@platforma-sdk/ui-vue 1.41.19 → 1.42.1

package/dist/components/PlMultiSequenceAlignment/data.js

@@ -1,293 +1,279 @@
-import { isJsonEqual as L } from "../../lib/util/helpers/dist/index.js";
-import { getRawPlatformaInstance as K, isLabelColumn as B, isLinkerColumn as Q, createRowSelectionColumn as Y } from "../../sdk/model/dist/index.js";
-import { ref as O, watch as Z } from "vue";
-import { chemicalPropertiesColorMap as I, colorizeSequencesByChemicalProperties as ee } from "./chemical-properties.js";
-import { parseMarkup as te, markupAlignedSequence as ne, markupColors as T, colorizeSequencesByMarkup as oe } from "./markup.js";
-import { multiSequenceAlignment as ae } from "./multi-sequence-alignment.js";
-import { getResidueCounts as re } from "./residue-counts.js";
-import { ensureError as se, canonicalizeJson as A, getAxisId as J, parseJson as D, matchAxisId as ie, pTableValue as q } from "../../lib/model/common/dist/index.js";
-const M = () => K().pFrameDriver, E = 1e3, Se = k(
-  le
-), xe = k(
-  ce
-), Ae = k(
-  pe
-), ve = k(
-  ue
+import { isJsonEqual as J } from "../../lib/util/helpers/dist/index.js";
+import { getRawPlatformaInstance as z, isLabelColumn as N, isLinkerColumn as W, createRowSelectionColumn as X } from "../../sdk/model/dist/index.js";
+import { ref as M, watch as G } from "vue";
+import { highlightByChemicalProperties as H } from "./chemical-properties.js";
+import { parseMarkup as K, markupAlignedSequence as Q, highlightByMarkup as Y } from "./markup.js";
+import { multiSequenceAlignment as Z } from "./multi-sequence-alignment.js";
+import { getResidueCounts as nn } from "./residue-counts.js";
+import { ensureError as tn, canonicalizeJson as A, getAxisId as E, parseJson as D, matchAxisId as en, pTableValue as q } from "../../lib/model/common/dist/index.js";
+const S = () => z().pFrameDriver, O = 1e3, gn = k(
+  an
+), hn = k(
+  on
+), wn = k(
+  rn
+), bn = k(
+  sn
 );
-async function le({
+async function an({
   pFrame: c,
-  sequenceColumnPredicate: t
+  sequenceColumnPredicate: e
 }) {
   if (!c) return;
-  const a = (await M().listColumns(c)).filter((i) => t(i)).map(({ spec: i, columnId: p }) => {
+  const t = (await S().listColumns(c)).values().filter((o) => e(o)).map(({ spec: o, columnId: u }) => {
     var m;
     return {
-      label: ((m = i.annotations) == null ? void 0 : m["pl7.app/label"]) ?? "Unlabelled column",
-      value: p
+      label: ((m = o.annotations) == null ? void 0 : m["pl7.app/label"]) ?? "Unlabelled column",
+      value: u
     };
-  }), s = a.map(({ value: i }) => i);
-  return { options: a, defaults: s };
+  }).toArray(), l = t.map(({ value: o }) => o);
+  return { options: t, defaults: l };
 }
-async function ce({
+async function on({
   pFrame: c,
-  sequenceColumnIds: t
+  sequenceColumnIds: e
 }) {
-  var f, x, w;
-  if (!c || !t) return;
-  const d = M(), l = await d.listColumns(c), a = /* @__PURE__ */ new Map(), s = new Map(t.flatMap((r) => {
-    const y = l.find(({ columnId: u }) => u === r);
-    if (!y)
-      throw new Error(`Couldn't find sequence column (ID: \`${r}\`).`);
-    return y.spec.axesSpec.map((u) => [A(J(u)), u]);
-  }));
-  for (const [r, y] of s.entries()) {
-    const u = D(r), g = l.find(
-      ({ spec: b }) => B(b) && ie(u, J(b.axesSpec[0]))
+  var f, h, b;
+  if (!c || !e) return;
+  const y = S(), p = await y.listColumns(c), t = /* @__PURE__ */ new Map(), l = new Map(
+    e.values().flatMap((i) => {
+      const d = p.find(({ columnId: a }) => a === i);
+      if (!d)
+        throw new Error(`Couldn't find sequence column (ID: \`${i}\`).`);
+      return d.spec.axesSpec.values().map((a) => [A(E(a)), a]);
+    })
+  );
+  for (const [i, d] of l.entries()) {
+    const a = D(i), g = p.find(
+      ({ spec: v }) => N(v) && en(a, E(v.axesSpec[0]))
     );
-    a.set(
-      g ? A({ type: "column", id: g.columnId }) : A({ type: "axis", id: u }),
-      ((f = g == null ? void 0 : g.spec.annotations) == null ? void 0 : f["pl7.app/label"]) ?? ((x = y.annotations) == null ? void 0 : x["pl7.app/label"]) ?? "Unlabelled axis"
+    t.set(
+      g ? A({ type: "column", id: g.columnId }) : A({ type: "axis", id: a }),
+      ((f = g == null ? void 0 : g.spec.annotations) == null ? void 0 : f["pl7.app/label"]) ?? ((h = d.annotations) == null ? void 0 : h["pl7.app/label"]) ?? "Unlabelled axis"
     );
   }
-  const { hits: i } = await d.findColumns(c, {
+  const { hits: o } = await y.findColumns(c, {
     columnFilter: {},
-    compatibleWith: Array.from(
-      s.keys(),
-      (r) => D(r)
-    ),
+    compatibleWith: l.keys().map((i) => D(i)).toArray(),
     strictlyCompatible: !1
   });
-  for (const { columnId: r, spec: y } of i) {
-    const u = A({ type: "column", id: r });
-    a.has(u) || a.set(
-      u,
-      ((w = y.annotations) == null ? void 0 : w["pl7.app/label"]) ?? "Unlabelled column"
+  for (const { columnId: i, spec: d } of o) {
+    const a = A({ type: "column", id: i });
+    t.has(a) || t.set(
+      a,
+      ((b = d.annotations) == null ? void 0 : b["pl7.app/label"]) ?? "Unlabelled column"
     );
   }
-  const p = Array.from(a).map(
-    ([r, y]) => ({ label: y, value: D(r) })
-  ), m = p.filter(({ value: r }) => {
-    if (r.type === "axis") return !0;
-    const y = l.find(({ columnId: u }) => u === r.id);
-    return y && B(y.spec);
-  }).map(({ value: r }) => r);
-  return { options: p, defaults: m };
+  const u = t.entries().map(([i, d]) => ({ label: d, value: D(i) })).toArray(), m = u.values().filter(({ value: i }) => {
+    if (i.type === "axis") return !0;
+    const d = p.find(({ columnId: a }) => a === i.id);
+    return d && N(d.spec);
+  }).map(({ value: i }) => i).toArray();
+  return { options: u, defaults: m };
 }
-async function pe({
+async function rn({
   pFrame: c,
-  sequenceColumnIds: t
+  sequenceColumnIds: e
 }) {
-  if (!c || (t == null ? void 0 : t.length) !== 1) return;
-  const l = await M().listColumns(c), a = l.find(
-    (s) => s.columnId === t[0]
+  if (!c || (e == null ? void 0 : e.length) !== 1) return;
+  const p = await S().listColumns(c), t = p.find(
+    (l) => l.columnId === e[0]
   );
-  if (!a)
+  if (!t)
     throw new Error(
-      `Couldn't find sequence column (ID: \`${t[0]}\`).`
+      `Couldn't find sequence column (ID: \`${e[0]}\`).`
     );
-  return l.filter(
-    (s) => {
-      var i;
-      return ((i = s.spec.annotations) == null ? void 0 : i["pl7.app/sequence/isAnnotation"]) === "true" && L(a.spec.axesSpec, s.spec.axesSpec) && Object.entries(a.spec.domain ?? {}).every(([p, m]) => {
+  return p.values().filter(
+    (l) => {
+      var o;
+      return ((o = l.spec.annotations) == null ? void 0 : o["pl7.app/sequence/isAnnotation"]) === "true" && J(t.spec.axesSpec, l.spec.axesSpec) && Object.entries(t.spec.domain ?? {}).every(([u, m]) => {
         var f;
-        return ((f = s.spec.domain) == null ? void 0 : f[p]) === m;
+        return ((f = l.spec.domain) == null ? void 0 : f[u]) === m;
       });
     }
-  ).map(({ columnId: s, spec: i }) => {
-    var p;
+  ).map(({ columnId: l, spec: o }) => {
+    var u;
     return {
-      value: s,
-      label: ((p = i.annotations) == null ? void 0 : p["pl7.app/label"]) ?? "Unlabelled column"
+      value: l,
+      label: ((u = o.annotations) == null ? void 0 : u["pl7.app/label"]) ?? "Unlabelled column"
     };
-  });
+  }).toArray();
 }
-async function ue({
+async function sn({
   pframe: c,
-  sequenceColumnIds: t,
-  labelColumnIds: d,
-  markupColumnId: l,
-  selection: a,
-  colorScheme: s,
-  alignmentParams: i
+  sequenceColumnIds: e,
+  labelColumnIds: y,
+  selection: p,
+  colorScheme: t,
+  alignmentParams: l
 }) {
-  var $, j, N, _;
-  if (!c || !(t != null && t.length) || !d) return;
-  const p = M(), m = await p.listColumns(c), f = m.filter((e) => Q(e.spec)), x = Y({ selection: a });
-  let w = {
+  var F, I;
+  if (!c || !(e != null && e.length) || !y) return;
+  const o = S(), u = await o.listColumns(c), m = u.filter((n) => W(n.spec)), f = X({ selection: p });
+  let h = {
     type: "inner",
-    entries: t.map((e) => ({
+    entries: e.map((n) => ({
       type: "column",
-      column: e
+      column: n
     }))
   };
-  f.length > 0 && (w = {
+  m.length > 0 && (h = {
     type: "outer",
-    primary: w,
-    secondary: f.map(({ columnId: e }) => ({
+    primary: h,
+    secondary: m.map(({ columnId: n }) => ({
       type: "column",
-      column: e
+      column: n
     }))
-  }), x && (w = {
+  }), f && (h = {
     type: "inner",
     entries: [
-      w,
+      h,
       {
         type: "inlineColumn",
-        column: x
+        column: f
       }
     ]
   });
-  const r = d.flatMap((e) => e.type !== "column" ? [] : { type: "column", column: e.id });
-  l && r.push({ type: "column", column: l });
-  const y = Array.from(
-    new Set(t.flatMap((e) => {
-      const n = m.find(({ columnId: o }) => o === e);
-      if (!n)
-        throw new Error(`Couldn't find sequence column (ID: ${e})`);
-      return n.spec.axesSpec.map((o) => A(J(o)));
-    }))
-  ).sort().map((e) => ({
-    column: { type: "axis", id: D(e) },
+  const b = y.flatMap((n) => n.type !== "column" ? [] : { type: "column", column: n.id });
+  t.type === "markup" && b.push({ type: "column", column: t.columnId });
+  const i = Array.from(
+    new Set(
+      e.values().flatMap((n) => {
+        const r = u.find(({ columnId: s }) => s === n);
+        if (!r)
+          throw new Error(`Couldn't find sequence column (ID: ${n})`);
+        return r.spec.axesSpec.map((s) => A(E(s)));
+      })
+    )
+  ).sort().map((n) => ({
+    column: { type: "axis", id: D(n) },
     ascending: !0,
     naAndAbsentAreLeastValues: !0
-  })), u = {
+  })), d = {
     src: {
       type: "outer",
-      primary: w,
-      secondary: r
+      primary: h,
+      secondary: b
     },
     filters: [],
-    sorting: y
-  }, g = await p.calculateTableData(
+    sorting: i
+  }, a = await o.calculateTableData(
     c,
-    JSON.parse(JSON.stringify(u)),
+    JSON.parse(JSON.stringify(d)),
     {
       offset: 0,
       // +1 is a hack to check whether the selection is over the limit
-      length: E + 1
+      length: O + 1
     }
   );
-  let b = (g == null ? void 0 : g[0].data.data.length) ?? 0, P = !1;
-  b > E && (b = E, P = !0);
-  const R = t.map((e) => {
-    const n = g.find(({ spec: o }) => o.id === e);
-    if (!n)
-      throw new Error(`Couldn't find sequence column (ID: \`${e}\`).`);
-    return n;
-  }), V = d.map((e) => {
-    const n = g.find(({ spec: o }) => {
-      if (e.type === "axis" && o.type === "axis")
-        return L(e.id, o.id);
-      if (e.type === "column" && o.type === "column")
-        return e.id === o.id;
+  let g = (a == null ? void 0 : a[0].data.data.length) ?? 0, v = !1;
+  g > O && (g = O, v = !0);
+  const L = e.map((n) => {
+    const r = a.find(({ spec: s }) => s.id === n);
+    if (!r)
+      throw new Error(`Couldn't find sequence column (ID: \`${n}\`).`);
+    return r;
+  }), _ = y.map((n) => {
+    const r = a.find(({ spec: s }) => {
+      if (n.type === "axis" && s.type === "axis")
+        return J(n.id, s.id);
+      if (n.type === "column" && s.type === "column")
+        return n.id === s.id;
     });
-    if (!n)
-      throw new Error(`Couldn't find label column (ID: \`${e}\`).`);
-    return n;
-  }), C = l && g.find(({ spec: e }) => e.id === l), W = await Promise.all(
-    R.map(
-      (e) => ae(
+    if (!r)
+      throw new Error(`Couldn't find label column (ID: \`${n}\`).`);
+    return r;
+  }), j = await Promise.all(
+    L.map(
+      (n) => Z(
         Array.from(
-          { length: b },
-          (n, o) => {
-            var h;
-            return ((h = q(e.data, o, { na: "", absent: "" })) == null ? void 0 : h.toString()) ?? "";
+          { length: g },
+          (r, s) => {
+            var w;
+            return ((w = q(n.data, s, { na: "", absent: "" })) == null ? void 0 : w.toString()) ?? "";
           }
         ),
-        i
+        l
       )
     )
-  ), F = Array.from(
-    { length: b },
-    (e, n) => W.map((o) => o[n])
-  ), X = R.map(
-    (e) => {
-      var n;
-      return ((n = e.spec.spec.annotations) == null ? void 0 : n["pl7.app/label"]) ?? "Unlabelled column";
+  ), R = Array.from(
+    { length: g },
+    (n, r) => j.map((s) => s[r])
+  ), B = L.map(
+    (n) => {
+      var r;
+      return ((r = n.spec.spec.annotations) == null ? void 0 : r["pl7.app/label"]) ?? "Unlabelled column";
     }
-  ), G = Array.from(
-    { length: b },
-    (e, n) => V.map(
-      (o) => {
-        var h;
-        return ((h = q(o.data, n, { na: "", absent: "" })) == null ? void 0 : h.toString()) ?? "";
+  ), T = Array.from(
+    { length: g },
+    (n, r) => _.map(
+      (s) => {
+        var w;
+        return ((w = q(s.data, r, { na: "", absent: "" })) == null ? void 0 : w.toString()) ?? "";
       }
     )
-  ), v = F.map((e) => e.join(" ")), U = re(v), S = {
-    sequences: v,
-    sequenceNames: X,
-    labelsRows: G,
-    exceedsLimit: P,
-    residueCounts: U
+  ), x = R.map((n) => n.join(" ")), $ = nn(x), C = {
+    sequences: x,
+    sequenceNames: B,
+    labelRows: T,
+    exceedsLimit: v,
+    residueCounts: $
   };
-  if (C) {
-    const e = JSON.parse(
-      (($ = C.spec.spec.annotations) == null ? void 0 : $["pl7.app/sequence/annotation/mapping"]) ?? "{}"
-    ), n = Array.from(
-      { length: b },
-      (o, h) => {
-        var z;
-        const H = te(
-          ((z = q(C.data, h, { na: "", absent: "" })) == null ? void 0 : z.toString()) ?? ""
+  if (t.type === "chemical-properties")
+    C.highlightImage = H({
+      sequences: x,
+      residueCounts: $
+    });
+  else if (t.type === "markup") {
+    const n = a.find(
+      ({ spec: w }) => w.id === t.columnId
+    );
+    if (!n)
+      throw new Error(
+        `Couldn't find markup column (ID: \`${t.columnId}\`).`
+      );
+    const r = Array.from(
+      { length: g },
+      (w, P) => {
+        var U;
+        const V = K(
+          ((U = q(n.data, P, { na: "", absent: "" })) == null ? void 0 : U.toString()) ?? ""
         );
-        return ne(F[h][0], H);
+        return Q(R[P][0], V);
       }
+    ), s = JSON.parse(
+      ((F = n.spec.spec.annotations) == null ? void 0 : F["pl7.app/sequence/annotation/mapping"]) ?? "{}"
     );
-    S.markup = { labels: e, data: n };
-  }
-  if (s.type === "chemical-properties") {
-    const e = I;
-    S.highlightImage = {
-      blob: await ee({
-        sequences: v,
-        residueCounts: U,
-        colorMap: e
-      }),
-      colorMap: e
-    };
-  } else if (s.type === "markup") {
-    const e = Object.fromEntries(
-      Object.entries(
-        ((j = S.markup) == null ? void 0 : j.labels) ?? {}
-      ).map(([n, o], h) => [
-        n,
-        { label: o, color: T[h % T.length] }
-      ])
-    );
-    S.highlightImage = {
-      blob: await oe({
-        markupRows: ((N = S.markup) == null ? void 0 : N.data) ?? [],
-        colorMap: e,
-        columnCount: ((_ = v.at(0)) == null ? void 0 : _.length) ?? 0
-      }),
-      colorMap: e
-    };
+    C.highlightImage = Y({
+      markupRows: r,
+      columnCount: ((I = x.at(0)) == null ? void 0 : I.length) ?? 0,
+      labels: s
+    });
   }
-  return S;
+  return C;
 }
 function k(c) {
-  const t = O(), d = O(!0), l = O();
-  let a;
-  return (s) => (Z(s, async (i, p) => {
-    if (L(i, p)) return;
-    const m = a = Symbol();
+  const e = M(), y = M(!0), p = M();
+  let t;
+  return (l) => (G(l, async (o, u) => {
+    if (J(o, u)) return;
+    const m = t = Symbol();
     try {
-      l.value = void 0, d.value = !0;
-      const f = await c(i);
-      m === a && (t.value = f);
+      p.value = void 0, y.value = !0;
+      const f = await c(o);
+      m === t && (e.value = f);
     } catch (f) {
-      console.error(f), m === a && (l.value = se(f));
+      console.error(f), m === t && (p.value = tn(f));
     } finally {
-      m === a && (d.value = !1);
+      m === t && (y.value = !1);
     }
-  }, { immediate: !0 }), { data: t, isLoading: d, error: l });
+  }, { immediate: !0 }), { data: e, isLoading: y, error: p });
 }
 export {
-  E as sequenceLimit,
-  xe as useLabelColumnsOptions,
-  Ae as useMarkupColumnsOptions,
-  ve as useMultipleAlignmentData,
-  Se as useSequenceColumnsOptions
+  O as sequenceLimit,
+  hn as useLabelColumnsOptions,
+  wn as useMarkupColumnsOptions,
+  bn as useMultipleAlignmentData,
+  gn as useSequenceColumnsOptions
 };
 //# sourceMappingURL=data.js.map

package/dist/components/PlMultiSequenceAlignment/data.js.map

@@ -1 +1 @@
-{"version":3,"file":"data.js","sources":["../../../src/components/PlMultiSequenceAlignment/data.ts"],"sourcesContent":["import { isJsonEqual } from '@milaboratories/helpers';\nimport type { ListOptionNormalized } from '@milaboratories/uikit';\nimport {\n  type CalculateTableDataRequest,\n  type CanonicalizedJson,\n  canonicalizeJson,\n  createRowSelectionColumn,\n  ensureError,\n  getAxisId,\n  getRawPlatformaInstance,\n  isLabelColumn,\n  isLinkerColumn,\n  type JoinEntry,\n  matchAxisId,\n  parseJson,\n  type PColumnIdAndSpec,\n  type PFrameHandle,\n  type PlMultiSequenceAlignmentColorSchemeOption,\n  type PlMultiSequenceAlignmentSettings,\n  type PlSelectionModel,\n  type PObjectId,\n  type PTableColumnId,\n  type PTableSorting,\n  pTableValue,\n} from '@platforma-sdk/model';\nimport { ref, watch } from 'vue';\nimport {\n  chemicalPropertiesColorMap,\n  colorizeSequencesByChemicalProperties,\n} from './chemical-properties';\nimport {\n  colorizeSequencesByMarkup,\n  type Markup,\n  markupAlignedSequence,\n  markupColors,\n  parseMarkup,\n} from './markup';\nimport { multiSequenceAlignment } from './multi-sequence-alignment';\nimport { getResidueCounts } from './residue-counts';\nimport type { ColorMap, ResidueCounts } from './types';\n\nconst getPFrameDriver = () => getRawPlatformaInstance().pFrameDriver;\n\nexport const sequenceLimit = 1000;\n\nexport const useSequenceColumnsOptions = refreshOnDeepChange(\n  getSequenceColumnsOptions,\n);\n\nexport const useLabelColumnsOptions = refreshOnDeepChange(\n  getLabelColumnsOptions,\n);\n\nexport const useMarkupColumnsOptions = refreshOnDeepChange(\n  getMarkupColumnsOptions,\n);\n\nexport const useMultipleAlignmentData = refreshOnDeepChange(\n  getMultipleAlignmentData,\n);\n\nasync function getSequenceColumnsOptions({\n  pFrame,\n  sequenceColumnPredicate,\n}: {\n  pFrame: PFrameHandle | undefined;\n  sequenceColumnPredicate: (column: PColumnIdAndSpec) => boolean;\n}): Promise<OptionsWithDefaults<PObjectId> | undefined> {\n  if (!pFrame) return;\n\n  const pFrameDriver = getPFrameDriver();\n  const columns = await pFrameDriver.listColumns(pFrame);\n  const options = columns\n    .filter((column) => sequenceColumnPredicate(column))\n    .map(({ spec, columnId }) => ({\n      label: spec.annotations?.['pl7.app/label'] ?? 'Unlabelled column',\n      value: columnId,\n    }));\n  const defaults = options.map(({ value }) => value);\n  return { options, defaults };\n}\n\nasync function getLabelColumnsOptions({\n  pFrame,\n  sequenceColumnIds,\n}: {\n  pFrame: PFrameHandle | undefined;\n  sequenceColumnIds: PObjectId[] | undefined;\n}): Promise<OptionsWithDefaults<PTableColumnId> | undefined> {\n  if (!pFrame || !sequenceColumnIds) return;\n\n  const pFrameDriver = getPFrameDriver();\n  const columns = await pFrameDriver.listColumns(pFrame);\n  const optionMap = new Map<CanonicalizedJson<PTableColumnId>, string>();\n\n  const sequenceColumnsAxes = new Map(sequenceColumnIds.flatMap((id) => {\n    const column = columns.find(({ columnId }) => columnId === id);\n    if (!column) {\n      throw new Error(`Couldn't find sequence column (ID: \\`${id}\\`).`);\n    }\n    return column.spec.axesSpec\n      .map((spec) => [canonicalizeJson(getAxisId(spec)), spec]);\n  }));\n\n  for (const [axisIdJson, axisSpec] of sequenceColumnsAxes.entries()) {\n    const axisId = parseJson(axisIdJson);\n    const labelColumn = columns.find(({ spec }) =>\n      isLabelColumn(spec) && matchAxisId(axisId, getAxisId(spec.axesSpec[0])),\n    );\n    optionMap.set(\n      labelColumn\n        ? canonicalizeJson({ type: 'column', id: labelColumn.columnId })\n        : canonicalizeJson({ type: 'axis', id: axisId }),\n      labelColumn?.spec.annotations?.['pl7.app/label']\n      ?? axisSpec.annotations?.['pl7.app/label']\n      ?? 'Unlabelled axis',\n    );\n  }\n\n  const { hits: compatibleColumns } = await pFrameDriver.findColumns(pFrame, {\n    columnFilter: {},\n    compatibleWith: Array.from(\n      sequenceColumnsAxes.keys(),\n      (axisIdJson) => parseJson(axisIdJson),\n    ),\n    strictlyCompatible: false,\n  });\n\n  for (const { columnId, spec } of compatibleColumns) {\n    const columnIdJson = canonicalizeJson({ type: 'column', id: columnId });\n    if (optionMap.has(columnIdJson)) continue;\n    optionMap.set(\n      columnIdJson,\n      spec.annotations?.['pl7.app/label'] ?? 'Unlabelled column',\n    );\n  }\n\n  const options = Array.from(optionMap).map(\n    ([value, label]) => ({ label, value: parseJson(value) }),\n  );\n\n  const defaults = options\n    .filter(({ value }) => {\n      if (value.type === 'axis') return true;\n      const column = columns.find(({ columnId }) => columnId === value.id);\n      return column && isLabelColumn(column.spec);\n    })\n    .map(({ value }) => value);\n  return { options, defaults };\n}\n\nasync function getMarkupColumnsOptions({\n  pFrame,\n  sequenceColumnIds,\n}: {\n  pFrame: PFrameHandle | undefined;\n  sequenceColumnIds: PObjectId[] | undefined;\n}): Promise<ListOptionNormalized<PObjectId>[] | undefined> {\n  if (!pFrame || sequenceColumnIds?.length !== 1) return;\n\n  const pFrameDriver = getPFrameDriver();\n  const columns = await pFrameDriver.listColumns(pFrame);\n  const sequenceColumn = columns.find((column) =>\n    column.columnId === sequenceColumnIds[0],\n  );\n  if (!sequenceColumn) {\n    throw new Error(\n      `Couldn't find sequence column (ID: \\`${sequenceColumnIds[0]}\\`).`,\n    );\n  }\n  return columns\n    .filter((column) =>\n      column.spec.annotations?.['pl7.app/sequence/isAnnotation'] === 'true'\n      && isJsonEqual(sequenceColumn.spec.axesSpec, column.spec.axesSpec)\n      && Object.entries(sequenceColumn.spec.domain ?? {}).every((\n        [key, value],\n      ) => column.spec.domain?.[key] === value),\n    ).map(({ columnId, spec }) => ({\n      value: columnId,\n      label: spec.annotations?.['pl7.app/label'] ?? 'Unlabelled column',\n    }));\n}\n\nasync function getMultipleAlignmentData({\n  pframe,\n  sequenceColumnIds,\n  labelColumnIds,\n  markupColumnId,\n  selection,\n  colorScheme,\n  alignmentParams,\n}: {\n  pframe: PFrameHandle | undefined;\n  sequenceColumnIds: PObjectId[] | undefined;\n  labelColumnIds: PTableColumnId[] | undefined;\n  markupColumnId: PObjectId | undefined;\n  selection: PlSelectionModel | undefined;\n  colorScheme: PlMultiSequenceAlignmentColorSchemeOption;\n  alignmentParams: PlMultiSequenceAlignmentSettings['alignmentParams'];\n}): Promise<MultipleAlignmentData | undefined> {\n  if (!pframe || !sequenceColumnIds?.length || !labelColumnIds) return;\n\n  const pFrameDriver = getPFrameDriver();\n  const columns = await pFrameDriver.listColumns(pframe);\n  const linkerColumns = columns.filter((column) => isLinkerColumn(column.spec));\n\n  const filterColumn = createRowSelectionColumn({ selection });\n\n  // inner join of sequence columns\n  let primaryEntry: JoinEntry<PObjectId> = {\n    type: 'inner',\n    entries: sequenceColumnIds.map((column) => ({\n      type: 'column',\n      column,\n    })),\n  };\n\n  // if we have linkers, left join them\n  if (linkerColumns.length > 0) {\n    primaryEntry = {\n      type: 'outer',\n      primary: primaryEntry,\n      secondary: linkerColumns.map(({ columnId }) => ({\n        type: 'column',\n        column: columnId,\n      })),\n    };\n  }\n\n  // inner join with filters\n  if (filterColumn) {\n    primaryEntry = {\n      type: 'inner',\n      entries: [\n        primaryEntry,\n        {\n          type: 'inlineColumn',\n          column: filterColumn,\n        },\n      ],\n    };\n  }\n\n  // left join with labels\n  const secondaryEntry: JoinEntry<PObjectId>[] = labelColumnIds\n    .flatMap((column) => {\n      if (column.type !== 'column') return [];\n      return { type: 'column', column: column.id };\n    });\n\n  // and markup\n  if (markupColumnId) {\n    secondaryEntry.push({ type: 'column', column: markupColumnId });\n  }\n\n  const sorting: PTableSorting[] = Array.from(\n    new Set(sequenceColumnIds.flatMap((id) => {\n      const column = columns.find(({ columnId }) => columnId === id);\n      if (!column) {\n        throw new Error(`Couldn't find sequence column (ID: ${id})`);\n      }\n      return column.spec.axesSpec\n        .map((spec) => canonicalizeJson(getAxisId(spec)));\n    })),\n  )\n    .sort()\n    .map((id) => ({\n      column: { type: 'axis', id: parseJson(id) },\n      ascending: true,\n      naAndAbsentAreLeastValues: true,\n    }));\n\n  const request: CalculateTableDataRequest<PObjectId> = {\n    src: {\n      type: 'outer',\n      primary: primaryEntry,\n      secondary: secondaryEntry,\n    },\n    filters: [],\n    sorting,\n  };\n\n  const table = await pFrameDriver.calculateTableData(\n    pframe,\n    JSON.parse(JSON.stringify(request)),\n    {\n      offset: 0,\n      // +1 is a hack to check whether the selection is over the limit\n      length: sequenceLimit + 1,\n    },\n  );\n\n  let rowCount = table?.[0].data.data.length ?? 0;\n  let exceedsLimit = false;\n  if (rowCount > sequenceLimit) {\n    rowCount = sequenceLimit;\n    exceedsLimit = true;\n  }\n\n  const sequenceColumns = sequenceColumnIds.map((columnId) => {\n    const column = table.find(({ spec }) => spec.id === columnId);\n    if (!column) {\n      throw new Error(`Couldn't find sequence column (ID: \\`${columnId}\\`).`);\n    }\n    return column;\n  });\n\n  const labelColumns = labelColumnIds.map((labelColumn) => {\n    const column = table.find(({ spec }) => {\n      if (labelColumn.type === 'axis' && spec.type === 'axis') {\n        return isJsonEqual(labelColumn.id, spec.id);\n      }\n      if (labelColumn.type === 'column' && spec.type === 'column') {\n        return labelColumn.id === spec.id;\n      }\n    });\n    if (!column) {\n      throw new Error(`Couldn't find label column (ID: \\`${labelColumn}\\`).`);\n    }\n    return column;\n  });\n\n  const markupColumn = markupColumnId\n    && table.find(({ spec }) => spec.id === markupColumnId);\n\n  const alignedSequences = await Promise.all(\n    sequenceColumns.map((column) =>\n      multiSequenceAlignment(\n        Array.from(\n          { length: rowCount },\n          (_, row) =>\n            pTableValue(column.data, row, { na: '', absent: '' })?.toString()\n            ?? '',\n        ),\n        alignmentParams,\n      ),\n    ),\n  );\n\n  const sequences = Array.from(\n    { length: rowCount },\n    (_, row) => alignedSequences.map((column) => column[row]),\n  );\n\n  const sequenceNames = sequenceColumns.map((column) =>\n    column.spec.spec.annotations?.['pl7.app/label'] ?? 'Unlabelled column',\n  );\n\n  const labels = Array.from(\n    { length: rowCount },\n    (_, row) =>\n      labelColumns.map((column) =>\n        pTableValue(column.data, row, { na: '', absent: '' })?.toString() ?? '',\n      ),\n  );\n\n  const concatenatedSequences = sequences.map((row) => row.join(' '));\n  const residueCounts = getResidueCounts(concatenatedSequences);\n\n  const result: MultipleAlignmentData = {\n    sequences: concatenatedSequences,\n    sequenceNames,\n    labelsRows: labels,\n    exceedsLimit,\n    residueCounts,\n  };\n\n  if (markupColumn) {\n    const labels = JSON.parse(\n      markupColumn.spec.spec.annotations\n        ?.['pl7.app/sequence/annotation/mapping'] ?? '{}',\n    );\n    const data = Array.from(\n      { length: rowCount },\n      (_, row) => {\n        const markup = parseMarkup(\n          pTableValue(markupColumn.data, row, { na: '', absent: '' })\n            ?.toString()\n            ?? '',\n        );\n        return markupAlignedSequence(sequences[row][0], markup);\n      },\n    );\n    result.markup = { labels, data };\n  }\n\n  if (colorScheme.type === 'chemical-properties') {\n    const colorMap = chemicalPropertiesColorMap;\n    result.highlightImage = {\n      blob: await colorizeSequencesByChemicalProperties({\n        sequences: concatenatedSequences,\n        residueCounts,\n        colorMap,\n      }),\n      colorMap,\n    };\n  } else if (colorScheme.type === 'markup') {\n    const colorMap = Object.fromEntries(\n      Object.entries(\n        result.markup?.labels ?? {},\n      ).map(([id, label], index) => [\n        id,\n        { label, color: markupColors[index % markupColors.length] },\n      ]),\n    );\n    result.highlightImage = {\n      blob: await colorizeSequencesByMarkup({\n        markupRows: result.markup?.data ?? [],\n        colorMap,\n        columnCount: concatenatedSequences.at(0)?.length ?? 0,\n      }),\n      colorMap,\n    };\n  }\n\n  return result;\n}\n\nfunction refreshOnDeepChange<T, P>(cb: (params: P) => Promise<T>) {\n  const data = ref<T>();\n  const isLoading = ref(true);\n  const error = ref<Error>();\n  let requestId: symbol;\n  return (paramsGetter: () => P) => {\n    watch(paramsGetter, async (params, prevParams) => {\n      if (isJsonEqual(params, prevParams)) return;\n      const currentRequestId = requestId = Symbol();\n      try {\n        error.value = undefined;\n        isLoading.value = true;\n        const result = await cb(params);\n        if (currentRequestId === requestId) {\n          data.value = result;\n        }\n      } catch (err) {\n        console.error(err);\n        if (currentRequestId === requestId) {\n          error.value = ensureError(err);\n        }\n      } finally {\n        if (currentRequestId === requestId) {\n          isLoading.value = 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package/dist/components/PlMultiSequenceAlignment/markup.d.ts

@@ -1,4 +1,4 @@
-import { ColorMap } from './types';
+import { HighlightLegend } from './types';
 export type Markup = {
     id: string;
     start: number;
@@ -6,10 +6,12 @@ export type Markup = {
 }[];
 export declare function parseMarkup(row: string): Markup;
 export declare function markupAlignedSequence(alignedSequence: string, markup: Markup): Markup;
-export declare function colorizeSequencesByMarkup({ markupRows, columnCount, colorMap }: {
+export declare function highlightByMarkup({ markupRows, columnCount, labels }: {
     markupRows: Markup[];
     columnCount: number;
-    colorMap: ColorMap;
-}): Promise<Blob>;
-export declare const markupColors: string[];
+    labels: Record<string, string>;
+}): {
+    blob: Blob;
+    legend: HighlightLegend;
+};
 //# sourceMappingURL=markup.d.ts.map