@platforma-sdk/ui-vue 1.42.19 → 1.42.21

package/dist/components/PlMultiSequenceAlignment/data.js

@@ -1,37 +1,36 @@
-import { isJsonEqual as J } from "../../lib/util/helpers/dist/index.js";
-import { getRawPlatformaInstance as Z, isLabelColumn as N, isLinkerColumn as G, createRowSelectionColumn as H } from "../../sdk/model/dist/index.js";
-import { ref as M, watch as K } from "vue";
-import { highlightByChemicalProperties as Q } from "./chemical-properties.js";
-import { parseMarkup as X, markupAlignedSequence as Y, highlightByMarkup as nn } from "./markup.js";
-import { multiSequenceAlignment as tn } from "./multi-sequence-alignment.js";
-import { getResidueCounts as en } from "./residue-counts.js";
-import { ensureError as rn, readAnnotation as b, canonicalizeJson as v, getAxisId as O, parseJson as S, matchAxisId as an, readAnnotationJson as j, pTableValue as q, Annotation as g } from "../../lib/model/common/dist/index.js";
-const C = () => Z().pFrameDriver, E = 1e3, wn = L(
-  on
-), An = L(
-  sn
-), bn = L(
-  ln
-), vn = L(
-  cn
+import { isJsonEqual as J } from "../../lib/util/helpers/dist/objects.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, gt = k(
+  at
+), ht = k(
+  st
+), wt = k(
+  it
+), bt = k(
+  lt
 );
-async function on({
+async function at({
   pFrame: l,
   sequenceColumnPredicate: r
 }) {
   if (!l) return;
-  const t = (await C().listColumns(l)).values().filter((o) => r(o)).map(({ spec: o, columnId: f }) => ({
-    label: b(o, g.Label) ?? "Unlabeled column",
+  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 = t.map(({ value: o }) => o);
-  return { options: t, defaults: i };
+  })).toArray(), i = n.map(({ value: a }) => a);
+  return { options: n, defaults: i };
 }
-async function sn({
+async function st({
   pFrame: l,
   sequenceColumnIds: r
 }) {
   if (!l || !r) return;
-  const m = C(), p = await m.listColumns(l), t = /* @__PURE__ */ new Map(), i = new Map(
+  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)
@@ -41,78 +40,78 @@ async function sn({
   );
   for (const [e, s] of i.entries()) {
     const c = S(e), h = p.find(
-      ({ spec: x }) => N(x) && an(c, O(x.axesSpec[0]))
+      ({ spec: x }) => N(x) && K(c, O(x.axesSpec[0]))
     );
-    t.set(
+    n.set(
       h ? v({ type: "column", id: h.columnId }) : v({ type: "axis", id: c }),
-      b(h == null ? void 0 : h.spec, g.Label) ?? b(s, g.Label) ?? "Unlabeled axis"
+      A(h == null ? void 0 : h.spec, g.Label) ?? A(s, g.Label) ?? "Unlabeled axis"
     );
   }
-  const { hits: o } = await m.findColumns(l, {
+  const { hits: a } = await m.findColumns(l, {
     columnFilter: {},
     compatibleWith: i.keys().map((e) => S(e)).toArray(),
     strictlyCompatible: !1
   });
-  for (const { columnId: e, spec: s } of o) {
+  for (const { columnId: e, spec: s } of a) {
     const c = v({ type: "column", id: e });
-    t.has(c) || t.set(
+    n.has(c) || n.set(
       c,
-      b(s, g.Label) ?? "Unlabeled column"
+      A(s, g.Label) ?? "Unlabeled column"
     );
   }
-  const f = t.entries().map(([e, s]) => ({ label: s, value: S(e) })).toArray(), d = f.values().filter(({ value: e }) => {
+  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 };
 }
-async function ln({
+async function it({
   pFrame: l,
   sequenceColumnIds: r
 }) {
   if (!l || (r == null ? void 0 : r.length) !== 1) return;
-  const p = await C().listColumns(l), t = p.find(
+  const p = await C().listColumns(l), n = p.find(
     (i) => i.columnId === r[0]
   );
-  if (!t)
+  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(t.spec.axesSpec, i.spec.axesSpec) && Object.entries(t.spec.domain ?? {}).every(([o, f]) => {
+    (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[o]) === f;
+      return ((d = i.spec.domain) == null ? void 0 : d[a]) === f;
     })
-  ).map(({ columnId: i, spec: o }) => ({
+  ).map(({ columnId: i, spec: a }) => ({
     value: i,
-    label: b(o, g.Label) ?? "Unlabeled column"
+    label: A(a, g.Label) ?? "Unlabeled column"
   })).toArray();
 }
-async function cn({
+async function lt({
   pFrame: l,
   sequenceColumnIds: r,
   labelColumnIds: m,
   selection: p,
-  colorScheme: t,
+  colorScheme: n,
   alignmentParams: i
 }) {
-  var F;
+  var P;
   if (!l || !(r != null && r.length) || !m) return;
-  const o = C(), f = await o.listColumns(l), d = f.filter((n) => G(n.spec)), e = H({ selection: p });
+  const a = C(), f = await a.listColumns(l), d = f.filter((t) => Q(t.spec)), e = X({ selection: p });
   let s = {
     type: "inner",
-    entries: r.map((n) => ({
+    entries: r.map((t) => ({
       type: "column",
-      column: n
+      column: t
     }))
   };
   d.length > 0 && (s = {
     type: "outer",
     primary: s,
-    secondary: d.map(({ columnId: n }) => ({
+    secondary: d.map(({ columnId: t }) => ({
       type: "column",
-      column: n
+      column: t
     }))
   }), e && (s = {
     type: "inner",
@@ -124,19 +123,19 @@ async function cn({
       }
     ]
   });
-  const c = m.flatMap((n) => n.type !== "column" ? [] : { type: "column", column: n.id });
-  t.type === "markup" && c.push({ type: "column", column: t.columnId });
+  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(
     new Set(
-      r.values().flatMap((n) => {
-        const u = f.find(({ columnId: a }) => a === n);
+      r.values().flatMap((t) => {
+        const u = f.find(({ columnId: o }) => o === t);
         if (!u)
-          throw new Error(`Couldn't find sequence column (ID: ${n})`);
-        return u.spec.axesSpec.map((a) => v(O(a)));
+          throw new Error(`Couldn't find sequence column (ID: ${t})`);
+        return u.spec.axesSpec.map((o) => v(O(o)));
       })
     )
-  ).sort().map((n) => ({
-    column: { type: "axis", id: S(n) },
+  ).sort().map((t) => ({
+    column: { type: "axis", id: S(t) },
     ascending: !0,
     naAndAbsentAreLeastValues: !0
   })), x = {
@@ -147,7 +146,7 @@ async function cn({
     },
     filters: [],
     sorting: h
-  }, w = await o.calculateTableData(
+  }, w = await a.calculateTableData(
     l,
     JSON.parse(JSON.stringify(x)),
     {
@@ -156,109 +155,109 @@ async function cn({
       length: E + 1
     }
   );
-  let A = (w == null ? void 0 : w[0].data.data.length) ?? 0, I = !1;
-  A > E && (A = E, I = !0);
-  const R = r.map((n) => {
-    const u = w.find(({ spec: a }) => a.id === n);
+  let b = (w == null ? void 0 : w[0].data.data.length) ?? 0, I = !1;
+  b > E && (b = E, I = !0);
+  const R = r.map((t) => {
+    const u = w.find(({ spec: o }) => o.id === t);
     if (!u)
-      throw new Error(`Couldn't find sequence column (ID: \`${n}\`).`);
+      throw new Error(`Couldn't find sequence column (ID: \`${t}\`).`);
     return u;
-  }), z = m.map((n) => {
-    const u = w.find(({ spec: a }) => {
-      if (n.type === "axis" && a.type === "axis")
-        return J(n.id, a.id);
-      if (n.type === "column" && a.type === "column")
-        return n.id === a.id;
+  }), B = m.map((t) => {
+    const u = w.find(({ spec: o }) => {
+      if (t.type === "axis" && o.type === "axis")
+        return J(t.id, o.id);
+      if (t.type === "column" && o.type === "column")
+        return t.id === o.id;
     });
     if (!u)
-      throw new Error(`Couldn't find label column (ID: \`${n}\`).`);
+      throw new Error(`Couldn't find label column (ID: \`${t}\`).`);
     return u;
-  }), B = await Promise.all(
+  }), T = await Promise.all(
     R.map(
-      (n) => tn(
+      (t) => rt(
         Array.from(
-          { length: A },
-          (u, a) => {
+          { length: b },
+          (u, o) => {
             var y;
-            return ((y = q(n.data, a, { na: "", absent: "" })) == null ? void 0 : y.toString()) ?? "";
+            return ((y = M(t.data, o, { na: "", absent: "" })) == null ? void 0 : y.toString()) ?? "";
           }
         ),
         i
       )
     )
   ), $ = Array.from(
-    { length: A },
-    (n, u) => B.map((a) => a[u])
-  ), T = R.map(
-    (n) => b(n.spec.spec, g.Label) ?? "Unlabeled column"
-  ), V = Array.from(
-    { length: A },
-    (n, u) => z.map(
-      (a) => {
+    { 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 = q(a.data, u, { na: "", absent: "" })) == null ? void 0 : y.toString()) ?? "";
+        return ((y = M(o.data, u, { na: "", absent: "" })) == null ? void 0 : y.toString()) ?? "";
       }
     )
-  ), D = $.map((n) => n.join(" ")), U = en(D), k = {
+  ), D = $.map((t) => t.join(" ")), U = ot(D), L = {
     sequences: D,
-    sequenceNames: T,
-    labelRows: V,
+    sequenceNames: V,
+    labelRows: z,
     exceedsLimit: I,
     residueCounts: U
   };
-  if (t.type === "chemical-properties")
-    k.highlightImage = Q({
+  if (n.type === "chemical-properties")
+    L.highlightImage = Z({
       sequences: D,
       residueCounts: U
     });
-  else if (t.type === "markup") {
-    const n = w.find(
-      ({ spec: y }) => y.id === t.columnId
+  else if (n.type === "markup") {
+    const t = w.find(
+      ({ spec: y }) => y.id === n.columnId
     );
-    if (!n)
+    if (!t)
       throw new Error(
-        `Couldn't find markup column (ID: \`${t.columnId}\`).`
+        `Couldn't find markup column (ID: \`${n.columnId}\`).`
       );
     const u = Array.from(
-      { length: A },
-      (y, P) => {
-        var _;
-        const W = X(
-          ((_ = q(n.data, P, { na: "", absent: "" })) == null ? void 0 : _.toString()) ?? ""
+      { length: b },
+      (y, _) => {
+        var F;
+        const W = tt(
+          ((F = M(t.data, _, { na: "", absent: "" })) == null ? void 0 : F.toString()) ?? ""
         );
-        return Y($[P][0], W);
+        return nt($[_][0], W);
       }
-    ), a = j(n.spec.spec, g.Sequence.Annotation.Mapping) ?? {};
-    k.highlightImage = nn({
+    ), o = j(t.spec.spec, g.Sequence.Annotation.Mapping) ?? {};
+    L.highlightImage = et({
       markupRows: u,
-      columnCount: ((F = D.at(0)) == null ? void 0 : F.length) ?? 0,
-      labels: a
+      columnCount: ((P = D.at(0)) == null ? void 0 : P.length) ?? 0,
+      labels: o
     });
   }
-  return k;
+  return L;
 }
-function L(l) {
-  const r = M(), m = M(!0), p = M();
-  let t;
-  return (i) => (K(i, async (o, f) => {
-    if (J(o, f)) return;
-    const d = t = Symbol();
+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();
     try {
       p.value = void 0, m.value = !0;
-      const e = await l(o);
-      d === t && (r.value = e);
+      const e = await l(a);
+      d === n && (r.value = e);
     } catch (e) {
-      console.error(e), d === t && (p.value = rn(e));
+      console.error(e), d === n && (p.value = G(e));
     } finally {
-      d === t && (m.value = !1);
+      d === n && (m.value = !1);
     }
   }, { immediate: !0 }), { data: r, isLoading: m, error: p });
 }
 export {
   E as sequenceLimit,
-  An as useLabelColumnsOptions,
-  bn as useMarkupColumnsOptions,
-  vn as useMultipleAlignmentData,
-  wn as useSequenceColumnsOptions
+  ht as useLabelColumnsOptions,
+  wt as useMarkupColumnsOptions,
+  bt as useMultipleAlignmentData,
+  gt 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  readAnnotation,\n  Annotation,\n  readAnnotationJson,\n} from '@platforma-sdk/model';\nimport { ref, watch } from 'vue';\nimport { highlightByChemicalProperties } from './chemical-properties';\nimport {\n  highlightByMarkup,\n  markupAlignedSequence,\n  parseMarkup,\n} from './markup';\nimport { multiSequenceAlignment } from './multi-sequence-alignment';\nimport { getResidueCounts } from './residue-counts';\nimport type { HighlightLegend, 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.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  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(\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  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({ type: 'column', id: columnId } satisfies PTableColumnId);\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  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.values()\n    .filter((column) =>\n      !!readAnnotationJson(column.spec, Annotation.Sequence.IsAnnotation)\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: readAnnotation(spec, Annotation.Label) ?? 'Unlabeled column',\n    }))\n    .toArray();\n}\n\nasync function getMultipleAlignmentData({\n  pFrame,\n  sequenceColumnIds,\n  labelColumnIds,\n  selection,\n  colorScheme,\n  alignmentParams,\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}): 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 (colorScheme.type === 'markup') {\n    secondaryEntry.push({ type: 'column', column: colorScheme.columnId });\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: ${id})`);\n        }\n        return column.spec.axesSpec\n          .map((spec) => canonicalizeJson(getAxisId(spec)));\n      }),\n    ),\n  )\n    .sort()\n    .map((id) => ({\n      column: { type: 'axis', id: parseJson(id) },\n      ascending: true,\n      naAndAbsentAreLeastValues: true,\n    }));\n\n  const request: CalculateTableDataRequest<PObjectId> = {\n    src: {\n      type: 'outer',\n      primary: primaryEntry,\n      secondary: secondaryEntry,\n    },\n    filters: [],\n    sorting,\n  };\n\n  const table = await pFrameDriver.calculateTableData(\n    pFrame,\n    JSON.parse(JSON.stringify(request)),\n    {\n      offset: 0,\n      // +1 is a hack to check whether the selection is over the limit\n      length: sequenceLimit + 1,\n    },\n  );\n\n  let rowCount = table?.[0].data.data.length ?? 0;\n  let exceedsLimit = false;\n  if (rowCount > sequenceLimit) {\n    rowCount = sequenceLimit;\n    exceedsLimit = true;\n  }\n\n  const sequenceColumns = sequenceColumnIds.map((columnId) => {\n    const column = table.find(({ spec }) => spec.id === columnId);\n    if (!column) {\n      throw new Error(`Couldn't find sequence column (ID: \\`${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: \\`${labelColumn}\\`).`);\n    }\n    return column;\n  });\n\n  const alignedSequences = await Promise.all(\n    sequenceColumns.map((column) =>\n      multiSequenceAlignment(\n        Array.from(\n          { length: rowCount },\n          (_, row) =>\n            pTableValue(column.data, row, { na: '', absent: '' })?.toString()\n            ?? '',\n        ),\n        alignmentParams,\n      ),\n    ),\n  );\n\n  const sequences = Array.from(\n    { length: rowCount },\n    (_, row) => alignedSequences.map((column) => column[row]),\n  );\n\n  const sequenceNames = sequenceColumns.map((column) =>\n    readAnnotation(column.spec.spec, Annotation.Label) ?? 'Unlabeled column',\n  );\n\n  const labels = Array.from(\n    { length: rowCount },\n    (_, row) =>\n      labelColumns.map((column) =>\n        pTableValue(column.data, row, { na: '', absent: '' })?.toString() ?? '',\n      ),\n  );\n\n  const concatenatedSequences = sequences.map((row) => row.join(' '));\n  const residueCounts = getResidueCounts(concatenatedSequences);\n\n  const result: MultipleAlignmentData = {\n    sequences: concatenatedSequences,\n    sequenceNames,\n    labelRows: labels,\n    exceedsLimit,\n    residueCounts,\n  };\n\n  if (colorScheme.type === 'chemical-properties') {\n    result.highlightImage = highlightByChemicalProperties({\n      sequences: concatenatedSequences,\n      residueCounts,\n    });\n  } else if (colorScheme.type === 'markup') {\n    const markupColumn = table.find(({ spec }) =>\n      spec.id === colorScheme.columnId,\n    );\n    if (!markupColumn) {\n      throw new Error(\n        `Couldn't find markup column (ID: \\`${colorScheme.columnId}\\`).`,\n      );\n    }\n    const markupRows = 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    const labels = readAnnotationJson(markupColumn.spec.spec, Annotation.Sequence.Annotation.Mapping) ?? {};\n    result.highlightImage = highlightByMarkup({\n      markupRows,\n      columnCount: concatenatedSequences.at(0)?.length ?? 0,\n      labels,\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 = false;\n        }\n      }\n    }, { immediate: true });\n    return { data, isLoading, error };\n  };\n}\n\ntype MultipleAlignmentData = {\n  sequences: string[];\n  sequenceNames: string[];\n  labelRows: string[][];\n  residueCounts: ResidueCounts;\n  highlightImage?: {\n    blob: Blob;\n    legend: HighlightLegend;\n  };\n  exceedsLimit: boolean;\n};\n\ntype OptionsWithDefaults<T> = {\n  options: ListOptionNormalized<T>[];\n  defaults: T[];\n};\n"],"names":["getPFrameDriver","getRawPlatformaInstance","sequenceLimit","useSequenceColumnsOptions","refreshOnDeepChange","getSequenceColumnsOptions","useLabelColumnsOptions","getLabelColumnsOptions","useMarkupColumnsOptions","getMarkupColumnsOptions","useMultipleAlignmentData","getMultipleAlignmentData","pFrame","sequenceColumnPredicate","options","column","spec","columnId","readAnnotation","Annotation","defaults","value","sequenceColumnIds","pFrameDriver","columns","optionMap","sequenceColumnsAxes","id","canonicalizeJson","getAxisId","axisIdJson","axisSpec","axisId","parseJson","labelColumn","isLabelColumn","matchAxisId","compatibleColumns","columnIdJson","label","sequenceColumn","readAnnotationJson","isJsonEqual","key","_a","labelColumnIds","selection","colorScheme","alignmentParams","linkerColumns","isLinkerColumn","filterColumn","createRowSelectionColumn","primaryEntry","secondaryEntry","sorting","request","table","rowCount","exceedsLimit","sequenceColumns","labelColumns","alignedSequences","multiSequenceAlignment","_","row","pTableValue","sequences","sequenceNames","labels","concatenatedSequences","residueCounts","getResidueCounts","result","highlightByChemicalProperties","markupColumn","markupRows","markup","parseMarkup","markupAlignedSequence","highlightByMarkup","cb","data","ref","isLoading","error","requestId","paramsGetter","watch","params","prevParams","currentRequestId","err","ensureError"],"mappings":";;;;;;;;AAuCA,MAAMA,IAAkB,MAAMC,EAAA,EAA0B,cAE3CC,IAAgB,KAEhBC,KAA4BC;AAAA,EACvCC;AACF,GAEaC,KAAyBF;AAAA,EACpCG;AACF,GAEaC,KAA0BJ;AAAA,EACrCK;AACF,GAEaC,KAA2BN;AAAA,EACtCO;AACF;AAEA,eAAeN,GAA0B;AAAA,EACvC,QAAAO;AAAA,EACA,yBAAAC;AACF,GAGwD;AACtD,MAAI,CAACD,EAAQ;AAIb,QAAME,KADU,MADKd,EAAgB,EACF,YAAYY,CAAM,GAC7B,OAAA,EACrB,OAAO,CAACG,MAAWF,EAAwBE,CAAM,CAAC,EAClD,IAAI,CAAC,EAAE,MAAAC,GAAM,UAAAC,SAAgB;AAAA,IAC5B,OAAOC,EAAeF,GAAMG,EAAW,KAAK,KAAK;AAAA,IACjD,OAAOF;AAAA,EAAA,EACP,EACD,QAAQ,GACLG,IAAWN,EAAQ,IAAI,CAAC,EAAE,OAAAO,QAAYA,CAAK;AAC1C,SAAA,EAAE,SAAAP,GAAS,UAAAM,EAAS;AAC7B;AAEA,eAAeb,GAAuB;AAAA,EACpC,QAAAK;AAAA,EACA,mBAAAU;AACF,GAG6D;AACvD,MAAA,CAACV,KAAU,CAACU,EAAmB;AAEnC,QAAMC,IAAevB,EAAgB,GAC/BwB,IAAU,MAAMD,EAAa,YAAYX,CAAM,GAC/Ca,wBAAgB,IAA+C,GAE/DC,IAAsB,IAAI;AAAA,IAC9BJ,EAAkB,OAAA,EAAS,QAAQ,CAACK,MAAO;AACnC,YAAAZ,IAASS,EAAQ,KAAK,CAAC,EAAE,UAAAP,EAAS,MAAMA,MAAaU,CAAE;AAC7D,UAAI,CAACZ;AACH,cAAM,IAAI,MAAM,wCAAwCY,CAAE,MAAM;AAElE,aAAOZ,EAAO,KAAK,SAAS,OAAA,EACzB,IAAI,CAACC,MAAS,CAACY,EAAiBC,EAAUb,CAAI,CAAC,GAAGA,CAAI,CAAC;AAAA,IAC3D,CAAA;AAAA,EACH;AAEA,aAAW,CAACc,GAAYC,CAAQ,KAAKL,EAAoB,WAAW;AAC5D,UAAAM,IAASC,EAAUH,CAAU,GAC7BI,IAAcV,EAAQ;AAAA,MAAK,CAAC,EAAE,MAAAR,EAAK,MACvCmB,EAAcnB,CAAI,KAAKoB,GAAYJ,GAAQH,EAAUb,EAAK,SAAS,CAAC,CAAC,CAAC;AAAA,IACxE;AACU,IAAAS,EAAA;AAAA,MACRS,IACIN,EAAiB,EAAE,MAAM,UAAU,IAAIM,EAAY,SAAU,CAAA,IAC7DN,EAAiB,EAAE,MAAM,QAAQ,IAAII,GAAQ;AAAA,MACjDd,EAAegB,KAAA,gBAAAA,EAAa,MAAMf,EAAW,KAAK,KAC/CD,EAAea,GAAUZ,EAAW,KAAK,KACzC;AAAA,IACL;AAAA,EAAA;AAGF,QAAM,EAAE,MAAMkB,EAAA,IAAsB,MAAMd,EAAa,YAAYX,GAAQ;AAAA,IACzE,cAAc,CAAC;AAAA,IACf,gBAAgBc,EAAoB,KAAA,EACjC,IAAI,CAACI,MAAeG,EAAUH,CAAU,CAAC,EACzC,QAAQ;AAAA,IACX,oBAAoB;AAAA,EAAA,CACrB;AAED,aAAW,EAAE,UAAAb,GAAU,MAAAD,EAAK,KAAKqB,GAAmB;AAClD,UAAMC,IAAeV,EAAiB,EAAE,MAAM,UAAU,IAAIX,GAAmC;AAC3F,IAAAQ,EAAU,IAAIa,CAAY,KACpBb,EAAA;AAAA,MACRa;AAAA,MACApB,EAAeF,GAAMG,EAAW,KAAK,KAAK;AAAA,IAC5C;AAAA,EAAA;AAGF,QAAML,IAAUW,EAAU,UACvB,IAAI,CAAC,CAACJ,GAAOkB,CAAK,OAAO,EAAE,OAAAA,GAAO,OAAON,EAAUZ,CAAK,EAAE,EAAE,EAC5D,QAAQ,GAELD,IAAWN,EAAQ,OAAO,EAC7B,OAAO,CAAC,EAAE,OAAAO,QAAY;AACjB,QAAAA,EAAM,SAAS,OAAe,QAAA;AAC5B,UAAAN,IAASS,EAAQ,KAAK,CAAC,EAAE,UAAAP,QAAeA,MAAaI,EAAM,EAAE;AAC5D,WAAAN,KAAUoB,EAAcpB,EAAO,IAAI;AAAA,EAAA,CAC3C,EACA,IAAI,CAAC,EAAE,OAAAM,EAAM,MAAMA,CAAK,EACxB,QAAQ;AACJ,SAAA,EAAE,SAAAP,GAAS,UAAAM,EAAS;AAC7B;AAEA,eAAeX,GAAwB;AAAA,EACrC,QAAAG;AAAA,EACA,mBAAAU;AACF,GAG2D;AACzD,MAAI,CAACV,MAAUU,KAAA,gBAAAA,EAAmB,YAAW,EAAG;AAGhD,QAAME,IAAU,MADKxB,EAAgB,EACF,YAAYY,CAAM,GAC/C4B,IAAiBhB,EAAQ;AAAA,IAAK,CAACT,MACnCA,EAAO,aAAaO,EAAkB,CAAC;AAAA,EACzC;AACA,MAAI,CAACkB;AACH,UAAM,IAAI;AAAA,MACR,wCAAwClB,EAAkB,CAAC,CAAC;AAAA,IAC9D;AAEK,SAAAE,EAAQ,SACZ;AAAA,IAAO,CAACT,MACP,CAAC,CAAC0B,EAAmB1B,EAAO,MAAMI,EAAW,SAAS,YAAY,KAC/DuB,EAAYF,EAAe,KAAK,UAAUzB,EAAO,KAAK,QAAQ,KAC9D,OAAO,QAAQyB,EAAe,KAAK,UAAU,CAAA,CAAE,EAAE,MAAM,CACxD,CAACG,GAAKtB,CAAK,MACR;;AAAA,eAAAuB,IAAA7B,EAAO,KAAK,WAAZ,gBAAA6B,EAAqBD,QAAStB;AAAA,KAAK;AAAA,IACxC,IAAI,CAAC,EAAE,UAAAJ,GAAU,MAAAD,SAAY;AAAA,IAC7B,OAAOC;AAAA,IACP,OAAOC,EAAeF,GAAMG,EAAW,KAAK,KAAK;AAAA,EAAA,EACjD,EACD,QAAQ;AACb;AAEA,eAAeR,GAAyB;AAAA,EACtC,QAAAC;AAAA,EACA,mBAAAU;AAAA,EACA,gBAAAuB;AAAA,EACA,WAAAC;AAAA,EACA,aAAAC;AAAA,EACA,iBAAAC;AACF,GAO+C;;AAC7C,MAAI,CAACpC,KAAU,EAACU,KAAA,QAAAA,EAAmB,WAAU,CAACuB,EAAgB;AAE9D,QAAMtB,IAAevB,EAAgB,GAC/BwB,IAAU,MAAMD,EAAa,YAAYX,CAAM,GAC/CqC,IAAgBzB,EAAQ,OAAO,CAACT,MAAWmC,EAAenC,EAAO,IAAI,CAAC,GAEtEoC,IAAeC,EAAyB,EAAE,WAAAN,GAAW;AAG3D,MAAIO,IAAqC;AAAA,IACvC,MAAM;AAAA,IACN,SAAS/B,EAAkB,IAAI,CAACP,OAAY;AAAA,MAC1C,MAAM;AAAA,MACN,QAAAA;AAAA,IAAA,EACA;AAAA,EACJ;AAGI,EAAAkC,EAAc,SAAS,MACVI,IAAA;AAAA,IACb,MAAM;AAAA,IACN,SAASA;AAAA,IACT,WAAWJ,EAAc,IAAI,CAAC,EAAE,UAAAhC,SAAgB;AAAA,MAC9C,MAAM;AAAA,MACN,QAAQA;AAAA,IAAA,EACR;AAAA,EACJ,IAIEkC,MACaE,IAAA;AAAA,IACb,MAAM;AAAA,IACN,SAAS;AAAA,MACPA;AAAA,MACA;AAAA,QACE,MAAM;AAAA,QACN,QAAQF;AAAA,MAAA;AAAA,IACV;AAAA,EAEJ;AAIF,QAAMG,IAAyCT,EAC5C,QAAQ,CAAC9B,MACJA,EAAO,SAAS,WAAiB,CAAC,IAC/B,EAAE,MAAM,UAAU,QAAQA,EAAO,GAAG,CAC5C;AAGC,EAAAgC,EAAY,SAAS,YACvBO,EAAe,KAAK,EAAE,MAAM,UAAU,QAAQP,EAAY,UAAU;AAGtE,QAAMQ,IAA2B,MAAM;AAAA,IACrC,IAAI;AAAA,MACFjC,EAAkB,OAAA,EAAS,QAAQ,CAACK,MAAO;AACnC,cAAAZ,IAASS,EAAQ,KAAK,CAAC,EAAE,UAAAP,EAAS,MAAMA,MAAaU,CAAE;AAC7D,YAAI,CAACZ;AACH,gBAAM,IAAI,MAAM,sCAAsCY,CAAE,GAAG;AAEtD,eAAAZ,EAAO,KAAK,SAChB,IAAI,CAACC,MAASY,EAAiBC,EAAUb,CAAI,CAAC,CAAC;AAAA,MACnD,CAAA;AAAA,IAAA;AAAA,EAGF,EAAA,KACA,EAAA,IAAI,CAACW,OAAQ;AAAA,IACZ,QAAQ,EAAE,MAAM,QAAQ,IAAIM,EAAUN,CAAE,EAAE;AAAA,IAC1C,WAAW;AAAA,IACX,2BAA2B;AAAA,EAAA,EAC3B,GAEE6B,IAAgD;AAAA,IACpD,KAAK;AAAA,MACH,MAAM;AAAA,MACN,SAASH;AAAA,MACT,WAAWC;AAAA,IACb;AAAA,IACA,SAAS,CAAC;AAAA,IACV,SAAAC;AAAA,EACF,GAEME,IAAQ,MAAMlC,EAAa;AAAA,IAC/BX;AAAA,IACA,KAAK,MAAM,KAAK,UAAU4C,CAAO,CAAC;AAAA,IAClC;AAAA,MACE,QAAQ;AAAA;AAAA,MAER,QAAQtD,IAAgB;AAAA,IAAA;AAAA,EAE5B;AAEA,MAAIwD,KAAWD,KAAA,gBAAAA,EAAQ,GAAG,KAAK,KAAK,WAAU,GAC1CE,IAAe;AACnB,EAAID,IAAWxD,MACFwD,IAAAxD,GACIyD,IAAA;AAGjB,QAAMC,IAAkBtC,EAAkB,IAAI,CAACL,MAAa;AACpD,UAAAF,IAAS0C,EAAM,KAAK,CAAC,EAAE,MAAAzC,QAAWA,EAAK,OAAOC,CAAQ;AAC5D,QAAI,CAACF;AACH,YAAM,IAAI,MAAM,wCAAwCE,CAAQ,MAAM;AAEjE,WAAAF;AAAA,EAAA,CACR,GAEK8C,IAAehB,EAAe,IAAI,CAACX,MAAgB;AACvD,UAAMnB,IAAS0C,EAAM,KAAK,CAAC,EAAE,MAAAzC,QAAW;AACtC,UAAIkB,EAAY,SAAS,UAAUlB,EAAK,SAAS;AAC/C,eAAO0B,EAAYR,EAAY,IAAIlB,EAAK,EAAE;AAE5C,UAAIkB,EAAY,SAAS,YAAYlB,EAAK,SAAS;AAC1C,eAAAkB,EAAY,OAAOlB,EAAK;AAAA,IACjC,CACD;AACD,QAAI,CAACD;AACH,YAAM,IAAI,MAAM,qCAAqCmB,CAAW,MAAM;AAEjE,WAAAnB;AAAA,EAAA,CACR,GAEK+C,IAAmB,MAAM,QAAQ;AAAA,IACrCF,EAAgB;AAAA,MAAI,CAAC7C,MACnBgD;AAAA,QACE,MAAM;AAAA,UACJ,EAAE,QAAQL,EAAS;AAAA,UACnB,CAACM,GAAGC,MACF;;AAAAC,qBAAAA,IAAAA,EAAYnD,EAAO,MAAMkD,GAAK,EAAE,IAAI,IAAI,QAAQ,GAAA,CAAI,MAApDC,gBAAAA,EAAuD,eACpD;AAAA;AAAA,QACP;AAAA,QACAlB;AAAA,MAAA;AAAA,IACF;AAAA,EAEJ,GAEMmB,IAAY,MAAM;AAAA,IACtB,EAAE,QAAQT,EAAS;AAAA,IACnB,CAACM,GAAGC,MAAQH,EAAiB,IAAI,CAAC/C,MAAWA,EAAOkD,CAAG,CAAC;AAAA,EAC1D,GAEMG,IAAgBR,EAAgB;AAAA,IAAI,CAAC7C,MACzCG,EAAeH,EAAO,KAAK,MAAMI,EAAW,KAAK,KAAK;AAAA,EACxD,GAEMkD,IAAS,MAAM;AAAA,IACnB,EAAE,QAAQX,EAAS;AAAA,IACnB,CAACM,GAAGC,MACFJ,EAAa;AAAA,MAAI,CAAC9C,MAAA;;AAChBmD,iBAAAA,IAAAA,EAAYnD,EAAO,MAAMkD,GAAK,EAAE,IAAI,IAAI,QAAQ,IAAI,MAApDC,gBAAAA,EAAuD,eAAc;AAAA;AAAA,IAAA;AAAA,EAE3E,GAEMI,IAAwBH,EAAU,IAAI,CAACF,MAAQA,EAAI,KAAK,GAAG,CAAC,GAC5DM,IAAgBC,GAAiBF,CAAqB,GAEtDG,IAAgC;AAAA,IACpC,WAAWH;AAAA,IACX,eAAAF;AAAA,IACA,WAAWC;AAAA,IACX,cAAAV;AAAA,IACA,eAAAY;AAAA,EACF;AAEI,MAAAxB,EAAY,SAAS;AACvB,IAAA0B,EAAO,iBAAiBC,EAA8B;AAAA,MACpD,WAAWJ;AAAA,MACX,eAAAC;AAAA,IAAA,CACD;AAAA,WACQxB,EAAY,SAAS,UAAU;AACxC,UAAM4B,IAAelB,EAAM;AAAA,MAAK,CAAC,EAAE,MAAAzC,EACjC,MAAAA,EAAK,OAAO+B,EAAY;AAAA,IAC1B;AACA,QAAI,CAAC4B;AACH,YAAM,IAAI;AAAA,QACR,sCAAsC5B,EAAY,QAAQ;AAAA,MAC5D;AAEF,UAAM6B,IAAa,MAAM;AAAA,MACvB,EAAE,QAAQlB,EAAS;AAAA,MACnB,CAACM,GAAGC,MAAQ;;AACV,cAAMY,IAASC;AAAA,YACbZ,IAAAA,EAAYS,EAAa,MAAMV,GAAK,EAAE,IAAI,IAAI,QAAQ,IAAI,MAA1DC,gBAAAA,EACI,eACC;AAAA,QACP;AACA,eAAOa,EAAsBZ,EAAUF,CAAG,EAAE,CAAC,GAAGY,CAAM;AAAA,MAAA;AAAA,IAE1D,GACMR,IAAS5B,EAAmBkC,EAAa,KAAK,MAAMxD,EAAW,SAAS,WAAW,OAAO,KAAK,CAAC;AACtG,IAAAsD,EAAO,iBAAiBO,GAAkB;AAAA,MACxC,YAAAJ;AAAA,MACA,eAAahC,IAAA0B,EAAsB,GAAG,CAAC,MAA1B,gBAAA1B,EAA6B,WAAU;AAAA,MACpD,QAAAyB;AAAAA,IAAA,CACD;AAAA,EAAA;AAGI,SAAAI;AACT;AAEA,SAASrE,EAA0B6E,GAA+B;AAChE,QAAMC,IAAOC,EAAO,GACdC,IAAYD,EAAI,EAAI,GACpBE,IAAQF,EAAW;AACrB,MAAAG;AACJ,SAAO,CAACC,OACAC,EAAAD,GAAc,OAAOE,GAAQC,MAAe;AAC5C,QAAAhD,EAAY+C,GAAQC,CAAU,EAAG;AAC/B,UAAAC,IAAmBL,IAAY,OAAO;AACxC,QAAA;AACF,MAAAD,EAAM,QAAQ,QACdD,EAAU,QAAQ;AACZ,YAAAX,IAAS,MAAMQ,EAAGQ,CAAM;AAC9B,MAAIE,MAAqBL,MACvBJ,EAAK,QAAQT;AAAA,aAERmB,GAAK;AACZ,cAAQ,MAAMA,CAAG,GACbD,MAAqBL,MACjBD,EAAA,QAAQQ,GAAYD,CAAG;AAAA,IAC/B,UACA;AACA,MAAID,MAAqBL,MACvBF,EAAU,QAAQ;AAAA,IACpB;AAAA,EACF,GACC,EAAE,WAAW,IAAM,GACf,EAAE,MAAAF,GAAM,WAAAE,GAAW,OAAAC,EAAM;AAEpC;"}
+{"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  readAnnotation,\n  Annotation,\n  readAnnotationJson,\n} from '@platforma-sdk/model';\nimport { ref, watch } from 'vue';\nimport { highlightByChemicalProperties } from './chemical-properties';\nimport {\n  highlightByMarkup,\n  markupAlignedSequence,\n  parseMarkup,\n} from './markup';\nimport { multiSequenceAlignment } from './multi-sequence-alignment';\nimport { getResidueCounts } from './residue-counts';\nimport type { HighlightLegend, 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.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  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(\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  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({ type: 'column', id: columnId } satisfies PTableColumnId);\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  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.values()\n    .filter((column) =>\n      !!readAnnotationJson(column.spec, Annotation.Sequence.IsAnnotation)\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: readAnnotation(spec, Annotation.Label) ?? 'Unlabeled column',\n    }))\n    .toArray();\n}\n\nasync function getMultipleAlignmentData({\n  pFrame,\n  sequenceColumnIds,\n  labelColumnIds,\n  selection,\n  colorScheme,\n  alignmentParams,\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}): 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 (colorScheme.type === 'markup') {\n    secondaryEntry.push({ type: 'column', column: colorScheme.columnId });\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: ${id})`);\n        }\n        return column.spec.axesSpec\n          .map((spec) => canonicalizeJson(getAxisId(spec)));\n      }),\n    ),\n  )\n    .sort()\n    .map((id) => ({\n      column: { type: 'axis', id: parseJson(id) },\n      ascending: true,\n      naAndAbsentAreLeastValues: true,\n    }));\n\n  const request: CalculateTableDataRequest<PObjectId> = {\n    src: {\n      type: 'outer',\n      primary: primaryEntry,\n      secondary: secondaryEntry,\n    },\n    filters: [],\n    sorting,\n  };\n\n  const table = await pFrameDriver.calculateTableData(\n    pFrame,\n    JSON.parse(JSON.stringify(request)),\n    {\n      offset: 0,\n      // +1 is a hack to check whether the selection is over the limit\n      length: sequenceLimit + 1,\n    },\n  );\n\n  let rowCount = table?.[0].data.data.length ?? 0;\n  let exceedsLimit = false;\n  if (rowCount > sequenceLimit) {\n    rowCount = sequenceLimit;\n    exceedsLimit = true;\n  }\n\n  const sequenceColumns = sequenceColumnIds.map((columnId) => {\n    const column = table.find(({ spec }) => spec.id === columnId);\n    if (!column) {\n      throw new Error(`Couldn't find sequence column (ID: \\`${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: \\`${labelColumn}\\`).`);\n    }\n    return column;\n  });\n\n  const alignedSequences = await Promise.all(\n    sequenceColumns.map((column) =>\n      multiSequenceAlignment(\n        Array.from(\n          { length: rowCount },\n          (_, row) =>\n            pTableValue(column.data, row, { na: '', absent: '' })?.toString()\n            ?? '',\n        ),\n        alignmentParams,\n      ),\n    ),\n  );\n\n  const sequences = Array.from(\n    { length: rowCount },\n    (_, row) => alignedSequences.map((column) => column[row]),\n  );\n\n  const sequenceNames = sequenceColumns.map((column) =>\n    readAnnotation(column.spec.spec, Annotation.Label) ?? 'Unlabeled column',\n  );\n\n  const labels = Array.from(\n    { length: rowCount },\n    (_, row) =>\n      labelColumns.map((column) =>\n        pTableValue(column.data, row, { na: '', absent: '' })?.toString() ?? '',\n      ),\n  );\n\n  const concatenatedSequences = sequences.map((row) => row.join(' '));\n  const residueCounts = getResidueCounts(concatenatedSequences);\n\n  const result: MultipleAlignmentData = {\n    sequences: concatenatedSequences,\n    sequenceNames,\n    labelRows: labels,\n    exceedsLimit,\n    residueCounts,\n  };\n\n  if (colorScheme.type === 'chemical-properties') {\n    result.highlightImage = highlightByChemicalProperties({\n      sequences: concatenatedSequences,\n      residueCounts,\n    });\n  } else if (colorScheme.type === 'markup') {\n    const markupColumn = table.find(({ spec }) =>\n      spec.id === colorScheme.columnId,\n    );\n    if (!markupColumn) {\n      throw new Error(\n        `Couldn't find markup column (ID: \\`${colorScheme.columnId}\\`).`,\n      );\n    }\n    const markupRows = 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    const labels = readAnnotationJson(markupColumn.spec.spec, Annotation.Sequence.Annotation.Mapping) ?? {};\n    result.highlightImage = highlightByMarkup({\n      markupRows,\n      columnCount: concatenatedSequences.at(0)?.length ?? 0,\n      labels,\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 = false;\n        }\n      }\n    }, { immediate: true });\n    return { data, isLoading, error };\n  };\n}\n\ntype MultipleAlignmentData = {\n  sequences: string[];\n  sequenceNames: string[];\n  labelRows: string[][];\n  residueCounts: ResidueCounts;\n  highlightImage?: {\n    blob: Blob;\n    legend: HighlightLegend;\n  };\n  exceedsLimit: boolean;\n};\n\ntype OptionsWithDefaults<T> = {\n  options: ListOptionNormalized<T>[];\n  defaults: T[];\n};\n"],"names":["getPFrameDriver","getRawPlatformaInstance","sequenceLimit","useSequenceColumnsOptions","refreshOnDeepChange","getSequenceColumnsOptions","useLabelColumnsOptions","getLabelColumnsOptions","useMarkupColumnsOptions","getMarkupColumnsOptions","useMultipleAlignmentData","getMultipleAlignmentData","pFrame","sequenceColumnPredicate","options","column","spec","columnId","readAnnotation","Annotation","defaults","value","sequenceColumnIds","pFrameDriver","columns","optionMap","sequenceColumnsAxes","id","canonicalizeJson","getAxisId","axisIdJson","axisSpec","axisId","parseJson","labelColumn","isLabelColumn","matchAxisId","compatibleColumns","columnIdJson","label","sequenceColumn","readAnnotationJson","isJsonEqual","key","_a","labelColumnIds","selection","colorScheme","alignmentParams","linkerColumns","isLinkerColumn","filterColumn","createRowSelectionColumn","primaryEntry","secondaryEntry","sorting","request","table","rowCount","exceedsLimit","sequenceColumns","labelColumns","alignedSequences","multiSequenceAlignment","_","row","pTableValue","sequences","sequenceNames","labels","concatenatedSequences","residueCounts","getResidueCounts","result","highlightByChemicalProperties","markupColumn","markupRows","markup","parseMarkup","markupAlignedSequence","highlightByMarkup","cb","data","ref","isLoading","error","requestId","paramsGetter","watch","params","prevParams","currentRequestId","err","ensureError"],"mappings":";;;;;;;AAuCA,MAAMA,IAAkB,MAAMC,EAAA,EAA0B,cAE3CC,IAAgB,KAEhBC,KAA4BC;AAAA,EACvCC;AACF,GAEaC,KAAyBF;AAAA,EACpCG;AACF,GAEaC,KAA0BJ;AAAA,EACrCK;AACF,GAEaC,KAA2BN;AAAA,EACtCO;AACF;AAEA,eAAeN,GAA0B;AAAA,EACvC,QAAAO;AAAA,EACA,yBAAAC;AACF,GAGwD;AACtD,MAAI,CAACD,EAAQ;AAIb,QAAME,KADU,MADKd,EAAA,EACc,YAAYY,CAAM,GAC7B,OAAA,EACrB,OAAO,CAACG,MAAWF,EAAwBE,CAAM,CAAC,EAClD,IAAI,CAAC,EAAE,MAAAC,GAAM,UAAAC,SAAgB;AAAA,IAC5B,OAAOC,EAAeF,GAAMG,EAAW,KAAK,KAAK;AAAA,IACjD,OAAOF;AAAA,EAAA,EACP,EACD,QAAA,GACGG,IAAWN,EAAQ,IAAI,CAAC,EAAE,OAAAO,EAAA,MAAYA,CAAK;AACjD,SAAO,EAAE,SAAAP,GAAS,UAAAM,EAAA;AACpB;AAEA,eAAeb,GAAuB;AAAA,EACpC,QAAAK;AAAA,EACA,mBAAAU;AACF,GAG6D;AAC3D,MAAI,CAACV,KAAU,CAACU,EAAmB;AAEnC,QAAMC,IAAevB,EAAA,GACfwB,IAAU,MAAMD,EAAa,YAAYX,CAAM,GAC/Ca,wBAAgB,IAAA,GAEhBC,IAAsB,IAAI;AAAA,IAC9BJ,EAAkB,OAAA,EAAS,QAAQ,CAACK,MAAO;AACzC,YAAMZ,IAASS,EAAQ,KAAK,CAAC,EAAE,UAAAP,EAAA,MAAeA,MAAaU,CAAE;AAC7D,UAAI,CAACZ;AACH,cAAM,IAAI,MAAM,wCAAwCY,CAAE,MAAM;AAElE,aAAOZ,EAAO,KAAK,SAAS,OAAA,EACzB,IAAI,CAACC,MAAS,CAACY,EAAiBC,EAAUb,CAAI,CAAC,GAAGA,CAAI,CAAC;AAAA,IAC5D,CAAC;AAAA,EAAA;AAGH,aAAW,CAACc,GAAYC,CAAQ,KAAKL,EAAoB,WAAW;AAClE,UAAMM,IAASC,EAAUH,CAAU,GAC7BI,IAAcV,EAAQ;AAAA,MAAK,CAAC,EAAE,MAAAR,EAAA,MAClCmB,EAAcnB,CAAI,KAAKoB,EAAYJ,GAAQH,EAAUb,EAAK,SAAS,CAAC,CAAC,CAAC;AAAA,IAAA;AAExE,IAAAS,EAAU;AAAA,MACRS,IACIN,EAAiB,EAAE,MAAM,UAAU,IAAIM,EAAY,SAAA,CAAU,IAC7DN,EAAiB,EAAE,MAAM,QAAQ,IAAII,GAAQ;AAAA,MACjDd,EAAegB,KAAA,gBAAAA,EAAa,MAAMf,EAAW,KAAK,KAC/CD,EAAea,GAAUZ,EAAW,KAAK,KACzC;AAAA,IAAA;AAAA,EAEP;AAEA,QAAM,EAAE,MAAMkB,EAAA,IAAsB,MAAMd,EAAa,YAAYX,GAAQ;AAAA,IACzE,cAAc,CAAA;AAAA,IACd,gBAAgBc,EAAoB,KAAA,EACjC,IAAI,CAACI,MAAeG,EAAUH,CAAU,CAAC,EACzC,QAAA;AAAA,IACH,oBAAoB;AAAA,EAAA,CACrB;AAED,aAAW,EAAE,UAAAb,GAAU,MAAAD,EAAA,KAAUqB,GAAmB;AAClD,UAAMC,IAAeV,EAAiB,EAAE,MAAM,UAAU,IAAIX,GAAmC;AAC/F,IAAIQ,EAAU,IAAIa,CAAY,KAC9Bb,EAAU;AAAA,MACRa;AAAA,MACApB,EAAeF,GAAMG,EAAW,KAAK,KAAK;AAAA,IAAA;AAAA,EAE9C;AAEA,QAAML,IAAUW,EAAU,QAAA,EACvB,IAAI,CAAC,CAACJ,GAAOkB,CAAK,OAAO,EAAE,OAAAA,GAAO,OAAON,EAAUZ,CAAK,EAAA,EAAI,EAC5D,QAAA,GAEGD,IAAWN,EAAQ,OAAA,EACtB,OAAO,CAAC,EAAE,OAAAO,QAAY;AACrB,QAAIA,EAAM,SAAS,OAAQ,QAAO;AAClC,UAAMN,IAASS,EAAQ,KAAK,CAAC,EAAE,UAAAP,QAAeA,MAAaI,EAAM,EAAE;AACnE,WAAON,KAAUoB,EAAcpB,EAAO,IAAI;AAAA,EAC5C,CAAC,EACA,IAAI,CAAC,EAAE,OAAAM,EAAA,MAAYA,CAAK,EACxB,QAAA;AACH,SAAO,EAAE,SAAAP,GAAS,UAAAM,EAAA;AACpB;AAEA,eAAeX,GAAwB;AAAA,EACrC,QAAAG;AAAA,EACA,mBAAAU;AACF,GAG2D;AACzD,MAAI,CAACV,MAAUU,KAAA,gBAAAA,EAAmB,YAAW,EAAG;AAGhD,QAAME,IAAU,MADKxB,EAAA,EACc,YAAYY,CAAM,GAC/C4B,IAAiBhB,EAAQ;AAAA,IAAK,CAACT,MACnCA,EAAO,aAAaO,EAAkB,CAAC;AAAA,EAAA;AAEzC,MAAI,CAACkB;AACH,UAAM,IAAI;AAAA,MACR,wCAAwClB,EAAkB,CAAC,CAAC;AAAA,IAAA;AAGhE,SAAOE,EAAQ,SACZ;AAAA,IAAO,CAACT,MACP,CAAC,CAAC0B,EAAmB1B,EAAO,MAAMI,EAAW,SAAS,YAAY,KAC/DuB,EAAYF,EAAe,KAAK,UAAUzB,EAAO,KAAK,QAAQ,KAC9D,OAAO,QAAQyB,EAAe,KAAK,UAAU,CAAA,CAAE,EAAE,MAAM,CACxD,CAACG,GAAKtB,CAAK,MAAA;;AACR,eAAAuB,IAAA7B,EAAO,KAAK,WAAZ,gBAAA6B,EAAqBD,QAAStB;AAAA,KAAK;AAAA,EAAA,EACxC,IAAI,CAAC,EAAE,UAAAJ,GAAU,MAAAD,SAAY;AAAA,IAC7B,OAAOC;AAAA,IACP,OAAOC,EAAeF,GAAMG,EAAW,KAAK,KAAK;AAAA,EAAA,EACjD,EACD,QAAA;AACL;AAEA,eAAeR,GAAyB;AAAA,EACtC,QAAAC;AAAA,EACA,mBAAAU;AAAA,EACA,gBAAAuB;AAAA,EACA,WAAAC;AAAA,EACA,aAAAC;AAAA,EACA,iBAAAC;AACF,GAO+C;;AAC7C,MAAI,CAACpC,KAAU,EAACU,KAAA,QAAAA,EAAmB,WAAU,CAACuB,EAAgB;AAE9D,QAAMtB,IAAevB,EAAA,GACfwB,IAAU,MAAMD,EAAa,YAAYX,CAAM,GAC/CqC,IAAgBzB,EAAQ,OAAO,CAACT,MAAWmC,EAAenC,EAAO,IAAI,CAAC,GAEtEoC,IAAeC,EAAyB,EAAE,WAAAN,GAAW;AAG3D,MAAIO,IAAqC;AAAA,IACvC,MAAM;AAAA,IACN,SAAS/B,EAAkB,IAAI,CAACP,OAAY;AAAA,MAC1C,MAAM;AAAA,MACN,QAAAA;AAAA,IAAA,EACA;AAAA,EAAA;AAIJ,EAAIkC,EAAc,SAAS,MACzBI,IAAe;AAAA,IACb,MAAM;AAAA,IACN,SAASA;AAAA,IACT,WAAWJ,EAAc,IAAI,CAAC,EAAE,UAAAhC,SAAgB;AAAA,MAC9C,MAAM;AAAA,MACN,QAAQA;AAAA,IAAA,EACR;AAAA,EAAA,IAKFkC,MACFE,IAAe;AAAA,IACb,MAAM;AAAA,IACN,SAAS;AAAA,MACPA;AAAA,MACA;AAAA,QACE,MAAM;AAAA,QACN,QAAQF;AAAA,MAAA;AAAA,IACV;AAAA,EACF;AAKJ,QAAMG,IAAyCT,EAC5C,QAAQ,CAAC9B,MACJA,EAAO,SAAS,WAAiB,CAAA,IAC9B,EAAE,MAAM,UAAU,QAAQA,EAAO,GAAA,CACzC;AAGH,EAAIgC,EAAY,SAAS,YACvBO,EAAe,KAAK,EAAE,MAAM,UAAU,QAAQP,EAAY,UAAU;AAGtE,QAAMQ,IAA2B,MAAM;AAAA,IACrC,IAAI;AAAA,MACFjC,EAAkB,OAAA,EAAS,QAAQ,CAACK,MAAO;AACzC,cAAMZ,IAASS,EAAQ,KAAK,CAAC,EAAE,UAAAP,EAAA,MAAeA,MAAaU,CAAE;AAC7D,YAAI,CAACZ;AACH,gBAAM,IAAI,MAAM,sCAAsCY,CAAE,GAAG;AAE7D,eAAOZ,EAAO,KAAK,SAChB,IAAI,CAACC,MAASY,EAAiBC,EAAUb,CAAI,CAAC,CAAC;AAAA,MACpD,CAAC;AAAA,IAAA;AAAA,EACH,EAEC,KAAA,EACA,IAAI,CAACW,OAAQ;AAAA,IACZ,QAAQ,EAAE,MAAM,QAAQ,IAAIM,EAAUN,CAAE,EAAA;AAAA,IACxC,WAAW;AAAA,IACX,2BAA2B;AAAA,EAAA,EAC3B,GAEE6B,IAAgD;AAAA,IACpD,KAAK;AAAA,MACH,MAAM;AAAA,MACN,SAASH;AAAA,MACT,WAAWC;AAAA,IAAA;AAAA,IAEb,SAAS,CAAA;AAAA,IACT,SAAAC;AAAA,EAAA,GAGIE,IAAQ,MAAMlC,EAAa;AAAA,IAC/BX;AAAA,IACA,KAAK,MAAM,KAAK,UAAU4C,CAAO,CAAC;AAAA,IAClC;AAAA,MACE,QAAQ;AAAA;AAAA,MAER,QAAQtD,IAAgB;AAAA,IAAA;AAAA,EAC1B;AAGF,MAAIwD,KAAWD,KAAA,gBAAAA,EAAQ,GAAG,KAAK,KAAK,WAAU,GAC1CE,IAAe;AACnB,EAAID,IAAWxD,MACbwD,IAAWxD,GACXyD,IAAe;AAGjB,QAAMC,IAAkBtC,EAAkB,IAAI,CAACL,MAAa;AAC1D,UAAMF,IAAS0C,EAAM,KAAK,CAAC,EAAE,MAAAzC,QAAWA,EAAK,OAAOC,CAAQ;AAC5D,QAAI,CAACF;AACH,YAAM,IAAI,MAAM,wCAAwCE,CAAQ,MAAM;AAExE,WAAOF;AAAA,EACT,CAAC,GAEK8C,IAAehB,EAAe,IAAI,CAACX,MAAgB;AACvD,UAAMnB,IAAS0C,EAAM,KAAK,CAAC,EAAE,MAAAzC,QAAW;AACtC,UAAIkB,EAAY,SAAS,UAAUlB,EAAK,SAAS;AAC/C,eAAO0B,EAAYR,EAAY,IAAIlB,EAAK,EAAE;AAE5C,UAAIkB,EAAY,SAAS,YAAYlB,EAAK,SAAS;AACjD,eAAOkB,EAAY,OAAOlB,EAAK;AAAA,IAEnC,CAAC;AACD,QAAI,CAACD;AACH,YAAM,IAAI,MAAM,qCAAqCmB,CAAW,MAAM;AAExE,WAAOnB;AAAA,EACT,CAAC,GAEK+C,IAAmB,MAAM,QAAQ;AAAA,IACrCF,EAAgB;AAAA,MAAI,CAAC7C,MACnBgD;AAAA,QACE,MAAM;AAAA,UACJ,EAAE,QAAQL,EAAA;AAAA,UACV,CAACM,GAAGC,MAAA;;AACF,qBAAArB,IAAAsB,EAAYnD,EAAO,MAAMkD,GAAK,EAAE,IAAI,IAAI,QAAQ,GAAA,CAAI,MAApD,gBAAArB,EAAuD,eACpD;AAAA;AAAA,QAAA;AAAA,QAEPI;AAAA,MAAA;AAAA,IACF;AAAA,EACF,GAGImB,IAAY,MAAM;AAAA,IACtB,EAAE,QAAQT,EAAA;AAAA,IACV,CAACM,GAAGC,MAAQH,EAAiB,IAAI,CAAC/C,MAAWA,EAAOkD,CAAG,CAAC;AAAA,EAAA,GAGpDG,IAAgBR,EAAgB;AAAA,IAAI,CAAC7C,MACzCG,EAAeH,EAAO,KAAK,MAAMI,EAAW,KAAK,KAAK;AAAA,EAAA,GAGlDkD,IAAS,MAAM;AAAA,IACnB,EAAE,QAAQX,EAAA;AAAA,IACV,CAACM,GAAGC,MACFJ,EAAa;AAAA,MAAI,CAAC9C,MAAA;;AAChB,iBAAA6B,IAAAsB,EAAYnD,EAAO,MAAMkD,GAAK,EAAE,IAAI,IAAI,QAAQ,IAAI,MAApD,gBAAArB,EAAuD,eAAc;AAAA;AAAA,IAAA;AAAA,EACvE,GAGE0B,IAAwBH,EAAU,IAAI,CAACF,MAAQA,EAAI,KAAK,GAAG,CAAC,GAC5DM,IAAgBC,GAAiBF,CAAqB,GAEtDG,IAAgC;AAAA,IACpC,WAAWH;AAAA,IACX,eAAAF;AAAA,IACA,WAAWC;AAAA,IACX,cAAAV;AAAA,IACA,eAAAY;AAAA,EAAA;AAGF,MAAIxB,EAAY,SAAS;AACvB,IAAA0B,EAAO,iBAAiBC,EAA8B;AAAA,MACpD,WAAWJ;AAAA,MACX,eAAAC;AAAA,IAAA,CACD;AAAA,WACQxB,EAAY,SAAS,UAAU;AACxC,UAAM4B,IAAelB,EAAM;AAAA,MAAK,CAAC,EAAE,MAAAzC,EAAA,MACjCA,EAAK,OAAO+B,EAAY;AAAA,IAAA;AAE1B,QAAI,CAAC4B;AACH,YAAM,IAAI;AAAA,QACR,sCAAsC5B,EAAY,QAAQ;AAAA,MAAA;AAG9D,UAAM6B,IAAa,MAAM;AAAA,MACvB,EAAE,QAAQlB,EAAA;AAAA,MACV,CAACM,GAAGC,MAAQ;;AACV,cAAMY,IAASC;AAAA,YACblC,IAAAsB,EAAYS,EAAa,MAAMV,GAAK,EAAE,IAAI,IAAI,QAAQ,IAAI,MAA1D,gBAAArB,EACI,eACC;AAAA,QAAA;AAEP,eAAOmC,GAAsBZ,EAAUF,CAAG,EAAE,CAAC,GAAGY,CAAM;AAAA,MACxD;AAAA,IAAA,GAEIR,IAAS5B,EAAmBkC,EAAa,KAAK,MAAMxD,EAAW,SAAS,WAAW,OAAO,KAAK,CAAA;AACrG,IAAAsD,EAAO,iBAAiBO,GAAkB;AAAA,MACxC,YAAAJ;AAAA,MACA,eAAahC,IAAA0B,EAAsB,GAAG,CAAC,MAA1B,gBAAA1B,EAA6B,WAAU;AAAA,MACpD,QAAAyB;AAAAA,IAAA,CACD;AAAA,EACH;AAEA,SAAOI;AACT;AAEA,SAASrE,EAA0B6E,GAA+B;AAChE,QAAMC,IAAOC,EAAA,GACPC,IAAYD,EAAI,EAAI,GACpBE,IAAQF,EAAA;AACd,MAAIG;AACJ,SAAO,CAACC,OACNC,EAAMD,GAAc,OAAOE,GAAQC,MAAe;AAChD,QAAIhD,EAAY+C,GAAQC,CAAU,EAAG;AACrC,UAAMC,IAAmBL,IAAY,OAAA;AACrC,QAAI;AACF,MAAAD,EAAM,QAAQ,QACdD,EAAU,QAAQ;AAClB,YAAMX,IAAS,MAAMQ,EAAGQ,CAAM;AAC9B,MAAIE,MAAqBL,MACvBJ,EAAK,QAAQT;AAAA,IAEjB,SAASmB,GAAK;AACZ,cAAQ,MAAMA,CAAG,GACbD,MAAqBL,MACvBD,EAAM,QAAQQ,EAAYD,CAAG;AAAA,IAEjC,UAAA;AACE,MAAID,MAAqBL,MACvBF,EAAU,QAAQ;AAAA,IAEtB;AAAA,EACF,GAAG,EAAE,WAAW,IAAM,GACf,EAAE,MAAAF,GAAM,WAAAE,GAAW,OAAAC,EAAA;AAE9B;"}

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

@@ -1,2 +1 @@
 export { default as PlMultiSequenceAlignment } from './PlMultiSequenceAlignment.vue';
-//# sourceMappingURL=index.d.ts.map

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

@@ -14,4 +14,3 @@ export declare function highlightByMarkup({ markupRows, columnCount, labels }: {
     blob: Blob;
     legend: HighlightLegend;
 };
-//# sourceMappingURL=markup.d.ts.map

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

@@ -1 +1 @@
-{"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      .filter(([id]) => linesById.has(id))\n      .map(([id, label], index) => [\n        id,\n        {\n          label,\n          color: markupColors[index % markupColors.length],\n        },\n      ]),\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;AACxC,SAAA,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;AACG,WAAA;AAAA,MACL,IAAIA,EAAY;AAAA,MAChB,OAAAC;AAAA,MACA,QAAAC;AAAA,IACF;AAAA,EAAA,CACD;AACH;AAEgB,SAAAC,EACdC,GACAC,GACQ;AACR,QAAMC,IAAWF,EAAgB,MAAM,EAAE,EAAE;AAAA,IACzC,CAACG,GAAKC,GAAMC,OACND,MAAS,OAASD,EAAA,KAAKE,CAAK,GACzBF;AAAA,IAET,CAAA;AAAA,EACF;AAUO,SATUF,EAAO,IAAI,CAACK,MAAY;AACjC,UAAAT,IAAQK,EAASI,EAAQ,KAAK,GAC9BC,IAAML,EAASI,EAAQ,QAAQA,EAAQ,SAAS,CAAC,IAAI;AACpD,WAAA;AAAA,MACL,IAAIA,EAAQ;AAAA,MACZ,OAAAT;AAAA,MACA,QAAQU,IAAMV;AAAA,IAChB;AAAA,EAAA,CACD;AAEH;AAEO,SAASW,EACd,EAAE,YAAAC,GAAY,aAAAC,GAAa,QAAAC,KAKc;AACnC,QAAAC,wBAIK,IAAI;AACf,aAAW,CAAClB,GAAKO,CAAM,KAAKQ,EAAW;AACrC,eAAW,EAAE,IAAAI,GAAI,OAAAhB,GAAO,QAAAC,EAAA,KAAYG,GAAQ;AACtC,UAAAa,IAASF,EAAU,IAAIC,CAAE;AAC7B,MAAKC,KAAQF,EAAU,IAAIC,GAAIC,IAAS,EAAE,GAC1CA,EAAO,KAAK,EAAE,KAAApB,GAAK,OAAAG,GAAO,QAAAC,GAAQ;AAAA,IAAA;AAGtC,QAAMiB,IAA0B,OAAO;AAAA,IACrC,OAAO,QAAQJ,CAAM,EAClB,OAAO,CAAC,CAACE,CAAE,MAAMD,EAAU,IAAIC,CAAE,CAAC,EAClC,IAAI,CAAC,CAACA,GAAIG,CAAK,GAAGX,MAAU;AAAA,MAC3BQ;AAAA,MACA;AAAA,QACE,OAAAG;AAAA,QACA,OAAOC,EAAaZ,IAAQY,EAAa,MAAM;AAAA,MAAA;AAAA,IAElD,CAAA;AAAA,EACL;AAoBO,SAAA,EAAE,MAnBI,IAAI;AAAA,IACd,aAAY;AAEX,YAAM,oDADU,OAAOP,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;AACxB,YAAAC,IAAI,GAAGC,IAAI;AACf,mBAAW,EAAE,KAAA3B,GAAK,OAAAG,GAAO,QAAAC,EAAA,KAAYoB;AAC7B,gBAAA,IAAIrB,IAAQuB,CAAC,IAAI1B,IAAM,IAAI,IAAI2B,CAAC,IAAIvB,CAAM,IAChDsB,IAAIvB,IAAQC,GACZuB,IAAI3B,IAAM,IAAI;AAEV,cAAA;AAAA,MAAA;AAEF,YAAA;AAAA,IACR,EAAA,EAAK,QAAQ;AAAA,IACb,EAAE,MAAM,gBAAgB;AAAA,EAC1B,GACe,QAAAqB,EAAO;AACxB;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;"}
+{"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      .filter(([id]) => linesById.has(id))\n      .map(([id, label], index) => [\n        id,\n        {\n          label,\n          color: markupColors[index % markupColors.length],\n        },\n      ]),\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,OAAO,CAAC,CAACE,CAAE,MAAMD,EAAU,IAAIC,CAAE,CAAC,EAClC,IAAI,CAAC,CAACA,GAAIG,CAAK,GAAGX,MAAU;AAAA,MAC3BQ;AAAA,MACA;AAAA,QACE,OAAAG;AAAA,QACA,OAAOC,EAAaZ,IAAQY,EAAa,MAAM;AAAA,MAAA;AAAA,IACjD,CACD;AAAA,EAAA;AAqBL,SAAO,EAAE,MAnBI,IAAI;AAAA,IACd,aAAY;AAEX,YAAM,oDADU,OAAOP,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

@@ -1,4 +1,3 @@
 import { PlMultiSequenceAlignmentModel } from '@platforma-sdk/model';
 import { Ref } from 'vue';
 export declare function runMigrations(model: Ref<PlMultiSequenceAlignmentModel>): void;
-//# sourceMappingURL=migrations.d.ts.map

package/dist/components/PlMultiSequenceAlignment/migrations.js

@@ -1,7 +1,6 @@
-import "../../sdk/model/dist/index.js";
-import { parseJson as s } from "../../lib/model/common/dist/index.js";
+import { parseJson as s } from "@platforma-sdk/model";
 const e = 1;
-function l(r) {
+function a(r) {
   const t = i(r.value);
   try {
     if (t < 1) {
@@ -18,6 +17,6 @@ function i(r) {
   return r.version !== void 0 ? r.version : Object.keys(r).length ? 0 : e;
 }
 export {
-  l as runMigrations
+  a as runMigrations
 };
 //# sourceMappingURL=migrations.js.map

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

@@ -1 +1 @@
-{"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 = 1;\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  } 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","error"],"mappings":";;AAQA,MAAMA,IAAgB;AAEf,SAASC,EAAcC,GAA2C;AACjE,QAAAC,IAAiBC,EAAkBF,EAAM,KAAK;AAChD,MAAA;AACF,QAAIC,IAAiB,GAAG;AAChB,YAAAE,IAAoBH,EAAM,MAAM;AAGtC,MAAIG,MACIH,EAAA,MAAM,iBAAiBG,EAC1B,IAAI,CAACC,MAAOC,EAAUD,CAAE,CAAC;AAAA,IAC9B;AAAA,WAEKE,GAAO;AACd,YAAQ,MAAMA,CAAK,GACnBN,EAAM,QAAQ,CAAC;AAAA,EAAA,UACf;AACA,IAAAA,EAAM,MAAM,UAAUF;AAAA,EAAA;AAE1B;AAQA,SAASI,EAAkBF,GAAsC;AAC/D,SAAIA,EAAM,YAAY,SAAkBA,EAAM,UAC1C,OAAO,KAAKA,CAAK,EAAE,SAAe,IAC/BF;AACT;"}
+{"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 = 1;\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  } 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","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;AAAA,EACF,SAASE,GAAO;AACd,YAAQ,MAAMA,CAAK,GACnBN,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.d.ts

@@ -5,4 +5,3 @@ export declare const defaultAlignmentParams: {
     tgpe: number;
 };
 export declare function multiSequenceAlignment(sequences: string[], alignmentParams?: PlMultiSequenceAlignmentModel['alignmentParams']): Promise<string[]>;
-//# sourceMappingURL=multi-sequence-alignment.d.ts.map

package/dist/components/PlMultiSequenceAlignment/multi-sequence-alignment.js.map

@@ -1 +1 @@
-{"version":3,"file":"multi-sequence-alignment.js","sources":["../../../src/components/PlMultiSequenceAlignment/multi-sequence-alignment.ts"],"sourcesContent":["import Aioli from '@milaboratories/biowasm-tools';\nimport type { PlMultiSequenceAlignmentModel } from '@platforma-sdk/model';\nimport { objectHash } from '../../objectHash';\n\nconst cache = new Map<string, string[]>();\n\nexport const defaultAlignmentParams = {\n  gpo: 5.5,\n  gpe: 2.0,\n  tgpe: 1.0,\n} satisfies PlMultiSequenceAlignmentModel['alignmentParams'];\n\nconst getCli = (() => {\n  let cli: Aioli;\n  return async () => {\n    if (!cli) {\n      cli = await new Aioli(['kalign']);\n    }\n    return cli;\n  };\n})();\n\nexport async function multiSequenceAlignment(\n  sequences: string[],\n  alignmentParams: PlMultiSequenceAlignmentModel['alignmentParams'] =\n  defaultAlignmentParams,\n): Promise<string[]> {\n  if (sequences.length < 2) return sequences;\n  const hash = await objectHash([sequences, alignmentParams]);\n  let result = cache.get(hash);\n  if (result) return result;\n  const CLI = await getCli();\n  const params = {\n    input: `/shared/data/input-${hash}`,\n    output: `/shared/data/output-${hash}`,\n    ...alignmentParams,\n  };\n  CLI.mount(\n    new File(\n      sequences.map((sequence, index) => `>${index}\\n${sequence}\\n`),\n      // HACK: remove when mount will handle mounts properly\n      params.input.split('/').at(-1)!,\n    ),\n  );\n  await CLI.exec(`kalign ${\n    Object.entries(params)\n      .map(([key, value]) => `--${key} ${value}`)\n      .join(' ')\n  }`);\n  const output = await CLI.cat(params.output);\n  result = parseKalignOutput(output);\n  cache.set(hash, result);\n  return result;\n}\n\nfunction parseKalignOutput(output: string): string[] {\n  const result: string[] = [];\n  let index = -1;\n  for (let line of output.split('\\n')) {\n    line = line.trim();\n    if (!line) {\n      continue;\n    }\n    if (line.startsWith('>')) {\n      index += 1;\n      continue;\n    }\n    if (index >= 0) {\n      result[index] = (result[index] ?? '').concat(line);\n    }\n  }\n  return result;\n}\n\nif (import.meta.vitest) {\n  const { test, expect } = import.meta.vitest;\n\n  test('parseKalignOutput', () => {\n    const serialized = `some garbage\n[some more garbage]\n>1aab_\nGKGDPKKPRG-KMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKF\nEDMAKADKARYEREMKTY-IPPKGE---------\n>1j46_A\n-----MQDRV-KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPF\nFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK---\n>1k99_A\nMKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKY\nIQDFQREKQ-EFERNLARFREDHPDLIQNAKK--\n>2lef_A\n-----MHI---KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKY\nYELARKERQLHMQLYPGWSARDNYGKKKKRKREK`;\n\n    expect(parseKalignOutput(serialized)).toEqual([\n      'GKGDPKKPRG-KMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY-IPPKGE---------',\n      '-----MQDRV-KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK---',\n      'MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQ-EFERNLARFREDHPDLIQNAKK--',\n      '-----MHI---KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK',\n    ]);\n  });\n}\n"],"names":["cache","defaultAlignmentParams","getCli","cli","Aioli","multiSequenceAlignment","sequences","alignmentParams","hash","objectHash","result","CLI","params","sequence","index","key","value","output","parseKalignOutput","line"],"mappings":";;AAIA,MAAMA,wBAAY,IAAsB,GAE3BC,IAAyB;AAAA,EACpC,KAAK;AAAA,EACL,KAAK;AAAA,EACL,MAAM;AACR,GAEMC,IAAgB,uBAAA;AAChB,MAAAC;AACJ,SAAO,aACAA,MACHA,IAAM,MAAM,IAAIC,EAAM,CAAC,QAAQ,CAAC,IAE3BD;AAEX,GAAG;AAEmB,eAAAE,EACpBC,GACAC,IACAN,GACmB;AACf,MAAAK,EAAU,SAAS,EAAU,QAAAA;AACjC,QAAME,IAAO,MAAMC,EAAW,CAACH,GAAWC,CAAe,CAAC;AACtD,MAAAG,IAASV,EAAM,IAAIQ,CAAI;AAC3B,MAAIE,EAAe,QAAAA;AACb,QAAAC,IAAM,MAAMT,EAAO,GACnBU,IAAS;AAAA,IACb,OAAO,sBAAsBJ,CAAI;AAAA,IACjC,QAAQ,uBAAuBA,CAAI;AAAA,IACnC,GAAGD;AAAA,EACL;AACI,EAAAI,EAAA;AAAA,IACF,IAAI;AAAA,MACFL,EAAU,IAAI,CAACO,GAAUC,MAAU,IAAIA,CAAK;AAAA,EAAKD,CAAQ;AAAA,CAAI;AAAA;AAAA,MAE7DD,EAAO,MAAM,MAAM,GAAG,EAAE,GAAG,EAAE;AAAA,IAAA;AAAA,EAEjC,GACM,MAAAD,EAAI,KAAK,UACb,OAAO,QAAQC,CAAM,EAClB,IAAI,CAAC,CAACG,GAAKC,CAAK,MAAM,KAAKD,CAAG,IAAIC,CAAK,EAAE,EACzC,KAAK,GAAG,CACb,EAAE;AACF,QAAMC,IAAS,MAAMN,EAAI,IAAIC,EAAO,MAAM;AAC1C,SAAAF,IAASQ,EAAkBD,CAAM,GAC3BjB,EAAA,IAAIQ,GAAME,CAAM,GACfA;AACT;AAEA,SAASQ,EAAkBD,GAA0B;AACnD,QAAMP,IAAmB,CAAC;AAC1B,MAAII,IAAQ;AACZ,WAASK,KAAQF,EAAO,MAAM;AAAA,CAAI;AAEhC,QADAE,IAAOA,EAAK,KAAK,GACb,EAACA,GAGD;AAAA,UAAAA,EAAK,WAAW,GAAG,GAAG;AACf,QAAAL,KAAA;AACT;AAAA,MAAA;AAEF,MAAIA,KAAS,MACXJ,EAAOI,CAAK,KAAKJ,EAAOI,CAAK,KAAK,IAAI,OAAOK,CAAI;AAAA;AAG9C,SAAAT;AACT;"}
+{"version":3,"file":"multi-sequence-alignment.js","sources":["../../../src/components/PlMultiSequenceAlignment/multi-sequence-alignment.ts"],"sourcesContent":["import Aioli from '@milaboratories/biowasm-tools';\nimport type { PlMultiSequenceAlignmentModel } from '@platforma-sdk/model';\nimport { objectHash } from '../../objectHash';\n\nconst cache = new Map<string, string[]>();\n\nexport const defaultAlignmentParams = {\n  gpo: 5.5,\n  gpe: 2.0,\n  tgpe: 1.0,\n} satisfies PlMultiSequenceAlignmentModel['alignmentParams'];\n\nconst getCli = (() => {\n  let cli: Aioli;\n  return async () => {\n    if (!cli) {\n      cli = await new Aioli(['kalign']);\n    }\n    return cli;\n  };\n})();\n\nexport async function multiSequenceAlignment(\n  sequences: string[],\n  alignmentParams: PlMultiSequenceAlignmentModel['alignmentParams'] =\n  defaultAlignmentParams,\n): Promise<string[]> {\n  if (sequences.length < 2) return sequences;\n  const hash = await objectHash([sequences, alignmentParams]);\n  let result = cache.get(hash);\n  if (result) return result;\n  const CLI = await getCli();\n  const params = {\n    input: `/shared/data/input-${hash}`,\n    output: `/shared/data/output-${hash}`,\n    ...alignmentParams,\n  };\n  CLI.mount(\n    new File(\n      sequences.map((sequence, index) => `>${index}\\n${sequence}\\n`),\n      // HACK: remove when mount will handle mounts properly\n      params.input.split('/').at(-1)!,\n    ),\n  );\n  await CLI.exec(`kalign ${\n    Object.entries(params)\n      .map(([key, value]) => `--${key} ${value}`)\n      .join(' ')\n  }`);\n  const output = await CLI.cat(params.output);\n  result = parseKalignOutput(output);\n  cache.set(hash, result);\n  return result;\n}\n\nfunction parseKalignOutput(output: string): string[] {\n  const result: string[] = [];\n  let index = -1;\n  for (let line of output.split('\\n')) {\n    line = line.trim();\n    if (!line) {\n      continue;\n    }\n    if (line.startsWith('>')) {\n      index += 1;\n      continue;\n    }\n    if (index >= 0) {\n      result[index] = (result[index] ?? '').concat(line);\n    }\n  }\n  return result;\n}\n\nif (import.meta.vitest) {\n  const { test, expect } = import.meta.vitest;\n\n  test('parseKalignOutput', () => {\n    const serialized = `some garbage\n[some more garbage]\n>1aab_\nGKGDPKKPRG-KMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKF\nEDMAKADKARYEREMKTY-IPPKGE---------\n>1j46_A\n-----MQDRV-KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPF\nFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK---\n>1k99_A\nMKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKY\nIQDFQREKQ-EFERNLARFREDHPDLIQNAKK--\n>2lef_A\n-----MHI---KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKY\nYELARKERQLHMQLYPGWSARDNYGKKKKRKREK`;\n\n    expect(parseKalignOutput(serialized)).toEqual([\n      'GKGDPKKPRG-KMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY-IPPKGE---------',\n      '-----MQDRV-KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK---',\n      'MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQ-EFERNLARFREDHPDLIQNAKK--',\n      '-----MHI---KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK',\n    ]);\n  });\n}\n"],"names":["cache","defaultAlignmentParams","getCli","cli","Aioli","multiSequenceAlignment","sequences","alignmentParams","hash","objectHash","result","CLI","params","sequence","index","key","value","output","parseKalignOutput","line"],"mappings":";;AAIA,MAAMA,wBAAY,IAAA,GAELC,IAAyB;AAAA,EACpC,KAAK;AAAA,EACL,KAAK;AAAA,EACL,MAAM;AACR,GAEMC,IAAU,uBAAM;AACpB,MAAIC;AACJ,SAAO,aACAA,MACHA,IAAM,MAAM,IAAIC,EAAM,CAAC,QAAQ,CAAC,IAE3BD;AAEX,GAAA;AAEA,eAAsBE,EACpBC,GACAC,IACAN,GACmB;AACnB,MAAIK,EAAU,SAAS,EAAG,QAAOA;AACjC,QAAME,IAAO,MAAMC,EAAW,CAACH,GAAWC,CAAe,CAAC;AAC1D,MAAIG,IAASV,EAAM,IAAIQ,CAAI;AAC3B,MAAIE,EAAQ,QAAOA;AACnB,QAAMC,IAAM,MAAMT,EAAA,GACZU,IAAS;AAAA,IACb,OAAO,sBAAsBJ,CAAI;AAAA,IACjC,QAAQ,uBAAuBA,CAAI;AAAA,IACnC,GAAGD;AAAA,EAAA;AAEL,EAAAI,EAAI;AAAA,IACF,IAAI;AAAA,MACFL,EAAU,IAAI,CAACO,GAAUC,MAAU,IAAIA,CAAK;AAAA,EAAKD,CAAQ;AAAA,CAAI;AAAA;AAAA,MAE7DD,EAAO,MAAM,MAAM,GAAG,EAAE,GAAG,EAAE;AAAA,IAAA;AAAA,EAC/B,GAEF,MAAMD,EAAI,KAAK,UACb,OAAO,QAAQC,CAAM,EAClB,IAAI,CAAC,CAACG,GAAKC,CAAK,MAAM,KAAKD,CAAG,IAAIC,CAAK,EAAE,EACzC,KAAK,GAAG,CACb,EAAE;AACF,QAAMC,IAAS,MAAMN,EAAI,IAAIC,EAAO,MAAM;AAC1C,SAAAF,IAASQ,EAAkBD,CAAM,GACjCjB,EAAM,IAAIQ,GAAME,CAAM,GACfA;AACT;AAEA,SAASQ,EAAkBD,GAA0B;AACnD,QAAMP,IAAmB,CAAA;AACzB,MAAII,IAAQ;AACZ,WAASK,KAAQF,EAAO,MAAM;AAAA,CAAI;AAEhC,QADAE,IAAOA,EAAK,KAAA,GACR,EAACA,GAGL;AAAA,UAAIA,EAAK,WAAW,GAAG,GAAG;AACxB,QAAAL,KAAS;AACT;AAAA,MACF;AACA,MAAIA,KAAS,MACXJ,EAAOI,CAAK,KAAKJ,EAAOI,CAAK,KAAK,IAAI,OAAOK,CAAI;AAAA;AAGrD,SAAOT;AACT;"}

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

@@ -1,3 +1,2 @@
 import { ResidueCounts } from './types';
 export declare function getResidueCounts(alignedSequences: string[]): ResidueCounts;
-//# sourceMappingURL=residue-counts.d.ts.map