@weng-lab/visualization 1.3.0-beta.1 → 1.3.1

package/dist/visualization.es697.js

@@ -0,0 +1,40 @@
+import { clsx as y } from "./visualization.es193.js";
+function r(t, o, n = !1) {
+  const e = {
+    ...o
+  };
+  for (const f in t)
+    if (Object.prototype.hasOwnProperty.call(t, f)) {
+      const s = f;
+      if (s === "components" || s === "slots")
+        e[s] = {
+          ...t[s],
+          ...e[s]
+        };
+      else if (s === "componentsProps" || s === "slotProps") {
+        const l = t[s], c = o[s];
+        if (!c)
+          e[s] = l || {};
+        else if (!l)
+          e[s] = c;
+        else {
+          e[s] = {
+            ...c
+          };
+          for (const a in l)
+            if (Object.prototype.hasOwnProperty.call(l, a)) {
+              const i = a;
+              e[s][i] = r(l[i], c[i], n);
+            }
+        }
+      } else s === "className" && n && o.className ? e.className = y(t?.className, o?.className) : s === "style" && n && o.style ? e.style = {
+        ...t?.style,
+        ...o?.style
+      } : e[s] === void 0 && (e[s] = t[s]);
+    }
+  return e;
+}
+export {
+  r as default
+};
+//# sourceMappingURL=visualization.es697.js.map

package/dist/visualization.es697.js.map

@@ -0,0 +1 @@
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package/dist/visualization.es698.js

@@ -0,0 +1,22 @@
+import * as u from "react";
+let n = 0;
+function f(t) {
+  const [e, a] = u.useState(t), c = t || e;
+  return u.useEffect(() => {
+    e == null && (n += 1, a(`mui-${n}`));
+  }, [e]), c;
+}
+const o = {
+  ...u
+}, s = o.useId;
+function l(t) {
+  if (s !== void 0) {
+    const e = s();
+    return t ?? e;
+  }
+  return f(t);
+}
+export {
+  l as default
+};
+//# sourceMappingURL=visualization.es698.js.map

package/dist/visualization.es698.js.map

@@ -0,0 +1 @@
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package/dist/visualization.es699.js

@@ -0,0 +1,126 @@
+import * as f from "react";
+import e from "./visualization.es112.js";
+import { clsx as P } from "./visualization.es193.js";
+import { j as D } from "./visualization.es11.js";
+import R from "./visualization.es724.js";
+import B from "./visualization.es433.js";
+import E from "./visualization.es728.js";
+import F from "./visualization.es725.js";
+import { handleBreakpoints as h, resolveBreakpointValues as m, mergeBreakpointsInOrder as N } from "./visualization.es673.js";
+import S from "./visualization.es667.js";
+import G from "./visualization.es200.js";
+import M from "./visualization.es202.js";
+import { createUnarySpacing as U, getValue as O } from "./visualization.es661.js";
+const A = F(), _ = R("div", {
+  name: "MuiStack",
+  slot: "Root"
+});
+function $(o) {
+  return E({
+    props: o,
+    name: "MuiStack",
+    defaultTheme: A
+  });
+}
+function I(o, s) {
+  const c = f.Children.toArray(o).filter(Boolean);
+  return c.reduce((i, l, t) => (i.push(l), t < c.length - 1 && i.push(/* @__PURE__ */ f.cloneElement(s, {
+    key: `separator-${t}`
+  })), i), []);
+}
+const L = (o) => ({
+  row: "Left",
+  "row-reverse": "Right",
+  column: "Top",
+  "column-reverse": "Bottom"
+})[o], q = ({
+  ownerState: o,
+  theme: s
+}) => {
+  let c = {
+    display: "flex",
+    flexDirection: "column",
+    ...h({
+      theme: s
+    }, m({
+      values: o.direction,
+      breakpoints: s.breakpoints.values
+    }), (i) => ({
+      flexDirection: i
+    }))
+  };
+  if (o.spacing) {
+    const i = U(s), l = Object.keys(s.breakpoints.values).reduce((r, n) => ((typeof o.spacing == "object" && o.spacing[n] != null || typeof o.direction == "object" && o.direction[n] != null) && (r[n] = !0), r), {}), t = m({
+      values: o.direction,
+      base: l
+    }), a = m({
+      values: o.spacing,
+      base: l
+    });
+    typeof t == "object" && Object.keys(t).forEach((r, n, p) => {
+      if (!t[r]) {
+        const u = n > 0 ? t[p[n - 1]] : "column";
+        t[r] = u;
+      }
+    }), c = S(c, h({
+      theme: s
+    }, a, (r, n) => o.useFlexGap ? {
+      gap: O(i, r)
+    } : {
+      // The useFlexGap={false} implement relies on each child to give up control of the margin.
+      // We need to reset the margin to avoid double spacing.
+      "& > :not(style):not(style)": {
+        margin: 0
+      },
+      "& > :not(style) ~ :not(style)": {
+        [`margin${L(n ? t[n] : o.direction)}`]: O(i, r)
+      }
+    }));
+  }
+  return c = N(s.breakpoints, c), c;
+};
+function re(o = {}) {
+  const {
+    // This will allow adding custom styled fn (for example for custom sx style function)
+    createStyledComponent: s = _,
+    useThemeProps: c = $,
+    componentName: i = "MuiStack"
+  } = o, l = () => G({
+    root: ["root"]
+  }, (r) => M(i, r), {}), t = s(q), a = /* @__PURE__ */ f.forwardRef(function(r, n) {
+    const p = c(r), y = B(p), {
+      component: u = "div",
+      direction: b = "column",
+      spacing: j = 0,
+      divider: g,
+      children: v,
+      className: k,
+      useFlexGap: T = !1,
+      ...x
+    } = y, V = {
+      direction: b,
+      spacing: j,
+      useFlexGap: T
+    }, C = l();
+    return /* @__PURE__ */ D.jsx(t, {
+      as: u,
+      ownerState: V,
+      ref: n,
+      className: P(C.root, k),
+      ...x,
+      children: g ? I(v, g) : v
+    });
+  });
+  return process.env.NODE_ENV !== "production" && (a.propTypes = {
+    children: e.node,
+    direction: e.oneOfType([e.oneOf(["column-reverse", "column", "row-reverse", "row"]), e.arrayOf(e.oneOf(["column-reverse", "column", "row-reverse", "row"])), e.object]),
+    divider: e.node,
+    spacing: e.oneOfType([e.arrayOf(e.oneOfType([e.number, e.string])), e.number, e.object, e.string]),
+    sx: e.oneOfType([e.arrayOf(e.oneOfType([e.func, e.object, e.bool])), e.func, e.object])
+  }), a;
+}
+export {
+  re as default,
+  q as style
+};
+//# sourceMappingURL=visualization.es699.js.map

package/dist/visualization.es699.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"visualization.es699.js","sources":["../../../node_modules/.pnpm/@mui+system@7.2.0_@emotion+react@11.14.0_@types+react@19.1.8_react@19.1.0__@emotion+sty_7f3319f308133a2adcfe5767030e6962/node_modules/@mui/system/esm/Stack/createStack.js"],"sourcesContent":["'use client';\n\nimport * as React from 'react';\nimport PropTypes from 'prop-types';\nimport clsx from 'clsx';\nimport deepmerge from '@mui/utils/deepmerge';\nimport generateUtilityClass from '@mui/utils/generateUtilityClass';\nimport composeClasses from '@mui/utils/composeClasses';\nimport systemStyled from \"../styled/index.js\";\nimport useThemePropsSystem from \"../useThemeProps/index.js\";\nimport { extendSxProp } from \"../styleFunctionSx/index.js\";\nimport createTheme from \"../createTheme/index.js\";\nimport { handleBreakpoints, mergeBreakpointsInOrder, resolveBreakpointValues } from \"../breakpoints/index.js\";\nimport { createUnarySpacing, getValue } from \"../spacing/index.js\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nconst defaultTheme = createTheme();\n// widening Theme to any so that the consumer can own the theme structure.\nconst defaultCreateStyledComponent = systemStyled('div', {\n  name: 'MuiStack',\n  slot: 'Root'\n});\nfunction useThemePropsDefault(props) {\n  return useThemePropsSystem({\n    props,\n    name: 'MuiStack',\n    defaultTheme\n  });\n}\n\n/**\n * Return an array with the separator React element interspersed between\n * each React node of the input children.\n *\n * > joinChildren([1,2,3], 0)\n * [1,0,2,0,3]\n */\nfunction joinChildren(children, separator) {\n  const childrenArray = React.Children.toArray(children).filter(Boolean);\n  return childrenArray.reduce((output, child, index) => {\n    output.push(child);\n    if (index < childrenArray.length - 1) {\n      output.push(/*#__PURE__*/React.cloneElement(separator, {\n        key: `separator-${index}`\n      }));\n    }\n    return output;\n  }, []);\n}\nconst getSideFromDirection = direction => {\n  return {\n    row: 'Left',\n    'row-reverse': 'Right',\n    column: 'Top',\n    'column-reverse': 'Bottom'\n  }[direction];\n};\nexport const style = ({\n  ownerState,\n  theme\n}) => {\n  let styles = {\n    display: 'flex',\n    flexDirection: 'column',\n    ...handleBreakpoints({\n      theme\n    }, resolveBreakpointValues({\n      values: ownerState.direction,\n      breakpoints: theme.breakpoints.values\n    }), propValue => ({\n      flexDirection: propValue\n    }))\n  };\n  if (ownerState.spacing) {\n    const transformer = createUnarySpacing(theme);\n    const base = Object.keys(theme.breakpoints.values).reduce((acc, breakpoint) => {\n      if (typeof ownerState.spacing === 'object' && ownerState.spacing[breakpoint] != null || typeof ownerState.direction === 'object' && ownerState.direction[breakpoint] != null) {\n        acc[breakpoint] = true;\n      }\n      return acc;\n    }, {});\n    const directionValues = resolveBreakpointValues({\n      values: ownerState.direction,\n      base\n    });\n    const spacingValues = resolveBreakpointValues({\n      values: ownerState.spacing,\n      base\n    });\n    if (typeof directionValues === 'object') {\n      Object.keys(directionValues).forEach((breakpoint, index, breakpoints) => {\n        const directionValue = directionValues[breakpoint];\n        if (!directionValue) {\n          const previousDirectionValue = index > 0 ? directionValues[breakpoints[index - 1]] : 'column';\n          directionValues[breakpoint] = previousDirectionValue;\n        }\n      });\n    }\n    const styleFromPropValue = (propValue, breakpoint) => {\n      if (ownerState.useFlexGap) {\n        return {\n          gap: getValue(transformer, propValue)\n        };\n      }\n      return {\n        // The useFlexGap={false} implement relies on each child to give up control of the margin.\n        // We need to reset the margin to avoid double spacing.\n        '& > :not(style):not(style)': {\n          margin: 0\n        },\n        '& > :not(style) ~ :not(style)': {\n          [`margin${getSideFromDirection(breakpoint ? directionValues[breakpoint] : ownerState.direction)}`]: getValue(transformer, propValue)\n        }\n      };\n    };\n    styles = deepmerge(styles, handleBreakpoints({\n      theme\n    }, spacingValues, styleFromPropValue));\n  }\n  styles = mergeBreakpointsInOrder(theme.breakpoints, styles);\n  return styles;\n};\nexport default function createStack(options = {}) {\n  const {\n    // This will allow adding custom styled fn (for example for custom sx style function)\n    createStyledComponent = defaultCreateStyledComponent,\n    useThemeProps = useThemePropsDefault,\n    componentName = 'MuiStack'\n  } = options;\n  const useUtilityClasses = () => {\n    const slots = {\n      root: ['root']\n    };\n    return composeClasses(slots, slot => generateUtilityClass(componentName, slot), {});\n  };\n  const StackRoot = createStyledComponent(style);\n  const Stack = /*#__PURE__*/React.forwardRef(function Grid(inProps, ref) {\n    const themeProps = useThemeProps(inProps);\n    const props = extendSxProp(themeProps); // `color` type conflicts with html color attribute.\n    const {\n      component = 'div',\n      direction = 'column',\n      spacing = 0,\n      divider,\n      children,\n      className,\n      useFlexGap = false,\n      ...other\n    } = props;\n    const ownerState = {\n      direction,\n      spacing,\n      useFlexGap\n    };\n    const classes = useUtilityClasses();\n    return /*#__PURE__*/_jsx(StackRoot, {\n      as: component,\n      ownerState: ownerState,\n      ref: ref,\n      className: clsx(classes.root, className),\n      ...other,\n      children: divider ? joinChildren(children, divider) : children\n    });\n  });\n  process.env.NODE_ENV !== \"production\" ? 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package/dist/visualization.es7.js

@@ -0,0 +1,161 @@
+import { j as b } from "./visualization.es11.js";
+import { useState as q, useMemo as L, useRef as z, useCallback as x } from "react";
+import { ZoomFrame as te } from "./visualization.es57.js";
+import { RenderTree as se } from "./visualization.es58.js";
+import ae from "./visualization.es55.js";
+import ne from "./visualization.es54.js";
+import oe from "./visualization.es59.js";
+import ce from "./visualization.es60.js";
+import re from "./visualization.es61.js";
+import R from "./visualization.es62.js";
+import ie from "./visualization.es23.js";
+import le from "./visualization.es21.js";
+import { pathRadialStep as F } from "./visualization.es63.js";
+const ve = {
+  duration: 0.3,
+  ease: "easeInOut"
+}, de = () => 1, ue = (t, r, c) => r === 0 ? 0 : t / r * c, he = (t) => {
+  const r = /-?\d*\.?\d+[eE][+-]?\d+/g;
+  return t.replace(r, (c) => Number(c).toFixed(10).replace(/\.?0+$/, ""));
+}, G = (t) => (r) => {
+  const c = t(r);
+  return c ? he(c) : "";
+}, pe = G(F({
+  source: (t) => t.source,
+  target: (t) => t.target,
+  x: (t) => t?.x || 0,
+  y: (t) => t?.y || 0
+})), me = G(F({
+  source: (t) => t.source,
+  target: (t) => t.target,
+  x: (t) => t?.x || 0,
+  y: (t) => t?.branchLengthScaledRadius || 0
+})), be = (t, r) => {
+  t = t.replace(/^#/, "");
+  let c = parseInt(t.substring(0, 2), 16), d = parseInt(t.substring(2, 4), 16), u = parseInt(t.substring(4, 6), 16);
+  c = Math.round(c + (255 - c) * r), d = Math.round(d + (255 - d) * r), u = Math.round(u + (255 - u) * r);
+  const p = (g) => g.toString(16).padStart(2, "0");
+  return `#${p(c)}${p(d)}${p(u)}`;
+}, I = 500, Ee = I * 2;
+function Be({
+  width: t,
+  height: r,
+  data: c,
+  highlighted: d = [],
+  hovered: u = [],
+  leafFontSize: p = 8,
+  leafFontFamily: g = "Arial",
+  linkStrokeWidth: M = 1,
+  getColor: y = () => "black",
+  getLabel: U = (f) => f,
+  onBranchClick: S = () => null,
+  onLeafHoverChange: m,
+  labelPadding: J = 135,
+  defaultScaling: K = "scaled",
+  tooltipContents: X
+}) {
+  const [f, Q] = q(K === "scaled"), [T, V] = q(null), {
+    tooltipData: v,
+    tooltipLeft: C,
+    tooltipTop: W,
+    showTooltip: E,
+    hideTooltip: B
+  } = ae(), k = L(() => T ? [T, ...u] : u, [T, u]), {
+    TooltipInPortal: _
+  } = ne({
+    scroll: !0,
+    detectBounds: !0
+  }), P = z(null), Y = z(!1), j = (o, s) => {
+    P.current = s ? {
+      node: s,
+      x: o.clientX,
+      y: o.clientY
+    } : {
+      node: null,
+      x: 0,
+      y: 0
+    }, Y.current || (Y.current = !0, requestAnimationFrame(() => {
+      const i = P.current, e = i?.node ?? null;
+      V(e ? e.data.id : null), e && !e.children ? E({
+        tooltipData: e.data,
+        tooltipLeft: i.x,
+        tooltipTop: i.y
+      }) : B(), m && m(e ? e.leaves().map((n) => n.data.id) : []), Y.current = !1;
+    }));
+  }, N = Math.max(0, I - J), A = L(() => [2 * Math.PI, N], [N]), w = L(() => oe(c, (s) => s.children).sum((s) => s.children ? 0 : 1).sort((s, i) => {
+    const e = s.leaves().some((a) => a.data.id === "Homo_sapiens"), n = i.leaves().some((a) => a.data.id === "Homo_sapiens");
+    return e !== n ? e ? -1 : 1 : (s.value || 0) - (i.value || 0) || ce(s.data.branch_length ?? void 0, i.data.branch_length ?? void 0);
+  }), [c, y, N]), D = L(() => {
+    const o = re();
+    o.size(A), o.separation(de);
+    const s = o(w.copy());
+    let i = 0;
+    return s.each((e) => {
+      e.label = U(e.data.id);
+    }), s.eachAfter((e) => {
+      if (!e.children)
+        e.color = y(e.data.id);
+      else {
+        const n = e.children.map((h) => h.color), a = e.children[0].color, l = a !== null && n.every((h) => h === a);
+        e.color = l ? a : "#666";
+      }
+    }), s.eachBefore((e) => {
+      const a = (e.parent?.cumulativeBranchLength ?? 0) + (e.data.branch_length ?? 0);
+      a > i && (i = a), e.cumulativeBranchLength = a;
+    }), s.descendants().forEach((e) => {
+      const n = ue(e.cumulativeBranchLength ?? 0, i, N);
+      e.branchLengthScaledRadius = n;
+    }), s.descendants().forEach((e) => {
+      const [n, a] = R(e.x, e.y), [l, h] = R(e.x, e.branchLengthScaledRadius ?? 0);
+      e.baseNodeX = n, e.baseNodeY = a, e.scaledNodeX = l, e.scaledNodeY = h;
+    }), s.descendants().forEach((e) => {
+      const [n, a] = R(e.x, e.y), [l, h] = R(e.x, e.branchLengthScaledRadius ?? 0);
+      e.baseNodeX = n, e.baseNodeY = a, e.scaledNodeX = l, e.scaledNodeY = h;
+    }), s.descendants().forEach((e) => {
+      if (e.parent) {
+        const n = {
+          source: e.parent,
+          target: e
+        }, a = pe(n), l = me(n);
+        e.baseLinkPath = a, e.scaledLinkPath = l;
+      }
+    }), s.leaves().forEach((e) => {
+      e.baseLeafLinkExtension = {
+        x1: e.baseNodeX ?? 0,
+        x2: e.baseNodeX ?? 0,
+        y1: e.baseNodeY ?? 0,
+        y2: e.baseNodeY ?? 0
+      }, e.scaledLeafLinkExtension = {
+        x1: e.scaledNodeX ?? 0,
+        x2: e.baseNodeX ?? 0,
+        y1: e.scaledNodeY ?? 0,
+        y2: e.baseNodeY ?? 0
+      }, e.lightenedLinkExtColor = be(e.color ?? "#000000", 0.7);
+    }), s.each((e) => {
+      const a = !e.children ? d.includes(e.data.id) : e.leaves().some((l) => d.includes(l.data.id));
+      e.linkStrokeWidth = a ? M * 2 : M, e.labelStrokeWidth = a ? 0.7 : 0;
+    }), s.each((e) => {
+      const n = new Set(e.ancestors().map((l) => l.data.id)), a = new Set(e.descendants().map((l) => l.data.id));
+      e.ancestorIds = n, e.descendantIds = a;
+    }), s;
+  }, [c, A, N, w, d, M]), O = x(() => Q((o) => !o), []), $ = x((o, s) => {
+    j(o, s), !s.children && E({
+      tooltipData: s.data,
+      tooltipLeft: o.clientX,
+      tooltipTop: o.clientY
+    }), m && m(s.leaves().map((i) => i.data.id));
+  }, []), H = x((o, s) => {
+    j(o, null), B(), m && m([]);
+  }, []), Z = L(() => /* @__PURE__ */ b.jsx(ie, { top: I, left: I, children: /* @__PURE__ */ b.jsx(se, { node: D, hovered: k, leafFontFamily: g, leafFontSize: p, useBranchLengths: f, onNodeMouseMove: $, onNodeMouseLeave: H, onBranchClick: S }) }), [D, k, g, p, f, $, H, S]), ee = x((o) => /* @__PURE__ */ b.jsx(te, { zoom: o, totalWidth: t, totalHeight: r, toggleBranchLength: O, children: Z }), [t, r, O, Z]);
+  return t < 10 ? null : /* @__PURE__ */ b.jsxs("div", { children: [
+    /* @__PURE__ */ b.jsx(le, { width: t, height: r, scaleXMin: 0.8, scaleXMax: 4, scaleYMin: 0.8, scaleYMax: 4, children: ee }),
+    v && X && /* @__PURE__ */ b.jsx(_, { left: C, top: W, children: X(v.id) })
+  ] });
+}
+export {
+  Ee as TOTAL_INNER_DIAMETER,
+  I as TOTAL_INNER_RADIUS,
+  Be as default,
+  ve as useBranchLengthTransition
+};
+//# sourceMappingURL=visualization.es7.js.map

package/dist/visualization.es7.js.map

@@ -0,0 +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 } from \"@visx/zoom\";\nimport { ProvidedZoom } from \"@visx/zoom/lib/types\";\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}: 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        // 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        // Original sort\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]);\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    return clusterRoot;\n  }, [data, size, circleRadius, root, highlighted, linkStrokeWidth]);\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          node={rootNode}\n          hovered={hovered}\n          leafFontFamily={leafFontFamily}\n          leafFontSize={leafFontSize}\n          useBranchLengths={enableBranchLengths}\n          onNodeMouseMove={handleLeafOnMouseMove}\n          onNodeMouseLeave={handleLeafOnMouseLeave}\n          onBranchClick={onBranchClick}\n        />\n      </Group>\n    );\n  }, [\n    rootNode,\n    hovered,\n    leafFontFamily,\n    leafFontSize,\n    enableBranchLengths,\n    handleLeafOnMouseMove,\n    handleLeafOnMouseLeave,\n    onBranchClick,\n  ]);\n\n  const renderTreeInZoom = useCallback(\n    (zoom: ProvidedZoom<SVGSVGElement> & ZoomState) => {\n      return (\n        <ZoomFrame\n          zoom={zoom}\n          totalWidth={totalWidth}\n          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package/dist/visualization.es70.js

@@ -0,0 +1,36 @@
+import { j as s } from "./visualization.es11.js";
+import { c as f } from "./visualization.es85.js";
+import u from "./visualization.es103.js";
+const h = (i) => {
+  const t = f.c(7), {
+    left: e,
+    top: o,
+    data: r,
+    open: a,
+    pointTooltipBody: l
+  } = i;
+  if (!a || !r)
+    return null;
+  const c = e + 10;
+  let n;
+  t[0] !== r || t[1] !== l ? (n = l && r.point ? l(r.point) : Object.entries(r).map(d), t[0] = r, t[1] = l, t[2] = n) : n = t[2];
+  let p;
+  return t[3] !== c || t[4] !== n || t[5] !== o ? (p = /* @__PURE__ */ s.jsx(u, { left: c, top: o, children: n }), t[3] = c, t[4] = n, t[5] = o, t[6] = p) : p = t[6], p;
+};
+function m(i) {
+  return i.toUpperCase();
+}
+function d(i) {
+  const [t, e] = i, o = t.replace(/([a-z])([A-Z])/g, "$1 $2").replace(/^./, m);
+  return t === "outlier" ? /* @__PURE__ */ s.jsx("div", { children: /* @__PURE__ */ s.jsx("strong", { children: o }) }, t) : /* @__PURE__ */ s.jsxs("div", { children: [
+    /* @__PURE__ */ s.jsxs("strong", { children: [
+      o,
+      ": "
+    ] }),
+    typeof e == "string" ? e.length > 45 ? `${e.replace(/_/g, " ").slice(0, 45)}...` : e.replace(/_/g, " ") : String(e)
+  ] }, t);
+}
+export {
+  h as default
+};
+//# sourceMappingURL=visualization.es70.js.map

package/dist/visualization.es70.js.map

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+{"version":3,"file":"visualization.es70.js","sources":["../src/components/ViolinPlot/violinTooltip.tsx"],"sourcesContent":["import { TooltipWithBounds } from \"@visx/tooltip\";\nimport { TooltipProps } from \"./types\";\n\nconst ViolinTooltip = <T,>({ left, top, data, open, pointTooltipBody }: TooltipProps<T>) => {\n    if (!open || !data) return null;\n\n    return (\n        <TooltipWithBounds left={left + 10} top={top}>\n            {pointTooltipBody && data.point ? (\n                pointTooltipBody(data.point)\n            ) : (\n                Object.entries(data as Record<string, unknown>).map(([key, value]) => {\n                    const formattedKey = key\n                        .replace(/([a-z])([A-Z])/g, \"$1 $2\")\n                        .replace(/^./, str => str.toUpperCase());\n\n                    if (key === \"outlier\") {\n                        return (\n                            <div key={key}>\n                                <strong>{formattedKey}</strong>\n                            </div>\n                        );\n                    } else {\n                        return (\n                            <div key={key}>\n                                <strong>{formattedKey}: </strong>\n                                {typeof value === 'string'\n                                    ? (value.length > 45\n                                        ? `${value.replace(/_/g, \" \").slice(0, 45)}...`\n                                        : value.replace(/_/g, \" \"))\n                                    : String(value)}\n                            </div>\n                        );\n                    }\n                })\n            )}\n        </TooltipWithBounds>\n    );\n};\n\nexport default ViolinTooltip;\n"],"names":["ViolinTooltip","t0","$","_c","left","top","data","open","pointTooltipBody","t1","t2","point","Object","entries","map","_temp2","t3","TooltipWithBounds","_temp","str","toUpperCase","key","value","formattedKey","replace","jsx","jsxs","length","slice","String"],"mappings":";;;AAGA,MAAMA,IAAgBC,CAAAA,MAAA;AAAA,QAAAC,IAAAC,EAAAA,EAAA,CAAA,GAAK;AAAA,IAAAC,MAAAA;AAAAA,IAAAC,KAAAA;AAAAA,IAAAC,MAAAA;AAAAA,IAAAC,MAAAA;AAAAA,IAAAC,kBAAAA;AAAAA,EAAAA,IAAAP;AACvB,MAAI,CAACM,KAAD,CAAUD;AAAI,WAAS;AAGE,QAAAG,IAAAL,IAAO;AAAE,MAAAM;AAAA,EAAAR,EAAA,CAAA,MAAAI,KAAAJ,SAAAM,KAC7BE,IAAAF,KAAoBF,EAAIK,QACrBH,EAAiBF,EAAIK,KA0BzB,IAxBIC,OAAMC,QAASP,CAA+B,EAACQ,IAAKC,CAwBxD,GAACb,OAAAI,GAAAJ,OAAAM,GAAAN,OAAAQ,KAAAA,IAAAR,EAAA,CAAA;AAAA,MAAAc;AAAA,SAAAd,EAAA,CAAA,MAAAO,KAAAP,SAAAQ,KAAAR,EAAA,CAAA,MAAAG,KA5BLW,0BAACC,GAAA,EAAwB,MAAAR,GAAgBJ,KAAAA,GACpCK,UAAAA,GA4BL,GAAoBR,OAAAO,GAAAP,OAAAQ,GAAAR,OAAAG,GAAAH,OAAAc,KAAAA,IAAAd,EAAA,CAAA,GA7BpBc;AA6BoB;AAjCN,SAAAE,EAAAC,GAAA;AAAA,SAWwBA,EAAGC,YAAAA;AAAc;AAXzC,SAAAL,EAAAd,GAAA;AAQ+C,QAAA,CAAAoB,GAAAC,CAAA,IAAArB,GACjDsB,IAAqBF,EAAGG,QACX,mBAAmB,OAAO,EAACA,QAC3B,MAAMN,CAAwB;AAE3C,SAAIG,MAAQ,kCAEJ,OAAA,EACI,UAAAI,gBAAAA,EAAAA,IAAA,UAAA,eAAsB,MAC1B,2BAIA,OAAA,EACI,UAAA;AAAA,IAAAC,gBAAAA,OAAA,UAAA,EAASH,UAAAA;AAAAA,MAAAA;AAAAA,MAAa;AAAA,IAAA,GAAE;AAAA,IACvB,OAAOD,KAAU,WACXA,EAAKK,SAAU,KAAf,GACML,EAAKE,QAAS,MAAM,GAAG,EAACI,MAAO,GAAG,EAAE,CAAC,QACxCN,EAAKE,QAAS,MAAM,GAAG,IAC3BK,OAAOP,CAAK;AAAA,EAAA,EAAA,GANZD,CAOV;AAEP;"}

package/dist/visualization.es700.js

@@ -0,0 +1,51 @@
+import y from "./visualization.es770.js";
+import T from "./visualization.es771.js";
+import g from "./visualization.es707.js";
+import h from "./visualization.es772.js";
+function L(o, t) {
+  const {
+    className: c,
+    elementType: i,
+    ownerState: n,
+    externalForwardedProps: P,
+    internalForwardedProps: s,
+    shouldForwardComponentProp: p = !1,
+    ...a
+  } = t, {
+    component: l,
+    slots: r = {
+      [o]: void 0
+    },
+    slotProps: u = {
+      [o]: void 0
+    },
+    ...w
+  } = P, d = r[o] || i, f = y(u[o], n), {
+    props: {
+      component: m,
+      ...C
+    },
+    internalRef: S
+  } = T({
+    className: c,
+    ...a,
+    externalForwardedProps: o === "root" ? w : void 0,
+    externalSlotProps: f
+  }), F = g(S, f?.ref, t.ref), e = o === "root" ? m || l : m, x = h(d, {
+    ...o === "root" && !l && !r[o] && s,
+    ...o !== "root" && !r[o] && s,
+    ...C,
+    ...e && !p && {
+      as: e
+    },
+    ...e && p && {
+      component: e
+    },
+    ref: F
+  }, n);
+  return [d, x];
+}
+export {
+  L as default
+};
+//# sourceMappingURL=visualization.es700.js.map

package/dist/visualization.es700.js.map

@@ -0,0 +1 @@
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package/dist/visualization.es701.js

@@ -0,0 +1,11 @@
+import o from "./visualization.es203.js";
+import e from "./visualization.es202.js";
+function l(t) {
+  return e("MuiTooltip", t);
+}
+const r = o("MuiTooltip", ["popper", "popperInteractive", "popperArrow", "popperClose", "tooltip", "tooltipArrow", "touch", "tooltipPlacementLeft", "tooltipPlacementRight", "tooltipPlacementTop", "tooltipPlacementBottom", "arrow"]);
+export {
+  r as default,
+  l as getTooltipUtilityClass
+};
+//# sourceMappingURL=visualization.es701.js.map

package/dist/visualization.es701.js.map

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