@platforma-sdk/ui-vue 1.45.35 → 1.45.36

package/dist/components/PlMultiSequenceAlignment/data.js

@@ -1,370 +0,0 @@
-import { isJsonEqual as O } from "../../lib/util/helpers/dist/objects.js";
-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 = () => $().pFrameDriver, D = 1e3, we = E(
-  _
-), ge = E(
-  G
-), he = E(
-  K
-), be = E(
-  X
-);
-async function _({ pFrame: n, sequenceColumnPredicate: r }) {
-  if (!n) return;
-  const o = (await x().listColumns(n)).values().filter((i) => r(i)).map(({ spec: i, columnId: c }) => ({
-    label: C(i, h.Label) ?? "Unlabeled column",
-    value: c
-  })).toArray(), t = o.map(({ value: i }) => i);
-  return { options: o, defaults: t };
-}
-async function G({ pFrame: n, sequenceColumnIds: r }) {
-  if (!n || !r) return;
-  const a = x(), e = await a.listColumns(n), o = new Map(
-    r.values().flatMap((s) => {
-      const u = e.find(({ columnId: m }) => m === s);
-      if (!u)
-        throw new Error(`Couldn't find sequence column (ID: \`${s}\`).`);
-      return u.spec.axesSpec.values().map((m) => [v(S(m)), m]);
-    })
-  ), 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]))
-    );
-    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: i } = await a.findColumns(n, {
-    columnFilter: {},
-    compatibleWith: o.keys().map((s) => A(s)).toArray(),
-    strictlyCompatible: !1
-  });
-  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 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 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 }))
-  );
-  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 X({
-  pFrame: n,
-  sequenceColumnIds: r,
-  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((p) => ({
-      type: "column",
-      column: p
-    }))
-  };
-  c.length > 0 && (s = {
-    type: "outer",
-    primary: s,
-    secondary: c.map(({ columnId: p }) => ({
-      type: "column",
-      column: p
-    }))
-  }), l && (s = {
-    type: "inner",
-    entries: [
-      s,
-      {
-        type: "inlineColumn",
-        column: l
-      }
-    ]
-  });
-  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((p) => {
-        const b = i.find(({ columnId: y }) => y === p);
-        if (!b)
-          throw new Error(`Couldn't find sequence column (ID: ${p})`);
-        return b.spec.axesSpec.map((y) => v(S(y)));
-      })
-    )
-  ).sort().map((p) => ({
-    column: { type: "axis", id: A(p) },
-    ascending: !0,
-    naAndAbsentAreLeastValues: !0
-  })), d = {
-    src: {
-      type: "outer",
-      primary: s,
-      secondary: u
-    },
-    filters: [],
-    sorting: m
-  };
-  return t.calculateTableData(
-    n,
-    JSON.parse(JSON.stringify(d)),
-    {
-      offset: 0,
-      // +1 is a hack to check whether the selection is over the limit
-      length: D + 1
-    }
-  );
-}
-const te = (n, r) => n.map((a) => {
-  const e = r.find(({ spec: i }) => i.id === a);
-  if (!e)
-    throw new Error(`Couldn't find sequence column (ID: \`${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
-        ),
-        { 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")
-    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
-    });
-  }
-}
-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 {
-      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 {
-      s === o && (a.value = !1);
-    }
-  }, { immediate: !0 }), { data: r, isLoading: a, error: e });
-}
-export {
-  D as SEQUENCE_LIMIT,
-  ge as useLabelColumnsOptions,
-  he as useMarkupColumnsOptions,
-  be as useMultipleAlignmentData,
-  we as useSequenceColumnsOptions
-};
-//# sourceMappingURL=data.js.map

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

@@ -1 +0,0 @@
-{"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  Annotation,\n  type CalculateTableDataRequest,\n  type CalculateTableDataResponse,\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  readAnnotation,\n  readAnnotationJson,\n} from '@platforma-sdk/model';\nimport { onWatcherCleanup, ref, watch } from 'vue';\nimport { objectHash } from '../../objectHash';\nimport { highlightByChemicalProperties } from './chemical-properties';\nimport type { Markup } from './markup';\nimport {\n  highlightByMarkup,\n  markupAlignedSequence,\n  parseMarkup,\n} from './markup';\nimport type * as MultiSequenceAlignmentWorker from './multi-sequence-alignment.worker';\nimport type * as PhylogeneticTreeWorker from './phylogenetic-tree.worker';\nimport { getResidueCounts } from './residue-counts';\nimport type { HighlightLegend, ResidueCounts } from './types';\n\nconst getPFrameDriver = () => getRawPlatformaInstance().pFrameDriver;\n\nexport const SEQUENCE_LIMIT = 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({ pFrame, sequenceColumnPredicate }: {\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\n  const options = columns.values()\n    .filter((column) => sequenceColumnPredicate(column))\n    .map(({ spec, columnId }) => ({\n      label: readAnnotation(spec, Annotation.Label) ?? 'Unlabeled column',\n      value: columnId,\n    }))\n    .toArray();\n\n  const defaults = options.map(({ value }) => value);\n\n  return { options, defaults };\n}\n\nasync function getLabelColumnsOptions({ pFrame, sequenceColumnIds }: {\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\n  const sequenceColumnsAxes = new Map(\n    sequenceColumnIds.values().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.values()\n        .map((spec) => [canonicalizeJson(getAxisId(spec)), spec]);\n    }),\n  );\n\n  const optionMap = new Map<CanonicalizedJson<PTableColumnId>, string>();\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      readAnnotation(labelColumn?.spec, Annotation.Label)\n      ?? readAnnotation(axisSpec, Annotation.Label)\n      ?? 'Unlabeled axis',\n    );\n  }\n\n  const { hits: compatibleColumns } = await pFrameDriver.findColumns(pFrame, {\n    columnFilter: {},\n    compatibleWith: sequenceColumnsAxes.keys()\n      .map((axisIdJson) => parseJson(axisIdJson))\n      .toArray(),\n    strictlyCompatible: false,\n  });\n\n  for (const { columnId, spec } of compatibleColumns) {\n    const columnIdJson = canonicalizeJson<PTableColumnId>({\n      type: 'column',\n      id: columnId,\n    });\n    if (optionMap.has(columnIdJson)) continue;\n    optionMap.set(\n      columnIdJson,\n      readAnnotation(spec, Annotation.Label) ?? 'Unlabeled column',\n    );\n  }\n\n  const options = optionMap.entries()\n    .map(([value, label]) => ({ label, value: parseJson(value) }))\n    .toArray();\n\n  const defaults = options.values()\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    .toArray();\n\n  return { options, defaults };\n}\n\nasync function getMarkupColumnsOptions({ pFrame, sequenceColumnIds }: {\n  pFrame: PFrameHandle | undefined;\n  sequenceColumnIds: PObjectId[] | undefined;\n}): Promise<ListOptionNormalized<PObjectId[]>[] | undefined> {\n  if (!pFrame || !sequenceColumnIds) return;\n\n  const pFrameDriver = getPFrameDriver();\n  const columns = await pFrameDriver.listColumns(pFrame);\n\n  const sequenceColumns = sequenceColumnIds.map((columnId) => {\n    const column = columns.find((column) => column.columnId === columnId);\n    if (!column) {\n      throw new Error(\n        `Couldn't find sequence column (ID: \\`${sequenceColumnIds[0]}\\`).`,\n      );\n    }\n    return column;\n  });\n\n  const columnPairs = sequenceColumns\n    .flatMap((sequenceColumn) =>\n      columns\n        .filter((column) =>\n          readAnnotationJson(column.spec, Annotation.Sequence.IsAnnotation)\n          && isJsonEqual(sequenceColumn.spec.axesSpec, column.spec.axesSpec)\n          && Object.entries(sequenceColumn.spec.domain ?? {})\n            .every(([key, value]) => column.spec.domain?.[key] === value),\n        )\n        .map((markupColumn) => ({ markupColumn, sequenceColumn })),\n    );\n\n  const groupedByDomainDiff = Map.groupBy(\n    columnPairs,\n    ({ markupColumn, sequenceColumn }) => {\n      const domainDiff = Object.fromEntries(\n        Object.entries(markupColumn.spec.domain ?? {})\n          .filter(([key]) => sequenceColumn.spec.domain?.[key] == undefined),\n      );\n      return canonicalizeJson(domainDiff);\n    },\n  );\n\n  return groupedByDomainDiff.entries()\n    .map(([domainDiffJson, columnPairs]) => ({\n      label: Object.values(parseJson(domainDiffJson)).join(', '),\n      value: columnPairs.map(({ markupColumn }) => markupColumn.columnId),\n    }))\n    .toArray();\n}\n\nasync function getMultipleAlignmentData(\n  {\n    pFrame,\n    sequenceColumnIds,\n    labelColumnIds,\n    selection,\n    colorScheme,\n    alignmentParams,\n    shouldBuildPhylogeneticTree,\n  }: {\n    pFrame: PFrameHandle | undefined;\n    sequenceColumnIds: PObjectId[] | undefined;\n    labelColumnIds: PTableColumnId[] | undefined;\n    selection: PlSelectionModel | undefined;\n    colorScheme: PlMultiSequenceAlignmentColorSchemeOption;\n    alignmentParams: PlMultiSequenceAlignmentSettings['alignmentParams'];\n    shouldBuildPhylogeneticTree: boolean;\n  },\n  abortSignal: AbortSignal,\n): Promise<MultipleAlignmentData | undefined> {\n  if (!pFrame || !sequenceColumnIds?.length || !labelColumnIds) return;\n\n  const table = await getTableData({\n    pFrame,\n    sequenceColumnIds,\n    labelColumnIds,\n    selection,\n    colorScheme,\n  });\n\n  const rowCount = table.at(0)?.data.data.length ?? 0;\n\n  if (rowCount < 2) return;\n\n  const exceedsLimit = rowCount > SEQUENCE_LIMIT;\n  const rawSequences = extractSequences(sequenceColumnIds, table);\n  const labels = extractLabels(labelColumnIds, table);\n  const markups = colorScheme.type === 'markup'\n    ? extractMarkups(colorScheme.columnIds, table)\n    : undefined;\n\n  const highlightLegend: HighlightLegend = {};\n\n  const alignedSequences = await Promise.all(\n    rawSequences.map(async ({ name, rows }) => ({\n      name,\n      rows: await alignSequences(\n        rows,\n        JSON.parse(JSON.stringify(alignmentParams)),\n        abortSignal,\n      ),\n    })),\n  );\n\n  let phylogeneticTree: PhylogeneticTreeWorker.TreeNodeData[] | undefined;\n  if (shouldBuildPhylogeneticTree) {\n    phylogeneticTree = await buildPhylogeneticTree(\n      alignedSequences,\n      abortSignal,\n    );\n    const rowOrder = phylogeneticTree.values()\n      .filter(({ id }) => id >= 0)\n      .map(({ id }) => id)\n      .toArray();\n    for (const sequencesColumn of alignedSequences) {\n      sequencesColumn.rows = rowOrder.map((i) => sequencesColumn.rows[i]);\n    }\n    for (const labelsColumn of labels) {\n      labelsColumn.rows = rowOrder.map((i) => labelsColumn.rows[i]);\n    }\n    for (const markupsColumn of markups ?? []) {\n      markupsColumn.rows = rowOrder.map((i) => markupsColumn.rows[i]);\n    }\n  }\n\n  const sequences = await Promise.all(\n    alignedSequences.map(async ({ name, rows }, index) => {\n      const residueCounts = getResidueCounts(rows);\n      const image = generateHighlightImage({\n        colorScheme,\n        sequences: rows,\n        residueCounts,\n        markup: markups?.at(index),\n      });\n      if (image) {\n        Object.assign(highlightLegend, image.legend);\n      }\n      return {\n        name,\n        rows,\n        residueCounts,\n        ...image && {\n          highlightImageUrl: await blobToBase64(image.blob),\n        },\n      } satisfies MultipleAlignmentData['sequences'][number];\n    }),\n  );\n\n  return {\n    sequences,\n    labels,\n    ...Object.keys(highlightLegend).length && {\n      highlightLegend,\n    },\n    ...phylogeneticTree && {\n      phylogeneticTree,\n    },\n    exceedsLimit,\n  };\n}\n\nasync function getTableData(\n  { pFrame, sequenceColumnIds, labelColumnIds, selection, colorScheme }: {\n    pFrame: PFrameHandle;\n    sequenceColumnIds: PObjectId[];\n    labelColumnIds: PTableColumnId[];\n    selection: PlSelectionModel | undefined;\n    colorScheme: PlMultiSequenceAlignmentColorSchemeOption;\n  },\n): Promise<CalculateTableDataResponse> {\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 (colorScheme.type === 'markup') {\n    for (const column of colorScheme.columnIds) {\n      secondaryEntry.push({ type: 'column', column });\n    }\n  }\n\n  const sorting: PTableSorting[] = Array.from(\n    new Set(\n      sequenceColumnIds.values().flatMap((id) => {\n        const column = columns.find(({ columnId }) => columnId === id);\n        if (!column) {\n          throw new Error(`Couldn't find sequence column (ID: ${id})`);\n        }\n        return column.spec.axesSpec\n          .map((spec) => canonicalizeJson(getAxisId(spec)));\n      }),\n    ),\n  )\n    .sort()\n    .map((id) => ({\n      column: { type: 'axis', id: parseJson(id) },\n      ascending: true,\n      naAndAbsentAreLeastValues: true,\n    }));\n\n  const request: CalculateTableDataRequest<PObjectId> = {\n    src: {\n      type: 'outer',\n      primary: primaryEntry,\n      secondary: secondaryEntry,\n    },\n    filters: [],\n    sorting,\n  };\n\n  return pFrameDriver.calculateTableData(\n    pFrame,\n    JSON.parse(JSON.stringify(request)),\n    {\n      offset: 0,\n      // +1 is a hack to check whether the selection is over the limit\n      length: SEQUENCE_LIMIT + 1,\n    },\n  );\n}\n\nconst extractSequences = (\n  columnIds: PObjectId[],\n  table: CalculateTableDataResponse,\n): { name: string; rows: string[] }[] =>\n  columnIds.map((columnId) => {\n    const column = table.find(({ spec }) => spec.id === columnId);\n    if (!column) {\n      throw new Error(`Couldn't find sequence column (ID: \\`${columnId}\\`).`);\n    }\n    const name = readAnnotation(column.spec.spec, Annotation.Label)\n      ?? 'Unlabeled column';\n    const rows = column.data.data\n      .keys()\n      .take(SEQUENCE_LIMIT)\n      .map((row) =>\n        pTableValue(column.data, row, { absent: '', na: '' })?.toString()\n        ?? '',\n      )\n      .toArray();\n    return { name, rows };\n  });\n\nconst extractLabels = (\n  columnIds: PTableColumnId[],\n  table: CalculateTableDataResponse,\n): { rows: string[] }[] =>\n  columnIds.map((columnId) => {\n    const column = table.find(({ spec }) => {\n      if (columnId.type === 'axis' && spec.type === 'axis') {\n        return isJsonEqual(columnId.id, spec.id);\n      }\n      if (columnId.type === 'column' && spec.type === 'column') {\n        return columnId.id === spec.id;\n      }\n    });\n    if (!column) {\n      throw new Error(`Couldn't find label column (ID: \\`${columnId}\\`).`);\n    }\n    const rows = column.data.data\n      .keys()\n      .take(SEQUENCE_LIMIT)\n      .map((row) =>\n        pTableValue(column.data, row, { absent: '', na: '' })?.toString()\n        ?? 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[];\n    const hash = await objectHash(concatenatedSequences);\n    let result = cache.get(hash);\n    if (result) return result;\n    result = await runInWorker<\n      PhylogeneticTreeWorker.RequestMessage,\n      PhylogeneticTreeWorker.ResponseMessage\n    >(\n      new Worker(\n        new URL('./phylogenetic-tree.worker.ts', import.meta.url),\n        { type: 'module' },\n      ),\n      concatenatedSequences,\n      abortSignal,\n    );\n    cache.set(hash, result);\n    return result;\n  };\n})();\n\nconst runInWorker = <RequestMessage, ResponseMessage>(\n  worker: Worker,\n  message: RequestMessage,\n  abortSignal: AbortSignal,\n) =>\n  new Promise<ResponseMessage>((resolve, reject) => {\n    worker.addEventListener('message', ({ data }) => {\n      resolve(data);\n      worker.terminate();\n    });\n    worker.addEventListener('error', ({ error, message }) => {\n      reject(error ?? message);\n      worker.terminate();\n    });\n    abortSignal.addEventListener('abort', () => 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package/dist/components/PlMultiSequenceAlignment/index.d.ts

@@ -1 +0,0 @@
-export { default as PlMultiSequenceAlignment } from './PlMultiSequenceAlignment.vue';

package/dist/components/PlMultiSequenceAlignment/markup.d.ts

@@ -1,16 +0,0 @@
-import { HighlightLegend } from './types';
-export type Markup = {
-    id: string;
-    start: number;
-    length: number;
-}[];
-export declare function parseMarkup(row: string): Markup;
-export declare function markupAlignedSequence(alignedSequence: string, markup: Markup): Markup;
-export declare function highlightByMarkup({ markupRows, columnCount, labels }: {
-    markupRows: Markup[];
-    columnCount: number;
-    labels: Record<string, string>;
-}): {
-    blob: Blob;
-    legend: HighlightLegend;
-};

package/dist/components/PlMultiSequenceAlignment/markup.js

@@ -1,84 +0,0 @@
-function E(o) {
-  return Array.from(o.matchAll(
-    /(?<id>[^:]*):(?<start>[0-9A-Za-z]*)(?:\+(?<length>[0-9A-Za-z]*))?\|?/g
-  )).map((l) => {
-    const r = l.groups, n = Number.parseInt(r.start, 36), t = r.length ? Number.parseInt(r.length, 36) : 0;
-    return {
-      id: r.id,
-      start: n,
-      length: t
-    };
-  });
-}
-function f(o, l) {
-  const r = o.split("").reduce(
-    (t, a, e) => (a !== "-" && t.push(e), t),
-    []
-  );
-  return l.map((t) => {
-    const a = r[t.start], e = r[t.start + t.length - 1] + 1;
-    return {
-      id: t.id,
-      start: a,
-      length: e - a
-    };
-  });
-}
-function C({ markupRows: o, columnCount: l, labels: r }) {
-  const n = /* @__PURE__ */ new Map();
-  for (const [e, F] of o.entries())
-    for (const { id: s, start: u, length: c } of F) {
-      let i = n.get(s);
-      i || n.set(s, i = []), i.push({ row: e, start: u, length: c });
-    }
-  const t = Object.fromEntries(
-    Object.entries(r).map(
-      ([e, F], s) => [
-        e,
-        {
-          label: F,
-          color: g[s % g.length]
-        }
-      ]
-    ).filter(([e]) => n.has(e))
-  );
-  return { blob: new Blob(
-    function* () {
-      yield `<svg xmlns="http://www.w3.org/2000/svg" viewBox="${`0 0 ${l} ${o.length * 2}`}" stroke-width="2" preserveAspectRatio="none">`;
-      for (const [F, s] of n) {
-        const { color: u } = t[F];
-        yield `<path stroke="${u}" d="`;
-        let c = 0, i = 0;
-        for (const { row: d, start: p, length: h } of s)
-          yield `m${p - c},${d * 2 + 1 - i}h${h}`, c = p + h, i = d * 2 + 1;
-        yield '"/>';
-      }
-      yield "</svg>";
-    }().toArray(),
-    { type: "image/svg+xml" }
-  ), legend: t };
-}
-const g = [
-  "#E5F2FF",
-  "#FFE8E8",
-  "#F0EBFF",
-  "#FFFFE3",
-  "#E5F7E5",
-  "#FEEAFE",
-  "#FDEED6",
-  "#E8FDFE",
-  "#CCDFF2",
-  "#F2CCCD",
-  "#D5CCF2",
-  "#F2F2CC",
-  "#CCF2CC",
-  "#F2CCF2",
-  "#EFDDBF",
-  "#DEEEEF"
-];
-export {
-  C as highlightByMarkup,
-  f as markupAlignedSequence,
-  E as parseMarkup
-};
-//# sourceMappingURL=markup.js.map

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

@@ -1 +0,0 @@
-{"version":3,"file":"markup.js","sources":["../../../src/components/PlMultiSequenceAlignment/markup.ts"],"sourcesContent":["import type { HighlightLegend } from './types';\n\nexport type Markup = { id: string; start: number; length: number }[];\n\nexport function parseMarkup(row: string): Markup {\n  return Array.from(row.matchAll(\n    /(?<id>[^:]*):(?<start>[0-9A-Za-z]*)(?:\\+(?<length>[0-9A-Za-z]*))?\\|?/g,\n  )).map((match) => {\n    const matchGroups = match.groups as {\n      id: string;\n      start: string;\n      length: string | undefined;\n    };\n    const start = Number.parseInt(matchGroups.start, 36);\n    const length = matchGroups.length\n      ? Number.parseInt(matchGroups.length, 36)\n      : 0;\n    return {\n      id: matchGroups.id,\n      start,\n      length,\n    };\n  });\n}\n\nexport function markupAlignedSequence(\n  alignedSequence: string,\n  markup: Markup,\n): Markup {\n  const indexMap = alignedSequence.split('').reduce<number[]>(\n    (acc, char, index) => {\n      if (char !== '-') acc.push(index);\n      return acc;\n    },\n    [],\n  );\n  const adjusted = markup.map((segment) => {\n    const start = indexMap[segment.start];\n    const end = indexMap[segment.start + segment.length - 1] + 1;\n    return {\n      id: segment.id,\n      start: start,\n      length: end - start,\n    };\n  });\n  return adjusted;\n}\n\nexport function highlightByMarkup(\n  { markupRows, columnCount, labels }: {\n    markupRows: Markup[];\n    columnCount: number;\n    labels: Record<string, string>;\n  },\n): { blob: Blob; legend: HighlightLegend } {\n  const linesById: Map<string, {\n    row: number;\n    start: number;\n    length: number;\n  }[]> = new Map();\n  for (const [row, markup] of markupRows.entries()) {\n    for (const { id, start, length } of markup) {\n      let bucket = linesById.get(id);\n      if (!bucket) linesById.set(id, bucket = []);\n      bucket.push({ row, start, length });\n    }\n  }\n  const legend: HighlightLegend = Object.fromEntries(\n    Object.entries(labels)\n      .map(([id, label], index) =>\n        [\n          id,\n          {\n            label,\n            color: markupColors[index % markupColors.length],\n          },\n        ] as const,\n      )\n      .filter(([id]) => linesById.has(id)),\n  );\n  const blob = new Blob(\n    (function*() {\n      const viewBox = `0 0 ${columnCount} ${markupRows.length * 2}`;\n      yield `<svg xmlns=\"http://www.w3.org/2000/svg\" viewBox=\"${viewBox}\" stroke-width=\"2\" preserveAspectRatio=\"none\">`;\n      for (const [id, lines] of linesById) {\n        const { color } = legend[id];\n        yield `<path stroke=\"${color}\" d=\"`;\n        let x = 0, y = 0;\n        for (const { row, start, length } of lines) {\n          yield `m${start - x},${row * 2 + 1 - y}h${length}`;\n          x = start + length;\n          y = row * 2 + 1;\n        }\n        yield '\"/>';\n      }\n      yield '</svg>';\n    })().toArray(),\n    { type: 'image/svg+xml' },\n  );\n  return { blob, legend };\n}\n\nconst markupColors = [\n  '#E5F2FF',\n  '#FFE8E8',\n  '#F0EBFF',\n  '#FFFFE3',\n  '#E5F7E5',\n  '#FEEAFE',\n  '#FDEED6',\n  '#E8FDFE',\n  '#CCDFF2',\n  '#F2CCCD',\n  '#D5CCF2',\n  '#F2F2CC',\n  '#CCF2CC',\n  '#F2CCF2',\n  '#EFDDBF',\n  '#DEEEEF',\n];\n\nif (import.meta.vitest) {\n  const { test, expect } = import.meta.vitest;\n  test('annotateAlignedRow', () => {\n    const alignedSequence\n      = 'EVRLVESGGALVQPGGSLRLSCVAASGFTFINNWVTWVRQAPGKGLEWVANIKEDGSQKYYVDSVKGRFTISRDNAEKSVYLQMSSLRVDDTAVYYCAR------------GRAV----D---QWGQGTLVTVSS';\n    //   0         10        20        30        40        50        60        70        80        90        100       110       120       130\n    //   EVRLVESGGALVQPGGSLRLSCVAASGFTFINNWVTWVRQAPGKGLEWVANIKEDGSQKYYVDSVKGRFTISRDNAEKSVYLQMSSLRVDDTAVYYCARGRAVDQWGQGTLVTVSS\n    const markup = [\n      { id: '1', start: 0, length: 99 },\n      { id: '2', start: 99, length: 3 },\n      { id: '3', start: 102, length: 14 },\n    ];\n    const alignedMarkup = markupAlignedSequence(alignedSequence, markup);\n    expect(alignedMarkup).toEqual([\n      { id: '1', start: 0, length: 99 },\n      { id: '2', start: 111, length: 3 },\n      { id: '3', start: 114, length: 21 },\n    ]);\n  });\n}\n"],"names":["parseMarkup","row","match","matchGroups","start","length","markupAlignedSequence","alignedSequence","markup","indexMap","acc","char","index","segment","end","highlightByMarkup","markupRows","columnCount","labels","linesById","id","bucket","legend","label","markupColors","lines","color","x","y"],"mappings":"AAIO,SAASA,EAAYC,GAAqB;AAC/C,SAAO,MAAM,KAAKA,EAAI;AAAA,IACpB;AAAA,EAAA,CACD,EAAE,IAAI,CAACC,MAAU;AAChB,UAAMC,IAAcD,EAAM,QAKpBE,IAAQ,OAAO,SAASD,EAAY,OAAO,EAAE,GAC7CE,IAASF,EAAY,SACvB,OAAO,SAASA,EAAY,QAAQ,EAAE,IACtC;AACJ,WAAO;AAAA,MACL,IAAIA,EAAY;AAAA,MAChB,OAAAC;AAAA,MACA,QAAAC;AAAA,IAAA;AAAA,EAEJ,CAAC;AACH;AAEO,SAASC,EACdC,GACAC,GACQ;AACR,QAAMC,IAAWF,EAAgB,MAAM,EAAE,EAAE;AAAA,IACzC,CAACG,GAAKC,GAAMC,OACND,MAAS,OAAKD,EAAI,KAAKE,CAAK,GACzBF;AAAA,IAET,CAAA;AAAA,EAAC;AAWH,SATiBF,EAAO,IAAI,CAACK,MAAY;AACvC,UAAMT,IAAQK,EAASI,EAAQ,KAAK,GAC9BC,IAAML,EAASI,EAAQ,QAAQA,EAAQ,SAAS,CAAC,IAAI;AAC3D,WAAO;AAAA,MACL,IAAIA,EAAQ;AAAA,MACZ,OAAAT;AAAA,MACA,QAAQU,IAAMV;AAAA,IAAA;AAAA,EAElB,CAAC;AAEH;AAEO,SAASW,EACd,EAAE,YAAAC,GAAY,aAAAC,GAAa,QAAAC,KAKc;AACzC,QAAMC,wBAIK,IAAA;AACX,aAAW,CAAClB,GAAKO,CAAM,KAAKQ,EAAW;AACrC,eAAW,EAAE,IAAAI,GAAI,OAAAhB,GAAO,QAAAC,EAAA,KAAYG,GAAQ;AAC1C,UAAIa,IAASF,EAAU,IAAIC,CAAE;AAC7B,MAAKC,KAAQF,EAAU,IAAIC,GAAIC,IAAS,EAAE,GAC1CA,EAAO,KAAK,EAAE,KAAApB,GAAK,OAAAG,GAAO,QAAAC,GAAQ;AAAA,IACpC;AAEF,QAAMiB,IAA0B,OAAO;AAAA,IACrC,OAAO,QAAQJ,CAAM,EAClB;AAAA,MAAI,CAAC,CAACE,GAAIG,CAAK,GAAGX,MACjB;AAAA,QACEQ;AAAA,QACA;AAAA,UACE,OAAAG;AAAA,UACA,OAAOC,EAAaZ,IAAQY,EAAa,MAAM;AAAA,QAAA;AAAA,MACjD;AAAA,IACF,EAED,OAAO,CAAC,CAACJ,CAAE,MAAMD,EAAU,IAAIC,CAAE,CAAC;AAAA,EAAA;AAqBvC,SAAO,EAAE,MAnBI,IAAI;AAAA,IACd,aAAY;AAEX,YAAM,oDADU,OAAOH,CAAW,IAAID,EAAW,SAAS,CAAC,EACM;AACjE,iBAAW,CAACI,GAAIK,CAAK,KAAKN,GAAW;AACnC,cAAM,EAAE,OAAAO,EAAA,IAAUJ,EAAOF,CAAE;AAC3B,cAAM,iBAAiBM,CAAK;AAC5B,YAAIC,IAAI,GAAGC,IAAI;AACf,mBAAW,EAAE,KAAA3B,GAAK,OAAAG,GAAO,QAAAC,EAAA,KAAYoB;AACnC,gBAAM,IAAIrB,IAAQuB,CAAC,IAAI1B,IAAM,IAAI,IAAI2B,CAAC,IAAIvB,CAAM,IAChDsB,IAAIvB,IAAQC,GACZuB,IAAI3B,IAAM,IAAI;AAEhB,cAAM;AAAA,MACR;AACA,YAAM;AAAA,IACR,EAAA,EAAK,QAAA;AAAA,IACL,EAAE,MAAM,gBAAA;AAAA,EAAgB,GAEX,QAAAqB,EAAA;AACjB;AAEA,MAAME,IAAe;AAAA,EACnB;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AACF;"}

package/dist/components/PlMultiSequenceAlignment/migrations.d.ts

@@ -1,3 +0,0 @@
-import { PlMultiSequenceAlignmentModel } from '@platforma-sdk/model';
-import { Ref } from 'vue';
-export declare function runMigrations(model: Ref<PlMultiSequenceAlignmentModel>): void;

package/dist/components/PlMultiSequenceAlignment/migrations.js

@@ -1,24 +0,0 @@
-import { parseJson as u } from "@platforma-sdk/model";
-const o = 2;
-function l(r) {
-  var t;
-  const n = s(r.value);
-  try {
-    if (n < 1) {
-      const e = r.value.labelColumnIds;
-      e && (r.value.labelColumnIds = e.map((i) => u(i)));
-    }
-    n < 2 && ((t = r.value.colorScheme) == null ? void 0 : t.type) === "markup" && delete r.value.colorScheme;
-  } catch (e) {
-    console.error(e), r.value = {};
-  } finally {
-    r.value.version = o;
-  }
-}
-function s(r) {
-  return r.version !== void 0 ? r.version : Object.keys(r).length ? 0 : o;
-}
-export {
-  l as runMigrations
-};
-//# sourceMappingURL=migrations.js.map

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

@@ -1 +0,0 @@
-{"version":3,"file":"migrations.js","sources":["../../../src/components/PlMultiSequenceAlignment/migrations.ts"],"sourcesContent":["import {\n  type CanonicalizedJson,\n  parseJson,\n  type PlMultiSequenceAlignmentModel,\n  type PTableColumnId,\n} from '@platforma-sdk/model';\nimport { type Ref } from 'vue';\n\nconst latestVersion = 2;\n\nexport function runMigrations(model: Ref<PlMultiSequenceAlignmentModel>) {\n  const currentVersion = getCurrentVersion(model.value);\n  try {\n    if (currentVersion < 1) {\n      const oldLabelColumnIds = model.value.labelColumnIds as unknown as\n        | CanonicalizedJson<PTableColumnId>[]\n        | undefined;\n      if (oldLabelColumnIds) {\n        model.value.labelColumnIds = oldLabelColumnIds\n          .map((id) => parseJson(id));\n      }\n    }\n    if (currentVersion < 2) {\n      if (model.value.colorScheme?.type === 'markup') {\n        delete model.value.colorScheme;\n      }\n    }\n  } catch (error) {\n    console.error(error);\n    model.value = {};\n  } finally {\n    model.value.version = latestVersion;\n  }\n}\n\n/**\n * If a model has a version, return it.\n * If it doesn't, but contains anything at all, that's version 0,\n * which is a pre-versioning version.\n * Otherwise, emtpy model is treated as the latest model.\n */\nfunction getCurrentVersion(model: PlMultiSequenceAlignmentModel) {\n  if (model.version !== undefined) return model.version;\n  if (Object.keys(model).length) return 0;\n  return latestVersion;\n}\n"],"names":["latestVersion","runMigrations","model","currentVersion","getCurrentVersion","oldLabelColumnIds","id","parseJson","_a","error"],"mappings":";AAQA,MAAMA,IAAgB;AAEf,SAASC,EAAcC,GAA2C;;AACvE,QAAMC,IAAiBC,EAAkBF,EAAM,KAAK;AACpD,MAAI;AACF,QAAIC,IAAiB,GAAG;AACtB,YAAME,IAAoBH,EAAM,MAAM;AAGtC,MAAIG,MACFH,EAAM,MAAM,iBAAiBG,EAC1B,IAAI,CAACC,MAAOC,EAAUD,CAAE,CAAC;AAAA,IAEhC;AACA,IAAIH,IAAiB,OACfK,IAAAN,EAAM,MAAM,gBAAZ,gBAAAM,EAAyB,UAAS,YACpC,OAAON,EAAM,MAAM;AAAA,EAGzB,SAASO,GAAO;AACd,YAAQ,MAAMA,CAAK,GACnBP,EAAM,QAAQ,CAAA;AAAA,EAChB,UAAA;AACE,IAAAA,EAAM,MAAM,UAAUF;AAAA,EACxB;AACF;AAQA,SAASI,EAAkBF,GAAsC;AAC/D,SAAIA,EAAM,YAAY,SAAkBA,EAAM,UAC1C,OAAO,KAAKA,CAAK,EAAE,SAAe,IAC/BF;AACT;"}

package/dist/components/PlMultiSequenceAlignment/multi-sequence-alignment.worker.d.ts

@@ -1,6 +0,0 @@
-import { PlMultiSequenceAlignmentSettings } from '@platforma-sdk/model';
-export type RequestMessage = {
-    sequences: string[];
-    params: PlMultiSequenceAlignmentSettings['alignmentParams'];
-};
-export type ResponseMessage = string[];

package/dist/components/PlMultiSequenceAlignment/phylogenetic-tree.worker.d.ts

@@ -1,7 +0,0 @@
-export type RequestMessage = string[];
-export type ResponseMessage = TreeNodeData[];
-export interface TreeNodeData {
-    id: number;
-    length?: number;
-    parentId?: number;
-}

package/dist/components/PlMultiSequenceAlignment/residue-counts.d.ts

@@ -1,2 +0,0 @@
-import { ResidueCounts } from './types';
-export declare function getResidueCounts(alignedSequences: string[]): ResidueCounts;

package/dist/components/PlMultiSequenceAlignment/residue-counts.js

@@ -1,13 +0,0 @@
-function c(n) {
-  const e = [];
-  for (const r of n)
-    for (const [t, o] of r.split("").entries()) {
-      const s = e[t] ?? (e[t] = {});
-      s[o] = (s[o] ?? 0) + 1;
-    }
-  return e;
-}
-export {
-  c as getResidueCounts
-};
-//# sourceMappingURL=residue-counts.js.map

package/dist/components/PlMultiSequenceAlignment/residue-counts.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"residue-counts.js","sources":["../../../src/components/PlMultiSequenceAlignment/residue-counts.ts"],"sourcesContent":["import type { ResidueCounts } from './types';\n\nexport function getResidueCounts(\n  alignedSequences: string[],\n): ResidueCounts {\n  const columns: ResidueCounts = [];\n  for (const sequence of alignedSequences) {\n    for (const [columnIndex, residue] of sequence.split('').entries()) {\n      const column = columns[columnIndex] ??= {};\n      column[residue] = (column[residue] ?? 0) + 1;\n    }\n  }\n  return columns;\n}\n\nif (import.meta.vitest) {\n  const { test, expect } = import.meta.vitest;\n\n  test('getAlignmentStats', () => {\n    const alignedSequences = [\n      'GKGDPKKPRG-KMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY-IPPKGE---------',\n      '-----MQDRV-KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK---',\n      'MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQ-EFERNLARFREDHPDLIQNAKK--',\n      '-----MHI---KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK',\n    ];\n\n    expect(getResidueCounts(alignedSequences)).toEqual([\n      { '-': 2, 'G': 1, 'M': 1 },\n      { '-': 2, 'K': 2 },\n      { '-': 2, 'G': 1, 'K': 1 },\n      { '-': 2, 'D': 1, 'L': 1 },\n      { '-': 2, 'K': 1, 'P': 1 },\n      { K: 2, M: 2 },\n      { H: 2, K: 1, Q: 1 },\n      { D: 1, I: 1, P: 2 },\n      { '-': 1, 'D': 1, 'R': 2 },\n      { '-': 1, 'F': 1, 'G': 1, 'V': 1 },\n      { '-': 3, 'P': 1 },\n      { K: 4 },\n      { K: 2, M: 1, R: 1 },\n      { P: 3, S: 1 },\n      { L: 2, M: 1, S: 1 },\n      { N: 2, T: 1, Y: 1 },\n      { A: 3, P: 1 },\n      { F: 3, Y: 1 },\n      { F: 2, I: 1, M: 1 },\n      { L: 1, R: 1, V: 2 },\n      { F: 1, Q: 1, W: 1, Y: 1 },\n      { F: 1, M: 1, S: 1, T: 1 },\n      { K: 1, M: 1, R: 1, S: 1 },\n      { D: 1, E: 2, R: 1 },\n      { E: 1, K: 1, M: 1, Q: 1 },\n      { E: 1, R: 3 },\n      { A: 2, H: 1, R: 1 },\n      { K: 3, N: 1 },\n      { K: 1, M: 1, V: 1, Y: 1 },\n      { A: 2, K: 1, V: 1 },\n      { A: 1, H: 1, K: 1, L: 1 },\n      { E: 2, L: 1, P: 1 },\n      { D: 1, H: 1, N: 1, S: 1 },\n      { A: 1, P: 2, T: 1 },\n      { E: 1, L: 1, R: 1, S: 1 },\n      { K: 1, M: 2, V: 1 },\n      { E: 1, N: 1, R: 1, S: 1 },\n      { F: 1, N: 2, S: 1 },\n      { A: 1, L: 1, S: 2 },\n      { A: 1, D: 1, E: 2 },\n      { F: 1, I: 2, L: 1 },\n      { N: 1, S: 2, T: 1 },\n      { K: 3, Q: 1 },\n      { I: 2, K: 1, Q: 1 },\n      { C: 1, L: 3 },\n      { G: 2, S: 2 },\n      { E: 1, K: 1, R: 1, Y: 1 },\n      { K: 1, Q: 1, R: 2 },\n      { W: 3, Y: 1 },\n      { H: 1, K: 3 },\n      { A: 1, E: 1, M: 1, T: 1 },\n      { L: 3, M: 1 },\n      { P: 1, S: 2, T: 1 },\n      { A: 1, E: 2, R: 1 },\n      { A: 1, E: 1, K: 2 },\n      { E: 3, K: 1 },\n      { K: 3, Q: 1 },\n      { A: 1, G: 1, M: 1, W: 1 },\n      { K: 3, P: 1 },\n      { F: 2, Y: 2 },\n      { E: 1, F: 1, I: 1, Y: 1 },\n      { D: 1, E: 1, Q: 2 },\n      { D: 1, E: 1, L: 1, M: 1 },\n      { A: 3, F: 1 },\n      { K: 1, Q: 2, R: 1 },\n      { A: 1, K: 2, R: 1 },\n      { D: 1, E: 2, L: 1 },\n      { K: 2, Q: 1, R: 1 },\n      { A: 2, Q: 2 },\n      { '-': 1, 'L': 1, 'M': 1, 'R': 1 },\n      { E: 1, H: 2, Y: 1 },\n      { E: 1, F: 1, M: 1, R: 1 },\n      { E: 2, Q: 1, R: 1 },\n      { E: 1, K: 1, L: 1, R: 1 },\n      { M: 1, N: 1, Y: 2 },\n      { K: 1, L: 1, P: 2 },\n      { A: 1, G: 1, N: 1, T: 1 },\n      { R: 1, W: 1, Y: 2 },\n      { '-': 1, 'F': 1, 'K': 1, 'S': 1 },\n      { A: 1, I: 1, R: 1, Y: 1 },\n      { E: 1, P: 1, R: 2 },\n      { D: 2, P: 2 },\n      { H: 1, K: 1, N: 1, R: 1 },\n      { G: 1, P: 1, R: 1, Y: 1 },\n      { D: 1, E: 1, G: 1, K: 1 },\n      { '-': 1, 'A': 1, 'K': 1, 'L': 1 },\n      { '-': 1, 'I': 1, 'K': 2 },\n      { '-': 1, 'K': 1, 'M': 1, 'Q': 1 },\n      { '-': 1, 'K': 1, 'L': 1, 'N': 1 },\n      { '-': 1, 'A': 1, 'P': 1, 'R': 1 },\n      { '-': 1, 'K': 3 },\n      { '-': 2, 'K': 1, 'R': 1 },\n      { '-': 3, 'E': 1 },\n      { '-': 3, 'K': 1 },\n    ]);\n  });\n}\n"],"names":["getResidueCounts","alignedSequences","columns","sequence","columnIndex","residue","column"],"mappings":"AAEO,SAASA,EACdC,GACe;AACf,QAAMC,IAAyB,CAAA;AAC/B,aAAWC,KAAYF;AACrB,eAAW,CAACG,GAAaC,CAAO,KAAKF,EAAS,MAAM,EAAE,EAAE,WAAW;AACjE,YAAMG,IAASJ,EAAAE,OAAAF,EAAAE,KAAyB,CAAA;AACxC,MAAAE,EAAOD,CAAO,KAAKC,EAAOD,CAAO,KAAK,KAAK;AAAA,IAC7C;AAEF,SAAOH;AACT;"}

package/dist/components/PlMultiSequenceAlignment/settings.d.ts

@@ -1,2 +0,0 @@
-import { PlMultiSequenceAlignmentSettings } from '@platforma-sdk/model';
-export declare const defaultSettings: PlMultiSequenceAlignmentSettings;