@datagrok/bio 2.26.8 → 2.27.1

package/CHANGELOG.md

@@ -1,5 +1,9 @@
 # Bio changelog
 
+## 2.27.0 (2026-04-09)
+
+* Engine based MSA
+
 ## 2.26.5 (2026-04-01)
 
 ### Features

package/CLAUDE.md

@@ -44,7 +44,7 @@ Other packages depend on these implementations: **Helm**, **Peptides**, **Biostr
 |---|---|---|
 | `Bio \| Analyze \| Activity Cliffs...` | `activityCliffs` | Detects sequence pairs with similar structure but significant activity difference |
 | `Bio \| Analyze \| Sequence Space...` | `sequenceSpaceTopMenu` | UMAP/tSNE 2D projection of sequences by pairwise distance |
-| `Bio \| Analyze \| MSA...` | `multipleSequenceAlignmentDialog` | Multiple sequence alignment via kalign (WASM) or PepSeA (Docker) |
+| `Bio \| Analyze \| MSA...` | `multipleSequenceAlignmentDialog` | Multiple sequence alignment via kalign (WASM) for canonical sequences, or dynamically discovered engines (e.g. PepSeA Docker) for non-canonical |
 | `Bio \| Analyze \| Composition` | `compositionAnalysis` | Docks a WebLogo viewer for sequence composition |
 | `Bio \| Transform \| Convert Sequence Notation...` | `convertDialog` | FASTA ↔ SEPARATOR ↔ HELM ↔ BILN conversion |
 | `Bio \| Transform \| To Atomic Level...` | `toAtomicLevel` | Converts sequences to V3000 molfiles |
@@ -177,9 +177,38 @@ Key methods: `detectSeparator()`, `detectAlphabet()`, `getAlphabetSimilarity()`,
 
 | File | Purpose |
 |---|---|
-| `multiple-sequence-alignment.ts` | `multipleSequenceAlignment()` — core MSA via **kalign** (WebAssembly/Aioli). Supports per-cluster alignment, gap penalties, selected-rows-only mode. |
-| `multiple-sequence-alignment-ui.ts` | `multipleSequenceAlignmentUI()` — MSA dialog with column selection, alignment method (kalign vs PepSeA), gap penalties |
-| `pepsea.ts` | `pepseaAlignSequences()` — MSA for HELM peptides via **PepSeA Docker container** (mafft/linsi/ginsi methods) |
+| `multiple-sequence-alignment.ts` | `runKalign()` — core MSA via **kalign** (WebAssembly/Aioli). Supports per-cluster alignment, gap penalties, selected-rows-only mode. Used for canonical sequences (DNA/RNA/PT). |
+| `multiple-sequence-alignment-ui.ts` | `multipleSequenceAlignmentUI()` — MSA dialog with column selection, mode switching (kalign for canonical, dynamically discovered engines for non-canonical), per-cluster alignment, selected-rows-only. |
+| `pepsea.ts` | `alignWithPepsea()` / `runPepsea()` — MSA for HELM peptides via **PepSeA Docker container** (mafft/linsi/ginsi methods). Registered as a `sequenceMSA` engine via `pepseaMsa()` in `package.ts`. |
+
+##### Adding a New MSA Engine
+
+Non-canonical MSA engines are discovered dynamically via `DG.Func.find({meta: {role: 'sequenceMSA'}})`.
+To add a new alignment engine (in this or any other package):
+
+1. Register a function with `meta.role: 'sequenceMSA'` and `outputs: [{name: 'result', type: 'column'}]`.
+2. The **first parameter** must be a `column` input with `semType: 'Macromolecule'` — the sequences to align.
+3. All **remaining parameters** are engine-specific configuration (method, gap penalties, etc.) and will be rendered automatically in the MSA dialog under "Alignment parameters".
+4. The function must **create and return** the aligned output column with appropriate metadata tags (`meta.units`, `semType`, `aligned`, `alphabet`, `separator`, etc.). Different engines can produce different output notations (e.g. PepSeA produces separator notation with `.` delimiter).
+5. The MSA dialog handles clustering and row selection — the engine function receives a single column to align.
+
+Example (decorator style):
+```typescript
+@grok.decorators.func({
+  name: 'My Aligner',
+  description: 'Custom MSA engine',
+  meta: {role: 'sequenceMSA'},
+  outputs: [{name: 'result', type: 'column'}],
+})
+static async myAligner(
+  @grok.decorators.param({type: 'column', options: {semType: 'Macromolecule'}}) sequenceCol: DG.Column<string>,
+  @grok.decorators.param({type: 'double'}) gapOpen: number = 1.0,
+): Promise<DG.Column<string>> {
+  // Align sequences, create result column with metadata tags, return it.
+}
+```
+
+See `pepseaMsa()` in `package.ts` and `alignWithPepsea()` in `pepsea.ts` for a complete reference implementation.
 
 #### Seq Helper — `src/utils/seq-helper/`
 
@@ -351,7 +380,8 @@ Test entry point: `src/package-test.ts` — imports all test files, exports `tes
 | Sequence space (UMAP/tSNE) | `src/analysis/sequence-space.ts` |
 | Similarity/diversity viewers | `src/analysis/sequence-similarity-viewer.ts` / `sequence-diversity-viewer.ts` |
 | MSA (kalign) | `src/utils/multiple-sequence-alignment.ts` |
-| MSA (PepSeA Docker) | `src/utils/pepsea.ts` |
+| MSA (PepSeA Docker) | `src/utils/pepsea.ts` + `pepseaMsa()` in `src/package.ts` |
+| Adding MSA engines | See "Adding a New MSA Engine" in Multiple Sequence Alignment section |
 | Notation conversion | `src/utils/convert.ts` |
 | Seq → molfile conversion | `src/utils/sequence-to-mol.ts` |
 | HELM → molfile pipeline | `src/utils/helm-to-molfile/converter/` |

package/detectors.js

@@ -333,7 +333,8 @@ class BioPackageDetectors extends DG.Package {
         // const forbidden = this.checkForbiddenWoSeparator(stats.freq);
         col.meta.units = units;
         if (separator) col.setTag(SeqHandler.TAGS.separator, separator);
-        col.setTag(SeqHandler.TAGS.aligned, aligned);
+        if (!col.getTag(SeqHandler.TAGS.aligned))
+          col.setTag(SeqHandler.TAGS.aligned, aligned);
         col.setTag(SeqHandler.TAGS.alphabet, alphabet);
         if (alphabet === ALPHABET.UN) {
           // alphabetSize calculated on (sub)sample of data is incorrect
@@ -706,7 +707,8 @@ class BioPackageDetectors extends DG.Package {
           const isPotentiallyMSA = averageLength > 1 && std < 2; // if the average length is more than 1 and the std is less than 0.5, then it is potentially MSA
           column.setTag('units', notationInput.value);
           separatorInput.value && column.setTag('separator', separatorInput.value);
-          column.setTag('aligned', isPotentiallyMSA ? 'SEQ.MSA' : 'SEQ');
+          if (!column.getTag('aligned'))
+            column.setTag('aligned', isPotentiallyMSA ? 'SEQ.MSA' : 'SEQ');
           column.setTag('alphabet', defaultAlphabet);
           isMultichar && column.setTag('.alphabetIsMultichar', 'true');
           column.semType = 'Macromolecule';

package/dist/287.js

@@ -1,2 +1,2 @@
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annot.category;\n      const sevLabel = annot.severity ? ` [${severityLabels[annot.severity] ?? annot.severity}]` : '';\n      const rangeLabel = annot.start && annot.end ? ` (${annot.start}-${annot.end})` : '';\n      const schemeLabel = annot.sourceScheme ? ` ${annot.sourceScheme}` : '';\n\n      const removeBtn = ui.iconFA('trash', () => {\n        const updated = getColumnAnnotations(selectedCol).filter((a) => a.id !== annot.id);\n        setColumnAnnotations(selectedCol, updated);\n        df.fireValuesChanged();\n        refreshList();\n      }, 'Delete');\n      removeBtn.style.cursor = 'pointer';\n      removeBtn.style.color = '#999';\n      removeBtn.style.marginLeft = '8px';\n      const originalColor = annot.color ?? '#ccc';\n      let currentColor = originalColor;\n      const colorSwatch = ui.div([], {style: {\n        width: '12px', height: '12px', borderRadius: '2px',\n        backgroundColor: currentColor, display: 'inline-block', marginRight: '6px',\n        flexShrink: '0', cursor: 'pointer',\n      }});\n\n      ui.colorPicker(DG.Color.fromHtml(annot.color ?? '#ccc'), (newColor) => {\n        currentColor = DG.Color.toHtml(newColor);\n      }, colorSwatch, () => {\n        const updated = getColumnAnnotations(selectedCol).map((a) => a.id === annot.id ? {...a, color: currentColor} : a);\n        setColumnAnnotations(selectedCol, updated);\n        df.fireValuesChanged();\n        refreshList();\n      }, () => {\n        currentColor = originalColor;\n        colorSwatch.style.backgroundColor = currentColor;\n      });\n\n      const row = ui.divH([\n        colorSwatch,\n        ui.divText(`${annot.name}${rangeLabel}${schemeLabel}${sevLabel}`, {style: {flex: '1', fontSize: '12px', padding: '4px'}}),\n        ui.divText(catLabel, {style: {color: '#888', fontSize: '11px', marginRight: '8px'}}),\n        removeBtn,\n      ], {style: {alignItems: 'center', padding: '4px 0', borderBottom: '1px solid #eee'}});\n\n      listDiv.append(row);\n    }\n  }\n\n  refreshList();\n\n  const clearBtn = ui.button('Clear All', () => {\n    clearAnnotations(df, selectedCol);\n    df.fireValuesChanged();\n    refreshList();\n    grok.shell.info('All annotations cleared');\n  });\n\n  const dialog = ui.dialog({title: 'Manage Annotations'})\n    .add(ui.inputs([colInput]))\n    .add(ui.h3('Annotations'))\n    .add(listDiv)\n    .add(ui.divH([clearBtn], {style: {marginTop: '8px'}}))\n    .onOK(() => {});\n\n  dialog.show();\n}\n"],"names":["categoryLabels","Structure","Liability","PTM","Custom","severityLabels","High","Medium","Low","Info","showAnnotationManagerDialog","df","tv","dataFrame","warning","seqCols","columns","bySemTypeAll","MACROMOLECULE","length","selectedCol","colInput","column","table","value","filter","col","semType","onValueChanged","refreshList","listDiv","style","maxHeight","overflowY","paddingRight","innerHTML","annotations","annot","catLabel","category","sevLabel","severity","rangeLabel","start","end","schemeLabel","sourceScheme","removeBtn","updated","a","id","fireValuesChanged","cursor","color","marginLeft","originalColor","currentColor","colorSwatch","width","height","borderRadius","backgroundColor","display","marginRight","flexShrink","fromHtml","newColor","toHtml","map","row","name","flex","fontSize","padding","alignItems","borderBottom","append","clearBtn","info","title","add","marginTop","onOK","show"],"sourceRoot":""}

package/dist/422.js

@@ -1,2 +1,2 @@
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 //# sourceMappingURL=422.js.map

package/dist/422.js.map

@@ -1 +1 @@
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eslint-disable max-len */\nimport * as DG from 'datagrok-api/dg';\n\nimport {ISeqHandler} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';\nimport {\n  SeqAnnotation, SeqAnnotationHit, RowAnnotationData,\n  AnnotationVisualType, AnnotationCategory, LiabilitySeverity,\n  ANNOTATION_COLORS,\n} from '@datagrok-libraries/bio/src/utils/macromolecule/annotations';\nimport {\n  getOrCreateAnnotationColumn, setColumnAnnotations, setRowAnnotations,\n  getColumnAnnotations, getRowAnnotations, mergeRowHits,\n} from './annotation-manager';\n\n/** A single liability scanning rule. */\nexport interface LiabilityRule {\n  id: string;\n  name: string;\n  pattern: RegExp;\n  length: number;\n  severity: LiabilitySeverity;\n  /** Sub-category for grouping (e.g. \"deamidation\", \"oxidation\") */\n  ruleCategory: string;\n  color: string;\n  enabled: boolean;\n}\n\n/** Built-in liability rules for antibody engineering. */\nexport const BUILTIN_LIABILITY_RULES: LiabilityRule[] = [\n  {id: 'deamid-ng', name: 'Deamidation (NG)', pattern: /NG/g, length: 2, severity: LiabilitySeverity.High, ruleCategory: 'deamidation', color: ANNOTATION_COLORS.liability.deamidation, enabled: true},\n  {id: 'deamid-ns', name: 'Deamidation (NS)', pattern: /NS/g, length: 2, severity: LiabilitySeverity.Medium, ruleCategory: 'deamidation', color: ANNOTATION_COLORS.liability.deamidation, enabled: true},\n  {id: 'deamid-na', name: 'Deamidation (NA)', pattern: /NA/g, length: 2, severity: LiabilitySeverity.Low, ruleCategory: 'deamidation', color: ANNOTATION_COLORS.liability.deamidation, enabled: true},\n  {id: 'deamid-nd', name: 'Deamidation (ND)', pattern: /ND/g, length: 2, severity: LiabilitySeverity.Low, ruleCategory: 'deamidation', color: ANNOTATION_COLORS.liability.deamidation, enabled: true},\n  {id: 'deamid-nt', name: 'Deamidation (NT)', pattern: /NT/g, length: 2, severity: LiabilitySeverity.Low, ruleCategory: 'deamidation', color: ANNOTATION_COLORS.liability.deamidation, enabled: true},\n  {id: 'isom-dg', name: 'Isomerization (DG)', pattern: /DG/g, length: 2, severity: LiabilitySeverity.High, ruleCategory: 'isomerization', color: ANNOTATION_COLORS.liability.isomerization, enabled: true},\n  {id: 'isom-ds', name: 'Isomerization (DS)', pattern: /DS/g, length: 2, severity: LiabilitySeverity.Medium, ruleCategory: 'isomerization', color: ANNOTATION_COLORS.liability.isomerization, enabled: true},\n  {id: 'oxid-m', name: 'Oxidation (Met)', pattern: /M/g, length: 1, severity: LiabilitySeverity.Medium, ruleCategory: 'oxidation', color: ANNOTATION_COLORS.liability.oxidation, enabled: true},\n  {id: 'oxid-w', name: 'Oxidation (Trp)', pattern: /W/g, length: 1, severity: LiabilitySeverity.Low, ruleCategory: 'oxidation', color: ANNOTATION_COLORS.liability.oxidation, enabled: true},\n  {id: 'glyco-nxst', name: 'N-glycosylation', pattern: /N[^P][ST]/g, length: 3, severity: LiabilitySeverity.High, ruleCategory: 'glycosylation', color: ANNOTATION_COLORS.liability.glycosylation, enabled: true},\n  {id: 'free-cys', name: 'Free Cysteine', pattern: /C/g, length: 1, severity: LiabilitySeverity.Info, ruleCategory: 'freeCysteine', color: ANNOTATION_COLORS.liability.freeCysteine, enabled: false},\n];\n\n/** Extracts a canonical single-letter string from a sequence handler for a given row. */\nfunction getCanonicalString(sh: ISeqHandler, rowIdx: number): string {\n  const splitted = sh.getSplitted(rowIdx);\n  const chars: string[] = new Array(splitted.length);\n  for (let i = 0; i < splitted.length; i++)\n    chars[i] = splitted.getOriginal(i);\n  return chars.join('');\n}\n\nexport interface ScanLiabilitiesResult {\n  annotations: SeqAnnotation[];\n  rowData: RowAnnotationData[];\n  totalHits: number;\n}\n\n/** Scans all rows of a macromolecule column for liability motifs.\n *  Returns column-level SeqAnnotation entries + per-row SeqAnnotationHit arrays. */\nexport function scanLiabilities(\n  col: DG.Column<string>,\n  sh: ISeqHandler,\n  rules: LiabilityRule[],\n): ScanLiabilitiesResult {\n  const enabledRules = rules.filter((r) => r.enabled);\n  const posList = sh.posList;\n\n  // Track which rules had hits\n  const ruleHitCounts = new Map<string, number>();\n\n  const rowData: RowAnnotationData[] = new Array(col.length);\n  let totalHits = 0;\n\n  for (let rowIdx = 0; rowIdx < col.length; rowIdx++) {\n    const seq = getCanonicalString(sh, rowIdx);\n    const hits: SeqAnnotationHit[] = [];\n\n    for (const rule of enabledRules) {\n      // Reset regex lastIndex for global patterns\n      rule.pattern.lastIndex = 0;\n      let match: RegExpExecArray | null;\n      while ((match = rule.pattern.exec(seq)) !== null) {\n        hits.push({\n          annotationId: rule.id,\n          positionIndex: match.index,\n          positionName: match.index < posList.length ? posList[match.index] : undefined,\n          matchedMonomers: match[0],\n        });\n        ruleHitCounts.set(rule.id, (ruleHitCounts.get(rule.id) ?? 0) + 1);\n        totalHits++;\n      }\n    }\n    rowData[rowIdx] = hits;\n  }\n\n  // Build column-level annotations only for rules that had hits\n  const annotations: SeqAnnotation[] = enabledRules\n    .filter((r) => ruleHitCounts.has(r.id))\n    .map((r) => ({\n      id: r.id,\n      name: r.name,\n      description: `${r.ruleCategory} liability pattern (${ruleHitCounts.get(r.id)} hits)`,\n      start: null,\n      end: null,\n      visualType: r.length === 1 ? AnnotationVisualType.Point : AnnotationVisualType.Motif,\n      category: AnnotationCategory.Liability,\n      color: r.color,\n      severity: r.severity,\n      motifPattern: r.pattern.source,\n      autoGenerated: true,\n    }));\n\n  return {annotations, rowData, totalHits};\n}\n\n/** Applies liability scan results to the DataFrame (writes tags + companion column). */\nexport function applyLiabilityScanResults(\n  df: DG.DataFrame,\n  seqCol: DG.Column<string>,\n  result: ScanLiabilitiesResult,\n): void {\n  // Merge with existing annotations, removing old liability entries\n  const existing = getColumnAnnotations(seqCol)\n    .filter((a) => a.category !== AnnotationCategory.Liability);\n  setColumnAnnotations(seqCol, [...existing, ...result.annotations]);\n\n  // Write per-row data to hidden companion column, preserving region hits from numbering\n  const annotCol = getOrCreateAnnotationColumn(df, seqCol);\n  for (let i = 0; i < result.rowData.length; i++) {\n    const existingHits = getRowAnnotations(annotCol, i) ?? [];\n    setRowAnnotations(annotCol, i, mergeRowHits(existingHits, result.rowData[i], false, true));\n  }\n}\n\n/** Creates a liability summary count column (total hits per row). */\nexport function createLiabilitySummaryColumn(\n  df: DG.DataFrame,\n  seqCol: DG.Column<string>,\n  result: ScanLiabilitiesResult,\n): DG.Column<number> {\n  const colName = `${seqCol.name}_liability_count`;\n  const counts = result.rowData.map((hits) => hits.length);\n  const col = df.columns.addNewInt(colName);\n  for (let i = 0; i < counts.length; i++)\n    col.set(i, counts[i]);\n  return col;\n}\n","import * as grok from 'datagrok-api/grok';\nimport * as ui from 'datagrok-api/ui';\nimport * as DG from 'datagrok-api/dg';\n\nimport {_package} from '../../package';\nimport {\n  BUILTIN_LIABILITY_RULES, LiabilityRule, scanLiabilities,\n  applyLiabilityScanResults, createLiabilitySummaryColumn,\n} from './liability-scanner';\nimport {LiabilitySeverity} from '@datagrok-libraries/bio/src/utils/macromolecule/annotations';\n\nconst severityLabels: Record<string, string> = {\n  [LiabilitySeverity.High]: 'High',\n  [LiabilitySeverity.Medium]: 'Medium',\n  [LiabilitySeverity.Low]: 'Low',\n  [LiabilitySeverity.Info]: 'Info',\n};\n\nexport function showLiabilityScannerDialog(): void {\n  const df = grok.shell.tv?.dataFrame;\n  if (!df) {\n    grok.shell.warning('No table open');\n    return;\n  }\n\n  const seqCols = df.columns.bySemTypeAll(DG.SEMTYPE.MACROMOLECULE);\n  if (seqCols.length === 0) {\n    grok.shell.warning('No macromolecule columns found');\n    return;\n  }\n\n  const rules = BUILTIN_LIABILITY_RULES.map((r) => ({...r, pattern: new RegExp(r.pattern.source, 'g')}));\n\n  const tableInput = ui.input.table('Table', {value: df});\n  const seqInput = ui.input.column('Sequence', {\n    table: df, value: seqCols[0],\n    filter: (col: DG.Column) => col.semType === DG.SEMTYPE.MACROMOLECULE,\n  });\n\n  // Rule checkboxes\n  const ruleChecks: {rule: LiabilityRule; input: DG.InputBase<boolean>}[] = [];\n  const rulesDiv = ui.divV([]);\n  for (const rule of rules) {\n    const check = ui.input.bool(rule.name, {\n      value: rule.enabled,\n      tooltipText: `Severity: ${severityLabels[rule.severity] ?? rule.severity}`,\n    });\n    ruleChecks.push({rule, input: check});\n    rulesDiv.append(check.root);\n  }\n\n  const highlightInput = ui.input.bool('Highlight in cell renderer', {value: true});\n  const annotColInput = ui.input.bool('Create annotation column', {value: true});\n  const summaryInput = ui.input.bool('Create summary count column', {value: false});\n\n  const dialog = ui.dialog({title: 'Scan Sequence Liabilities'})\n    .add(ui.inputs([tableInput, seqInput]))\n    .add(ui.h3('Rules'))\n    .add(rulesDiv)\n    .add(ui.h3('Output'))\n    .add(ui.inputs([highlightInput, annotColInput, summaryInput]))\n    .onOK(() => {\n      try {\n        const seqCol = seqInput.value!;\n        const sh = _package.seqHelper.getSeqHandler(seqCol);\n\n        // Apply checkbox state\n        for (const {rule, input} of ruleChecks)\n          rule.enabled = input.value;\n\n        const result = scanLiabilities(seqCol, sh, rules);\n\n        if (annotColInput.value || highlightInput.value)\n          applyLiabilityScanResults(df, seqCol, result);\n\n        if (summaryInput.value)\n          createLiabilitySummaryColumn(df, seqCol, result);\n\n        grok.shell.info(`Liability scan: ${result.totalHits} hits found across ${result.annotations.length} rules`);\n        df.fireValuesChanged();\n      } catch (err: any) {\n        grok.shell.error(`Liability scan failed: ${err.message ?? err}`);\n        console.error(err);\n      }\n    });\n\n  dialog.show();\n}\n"],"names":["BUILTIN_LIABILITY_RULES","id","name","pattern","length","severity","High","ruleCategory","color","liability","deamidation","enabled","Medium","Low","isomerization","oxidation","glycosylation","Info","freeCysteine","getCanonicalString","sh","rowIdx","splitted","getSplitted","chars","Array","i","getOriginal","join","severityLabels","showLiabilityScannerDialog","df","tv","dataFrame","warning","seqCols","columns","bySemTypeAll","MACROMOLECULE","rules","map","r","RegExp","source","tableInput","table","value","seqInput","column","filter","col","semType","ruleChecks","rulesDiv","rule","check","bool","tooltipText","push","input","append","root","highlightInput","annotColInput","summaryInput","dialog","title","add","onOK","seqCol","_package","seqHelper","getSeqHandler","result","enabledRules","posList","ruleHitCounts","Map","rowData","totalHits","seq","hits","match","lastIndex","exec","annotationId","positionIndex","index","positionName","undefined","matchedMonomers","set","get","annotations","has","description","start","end","visualType","Point","Motif","category","Liability","motifPattern","autoGenerated","scanLiabilities","existing","a","annotCol","existingHits","applyLiabilityScanResults","colName","counts","addNewInt","createLiabilitySummaryColumn","info","fireValuesChanged","err","error","message","console","show"],"sourceRoot":""}
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eslint-disable max-len */\nimport * as DG from 'datagrok-api/dg';\n\nimport {ISeqHandler} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-handler';\nimport {\n  SeqAnnotation, SeqAnnotationHit, RowAnnotationData,\n  AnnotationVisualType, AnnotationCategory, LiabilitySeverity,\n  ANNOTATION_COLORS,\n} from '@datagrok-libraries/bio/src/utils/macromolecule/annotations';\nimport {\n  getOrCreateAnnotationColumn, setColumnAnnotations, setRowAnnotations,\n  getColumnAnnotations, getRowAnnotations, mergeRowHits,\n} from './annotation-manager';\n\n/** A single liability scanning rule. */\nexport interface LiabilityRule {\n  id: string;\n  name: string;\n  pattern: RegExp;\n  length: number;\n  severity: LiabilitySeverity;\n  /** Sub-category for grouping (e.g. \"deamidation\", \"oxidation\") */\n  ruleCategory: string;\n  color: string;\n  enabled: boolean;\n}\n\n/** Built-in liability rules for antibody engineering. */\nexport const BUILTIN_LIABILITY_RULES: LiabilityRule[] = [\n  {id: 'deamid-ng', name: 'Deamidation (NG)', pattern: /NG/g, length: 2, severity: LiabilitySeverity.High, ruleCategory: 'deamidation', color: ANNOTATION_COLORS.liability.deamidation, enabled: true},\n  {id: 'deamid-ns', name: 'Deamidation (NS)', pattern: /NS/g, length: 2, severity: LiabilitySeverity.Medium, ruleCategory: 'deamidation', color: ANNOTATION_COLORS.liability.deamidation, enabled: true},\n  {id: 'deamid-na', name: 'Deamidation (NA)', pattern: /NA/g, length: 2, severity: LiabilitySeverity.Low, ruleCategory: 'deamidation', color: ANNOTATION_COLORS.liability.deamidation, enabled: true},\n  {id: 'deamid-nd', name: 'Deamidation (ND)', pattern: /ND/g, length: 2, severity: LiabilitySeverity.Low, ruleCategory: 'deamidation', color: ANNOTATION_COLORS.liability.deamidation, enabled: true},\n  {id: 'deamid-nt', name: 'Deamidation (NT)', pattern: /NT/g, length: 2, severity: LiabilitySeverity.Low, ruleCategory: 'deamidation', color: ANNOTATION_COLORS.liability.deamidation, enabled: true},\n  {id: 'isom-dg', name: 'Isomerization (DG)', pattern: /DG/g, length: 2, severity: LiabilitySeverity.High, ruleCategory: 'isomerization', color: ANNOTATION_COLORS.liability.isomerization, enabled: true},\n  {id: 'isom-ds', name: 'Isomerization (DS)', pattern: /DS/g, length: 2, severity: LiabilitySeverity.Medium, ruleCategory: 'isomerization', color: ANNOTATION_COLORS.liability.isomerization, enabled: true},\n  {id: 'oxid-m', name: 'Oxidation (Met)', pattern: /M/g, length: 1, severity: LiabilitySeverity.Medium, ruleCategory: 'oxidation', color: ANNOTATION_COLORS.liability.oxidation, enabled: true},\n  {id: 'oxid-w', name: 'Oxidation (Trp)', pattern: /W/g, length: 1, severity: LiabilitySeverity.Low, ruleCategory: 'oxidation', color: ANNOTATION_COLORS.liability.oxidation, enabled: true},\n  {id: 'glyco-nxst', name: 'N-glycosylation', pattern: /N[^P][ST]/g, length: 3, severity: LiabilitySeverity.High, ruleCategory: 'glycosylation', color: ANNOTATION_COLORS.liability.glycosylation, enabled: true},\n  {id: 'free-cys', name: 'Free Cysteine', pattern: /C/g, length: 1, severity: LiabilitySeverity.Info, ruleCategory: 'freeCysteine', color: ANNOTATION_COLORS.liability.freeCysteine, enabled: false},\n];\n\n/** Extracts a canonical single-letter string from a sequence handler for a given row. */\nfunction getCanonicalString(sh: ISeqHandler, rowIdx: number): string {\n  const splitted = sh.getSplitted(rowIdx);\n  const chars: string[] = new Array(splitted.length);\n  for (let i = 0; i < splitted.length; i++)\n    chars[i] = splitted.getOriginal(i);\n  return chars.join('');\n}\n\nexport interface ScanLiabilitiesResult {\n  annotations: SeqAnnotation[];\n  rowData: RowAnnotationData[];\n  totalHits: number;\n}\n\n/** Scans all rows of a macromolecule column for liability motifs.\n *  Returns column-level SeqAnnotation entries + per-row SeqAnnotationHit arrays. */\nexport function scanLiabilities(\n  col: DG.Column<string>,\n  sh: ISeqHandler,\n  rules: LiabilityRule[],\n): ScanLiabilitiesResult {\n  const enabledRules = rules.filter((r) => r.enabled);\n  const posList = sh.posList;\n\n  // Track which rules had hits\n  const ruleHitCounts = new Map<string, number>();\n\n  const rowData: RowAnnotationData[] = new Array(col.length);\n  let totalHits = 0;\n\n  for (let rowIdx = 0; rowIdx < col.length; rowIdx++) {\n    const seq = getCanonicalString(sh, rowIdx);\n    const hits: SeqAnnotationHit[] = [];\n\n    for (const rule of enabledRules) {\n      // Reset regex lastIndex for global patterns\n      rule.pattern.lastIndex = 0;\n      let match: RegExpExecArray | null;\n      while ((match = rule.pattern.exec(seq)) !== null) {\n        hits.push({\n          annotationId: rule.id,\n          positionIndex: match.index,\n          positionName: match.index < posList.length ? posList[match.index] : undefined,\n          matchedMonomers: match[0],\n        });\n        ruleHitCounts.set(rule.id, (ruleHitCounts.get(rule.id) ?? 0) + 1);\n        totalHits++;\n      }\n    }\n    rowData[rowIdx] = hits;\n  }\n\n  // Build column-level annotations only for rules that had hits\n  const annotations: SeqAnnotation[] = enabledRules\n    .filter((r) => ruleHitCounts.has(r.id))\n    .map((r) => ({\n      id: r.id,\n      name: r.name,\n      description: `${r.ruleCategory} liability pattern (${ruleHitCounts.get(r.id)} hits)`,\n      start: null,\n      end: null,\n      visualType: r.length === 1 ? AnnotationVisualType.Point : AnnotationVisualType.Motif,\n      category: AnnotationCategory.Liability,\n      color: r.color,\n      severity: r.severity,\n      motifPattern: r.pattern.source,\n      autoGenerated: true,\n    }));\n\n  return {annotations, rowData, totalHits};\n}\n\n/** Applies liability scan results to the DataFrame (writes tags + companion column). */\nexport function applyLiabilityScanResults(\n  df: DG.DataFrame,\n  seqCol: DG.Column<string>,\n  result: ScanLiabilitiesResult,\n): void {\n  // Merge with existing annotations, removing old liability entries\n  const existing = getColumnAnnotations(seqCol)\n    .filter((a) => a.category !== AnnotationCategory.Liability);\n  setColumnAnnotations(seqCol, [...existing, ...result.annotations]);\n\n  // Write per-row data to hidden companion column, preserving region hits from numbering\n  const annotCol = getOrCreateAnnotationColumn(df, seqCol);\n  for (let i = 0; i < result.rowData.length; i++) {\n    const existingHits = getRowAnnotations(annotCol, i) ?? [];\n    setRowAnnotations(annotCol, i, mergeRowHits(existingHits, result.rowData[i], false, true));\n  }\n}\n\n/** Creates a liability summary count column (total hits per row). */\nexport function createLiabilitySummaryColumn(\n  df: DG.DataFrame,\n  seqCol: DG.Column<string>,\n  result: ScanLiabilitiesResult,\n): DG.Column<number> {\n  const colName = `${seqCol.name}_liability_count`;\n  const counts = result.rowData.map((hits) => hits.length);\n  const col = df.columns.addNewInt(colName);\n  for (let i = 0; i < counts.length; i++)\n    col.set(i, counts[i]);\n  return col;\n}\n","import * as grok from 'datagrok-api/grok';\nimport * as ui from 'datagrok-api/ui';\nimport * as DG from 'datagrok-api/dg';\n\nimport {_package} from '../../package';\nimport {\n  BUILTIN_LIABILITY_RULES, LiabilityRule, scanLiabilities,\n  applyLiabilityScanResults, createLiabilitySummaryColumn,\n} from './liability-scanner';\nimport {LiabilitySeverity} from '@datagrok-libraries/bio/src/utils/macromolecule/annotations';\n\nconst severityLabels: Record<string, string> = {\n  [LiabilitySeverity.High]: 'High',\n  [LiabilitySeverity.Medium]: 'Medium',\n  [LiabilitySeverity.Low]: 'Low',\n  [LiabilitySeverity.Info]: 'Info',\n};\n\nexport function showLiabilityScannerDialog(): void {\n  const df = grok.shell.tv?.dataFrame;\n  if (!df) {\n    grok.shell.warning('No table open');\n    return;\n  }\n\n  const seqCols = df.columns.bySemTypeAll(DG.SEMTYPE.MACROMOLECULE);\n  if (seqCols.length === 0) {\n    grok.shell.warning('No macromolecule columns found');\n    return;\n  }\n\n  const rules = BUILTIN_LIABILITY_RULES.map((r) => ({...r, pattern: new RegExp(r.pattern.source, 'g')}));\n\n  const tableInput = ui.input.table('Table', {value: df});\n  const seqInput = ui.input.column('Sequence', {\n    table: df, value: seqCols[0],\n    filter: (col: DG.Column) => col.semType === DG.SEMTYPE.MACROMOLECULE,\n  });\n\n  // Rule checkboxes\n  const ruleChecks: {rule: LiabilityRule; input: DG.InputBase<boolean>}[] = [];\n  const rulesDiv = ui.divV([]);\n  for (const rule of rules) {\n    const check = ui.input.bool(rule.name, {\n      value: rule.enabled,\n      tooltipText: `Severity: ${severityLabels[rule.severity] ?? rule.severity}`,\n    });\n    ruleChecks.push({rule, input: check});\n    rulesDiv.append(check.root);\n  }\n\n  const highlightInput = ui.input.bool('Highlight in cell renderer', {value: true});\n  const annotColInput = ui.input.bool('Create annotation column', {value: true});\n  const summaryInput = ui.input.bool('Create summary count column', {value: false});\n\n  const dialog = ui.dialog({title: 'Scan Sequence Liabilities'})\n    .add(ui.inputs([tableInput, seqInput]))\n    .add(ui.h3('Rules'))\n    .add(rulesDiv)\n    .add(ui.h3('Output'))\n    .add(ui.inputs([highlightInput, annotColInput, summaryInput]))\n    .onOK(() => {\n      try {\n        const seqCol = seqInput.value!;\n        const sh = _package.seqHelper.getSeqHandler(seqCol);\n\n        // Apply checkbox state\n        for (const {rule, input} of ruleChecks)\n          rule.enabled = input.value;\n\n        const result = scanLiabilities(seqCol, sh, rules);\n\n        if (annotColInput.value || highlightInput.value)\n          applyLiabilityScanResults(df, seqCol, result);\n\n        if (summaryInput.value)\n          createLiabilitySummaryColumn(df, seqCol, result);\n\n        grok.shell.info(`Liability scan: ${result.totalHits} hits found across ${result.annotations.length} rules`);\n        df.fireValuesChanged();\n      } catch (err: any) {\n        grok.shell.error(`Liability scan failed: ${err.message ?? err}`);\n        console.error(err);\n      }\n    });\n\n  dialog.show();\n}\n"],"names":["BUILTIN_LIABILITY_RULES","id","name","pattern","length","severity","High","ruleCategory","color","liability","deamidation","enabled","Medium","Low","isomerization","oxidation","glycosylation","Info","freeCysteine","getCanonicalString","sh","rowIdx","splitted","getSplitted","chars","Array","i","getOriginal","join","severityLabels","showLiabilityScannerDialog","df","tv","dataFrame","warning","seqCols","columns","bySemTypeAll","MACROMOLECULE","rules","map","r","RegExp","source","tableInput","table","value","seqInput","column","filter","col","semType","ruleChecks","rulesDiv","rule","check","bool","tooltipText","push","input","append","root","highlightInput","annotColInput","summaryInput","dialog","title","add","onOK","seqCol","_package","seqHelper","getSeqHandler","result","enabledRules","posList","ruleHitCounts","Map","rowData","totalHits","seq","hits","match","lastIndex","exec","annotationId","positionIndex","index","positionName","undefined","matchedMonomers","set","get","annotations","has","description","start","end","visualType","Point","Motif","category","Liability","motifPattern","autoGenerated","scanLiabilities","existing","a","annotCol","existingHits","applyLiabilityScanResults","colName","counts","addNewInt","createLiabilitySummaryColumn","info","fireValuesChanged","err","error","message","console","show"],"sourceRoot":""}