@platforma-sdk/ui-vue 1.41.17 → 1.42.0

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: 'polar',\n    rules: [\n      { groups: ['N'], threshold: 0.5 },\n      { groups: [...'ND'], threshold: 0.85 },\n    ],\n  },\n  {\n    residues: 'Q',\n    category: 'polar',\n    rules: [\n      { groups: ['KR'], threshold: 0.6 },\n      { groups: ['QE'], threshold: 0.5 },\n      { groups: [...'QTKR'], threshold: 0.85 },\n    ],\n  },\n  {\n    residues: 'ST',\n    category: 'polar',\n    rules: [\n      { groups: ['WLVIMAFCYHP'], threshold: 0.6 },\n      { groups: ['TS'], threshold: 0.5 },\n      { groups: [...'ST'], threshold: 0.85 },\n    ],\n  },\n  {\n    residues: 'C',\n    category: 'cysteine',\n    rules: [\n      { groups: ['C'], threshold: 0.85 },\n    ],\n  },\n  {\n    residues: 'G',\n    category: 'glycine',\n    rules: [\n      { groups: ['G'], threshold: 0 },\n    ],\n  },\n  {\n    residues: 'P',\n    category: 'proline',\n    rules: [\n      { groups: ['P'], threshold: 0 },\n    ],\n  },\n  {\n    residues: 'HY',\n    category: 'aromatic',\n    rules: [\n      { groups: ['WLVIMAFCYHP'], threshold: 0.6 },\n      { groups: [...'WYACPQFHILMV'], threshold: 0.85 },\n    ],\n  },\n];\n\ntype Criteria = {\n  residues: string;\n  category: ChemicalCategory;\n  rules: {\n    groups: string[];\n    threshold: number;\n  }[];\n};\n"],"names":["chemicalPropertiesColorMap","colorizeSequencesByChemicalProperties","sequences","residueCounts","colorMap","_a","_b","_c","_d","canvas","context","chemicalProperties","getAlignmentChemicalProperties","rowIndex","sequence","columnIndex","residue","category","residues","rowCount","column","categoryCriterion","rules","groups","threshold","group","acc"],"mappings":"AAEO,MAAMA,IAAuC;AAAA,EAClD,aAAa;AAAA,IACX,OAAO;AAAA,IACP,OAAO;AAAA,EACT;AAAA,EACA,gBAAgB;AAAA,IACd,OAAO;AAAA,IACP,OAAO;AAAA,EACT;AAAA,EACA,gBAAgB;AAAA,IACd,OAAO;AAAA,IACP,OAAO;AAAA,EACT;AAAA,EACA,OAAO;AAAA,IACL,OAAO;AAAA,IACP,OAAO;AAAA,EACT;AAAA,EACA,UAAU;AAAA,IACR,OAAO;AAAA,IACP,OAAO;AAAA,EACT;AAAA,EACA,SAAS;AAAA,IACP,OAAO;AAAA,IACP,OAAO;AAAA,EACT;AAAA,EACA,SAAS;AAAA,IACP,OAAO;AAAA,IACP,OAAO;AAAA,EACT;AAAA,EACA,UAAU;AAAA,IACR,OAAO;AAAA,IACP,OAAO;AAAA,EAAA;AAEX;AAIO,SAASC,EACd,EAAE,WAAAC,GAAW,eAAAC,GAAe,UAAAC,KAKb;AA3CV,MAAAC,GAAAC,GAAAC,GAAAC;AA4CL,QAAMC,IAAS,IAAI;AAAA,MACjBJ,IAAAH,EAAU,CAAC,MAAX,gBAAAG,EAAc,WAAU;AAAA,IACxBH,EAAU;AAAA,EACZ,GACMQ,IAAUD,EAAO,WAAW,IAAI,GAChCE,IAAqBC,EAA+B;AAAA,IACxD,eAAAT;AAAA,IACA,UAAUD,EAAU;AAAA,EAAA,CACrB;AACD,aAAW,CAACW,GAAUC,CAAQ,KAAKZ,EAAU;AAChC,eAAA,CAACa,GAAaC,CAAO,KAAKF,EAAS,MAAM,EAAE,EAAE,WAAW;AACjE,YAAMG,KAAWV,KAAAD,IAAAK,EACd,GAAGI,CAAW,MADA,gBAAAT,EAEb,KAAK,CAAC,EAAE,UAAAY,EAAe,MAAAA,EAAS,SAASF,CAAO,OAFnC,gBAAAT,EAGb;AAGJ,MAFI,CAACU,KAED,GADUT,IAAAJ,EAASa,CAAQ,MAAjB,QAAAT,EAAoB,WAE1BE,EAAA,YAAYN,EAASa,CAAQ,EAAE,OACvCP,EAAQ,SAASK,GAAaF,GAAU,GAAG,CAAC;AAAA,IAAA;AAGhD,SAAOJ,EAAO,cAAc;AAC9B;AAEA,MAAMG,IAAiC,CACrC,EAAE,eAAAT,GAAe,UAAAgB,EAAS;AAAA;AAAA;AAAA,EAO1BhB,EAAc,IAAI,CAACiB;AAAA;AAAA,IAEjBC,EACG;AAAA,MAAO,CAAC,EAAE,OAAAC,EAAM;AAAA;AAAA,QAEfA,EAAM;AAAA,UAAK,CAAC,EAAE,QAAAC,GAAQ,WAAAC,EAAU;AAAA;AAAA,YAE9BD,EAAO,KAAK,CAACE,MAEQA,EAAM,MAAM,EAAE,EAAE;AAAA,cACjC,CAACC,GAAKV,MAAYU,KAAON,EAAOJ,CAAO,KAAK;AAAA,cAC5C;AAAA,YACF,IAEoBG,IAAWK,CAChC;AAAA;AAAA,QAAA;AAAA;AAAA,IACH,EAED,IAAI,CAAC,EAAE,UAAAN,GAAU,UAAAD,SAAgB,EAAE,UAAAC,GAAU,UAAAD,IAAW;AAAA,GAC5D;AAAA,GAQGI,IAAgC;AAAA,EACpC;AAAA,IACE,UAAU;AAAA,IACV,UAAU;AAAA,IACV,OAAO;AAAA,MACL,EAAE,QAAQ,CAAC,aAAa,GAAG,WAAW,IAAI;AAAA,IAAA;AAAA,EAE9C;AAAA,EACA;AAAA,IACE,UAAU;AAAA,IACV,UAAU;AAAA,IACV,OAAO;AAAA,MACL,EAAE,QAAQ,CAAC,IAAI,GAAG,WAAW,IAAI;AAAA,MACjC,EAAE,QAAQ,CAAC,GAAG,KAAK,GAAG,WAAW,IAAI;AAAA,IAAA;AAAA,EAEzC;AAAA,EACA;AAAA,IACE,UAAU;AAAA,IACV,UAAU;AAAA,IACV,OAAO;AAAA,MACL,EAAE,QAAQ,CAAC,IAAI,GAAG,WAAW,IAAI;AAAA,MACjC,EAAE,QAAQ,CAAC,IAAI,GAAG,WAAW,IAAI;AAAA,MACjC,EAAE,QAAQ,CAAC,IAAI,GAAG,WAAW,IAAI;AAAA,MACjC,EAAE,QAAQ,CAAC,GAAG,KAAK,GAAG,WAAW,KAAK;AAAA,IAAA;AAAA,EAE1C;AAAA,EACA;AAAA,IACE,UAAU;AAAA,IACV,UAAU;AAAA,IACV,OAAO;AAAA,MACL,EAAE,QAAQ,CAAC,IAAI,GAAG,WAAW,IAAI;AAAA,MACjC,EAAE,QAAQ,CAAC,GAAG,KAAK,GAAG,WAAW,KAAK;AAAA,MACtC,EAAE,QAAQ,CAAC,IAAI,GAAG,WAAW,IAAI;AAAA,IAAA;AAAA,EAErC;AAAA,EACA;AAAA,IACE,UAAU;AAAA,IACV,UAAU;AAAA,IACV,OAAO;AAAA,MACL,EAAE,QAAQ,CAAC,GAAG,GAAG,WAAW,IAAI;AAAA,MAChC,EAAE,QAAQ,CAAC,GAAG,IAAI,GAAG,WAAW,KAAK;AAAA,IAAA;AAAA,EAEzC;AAAA,EACA;AAAA,IACE,UAAU;AAAA,IACV,UAAU;AAAA,IACV,OAAO;AAAA,MACL,EAAE,QAAQ,CAAC,IAAI,GAAG,WAAW,IAAI;AAAA,MACjC,EAAE,QAAQ,CAAC,IAAI,GAAG,WAAW,IAAI;AAAA,MACjC,EAAE,QAAQ,CAAC,GAAG,MAAM,GAAG,WAAW,KAAK;AAAA,IAAA;AAAA,EAE3C;AAAA,EACA;AAAA,IACE,UAAU;AAAA,IACV,UAAU;AAAA,IACV,OAAO;AAAA,MACL,EAAE,QAAQ,CAAC,aAAa,GAAG,WAAW,IAAI;AAAA,MAC1C,EAAE,QAAQ,CAAC,IAAI,GAAG,WAAW,IAAI;AAAA,MACjC,EAAE,QAAQ,CAAC,GAAG,IAAI,GAAG,WAAW,KAAK;AAAA,IAAA;AAAA,EAEzC;AAAA,EACA;AAAA,IACE,UAAU;AAAA,IACV,UAAU;AAAA,IACV,OAAO;AAAA,MACL,EAAE,QAAQ,CAAC,GAAG,GAAG,WAAW,KAAK;AAAA,IAAA;AAAA,EAErC;AAAA,EACA;AAAA,IACE,UAAU;AAAA,IACV,UAAU;AAAA,IACV,OAAO;AAAA,MACL,EAAE,QAAQ,CAAC,GAAG,GAAG,WAAW,EAAE;AAAA,IAAA;AAAA,EAElC;AAAA,EACA;AAAA,IACE,UAAU;AAAA,IACV,UAAU;AAAA,IACV,OAAO;AAAA,MACL,EAAE,QAAQ,CAAC,GAAG,GAAG,WAAW,EAAE;AAAA,IAAA;AAAA,EAElC;AAAA,EACA;AAAA,IACE,UAAU;AAAA,IACV,UAAU;AAAA,IACV,OAAO;AAAA,MACL,EAAE,QAAQ,CAAC,aAAa,GAAG,WAAW,IAAI;AAAA,MAC1C,EAAE,QAAQ,CAAC,GAAG,cAAc,GAAG,WAAW,KAAK;AAAA,IAAA;AAAA,EACjD;AAEJ;"}
+{"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;
 };

package/dist/components/PlMultiSequenceAlignment/data.d.ts.map

@@ -1 +1 @@
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package/dist/components/PlMultiSequenceAlignment/data.js

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