY + padding + LABEL_GAP + LABEL_HEIGHT + 10,\n    nodes,\n    edges: shiftedEdges,\n  };\n}\n\nfunction shiftPath(pathData: string, dx: number, dy: number): string {\n  return pathData.replace(\n    /([ML])\\s*([\\d.-]+)\\s+([\\d.-]+)/g,\n    (_match, cmd: string, xStr: string, yStr: string) => {\n      const x = parseFloat(xStr) + dx;\n      const y = parseFloat(yStr) + dy;\n      return `${cmd} ${x} ${y}`;\n    }\n  );\n}\n","/**\n * Auto-derive a LegendSpec from a pedigree AST.\n *\n * Pedigree-specific encodings:\n *   1. Trait fills (the legacy `legend: trait_id = \"Label\" (fill: ...)`\n *      directive) — merged into the unified system as a TRAITS section.\n *   2. Symbols (carriers, deceased, proband, etc.) — only when used.\n *\n * The standard square=Male / circle=Female convention is universal McGoldrick\n * and is excluded by default (matches genogram behavior).\n */\n\nimport type {\n  DiagramAST,\n  GeneticStatus,\n  LegendItem,\n  LegendSection,\n  LegendSpec,\n  Sex,\n} from \"../../core/types\";\nimport type { ResolvedTheme, PersonTokens } from \"../../core/theme\";\n\nconst SECTIONS: LegendSection[] = [\n  { id: \"status\", title: \"Genetic status\" },\n  { id: \"traits\", title: \"Traits\" },\n  { id: \"symbols\", title: \"Symbols\" },\n];\n\nconst OBVIOUS_SEX: ReadonlySet<Sex> = new Set<Sex>([\"male\", \"female\"]);\n\nexport function buildPedigreeLegend(\n  ast: DiagramAST,\n  theme: ResolvedTheme<PersonTokens>\n): LegendSpec {\n  const items: LegendItem[] = [];\n\n  // Genetic status: standard pedigree-chart encoding (unaffected omitted —\n  // it's the universal default).\n  const statusUsed = new Set<GeneticStatus>();\n  for (const ind of ast.individuals) {\n    if (ind.geneticStatus && ind.geneticStatus !== \"unaffected\") {\n      statusUsed.add(ind.geneticStatus);\n    }\n  }\n  const statusOrder: GeneticStatus[] = [\n    \"affected\",\n    \"carrier\",\n    \"carrier-x\",\n    \"obligate-carrier\",\n    \"presymptomatic\",\n  ];\n  for (const s of statusOrder) {\n    if (!statusUsed.has(s)) continue;\n    items.push(geneticStatusItem(s, theme));\n  }\n\n  // Legacy trait legend entries (when DSL uses `legend: cf = \"Cystic Fibrosis\"`).\n  if (ast.legend && ast.legend.length > 0) {\n    for (const entry of ast.legend) {\n      const isFull = !entry.fill || entry.fill === \"full\";\n      items.push({\n        key: entry.id,\n        label: entry.label,\n        kind: isFull ? \"fill\" : \"fill-pattern\",\n        color: entry.color ?? theme.conditionFill,\n        shape: isFull ? undefined : entry.fill,\n        section: \"traits\",\n      });\n    }\n  }\n\n  // Non-obvious sex shapes (unknown / nonbinary / intersex).\n  const sexUsed = new Set<Sex>();\n  for (const ind of ast.individuals) sexUsed.add(ind.sex);\n  const sexOrder: Sex[] = [\"unknown\", \"other\", \"nonbinary\", \"intersex\"];\n  for (const s of sexOrder) {\n    if (!sexUsed.has(s) || OBVIOUS_SEX.has(s)) continue;\n    items.push({\n      key: `sex.${s}`,\n      label: sexLabel(s),\n      kind: \"shape\",\n      shape: \"diamond\",\n      fill: theme.unknownFill,\n      color: theme.stroke,\n      section: \"symbols\",\n    });\n  }\n\n  // Deceased\n  const hasDeceased = ast.individuals.some((i) => i.status === \"deceased\");\n  if (hasDeceased) {\n    items.push({\n      key: \"status.deceased\",\n      label: \"Deceased\",\n      kind: \"marker\",\n      marker: \"slash\",\n      color: theme.deceasedMark,\n      section: \"symbols\",\n    });\n  }\n\n  // Proband / consultand markers\n  const hasProband = ast.individuals.some((i) => i.markers?.includes(\"proband\"));\n  if (hasProband) {\n    items.push({\n      key: \"marker.proband\",\n      label: \"Proband (P) — first affected case identified\",\n      kind: \"marker\",\n      marker: \"P\",\n      section: \"symbols\",\n    });\n  }\n  const hasConsultand = ast.individuals.some((i) => i.markers?.includes(\"consultand\"));\n  if (hasConsultand) {\n    items.push({\n      key: \"marker.consultand\",\n      label: \"Consultand (C)\",\n      kind: \"marker\",\n      marker: \"C\",\n      section: \"symbols\",\n    });\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 geneticStatusItem(\n  s: GeneticStatus,\n  theme: ResolvedTheme<PersonTokens>\n): LegendItem {\n  switch (s) {\n    case \"affected\":\n      return {\n        key: `status.${s}`,\n        label: \"Affected\",\n        kind: \"fill\",\n        color: theme.conditionFill,\n        section: \"status\",\n      };\n    case \"carrier\":\n      return {\n        key: `status.${s}`,\n        label: \"Carrier\",\n        kind: \"fill-pattern\",\n        color: theme.conditionFill,\n        shape: \"half-left\",\n        section: \"status\",\n      };\n    case \"carrier-x\":\n      return {\n        key: `status.${s}`,\n        label: \"X-linked carrier\",\n        kind: \"marker\",\n        marker: \"dot\",\n        color: theme.conditionFill,\n        section: \"status\",\n      };\n    case \"obligate-carrier\":\n      return {\n        key: `status.${s}`,\n        label: \"Obligate carrier\",\n        kind: \"marker\",\n        marker: \"dot\",\n        color: theme.conditionFill,\n        section: \"status\",\n      };\n    case \"presymptomatic\":\n      return {\n        key: `status.${s}`,\n        label: \"Presymptomatic\",\n        kind: \"line\",\n        color: theme.conditionFill,\n        pattern: \"solid\",\n        strokeWidth: 2,\n        section: \"status\",\n      };\n    default:\n      return {\n        key: `status.${s}`,\n        label: humanize(s),\n        kind: \"fill\",\n        color: theme.conditionFill,\n        section: \"status\",\n      };\n  }\n}\n\nfunction sexLabel(s: Sex): string {\n  switch (s) {\n    case \"unknown\": return \"Unknown sex\";\n    case \"other\": return \"Other\";\n    case \"nonbinary\": return \"Non-binary\";\n    case \"intersex\": return \"Intersex\";\n    default: return s;\n  }\n}\n\nfunction humanize(s: string): string {\n  return s.replace(/[-_]+/g, \" \").replace(/\\b\\w/g, (c) => c.toUpperCase());\n}\n","import type {\n  LayoutResult,\n  LayoutNode,\n  LayoutEdge,\n  RenderConfig,\n  Individual,\n  DiagramAST,\n} from \"../../core/types\";\nimport {\n  svgRoot,\n  el,\n  group,\n  rect,\n  circle,\n  polygon,\n  line,\n  text,\n  title,\n  desc,\n  defs,\n  path,\n} from \"../../core/svg\";\nimport { cssCustomProperties, resolvePersonTheme, STROKE_WIDTH, type ResolvedTheme, type PersonTokens } from \"../../core/theme\";\nimport { applyLegendOverrides, renderLegend as renderLegendCore } from \"../../core/legend\";\nimport { buildPedigreeLegend } from \"./legend\";\n\n// ─── Public API ─────────────────────────────────────────────\n\nexport function renderPedigree(\n  layout: LayoutResult,\n  config: RenderConfig,\n  ast?: DiagramAST\n): string {\n  const t = resolvePersonTheme(config.theme);\n  const defsStr = buildDefs(layout.nodes, t);\n  const styleStr = buildStyles(config, t);\n\n  const genGroups = groupByGeneration(layout.nodes);\n  const edgeLayers = renderEdges(layout.edges);\n  const nodeLayers = renderNodes(genGroups);\n  const labelLayer = renderLabels(layout.nodes, genGroups, config);\n  const genLabels = renderGenerationLabels(genGroups, config);\n\n  const nodeCount = layout.nodes.length;\n  const genCount = genGroups.size;\n\n  const diagramTitle = ast?.metadata?.title ?? \"Pedigree\";\n\n  const layers: string[] = [\n    title(diagramTitle),\n    desc(`Pedigree chart with ${nodeCount} individuals across ${genCount} generations`),\n    defsStr,\n    styleStr,\n  ];\n\n  // Defer chart-content push until legend bbox is known so we can center.\n  const chartContent = [genLabels, edgeLayers, ...nodeLayers, labelLayer];\n\n  let finalWidth = layout.width;\n  let finalHeight = layout.height;\n  let legendSvg = \"\";\n\n  if (ast) {\n    const autoSpec = buildPedigreeLegend(ast, t);\n    const finalSpec = applyLegendOverrides(autoSpec, ast.legendOverrides);\n    if (finalSpec.mode === \"on\" && finalSpec.items.length > 0) {\n      const { svg, bbox: lb } = renderLegendCore(\n        finalSpec,\n        {\n          canvasWidth: layout.width,\n          canvasHeight: layout.height,\n          padding: 16,\n        },\n        t,\n        { fontFamily: config.fontFamily, fontSize: config.fontSize }\n      );\n      if (svg) {\n        legendSvg = svg;\n        const overflowX = lb.x + lb.w + 8;\n        const overflowY = lb.y + lb.h + 8;\n        if (overflowX > finalWidth) finalWidth = overflowX;\n        if (overflowY > finalHeight) finalHeight = overflowY;\n      }\n    }\n  }\n\n  const chartXOffset = Math.max(0, (finalWidth - layout.width) / 2);\n  layers.push(\n    group(\n      { transform: chartXOffset > 0 ? `translate(${chartXOffset}, 0)` : undefined },\n      chartContent\n    )\n  );\n  if (legendSvg) layers.push(legendSvg);\n\n  return svgRoot(\n    {\n      viewBox: `0 0 ${finalWidth} ${finalHeight}`,\n      class: \"schematex-diagram schematex-pedigree\",\n      width: finalWidth,\n      height: finalHeight,\n    },\n    layers\n  );\n}\n\n// ─── Defs ──────────────────────────────────────────────────\n\nfunction buildDefs(nodes: LayoutNode[], t: ResolvedTheme<PersonTokens>): string {\n  const children: string[] = [];\n  const needs = new Set<string>();\n\n  for (const n of nodes) {\n    const gs = n.individual.geneticStatus;\n    if (gs) needs.add(gs);\n  }\n\n  if (needs.has(\"carrier\")) {\n    children.push(\n      el(\"clipPath\", { id: \"schematex-pedigree-clip-carrier-rect\" }, [\n        rect({ x: \"0\", y: \"0\", width: \"50%\", height: \"100%\" }),\n      ]),\n      el(\"clipPath\", { id: \"schematex-pedigree-clip-carrier-circle\" }, [\n        rect({ x: \"-50\", y: \"-50\", width: \"50\", height: \"100\" }),\n      ])\n    );\n  }\n\n  // Proband arrow marker\n  children.push(\n    el(\"marker\", {\n      id: \"schematex-pedigree-proband-arrow\",\n      viewBox: \"0 0 10 10\",\n      refX: \"0\",\n      refY: \"5\",\n      markerWidth: \"8\",\n      markerHeight: \"8\",\n      orient: \"auto-start-reverse\",\n    }, [\n      path({ d: \"M 0 0 L 10 5 L 0 10 z\", fill: t.stroke }),\n    ])\n  );\n\n  return defs(children);\n}\n\n// ─── Styles ────────────────────────────────────────────────\n\nfunction buildStyles(config: RenderConfig, t: ResolvedTheme<PersonTokens>): string {\n  const css = `\n.schematex-pedigree {${cssCustomProperties(t)}\n}\n.schematex-pedigree-shape { fill: ${t.fill}; stroke: ${t.stroke}; stroke-width: ${STROKE_WIDTH.normal}; stroke-linejoin: round; }\n.schematex-pedigree-label { font-family: ${config.fontFamily}; font-size: ${config.fontSize}px; text-anchor: middle; fill: ${t.text}; }\n.schematex-pedigree-gen-label { font-family: ${config.fontFamily}; font-size: 14px; font-weight: bold; fill: ${t.text}; text-anchor: middle; }\n.schematex-pedigree-edge { stroke: ${t.stroke}; stroke-width: ${STROKE_WIDTH.normal}; fill: none; stroke-linecap: round; stroke-linejoin: round; }\n.schematex-pedigree-deceased-mark { stroke: ${t.deceasedMark}; stroke-width: ${STROKE_WIDTH.normal}; stroke-linecap: round; }\n.schematex-pedigree-affected-fill { fill: ${t.conditionFill}; }\n.schematex-pedigree-carrier-fill { fill: ${t.conditionFill}; }\n.schematex-pedigree-carrier-x-dot { fill: ${t.conditionFill}; }\n.schematex-pedigree-presymptomatic-mark { stroke: ${t.conditionFill}; stroke-width: ${STROKE_WIDTH.normal}; }\n.schematex-pedigree-proband-arrow-line { stroke: ${t.stroke}; stroke-width: ${STROKE_WIDTH.normal}; fill: none; marker-end: url(#schematex-pedigree-proband-arrow); }\n.schematex-pedigree-proband-label { font-family: ${config.fontFamily}; font-size: 10px; font-weight: bold; fill: ${t.stroke}; }\n.schematex-pedigree-loss-shape { fill: ${t.stroke}; stroke: ${t.stroke}; stroke-width: ${STROKE_WIDTH.normal}; stroke-linejoin: round; }\n.schematex-pedigree-tab-slash { stroke: ${t.deceasedMark}; stroke-width: ${STROKE_WIDTH.normal}; stroke-linecap: round; }\n.schematex-pedigree-status-label { font-family: ${config.fontFamily}; font-size: 10px; font-weight: bold; fill: ${t.text}; }\n.schematex-pedigree-legend { font-family: ${config.fontFamily}; font-size: 11px; fill: ${t.text}; }\n.schematex-pedigree-legend-box { fill: ${t.fill}; stroke: ${t.neutral}; stroke-width: 1; }\n`;\n  return el(\"style\", {}, css);\n}\n\n// ─── Edges ─────────────────────────────────────────────────\n\nfunction renderEdges(edges: LayoutEdge[]): string {\n  const children: string[] = [];\n\n  for (const edge of edges) {\n    const relType = edge.relationship.type;\n    const cssClass = `schematex-pedigree-edge schematex-pedigree-edge-${relType}`;\n\n    const elements: string[] = [\n      el(\"path\", { d: edge.path, class: \"schematex-pedigree-edge-path\" }),\n    ];\n\n    if (relType === \"separated\") {\n      const mid = pathMidpoint(edge.path);\n      if (mid) {\n        elements.push(\n          line({\n            x1: mid.x - 4, y1: mid.y - 6,\n            x2: mid.x + 4, y2: mid.y + 6,\n            class: \"schematex-pedigree-edge\",\n          })\n        );\n      }\n    }\n\n    children.push(\n      group({ class: cssClass, \"data-from\": edge.from, \"data-to\": edge.to }, elements)\n    );\n  }\n\n  return group({ class: \"schematex-pedigree-edges\" }, children);\n}\n\nfunction pathMidpoint(pathData: string): { x: number; y: number } | null {\n  const coords = pathData.match(/[\\d.-]+/g);\n  if (!coords || coords.length < 4) return null;\n  return {\n    x: (parseFloat(coords[0]) + parseFloat(coords[2])) / 2,\n    y: (parseFloat(coords[1]) + parseFloat(coords[3])) / 2,\n  };\n}\n\n// ─── Nodes ─────────────────────────────────────────────────\n\nfunction groupByGeneration(nodes: LayoutNode[]): Map<number, LayoutNode[]> {\n  const groups = new Map<number, LayoutNode[]>();\n  for (const node of nodes) {\n    const grp = groups.get(node.generation) ?? [];\n    grp.push(node);\n    groups.set(node.generation, grp);\n  }\n  return groups;\n}\n\nfunction renderNodes(genGroups: Map<number, LayoutNode[]>): string[] {\n  const layers: string[] = [];\n  const sortedGens = Array.from(genGroups.keys()).sort((a, b) => a - b);\n\n  for (const genIdx of sortedGens) {\n    const nodes = genGroups.get(genIdx) ?? [];\n    const nodeElements: string[] = [];\n\n    for (const node of nodes) {\n      const cx = node.x + node.width / 2;\n      const cy = node.y + node.height / 2;\n      nodeElements.push(renderPedigreeSymbol(node.individual, cx, cy, node.width));\n    }\n\n    layers.push(\n      group(\n        { class: `schematex-pedigree-generation schematex-pedigree-generation-${genIdx}`, \"data-generation\": genIdx },\n        nodeElements\n      )\n    );\n  }\n\n  return layers;\n}\n\nfunction renderPedigreeSymbol(\n  ind: Individual,\n  x: number,\n  y: number,\n  size: number\n): string {\n  const half = size / 2;\n  const classes = [\"schematex-pedigree-node\", `schematex-pedigree-${ind.sex === \"other\" ? \"unknown\" : ind.sex}`];\n  if (ind.status === \"deceased\") classes.push(\"schematex-pedigree-deceased\");\n  if (ind.geneticStatus) classes.push(`schematex-pedigree-${ind.geneticStatus}`);\n\n  const titleText = formatTitle(ind);\n  const children: string[] = [title(titleText)];\n\n  // NSGC pregnancy-loss: filled point-down triangle (~60% size). TAB adds slash; Ectopic adds \"ECT\".\n  const pregLoss = ind.status === \"sab\" || ind.status === \"tab\" || ind.status === \"ectopic\";\n  if (pregLoss) {\n    classes.push(`schematex-pedigree-${ind.status}`);\n    const t = half * 0.6;\n    children.push(\n      polygon({\n        points: `${-t},${-t} ${t},${-t} 0,${t}`,\n        class: `schematex-pedigree-loss-shape schematex-pedigree-${ind.status}-shape`,\n      })\n    );\n    if (ind.status === \"tab\") {\n      children.push(\n        line({\n          x1: -t * 1.1, y1: t * 1.1, x2: t * 1.1, y2: -t * 1.1,\n          class: \"schematex-pedigree-tab-slash\",\n        })\n      );\n    }\n    if (ind.status === \"ectopic\") {\n      children.push(\n        text(\n          { x: 0, y: t + 14, class: \"schematex-pedigree-status-label\", \"text-anchor\": \"middle\" },\n          \"ECT\"\n        )\n      );\n    }\n    // Skip regular shape + genetic-status fills — not applicable.\n    return group(\n      {\n        class: classes.join(\" \"),\n        \"data-individual-id\": ind.id,\n        transform: `translate(${x}, ${y})`,\n      },\n      children\n    );\n  }\n\n  // Base shape\n  children.push(baseShape(ind.sex, half));\n\n  // Stillborn: keep the sex-based shape, add an \"SB\" label below.\n  if (ind.status === \"stillborn\") {\n    classes.push(\"schematex-pedigree-stillborn\");\n    children.push(\n      text(\n        { x: 0, y: half + 14, class: \"schematex-pedigree-status-label\", \"text-anchor\": \"middle\" },\n        \"SB\"\n      )\n    );\n  }\n\n  // Genetic status fills\n  const gs = ind.geneticStatus;\n  if (gs === \"affected\") {\n    children.push(affectedFill(ind.sex, half));\n  } else if (gs === \"carrier\") {\n    children.push(carrierFill(ind.sex, half));\n  } else if (gs === \"carrier-x\" || gs === \"obligate-carrier\") {\n    children.push(carrierDot(half));\n  }\n\n  // Presymptomatic vertical line\n  if (gs === \"presymptomatic\") {\n    children.push(\n      line({ x1: 0, y1: -half, x2: 0, y2: half, class: \"schematex-pedigree-presymptomatic-mark\" })\n    );\n  }\n\n  // Deceased: diagonal slash (pedigree uses / not X)\n  if (ind.status === \"deceased\") {\n    const ext = ind.sex === \"female\" ? half * 0.707 : half;\n    children.push(\n      line({ x1: ext, y1: -ext, x2: -ext, y2: ext, class: \"schematex-pedigree-deceased-mark\" })\n    );\n  }\n\n  // Proband arrow\n  if (ind.markers?.includes(\"proband\")) {\n    const arrowLen = 20;\n    children.push(\n      line({\n        x1: -half - arrowLen, y1: half + arrowLen,\n        x2: -half - 2, y2: half + 2,\n        class: \"schematex-pedigree-proband-arrow-line\",\n      }),\n      text(\n        { x: -half - arrowLen - 4, y: half + arrowLen + 4, class: \"schematex-pedigree-proband-label\", \"text-anchor\": \"end\" },\n        \"P\"\n      )\n    );\n  }\n\n  // Consultand arrow\n  if (ind.markers?.includes(\"consultand\")) {\n    const arrowLen = 20;\n    children.push(\n      line({\n        x1: -half - arrowLen, y1: half + arrowLen,\n        x2: -half - 2, y2: half + 2,\n        class: \"schematex-pedigree-proband-arrow-line\",\n      }),\n      text(\n        { x: -half - arrowLen - 4, y: half + arrowLen + 4, class: \"schematex-pedigree-proband-label\", \"text-anchor\": \"end\" },\n        \"C\"\n      )\n    );\n  }\n\n  // Evaluated marker\n  if (ind.markers?.includes(\"evaluated\")) {\n    children.push(\n      text(\n        { x: 0, y: -half - 4, class: \"schematex-pedigree-proband-label\", \"text-anchor\": \"middle\" },\n        \"E\"\n      )\n    );\n  }\n\n  return group(\n    {\n      class: classes.join(\" \"),\n      \"data-individual-id\": ind.id,\n      transform: `translate(${x}, ${y})`,\n    },\n    children\n  );\n}\n\nfunction baseShape(sex: Individual[\"sex\"], half: number): string {\n  switch (sex) {\n    case \"male\":\n      return rect({ x: -half, y: -half, width: half * 2, height: half * 2, class: \"schematex-pedigree-shape\" });\n    case \"female\":\n      return circle({ cx: 0, cy: 0, r: half, class: \"schematex-pedigree-shape\" });\n    default:\n      return polygon({ points: `0,${-half} ${half},0 0,${half} ${-half},0`, class: \"schematex-pedigree-shape\" });\n  }\n}\n\nfunction affectedFill(sex: Individual[\"sex\"], half: number): string {\n  const attrs = { class: \"schematex-pedigree-affected-fill\" };\n  switch (sex) {\n    case \"male\":\n      return rect({ x: -half, y: -half, width: half * 2, height: half * 2, ...attrs });\n    case \"female\":\n      return circle({ cx: 0, cy: 0, r: half, ...attrs });\n    default:\n      return polygon({ points: `0,${-half} ${half},0 0,${half} ${-half},0`, ...attrs });\n  }\n}\n\nfunction carrierFill(sex: Individual[\"sex\"], half: number): string {\n  const clipSuffix = sex === \"female\" ? \"circle\" : \"rect\";\n  const attrs = {\n    class: \"schematex-pedigree-carrier-fill\",\n    \"clip-path\": `url(#schematex-pedigree-clip-carrier-${clipSuffix})`,\n  };\n  switch (sex) {\n    case \"male\":\n      return rect({ x: -half, y: -half, width: half * 2, height: half * 2, ...attrs });\n    case \"female\":\n      return circle({ cx: 0, cy: 0, r: half, ...attrs });\n    default:\n      return polygon({ points: `0,${-half} ${half},0 0,${half} ${-half},0`, ...attrs });\n  }\n}\n\nfunction carrierDot(half: number): string {\n  return circle({ cx: 0, cy: 0, r: half * 0.15, class: \"schematex-pedigree-carrier-x-dot\" });\n}\n\nfunction formatTitle(ind: Individual): string {\n  const name = ind.label.charAt(0).toUpperCase() + ind.label.slice(1);\n  if (ind.geneticStatus && ind.geneticStatus !== \"unaffected\") {\n    return `${name} (${ind.geneticStatus})`;\n  }\n  return name;\n}\n\n// ─── Labels ────────────────────────────────────────────────\n\nfunction renderLabels(\n  nodes: LayoutNode[],\n  genGroups: Map<number, LayoutNode[]>,\n  config: RenderConfig\n): string {\n  const labels: string[] = [];\n\n  // Build per-generation numbering\n  const genNumbering = new Map<string, string>();\n  const sortedGens = Array.from(genGroups.keys()).sort((a, b) => a - b);\n  for (const genIdx of sortedGens) {\n    const genNodes = genGroups.get(genIdx) ?? [];\n    const sorted = [...genNodes].sort((a, b) => a.x - b.x);\n    const romanNum = toRoman(genIdx + 1);\n    for (let i = 0; i < sorted.length; i++) {\n      genNumbering.set(sorted[i].id, `${romanNum}-${i + 1}`);\n    }\n  }\n\n  for (const node of nodes) {\n    const ind = node.individual;\n    const cx = node.x + node.width / 2;\n    const labelY = node.y + node.height + 6 + config.fontSize;\n\n    const pedigreeId = genNumbering.get(ind.id) ?? ind.id;\n    const displayLabel = ind.label !== ind.id ? ind.label : pedigreeId;\n\n    labels.push(\n      text(\n        { x: cx, y: labelY, class: \"schematex-pedigree-label\", \"data-individual-id\": ind.id },\n        displayLabel\n      )\n    );\n  }\n\n  return group({ class: \"schematex-pedigree-labels\" }, labels);\n}\n\n// ─── Generation Labels ─────────────────────────────────────\n\nfunction renderGenerationLabels(\n  genGroups: Map<number, LayoutNode[]>,\n  _config: RenderConfig\n): string {\n  const labels: string[] = [];\n  const sortedGens = Array.from(genGroups.keys()).sort((a, b) => a - b);\n\n  for (const genIdx of sortedGens) {\n    const nodes = genGroups.get(genIdx) ?? [];\n    if (nodes.length === 0) continue;\n\n    const midY = nodes[0].y + nodes[0].height / 2;\n    const roman = toRoman(genIdx + 1);\n\n    labels.push(\n      text(\n        { x: 25, y: midY + 5, class: \"schematex-pedigree-gen-label\" },\n        roman\n      )\n    );\n  }\n\n  return group({ class: \"schematex-pedigree-generation-labels\" }, labels);\n}\n\n// ─── Legend ────────────────────────────────────────────────\n// (moved to ./legend.ts; rendered via core/legend)\n\n// ─── Helpers ───────────────────────────────────────────────\n\nfunction toRoman(n: number): string {\n  const vals = [1000, 900, 500, 400, 100, 90, 50, 40, 10, 9, 5, 4, 1];\n  const syms = [\"M\", \"CM\", \"D\", \"CD\", \"C\", \"XC\", \"L\", \"XL\", \"X\", \"IX\", \"V\", \"IV\", \"I\"];\n  let result = \"\";\n  for (let i = 0; i < vals.length; i++) {\n    while (n >= vals[i]) {\n      result += syms[i];\n      n -= vals[i];\n    }\n  }\n  return result;\n}\n","import type { DiagramPlugin, RenderConfig } from \"../../core/types\";\nimport { parsePedigree, PedigreeParseError } from \"./parser\";\nimport { layoutPedigree } from \"./layout\";\nimport { renderPedigree } from \"./renderer\";\n\nexport const pedigree: DiagramPlugin = {\n  type: \"pedigree\",\n\n  detect(text: string): boolean {\n    const firstLine = text.trim().split(\"\\n\")[0]?.trim().toLowerCase() ?? \"\";\n    return firstLine === \"pedigree\" || firstLine.startsWith(\"pedigree \");\n  },\n\n  parse: parsePedigree,\n\n  render(text: string, config?: RenderConfig): string {\n    const ast = parsePedigree(text);\n    const layoutConfig = {\n      nodeSpacingX: 80,\n      nodeSpacingY: 100,\n      nodeWidth: 40,\n      nodeHeight: 40,\n    };\n    const layout = layoutPedigree(ast, layoutConfig);\n    const renderConfig: RenderConfig = {\n      fontFamily: config?.fontFamily ?? \"system-ui, -apple-system, sans-serif\",\n      fontSize: config?.fontSize ?? 12,\n      theme: config?.theme ?? \"default\",\n      padding: config?.padding ?? 20,\n    };\n    return renderPedigree(layout, renderConfig, ast);\n  },\n};\n\nexport { parsePedigree, PedigreeParseError, layoutPedigree, renderPedigree };\n"]}

package/dist/{chunk-CWZKP3CJ.cjs → chunk-CQP5YHVK.cjs}

@@ -630,7 +630,6 @@ function buildCSS(ast, t) {
   return `
 .schematex-phylo {${chunkD7EHZFK4_cjs.cssCustomProperties(t)}
   font-family: system-ui, -apple-system, sans-serif;
-  background: ${t.bg};
 }
 .schematex-phylo-branch { fill: none; stroke: ${t.text}; stroke-width: ${chunkD7EHZFK4_cjs.STROKE_WIDTH.normal}; stroke-linecap: round; }
 .schematex-phylo-branch-connector { fill: none; stroke: ${t.text}; stroke-width: ${chunkD7EHZFK4_cjs.STROKE_WIDTH.normal}; }
@@ -892,5 +891,5 @@ exports.layoutPhylo = layoutPhylo;
 exports.parsePhylo = parsePhylo;
 exports.phylo = phylo;
 exports.renderPhylo = renderPhylo;
-//# sourceMappingURL=chunk-CWZKP3CJ.cjs.map
-//# sourceMappingURL=chunk-CWZKP3CJ.cjs.map
+//# sourceMappingURL=chunk-CQP5YHVK.cjs.map
+//# sourceMappingURL=chunk-CQP5YHVK.cjs.map

package/dist/chunk-CQP5YHVK.cjs.map

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 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  let title: string | undefined;\n  const titleMatch = headerLine.match(/\"([^\"]+)\"/);\n  if (titleMatch) title = titleMatch[1];\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"]}

package/dist/{chunk-QXL7AY2H.cjs → chunk-CS67UBP3.cjs}

@@ -612,7 +612,7 @@ function renderBlockDiagram(ast) {
   const { width } = layout;
   const height = layout.height + titleOffset;
   const css = `
-.schematex-bd { background: #fff; font-family: system-ui, -apple-system, sans-serif; }
+.schematex-bd { font-family: system-ui, -apple-system, sans-serif; }
 .schematex-bd-block { stroke: #333; stroke-width: 2; }
 .schematex-bd-tf { font: italic 14px serif; fill: #111; }
 .schematex-bd-block-name { font: 10px sans-serif; fill: #666; }
@@ -807,5 +807,5 @@ exports.blockdiagram = blockdiagram;
 exports.layoutBlockDiagram = layoutBlockDiagram;
 exports.parseBlockDiagram = parseBlockDiagram;
 exports.renderBlockDiagram = renderBlockDiagram;
-//# sourceMappingURL=chunk-QXL7AY2H.cjs.map
-//# sourceMappingURL=chunk-QXL7AY2H.cjs.map
+//# sourceMappingURL=chunk-CS67UBP3.cjs.map
+//# sourceMappingURL=chunk-CS67UBP3.cjs.map