@platforma-sdk/ui-vue 1.42.53 → 1.43.0

package/dist/components/PlMultiSequenceAlignment/data.js

@@ -1,264 +1,371 @@
-import { isJsonEqual as J } from "../../lib/util/helpers/dist/objects.js";
+import { isJsonEqual as O } from "../../lib/util/helpers/dist/objects.js";
 import "../../lib/util/helpers/dist/test_timeouts.js";
-import { ensureError as G, getRawPlatformaInstance as H, readAnnotation as A, Annotation as g, canonicalizeJson as v, getAxisId as O, parseJson as S, isLabelColumn as N, matchAxisId as K, readAnnotationJson as j, isLinkerColumn as Q, createRowSelectionColumn as X, pTableValue as M } from "@platforma-sdk/model";
-import { ref as q, watch as Y } from "vue";
-import { highlightByChemicalProperties as Z } from "./chemical-properties.js";
-import { parseMarkup as tt, markupAlignedSequence as nt, highlightByMarkup as et } from "./markup.js";
-import { multiSequenceAlignment as rt } from "./multi-sequence-alignment.js";
-import { getResidueCounts as ot } from "./residue-counts.js";
-const C = () => H().pFrameDriver, E = 1e3, ht = k(
-  at
-), wt = k(
-  st
-), bt = k(
-  it
-), At = k(
-  lt
+import { ensureError as T, getRawPlatformaInstance as $, readAnnotation as C, Annotation as h, canonicalizeJson as v, getAxisId as S, parseJson as A, isLabelColumn as j, matchAxisId as B, readAnnotationJson as J, isLinkerColumn as N, createRowSelectionColumn as W, pTableValue as R } from "@platforma-sdk/model";
+import { ref as M, watch as F, onWatcherCleanup as H } from "vue";
+import { objectHash as I } from "../../objectHash.js";
+import { highlightByChemicalProperties as V } from "./chemical-properties.js";
+import { parseMarkup as z, highlightByMarkup as Q, markupAlignedSequence as Y } from "./markup.js";
+import { getResidueCounts as Z } from "./residue-counts.js";
+const x = () => $().pFrameDriver, D = 1e3, ge = E(
+  _
+), he = E(
+  G
+), be = E(
+  K
+), ve = E(
+  X
 );
-async function at({
-  pFrame: l,
-  sequenceColumnPredicate: r
-}) {
-  if (!l) return;
-  const n = (await C().listColumns(l)).values().filter((a) => r(a)).map(({ spec: a, columnId: f }) => ({
-    label: A(a, g.Label) ?? "Unlabeled column",
-    value: f
-  })).toArray(), i = n.map(({ value: a }) => a);
-  return { options: n, defaults: i };
+async function _({ pFrame: n, sequenceColumnPredicate: r }) {
+  if (!n) return;
+  const o = (await x().listColumns(n)).values().filter((i) => r(i)).map(({ spec: i, columnId: c }) => ({
+    label: C(i, h.Label) ?? "Unlabeled column",
+    value: c
+  })).toArray(), t = o.map(({ value: i }) => i);
+  return { options: o, defaults: t };
 }
-async function st({
-  pFrame: l,
-  sequenceColumnIds: r
-}) {
-  if (!l || !r) return;
-  const m = C(), p = await m.listColumns(l), n = /* @__PURE__ */ new Map(), i = new Map(
-    r.values().flatMap((e) => {
-      const s = p.find(({ columnId: c }) => c === e);
-      if (!s)
-        throw new Error(`Couldn't find sequence column (ID: \`${e}\`).`);
-      return s.spec.axesSpec.values().map((c) => [v(O(c)), c]);
+async function G({ pFrame: n, sequenceColumnIds: r }) {
+  if (!n || !r) return;
+  const a = x(), e = await a.listColumns(n), o = new Map(
+    r.values().flatMap((s) => {
+      const u = e.find(({ columnId: m }) => m === s);
+      if (!u)
+        throw new Error(`Couldn't find sequence column (ID: \`${s}\`).`);
+      return u.spec.axesSpec.values().map((m) => [v(S(m)), m]);
     })
-  );
-  for (const [e, s] of i.entries()) {
-    const c = S(e), h = p.find(
-      ({ spec: x }) => N(x) && K(c, O(x.axesSpec[0]))
+  ), t = /* @__PURE__ */ new Map();
+  for (const [s, u] of o.entries()) {
+    const m = A(s), d = e.find(
+      ({ spec: p }) => j(p) && B(m, S(p.axesSpec[0]))
     );
-    n.set(
-      h ? v({ type: "column", id: h.columnId }) : v({ type: "axis", id: c }),
-      A(h == null ? void 0 : h.spec, g.Label) ?? A(s, g.Label) ?? "Unlabeled axis"
+    t.set(
+      d ? v({ type: "column", id: d.columnId }) : v({ type: "axis", id: m }),
+      C(d == null ? void 0 : d.spec, h.Label) ?? C(u, h.Label) ?? "Unlabeled axis"
     );
   }
-  const { hits: a } = await m.findColumns(l, {
+  const { hits: i } = await a.findColumns(n, {
     columnFilter: {},
-    compatibleWith: i.keys().map((e) => S(e)).toArray(),
+    compatibleWith: o.keys().map((s) => A(s)).toArray(),
     strictlyCompatible: !1
   });
-  for (const { columnId: e, spec: s } of a) {
-    const c = v({ type: "column", id: e });
-    n.has(c) || n.set(
-      c,
-      A(s, g.Label) ?? "Unlabeled column"
+  for (const { columnId: s, spec: u } of i) {
+    const m = v({
+      type: "column",
+      id: s
+    });
+    t.has(m) || t.set(
+      m,
+      C(u, h.Label) ?? "Unlabeled column"
     );
   }
-  const f = n.entries().map(([e, s]) => ({ label: s, value: S(e) })).toArray(), d = f.values().filter(({ value: e }) => {
-    if (e.type === "axis") return !0;
-    const s = p.find(({ columnId: c }) => c === e.id);
-    return s && N(s.spec);
-  }).map(({ value: e }) => e).toArray();
-  return { options: f, defaults: d };
+  const c = t.entries().map(([s, u]) => ({ label: u, value: A(s) })).toArray(), l = c.values().filter(({ value: s }) => {
+    if (s.type === "axis") return !0;
+    const u = e.find(({ columnId: m }) => m === s.id);
+    return u && j(u.spec);
+  }).map(({ value: s }) => s).toArray();
+  return { options: c, defaults: l };
 }
-async function it({
-  pFrame: l,
-  sequenceColumnIds: r
-}) {
-  if (!l || (r == null ? void 0 : r.length) !== 1) return;
-  const p = await C().listColumns(l), n = p.find(
-    (i) => i.columnId === r[0]
+async function K({ pFrame: n, sequenceColumnIds: r }) {
+  if (!n || !r) return;
+  const e = await x().listColumns(n), t = r.map((c) => {
+    const l = e.find((s) => s.columnId === c);
+    if (!l)
+      throw new Error(
+        `Couldn't find sequence column (ID: \`${r[0]}\`).`
+      );
+    return l;
+  }).flatMap(
+    (c) => e.filter(
+      (l) => J(l.spec, h.Sequence.IsAnnotation) && O(c.spec.axesSpec, l.spec.axesSpec) && Object.entries(c.spec.domain ?? {}).every(([s, u]) => {
+        var m;
+        return ((m = l.spec.domain) == null ? void 0 : m[s]) === u;
+      })
+    ).map((l) => ({ markupColumn: l, sequenceColumn: c }))
   );
-  if (!n)
-    throw new Error(
-      `Couldn't find sequence column (ID: \`${r[0]}\`).`
-    );
-  return p.values().filter(
-    (i) => !!j(i.spec, g.Sequence.IsAnnotation) && J(n.spec.axesSpec, i.spec.axesSpec) && Object.entries(n.spec.domain ?? {}).every(([a, f]) => {
-      var d;
-      return ((d = i.spec.domain) == null ? void 0 : d[a]) === f;
-    })
-  ).map(({ columnId: i, spec: a }) => ({
-    value: i,
-    label: A(a, g.Label) ?? "Unlabeled column"
+  return Map.groupBy(
+    t,
+    ({ markupColumn: c, sequenceColumn: l }) => {
+      const s = Object.fromEntries(
+        Object.entries(c.spec.domain ?? {}).filter(([u]) => {
+          var m;
+          return ((m = l.spec.domain) == null ? void 0 : m[u]) == null;
+        })
+      );
+      return v(s);
+    }
+  ).entries().map(([c, l]) => ({
+    label: Object.values(A(c)).join(", "),
+    value: l.map(({ markupColumn: s }) => s.columnId)
   })).toArray();
 }
-async function lt({
-  pFrame: l,
+async function X({
+  pFrame: n,
   sequenceColumnIds: r,
-  labelColumnIds: m,
-  selection: p,
-  colorScheme: n,
-  alignmentParams: i
-}) {
-  var P;
-  if (!l || !(r != null && r.length) || !m) return;
-  const a = C(), f = await a.listColumns(l), d = f.filter((t) => Q(t.spec)), e = X({ selection: p });
+  labelColumnIds: a,
+  selection: e,
+  colorScheme: o,
+  alignmentParams: t,
+  shouldBuildPhylogeneticTree: i
+}, c) {
+  var q;
+  if (!n || !(r != null && r.length) || !a) return;
+  const l = await ee({
+    pFrame: n,
+    sequenceColumnIds: r,
+    labelColumnIds: a,
+    selection: e,
+    colorScheme: o
+  }), s = ((q = l.at(0)) == null ? void 0 : q.data.data.length) ?? 0;
+  if (s < 2) return;
+  const u = s > D, m = te(r, l), d = ne(a, l), p = o.type === "markup" ? re(o.columnIds, l) : void 0, b = {}, y = await Promise.all(
+    m.map(async ({ name: w, rows: f }) => ({
+      name: w,
+      rows: await ae(
+        f,
+        JSON.parse(JSON.stringify(t)),
+        c
+      )
+    }))
+  );
+  let L;
+  if (i) {
+    L = await ie(
+      y,
+      c
+    );
+    const w = L.values().filter(({ id: f }) => f >= 0).map(({ id: f }) => f).toArray();
+    for (const f of y)
+      f.rows = w.map((g) => f.rows[g]);
+    for (const f of d)
+      f.rows = w.map((g) => f.rows[g]);
+    for (const f of p ?? [])
+      f.rows = w.map((g) => f.rows[g]);
+  }
+  return {
+    sequences: await Promise.all(
+      y.map(async ({ name: w, rows: f }, g) => {
+        const U = Z(f), k = oe({
+          colorScheme: o,
+          sequences: f,
+          residueCounts: U,
+          markup: p == null ? void 0 : p.at(g)
+        });
+        return k && Object.assign(b, k.legend), {
+          name: w,
+          rows: f,
+          residueCounts: U,
+          ...k && {
+            highlightImageUrl: await se(k.blob)
+          }
+        };
+      })
+    ),
+    labels: d,
+    ...Object.keys(b).length && {
+      highlightLegend: b
+    },
+    ...L && {
+      phylogeneticTree: L
+    },
+    exceedsLimit: u
+  };
+}
+async function ee({ pFrame: n, sequenceColumnIds: r, labelColumnIds: a, selection: e, colorScheme: o }) {
+  const t = x(), i = await t.listColumns(n), c = i.filter((p) => N(p.spec)), l = W({ selection: e });
   let s = {
     type: "inner",
-    entries: r.map((t) => ({
+    entries: r.map((p) => ({
       type: "column",
-      column: t
+      column: p
     }))
   };
-  d.length > 0 && (s = {
+  c.length > 0 && (s = {
     type: "outer",
     primary: s,
-    secondary: d.map(({ columnId: t }) => ({
+    secondary: c.map(({ columnId: p }) => ({
       type: "column",
-      column: t
+      column: p
     }))
-  }), e && (s = {
+  }), l && (s = {
     type: "inner",
     entries: [
       s,
       {
         type: "inlineColumn",
-        column: e
+        column: l
       }
     ]
   });
-  const c = m.flatMap((t) => t.type !== "column" ? [] : { type: "column", column: t.id });
-  n.type === "markup" && c.push({ type: "column", column: n.columnId });
-  const h = Array.from(
+  const u = a.flatMap((p) => p.type !== "column" ? [] : { type: "column", column: p.id });
+  if (o.type === "markup")
+    for (const p of o.columnIds)
+      u.push({ type: "column", column: p });
+  const m = Array.from(
     new Set(
-      r.values().flatMap((t) => {
-        const u = f.find(({ columnId: o }) => o === t);
-        if (!u)
-          throw new Error(`Couldn't find sequence column (ID: ${t})`);
-        return u.spec.axesSpec.map((o) => v(O(o)));
+      r.values().flatMap((p) => {
+        const b = i.find(({ columnId: y }) => y === p);
+        if (!b)
+          throw new Error(`Couldn't find sequence column (ID: ${p})`);
+        return b.spec.axesSpec.map((y) => v(S(y)));
       })
     )
-  ).sort().map((t) => ({
-    column: { type: "axis", id: S(t) },
+  ).sort().map((p) => ({
+    column: { type: "axis", id: A(p) },
     ascending: !0,
     naAndAbsentAreLeastValues: !0
-  })), x = {
+  })), d = {
     src: {
       type: "outer",
       primary: s,
-      secondary: c
+      secondary: u
     },
     filters: [],
-    sorting: h
-  }, w = await a.calculateTableData(
-    l,
-    JSON.parse(JSON.stringify(x)),
+    sorting: m
+  };
+  return t.calculateTableData(
+    n,
+    JSON.parse(JSON.stringify(d)),
     {
       offset: 0,
       // +1 is a hack to check whether the selection is over the limit
-      length: E + 1
+      length: D + 1
     }
   );
-  let b = (w == null ? void 0 : w[0].data.data.length) ?? 0, I = !1;
-  b > E && (b = E, I = !0);
-  const R = r.map((t) => {
-    const u = w.find(({ spec: o }) => o.id === t);
-    if (!u)
-      throw new Error(`Couldn't find sequence column (ID: \`${t}\`).`);
-    return u;
-  }), B = m.map((t) => {
-    const u = w.find(({ spec: o }) => {
-      if (t.type === "axis" && o.type === "axis")
-        return J(t.id, o.id);
-      if (t.type === "column" && o.type === "column")
-        return t.id === o.id;
-    });
-    if (!u)
-      throw new Error(`Couldn't find label column (ID: \`${t}\`).`);
-    return u;
-  }), T = await Promise.all(
-    R.map(
-      (t) => rt(
-        Array.from(
-          { length: b },
-          (u, o) => {
-            var y;
-            return ((y = M(t.data, o, { na: "", absent: "" })) == null ? void 0 : y.toString()) ?? "";
-          }
+}
+const te = (n, r) => n.map((a) => {
+  const e = r.find(({ spec: i }) => i.id === a);
+  if (!e)
+    throw new Error(`Couldn't find sequence column (ID: \`${a}\`).`);
+  const o = C(e.spec.spec, h.Label) ?? "Unlabeled column", t = e.data.data.keys().take(D).map(
+    (i) => {
+      var c;
+      return ((c = R(e.data, i, { absent: "", na: "" })) == null ? void 0 : c.toString()) ?? "";
+    }
+  ).toArray();
+  return { name: o, rows: t };
+}), ne = (n, r) => n.map((a) => {
+  const e = r.find(({ spec: t }) => {
+    if (a.type === "axis" && t.type === "axis")
+      return O(a.id, t.id);
+    if (a.type === "column" && t.type === "column")
+      return a.id === t.id;
+  });
+  if (!e)
+    throw new Error(`Couldn't find label column (ID: \`${a}\`).`);
+  return { rows: e.data.data.keys().take(D).map(
+    (t) => {
+      var i;
+      return ((i = R(e.data, t, { absent: "", na: "" })) == null ? void 0 : i.toString()) ?? "";
+    }
+  ).toArray() };
+}), re = (n, r) => n.map((a) => {
+  const e = r.find(({ spec: i }) => i.id === a);
+  if (!e)
+    throw new Error(`Couldn't find markup column (ID: \`${a}\`).`);
+  const o = J(
+    e.spec.spec,
+    h.Sequence.Annotation.Mapping
+  ) ?? {}, t = e.data.data.keys().take(D).map(
+    (i) => {
+      var c;
+      return z(
+        ((c = R(e.data, i, { absent: "", na: "" })) == null ? void 0 : c.toString()) ?? ""
+      );
+    }
+  ).toArray();
+  return { labels: o, rows: t };
+}), ae = /* @__PURE__ */ (() => {
+  const n = /* @__PURE__ */ new Map();
+  return async (r, a, e) => {
+    const o = await I([r, a]);
+    let t = n.get(o);
+    return t || (t = await P(
+      new Worker(
+        new URL(
+          /* @vite-ignore */
+          "" + new URL("../../assets/multi-sequence-alignment.worker-Cm0gZp19.js", import.meta.url).href,
+          import.meta.url
         ),
-        i
-      )
-    )
-  ), $ = Array.from(
-    { length: b },
-    (t, u) => T.map((o) => o[u])
-  ), V = R.map(
-    (t) => A(t.spec.spec, g.Label) ?? "Unlabeled column"
-  ), z = Array.from(
-    { length: b },
-    (t, u) => B.map(
-      (o) => {
-        var y;
-        return ((y = M(o.data, u, { na: "", absent: "" })) == null ? void 0 : y.toString()) ?? "";
-      }
-    )
-  ), D = $.map((t) => t.join(" ")), U = ot(D), L = {
-    sequences: D,
-    sequenceNames: V,
-    labelRows: z,
-    exceedsLimit: I,
-    residueCounts: U
+        { type: "module" }
+      ),
+      { sequences: r, params: a },
+      e
+    ), n.set(o, t), t);
   };
+})();
+function oe({ colorScheme: n, sequences: r, residueCounts: a, markup: e }) {
+  var o;
   if (n.type === "chemical-properties")
-    L.highlightImage = Z({
-      sequences: D,
-      residueCounts: U
-    });
-  else if (n.type === "markup") {
-    const t = w.find(
-      ({ spec: y }) => y.id === n.columnId
-    );
-    if (!t)
-      throw new Error(
-        `Couldn't find markup column (ID: \`${n.columnId}\`).`
-      );
-    const u = Array.from(
-      { length: b },
-      (y, _) => {
-        var F;
-        const W = tt(
-          ((F = M(t.data, _, { na: "", absent: "" })) == null ? void 0 : F.toString()) ?? ""
-        );
-        return nt($[_][0], W);
-      }
-    ), o = j(t.spec.spec, g.Sequence.Annotation.Mapping) ?? {};
-    L.highlightImage = et({
-      markupRows: u,
-      columnCount: ((P = D.at(0)) == null ? void 0 : P.length) ?? 0,
-      labels: o
+    return V({ sequences: r, residueCounts: a });
+  if (n.type === "markup") {
+    if (!e)
+      throw new Error("Missing markup data.");
+    return Q({
+      markupRows: r.map((t, i) => {
+        const c = e.rows.at(i);
+        if (!c) throw new Error(`Missing markup for row ${i}.`);
+        return Y(t, c);
+      }),
+      columnCount: ((o = r.at(0)) == null ? void 0 : o.length) ?? 0,
+      labels: e.labels
     });
   }
-  return L;
 }
-function k(l) {
-  const r = q(), m = q(!0), p = q();
-  let n;
-  return (i) => (Y(i, async (a, f) => {
-    if (J(a, f)) return;
-    const d = n = Symbol();
+const se = (n) => new Promise((r, a) => {
+  const e = new FileReader();
+  e.addEventListener("load", () => r(e.result)), e.addEventListener("error", () => a(e.error)), e.readAsDataURL(n);
+}), ie = /* @__PURE__ */ (() => {
+  const n = /* @__PURE__ */ new Map();
+  return async (r, a) => {
+    var i;
+    const e = ((i = r.at(0)) == null ? void 0 : i.rows.keys().map((c) => r.map((l) => l.rows.at(c) ?? "").join("")).toArray()) ?? [], o = await I(e);
+    let t = n.get(o);
+    return t || (t = await P(
+      new Worker(
+        new URL(
+          /* @vite-ignore */
+          "" + new URL("../../assets/phylogenetic-tree.worker-4CrExYEo.js", import.meta.url).href,
+          import.meta.url
+        ),
+        { type: "module" }
+      ),
+      e,
+      a
+    ), n.set(o, t), t);
+  };
+})(), P = (n, r, a) => new Promise((e, o) => {
+  n.addEventListener("message", ({ data: t }) => {
+    e(t), n.terminate();
+  }), n.addEventListener("error", ({ error: t, message: i }) => {
+    o(t ?? i), n.terminate();
+  }), a.addEventListener("abort", () => {
+    o(a.reason), n.terminate();
+  }), n.postMessage(r);
+});
+function E(n) {
+  const r = M(), a = M(!0), e = M();
+  let o;
+  return (t) => (F(t, async (i, c) => {
+    if (O(i, c)) return;
+    const l = new AbortController(), s = o = Symbol();
+    H(() => {
+      l.abort();
+    });
     try {
-      p.value = void 0, m.value = !0;
-      const e = await l(a);
-      d === n && (r.value = e);
-    } catch (e) {
-      console.error(e), d === n && (p.value = G(e));
+      e.value = void 0, a.value = !0;
+      const u = await n(i, l.signal);
+      s === o && (r.value = u);
+    } catch (u) {
+      console.error(u), s === o && (e.value = T(u));
     } finally {
-      d === n && (m.value = !1);
+      s === o && (a.value = !1);
     }
-  }, { immediate: !0 }), { data: r, isLoading: m, error: p });
+  }, { immediate: !0 }), { data: r, isLoading: a, error: e });
 }
 export {
-  E as sequenceLimit,
-  wt as useLabelColumnsOptions,
-  bt as useMarkupColumnsOptions,
-  At as useMultipleAlignmentData,
-  ht as useSequenceColumnsOptions
+  D as SEQUENCE_LIMIT,
+  he as useLabelColumnsOptions,
+  be as useMarkupColumnsOptions,
+  ve as useMultipleAlignmentData,
+  ge as useSequenceColumnsOptions
 };
 //# sourceMappingURL=data.js.map