schematex 0.6.9 → 0.7.0

package/dist/chunk-JAYJ2G4R.cjs.map

@@ -0,0 +1 @@
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\"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   * Dendrogram (hierarchical-clustering) mode flag. Dendrogram is a phylo-local\n   * mode layered on top of the cladogram base `mode`; it is carried in AST\n   * metadata (not the shared `PhyloMode` union) so the dendrogram feature stays\n   * isolated inside the phylo folder.\n   */\n  dendrogram?: boolean;\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(/^[\"']|[\"']$/g, \"\");\n\n    switch (key) {\n      case \"layout\":\n        if ([\"rectangular\", \"slanted\", \"circular\", \"unrooted\"].includes(val)) {\n          result.layout = val as PhyloLayout;\n        }\n        break;\n      case \"mode\":\n        if ([\"phylogram\", \"cladogram\", \"chronogram\"].includes(val)) {\n          result.mode = val as PhyloMode;\n        } else if (val === \"dendrogram\") {\n          // Dendrogram is a phylo-local mode (not in the shared PhyloMode\n          // union). It reuses the cladogram base for any code that only knows\n          // the standard modes, and is flagged separately for the dendrogram\n          // layout/renderer.\n          result.mode = \"cladogram\";\n          result.dendrogram = true;\n        }\n        break;\n      case \"branch-width\":\n        result.branchWidth = Number(val);\n        break;\n      case \"openAngle\":\n        result.openAngle = Number(val);\n        break;\n      case \"mrsd\":\n        result.mrsd = val;\n        break;\n    }\n  }\n\n  if (result.layout === \"unrooted\") {\n    result.unrooted = true;\n  }\n\n  return result;\n}\n\nfunction parseCladeLine(line: string): CladeDef | null {\n  // clade ID = (member1, member2, ...) [color: \"#hex\", label: \"text\", highlight: mode]\n  const match = line.match(\n    /^clade\\s+(\\S+)\\s*=\\s*\\(([^)]+)\\)\\s*(?:\\[([^\\]]*)\\])?\\s*$/\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  let cut: number | 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    // Cut line (dendrogram threshold): \"cut 1.5\" or \"cut: 1.5\"\n    if (/^cut\\b/i.test(trimmed)) {\n      const cutStr = trimmed.replace(/^cut\\s*:?\\s*/i, \"\").trim();\n      const cutVal = Number(cutStr);\n      if (!Number.isNaN(cutVal)) cut = cutVal;\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  // Dendrogram mode + cut threshold are phylo-local concerns carried in\n  // metadata so the dendrogram feature stays inside the phylo folder without\n  // extending the shared PhyloMode union or PhyloTreeAST interface.\n  const metadata: Record<string, string> = {};\n  if (headerProps.dendrogram) metadata.dendrogram = \"true\";\n  if (cut !== undefined) metadata.cut = String(cut);\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\";\nimport type { PhyloLayoutResult, PhyloBranch } from \"./layout\";\n\n// ─── Dendrogram (hierarchical-clustering tree) ───────────────\n//\n// A dendrogram differs from a cladogram in that internal nodes are positioned\n// at their *merge height* (the cluster distance at which two sub-clusters\n// join). Leaves all align at the baseline (height 0). Connectors are\n// rectangular \"elbow\" U-shapes. An optional `cut` threshold slices the tree\n// into flat clusters, each drawn in a distinct colour.\n//\n// Convention (matching the rest of the phylo engine — root on the left,\n// tips on the right):\n//   - height 0  → rightmost  (leaves)\n//   - maxHeight → leftmost   (root)\n//   - x = PADDING_LEFT + (maxHeight - height) * scale\n//\n// This module is phylo-local: dendrogram mode is flagged via\n// `ast.metadata.dendrogram === \"true\"` rather than the shared PhyloMode union.\n\nconst TIP_SPACING = 24;\nconst PADDING_LEFT = 20;\nconst PADDING_RIGHT = 20;\nconst PADDING_TOP = 24;\nconst PADDING_BOTTOM = 52;\n\n/** Is this AST a dendrogram (phylo-local mode carried in metadata)? */\nexport function isDendrogram(ast: PhyloTreeAST): boolean {\n  return ast.metadata?.dendrogram === \"true\";\n}\n\n/** Parsed cut threshold, or undefined when no `cut` directive was given. */\nexport function getCut(ast: PhyloTreeAST): number | undefined {\n  const raw = ast.metadata?.cut;\n  if (raw === undefined) return undefined;\n  const val = Number(raw);\n  return Number.isNaN(val) ? undefined : val;\n}\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 estimateLabelWidth(node: PhyloNode): number {\n  const label = node.label ?? node.id;\n  return label.length * 7.2 + 6;\n}\n\n/**\n * Merge height of a node = the cophenetic height at which its sub-clusters\n * join, computed as the maximum branch-length distance from this node down to\n * any descendant tip. Leaves have height 0. This is the standard\n * hierarchical-clustering interpretation and is stable for arbitrary\n * branch-length inputs.\n */\nfunction computeHeights(node: PhyloNode, out: Map<string, number>): number {\n  if (node.isLeaf) {\n    out.set(node.id, 0);\n    return 0;\n  }\n  let max = 0;\n  for (const child of node.children) {\n    const childHeight = computeHeights(child, out);\n    const branch = child.branchLength ?? 0;\n    const reach = childHeight + branch;\n    if (reach > max) max = reach;\n  }\n  out.set(node.id, max);\n  return max;\n}\n\n/**\n * Compute flat clusters produced by a horizontal/vertical cut at `cutValue`.\n * A cluster is the maximal subtree rooted at a node whose merge height is\n * <= cutValue but whose parent's merge height is > cutValue (i.e. the cut line\n * severs the edge above it). Returns one entry per cluster: the cluster's root\n * node and the set of leaf ids it contains.\n */\nexport interface DendrogramCluster {\n  rootId: string;\n  leafIds: string[];\n}\n\nexport function computeClusters(\n  ast: PhyloTreeAST,\n  heights: Map<string, number>,\n  cutValue: number\n): DendrogramCluster[] {\n  const clusters: DendrogramCluster[] = [];\n\n  function visit(node: PhyloNode, parentHeight: number): void {\n    const h = heights.get(node.id) ?? 0;\n    // The edge entering `node` crosses the cut line when the parent merges\n    // above the cut but this node merges at/below it. The root is treated as\n    // having an infinite parent height.\n    if (h <= cutValue && parentHeight > cutValue) {\n      clusters.push({ rootId: node.id, leafIds: collectLeaves(node).map((l) => l.id) });\n      return;\n    }\n    // Node merges above the cut — descend; its children may form clusters.\n    if (h > cutValue) {\n      for (const child of node.children) visit(child, h);\n    } else {\n      // h <= cut and parent <= cut: already inside a containing cluster — this\n      // branch is unreachable for the root call but kept for completeness.\n      clusters.push({ rootId: node.id, leafIds: collectLeaves(node).map((l) => l.id) });\n    }\n  }\n\n  visit(ast.root, Number.POSITIVE_INFINITY);\n  return clusters;\n}\n\nexport function layoutDendrogram(ast: PhyloTreeAST): PhyloLayoutResult {\n  const leaves = collectLeaves(ast.root);\n  const numLeaves = leaves.length;\n\n  const heights = new Map<string, number>();\n  const maxHeight = computeHeights(ast.root, heights);\n\n  const maxLabelWidth = Math.max(...leaves.map(estimateLabelWidth), 60);\n  const availableWidth = Math.max(320, numLeaves * 36 + maxLabelWidth + 120);\n  const plotWidth = availableWidth - PADDING_LEFT - PADDING_RIGHT - maxLabelWidth;\n\n  // Pixels per unit of merge height.\n  const scale = maxHeight > 0 ? plotWidth / maxHeight : plotWidth;\n\n  // Baseline (height 0) sits at the right edge of the plot; root at the left.\n  const baselineX = PADDING_LEFT + plotWidth;\n  const heightToX = (h: number): number => baselineX - h * scale;\n\n  const nodeMap = new Map<string, PhyloLayoutNode>();\n\n  // Step 1: leaf Y in-order, leaf X pinned to baseline.\n  let leafIdx = 0;\n  function assignLeaf(node: PhyloNode): void {\n    if (node.isLeaf) {\n      const y = PADDING_TOP + leafIdx * TIP_SPACING;\n      nodeMap.set(node.id, { node, x: baselineX, y });\n      leafIdx++;\n      return;\n    }\n    for (const child of node.children) assignLeaf(child);\n  }\n  assignLeaf(ast.root);\n\n  // Step 2: internal Y = midpoint of children; X from merge height.\n  function assignInternal(node: PhyloNode): number {\n    const existing = nodeMap.get(node.id);\n    if (node.isLeaf && existing) return existing.y;\n    const childYs = node.children.map(assignInternal);\n    const y = (Math.min(...childYs) + Math.max(...childYs)) / 2;\n    const x = heightToX(heights.get(node.id) ?? 0);\n    if (existing) {\n      existing.y = y;\n      existing.x = x;\n    } else {\n      nodeMap.set(node.id, { node, x, y });\n    }\n    return y;\n  }\n  assignInternal(ast.root);\n\n  // Optional cut → assign each leaf a cluster index for colouring.\n  const cut = getCut(ast);\n  const leafCluster = new Map<string, number>();\n  let clusterCount = 0;\n  if (cut !== undefined) {\n    const clusters = computeClusters(ast, heights, cut);\n    clusterCount = clusters.length;\n    clusters.forEach((cluster, idx) => {\n      for (const leafId of cluster.leafIds) leafCluster.set(leafId, idx);\n    });\n  }\n\n  /** Cluster index for an internal node's outgoing edge, when its whole\n   * subtree lies in a single cut cluster; otherwise undefined (above the cut). */\n  function subtreeCluster(node: PhyloNode): number | undefined {\n    const ids = collectLeaves(node).map((l) => l.id);\n    const first = leafCluster.get(ids[0]);\n    if (first === undefined) return undefined;\n    for (const id of ids) {\n      if (leafCluster.get(id) !== first) return undefined;\n    }\n    return first;\n  }\n\n  // Step 3: rectangular elbow connectors.\n  const branches: PhyloBranch[] = [];\n\n  function generate(node: PhyloNode): void {\n    if (node.children.length === 0) return;\n    const parent = nodeMap.get(node.id);\n    if (!parent) return;\n\n    const childLayouts = node.children\n      .map((c) => nodeMap.get(c.id))\n      .filter((l): l is PhyloLayoutNode => l !== undefined);\n    if (childLayouts.length === 0) return;\n\n    const minY = Math.min(...childLayouts.map((c) => c.y));\n    const maxY = Math.max(...childLayouts.map((c) => c.y));\n\n    // Vertical bar of the U at the node's merge-height X, spanning children.\n    branches.push({\n      path: `M ${parent.x},${minY} V ${maxY}`,\n      fromId: node.id,\n      toId: node.id,\n      isConnector: true,\n    });\n\n    // Horizontal arm of the U out to each child's X.\n    for (const child of node.children) {\n      const childLayout = nodeMap.get(child.id);\n      if (!childLayout) continue;\n      const cluster = subtreeCluster(child);\n      branches.push({\n        path: `M ${parent.x},${childLayout.y} H ${childLayout.x}`,\n        fromId: node.id,\n        toId: child.id,\n        cladeId: cluster !== undefined ? `cut${cluster}` : undefined,\n        isConnector: false,\n      });\n    }\n\n    for (const child of node.children) generate(child);\n  }\n  generate(ast.root);\n\n  const allNodes = Array.from(nodeMap.values());\n  const maxX = Math.max(\n    ...allNodes.map((n) => n.x + (n.node.isLeaf ? estimateLabelWidth(n.node) : 0))\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    // Dendrogram-specific extras stashed for the renderer (see types below).\n    dendrogram: {\n      maxHeight,\n      baselineX,\n      plotLeftX: PADDING_LEFT,\n      scale,\n      cut,\n      clusterCount,\n      leafCluster,\n      heights,\n    },\n  };\n}\n","import type {\n  PhyloTreeAST,\n  PhyloNode,\n  PhyloLayoutNode,\n} from \"../../core/types\";\nimport { isDendrogram, layoutDendrogram } from \"./dendrogram\";\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  /** Present only for dendrogram mode — drives the height axis + cut line. */\n  dendrogram?: DendrogramExtras;\n}\n\n/** Dendrogram-only layout metadata (phylo-local; see ./dendrogram.ts). */\nexport interface DendrogramExtras {\n  /** Largest merge height in the tree (root's height). */\n  maxHeight: number;\n  /** X pixel of the height-0 baseline (where leaves align). */\n  baselineX: number;\n  /** X pixel of the plot's left edge (root / max height). */\n  plotLeftX: number;\n  /** Pixels per unit of merge height. */\n  scale: number;\n  /** Cut threshold value, when a `cut` directive was given. */\n  cut?: number;\n  /** Number of flat clusters produced by the cut (0 when no cut). */\n  clusterCount: number;\n  /** Leaf id → cluster index (empty when no cut). */\n  leafCluster: Map<string, number>;\n  /** Node id → merge height. */\n  heights: Map<string, 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  if (isDendrogram(ast)) {\n    return layoutDendrogram(ast);\n  }\n\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: ${color}; }`;\n  });\n\n  // Dendrogram cut-cluster colours. The cluster count is layout-dependent, so\n  // emit one class per palette entry keyed off the biology clade palette; the\n  // layout assigns each cluster an index `cut{i}` that maps to these.\n  const cutColors: string[] = [];\n  if (ast.metadata?.dendrogram === \"true\" && ast.metadata?.cut !== undefined) {\n    for (let i = 0; i < t.cladeColors.length; i++) {\n      cutColors.push(\n        `.schematex-phylo-clade-cut${i} { stroke: ${t.cladeColors[i % t.cladeColors.length]}; }`\n      );\n    }\n  }\n\n  return `\n.schematex-phylo {${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-dendro-axis line { stroke: ${t.text}; stroke-width: ${STROKE_WIDTH.thin}; }\n.schematex-phylo-dendro-axis text { font-size: 10px; fill: ${t.textMuted}; text-anchor: middle; }\n.schematex-phylo-dendro-cut { stroke: ${t.supportBad}; stroke-width: ${STROKE_WIDTH.normal}; stroke-dasharray: 5 4; fill: none; }\n.schematex-phylo-dendro-cut-label { font-size: 10px; fill: ${t.supportBad}; text-anchor: start; }\n${cutColors.join(\"\\n\")}\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// ─── Dendrogram Height Axis + Cut Line ──────────────────────\n\n/** \"Nice\" step for the height axis so ticks land on round numbers. */\nfunction niceStep(maxHeight: number, targetTicks: number): number {\n  if (maxHeight <= 0) return 1;\n  const rough = maxHeight / targetTicks;\n  const mag = Math.pow(10, Math.floor(Math.log10(rough)));\n  const norm = rough / mag;\n  let step: number;\n  if (norm < 1.5) step = 1;\n  else if (norm < 3) step = 2;\n  else if (norm < 7) step = 5;\n  else step = 10;\n  return step * mag;\n}\n\nfunction formatTick(value: number): string {\n  if (value === 0) return \"0\";\n  if (Math.abs(value) < 0.01) return value.toExponential(0);\n  return String(Math.round(value * 1000) / 1000);\n}\n\nfunction renderDendrogramAxis(\n  layout: PhyloLayoutResult,\n  t: ResolvedTheme<BiologyTokens>\n): string {\n  const d = layout.dendrogram;\n  if (!d) return \"\";\n\n  const axisY = layout.height - 28;\n  const elements: string[] = [];\n\n  // Axis baseline from root (left, max height) to tips (right, height 0).\n  elements.push(\n    line({ x1: d.plotLeftX, y1: axisY, x2: d.baselineX, y2: axisY })\n  );\n\n  const step = niceStep(d.maxHeight, 5);\n  for (let h = 0; h <= d.maxHeight + step * 0.001; h += step) {\n    const x = d.baselineX - h * d.scale;\n    elements.push(line({ x1: x, y1: axisY, x2: x, y2: axisY + 4 }));\n    elements.push(\n      text({ x, y: axisY + 16, \"text-anchor\": \"middle\" }, formatTick(h))\n    );\n  }\n\n  if (layout.ast.scaleLabel) {\n    elements.push(\n      text(\n        {\n          x: (d.plotLeftX + d.baselineX) / 2,\n          y: axisY + 28,\n          \"text-anchor\": \"middle\",\n          \"font-size\": \"9\",\n          fill: t.textMuted,\n        },\n        layout.ast.scaleLabel\n      )\n    );\n  }\n\n  return group({ class: \"schematex-phylo-dendro-axis\" }, elements);\n}\n\nfunction renderCutLine(layout: PhyloLayoutResult): string {\n  const d = layout.dendrogram;\n  if (!d || d.cut === undefined) return \"\";\n\n  const x = d.baselineX - d.cut * d.scale;\n  const topY = 8;\n  const bottomY = layout.height - 32;\n\n  return group({}, [\n    line({\n      x1: x,\n      y1: topY,\n      x2: x,\n      y2: bottomY,\n      class: \"schematex-phylo-dendro-cut\",\n    }),\n    text(\n      { x: x + 4, y: topY + 4, class: \"schematex-phylo-dendro-cut-label\" },\n      `cut = ${formatTick(d.cut)}`\n    ),\n  ]);\n}\n\n// ─── Main Renderer ──────────────────────────────────────────\n\nexport function renderPhylo(layout: PhyloLayoutResult): string {\n  const { ast, nodes, branches } = layout;\n  const t = resolveBiologyTheme(ast.metadata?.theme ?? \"default\");\n\n  const css = buildCSS(ast, t);\n\n  const titleOffset = ast.title ? 30 : 0;\n  const totalHeight = layout.height + titleOffset;\n  const totalWidth = layout.width;\n\n  // Build layers\n  const branchElements: string[] = [];\n  const nodeElements: string[] = [];\n  const labelElements: string[] = [];\n\n  // Branches\n  for (const branch of branches) {\n    const cladeIdx = branch.cladeId\n      ? ast.clades.findIndex((c) => c.id === branch.cladeId)\n      : -1;\n    const cladeColor =\n      cladeIdx >= 0\n        ? ast.clades[cladeIdx].color ?? t.cladeColors[cladeIdx % t.cladeColors.length]\n        : undefined;\n\n    const cls = branch.isConnector\n      ? \"schematex-phylo-branch schematex-phylo-branch-connector\"\n      : `schematex-phylo-branch schematex-phylo-branch-internal${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 (phylogram/chronogram) OR dendrogram height axis + cut line.\n  const isDendro = layout.dendrogram !== undefined;\n  const scaleBarEl = isDendro ? \"\" : renderScaleBar(layout, t, ast.scaleLabel);\n  const dendroAxisEl = isDendro ? renderDendrogramAxis(layout, t) : \"\";\n  const cutLineEl = isDendro ? renderCutLine(layout) : \"\";\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 isDendrogramMode = layout.dendrogram !== undefined;\n  const descMode = isDendrogramMode ? \"dendrogram\" : ast.mode;\n  const descTitle = isDendrogramMode ? \"Dendrogram\" : \"Phylogenetic Tree\";\n  const cutSuffix =\n    isDendrogramMode && layout.dendrogram?.cut !== undefined\n      ? `, cut at ${layout.dendrogram.cut} into ${layout.dendrogram.clusterCount} clusters`\n      : \"\";\n  const svgContent = [\n    title(`${descTitle}${ast.title ? `: ${ast.title}` : \"\"}`),\n    desc(\n      `${isDendrogramMode ? \"Dendrogram\" : \"Phylogenetic tree\"} with ${leafCount} taxa, ${descMode} mode, ${ast.layout} layout${cutSuffix}`\n    ),\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,${transformY})` : undefined },\n        [scaleBarEl]\n      )\n    );\n  }\n\n  if (dendroAxisEl) {\n    svgContent.push(\n      group(\n        { transform: transformY ? `translate(0,${transformY})` : undefined },\n        [dendroAxisEl]\n      )\n    );\n  }\n\n  if (cutLineEl) {\n    svgContent.push(\n      group(\n        { transform: transformY ? `translate(0,${transformY})` : undefined },\n        [cutLineEl]\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/diagrams/phylo/index.cjs

@@ -1,6 +1,6 @@
 'use strict';
 
-var chunkBL57NQKN_cjs = require('../../chunk-BL57NQKN.cjs');
+var chunkJAYJ2G4R_cjs = require('../../chunk-JAYJ2G4R.cjs');
 require('../../chunk-NZT5P2XZ.cjs');
 require('../../chunk-NAGUZFXX.cjs');
 require('../../chunk-3WNW5Y7P.cjs');
@@ -9,23 +9,23 @@ require('../../chunk-3WNW5Y7P.cjs');
 
 Object.defineProperty(exports, "PhyloParseError", {
   enumerable: true,
-  get: function () { return chunkBL57NQKN_cjs.PhyloParseError; }
+  get: function () { return chunkJAYJ2G4R_cjs.PhyloParseError; }
 });
 Object.defineProperty(exports, "layoutPhylo", {
   enumerable: true,
-  get: function () { return chunkBL57NQKN_cjs.layoutPhylo; }
+  get: function () { return chunkJAYJ2G4R_cjs.layoutPhylo; }
 });
 Object.defineProperty(exports, "parsePhylo", {
   enumerable: true,
-  get: function () { return chunkBL57NQKN_cjs.parsePhylo; }
+  get: function () { return chunkJAYJ2G4R_cjs.parsePhylo; }
 });
 Object.defineProperty(exports, "phylo", {
   enumerable: true,
-  get: function () { return chunkBL57NQKN_cjs.phylo; }
+  get: function () { return chunkJAYJ2G4R_cjs.phylo; }
 });
 Object.defineProperty(exports, "renderPhylo", {
   enumerable: true,
-  get: function () { return chunkBL57NQKN_cjs.renderPhylo; }
+  get: function () { return chunkJAYJ2G4R_cjs.renderPhylo; }
 });
 //# sourceMappingURL=index.cjs.map
 //# sourceMappingURL=index.cjs.map

package/dist/diagrams/phylo/index.d.cts

@@ -13,6 +13,27 @@ interface PhyloLayoutResult {
     branches: PhyloBranch[];
     ast: PhyloTreeAST;
     scale: number;
+    /** Present only for dendrogram mode — drives the height axis + cut line. */
+    dendrogram?: DendrogramExtras;
+}
+/** Dendrogram-only layout metadata (phylo-local; see ./dendrogram.ts). */
+interface DendrogramExtras {
+    /** Largest merge height in the tree (root's height). */
+    maxHeight: number;
+    /** X pixel of the height-0 baseline (where leaves align). */
+    baselineX: number;
+    /** X pixel of the plot's left edge (root / max height). */
+    plotLeftX: number;
+    /** Pixels per unit of merge height. */
+    scale: number;
+    /** Cut threshold value, when a `cut` directive was given. */
+    cut?: number;
+    /** Number of flat clusters produced by the cut (0 when no cut). */
+    clusterCount: number;
+    /** Leaf id → cluster index (empty when no cut). */
+    leafCluster: Map<string, number>;
+    /** Node id → merge height. */
+    heights: Map<string, number>;
 }
 interface PhyloBranch {
     path: string;

package/dist/diagrams/phylo/index.d.ts

@@ -13,6 +13,27 @@ interface PhyloLayoutResult {
     branches: PhyloBranch[];
     ast: PhyloTreeAST;
     scale: number;
+    /** Present only for dendrogram mode — drives the height axis + cut line. */
+    dendrogram?: DendrogramExtras;
+}
+/** Dendrogram-only layout metadata (phylo-local; see ./dendrogram.ts). */
+interface DendrogramExtras {
+    /** Largest merge height in the tree (root's height). */
+    maxHeight: number;
+    /** X pixel of the height-0 baseline (where leaves align). */
+    baselineX: number;
+    /** X pixel of the plot's left edge (root / max height). */
+    plotLeftX: number;
+    /** Pixels per unit of merge height. */
+    scale: number;
+    /** Cut threshold value, when a `cut` directive was given. */
+    cut?: number;
+    /** Number of flat clusters produced by the cut (0 when no cut). */
+    clusterCount: number;
+    /** Leaf id → cluster index (empty when no cut). */
+    leafCluster: Map<string, number>;
+    /** Node id → merge height. */
+    heights: Map<string, number>;
 }
 interface PhyloBranch {
     path: string;

package/dist/diagrams/phylo/index.js

@@ -1,4 +1,4 @@
-export { PhyloParseError, layoutPhylo, parsePhylo, phylo, renderPhylo } from '../../chunk-HL5PS6MG.js';
+export { PhyloParseError, layoutPhylo, parsePhylo, phylo, renderPhylo } from '../../chunk-EENA7KNU.js';
 import '../../chunk-UK6HF6PE.js';
 import '../../chunk-5IKOLUWK.js';
 import '../../chunk-SYYBKDL7.js';

package/dist/index.cjs

@@ -1,6 +1,6 @@
 'use strict';
 
-var chunk5IZL57YJ_cjs = require('./chunk-5IZL57YJ.cjs');
+var chunkHFATQXFN_cjs = require('./chunk-HFATQXFN.cjs');
 var chunkUHPGWO77_cjs = require('./chunk-UHPGWO77.cjs');
 var chunkJ3EPFZPX_cjs = require('./chunk-J3EPFZPX.cjs');
 var chunkSHMG7BVF_cjs = require('./chunk-SHMG7BVF.cjs');
@@ -14,7 +14,7 @@ var chunkNFZMNKOR_cjs = require('./chunk-NFZMNKOR.cjs');
 var chunk2SZJQVPN_cjs = require('./chunk-2SZJQVPN.cjs');
 var chunkKGOZBABH_cjs = require('./chunk-KGOZBABH.cjs');
 require('./chunk-3KRL2EGN.cjs');
-var chunkBL57NQKN_cjs = require('./chunk-BL57NQKN.cjs');
+var chunkJAYJ2G4R_cjs = require('./chunk-JAYJ2G4R.cjs');
 var chunk5FYPSIGD_cjs = require('./chunk-5FYPSIGD.cjs');
 require('./chunk-5UCXMYE7.cjs');
 var chunk2F45Y2ON_cjs = require('./chunk-2F45Y2ON.cjs');
@@ -111,10 +111,10 @@ var PID_CSS = ".lt-pid-equip{fill:#ffffff;stroke:#1d1d1d;stroke-width:1.6}.lt-pi
 function pidCatalog() {
   const out = [];
   const pad = 12;
-  for (const [id, g] of Object.entries(chunk5IZL57YJ_cjs.GEOMETRY)) {
+  for (const [id, g] of Object.entries(chunkHFATQXFN_cjs.GEOMETRY)) {
     let inner;
     try {
-      inner = chunk5IZL57YJ_cjs.renderEquip(id, "");
+      inner = chunkHFATQXFN_cjs.renderEquip(id, "");
     } catch {
       continue;
     }
@@ -224,11 +224,11 @@ var NETWORK_KINDS = [
 function networkCatalog() {
   const out = [];
   for (const kind of NETWORK_KINDS) {
-    const { w, h } = chunk5IZL57YJ_cjs.iconSize(kind);
+    const { w, h } = chunkHFATQXFN_cjs.iconSize(kind);
     const device = { id: kind, kind, label: humanize(kind), groups: [] };
     let inner;
     try {
-      inner = chunk5IZL57YJ_cjs.drawDeviceIcon(device, { x: 0, y: 0, w, h });
+      inner = chunkHFATQXFN_cjs.drawDeviceIcon(device, { x: 0, y: 0, w, h });
     } catch {
       continue;
     }
@@ -286,75 +286,75 @@ function getSymbolCatalog(type) {
 
 Object.defineProperty(exports, "bowtie", {
   enumerable: true,
-  get: function () { return chunk5IZL57YJ_cjs.bowtie; }
+  get: function () { return chunkHFATQXFN_cjs.bowtie; }
 });
 Object.defineProperty(exports, "decisiontree", {
   enumerable: true,
-  get: function () { return chunk5IZL57YJ_cjs.decisiontree; }
+  get: function () { return chunkHFATQXFN_cjs.decisiontree; }
 });
 Object.defineProperty(exports, "faulttree", {
   enumerable: true,
-  get: function () { return chunk5IZL57YJ_cjs.faulttree; }
+  get: function () { return chunkHFATQXFN_cjs.faulttree; }
 });
 Object.defineProperty(exports, "network", {
   enumerable: true,
-  get: function () { return chunk5IZL57YJ_cjs.network; }
+  get: function () { return chunkHFATQXFN_cjs.network; }
 });
 Object.defineProperty(exports, "parse", {
   enumerable: true,
-  get: function () { return chunk5IZL57YJ_cjs.parse; }
+  get: function () { return chunkHFATQXFN_cjs.parse; }
 });
 Object.defineProperty(exports, "parseResult", {
   enumerable: true,
-  get: function () { return chunk5IZL57YJ_cjs.parseResult; }
+  get: function () { return chunkHFATQXFN_cjs.parseResult; }
 });
 Object.defineProperty(exports, "pert", {
   enumerable: true,
-  get: function () { return chunk5IZL57YJ_cjs.pert; }
+  get: function () { return chunkHFATQXFN_cjs.pert; }
 });
 Object.defineProperty(exports, "petri", {
   enumerable: true,
-  get: function () { return chunk5IZL57YJ_cjs.petri; }
+  get: function () { return chunkHFATQXFN_cjs.petri; }
 });
 Object.defineProperty(exports, "pid", {
   enumerable: true,
-  get: function () { return chunk5IZL57YJ_cjs.pid; }
+  get: function () { return chunkHFATQXFN_cjs.pid; }
 });
 Object.defineProperty(exports, "prisma", {
   enumerable: true,
-  get: function () { return chunk5IZL57YJ_cjs.prisma; }
+  get: function () { return chunkHFATQXFN_cjs.prisma; }
 });
 Object.defineProperty(exports, "render", {
   enumerable: true,
-  get: function () { return chunk5IZL57YJ_cjs.render; }
+  get: function () { return chunkHFATQXFN_cjs.render; }
 });
 Object.defineProperty(exports, "renderPreview", {
   enumerable: true,
-  get: function () { return chunk5IZL57YJ_cjs.renderPreview; }
+  get: function () { return chunkHFATQXFN_cjs.renderPreview; }
 });
 Object.defineProperty(exports, "renderResult", {
   enumerable: true,
-  get: function () { return chunk5IZL57YJ_cjs.renderResult; }
+  get: function () { return chunkHFATQXFN_cjs.renderResult; }
 });
 Object.defineProperty(exports, "sequence", {
   enumerable: true,
-  get: function () { return chunk5IZL57YJ_cjs.sequence; }
+  get: function () { return chunkHFATQXFN_cjs.sequence; }
 });
 Object.defineProperty(exports, "state", {
   enumerable: true,
-  get: function () { return chunk5IZL57YJ_cjs.state; }
+  get: function () { return chunkHFATQXFN_cjs.state; }
 });
 Object.defineProperty(exports, "timeline", {
   enumerable: true,
-  get: function () { return chunk5IZL57YJ_cjs.timeline; }
+  get: function () { return chunkHFATQXFN_cjs.timeline; }
 });
 Object.defineProperty(exports, "umlclass", {
   enumerable: true,
-  get: function () { return chunk5IZL57YJ_cjs.umlclass; }
+  get: function () { return chunkHFATQXFN_cjs.umlclass; }
 });
 Object.defineProperty(exports, "usecase", {
   enumerable: true,
-  get: function () { return chunk5IZL57YJ_cjs.usecase; }
+  get: function () { return chunkHFATQXFN_cjs.usecase; }
 });
 Object.defineProperty(exports, "orgchart", {
   enumerable: true,
@@ -406,7 +406,7 @@ Object.defineProperty(exports, "pedigree", {
 });
 Object.defineProperty(exports, "phylo", {
   enumerable: true,
-  get: function () { return chunkBL57NQKN_cjs.phylo; }
+  get: function () { return chunkJAYJ2G4R_cjs.phylo; }
 });
 Object.defineProperty(exports, "sociogram", {
   enumerable: true,

package/dist/index.js

@@ -1,5 +1,5 @@
-import { iconSize, drawDeviceIcon, GEOMETRY, renderEquip } from './chunk-3DPWFWQU.js';
-export { bowtie, decisiontree, faulttree, network, parse, parseResult, pert, petri, pid, prisma, render, renderPreview, renderResult, sequence, state, timeline, umlclass, usecase } from './chunk-3DPWFWQU.js';
+import { iconSize, drawDeviceIcon, GEOMETRY, renderEquip } from './chunk-IFNNV54X.js';
+export { bowtie, decisiontree, faulttree, network, parse, parseResult, pert, petri, pid, prisma, render, renderPreview, renderResult, sequence, state, timeline, umlclass, usecase } from './chunk-IFNNV54X.js';
 export { orgchart } from './chunk-MPCSWRZC.js';
 import { EXTRA_SYMBOLS, SYMBOLS } from './chunk-2TUZ3QJA.js';
 export { circuit } from './chunk-2TUZ3QJA.js';
@@ -16,7 +16,7 @@ export { genogram } from './chunk-6NUAGU6O.js';
 export { ecomap } from './chunk-K2D6VFLP.js';
 export { pedigree } from './chunk-JN6FHUC6.js';
 import './chunk-2KTQ75LN.js';
-export { phylo } from './chunk-HL5PS6MG.js';
+export { phylo } from './chunk-EENA7KNU.js';
 export { sociogram } from './chunk-OFKRELZK.js';
 import './chunk-FO7BLCEW.js';
 export { timing } from './chunk-P26FCZP3.js';

package/dist/react.cjs

@@ -1,6 +1,6 @@
 'use strict';
 
-var chunk5IZL57YJ_cjs = require('./chunk-5IZL57YJ.cjs');
+var chunkHFATQXFN_cjs = require('./chunk-HFATQXFN.cjs');
 require('./chunk-UHPGWO77.cjs');
 require('./chunk-J3EPFZPX.cjs');
 require('./chunk-SHMG7BVF.cjs');
@@ -14,7 +14,7 @@ require('./chunk-NFZMNKOR.cjs');
 require('./chunk-2SZJQVPN.cjs');
 require('./chunk-KGOZBABH.cjs');
 require('./chunk-3KRL2EGN.cjs');
-require('./chunk-BL57NQKN.cjs');
+require('./chunk-JAYJ2G4R.cjs');
 require('./chunk-5FYPSIGD.cjs');
 require('./chunk-5UCXMYE7.cjs');
 require('./chunk-2F45Y2ON.cjs');
@@ -37,7 +37,7 @@ function SchematexDiagram({
   onError
 }) {
   const svg = react.useMemo(() => {
-    const result = chunk5IZL57YJ_cjs.renderResult(dsl, { type, theme, fontFamily, padding });
+    const result = chunkHFATQXFN_cjs.renderResult(dsl, { type, theme, fontFamily, padding });
     if (!result.ok) {
       onError?.(new Error(result.diagnostics[0]?.message ?? "Schematex render failed"));
     }

package/dist/react.js

@@ -1,4 +1,4 @@
-import { renderResult } from './chunk-3DPWFWQU.js';
+import { renderResult } from './chunk-IFNNV54X.js';
 import './chunk-MPCSWRZC.js';
 import './chunk-2TUZ3QJA.js';
 import './chunk-C7V57V6O.js';
@@ -12,7 +12,7 @@ import './chunk-6NUAGU6O.js';
 import './chunk-K2D6VFLP.js';
 import './chunk-JN6FHUC6.js';
 import './chunk-2KTQ75LN.js';
-import './chunk-HL5PS6MG.js';
+import './chunk-EENA7KNU.js';
 import './chunk-OFKRELZK.js';
 import './chunk-FO7BLCEW.js';
 import './chunk-P26FCZP3.js';

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "schematex",
-  "version": "0.6.9",
+  "version": "0.7.0",
   "description": "Every diagram a doctor, engineer, or lawyer would actually use. 36 industry-standard diagrams (genogram, pedigree, ladder logic, SLD, FBD, SFC, P&ID, UML class, UML use case, UML sequence, fault tree, bowtie, PRISMA, phylo, fishbone, entity structure, ...) from a text DSL. Free, fully open source, made for AI. Pure SVG, zero dependencies.",
   "type": "module",
   "main": "./dist/index.cjs",