taxonium-component/dist/SupplementaryAlignments-CebupL-v.js

React component for exploring large phylogenetic trees in the browser

import { jsxs as y, jsx as l } from "react/jsx-runtime";
import { B as A } from "./BaseCard-B_4xCCRV.js";
import { u as m, bn as B, q as C, bo as x, T as v, a as E, bp as D } from "./JBrowsePanel-ClL6pWQW.js";
import { useState as w, useEffect as R, lazy as L } from "react";
import { L as h } from "./Link-CoWt_Y7_.js";
import { n as M } from "./AlignmentsFeatureDetail-BVDBx0nB.js";
async function V({ view: t, feature: n }) {
  var s;
  const { assemblyManager: i } = m.getSession(t), a = n.get("CIGAR"), o = n.get("strand"), f = ((s = n.get("tags")) === null || s === void 0 ? void 0 : s.SA) || "", u = n.get("name"), e = B(a, 1), g = await i.waitForAssembly(t.assemblyNames[0]);
  if (!g)
    throw new Error("assembly not found");
  const p = C(f, n.id(), o, u, !0), r = n.toJSON();
  r.clipPos = e, r.strand = 1, r.mate = {
    refName: u,
    start: e,
    end: e + x(a)
  };
  const S = [r, ...p];
  for (const [d, c] of S.entries())
    c.refName = g.getCanonicalRefName(c.refName) || c.refName, c.syntenyId = d, c.mate.syntenyId = d, c.mate.uniqueId = `${c.uniqueId}_mate`;
  return S.sort((d, c) => d.clipPos - c.clipPos), S;
}
const q = L(() => import("./BreakendMultiLevelOptionDialog-B7SgVjat.js")), F = L(() => import("./BreakendSingleLevelOptionDialog-BXFzWPGw.js"));
function I({ model: t, feature: n }) {
  const { view: s } = t, [i, a] = w(), [o, f] = w();
  R(() => {
    (async () => {
      try {
        const e = await V({
          view: s,
          feature: new m.SimpleFeature(n)
        });
        a(e);
      } catch (e) {
        f(e), console.error(e);
      }
    })();
  }, [n, s]);
  const u = [];
  if (i)
    for (let e = 0; e < i.length - 1; e++)
      u.push([i[e], i[e + 1]]);
  return u.length ? y("div", { children: [l(v, { children: "Launch split view" }), o ? l(E.ErrorMessage, { error: o }) : null, l("ul", { children: u.map((e, g) => {
    const [p, r] = e;
    return y("li", { children: [p.refName, ":", m.toLocale(p.strand === 1 ? p.end : p.start), " ->", " ", r.refName, ":", m.toLocale(r.strand === 1 ? r.start : r.end), " ", l(O, { model: t, f1: p, f2: r }), " ", l(P, { model: t, f1: p, f2: r })] }, `${JSON.stringify(e)}-${g}`);
  }) })] }) : null;
}
function O({ model: t, f1: n, f2: s }) {
  return l(h, { href: "#", onClick: (i) => {
    i.preventDefault();
    const a = m.getSession(t);
    a.queueDialog((o) => [
      q,
      {
        handleClose: o,
        session: a,
        feature: new m.SimpleFeature({ ...n, mate: s }),
        view: t.view,
        assemblyName: t.view.displayedRegions[0].assemblyName
      }
    ]);
  }, children: "(top/bottom)" });
}
function P({ model: t, f1: n, f2: s }) {
  return l(h, { href: "#", onClick: (i) => {
    i.preventDefault();
    const a = m.getSession(t);
    a.queueDialog((o) => [
      F,
      {
        handleClose: o,
        session: a,
        feature: new m.SimpleFeature({ ...n, mate: s }),
        view: t.view,
        assemblyName: t.view.displayedRegions[0].assemblyName
      }
    ]);
  }, children: "(single row)" });
}
function T({ tag: t, model: n }) {
  return y("div", { children: [l(v, { children: "List of supplementary alignment locations" }), l("ul", { children: t.split(";").filter((s) => !!s).map((s, i) => {
    const [a, o, f, u] = s.split(","), e = D(u), g = Math.floor(e / 5), p = +o, r = +o + e, S = p - g, d = r + g, c = `${a}:${Math.max(1, S)}-${d}`, N = p.toLocaleString("en-US"), b = r.toLocaleString("en-US"), $ = `${a}:${N}-${b} (${f}) [${e}bp]`;
    return l("li", { children: l(h, { href: "#", onClick: async (k) => {
      k.preventDefault(), M(c, n);
    }, children: $ }) }, `${c}-${i}`);
  }) })] });
}
function H(t) {
  const { model: n, tag: s, feature: i } = t, a = m.getSession(n), { pluginManager: o } = m.getEnv(a);
  let f = !1;
  try {
    f = !!o.getViewType("BreakpointSplitView");
  } catch {
  }
  return y(A, { ...t, title: "Supplementary alignments", children: [l(T, { model: n, tag: s }), f ? l(I, { model: n, feature: i }) : null] });
}
export {
  H as default
};
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