@platforma-sdk/ui-vue 1.41.19 → 1.42.1

package/dist/components/PlMultiSequenceAlignment/chemical-properties.js

@@ -1,4 +1,49 @@
-const f = {
+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"
@@ -31,136 +76,57 @@ const f = {
     label: "Aromatic",
     color: "#A2F5FA"
   }
-};
-function m({ sequences: e, residueCounts: c, colorMap: s }) {
-  var t, g, l, h;
-  const o = new OffscreenCanvas(
-    ((t = e[0]) == null ? void 0 : t.length) ?? 0,
-    e.length
-  ), r = o.getContext("2d"), i = y({
-    residueCounts: c,
-    rowCount: e.length
-  });
-  for (const [n, d] of e.entries())
-    for (const [a, p] of d.split("").entries()) {
-      const u = (l = (g = i.at(a)) == null ? void 0 : g.find(({ residues: C }) => C.includes(p))) == null ? void 0 : l.category;
-      !u || !((h = s[u]) != null && h.color) || (r.fillStyle = s[u].color, r.fillRect(a, n, 1, 1));
-    }
-  return o.convertToBlob();
-}
-const y = ({ residueCounts: e, rowCount: c }) => (
-  // for every column in a residue counts table
-  // (e.g. table = [{ A: 3, R: 5, Q: 1}, { E: 4, T: 2 }, ...])
-  e.map((s) => (
-    // find all matching criterion
-    F.filter(
-      ({ rules: o }) => (
-        // by matching at least one rule
-        o.some(
-          ({ groups: r, threshold: i }) => (
-            // where at least one residue group
-            r.some((t) => t.split("").reduce(
-              (l, h) => l + (s[h] ?? 0),
-              0
-            ) > c * i)
-          )
-        )
-      )
-    ).map(({ residues: o, category: r }) => ({ residues: o, category: r }))
-  ))
-), F = [
-  {
-    residues: "ACILMFWV",
-    category: "hydrophobic",
-    rules: [
-      { groups: ["WLVIMAFCYHP"], threshold: 0.6 }
-    ]
-  },
-  {
-    residues: "KR",
-    category: "positiveCharge",
-    rules: [
-      { groups: ["KR"], threshold: 0.6 },
-      { groups: [..."KRQ"], threshold: 0.8 }
-    ]
-  },
-  {
-    residues: "E",
-    category: "negativeCharge",
-    rules: [
-      { groups: ["KR"], threshold: 0.6 },
-      { groups: ["QE"], threshold: 0.5 },
-      { groups: ["ED"], threshold: 0.5 },
-      { groups: [..."EQD"], threshold: 0.85 }
-    ]
-  },
-  {
-    residues: "D",
-    category: "negativeCharge",
-    rules: [
-      { groups: ["KR"], threshold: 0.6 },
-      { groups: [..."DEN"], threshold: 0.85 },
-      { groups: ["ED"], threshold: 0.5 }
-    ]
-  },
-  {
-    residues: "N",
-    category: "polar",
-    rules: [
-      { groups: ["N"], threshold: 0.5 },
-      { groups: [..."ND"], threshold: 0.85 }
-    ]
-  },
-  {
-    residues: "Q",
-    category: "polar",
-    rules: [
-      { groups: ["KR"], threshold: 0.6 },
-      { groups: ["QE"], threshold: 0.5 },
-      { groups: [..."QTKR"], threshold: 0.85 }
-    ]
-  },
-  {
-    residues: "ST",
-    category: "polar",
-    rules: [
-      { groups: ["WLVIMAFCYHP"], threshold: 0.6 },
-      { groups: ["TS"], threshold: 0.5 },
-      { groups: [..."ST"], threshold: 0.85 }
-    ]
-  },
-  {
-    residues: "C",
-    category: "cysteine",
-    rules: [
-      { groups: ["C"], threshold: 0.85 }
-    ]
-  },
-  {
-    residues: "G",
-    category: "glycine",
-    rules: [
-      { groups: ["G"], threshold: 0 }
-    ]
-  },
-  {
-    residues: "P",
-    category: "proline",
-    rules: [
-      { groups: ["P"], threshold: 0 }
-    ]
-  },
-  {
-    residues: "HY",
-    category: "aromatic",
-    rules: [
-      { groups: ["WLVIMAFCYHP"], threshold: 0.6 },
-      { groups: [..."WYACPQFHILMV"], threshold: 0.85 }
-    ]
-  }
+}, 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 {
-  f as chemicalPropertiesColorMap,
-  m as colorizeSequencesByChemicalProperties
+  E as highlightByChemicalProperties
 };
 //# sourceMappingURL=chemical-properties.js.map

package/dist/components/PlMultiSequenceAlignment/chemical-properties.js.map

@@ -1 +1 @@
-{"version":3,"file":"chemical-properties.js","sources":["../../../src/components/PlMultiSequenceAlignment/chemical-properties.ts"],"sourcesContent":["import type { ColorMap, ResidueCounts } from './types';\n\nexport const chemicalPropertiesColorMap: ColorMap = {\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};\n\nexport type ChemicalCategory = keyof typeof chemicalPropertiesColorMap;\n\nexport function colorizeSequencesByChemicalProperties(\n  { sequences, residueCounts, colorMap }: {\n    sequences: string[];\n    residueCounts: ResidueCounts;\n    colorMap: ColorMap;\n  },\n): Promise<Blob> {\n  const canvas = new OffscreenCanvas(\n    sequences[0]?.length ?? 0,\n    sequences.length,\n  );\n  const context = canvas.getContext('2d')!;\n  const chemicalProperties = getAlignmentChemicalProperties({\n    residueCounts,\n    rowCount: sequences.length,\n  });\n  for (const [rowIndex, sequence] of sequences.entries()) {\n    for (const [columnIndex, residue] of sequence.split('').entries()) {\n      const category = chemicalProperties\n        .at(columnIndex)\n        ?.find(({ residues }) => residues.includes(residue))\n        ?.category;\n      if (!category) continue;\n      const color = colorMap[category]?.color;\n      if (!color) continue;\n      context.fillStyle = colorMap[category].color;\n      context.fillRect(columnIndex, rowIndex, 1, 1);\n    }\n  }\n  return canvas.convertToBlob();\n}\n\nconst getAlignmentChemicalProperties = (\n  { residueCounts, rowCount }: {\n    residueCounts: ResidueCounts;\n    rowCount: number;\n  },\n): ColumnChemicalProperties[] =>\n  // for every column in a residue counts table\n  // (e.g. table = [{ A: 3, R: 5, Q: 1}, { E: 4, T: 2 }, ...])\n  residueCounts.map((column) => (\n    // find all matching criterion\n    categoryCriterion\n      .filter(({ rules }) =>\n        // by matching at least one rule\n        rules.some(({ groups, threshold }) =>\n          // where at least one residue group\n          groups.some((group) => {\n            // combined\n            const groupCount = group.split('').reduce(\n              (acc, residue) => acc + (column[residue] ?? 0),\n              0,\n            );\n            // is above the required threshold\n            return groupCount > rowCount * threshold;\n          }),\n        ),\n      )\n      .map(({ residues, category }) => ({ residues, category }))\n  ));\n\ntype ColumnChemicalProperties = {\n  residues: string;\n  category: ChemicalCategory;\n}[];\n\n/** @see {@link https://www.jalview.org/help/html/colourSchemes/clustal.html} */\nconst categoryCriterion: Criteria[] = [\n  {\n    residues: 'ACILMFWV',\n    category: 'hydrophobic',\n    rules: [\n      { groups: ['WLVIMAFCYHP'], threshold: 0.6 },\n    ],\n  },\n  {\n    residues: 'KR',\n    category: 'positiveCharge',\n    rules: [\n      { groups: ['KR'], threshold: 0.6 },\n      { groups: [...'KRQ'], threshold: 0.8 },\n    ],\n  },\n  {\n    residues: 'E',\n    category: 'negativeCharge',\n    rules: [\n      { groups: ['KR'], threshold: 0.6 },\n      { groups: ['QE'], threshold: 0.5 },\n      { groups: ['ED'], threshold: 0.5 },\n      { groups: [...'EQD'], threshold: 0.85 },\n    ],\n  },\n  {\n    residues: 'D',\n    category: 'negativeCharge',\n    rules: [\n      { groups: ['KR'], threshold: 0.6 },\n      { groups: [...'DEN'], threshold: 0.85 },\n      { groups: ['ED'], threshold: 0.5 },\n    ],\n  },\n  {\n    residues: 'N',\n    category: 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+{"version":3,"file":"chemical-properties.js","sources":["../../../src/components/PlMultiSequenceAlignment/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/components/PlMultiSequenceAlignment/data.d.ts

@@ -1,7 +1,6 @@
 import { ListOptionNormalized } from '@milaboratories/uikit';
 import { PColumnIdAndSpec, PFrameHandle, PlMultiSequenceAlignmentColorSchemeOption, PlMultiSequenceAlignmentSettings, PlSelectionModel, PObjectId, PTableColumnId } from '@platforma-sdk/model';
-import { Markup } from './markup';
-import { ColorMap, ResidueCounts } from './types';
+import { HighlightLegend, ResidueCounts } from './types';
 export declare const sequenceLimit = 1000;
 export declare const useSequenceColumnsOptions: (paramsGetter: () => {
     pFrame: PFrameHandle | undefined;
@@ -31,7 +30,6 @@ export declare const useMultipleAlignmentData: (paramsGetter: () => {
     pframe: PFrameHandle | undefined;
     sequenceColumnIds: PObjectId[] | undefined;
     labelColumnIds: PTableColumnId[] | undefined;
-    markupColumnId: PObjectId | undefined;
     selection: PlSelectionModel | undefined;
     colorScheme: PlMultiSequenceAlignmentColorSchemeOption;
     alignmentParams: PlMultiSequenceAlignmentSettings["alignmentParams"];
@@ -43,15 +41,11 @@ export declare const useMultipleAlignmentData: (paramsGetter: () => {
 type MultipleAlignmentData = {
     sequences: string[];
     sequenceNames: string[];
-    labelsRows: string[][];
+    labelRows: string[][];
     residueCounts: ResidueCounts;
-    markup?: {
-        labels: Record<string, string>;
-        data: Markup[];
-    };
     highlightImage?: {
         blob: Blob;
-        colorMap: ColorMap;
+        legend: HighlightLegend;
     };
     exceedsLimit: boolean;
 };

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