@weng-lab/visualization 2.2.2 → 2.3.1

package/dist/visualization.es7.js

@@ -1,43 +1,43 @@
-import { j as L } from "./visualization.es18.js";
-import { useState as G, useMemo as f, useRef as U, useCallback as M } from "react";
-import { ZoomFrame as oe } from "./visualization.es66.js";
-import { RenderTree as ce } from "./visualization.es67.js";
-import re from "./visualization.es28.js";
-import ie from "./visualization.es27.js";
-import le from "./visualization.es68.js";
-import de from "./visualization.es69.js";
-import ue from "./visualization.es70.js";
-import S from "./visualization.es71.js";
-import he from "./visualization.es25.js";
-import pe from "./visualization.es42.js";
-import { pathRadialStep as J } from "./visualization.es72.js";
-const je = {
+import { jsx as N, jsxs as oe } from "react/jsx-runtime";
+import { useState as G, useMemo as f, useRef as U, useCallback as R } from "react";
+import { ZoomFrame as ce } from "./visualization.es56.js";
+import { RenderTree as re } from "./visualization.es57.js";
+import ie from "./visualization.es53.js";
+import le from "./visualization.es58.js";
+import de from "./visualization.es59.js";
+import ue from "./visualization.es60.js";
+import he from "./visualization.es61.js";
+import S from "./visualization.es62.js";
+import pe from "./visualization.es24.js";
+import me from "./visualization.es49.js";
+import { pathRadialStep as J } from "./visualization.es63.js";
+const we = {
   duration: 0.3,
   ease: "easeInOut"
-}, me = () => 1, be = (t, i, r) => i === 0 ? 0 : t / i * r, ge = (t) => {
+}, be = () => 1, ge = (t, i, r) => i === 0 ? 0 : t / i * r, Le = (t) => {
   const i = /-?\d*\.?\d+[eE][+-]?\d+/g;
   return t.replace(i, (r) => Number(r).toFixed(10).replace(/\.?0+$/, ""));
 }, K = (t) => (i) => {
   const r = t(i);
-  return r ? ge(r) : "";
-}, Le = K(J({
+  return r ? Le(r) : "";
+}, Ne = K(J({
   source: (t) => t.source,
   target: (t) => t.target,
   x: (t) => t?.x || 0,
   y: (t) => t?.y || 0
-})), Ne = K(J({
+})), fe = K(J({
   source: (t) => t.source,
   target: (t) => t.target,
   x: (t) => t?.x || 0,
   y: (t) => t?.branchLengthScaledRadius || 0
-})), fe = (t, i) => {
+})), xe = (t, i) => {
   t = t.replace(/^#/, "");
   let r = parseInt(t.substring(0, 2), 16), u = parseInt(t.substring(2, 4), 16), h = parseInt(t.substring(4, 6), 16);
   r = Math.round(r + (255 - r) * i), u = Math.round(u + (255 - u) * i), h = Math.round(h + (255 - h) * i);
   const b = (x) => x.toString(16).padStart(2, "0");
   return `#${b(r)}${b(u)}${b(h)}`;
-}, y = 500, ke = y * 2;
-function we({
+}, y = 500, Ae = y * 2;
+function De({
   width: t,
   height: i,
   data: r,
@@ -59,15 +59,15 @@ function we({
     tooltipData: P,
     tooltipLeft: ee,
     tooltipTop: te,
-    showTooltip: j,
-    hideTooltip: k
-  } = re(), w = f(() => T ? [T, ...h] : h, [T, h]), {
+    showTooltip: k,
+    hideTooltip: w
+  } = ie(), A = f(() => T ? [T, ...h] : h, [T, h]), {
     TooltipInPortal: se
-  } = ie({
+  } = le({
     scroll: !0,
     detectBounds: !0
-  }), A = U(null), Y = U(!1), D = (c, s) => {
-    A.current = s ? {
+  }), D = U(null), Y = U(!1), j = (c, s) => {
+    D.current = s ? {
       node: s,
       x: c.clientX,
       y: c.clientY
@@ -76,23 +76,23 @@ function we({
       x: 0,
       y: 0
     }, Y.current || (Y.current = !0, requestAnimationFrame(() => {
-      const l = A.current, e = l?.node ?? null;
-      _(e ? e.data.id : null), e && !e.children ? j({
+      const l = D.current, e = l?.node ?? null;
+      _(e ? e.data.id : null), e && !e.children ? k({
         tooltipData: e.data,
         tooltipLeft: l.x,
         tooltipTop: l.y
-      }) : k(), g && g(e ? e.leaves().map((n) => n.data.id) : []), Y.current = !1;
+      }) : w(), g && g(e ? e.leaves().map((n) => n.data.id) : []), Y.current = !1;
     }));
-  }, N = Math.max(0, y - V), q = f(() => [2 * Math.PI, N], [N]), $ = f(() => le(r, (s) => s.children).sum((s) => s.children ? 0 : 1).sort((s, l) => {
+  }, L = Math.max(0, y - V), q = f(() => [2 * Math.PI, L], [L]), $ = f(() => de(r, (s) => s.children).sum((s) => s.children ? 0 : 1).sort((s, l) => {
     if (p) {
-      const a = new Map(p.map((d, R) => [d, R])), o = (d) => Math.min(...d.leaves().map((R) => a.get(R.data.id) ?? 1 / 0));
+      const a = new Map(p.map((d, M) => [d, M])), o = (d) => Math.min(...d.leaves().map((M) => a.get(M.data.id) ?? 1 / 0));
       return o(s) - o(l);
     }
     const e = s.leaves().some((a) => a.data.id === "Homo_sapiens"), n = l.leaves().some((a) => a.data.id === "Homo_sapiens");
-    return e !== n ? e ? -1 : 1 : (s.value || 0) - (l.value || 0) || de(s.data.branch_length ?? void 0, l.data.branch_length ?? void 0);
-  }), [r, X, N, p]), F = f(() => {
-    const c = ue();
-    c.size(q), c.separation(me);
+    return e !== n ? e ? -1 : 1 : (s.value || 0) - (l.value || 0) || ue(s.data.branch_length ?? void 0, l.data.branch_length ?? void 0);
+  }), [r, X, L, p]), F = f(() => {
+    const c = he();
+    c.size(q), c.separation(be);
     const s = c($.copy());
     let l = 0;
     if (s.each((e) => {
@@ -108,7 +108,7 @@ function we({
       const a = (e.parent?.cumulativeBranchLength ?? 0) + (e.data.branch_length ?? 0);
       a > l && (l = a), e.cumulativeBranchLength = a;
     }), s.descendants().forEach((e) => {
-      const n = be(e.cumulativeBranchLength ?? 0, l, N);
+      const n = ge(e.cumulativeBranchLength ?? 0, l, L);
       e.branchLengthScaledRadius = n;
     }), s.descendants().forEach((e) => {
       const [n, a] = S(e.x, e.y), [o, d] = S(e.x, e.branchLengthScaledRadius ?? 0);
@@ -121,7 +121,7 @@ function we({
         const n = {
           source: e.parent,
           target: e
-        }, a = Le(n), o = Ne(n);
+        }, a = Ne(n), o = fe(n);
         e.baseLinkPath = a, e.scaledLinkPath = o;
       }
     }), s.leaves().forEach((e) => {
@@ -135,7 +135,7 @@ function we({
         x2: e.baseNodeX ?? 0,
         y1: e.scaledNodeY ?? 0,
         y2: e.baseNodeY ?? 0
-      }, e.lightenedLinkExtColor = fe(e.color ?? "#000000", 0.7);
+      }, e.lightenedLinkExtColor = xe(e.color ?? "#000000", 0.7);
     }), s.each((e) => {
       const a = !e.children ? u.includes(e.data.id) : e.leaves().some((o) => u.includes(o.data.id));
       e.linkStrokeWidth = a ? I * 2 : I, e.labelStrokeWidth = a ? 0.7 : 0;
@@ -149,24 +149,24 @@ Requested: ` + o.join(", ") + `
 Achieved:  ` + d.join(", "));
     }
     return s;
-  }, [r, q, N, $, u, I, p]), H = M(() => W((c) => !c), []), Z = M((c, s) => {
-    D(c, s), !s.children && j({
+  }, [r, q, L, $, u, I, p]), H = R(() => W((c) => !c), []), Z = R((c, s) => {
+    j(c, s), !s.children && k({
       tooltipData: s.data,
       tooltipLeft: c.clientX,
       tooltipTop: c.clientY
     }), g && g(s.leaves().map((l) => l.data.id));
-  }, []), O = M((c, s) => {
-    D(c, null), k(), g && g([]);
-  }, []), z = f(() => /* @__PURE__ */ L.jsx(he, { top: y, left: y, children: /* @__PURE__ */ L.jsx(ce, { node: F, hovered: w, leafFontFamily: x, leafFontSize: b, useBranchLengths: v, onNodeMouseMove: Z, onNodeMouseLeave: O, onBranchClick: E }) }), [F, w, x, b, v, Z, O, E]), ae = M((c) => /* @__PURE__ */ L.jsx(oe, { zoom: c, totalWidth: t, totalHeight: i, toggleBranchLength: H, children: z }), [t, i, H, z]);
-  return t < 10 ? null : /* @__PURE__ */ L.jsxs("div", { children: [
-    /* @__PURE__ */ L.jsx(pe, { width: t, height: i, scaleXMin: 0.8, scaleXMax: 4, scaleYMin: 0.8, scaleYMax: 4, children: ae }),
-    P && B && /* @__PURE__ */ L.jsx(se, { left: ee, top: te, children: B(P.id) })
+  }, []), O = R((c, s) => {
+    j(c, null), w(), g && g([]);
+  }, []), z = f(() => /* @__PURE__ */ N(pe, { top: y, left: y, children: /* @__PURE__ */ N(re, { node: F, hovered: A, leafFontFamily: x, leafFontSize: b, useBranchLengths: v, onNodeMouseMove: Z, onNodeMouseLeave: O, onBranchClick: E }) }), [F, A, x, b, v, Z, O, E]), ae = R((c) => /* @__PURE__ */ N(ce, { zoom: c, totalWidth: t, totalHeight: i, toggleBranchLength: H, children: z }), [t, i, H, z]);
+  return t < 10 ? null : /* @__PURE__ */ oe("div", { children: [
+    /* @__PURE__ */ N(me, { width: t, height: i, scaleXMin: 0.8, scaleXMax: 4, scaleYMin: 0.8, scaleYMax: 4, children: ae }),
+    P && B && /* @__PURE__ */ N(se, { left: ee, top: te, children: B(P.id) })
   ] });
 }
 export {
-  ke as TOTAL_INNER_DIAMETER,
+  Ae as TOTAL_INNER_DIAMETER,
   y as TOTAL_INNER_RADIUS,
-  we as default,
-  je as useBranchLengthTransition
+  De as default,
+  we as useBranchLengthTransition
 };
 //# sourceMappingURL=visualization.es7.js.map

package/dist/visualization.es7.js.map

@@ -1 +1 @@
-{"version":3,"file":"visualization.es7.js","sources":["../src/components/PhyloTree/PhyloTree.tsx"],"sourcesContent":["import { useMemo, useState, useCallback, useRef, useEffect } from \"react\";\nimport { Group } from \"@visx/group\";\nimport { ascending } from \"@visx/vendor/d3-array\";\nimport { pathRadialStep } from \"@visx/shape\";\nimport { cluster as d3cluster, hierarchy as d3hierarchy } from \"d3-hierarchy\";\nimport { PhyloTreeProps, TreeItem, TreeLink, TreeNode, ZoomState } from \"./types\";\nimport { useTooltip, defaultStyles, useTooltipInPortal } from \"@visx/tooltip\";\nimport { Zoom, ProvidedZoom } from \"@visx/zoom\";\nimport { ZoomFrame } from \"./ZoomFrame\";\nimport { pointRadial } from \"d3-shape\";\nimport { RenderTree } from \"./RenderTree\";\n\n/**\n * Improvements that would make this scale better (as much as svg can):\n * - Combine links into fewer path elements\n *    - Requires having static hit detecting paths, but can create fewer <path> elements by combining link paths\n *    - Creates less work for the browser to update fewer, but more complex paths\n *    - Would need base branches grouped by color, selection path, external highlight path, and invisible static hit target paths for branch selection\n * - Remove hover interaction and opt for click only interactions\n * - If keeping hover behavior, define gapless areas between nodes to prevent -> hover NodeA, hover null, hover NodeB in favor of NodeA -> NodeB\n * - Define single hit area that takes in click event and determines what was hit\n */\n\nexport const useBranchLengthTransition = {\n  duration: 0.3,\n  ease: \"easeInOut\",\n} as const;\n\n// Keep spacing of all leaf nodes consistent\nconst separationFn = () => 1;\n\nconst getBranchLengthScaledY = (cumulativeBranchLength: number, maxBranchLength: number, innerRadius: number) => {\n  return maxBranchLength === 0 ? 0 : (cumulativeBranchLength / maxBranchLength) * innerRadius;\n};\n\n// Framer motion had issues with e notation\nconst rmSciNotation = (pathString: string) => {\n  // Regex to match scientific notation:\n  // optional sign, digits/dots, 'e' or 'E', optional sign, and exponent digits\n  const scientificRegex = /-?\\d*\\.?\\d+[eE][+-]?\\d+/g;\n\n  return pathString.replace(scientificRegex, (match) => {\n    // Convert the match to a Number and then back to a decimal string\n    const num = Number(match);\n\n    // Use toFixed() to ensure no new scientific notation is generated\n    // 10 decimal places is usually enough for SVG precision\n    return num.toFixed(10).replace(/\\.?0+$/, \"\");\n  });\n};\n\nconst withNoSciNotation =\n  <L extends TreeLink>(generator: (link: L) => string | null) =>\n  (link: L) => {\n    const path = generator(link);\n    return path ? rmSciNotation(path) : \"\";\n  };\n\nconst getLinkPath = withNoSciNotation(\n  pathRadialStep<TreeLink, TreeNode>({\n    source: (l) => l.source,\n    target: (l) => l.target,\n    x: (n) => n?.x || 0,\n    y: (n) => n?.y || 0,\n  })\n);\n\nconst getScaledLinkPath = withNoSciNotation(\n  pathRadialStep<TreeLink, TreeNode>({\n    source: (l) => l.source,\n    target: (l) => l.target,\n    x: (n) => n?.x || 0,\n    y: (n) => n?.branchLengthScaledRadius || 0,\n  })\n);\n\n/**\n * Lightens a hex color by blending it with white.\n * @param {string} hex - The input color, e.g. \"#336699\"\n * @param {number} factor - How much to lighten: 0 = no change, 1 = full white\n * @returns {string} - The lightened hex color\n */\nconst lightenHex = (hex: string, factor: number) => {\n  // Remove leading \"#\" if present\n  hex = hex.replace(/^#/, '');\n\n  // Parse r, g, b\n  let r = parseInt(hex.substring(0, 2), 16);\n  let g = parseInt(hex.substring(2, 4), 16);\n  let b = parseInt(hex.substring(4, 6), 16);\n\n  // Blend each channel toward 255 (white)\n  r = Math.round(r + (255 - r) * factor);\n  g = Math.round(g + (255 - g) * factor);\n  b = Math.round(b + (255 - b) * factor);\n\n  // Convert back to hex and pad with zeros\n  const toHex = (c: number) => c.toString(16).padStart(2, '0');\n  return `#${toHex(r)}${toHex(g)}${toHex(b)}`;\n}\n\n/**\n * For internal svg calculation only\n */\nexport const TOTAL_INNER_RADIUS = 500;\n/**\n * For internal svg calculation only (used to define viewbox in ZoomFrame)\n */\nexport const TOTAL_INNER_DIAMETER = TOTAL_INNER_RADIUS * 2;\n\nexport default function PhyloTree({\n  width: totalWidth,\n  height: totalHeight,\n  data,\n  highlighted = [],\n  hovered: externalHovered = [],\n  leafFontSize = 8,\n  leafFontFamily = \"Arial\",\n  linkStrokeWidth = 1,\n  getColor = () => \"black\",\n  getLabel = (id) => id,\n  onBranchClick = () => null,\n  onLeafHoverChange,\n  labelPadding = 135,\n  defaultScaling = \"scaled\",\n  tooltipContents,\n  leafOrder,\n}: PhyloTreeProps) {\n  const [enableBranchLengths, setEnableBranchLengths] = useState<boolean>(defaultScaling === \"scaled\");\n\n  const [internalHovered, setInternalHovered] = useState<string | null>(null)\n  const { tooltipData, tooltipLeft, tooltipTop, tooltipOpen, showTooltip, hideTooltip } = useTooltip<TreeItem>();\n\n  const hovered = useMemo(\n    () => (internalHovered ? [internalHovered, ...externalHovered] : externalHovered),\n    [internalHovered, externalHovered]\n  );\n\n  const { TooltipInPortal } = useTooltipInPortal({\n    scroll: true,\n    detectBounds: true,\n  });\n\n  interface PendingHover {\n    node: TreeNode | null;\n    x: number;\n    y: number;\n  }\n\n  const pendingRef = useRef<PendingHover | null>(null);\n  const frameRef = useRef(false);\n\n  /**\n   * Prevents hover updates more frequently than the browser can repaint by using requestAnimationFrame\n   */\n  const handleDebounceHover = (event: React.MouseEvent, node: TreeNode | null) => {\n    pendingRef.current = node \n      ? { node, x: event.clientX, y: event.clientY }\n      : { node: null, x: 0, y: 0 };\n\n    if (!frameRef.current) {\n      frameRef.current = true;\n\n      requestAnimationFrame(() => {\n        // Everything comes from the ref now — consistent snapshot\n        const pending = pendingRef.current;\n        const pendingNode = pending?.node ?? null;\n\n        setInternalHovered(pendingNode ? pendingNode.data.id : null);\n\n        if (pendingNode && !pendingNode.children) {\n          showTooltip({\n            tooltipData: pendingNode.data,\n            tooltipLeft: pending!.x,\n            tooltipTop: pending!.y,\n          });\n        } else {\n          hideTooltip();\n        }\n\n        if (onLeafHoverChange) {\n          onLeafHoverChange(\n            pendingNode ? pendingNode.leaves().map((leaf) => leaf.data.id) : []\n          );\n        }\n\n        frameRef.current = false;\n      });\n    }\n  };\n\n  const circleRadius = Math.max(0, TOTAL_INNER_RADIUS - labelPadding);\n\n  // This defines the arbitrary x/y coordinate system. For our radial layout X is the angle defined in radians, Y is radius. https://d3js.org/d3-hierarchy/cluster#cluster_size\n  const size: [number, number] = useMemo(() => [2 * Math.PI, circleRadius], [circleRadius]);\n\n  /* Construct root node */\n  const root = useMemo(() => {\n    const r = d3hierarchy(data, (d) => d.children)\n      // sorts first by least number of children, and then by branch length to create nice looking plot\n      .sum((d) => (d.children ? 0 : 1))\n      .sort((a, b) => {\n        if (leafOrder) {\n          const indexMap = new Map(leafOrder.map((id, i) => [id, i]));\n          const minIdx = (node: typeof a) =>\n            Math.min(...node.leaves().map((l) => indexMap.get(l.data.id) ?? Infinity));\n          return minIdx(a) - minIdx(b);\n        }\n\n        // Float the Homo_sapiens subtree to the end so it appears at the top\n        const aHasHuman = a.leaves().some((l) => l.data.id === \"Homo_sapiens\");\n        const bHasHuman = b.leaves().some((l) => l.data.id === \"Homo_sapiens\");\n        if (aHasHuman !== bHasHuman) return aHasHuman ? -1 : 1;\n\n        return (\n          (a.value || 0) - (b.value || 0) ||\n          ascending(a.data.branch_length ?? undefined, b.data.branch_length ?? undefined)\n        );\n      });\n    return r;\n  }, [data, getColor, circleRadius, leafOrder]);\n\n  /* Add layout/render properties */\n  const rootNode = useMemo(() => {\n    const clusterLayout = d3cluster<TreeItem>();\n    clusterLayout.size(size);\n    clusterLayout.separation(separationFn);\n    //copy root node so that the reference changes when this useMemo is rerun. Otherwise is modifying in place\n    const clusterRoot: TreeNode = clusterLayout(root.copy());\n\n    let maxBranchLength = 0;\n\n    clusterRoot.each((node) => {\n      node.label = getLabel(node.data.id)\n    })\n\n    // uniformLeafColor\n    clusterRoot.eachAfter((node) => {\n      //This node is visited after all of it's descendents. Allows us to look at immediate children to see if they have same color.\n      //For leaf nodes, there will be no children, so assign the color AND assign light\n      if (!node.children) {\n        node.color = getColor(node.data.id);\n      } else {\n        const childColors = node.children.map((x) => x.color);\n        const firstColor = node.children[0].color;\n        const allSame = firstColor !== null && childColors.every((color) => color === firstColor);\n        node.color = allSame ? firstColor : \"#666\";\n      }\n    });\n\n    // cumulativeBranchLength\n    clusterRoot.eachBefore((node) => {\n      const parentLen = node.parent?.cumulativeBranchLength ?? 0;\n      const cumulativeBranchLength = parentLen + (node.data.branch_length ?? 0);\n\n      if (cumulativeBranchLength > maxBranchLength) {\n        maxBranchLength = cumulativeBranchLength;\n      }\n      \n      node.cumulativeBranchLength = cumulativeBranchLength;\n    });\n    \n    // Add BranchLengthScaledRadius. Must come after cumulativeBranchLength\n    clusterRoot.descendants().forEach((node) => {\n      const branchLengthScaledRadius = getBranchLengthScaledY(\n        node.cumulativeBranchLength ?? 0,\n        maxBranchLength,\n        circleRadius\n      );\n\n      node.branchLengthScaledRadius = branchLengthScaledRadius;\n    })\n\n    // Base/Scaled X/Y. Must come after branchLengthScaledRadius assignment\n    clusterRoot.descendants().forEach((node) => {\n      const [baseNodeX, baseNodeY] = pointRadial(node.x, node.y);\n      const [scaledNodeX, scaledNodeY] = pointRadial(node.x, node.branchLengthScaledRadius ?? 0);\n\n      node.baseNodeX = baseNodeX;\n      node.baseNodeY = baseNodeY;\n      node.scaledNodeX = scaledNodeX;\n      node.scaledNodeY = scaledNodeY;\n    });\n\n    // Base/Scaled X/Y. Must come after branchLengthScaledRadius assignment\n    clusterRoot.descendants().forEach((node) => {\n      const [baseNodeX, baseNodeY] = pointRadial(node.x, node.y);\n      const [scaledNodeX, scaledNodeY] = pointRadial(node.x, node.branchLengthScaledRadius ?? 0);\n\n      node.baseNodeX = baseNodeX;\n      node.baseNodeY = baseNodeY;\n      node.scaledNodeX = scaledNodeX;\n      node.scaledNodeY = scaledNodeY;\n    });\n    \n    //Link Path gen must come after the above assignment of branchLengthScaledRadius\n    clusterRoot.descendants().forEach((node) => {\n      if (node.parent) {\n        const link = { source: node.parent, target: node };\n\n        const baseLinkPath = getLinkPath(link);\n        const scaledLinkPath = getScaledLinkPath(link);\n\n        node.baseLinkPath = baseLinkPath;\n        node.scaledLinkPath = scaledLinkPath;\n      }\n    });\n\n    clusterRoot.leaves().forEach((leaf) => {\n      leaf.baseLeafLinkExtension = {\n        x1: leaf.baseNodeX ?? 0,\n        x2: leaf.baseNodeX ?? 0,\n        y1: leaf.baseNodeY ?? 0,\n        y2: leaf.baseNodeY ?? 0,\n      };\n      leaf.scaledLeafLinkExtension = {\n        x1: leaf.scaledNodeX ?? 0,\n        x2: leaf.baseNodeX ?? 0,\n        y1: leaf.scaledNodeY ?? 0,\n        y2: leaf.baseNodeY ?? 0,\n      };\n      leaf.lightenedLinkExtColor = lightenHex(leaf.color ?? \"#000000\", 0.7);\n    })\n\n    // Highlighted state\n    clusterRoot.each((node) => {\n      //probably could do this more efficiently with .eachAfter\n      const isLeaf = !node.children\n      const isHighlighted = isLeaf ? highlighted.includes(node.data.id) : node.leaves().some(leaf => highlighted.includes(leaf.data.id))\n\n      node.linkStrokeWidth = isHighlighted ? linkStrokeWidth * 2 : linkStrokeWidth\n      node.labelStrokeWidth = isHighlighted ? 0.7 : 0\n    })\n    //Add ancestors and descendant IDs for faster static lookup on hover rerender\n    clusterRoot.each((node) => {\n      const ancestorIds = new Set(node.ancestors().map(node => node.data.id))\n      const descendantIds = new Set(node.descendants().map(node => node.data.id))\n      \n\n      node.ancestorIds = ancestorIds\n      node.descendantIds = descendantIds\n    })\n\n    if (leafOrder) {\n      const achievedOrder = clusterRoot.leaves().map((l) => l.data.id);\n      const treeLeafSet = new Set(achievedOrder);\n      const leafOrderSet = new Set(leafOrder);\n      const requestedFiltered = leafOrder.filter((id) => treeLeafSet.has(id));\n      const achievedFiltered = achievedOrder.filter((id) => leafOrderSet.has(id));\n      const mismatch = requestedFiltered.some((id, i) => id !== achievedFiltered[i]);\n      if (mismatch) {\n        console.error(\n          \"[PhyloTree] Requested leafOrder is not achievable given the tree topology.\\n\" +\n          \"Requested: \" + requestedFiltered.join(\", \") + \"\\n\" +\n          \"Achieved:  \" + achievedFiltered.join(\", \")\n        );\n      }\n    }\n\n    return clusterRoot;\n  }, [data, size, circleRadius, root, highlighted, linkStrokeWidth, leafOrder]);\n\n  const toggleBranchLength = useCallback(() => setEnableBranchLengths((prev) => !prev), []);\n\n  const handleLeafOnMouseMove = useCallback((event: React.MouseEvent<Element, MouseEvent>, node: TreeNode) => {\n    handleDebounceHover(event, node)\n    !node.children && showTooltip({\n      tooltipData: node.data,\n      tooltipLeft: event.clientX,\n      tooltipTop: event.clientY,\n    });\n    if (onLeafHoverChange) {\n      onLeafHoverChange(node.leaves().map(leaf => leaf.data.id))\n    }\n  }, []);\n\n  const handleLeafOnMouseLeave = useCallback((event: React.MouseEvent<Element, MouseEvent>, node: TreeNode) => {\n    handleDebounceHover(event, null)\n    hideTooltip();\n    if (onLeafHoverChange) {\n      onLeafHoverChange([])\n    }\n  }, []);\n\n  const treeContent = useMemo(() => {\n    return (\n      <Group top={TOTAL_INNER_RADIUS} left={TOTAL_INNER_RADIUS}>\n        <RenderTree\n   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+{"version":3,"file":"visualization.es7.js","sources":["../src/components/PhyloTree/PhyloTree.tsx"],"sourcesContent":["import { useMemo, useState, useCallback, useRef, useEffect } from \"react\";\nimport { Group } from \"@visx/group\";\nimport { ascending } from \"@visx/vendor/d3-array\";\nimport { pathRadialStep } from \"@visx/shape\";\nimport { cluster as d3cluster, hierarchy as d3hierarchy } from \"d3-hierarchy\";\nimport { PhyloTreeProps, TreeItem, TreeLink, TreeNode, ZoomState } from \"./types\";\nimport { useTooltip, defaultStyles, useTooltipInPortal } from \"@visx/tooltip\";\nimport { Zoom, ProvidedZoom } from \"@visx/zoom\";\nimport { ZoomFrame } from \"./ZoomFrame\";\nimport { pointRadial } from \"d3-shape\";\nimport { RenderTree } from \"./RenderTree\";\n\n/**\n * Improvements that would make this scale better (as much as svg can):\n * - Combine links into fewer path elements\n *    - Requires having static hit detecting paths, but can create fewer <path> elements by combining link paths\n *    - Creates less work for the browser to update fewer, but more complex paths\n *    - Would need base branches grouped by color, selection path, external highlight path, and invisible static hit target paths for branch selection\n * - Remove hover interaction and opt for click only interactions\n * - If keeping hover behavior, define gapless areas between nodes to prevent -> hover NodeA, hover null, hover NodeB in favor of NodeA -> NodeB\n * - Define single hit area that takes in click event and determines what was hit\n */\n\nexport const useBranchLengthTransition = {\n  duration: 0.3,\n  ease: \"easeInOut\",\n} as const;\n\n// Keep spacing of all leaf nodes consistent\nconst separationFn = () => 1;\n\nconst getBranchLengthScaledY = (cumulativeBranchLength: number, maxBranchLength: number, innerRadius: number) => {\n  return maxBranchLength === 0 ? 0 : (cumulativeBranchLength / maxBranchLength) * innerRadius;\n};\n\n// Framer motion had issues with e notation\nconst rmSciNotation = (pathString: string) => {\n  // Regex to match scientific notation:\n  // optional sign, digits/dots, 'e' or 'E', optional sign, and exponent digits\n  const scientificRegex = /-?\\d*\\.?\\d+[eE][+-]?\\d+/g;\n\n  return pathString.replace(scientificRegex, (match) => {\n    // Convert the match to a Number and then back to a decimal string\n    const num = Number(match);\n\n    // Use toFixed() to ensure no new scientific notation is generated\n    // 10 decimal places is usually enough for SVG precision\n    return num.toFixed(10).replace(/\\.?0+$/, \"\");\n  });\n};\n\nconst withNoSciNotation =\n  <L extends TreeLink>(generator: (link: L) => string | null) =>\n  (link: L) => {\n    const path = generator(link);\n    return path ? rmSciNotation(path) : \"\";\n  };\n\nconst getLinkPath = withNoSciNotation(\n  pathRadialStep<TreeLink, TreeNode>({\n    source: (l) => l.source,\n    target: (l) => l.target,\n    x: (n) => n?.x || 0,\n    y: (n) => n?.y || 0,\n  })\n);\n\nconst getScaledLinkPath = withNoSciNotation(\n  pathRadialStep<TreeLink, TreeNode>({\n    source: (l) => l.source,\n    target: (l) => l.target,\n    x: (n) => n?.x || 0,\n    y: (n) => n?.branchLengthScaledRadius || 0,\n  })\n);\n\n/**\n * Lightens a hex color by blending it with white.\n * @param {string} hex - The input color, e.g. \"#336699\"\n * @param {number} factor - How much to lighten: 0 = no change, 1 = full white\n * @returns {string} - The lightened hex color\n */\nconst lightenHex = (hex: string, factor: number) => {\n  // Remove leading \"#\" if present\n  hex = hex.replace(/^#/, '');\n\n  // Parse r, g, b\n  let r = parseInt(hex.substring(0, 2), 16);\n  let g = parseInt(hex.substring(2, 4), 16);\n  let b = parseInt(hex.substring(4, 6), 16);\n\n  // Blend each channel toward 255 (white)\n  r = Math.round(r + (255 - r) * factor);\n  g = Math.round(g + (255 - g) * factor);\n  b = Math.round(b + (255 - b) * factor);\n\n  // Convert back to hex and pad with zeros\n  const toHex = (c: number) => c.toString(16).padStart(2, '0');\n  return `#${toHex(r)}${toHex(g)}${toHex(b)}`;\n}\n\n/**\n * For internal svg calculation only\n */\nexport const TOTAL_INNER_RADIUS = 500;\n/**\n * For internal svg calculation only (used to define viewbox in ZoomFrame)\n */\nexport const TOTAL_INNER_DIAMETER = TOTAL_INNER_RADIUS * 2;\n\nexport default function PhyloTree({\n  width: totalWidth,\n  height: totalHeight,\n  data,\n  highlighted = [],\n  hovered: externalHovered = [],\n  leafFontSize = 8,\n  leafFontFamily = \"Arial\",\n  linkStrokeWidth = 1,\n  getColor = () => \"black\",\n  getLabel = (id) => id,\n  onBranchClick = () => null,\n  onLeafHoverChange,\n  labelPadding = 135,\n  defaultScaling = \"scaled\",\n  tooltipContents,\n  leafOrder,\n}: PhyloTreeProps) {\n  const [enableBranchLengths, setEnableBranchLengths] = useState<boolean>(defaultScaling === \"scaled\");\n\n  const [internalHovered, setInternalHovered] = useState<string | null>(null)\n  const { tooltipData, tooltipLeft, tooltipTop, tooltipOpen, showTooltip, hideTooltip } = useTooltip<TreeItem>();\n\n  const hovered = useMemo(\n    () => (internalHovered ? [internalHovered, ...externalHovered] : externalHovered),\n    [internalHovered, externalHovered]\n  );\n\n  const { TooltipInPortal } = useTooltipInPortal({\n    scroll: true,\n    detectBounds: true,\n  });\n\n  interface PendingHover {\n    node: TreeNode | null;\n    x: number;\n    y: number;\n  }\n\n  const pendingRef = useRef<PendingHover | null>(null);\n  const frameRef = useRef(false);\n\n  /**\n   * Prevents hover updates more frequently than the browser can repaint by using requestAnimationFrame\n   */\n  const handleDebounceHover = (event: React.MouseEvent, node: TreeNode | null) => {\n    pendingRef.current = node \n      ? { node, x: event.clientX, y: event.clientY }\n      : { node: null, x: 0, y: 0 };\n\n    if (!frameRef.current) {\n      frameRef.current = true;\n\n      requestAnimationFrame(() => {\n        // Everything comes from the ref now — consistent snapshot\n        const pending = pendingRef.current;\n        const pendingNode = pending?.node ?? null;\n\n        setInternalHovered(pendingNode ? pendingNode.data.id : null);\n\n        if (pendingNode && !pendingNode.children) {\n          showTooltip({\n            tooltipData: pendingNode.data,\n            tooltipLeft: pending!.x,\n            tooltipTop: pending!.y,\n          });\n        } else {\n          hideTooltip();\n        }\n\n        if (onLeafHoverChange) {\n          onLeafHoverChange(\n            pendingNode ? pendingNode.leaves().map((leaf) => leaf.data.id) : []\n          );\n        }\n\n        frameRef.current = false;\n      });\n    }\n  };\n\n  const circleRadius = Math.max(0, TOTAL_INNER_RADIUS - labelPadding);\n\n  // This defines the arbitrary x/y coordinate system. For our radial layout X is the angle defined in radians, Y is radius. https://d3js.org/d3-hierarchy/cluster#cluster_size\n  const size: [number, number] = useMemo(() => [2 * Math.PI, circleRadius], [circleRadius]);\n\n  /* Construct root node */\n  const root = useMemo(() => {\n    const r = d3hierarchy(data, (d) => d.children)\n      // sorts first by least number of children, and then by branch length to create nice looking plot\n      .sum((d) => (d.children ? 0 : 1))\n      .sort((a, b) => {\n        if (leafOrder) {\n          const indexMap = new Map(leafOrder.map((id, i) => [id, i]));\n          const minIdx = (node: typeof a) =>\n            Math.min(...node.leaves().map((l) => indexMap.get(l.data.id) ?? Infinity));\n          return minIdx(a) - minIdx(b);\n        }\n\n        // Float the Homo_sapiens subtree to the end so it appears at the top\n        const aHasHuman = a.leaves().some((l) => l.data.id === \"Homo_sapiens\");\n        const bHasHuman = b.leaves().some((l) => l.data.id === \"Homo_sapiens\");\n        if (aHasHuman !== bHasHuman) return aHasHuman ? -1 : 1;\n\n        return (\n          (a.value || 0) - (b.value || 0) ||\n          ascending(a.data.branch_length ?? undefined, b.data.branch_length ?? undefined)\n        );\n      });\n    return r;\n  }, [data, getColor, circleRadius, leafOrder]);\n\n  /* Add layout/render properties */\n  const rootNode = useMemo(() => {\n    const clusterLayout = d3cluster<TreeItem>();\n    clusterLayout.size(size);\n    clusterLayout.separation(separationFn);\n    //copy root node so that the reference changes when this useMemo is rerun. Otherwise is modifying in place\n    const clusterRoot: TreeNode = clusterLayout(root.copy());\n\n    let maxBranchLength = 0;\n\n    clusterRoot.each((node) => {\n      node.label = getLabel(node.data.id)\n    })\n\n    // uniformLeafColor\n    clusterRoot.eachAfter((node) => {\n      //This node is visited after all of it's descendents. Allows us to look at immediate children to see if they have same color.\n      //For leaf nodes, there will be no children, so assign the color AND assign light\n      if (!node.children) {\n        node.color = getColor(node.data.id);\n      } else {\n        const childColors = node.children.map((x) => x.color);\n        const firstColor = node.children[0].color;\n        const allSame = firstColor !== null && childColors.every((color) => color === firstColor);\n        node.color = allSame ? firstColor : \"#666\";\n      }\n    });\n\n    // cumulativeBranchLength\n    clusterRoot.eachBefore((node) => {\n      const parentLen = node.parent?.cumulativeBranchLength ?? 0;\n      const cumulativeBranchLength = parentLen + (node.data.branch_length ?? 0);\n\n      if (cumulativeBranchLength > maxBranchLength) {\n        maxBranchLength = cumulativeBranchLength;\n      }\n      \n      node.cumulativeBranchLength = cumulativeBranchLength;\n    });\n    \n    // Add BranchLengthScaledRadius. Must come after cumulativeBranchLength\n    clusterRoot.descendants().forEach((node) => {\n      const branchLengthScaledRadius = getBranchLengthScaledY(\n        node.cumulativeBranchLength ?? 0,\n        maxBranchLength,\n        circleRadius\n      );\n\n      node.branchLengthScaledRadius = branchLengthScaledRadius;\n    })\n\n    // Base/Scaled X/Y. Must come after branchLengthScaledRadius assignment\n    clusterRoot.descendants().forEach((node) => {\n      const [baseNodeX, baseNodeY] = pointRadial(node.x, node.y);\n      const [scaledNodeX, scaledNodeY] = pointRadial(node.x, node.branchLengthScaledRadius ?? 0);\n\n      node.baseNodeX = baseNodeX;\n      node.baseNodeY = baseNodeY;\n      node.scaledNodeX = scaledNodeX;\n      node.scaledNodeY = scaledNodeY;\n    });\n\n    // Base/Scaled X/Y. Must come after branchLengthScaledRadius assignment\n    clusterRoot.descendants().forEach((node) => {\n      const [baseNodeX, baseNodeY] = pointRadial(node.x, node.y);\n      const [scaledNodeX, scaledNodeY] = pointRadial(node.x, node.branchLengthScaledRadius ?? 0);\n\n      node.baseNodeX = baseNodeX;\n      node.baseNodeY = baseNodeY;\n      node.scaledNodeX = scaledNodeX;\n      node.scaledNodeY = scaledNodeY;\n    });\n    \n    //Link Path gen must come after the above assignment of branchLengthScaledRadius\n    clusterRoot.descendants().forEach((node) => {\n      if (node.parent) {\n        const link = { source: node.parent, target: node };\n\n        const baseLinkPath = getLinkPath(link);\n        const scaledLinkPath = getScaledLinkPath(link);\n\n        node.baseLinkPath = baseLinkPath;\n        node.scaledLinkPath = scaledLinkPath;\n      }\n    });\n\n    clusterRoot.leaves().forEach((leaf) => {\n      leaf.baseLeafLinkExtension = {\n        x1: leaf.baseNodeX ?? 0,\n    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Set(node.ancestors().map(node => node.data.id))\n      const descendantIds = new Set(node.descendants().map(node => node.data.id))\n      \n\n      node.ancestorIds = ancestorIds\n      node.descendantIds = descendantIds\n    })\n\n    if (leafOrder) {\n      const achievedOrder = clusterRoot.leaves().map((l) => l.data.id);\n      const treeLeafSet = new Set(achievedOrder);\n      const leafOrderSet = new Set(leafOrder);\n      const requestedFiltered = leafOrder.filter((id) => treeLeafSet.has(id));\n      const achievedFiltered = achievedOrder.filter((id) => leafOrderSet.has(id));\n      const mismatch = requestedFiltered.some((id, i) => id !== achievedFiltered[i]);\n      if (mismatch) {\n        console.error(\n          \"[PhyloTree] Requested leafOrder is not achievable given the tree topology.\\n\" +\n          \"Requested: \" + requestedFiltered.join(\", \") + \"\\n\" +\n          \"Achieved:  \" + achievedFiltered.join(\", \")\n        );\n      }\n    }\n\n    return 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package/dist/visualization.es70.js

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-  return e;
-}
-function S(e) {
-  for (var n; n = e.children; ) e = n[n.length - 1];
-  return e;
+import { jsxs as n, jsx as c } from "react/jsx-runtime";
+import { c as b } from "react/compiler-runtime";
+import { useState as S, useImperativeHandle as v } from "react";
+import _ from "./visualization.es55.js";
+const H = (t) => {
+  const e = b(10), {
+    multiSeries: d,
+    tooltipBody: i,
+    ref: h
+  } = t;
+  let r;
+  e[0] === /* @__PURE__ */ Symbol.for("react.memo_cache_sentinel") ? (r = {
+    open: !1
+  }, e[0] = r) : r = e[0];
+  const [p, u] = S(r);
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+  H as default
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package/dist/visualization.es71.js

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+import { jsx as g } from "react/jsx-runtime";
+import { memo as X, useState as v } from "react";
+import { getAnimationProps as w } from "./visualization.es20.js";
+import { motion as x } from "./visualization.es25.js";
+import B from "./visualization.es93.js";
+const E = X(({
+  bin: r,
+  x: p,
+  barWidth: l,
+  yScale: n,
+  animationType: c,
+  binIndex: f,
+  svgRef: i,
+  tooltipRef: s,
+  onBarClicked: u
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+    s.current?.show(r, e ? t.clientX - e.left + 10 : t.pageX, e ? t.clientY - e.top : t.pageY);
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+    m(!1), s.current?.hide();
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+  }, onClick: () => u?.(r) }, `seg-${e}`)) });
+});
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-  n as default
+  E as default
 };
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+{"version":3,"file":"visualization.es71.js","sources":["../src/components/Histogram/HistogramBar.tsx"],"sourcesContent":["import React, { memo, useState } from 'react';\nimport { Bar } from '@visx/shape';\nimport { motion } from 'framer-motion';\nimport { getAnimationProps, AnimationType } from '../../utility';\nimport { HistogramBin } from './types';\nimport { HistogramTooltipHandle } from './HistogramTooltip';\n\nexport interface HistogramBarProps {\n    bin: HistogramBin;\n    x: number;\n    barWidth: number;\n    yScale: (v: number) => number;\n    animationType?: AnimationType;\n    binIndex: number;\n    svgRef: React.RefObject<SVGSVGElement | null>;\n    tooltipRef: React.RefObject<HistogramTooltipHandle | null>;\n    onBarClicked?: (bin: HistogramBin) => void;\n}\n\n//memoize so that entire chart doesnt re-render on hover, just the hovered bar\nconst HistogramBar = memo(({ bin, x, barWidth, yScale, animationType, binIndex, svgRef, tooltipRef, onBarClicked }: HistogramBarProps) => {\n    const [isHovered, setIsHovered] = useState(false);\n\n    const Wrapper = animationType ? motion.g : 'g';\n    const animProps = getAnimationProps(animationType, binIndex);\n\n    let totCount = 0;\n    const segments = bin.series.map((s, si) => {\n        const start = totCount;\n        totCount += s.count;\n        return { s, si, segY: yScale(start + s.count), segHeight: Math.max(yScale(start) - yScale(start + s.count), 0) };\n    });\n\n    return (\n        <Wrapper\n            {...animProps}\n            onMouseEnter={(e: React.MouseEvent) => {\n                setIsHovered(true);\n                const rect = svgRef.current?.getBoundingClientRect();\n                tooltipRef.current?.show(bin, rect ? e.clientX - rect.left + 10 : e.pageX, rect ? e.clientY - rect.top : e.pageY);\n            }}\n            onMouseMove={(e: React.MouseEvent) => {\n                const rect = svgRef.current?.getBoundingClientRect();\n                tooltipRef.current?.show(bin, rect ? e.clientX - rect.left + 10 : e.pageX, rect ? e.clientY - rect.top : e.pageY);\n            }}\n            onMouseLeave={() => {\n                setIsHovered(false);\n                tooltipRef.current?.hide();\n            }}\n        >\n            {segments.map(({ s, si, segY, segHeight }) => (\n                <Bar\n                    key={`seg-${si}`}\n                    x={x}\n                    y={segY}\n                    width={barWidth}\n                    height={segHeight}\n                    fill={s.color}\n                    opacity={0.85}\n                    stroke={isHovered ? '#000000' : 'none'}\n                    style={{ cursor: onBarClicked ? 'pointer' : 'default' }}\n                    onClick={() => onBarClicked?.(bin)}\n                />\n            ))}\n        </Wrapper>\n    );\n});\n\nexport default HistogramBar;\n"],"names":["HistogramBar","memo","bin","x","barWidth","yScale","animationType","binIndex","svgRef","tooltipRef","onBarClicked","isHovered","setIsHovered","useState","Wrapper","motion","g","animProps","getAnimationProps","totCount","segments","series","map","s","si","start","count","segY","segHeight","Math","max","e","rect","current","getBoundingClientRect","show","clientX","left","pageX","clientY","top","pageY","hide","jsx","Bar","color","cursor"],"mappings":";;;;;AAoBA,MAAMA,IAAeC,EAAK,CAAC;AAAA,EAAEC,KAAAA;AAAAA,EAAKC,GAAAA;AAAAA,EAAGC,UAAAA;AAAAA,EAAUC,QAAAA;AAAAA,EAAQC,eAAAA;AAAAA,EAAeC,UAAAA;AAAAA,EAAUC,QAAAA;AAAAA,EAAQC,YAAAA;AAAAA,EAAYC,cAAAA;AAAgC,MAAM;AACtI,QAAM,CAACC,GAAWC,CAAY,IAAIC,EAAS,EAAK,GAE1CC,IAAUR,IAAgBS,EAAOC,IAAI,KACrCC,IAAYC,EAAkBZ,GAAeC,CAAQ;AAE3D,MAAIY,IAAW;AACf,QAAMC,IAAWlB,EAAImB,OAAOC,IAAI,CAACC,GAAGC,MAAO;AACvC,UAAMC,IAAQN;AACdA,WAAAA,KAAYI,EAAEG,OACP;AAAA,MAAEH,GAAAA;AAAAA,MAAGC,IAAAA;AAAAA,MAAIG,MAAMtB,EAAOoB,IAAQF,EAAEG,KAAK;AAAA,MAAGE,WAAWC,KAAKC,IAAIzB,EAAOoB,CAAK,IAAIpB,EAAOoB,IAAQF,EAAEG,KAAK,GAAG,CAAC;AAAA,IAAA;AAAA,EACjH,CAAC;AAED,2BACKZ,GAAA,EACG,GAAIG,GACJ,cAAc,CAACc,MAAwB;AACnCnB,IAAAA,EAAa,EAAI;AACjB,UAAMoB,IAAOxB,EAAOyB,SAASC,sBAAAA;AAC7BzB,IAAAA,EAAWwB,SAASE,KAAKjC,GAAK8B,IAAOD,EAAEK,UAAUJ,EAAKK,OAAO,KAAKN,EAAEO,OAAON,IAAOD,EAAEQ,UAAUP,EAAKQ,MAAMT,EAAEU,KAAK;AAAA,EACpH,GACA,aAAa,CAACV,MAAwB;AAClC,UAAMC,IAAOxB,EAAOyB,SAASC,sBAAAA;AAC7BzB,IAAAA,EAAWwB,SAASE,KAAKjC,GAAK8B,IAAOD,EAAEK,UAAUJ,EAAKK,OAAO,KAAKN,EAAEO,OAAON,IAAOD,EAAEQ,UAAUP,EAAKQ,MAAMT,EAAEU,KAAK;AAAA,EACpH,GACA,cAAc,MAAM;AAChB7B,IAAAA,EAAa,EAAK,GAClBH,EAAWwB,SAASS,KAAAA;AAAAA,EACxB,GAECtB,UAAAA,EAASE,IAAI,CAAC;AAAA,IAAEC,GAAAA;AAAAA,IAAGC,IAAAA;AAAAA,IAAIG,MAAAA;AAAAA,IAAMC,WAAAA;AAAAA,EAAAA,MAC1B,gBAAAe,EAACC,GAAA,EAEG,GAAAzC,GACA,GAAGwB,GACH,OAAOvB,GACP,QAAQwB,GACR,MAAML,EAAEsB,OACR,SAAS,MACT,QAAQlC,IAAY,YAAY,QAChC,OAAO;AAAA,IAAEmC,QAAQpC,IAAe,YAAY;AAAA,EAAA,GAC5C,SAAS,MAAMA,IAAeR,CAAG,KAT5B,OAAOsB,CAAE,EASqB,CAE1C,GACL;AAER,CAAC;"}