@sjcrh/proteinpaint-client 2.191.4 → 2.192.0

package/dist/chunk-VQZ2Z5YU.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/d3-hierarchy/src/hierarchy/count.js", "../../node_modules/d3-hierarchy/src/hierarchy/each.js", "../../node_modules/d3-hierarchy/src/hierarchy/eachBefore.js", "../../node_modules/d3-hierarchy/src/hierarchy/eachAfter.js", "../../node_modules/d3-hierarchy/src/hierarchy/find.js", "../../node_modules/d3-hierarchy/src/hierarchy/sum.js", "../../node_modules/d3-hierarchy/src/hierarchy/sort.js", "../../node_modules/d3-hierarchy/src/hierarchy/path.js", "../../node_modules/d3-hierarchy/src/hierarchy/ancestors.js", "../../node_modules/d3-hierarchy/src/hierarchy/descendants.js", "../../node_modules/d3-hierarchy/src/hierarchy/leaves.js", "../../node_modules/d3-hierarchy/src/hierarchy/links.js", "../../node_modules/d3-hierarchy/src/hierarchy/iterator.js", "../../node_modules/d3-hierarchy/src/hierarchy/index.js", "../../node_modules/d3-hierarchy/src/array.js", "../../node_modules/d3-hierarchy/src/lcg.js", "../../node_modules/d3-hierarchy/src/pack/enclose.js", "../../node_modules/d3-hierarchy/src/pack/siblings.js", "../../node_modules/d3-hierarchy/src/treemap/round.js", "../../node_modules/d3-hierarchy/src/treemap/dice.js", "../../node_modules/d3-hierarchy/src/partition.js", "../../node_modules/d3-hierarchy/src/accessors.js", "../../node_modules/d3-hierarchy/src/stratify.js"],
+  "sourcesContent": ["function count(node) {\n  var sum = 0,\n      children = node.children,\n      i = children && children.length;\n  if (!i) sum = 1;\n  else while (--i >= 0) sum += children[i].value;\n  node.value = sum;\n}\n\nexport default function() {\n  return this.eachAfter(count);\n}\n", "export default function(callback, that) {\n  let index = -1;\n  for (const node of this) {\n    callback.call(that, node, ++index, this);\n  }\n  return this;\n}\n", "export default function(callback, that) {\n  var node = this, nodes = [node], children, i, index = -1;\n  while (node = nodes.pop()) {\n    callback.call(that, node, ++index, this);\n    if (children = node.children) {\n      for (i = children.length - 1; i >= 0; --i) {\n        nodes.push(children[i]);\n      }\n    }\n  }\n  return this;\n}\n", "export default function(callback, that) {\n  var node = this, nodes = [node], next = [], children, i, n, index = -1;\n  while (node = nodes.pop()) {\n    next.push(node);\n    if (children = node.children) {\n      for (i = 0, n = children.length; i < n; ++i) {\n        nodes.push(children[i]);\n      }\n    }\n  }\n  while (node = next.pop()) {\n    callback.call(that, node, ++index, this);\n  }\n  return this;\n}\n", "export default function(callback, that) {\n  let index = -1;\n  for (const node of this) {\n    if (callback.call(that, node, ++index, this)) {\n      return node;\n    }\n  }\n}\n", "export default function(value) {\n  return this.eachAfter(function(node) {\n    var sum = +value(node.data) || 0,\n        children = node.children,\n        i = children && children.length;\n    while (--i >= 0) sum += children[i].value;\n    node.value = sum;\n  });\n}\n", "export default function(compare) {\n  return this.eachBefore(function(node) {\n    if (node.children) {\n      node.children.sort(compare);\n    }\n  });\n}\n", "export default function(end) {\n  var start = this,\n      ancestor = leastCommonAncestor(start, end),\n      nodes = [start];\n  while (start !== ancestor) {\n    start = start.parent;\n    nodes.push(start);\n  }\n  var k = nodes.length;\n  while (end !== ancestor) {\n    nodes.splice(k, 0, end);\n    end = end.parent;\n  }\n  return nodes;\n}\n\nfunction leastCommonAncestor(a, b) {\n  if (a === b) return a;\n  var aNodes = a.ancestors(),\n      bNodes = b.ancestors(),\n      c = null;\n  a = aNodes.pop();\n  b = bNodes.pop();\n  while (a === b) {\n    c = a;\n    a = aNodes.pop();\n    b = bNodes.pop();\n  }\n  return c;\n}\n", "export default function() {\n  var node = this, nodes = [node];\n  while (node = node.parent) {\n    nodes.push(node);\n  }\n  return nodes;\n}\n", "export default function() {\n  return Array.from(this);\n}\n", "export default function() {\n  var leaves = [];\n  this.eachBefore(function(node) {\n    if (!node.children) {\n      leaves.push(node);\n    }\n  });\n  return leaves;\n}\n", "export default function() {\n  var root = this, links = [];\n  root.each(function(node) {\n    if (node !== root) { // Don\u2019t include the root\u2019s parent, if any.\n      links.push({source: node.parent, target: node});\n    }\n  });\n  return links;\n}\n", "export default function*() {\n  var node = this, current, next = [node], children, i, n;\n  do {\n    current = next.reverse(), next = [];\n    while (node = current.pop()) {\n      yield node;\n      if (children = node.children) {\n        for (i = 0, n = children.length; i < n; ++i) {\n          next.push(children[i]);\n        }\n      }\n    }\n  } while (next.length);\n}\n", "import node_count from \"./count.js\";\nimport node_each from \"./each.js\";\nimport node_eachBefore from \"./eachBefore.js\";\nimport node_eachAfter from \"./eachAfter.js\";\nimport node_find from \"./find.js\";\nimport node_sum from \"./sum.js\";\nimport node_sort from \"./sort.js\";\nimport node_path from \"./path.js\";\nimport node_ancestors from \"./ancestors.js\";\nimport node_descendants from \"./descendants.js\";\nimport node_leaves from \"./leaves.js\";\nimport node_links from \"./links.js\";\nimport node_iterator from \"./iterator.js\";\n\nexport default function hierarchy(data, children) {\n  if (data instanceof Map) {\n    data = [undefined, data];\n    if (children === undefined) children = mapChildren;\n  } else if (children === undefined) {\n    children = objectChildren;\n  }\n\n  var root = new Node(data),\n      node,\n      nodes = [root],\n      child,\n      childs,\n      i,\n      n;\n\n  while (node = nodes.pop()) {\n    if ((childs = children(node.data)) && (n = (childs = Array.from(childs)).length)) {\n      node.children = childs;\n      for (i = n - 1; i >= 0; --i) {\n        nodes.push(child = childs[i] = new Node(childs[i]));\n        child.parent = node;\n        child.depth = node.depth + 1;\n      }\n    }\n  }\n\n  return root.eachBefore(computeHeight);\n}\n\nfunction node_copy() {\n  return hierarchy(this).eachBefore(copyData);\n}\n\nfunction objectChildren(d) {\n  return d.children;\n}\n\nfunction mapChildren(d) {\n  return Array.isArray(d) ? d[1] : null;\n}\n\nfunction copyData(node) {\n  if (node.data.value !== undefined) node.value = node.data.value;\n  node.data = node.data.data;\n}\n\nexport function computeHeight(node) {\n  var height = 0;\n  do node.height = height;\n  while ((node = node.parent) && (node.height < ++height));\n}\n\nexport function Node(data) {\n  this.data = data;\n  this.depth =\n  this.height = 0;\n  this.parent = null;\n}\n\nNode.prototype = hierarchy.prototype = {\n  constructor: Node,\n  count: node_count,\n  each: node_each,\n  eachAfter: node_eachAfter,\n  eachBefore: node_eachBefore,\n  find: node_find,\n  sum: node_sum,\n  sort: node_sort,\n  path: node_path,\n  ancestors: node_ancestors,\n  descendants: node_descendants,\n  leaves: node_leaves,\n  links: node_links,\n  copy: node_copy,\n  [Symbol.iterator]: node_iterator\n};\n", "export default function(x) {\n  return typeof x === \"object\" && \"length\" in x\n    ? x // Array, TypedArray, NodeList, array-like\n    : Array.from(x); // Map, Set, iterable, string, or anything else\n}\n\nexport function shuffle(array, random) {\n  let m = array.length,\n      t,\n      i;\n\n  while (m) {\n    i = random() * m-- | 0;\n    t = array[m];\n    array[m] = array[i];\n    array[i] = t;\n  }\n\n  return array;\n}\n", "// https://en.wikipedia.org/wiki/Linear_congruential_generator#Parameters_in_common_use\nconst a = 1664525;\nconst c = 1013904223;\nconst m = 4294967296; // 2^32\n\nexport default function() {\n  let s = 1;\n  return () => (s = (a * s + c) % m) / m;\n}\n", "import {shuffle} from \"../array.js\";\nimport lcg from \"../lcg.js\";\n\nexport default function(circles) {\n  return packEncloseRandom(circles, lcg());\n}\n\nexport function packEncloseRandom(circles, random) {\n  var i = 0, n = (circles = shuffle(Array.from(circles), random)).length, B = [], p, e;\n\n  while (i < n) {\n    p = circles[i];\n    if (e && enclosesWeak(e, p)) ++i;\n    else e = encloseBasis(B = extendBasis(B, p)), i = 0;\n  }\n\n  return e;\n}\n\nfunction extendBasis(B, p) {\n  var i, j;\n\n  if (enclosesWeakAll(p, B)) return [p];\n\n  // If we get here then B must have at least one element.\n  for (i = 0; i < B.length; ++i) {\n    if (enclosesNot(p, B[i])\n        && enclosesWeakAll(encloseBasis2(B[i], p), B)) {\n      return [B[i], p];\n    }\n  }\n\n  // If we get here then B must have at least two elements.\n  for (i = 0; i < B.length - 1; ++i) {\n    for (j = i + 1; j < B.length; ++j) {\n      if (enclosesNot(encloseBasis2(B[i], B[j]), p)\n          && enclosesNot(encloseBasis2(B[i], p), B[j])\n          && enclosesNot(encloseBasis2(B[j], p), B[i])\n          && enclosesWeakAll(encloseBasis3(B[i], B[j], p), B)) {\n        return [B[i], B[j], p];\n      }\n    }\n  }\n\n  // If we get here then something is very wrong.\n  throw new Error;\n}\n\nfunction enclosesNot(a, b) {\n  var dr = a.r - b.r, dx = b.x - a.x, dy = b.y - a.y;\n  return dr < 0 || dr * dr < dx * dx + dy * dy;\n}\n\nfunction enclosesWeak(a, b) {\n  var dr = a.r - b.r + Math.max(a.r, b.r, 1) * 1e-9, dx = b.x - a.x, dy = b.y - a.y;\n  return dr > 0 && dr * dr > dx * dx + dy * dy;\n}\n\nfunction enclosesWeakAll(a, B) {\n  for (var i = 0; i < B.length; ++i) {\n    if (!enclosesWeak(a, B[i])) {\n      return false;\n    }\n  }\n  return true;\n}\n\nfunction encloseBasis(B) {\n  switch (B.length) {\n    case 1: return encloseBasis1(B[0]);\n    case 2: return encloseBasis2(B[0], B[1]);\n    case 3: return encloseBasis3(B[0], B[1], B[2]);\n  }\n}\n\nfunction encloseBasis1(a) {\n  return {\n    x: a.x,\n    y: a.y,\n    r: a.r\n  };\n}\n\nfunction encloseBasis2(a, b) {\n  var x1 = a.x, y1 = a.y, r1 = a.r,\n      x2 = b.x, y2 = b.y, r2 = b.r,\n      x21 = x2 - x1, y21 = y2 - y1, r21 = r2 - r1,\n      l = Math.sqrt(x21 * x21 + y21 * y21);\n  return {\n    x: (x1 + x2 + x21 / l * r21) / 2,\n    y: (y1 + y2 + y21 / l * r21) / 2,\n    r: (l + r1 + r2) / 2\n  };\n}\n\nfunction encloseBasis3(a, b, c) {\n  var x1 = a.x, y1 = a.y, r1 = a.r,\n      x2 = b.x, y2 = b.y, r2 = b.r,\n      x3 = c.x, y3 = c.y, r3 = c.r,\n      a2 = x1 - x2,\n      a3 = x1 - x3,\n      b2 = y1 - y2,\n      b3 = y1 - y3,\n      c2 = r2 - r1,\n      c3 = r3 - r1,\n      d1 = x1 * x1 + y1 * y1 - r1 * r1,\n      d2 = d1 - x2 * x2 - y2 * y2 + r2 * r2,\n      d3 = d1 - x3 * x3 - y3 * y3 + r3 * r3,\n      ab = a3 * b2 - a2 * b3,\n      xa = (b2 * d3 - b3 * d2) / (ab * 2) - x1,\n      xb = (b3 * c2 - b2 * c3) / ab,\n      ya = (a3 * d2 - a2 * d3) / (ab * 2) - y1,\n      yb = (a2 * c3 - a3 * c2) / ab,\n      A = xb * xb + yb * yb - 1,\n      B = 2 * (r1 + xa * xb + ya * yb),\n      C = xa * xa + ya * ya - r1 * r1,\n      r = -(Math.abs(A) > 1e-6 ? (B + Math.sqrt(B * B - 4 * A * C)) / (2 * A) : C / B);\n  return {\n    x: x1 + xa + xb * r,\n    y: y1 + ya + yb * r,\n    r: r\n  };\n}\n", "import array from \"../array.js\";\nimport lcg from \"../lcg.js\";\nimport {packEncloseRandom} from \"./enclose.js\";\n\nfunction place(b, a, c) {\n  var dx = b.x - a.x, x, a2,\n      dy = b.y - a.y, y, b2,\n      d2 = dx * dx + dy * dy;\n  if (d2) {\n    a2 = a.r + c.r, a2 *= a2;\n    b2 = b.r + c.r, b2 *= b2;\n    if (a2 > b2) {\n      x = (d2 + b2 - a2) / (2 * d2);\n      y = Math.sqrt(Math.max(0, b2 / d2 - x * x));\n      c.x = b.x - x * dx - y * dy;\n      c.y = b.y - x * dy + y * dx;\n    } else {\n      x = (d2 + a2 - b2) / (2 * d2);\n      y = Math.sqrt(Math.max(0, a2 / d2 - x * x));\n      c.x = a.x + x * dx - y * dy;\n      c.y = a.y + x * dy + y * dx;\n    }\n  } else {\n    c.x = a.x + c.r;\n    c.y = a.y;\n  }\n}\n\nfunction intersects(a, b) {\n  var dr = a.r + b.r - 1e-6, dx = b.x - a.x, dy = b.y - a.y;\n  return dr > 0 && dr * dr > dx * dx + dy * dy;\n}\n\nfunction score(node) {\n  var a = node._,\n      b = node.next._,\n      ab = a.r + b.r,\n      dx = (a.x * b.r + b.x * a.r) / ab,\n      dy = (a.y * b.r + b.y * a.r) / ab;\n  return dx * dx + dy * dy;\n}\n\nfunction Node(circle) {\n  this._ = circle;\n  this.next = null;\n  this.previous = null;\n}\n\nexport function packSiblingsRandom(circles, random) {\n  if (!(n = (circles = array(circles)).length)) return 0;\n\n  var a, b, c, n, aa, ca, i, j, k, sj, sk;\n\n  // Place the first circle.\n  a = circles[0], a.x = 0, a.y = 0;\n  if (!(n > 1)) return a.r;\n\n  // Place the second circle.\n  b = circles[1], a.x = -b.r, b.x = a.r, b.y = 0;\n  if (!(n > 2)) return a.r + b.r;\n\n  // Place the third circle.\n  place(b, a, c = circles[2]);\n\n  // Initialize the front-chain using the first three circles a, b and c.\n  a = new Node(a), b = new Node(b), c = new Node(c);\n  a.next = c.previous = b;\n  b.next = a.previous = c;\n  c.next = b.previous = a;\n\n  // Attempt to place each remaining circle\u2026\n  pack: for (i = 3; i < n; ++i) {\n    place(a._, b._, c = circles[i]), c = new Node(c);\n\n    // Find the closest intersecting circle on the front-chain, if any.\n    // \u201CCloseness\u201D is determined by linear distance along the front-chain.\n    // \u201CAhead\u201D or \u201Cbehind\u201D is likewise determined by linear distance.\n    j = b.next, k = a.previous, sj = b._.r, sk = a._.r;\n    do {\n      if (sj <= sk) {\n        if (intersects(j._, c._)) {\n          b = j, a.next = b, b.previous = a, --i;\n          continue pack;\n        }\n        sj += j._.r, j = j.next;\n      } else {\n        if (intersects(k._, c._)) {\n          a = k, a.next = b, b.previous = a, --i;\n          continue pack;\n        }\n        sk += k._.r, k = k.previous;\n      }\n    } while (j !== k.next);\n\n    // Success! Insert the new circle c between a and b.\n    c.previous = a, c.next = b, a.next = b.previous = b = c;\n\n    // Compute the new closest circle pair to the centroid.\n    aa = score(a);\n    while ((c = c.next) !== b) {\n      if ((ca = score(c)) < aa) {\n        a = c, aa = ca;\n      }\n    }\n    b = a.next;\n  }\n\n  // Compute the enclosing circle of the front chain.\n  a = [b._], c = b; while ((c = c.next) !== b) a.push(c._); c = packEncloseRandom(a, random);\n\n  // Translate the circles to put the enclosing circle around the origin.\n  for (i = 0; i < n; ++i) a = circles[i], a.x -= c.x, a.y -= c.y;\n\n  return c.r;\n}\n\nexport default function(circles) {\n  packSiblingsRandom(circles, lcg());\n  return circles;\n}\n", "export default function(node) {\n  node.x0 = Math.round(node.x0);\n  node.y0 = Math.round(node.y0);\n  node.x1 = Math.round(node.x1);\n  node.y1 = Math.round(node.y1);\n}\n", "export default function(parent, x0, y0, x1, y1) {\n  var nodes = parent.children,\n      node,\n      i = -1,\n      n = nodes.length,\n      k = parent.value && (x1 - x0) / parent.value;\n\n  while (++i < n) {\n    node = nodes[i], node.y0 = y0, node.y1 = y1;\n    node.x0 = x0, node.x1 = x0 += node.value * k;\n  }\n}\n", "import roundNode from \"./treemap/round.js\";\nimport treemapDice from \"./treemap/dice.js\";\n\nexport default function() {\n  var dx = 1,\n      dy = 1,\n      padding = 0,\n      round = false;\n\n  function partition(root) {\n    var n = root.height + 1;\n    root.x0 =\n    root.y0 = padding;\n    root.x1 = dx;\n    root.y1 = dy / n;\n    root.eachBefore(positionNode(dy, n));\n    if (round) root.eachBefore(roundNode);\n    return root;\n  }\n\n  function positionNode(dy, n) {\n    return function(node) {\n      if (node.children) {\n        treemapDice(node, node.x0, dy * (node.depth + 1) / n, node.x1, dy * (node.depth + 2) / n);\n      }\n      var x0 = node.x0,\n          y0 = node.y0,\n          x1 = node.x1 - padding,\n          y1 = node.y1 - padding;\n      if (x1 < x0) x0 = x1 = (x0 + x1) / 2;\n      if (y1 < y0) y0 = y1 = (y0 + y1) / 2;\n      node.x0 = x0;\n      node.y0 = y0;\n      node.x1 = x1;\n      node.y1 = y1;\n    };\n  }\n\n  partition.round = function(x) {\n    return arguments.length ? (round = !!x, partition) : round;\n  };\n\n  partition.size = function(x) {\n    return arguments.length ? (dx = +x[0], dy = +x[1], partition) : [dx, dy];\n  };\n\n  partition.padding = function(x) {\n    return arguments.length ? (padding = +x, partition) : padding;\n  };\n\n  return partition;\n}\n", "export function optional(f) {\n  return f == null ? null : required(f);\n}\n\nexport function required(f) {\n  if (typeof f !== \"function\") throw new Error;\n  return f;\n}\n", "import {optional} from \"./accessors.js\";\nimport {Node, computeHeight} from \"./hierarchy/index.js\";\n\nvar preroot = {depth: -1},\n    ambiguous = {},\n    imputed = {};\n\nfunction defaultId(d) {\n  return d.id;\n}\n\nfunction defaultParentId(d) {\n  return d.parentId;\n}\n\nexport default function() {\n  var id = defaultId,\n      parentId = defaultParentId,\n      path;\n\n  function stratify(data) {\n    var nodes = Array.from(data),\n        currentId = id,\n        currentParentId = parentId,\n        n,\n        d,\n        i,\n        root,\n        parent,\n        node,\n        nodeId,\n        nodeKey,\n        nodeByKey = new Map;\n\n    if (path != null) {\n      const I = nodes.map((d, i) => normalize(path(d, i, data)));\n      const P = I.map(parentof);\n      const S = new Set(I).add(\"\");\n      for (const i of P) {\n        if (!S.has(i)) {\n          S.add(i);\n          I.push(i);\n          P.push(parentof(i));\n          nodes.push(imputed);\n        }\n      }\n      currentId = (_, i) => I[i];\n      currentParentId = (_, i) => P[i];\n    }\n\n    for (i = 0, n = nodes.length; i < n; ++i) {\n      d = nodes[i], node = nodes[i] = new Node(d);\n      if ((nodeId = currentId(d, i, data)) != null && (nodeId += \"\")) {\n        nodeKey = node.id = nodeId;\n        nodeByKey.set(nodeKey, nodeByKey.has(nodeKey) ? ambiguous : node);\n      }\n      if ((nodeId = currentParentId(d, i, data)) != null && (nodeId += \"\")) {\n        node.parent = nodeId;\n      }\n    }\n\n    for (i = 0; i < n; ++i) {\n      node = nodes[i];\n      if (nodeId = node.parent) {\n        parent = nodeByKey.get(nodeId);\n        if (!parent) throw new Error(\"missing: \" + nodeId);\n        if (parent === ambiguous) throw new Error(\"ambiguous: \" + nodeId);\n        if (parent.children) parent.children.push(node);\n        else parent.children = [node];\n        node.parent = parent;\n      } else {\n        if (root) throw new Error(\"multiple roots\");\n        root = node;\n      }\n    }\n\n    if (!root) throw new Error(\"no root\");\n\n    // When imputing internal nodes, only introduce roots if needed.\n    // Then replace the imputed marker data with null.\n    if (path != null) {\n      while (root.data === imputed && root.children.length === 1) {\n        root = root.children[0], --n;\n      }\n      for (let i = nodes.length - 1; i >= 0; --i) {\n        node = nodes[i];\n        if (node.data !== imputed) break;\n        node.data = null;\n      }\n    }\n\n    root.parent = preroot;\n    root.eachBefore(function(node) { node.depth = node.parent.depth + 1; --n; }).eachBefore(computeHeight);\n    root.parent = null;\n    if (n > 0) throw new Error(\"cycle\");\n\n    return root;\n  }\n\n  stratify.id = function(x) {\n    return arguments.length ? (id = optional(x), stratify) : id;\n  };\n\n  stratify.parentId = function(x) {\n    return arguments.length ? (parentId = optional(x), stratify) : parentId;\n  };\n\n  stratify.path = function(x) {\n    return arguments.length ? (path = optional(x), stratify) : path;\n  };\n\n  return stratify;\n}\n\n// To normalize a path, we coerce to a string, strip the trailing slash if any\n// (as long as the trailing slash is not immediately preceded by another slash),\n// and add leading slash if missing.\nfunction normalize(path) {\n  path = `${path}`;\n  let i = path.length;\n  if (slash(path, i - 1) && !slash(path, i - 2)) path = path.slice(0, -1);\n  return path[0] === \"/\" ? path : `/${path}`;\n}\n\n// Walk backwards to find the first slash that is not the leading slash, e.g.:\n// \"/foo/bar\" \u21E5 \"/foo\", \"/foo\" \u21E5 \"/\", \"/\" \u21A6 \"\". (The root is special-cased\n// because the id of the root must be a truthy value.)\nfunction parentof(path) {\n  let i = path.length;\n  if (i < 2) return \"\";\n  while (--i > 1) if (slash(path, i)) break;\n  return path.slice(0, i);\n}\n\n// Slashes can be escaped; to determine whether a slash is a path delimiter, we\n// count the number of preceding backslashes escaping the forward slash: an odd\n// number indicates an escaped forward slash.\nfunction slash(path, i) {\n  if (path[i] === \"/\") {\n    let k = 0;\n    while (i > 0 && path[--i] === \"\\\\\") ++k;\n    if ((k & 1) === 0) return true;\n  }\n  return false;\n}\n"],
+  "mappings": 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+  "names": ["a", "c", "m", "a", "c", "a2", "c2", "a", "c", "a2", "Node", "dy", "d", "i", "node"]
+}

package/dist/chunk-W5OEFZCR.js

@@ -0,0 +1,254 @@
+import {
+  getMclassSorter,
+  getSampleGroupSorter,
+  getSampleSorter,
+  getTermSorter
+} from "./chunk-WXSRK3XR.js";
+import {
+  sample_match_termvaluesetting
+} from "./chunk-7IYJZZQI.js";
+import {
+  dtcnv,
+  dtfusionrna,
+  dtgeneexpression,
+  dtsnvindel
+} from "./chunk-ZF6HNVYD.js";
+import {
+  __export
+} from "./chunk-HFNDKYVF.js";
+
+// plots/matrix/matrix.groups.js
+var matrix_groups_exports = {};
+__export(matrix_groups_exports, {
+  classifyValues: () => classifyValues,
+  getSampleGroups: () => getSampleGroups,
+  getSampleOrder: () => getSampleOrder,
+  getTermOrder: () => getTermOrder,
+  stackSiblingCellsByClass: () => stackSiblingCellsByClass
+});
+function getTermOrder(data) {
+  const s = this.settings.matrix;
+  this.termSorter = getTermSorter(this, s);
+  const termOrder = [];
+  let totalIndex = 0, visibleGrpIndex = 0, numClusterTerms = 0;
+  this.mclassSorter = getMclassSorter(this);
+  for (const [grpIndex, grp] of this.termGroups.entries()) {
+    const lst = [];
+    for (const [index, tw] of grp.lst.entries()) {
+      const counts = { samples: 0, hits: 0 };
+      const countedSamples = /* @__PURE__ */ new Set();
+      for (const sd of data.lst) {
+        if (countedSamples.has(sd.sample)) continue;
+        countedSamples.add(sd.sample);
+        const anno = sd[tw.$id];
+        if (anno) {
+          const { filteredValues, countedValues, renderedValues } = this.classifyValues(anno, tw, grp, s, sd);
+          anno.filteredValues = filteredValues;
+          anno.countedValues = countedValues;
+          anno.renderedValues = renderedValues;
+          if (anno.countedValues?.length) {
+            const v = tw.term.values?.[anno.value];
+            if (v?.uncountable) continue;
+            counts.samples += 1;
+            counts.hits += anno.countedValues.length;
+            if (tw.q?.mode == "continuous") {
+              const v2 = anno.value;
+              if (!("minval" in counts) || counts.minval > v2) counts.minval = v2;
+              if (!("maxval" in counts) || counts.maxval < v2) counts.maxval = v2;
+            }
+          }
+        }
+      }
+      if (grp.type != "hierCluster" || counts.samples) lst.push({ tw, counts, index });
+      if (grp.type == "hierCluster") numClusterTerms++;
+    }
+    const termSorter = grp.sortTermsBy || grp.type == "hierCluster" ? getTermSorter(this, s, grp) : this.termSorter;
+    const processedLst = lst.filter((t) => {
+      if ("minNumSamples" in t.tw) return t.tw.minNumSamples <= t.counts.samples;
+      if (!grp.settings) return true;
+      return !("minNumSamples" in grp.settings) || t.counts.samples >= grp.settings.minNumSamples;
+    }).sort(termSorter);
+    if (!processedLst.length) continue;
+    for (const [index, t] of processedLst.entries()) {
+      const { tw, counts } = t;
+      const ref = data.refs.byTermId[t.tw.$id] || {};
+      termOrder.push({
+        grp,
+        grpIndex,
+        visibleGrpIndex,
+        tw,
+        index,
+        // rendered index
+        lstIndex: t.index,
+        // as-listed index, before applying term filters
+        processedLst,
+        prevGrpTotalIndex: totalIndex,
+        totalIndex: totalIndex + index,
+        ref,
+        allCounts: counts
+        // note: term label will be assigned after sample counts are known
+        // label: t.tw.label || t.tw.term.name,
+      });
+    }
+    totalIndex += processedLst.length;
+    visibleGrpIndex += 1;
+  }
+  this.numTerms = termOrder.length;
+  this.numClusterTerms = numClusterTerms;
+  return termOrder;
+}
+function getSampleGroups(data) {
+  const s = this.settings.matrix;
+  const defaultSampleGrp = {
+    id: this.config.divideBy?.$id,
+    name: this.config.divideBy ? "Not annotated" : "",
+    lst: []
+  };
+  const sampleGroups = /* @__PURE__ */ new Map();
+  const term = this.config.divideBy?.term || {};
+  const $id = this.config.divideBy?.$id || "-";
+  const exclude = this.config.divideBy?.exclude || [];
+  const values = term.values || {};
+  const ref = data.refs.byTermId[$id] || {};
+  for (const row of data.lst) {
+    if ($id in row) {
+      const key = row[$id].key;
+      const name = key in values && values[key].label ? values[key].label : key;
+      if (!sampleGroups.has(key)) {
+        const grp = {
+          name: `${name}`,
+          // convert to a string
+          id: key,
+          lst: [],
+          tw: this.config.divideBy,
+          legendGroups: {},
+          isExcluded: exclude.includes(key)
+        };
+        if (ref.bins && s.sortSampleGrpsBy == "name") grp.order = ref.bins.findIndex((bin) => bin.name == key);
+        else delete grp.order;
+        sampleGroups.set(key, grp);
+      }
+      sampleGroups.get(key).lst.push(row);
+    } else {
+      defaultSampleGrp.lst.push(row);
+    }
+  }
+  const sampleGrpsArr = [...sampleGroups.values()];
+  const n = sampleGroups.size;
+  if (n > 100 && sampleGrpsArr.filter((sg) => sg.lst.length < 3).length > 0.8 * n) {
+    const l = s.controlLabels;
+    throw `Did not group ${l.samples} by "${term.name}": too many ${l.sample} groups (${n}), with the majority of groups having <= 2 ${l.samples} per group.`;
+  }
+  if (defaultSampleGrp.lst.length && !sampleGroups.size) {
+    sampleGroups.set(void 0, defaultSampleGrp);
+    sampleGrpsArr.push(...sampleGroups.values());
+  }
+  this.asListedSampleOrder = [];
+  for (const grp of sampleGrpsArr) {
+    this.asListedSampleOrder.push(...grp.lst.map((s2) => s2.sample));
+  }
+  const selectedDictTerms = this.termOrder.filter((t) => t.tw.sortSamples && t.tw.term.type != "geneVariant");
+  const noGrpSampleSorter = getSampleSorter(this, s, data.lst, {
+    skipSorter: (p, tw) => !p.types?.includes("geneVariant") && selectedDictTerms.find((t) => t.tw.$id === tw.$id)
+  });
+  const noGrpSampleOrder = data.lst.sort(noGrpSampleSorter);
+  const allowedSamples = noGrpSampleOrder.slice(0, s.maxSample);
+  const dataFilter = (d) => allowedSamples.includes(d);
+  const hitsPerSample = (t, c) => t + (typeof c == "object" && c.countedValues?.length ? 1 : 0);
+  const countHits = (total, d) => total + (Object.values(d).reduce(hitsPerSample, 0) ? 1 : 0);
+  const grpLstSampleSorter = getSampleSorter(this, s, data.lst);
+  for (const grp of sampleGrpsArr) {
+    grp.lst = grp.lst.filter(dataFilter);
+    grp.totalCountedValues = grp.lst.reduce(countHits, 0);
+    grp.lst.sort(grpLstSampleSorter);
+  }
+  const sampleGrpSorter = getSampleGroupSorter(this);
+  return sampleGrpsArr.sort(sampleGrpSorter);
+}
+function getSampleOrder(data) {
+  const s = this.settings.matrix;
+  this.visibleSampleGrps = /* @__PURE__ */ new Set();
+  const sampleOrder = [];
+  let total = 0, numHiddenGrps = 0;
+  for (const [grpIndex, grp] of this.sampleGroups.entries()) {
+    if (!grp.lst.length) continue;
+    if (grp.isExcluded) numHiddenGrps++;
+    let processedLst = grp.lst;
+    for (const [index, row] of processedLst.entries()) {
+      sampleOrder.push({
+        grp,
+        grpIndex: grpIndex - numHiddenGrps,
+        // : this.sampleGroups.length,
+        row,
+        index,
+        prevGrpTotalIndex: total,
+        totalIndex: total + index,
+        totalHtAdjustments: 0,
+        // may be required when transposed???
+        grpTotals: { htAdjustment: 0 },
+        // may be required when transposed???
+        processedLst
+      });
+    }
+    if (!grp.isExcluded) total += processedLst.length;
+    this.visibleSampleGrps.add(grp);
+  }
+  this.unfilteredSampleOrder = sampleOrder;
+  return sampleOrder.filter((so) => !so.grp.isExcluded);
+}
+function classifyValues(anno, tw, grp, s, sample) {
+  const values = "value" in anno ? [anno.value] : anno.values;
+  if (!values) return { filteredValues: null, countedValues: null, renderedValues: null };
+  const isSpecific = [tw.valueFilter || grp.valueFilter].filter((v) => v && true);
+  if (isSpecific.length && isSpecific[0].type !== "tvs" && isSpecific[0].type !== "tvslst")
+    throw `unknown matrix value filter type='${isSpecific.type}'`;
+  let filteredValues = !isSpecific.length ? values : values.filter((v) => sample_match_termvaluesetting(v, isSpecific[0], tw.term, sample));
+  const renderedValues = [];
+  if (tw.term.type == "geneVariant" && tw.q?.type == "values") {
+    filteredValues.sort(this.mclassSorter);
+    if (s.cellEncoding == "") renderedValues.push(...filteredValues);
+    else {
+      const sortedFilteredValues = [];
+      for (const dt of [dtcnv, dtsnvindel, dtfusionrna, dtgeneexpression]) {
+        const v = dt == dtgeneexpression ? filteredValues.find((v2) => v2.dt === dt) : filteredValues.find((v2) => v2.dt === dt && v2.class !== "WT" && v2.class !== "Blank");
+        if (v) renderedValues.push(v);
+        const oneDtV = filteredValues.filter((v2) => v2.dt === dt);
+        sortedFilteredValues.push(...oneDtV);
+      }
+      filteredValues = sortedFilteredValues;
+    }
+  } else {
+    renderedValues.push(...filteredValues);
+  }
+  return {
+    filteredValues,
+    countedValues: filteredValues.filter((v) => {
+      if (tw.term.type == "geneVariant") {
+        if (tw.q?.type == "predefined-groupset" || tw.q?.type == "custom-groupset") {
+          const groupset = tw.q.type == "predefined-groupset" ? tw.term.groupsetting.lst[tw.q.predefined_groupset_idx] : tw.q.customset;
+          if (!groupset) throw "groupset not found";
+          const group = groupset.groups[0];
+          if (v != group.name) return false;
+        } else {
+          if (v.class == "WT" || v.class == "Blank" || s.geneVariantCountSamplesSkipMclass.includes(v.class))
+            return false;
+        }
+      }
+      return true;
+    }),
+    renderedValues
+  };
+}
+function stackSiblingCellsByClass(a, b) {
+  return a.class === b.class ? 0 : a.class === "Blank" ? 1 : b.class == "Blank" ? -1 : a.class < b.class ? -1 : 1;
+}
+
+export {
+  getTermOrder,
+  getSampleGroups,
+  getSampleOrder,
+  classifyValues,
+  stackSiblingCellsByClass,
+  matrix_groups_exports
+};
+//# sourceMappingURL=chunk-W5OEFZCR.js.map