@milaboratories/multi-sequence-alignment 1.45.0

package/dist/cell-size.d.ts

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+export declare const cellSize: {
+    inline: number;
+    block: number;
+};

package/dist/cell-size.js

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+const e = {
+  inline: 20,
+  block: 24
+};
+export {
+  e as cellSize
+};
+//# sourceMappingURL=cell-size.js.map

package/dist/cell-size.js.map

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+{"version":3,"file":"cell-size.js","sources":["../src/cell-size.ts"],"sourcesContent":["export const cellSize = {\n  inline: 20,\n  block: 24,\n};\n"],"names":["cellSize"],"mappings":"AAAO,MAAMA,IAAW;AAAA,EACtB,QAAQ;AAAA,EACR,OAAO;AACT;"}

package/dist/chemical-properties.d.ts

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+import { HighlightLegend, ResidueCounts } from './types';
+export declare function highlightByChemicalProperties({ sequences, residueCounts }: {
+    sequences: string[];
+    residueCounts: ResidueCounts;
+}): {
+    blob: Blob;
+    legend: HighlightLegend;
+};
+declare const chemicalPropertiesColorScheme: {
+    hydrophobic: {
+        label: string;
+        color: string;
+    };
+    positiveCharge: {
+        label: string;
+        color: string;
+    };
+    negativeCharge: {
+        label: string;
+        color: string;
+    };
+    polar: {
+        label: string;
+        color: string;
+    };
+    cysteine: {
+        label: string;
+        color: string;
+    };
+    glycine: {
+        label: string;
+        color: string;
+    };
+    proline: {
+        label: string;
+        color: string;
+    };
+    aromatic: {
+        label: string;
+        color: string;
+    };
+};
+export type ChemicalCategory = keyof typeof chemicalPropertiesColorScheme;
+export {};

package/dist/chemical-properties.js

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+function E({ sequences: t, residueCounts: g }) {
+  var C, h, u;
+  const i = [], c = v({
+    residueCounts: g,
+    rowCount: t.length
+  }), n = ((C = t.at(0)) == null ? void 0 : C.length) ?? 0, l = t.length;
+  for (let e = 0; e < n; e += 1)
+    for (let o = 0; o < l; o += 1) {
+      const F = t[o][e], d = (u = (h = c.at(e)) == null ? void 0 : h.find(({ residues: a }) => a.includes(F))) == null ? void 0 : u.category;
+      if (!d) continue;
+      const r = i.at(-1);
+      r && r.category === d && r.column === e && r.start + r.length === o ? r.length += 1 : i.push({ category: d, column: e, start: o, length: 1 });
+    }
+  const s = Map.groupBy(i, ({ category: e }) => e), y = new Blob(
+    (function* () {
+      var o;
+      yield `<svg xmlns="http://www.w3.org/2000/svg" viewBox="${`0 0 ${n * 2} ${l}`}" stroke-width="2" preserveAspectRatio="none">`;
+      for (const [F, d] of s) {
+        const r = (o = P[F]) == null ? void 0 : o.color;
+        if (!r) continue;
+        yield `<path stroke="${r}" d="`;
+        let a = 0, A = 0;
+        for (const { column: m, start: b, length: f } of d)
+          yield `m${m * 2 + 1 - a},${b - A}v${f}`, a = m * 2 + 1, A = b + f;
+        yield '"/>';
+      }
+      yield "</svg>";
+    })().toArray(),
+    { type: "image/svg+xml" }
+  ), p = Object.fromEntries(
+    Object.entries(P).filter(([e]) => s.has(e))
+  );
+  return { blob: y, legend: p };
+}
+const v = ({ residueCounts: t, rowCount: g }) => t.map((i) => {
+  const c = /* @__PURE__ */ new Set();
+  return D.filter(
+    ({ residues: n, rules: l }) => n.split("").some((s) => s in i) && (!l || l.split("").map(
+      (s) => [s, w[s]]
+    ).some(([s, { residues: y, threshold: p }]) => {
+      if (c.has(s)) return !0;
+      const h = y.split("").reduce((u, e) => u + (i[e] ?? 0), 0) >= g * p;
+      return h && c.add(s), h;
+    }))
+  );
+}), P = {
+  hydrophobic: {
+    label: "Hydrophobic",
+    color: "#99CCFF"
+  },
+  positiveCharge: {
+    label: "Positive Charged",
+    color: "#FFA2A3"
+  },
+  negativeCharge: {
+    label: "Negative Charged",
+    color: "#C1ADFF"
+  },
+  polar: {
+    label: "Polar",
+    color: "#99E099"
+  },
+  cysteine: {
+    label: "Cysteines",
+    color: "#FAAAFA"
+  },
+  glycine: {
+    label: "Glycines",
+    color: "#F7BC5D"
+  },
+  proline: {
+    label: "Prolines",
+    color: "#FFFF8F"
+  },
+  aromatic: {
+    label: "Aromatic",
+    color: "#A2F5FA"
+  }
+}, w = {
+  "%": { residues: "WLVIMAFCYHP", threshold: 0.6 },
+  "#": { residues: "WLVIMAFCYHP", threshold: 0.8 },
+  "-": { residues: "ED", threshold: 0.5 },
+  "+": { residues: "KR", threshold: 0.6 },
+  g: { residues: "G", threshold: 0.5 },
+  n: { residues: "N", threshold: 0.5 },
+  q: { residues: "QE", threshold: 0.5 },
+  p: { residues: "P", threshold: 0.5 },
+  t: { residues: "TS", threshold: 0.5 },
+  A: { residues: "A", threshold: 0.85 },
+  C: { residues: "C", threshold: 0.85 },
+  D: { residues: "D", threshold: 0.85 },
+  E: { residues: "E", threshold: 0.85 },
+  F: { residues: "F", threshold: 0.85 },
+  G: { residues: "G", threshold: 0.85 },
+  H: { residues: "H", threshold: 0.85 },
+  I: { residues: "I", threshold: 0.85 },
+  K: { residues: "K", threshold: 0.85 },
+  L: { residues: "L", threshold: 0.85 },
+  M: { residues: "M", threshold: 0.85 },
+  N: { residues: "N", threshold: 0.85 },
+  P: { residues: "P", threshold: 0.85 },
+  Q: { residues: "Q", threshold: 0.85 },
+  R: { residues: "R", threshold: 0.85 },
+  S: { residues: "S", threshold: 0.85 },
+  T: { residues: "T", threshold: 0.85 },
+  V: { residues: "V", threshold: 0.85 },
+  W: { residues: "W", threshold: 0.85 },
+  Y: { residues: "Y", threshold: 0.85 }
+}, D = [
+  { residues: "G", category: "glycine", rules: "" },
+  { residues: "P", category: "proline", rules: "" },
+  { residues: "T", category: "polar", rules: "tST%#" },
+  { residues: "S", category: "polar", rules: "tST#" },
+  { residues: "N", category: "polar", rules: "nND" },
+  { residues: "Q", category: "polar", rules: "qQE+KR" },
+  // criteria below has to go before the other criteria for C,
+  // otherwise it will never match
+  { residues: "C", category: "cysteine", rules: "C" },
+  { residues: "WLVIMF", category: "hydrophobic", rules: "%#ACFHILMVWYPp" },
+  // below there was an 's' rule too,
+  // but no definition of such rule was provided
+  { residues: "A", category: "hydrophobic", rules: "%#ACFHILMVWYPpTSG" },
+  { residues: "C", category: "hydrophobic", rules: "%#AFHILMVWYSPp" },
+  { residues: "HY", category: "aromatic", rules: "%#ACFHILMVWYPp" },
+  { residues: "E", category: "negativeCharge", rules: "-DEqQ" },
+  { residues: "D", category: "negativeCharge", rules: "-DEnN" },
+  { residues: "KR", category: "positiveCharge", rules: "+KRQ" }
+];
+export {
+  E as highlightByChemicalProperties
+};
+//# sourceMappingURL=chemical-properties.js.map

package/dist/chemical-properties.js.map

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+{"version":3,"file":"chemical-properties.js","sources":["../src/chemical-properties.ts"],"sourcesContent":["import type { HighlightLegend, ResidueCounts } from './types';\n\nexport function highlightByChemicalProperties(\n  { sequences, residueCounts }: {\n    sequences: string[];\n    residueCounts: ResidueCounts;\n  },\n): { blob: Blob; legend: HighlightLegend } {\n  const lines: {\n    category: ChemicalCategory;\n    column: number;\n    start: number;\n    length: number;\n  }[] = [];\n  const chemicalProperties = getAlignmentChemicalProperties({\n    residueCounts,\n    rowCount: sequences.length,\n  });\n  const width = sequences.at(0)?.length ?? 0;\n  const height = sequences.length;\n  for (let column = 0; column < width; column += 1) {\n    for (let row = 0; row < height; row += 1) {\n      const residue = sequences[row][column];\n      const category = chemicalProperties\n        .at(column)\n        ?.find(({ residues }) => residues.includes(residue))\n        ?.category;\n      if (!category) continue;\n      const lastLine = lines.at(-1);\n      if (\n        lastLine\n        && lastLine.category === category\n        && lastLine.column === column\n        && lastLine.start + lastLine.length === row\n      ) {\n        lastLine.length += 1;\n      } else {\n        lines.push({ category, column, start: row, length: 1 });\n      }\n    }\n  }\n  const linesByCategory = Map.groupBy(lines, ({ category }) => category);\n  const blob = new Blob(\n    (function*() {\n      const viewBox = `0 0 ${width * 2} ${height}`;\n      yield `<svg xmlns=\"http://www.w3.org/2000/svg\" viewBox=\"${viewBox}\" stroke-width=\"2\" preserveAspectRatio=\"none\">`;\n      for (const [category, lines] of linesByCategory) {\n        const color = chemicalPropertiesColorScheme[category]?.color;\n        if (!color) continue;\n        yield `<path stroke=\"${color}\" d=\"`;\n        let x = 0, y = 0;\n        for (const { column, start, length } of lines) {\n          yield `m${column * 2 + 1 - x},${start - y}v${length}`;\n          x = column * 2 + 1;\n          y = start + length;\n        }\n        yield '\"/>';\n      }\n      yield '</svg>';\n    })().toArray(),\n    { type: 'image/svg+xml' },\n  );\n  const legend = Object.fromEntries(\n    Object.entries(chemicalPropertiesColorScheme)\n      .filter(([color]) => linesByCategory.has(color as ChemicalCategory)),\n  );\n  return { blob, legend };\n}\n\nconst getAlignmentChemicalProperties = (\n  { residueCounts, rowCount }: {\n    residueCounts: ResidueCounts;\n    rowCount: number;\n  },\n): ColumnChemicalProperties[] =>\n  residueCounts.map((column) => {\n    const matchedRules = new Set<string>();\n    return categoryCriterion.filter(({ residues, rules }) =>\n      residues.split('').some((residue) => residue in column)\n      && (!rules || rules.split('').map((ruleName) =>\n        [ruleName, ruleDefinitions[ruleName as RuleName]] as const,\n      ).some(([ruleName, { residues, threshold }]) => {\n        if (matchedRules.has(ruleName)) return true;\n        const groupCount = residues.split('')\n          .reduce((acc, residue) => acc + (column[residue] ?? 0), 0);\n        const matches = groupCount >= rowCount * threshold;\n        if (matches) matchedRules.add(ruleName);\n        return matches;\n      })),\n    );\n  });\n\ntype ColumnChemicalProperties = {\n  residues: string;\n  category: ChemicalCategory;\n}[];\n\nconst chemicalPropertiesColorScheme = {\n  hydrophobic: {\n    label: 'Hydrophobic',\n    color: '#99CCFF',\n  },\n  positiveCharge: {\n    label: 'Positive Charged',\n    color: '#FFA2A3',\n  },\n  negativeCharge: {\n    label: 'Negative Charged',\n    color: '#C1ADFF',\n  },\n  polar: {\n    label: 'Polar',\n    color: '#99E099',\n  },\n  cysteine: {\n    label: 'Cysteines',\n    color: '#FAAAFA',\n  },\n  glycine: {\n    label: 'Glycines',\n    color: '#F7BC5D',\n  },\n  proline: {\n    label: 'Prolines',\n    color: '#FFFF8F',\n  },\n  aromatic: {\n    label: 'Aromatic',\n    color: '#A2F5FA',\n  },\n} satisfies HighlightLegend;\n\nexport type ChemicalCategory = keyof typeof chemicalPropertiesColorScheme;\n\n/*\n * Below taken mostly from\n * https://www.rbvi.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/multalignviewer/colprot.par}\n */\n\nconst ruleDefinitions = {\n  '%': { residues: 'WLVIMAFCYHP', threshold: 0.6 },\n  '#': { residues: 'WLVIMAFCYHP', threshold: 0.8 },\n  '-': { residues: 'ED', threshold: 0.5 },\n  '+': { residues: 'KR', threshold: 0.6 },\n  'g': { residues: 'G', threshold: 0.5 },\n  'n': { residues: 'N', threshold: 0.5 },\n  'q': { residues: 'QE', threshold: 0.5 },\n  'p': { residues: 'P', threshold: 0.5 },\n  't': { residues: 'TS', threshold: 0.5 },\n  'A': { residues: 'A', threshold: 0.85 },\n  'C': { residues: 'C', threshold: 0.85 },\n  'D': { residues: 'D', threshold: 0.85 },\n  'E': { residues: 'E', threshold: 0.85 },\n  'F': { residues: 'F', threshold: 0.85 },\n  'G': { residues: 'G', threshold: 0.85 },\n  'H': { residues: 'H', threshold: 0.85 },\n  'I': { residues: 'I', threshold: 0.85 },\n  'K': { residues: 'K', threshold: 0.85 },\n  'L': { residues: 'L', threshold: 0.85 },\n  'M': { residues: 'M', threshold: 0.85 },\n  'N': { residues: 'N', threshold: 0.85 },\n  'P': { residues: 'P', threshold: 0.85 },\n  'Q': { residues: 'Q', threshold: 0.85 },\n  'R': { residues: 'R', threshold: 0.85 },\n  'S': { residues: 'S', threshold: 0.85 },\n  'T': { residues: 'T', threshold: 0.85 },\n  'V': { residues: 'V', threshold: 0.85 },\n  'W': { residues: 'W', threshold: 0.85 },\n  'Y': { residues: 'Y', threshold: 0.85 },\n};\n\ntype RuleName = keyof typeof ruleDefinitions;\n\nconst categoryCriterion: Criteria[] = [\n  { residues: 'G', category: 'glycine', rules: '' },\n  { residues: 'P', category: 'proline', rules: '' },\n  { residues: 'T', category: 'polar', rules: 'tST%#' },\n  { residues: 'S', category: 'polar', rules: 'tST#' },\n  { residues: 'N', category: 'polar', rules: 'nND' },\n  { residues: 'Q', category: 'polar', rules: 'qQE+KR' },\n  // criteria below has to go before the other criteria for C,\n  // otherwise it will never match\n  { residues: 'C', category: 'cysteine', rules: 'C' },\n  { residues: 'WLVIMF', category: 'hydrophobic', rules: '%#ACFHILMVWYPp' },\n  // below there was an 's' rule too,\n  // but no definition of such rule was provided\n  { residues: 'A', category: 'hydrophobic', rules: '%#ACFHILMVWYPpTSG' },\n  { residues: 'C', category: 'hydrophobic', rules: '%#AFHILMVWYSPp' },\n  { residues: 'HY', category: 'aromatic', rules: '%#ACFHILMVWYPp' },\n  { residues: 'E', category: 'negativeCharge', rules: '-DEqQ' },\n  { residues: 'D', category: 'negativeCharge', rules: '-DEnN' },\n  { residues: 'KR', category: 'positiveCharge', rules: '+KRQ' },\n];\n\ntype Criteria = {\n  residues: string;\n  category: ChemicalCategory;\n  rules: 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package/dist/data.d.ts

@@ -0,0 +1,61 @@
+import { ListOptionNormalized } from '@milaboratories/uikit';
+import { PColumnIdAndSpec, PFrameHandle, PlMultiSequenceAlignmentColorSchemeOption, PlMultiSequenceAlignmentSettings, PlSelectionModel, PObjectId, PTableColumnId } from '@platforma-sdk/model';
+import { HighlightLegend, ResidueCounts } from './types';
+import type * as PhylogeneticTreeWorker from './phylogenetic-tree.worker';
+export declare const SEQUENCE_LIMIT = 1000;
+export declare const useSequenceColumnsOptions: (paramsGetter: () => {
+    pFrame: PFrameHandle | undefined;
+    sequenceColumnPredicate: (column: PColumnIdAndSpec) => boolean;
+}) => {
+    data: import('vue').Ref<OptionsWithDefaults<PObjectId> | undefined, OptionsWithDefaults<PObjectId> | undefined>;
+    isLoading: import('vue').Ref<boolean, boolean>;
+    error: import('vue').Ref<Error | undefined, Error | undefined>;
+};
+export declare const useLabelColumnsOptions: (paramsGetter: () => {
+    pFrame: PFrameHandle | undefined;
+    sequenceColumnIds: PObjectId[] | undefined;
+}) => {
+    data: import('vue').Ref<OptionsWithDefaults<PTableColumnId> | undefined, OptionsWithDefaults<PTableColumnId> | undefined>;
+    isLoading: import('vue').Ref<boolean, boolean>;
+    error: import('vue').Ref<Error | undefined, Error | undefined>;
+};
+export declare const useMarkupColumnsOptions: (paramsGetter: () => {
+    pFrame: PFrameHandle | undefined;
+    sequenceColumnIds: PObjectId[] | undefined;
+}) => {
+    data: import('vue').Ref<ListOptionNormalized<PObjectId[]>[] | undefined, ListOptionNormalized<PObjectId[]>[] | undefined>;
+    isLoading: import('vue').Ref<boolean, boolean>;
+    error: import('vue').Ref<Error | undefined, Error | undefined>;
+};
+export declare const useMultipleAlignmentData: (paramsGetter: () => {
+    pFrame: PFrameHandle | undefined;
+    sequenceColumnIds: PObjectId[] | undefined;
+    labelColumnIds: PTableColumnId[] | undefined;
+    selection: PlSelectionModel | undefined;
+    colorScheme: PlMultiSequenceAlignmentColorSchemeOption;
+    alignmentParams: PlMultiSequenceAlignmentSettings["alignmentParams"];
+    shouldBuildPhylogeneticTree: boolean;
+}) => {
+    data: import('vue').Ref<MultipleAlignmentData | undefined, MultipleAlignmentData | undefined>;
+    isLoading: import('vue').Ref<boolean, boolean>;
+    error: import('vue').Ref<Error | undefined, Error | undefined>;
+};
+type MultipleAlignmentData = {
+    sequences: {
+        name: string;
+        rows: string[];
+        residueCounts: ResidueCounts;
+        highlightImageUrl?: string;
+    }[];
+    labels: {
+        rows: string[];
+    }[];
+    highlightLegend?: HighlightLegend;
+    phylogeneticTree?: PhylogeneticTreeWorker.TreeNodeData[];
+    exceedsLimit: boolean;
+};
+type OptionsWithDefaults<T> = {
+    options: ListOptionNormalized<T>[];
+    defaults: T[];
+};
+export {};

package/dist/data.js

@@ -0,0 +1,370 @@
+import { isJsonEqual as O } from "./node_modules/.pnpm/@milaboratories_helpers@1.12.0/node_modules/@milaboratories/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 "@platforma-sdk/ui-vue";
+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