@weng-lab/visualization 2.4.2 → 2.5.0

package/dist/visualization.es154.js

@@ -1,18 +1,75 @@
-function p(t) {
-  for (var e = this, r = n(e, t), o = [e]; e !== r; )
-    e = e.parent, o.push(e);
-  for (var s = o.length; t !== r; )
-    o.splice(s, 0, t), t = t.parent;
-  return o;
+import { useMemo as f } from "react";
+import S from "./visualization.es157.js";
+import A from "./visualization.es155.js";
+function b(i) {
+  return typeof i == "number";
 }
-function n(t, e) {
-  if (t === e) return t;
-  var r = t.ancestors(), o = e.ancestors(), s = null;
-  for (t = r.pop(), e = o.pop(); t === e; )
-    s = t, t = r.pop(), e = o.pop();
-  return s;
+function D(i) {
+  return (
+    // number that is not NaN or Infinity
+    typeof i == "number" && Number.isFinite(i) || // for percentage
+    typeof i == "string"
+  );
+}
+function M(i) {
+  const {
+    verticalAnchor: m = "end",
+    scaleToFit: o = !1,
+    angle: p,
+    width: n,
+    lineHeight: w = "1em",
+    capHeight: g = "0.71em",
+    // Magic number from d3
+    children: c,
+    style: $,
+    ...L
+  } = i, {
+    x: d = 0,
+    y: h = 0
+  } = L, u = !D(d) || !D(h), {
+    wordsWithWidth: x,
+    spaceWidth: y
+  } = f(() => ({
+    wordsWithWidth: (c == null ? [] : c.toString().split(/(?:(?!\u00A0+)\s+)/)).map((s) => ({
+      word: s,
+      wordWidth: A(s, $) || 0
+    })),
+    spaceWidth: A(" ", $) || 0
+  }), [c, $]), e = f(() => u ? [] : n || o ? x.reduce((t, s) => {
+    let {
+      word: l,
+      wordWidth: a
+    } = s;
+    const r = t[t.length - 1];
+    if (r && (n == null || o || (r.width || 0) + a + y < n))
+      r.words.push(l), r.width = r.width || 0, r.width += a + y;
+    else {
+      const W = {
+        words: [l],
+        width: a
+      };
+      t.push(W);
+    }
+    return t;
+  }, []) : [{
+    words: c == null ? [] : c.toString().split(/(?:(?!\u00A0+)\s+)/)
+  }], [u, n, o, c, x, y]), N = f(() => u ? "" : m === "start" ? S(`calc(${g})`) : m === "middle" ? S(`calc(${(e.length - 1) / 2} * -${w} + (${g} / 2))`) : S(`calc(${e.length - 1} * -${w})`), [u, m, g, e.length, w]), X = f(() => {
+    const t = [];
+    if (u)
+      return "";
+    if (b(d) && b(h) && b(n) && o && e.length > 0) {
+      const s = e[0].width || 1, l = o === "shrink-only" ? Math.min(n / s, 1) : n / s, a = l, r = d - l * d, W = h - a * h;
+      t.push(`matrix(${l}, 0, 0, ${a}, ${r}, ${W})`);
+    }
+    return p && t.push(`rotate(${p}, ${d}, ${h})`), t.length > 0 ? t.join(" ") : "";
+  }, [u, d, h, n, o, e, p]);
+  return {
+    wordsByLines: e,
+    startDy: N,
+    transform: X
+  };
 }
 export {
-  p as default
+  M as default
 };
 //# sourceMappingURL=visualization.es154.js.map

package/dist/visualization.es154.js.map

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package/dist/visualization.es155.js

@@ -1,9 +1,20 @@
-function t() {
-  for (var e = this, n = [e]; e = e.parent; )
-    n.push(e);
-  return n;
+import r from "./visualization.es156.js";
+const o = "__react_svg_text_measurement_id";
+function s(n, i) {
+  if (typeof document > "u") return null;
+  try {
+    let e = document.getElementById(o);
+    if (!e) {
+      const t = document.createElementNS("http://www.w3.org/2000/svg", "svg");
+      t.setAttribute("aria-hidden", "true"), t.style.width = "0", t.style.height = "0", t.style.position = "absolute", t.style.top = "-100%", t.style.left = "-100%", e = document.createElementNS("http://www.w3.org/2000/svg", "text"), e.setAttribute("id", o), t.appendChild(e), document.body.appendChild(t);
+    }
+    return Object.assign(e.style, i), e.textContent = n, e.getComputedTextLength();
+  } catch {
+    return null;
+  }
 }
+const l = r(s, (n, i) => `${n}_${JSON.stringify(i)}`);
 export {
-  t as default
+  l as default
 };
 //# sourceMappingURL=visualization.es155.js.map

package/dist/visualization.es155.js.map

@@ -1 +1 @@
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package/dist/visualization.es156.js

@@ -1,7 +1,15 @@
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+function i(a, s) {
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+  return function() {
+    for (var o = arguments.length, n = new Array(o), t = 0; t < o; t++)
+      n[t] = arguments[t];
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+    if (e.has(r)) return e.get(r);
+    const u = a.apply(this, n);
+    return e.set(r, u), u;
+  };
 }
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-  e as default
+  i as default
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package/dist/visualization.es157.js

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-function n() {
-  var e = [];
-  return this.eachBefore(function(a) {
-    a.children || e.push(a);
-  }), e;
-}
+import { getDefaultExportFromCjs as r } from "./visualization.es227.js";
+import { __require as e } from "./visualization.es270.js";
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+const a = /* @__PURE__ */ r(o);
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+  a as default
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-  var r = this, n = [];
-  return r.each(function(t) {
-    t !== r && n.push({ source: t.parent, target: t });
-  }), n;
+import l from "./visualization.es144.js";
+import { jsx as o } from "react/jsx-runtime";
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+  let {
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package/dist/visualization.es159.js

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-  do
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-      if (yield e, i = e.children)
-        for (r = 0, h = i.length; r < h; ++r)
-          n.push(i[r]);
-  while (n.length);
+function e(t) {
+  return t?.[0];
+}
+function n(t) {
+  return t?.[1];
 }
 export {
-  l as default
+  e as getFirstItem,
+  n as getSecondItem
 };
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package/dist/visualization.es16.js

@@ -1,14 +1,273 @@
-const e = (s, t, o) => {
-  const r = {};
-  return o && o.forEach((c) => r[c] = 0), s?.forEach((c) => {
-    r[c[t]] ? r[c[t]]++ : r[c[t]] = 1;
-  }), r;
+import { jsxs as A, jsx as a } from "react/jsx-runtime";
+import { useState as P, useRef as D, useEffect as M, useCallback as Z, useMemo as y } from "react";
+import It from "@mui/material/Tooltip";
+import At from "@mui/icons-material/InfoOutlined";
+import Lt from "./visualization.es24.js";
+import xt from "./visualization.es35.js";
+import wt from "./visualization.es23.js";
+import q from "./visualization.es25.js";
+import Dt from "./visualization.es32.js";
+import Mt from "./visualization.es51.js";
+import { defaultStyles as yt } from "./visualization.es31.js";
+import Gt from "./visualization.es52.js";
+const et = {
+  A: "#05ac05",
+  C: "#1668cb",
+  G: "#ffb700",
+  T: "#fd1414",
+  N: "#555555",
+  M: "#984ea3",
+  "-": "#d4d4d4",
+  "*": "#ffffff"
+}, K = {
+  A: "A",
+  C: "C",
+  G: "G",
+  T: "T",
+  N: "N Unresolved",
+  M: "Ambiguous Alignment",
+  "-": "Gap",
+  "*": "Absent"
+}, V = ["A", "C", "G", "T", "N", "M", "*", "-"], _t = `
+  Each column is a position in the human cCRE, and each row shows the
+  corresponding aligned state in another mammalian genome. A, C, G, and
+  T indicate the nucleotide aligned to that human position. N indicates that
+  the target genome has an unresolved base at that position. Ambiguous
+  alignment indicates that this human cCRE position aligns to more than
+  one location in the target genome, and those aligned locations contain
+  different nucleotides. Because the alignment does not support a single
+  target base, the position is not assigned A, C, G, or T. Absent indicates
+  that the human position could not be aligned to that species. Gap
+  indicates that the alignment covers this region, but this species has a gap
+  relative to the human cCRE.
+`, Ct = Gt({
+  domain: V,
+  range: V.map((s) => et[s])
+}), nt = 24, Rt = 16, ot = 16, st = 3, J = nt + Rt + st * ot, N = 12, x = 12, G = 10, L = x + G + N + G, Ht = 1, Pt = 50, Q = 1.15, O = 5, tt = (s, f, m) => Math.min(0, Math.max(m * (1 - f), s)), qt = ({
+  data: s,
+  width: f,
+  height: m,
+  getLabel: it,
+  getOrderColor: at,
+  getOrder: rt,
+  hovered: _ = [],
+  highlighted: lt = [],
+  onHoverChange: B = () => null,
+  tooltipContents: j
+}) => {
+  const [v, ct] = P(null), [o, z] = P({
+    scaleX: 1,
+    translateX: 0
+  }), [W, C] = P(!1), T = D(o), Y = D(0), k = D(0);
+  M(() => {
+    T.current = o;
+  }, [o]);
+  const X = Z((t) => {
+    t !== v && (ct(t), B(t));
+  }, [v, B]), E = y(() => v ? [v, ..._] : _, [v, _]), {
+    tooltipData: F,
+    tooltipLeft: ht,
+    tooltipTop: dt,
+    showTooltip: U,
+    hideTooltip: R
+  } = Lt(), {
+    TooltipInPortal: pt
+  } = xt({
+    scroll: !0,
+    detectBounds: !0
+  }), w = Object.keys(s).length, c = Object.values(s)[0]?.length ?? 0, i = f - L, d = m - J, H = y(() => {
+    const t = Object.keys(s).map((e) => [e, {
+      id: e,
+      label: it(e),
+      order: rt(e),
+      color: at(e)
+    }]);
+    return new Map(t);
+  }, [s]), b = D(null);
+  M(() => {
+    const t = b.current;
+    if (!t) return;
+    const e = (n) => {
+      n.preventDefault();
+      const h = t.getBoundingClientRect(), g = n.clientX - h.left, {
+        scaleX: r,
+        translateX: p
+      } = T.current, u = n.deltaY < 0 ? Q : 1 / Q, l = Math.max(Ht, Math.min(Pt, r * u)), S = g - (g - p) * (l / r), I = tt(S, l, i);
+      z({
+        scaleX: l,
+        translateX: I
+      });
+    };
+    return t.addEventListener("wheel", e, {
+      passive: !1
+    }), () => t.removeEventListener("wheel", e);
+  }, [i]), M(() => {
+    const t = b.current;
+    if (!t) return;
+    const e = (n) => {
+      n.touches.length === 1 && n.preventDefault();
+    };
+    return t.addEventListener("touchstart", e, {
+      passive: !1
+    }), t.addEventListener("touchmove", e, {
+      passive: !1
+    }), () => {
+      t.removeEventListener("touchstart", e), t.removeEventListener("touchmove", e);
+    };
+  }, []), M(() => {
+    const t = b.current;
+    if (!t) return;
+    const e = t.getContext("2d");
+    if (!e) return;
+    const n = window.devicePixelRatio || 1;
+    t.width = i * n, t.height = d * n, t.style.width = `${i}px`, t.style.height = `${d}px`, e.setTransform(1, 0, 0, 1, 0, 0), e.clearRect(0, 0, t.width, t.height);
+    const h = t.width / c * o.scaleX, g = t.height / w, r = o.translateX * n;
+    e.setTransform(h, 0, 0, g, r, 0), Object.entries(s).forEach(([p, u], l) => {
+      u.forEach((S, I) => {
+        e.fillStyle = et[S], e.globalAlpha = E.length && !E.includes(p) ? 0.3 : 1, e.fillRect(I, l, 1, 1), e.globalAlpha = 1;
+      });
+    });
+  }, [s, i, d, c, w, E, o]);
+  const ut = Z((t) => {
+    const {
+      scaleX: e,
+      translateX: n
+    } = T.current;
+    return Math.floor((t - n) / i * (c / e));
+  }, [i, c]), mt = (t) => {
+    C(!0), Y.current = t.clientX, k.current = T.current.translateX, t.currentTarget.setPointerCapture(t.pointerId);
+  }, gt = (t) => {
+    const e = b.current;
+    if (!e) return;
+    if (W) {
+      const S = t.clientX - Y.current, I = tt(k.current + S, T.current.scaleX, i);
+      z((St) => ({
+        ...St,
+        translateX: I
+      }));
+      return;
+    }
+    const n = e.getBoundingClientRect(), h = t.clientX - n.left, g = t.clientY - n.top, r = ut(h), p = Math.floor(g / n.height * w), u = Object.keys(s)[p], l = s[u]?.[r];
+    r >= 0 && r < c && p >= 0 && p < w ? (X(u), U({
+      tooltipTop: t.clientY,
+      tooltipLeft: t.clientX,
+      tooltipData: {
+        position: r,
+        char: l,
+        charLabel: l != null ? K[l] : void 0,
+        ...H.get(u)
+      }
+    })) : (X(null), R());
+  }, ft = () => {
+    C(!1);
+  }, vt = () => {
+    C(!1), X(null), R();
+  }, Tt = (t, e) => {
+    X(e.id), U({
+      tooltipLeft: t.clientX,
+      tooltipTop: t.clientY,
+      tooltipData: e
+    });
+  }, Xt = (t, e) => {
+    X(null), R();
+  }, Et = y(() => wt({
+    domain: [0, c - 1],
+    range: [o.translateX, i * o.scaleX + o.translateX]
+  }), [c, i, o]), $ = y(() => [...H.values()], [H]), bt = i + O;
+  return f < 10 || m < 10 ? null : /* @__PURE__ */ A("div", { style: {
+    position: "relative",
+    width: f,
+    height: m
+  }, children: [
+    /* @__PURE__ */ A("svg", { width: L, height: m, style: {
+      top: 0,
+      left: 0,
+      position: "absolute"
+    }, children: [
+      $.map((t, e) => {
+        const n = d / $.length;
+        return /* @__PURE__ */ A("g", { onMouseMove: (h) => Tt(h, t), onMouseLeave: (h) => Xt(), opacity: E.length && !E.includes(t.id) ? 0.3 : 1, children: [
+          lt.includes(t.id) && /* @__PURE__ */ a("rect", { width: x, height: n, x: 0, y: n * e, fill: t.color, shapeRendering: "crispEdges" }),
+          /* @__PURE__ */ a("rect", { width: N, height: n, x: x + G, y: n * e, fill: t.color, shapeRendering: "crispEdges" })
+        ] }, e);
+      }),
+      /* @__PURE__ */ a(q, { angle: 270, textAnchor: "end", verticalAnchor: "middle", fontSize: 12, x: 0.5 * x, y: d + 2, children: "Highlight" }),
+      /* @__PURE__ */ a(q, { angle: 270, textAnchor: "end", verticalAnchor: "middle", fontSize: 12, x: x + G + 0.5 * N, y: d + 2, children: "Species" })
+    ] }),
+    /* @__PURE__ */ a("canvas", { ref: b, onPointerDown: mt, onPointerMove: gt, onPointerUp: ft, onPointerLeave: vt, style: {
+      position: "absolute",
+      left: L,
+      cursor: W ? "grabbing" : o.scaleX > 1 ? "grab" : "default"
+    } }),
+    /* @__PURE__ */ a("svg", { width: bt, height: J, style: {
+      position: "absolute",
+      //position it into the other svg by AXIS_LEFT_PADDING to fix axis cutoff of 0 at first load.
+      //can't fix with overflow visible since on zoom the axis needs to be clipped
+      left: L - O,
+      bottom: 0,
+      pointerEvents: "none",
+      overflow: "hidden"
+    }, children: /* @__PURE__ */ a(Dt, { scale: Et, numTicks: Math.min(c, Math.round(10 * o.scaleX)), left: O }) }),
+    /* @__PURE__ */ A("div", { style: {
+      position: "absolute",
+      top: d + nt,
+      left: L,
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+      display: "flex",
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+      alignItems: "center",
+      gap: 2,
+      fontSize: 12,
+      pointerEvents: "none"
+    }, children: [
+      /* @__PURE__ */ A("div", { style: {
+        position: "relative",
+        width: "100%",
+        textAlign: "center"
+      }, children: [
+        "Position in cCRE",
+        /* @__PURE__ */ a("span", { style: {
+          position: "absolute",
+          right: 0,
+          top: 0
+        }, children: `${o.scaleX.toFixed(1)}×` })
+      ] }),
+      /* @__PURE__ */ a(
+        Mt,
+        {
+          scale: Ct,
+          direction: "row",
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+          shapeWidth: 11,
+          shapeHeight: 11,
+          itemMargin: "0 10px 0 0",
+          labelMargin: "0 0 0 0px",
+          labelFormat: (t) => K[t],
+          shapeStyle: () => ({
+            border: "1px solid rgba(0,0,0,0.25)"
+          }),
+          style: {
+            display: "flex",
+            flexWrap: "wrap",
+            justifyContent: "center",
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+        }
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+    ] }),
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+      position: "absolute",
+      bottom: 4,
+      right: 4,
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+      cursor: "help"
+    } }) })
+  ] });
 };
-function n(s) {
-  return Object.fromEntries(Object.entries(s).sort(([, t], [, o]) => o - t));
-}
 export {
-  e as getProportionsFromArray,
-  n as sortObjectByValueDesc
+  qt as SequenceAlignmentPlot
 };
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