@datagrok/peptides 0.8.12 → 0.8.15

package/src/widgets/peptide-molecule.ts

@@ -1,8 +1,8 @@
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
-// import {ChemPalette} from '../utils/chem-palette';
-import {PeptidesController} from '../peptides';
+import * as C from '../utils/constants';
+import {PeptidesModel} from '../model';
 
 /**
  * 3D representation widget of peptide molecule.
@@ -11,40 +11,63 @@ import {PeptidesController} from '../peptides';
  * @param {string} pep Peptide string.
  * @return {Promise<DG.Widget>} Widget.
  */
-export async function peptideMoleculeWidget(pep: string): Promise<DG.Widget> {
+export async function peptideMoleculeWidget(pep: string, currentTable: DG.DataFrame): Promise<DG.Widget> {
   const pi = DG.TaskBarProgressIndicator.create('Creating NGL view');
+  const separator = currentTable.columns.bySemType(C.SEM_TYPES.ALIGNED_SEQUENCE)!.tags[C.TAGS.SEPARATOR];
 
-  const smiles = getMolecule(pep);
-  if (smiles == '')
-    return new DG.Widget(ui.divH([]));
+  let widgetHost;
+  let smiles = '';
+  let molfileStr = '';
+  try {
+    try {
+      const params = {table: currentTable};
+      const result = await grok.functions.call('Customerextensions:getPeptideStructure', params) as string[];
+      if (result.length !== 0) {
+        smiles = result[0];
+        molfileStr = result[1];
+        throw new Error(`Found structure in DB`);
+      }
 
+      smiles = getMolecule(pep, separator);
+      if (smiles == '')
+        throw new Error('Couldn\'t get smiles');
 
-  let molfileStr = (await grok.functions.call('Peptides:SmiTo3D', {smiles}));
+      molfileStr = (await grok.functions.call('Peptides:SmiTo3D', {smiles})) as string;
+    } catch (e) {
+      console.warn(e);
+    }
 
-  molfileStr = molfileStr.replaceAll('\\n', '\n'); ;
-  const stringBlob = new Blob([molfileStr], {type: 'text/plain'});
-  const nglHost = ui.div([], {classes: 'd4-ngl-viewer', id: 'ngl-3d-host'});
+    try {
+      molfileStr = molfileStr.replaceAll('\\n', '\n');
+      const stringBlob = new Blob([molfileStr], {type: 'text/plain'});
+      const nglHost = ui.div([], {classes: 'd4-ngl-viewer', id: 'ngl-3d-host'});
 
-  //@ts-ignore
-  const stage = new NGL.Stage(nglHost, {backgroundColor: 'white'});
-  //@ts-ignore
-  stage.loadFile(stringBlob, {ext: 'sdf'}).then(function(comp: NGL.StructureComponent) {
-    stage.setSize(300, 300);
-    comp.addRepresentation('ball+stick');
-    comp.autoView();
-  });
-  const sketch = grok.chem.svgMol(smiles);
-  const panel = ui.divH([sketch]);
+      //@ts-ignore
+      const stage = new NGL.Stage(nglHost, {backgroundColor: 'white'});
+      //@ts-ignore
+      stage.loadFile(stringBlob, {ext: 'sdf'}).then(function(comp: NGL.StructureComponent) {
+        stage.setSize(300, 300);
+        comp.addRepresentation('ball+stick');
+        comp.autoView();
+      });
+      const sketch = grok.chem.svgMol(molfileStr);
+      const panel = ui.divH([sketch]);
 
+      widgetHost = ui.div([panel, nglHost]);
+    } catch (e) {
+      widgetHost = ui.divText('Couldn\'t get peptide structure');
+    }
+  } catch (e) {
+    widgetHost = ui.divText('Couldn\'t get peptide structure');
+  }
   pi.close();
-
-  return new DG.Widget(ui.div([panel, nglHost]));
+  return new DG.Widget(widgetHost);
 }
 
-export function getMolecule(pep: string): string {
-  const split = pep.split('-');
+export function getMolecule(pep: string, separator: string): string {
+  const split = pep.split(separator);
   const mols = [];
-  const chemPalette = PeptidesController.chemPalette;
+  const chemPalette = PeptidesModel.chemPalette;
   for (let i = 1; i < split.length - 1; i++) {
     if (split[i] in chemPalette.AASmiles) {
       const aar = chemPalette.AASmiles[split[i]];

package/src/widgets/subst-table.ts

@@ -1,73 +1,58 @@
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
-import { PeptidesController } from '../peptides';
+import * as C from '../utils/constants';
+import * as type from '../utils/types';
+import {PeptidesModel} from '../model';
 
 export async function substitutionsWidget(table: DG.DataFrame): Promise<DG.Widget> {
-  const controller = await PeptidesController.getInstance(table);
-  controller.init(table);
-  const substTable = controller.getSubstitutions();
+  const model = await PeptidesModel.getInstance(table);
+  const substInfo = model.substitutionsInfo;
+  const currentCell = model.getCurrentAARandPos();
 
-  if (!substTable)
+  if (currentCell.aar === currentCell.pos)
     return new DG.Widget(ui.label('No substitution table generated'));
 
-  const dfRowCount = substTable.rowCount;
-  const aminoInputFrom = ui.stringInput('from', '');
-  const aminoInputTo = ui.stringInput('to', '');
-  const fromToMap: {[key: string]: DG.BitSet} = {};
-  let aminoFrom = '';
-  let aminoTo = '';
-  const initialCol: DG.Column = substTable.getCol('Initial');
-  const substitutedCol: DG.Column = substTable.getCol('Substituted');
-
-  initialCol.semType = 'alignedSequenceDifference';
-  initialCol.name = 'Substitution';
-  // substTable.columns.remove('Substituted');
-  // const substCol = table.getCol('Substitution');
-
-  for (let i = 0; i < dfRowCount; ++i) {
-    // const [from, to] = substCol!.get(i).split('#');
-    const from = initialCol.get(i);
-    const to = substitutedCol.get(i);
-    const aminosFrom: [] = from.split('-');
-    const aminosTo: [] = to.split('-');
-
-    for (let j = 0; j < aminosFrom.length; ++j) {
-      if (aminosFrom[j] != aminosTo[j]) {
-        const idx = `${getAmino(aminosFrom[j])}#${getAmino(aminosTo[j])}`;
+  const substitutionsMap =
+    substInfo.get(currentCell.aar)?.get(currentCell.pos) as Map<number, type.UTypedArray> | undefined;
+  if (typeof substitutionsMap === 'undefined')
+    return new DG.Widget(ui.label('No substitution table generated'));
 
-        if (!(idx in fromToMap))
-          fromToMap[idx] = DG.BitSet.create(dfRowCount);
-        fromToMap[idx].set(i, true);
-      }
+  const substitutionsArray: string[] = [];
+  const deltaArray: number[] = [];
+  const substitutedToArray: string[] = [];
+  // const alignedSeqCol = table.getCol(C.COLUMNS_NAMES.ALIGNED_SEQUENCE);
+  // const activityScaledCol = table.getCol(C.COLUMNS_NAMES.ACTIVITY_SCALED);
+  const alignedSeqCol = table.columns.bySemType(C.SEM_TYPES.ALIGNED_SEQUENCE)!;
+  const activityScaledCol = table.columns.bySemType(C.SEM_TYPES.ACTIVITY_SCALED)!;
+  const posCol = table.getCol(currentCell.pos);
+  for (const [referenceIdx, indexArray] of substitutionsMap.entries()) {
+    const baseSequence = alignedSeqCol.get(referenceIdx);
+    const baseActivity = activityScaledCol.get(referenceIdx);
+    for (const subIdx of indexArray) {
+      substitutionsArray.push(`${baseSequence}#${alignedSeqCol.get(subIdx)}`);
+      deltaArray.push(baseActivity - activityScaledCol.get(subIdx));
+      substitutedToArray.push(posCol.get(subIdx));
     }
   }
-
-  for (let i = 0; i < initialCol.length; ++i) {
-    const sequenceDifference = `${initialCol.get(i)}#${substitutedCol.get(i)}`;
-    initialCol.set(i, sequenceDifference);
-  }
-
-  aminoInputFrom.onInput(() => {
-    aminoFrom = getAmino(aminoInputFrom.value);
-    const fromKey = `${aminoFrom}#${aminoTo}`;
-    if (fromKey in fromToMap)
-      substTable.selection.copyFrom(fromToMap[fromKey]);
-  });
-
-  aminoInputTo.onInput(() => {
-    aminoTo = getAmino(aminoInputTo.value);
-    const toKey = `${aminoFrom}#${aminoTo}`;
-    if (toKey in fromToMap)
-      substTable.selection.copyFrom(fromToMap[toKey]);
+  const substCol = DG.Column.fromStrings('Substiutions', substitutionsArray);
+  substCol.semType = C.SEM_TYPES.ALIGNED_SEQUENCE_DIFFERENCE;
+  const toColName = '~to';
+  const hiddenSubstToAarCol = DG.Column.fromStrings(toColName, substitutedToArray);
+  const substTable =
+    DG.DataFrame.fromColumns([substCol, DG.Column.fromList('double', 'Delta', deltaArray), hiddenSubstToAarCol]);
+
+  const aminoToInput = ui.stringInput('Substituted to:', '', () => {
+    const substitutedToAar = aminoToInput.stringValue;
+    if (substitutedToAar != '')
+      substTable.filter.init((idx) => hiddenSubstToAarCol.get(idx) === substitutedToAar);
+    else
+      substTable.filter.setAll(true);
   });
 
   const grid = substTable.plot.grid();
   grid.props.allowEdit = false;
-  grid.root.style.width = 'auto';
-  grid.root.style.height = '150px';
-  return new DG.Widget(ui.divV([aminoInputFrom.root, aminoInputTo.root, grid.root]));
-}
-
-function getAmino(amino: string): string {
-  return amino === '' ? '-' : amino;
+  const gridRoot = grid.root;
+  gridRoot.style.width = 'auto';
+  gridRoot.style.height = '150px';
+  return new DG.Widget(ui.divV([aminoToInput.root, gridRoot]));
 }

package/src/workers/dimensionality-reducer.ts

@@ -1,6 +1,5 @@
 import {DimensionalityReducer, KnownMethods} from '@datagrok-libraries/ml/src/reduce-dimensionality';
 import {KnownMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
-import {Coordinates} from '@datagrok-libraries/utils/src/type-declarations';
 
 /**
  * Worker thread receiving data function.
@@ -8,23 +7,24 @@ import {Coordinates} from '@datagrok-libraries/utils/src/type-declarations';
  * @param {any[]} columnData Samples to process.
  * @param {string} method Embedding method.
  * @param {string} measure Distance metric.
- * @param {number} cyclesCount Number of cycles to repeat.
- * @return {Coordinates} Embedding.
+ * @param {any} options Options to pass to algorithm.
+ * @return {any} Embedding (and distance matrix where applicable).
  */
-function onMessage(columnData: any[], method: KnownMethods, measure: KnownMetrics, cyclesCount: number): Coordinates {
+function onMessage(columnData: any[], method: KnownMethods, measure: KnownMetrics, options: any): any {
   const reducer = new DimensionalityReducer(
     columnData,
     method,
     measure,
-    {cycles: cyclesCount},
+    options,
   );
   return reducer.transform(true);
 }
 
-self.onmessage = ({data: {columnData, method, measure, cyclesCount}}) => {
-  const embedding = onMessage(columnData, method, measure, cyclesCount);
+self.onmessage = ({data: {columnData, method, measure, options}}): void => {
+  const embedding = onMessage(columnData, method, measure, options);
   self.postMessage({
-    embedding: embedding,
+    distance: embedding.distance,
+    embedding: embedding.embedding,
   });
 };
 

package/{test-Peptides-414a1874a71a-2f1c6575.html → test-Peptides-e702a345ac13-2a8c8b59.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=414a1874a71a. Commit 2f1c6575.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=e702a345ac13. Commit 2a8c8b59.</title><style type="text/css">html,
 body {
   font-family: Arial, Helvetica, sans-serif;
   font-size: 1rem;
@@ -229,21 +229,14 @@ header {
   font-size: 1rem;
   padding: 0 0.5rem;
 }
-</style></head><body><div id="jesthtml-content"><header><h1 id="title">Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=414a1874a71a. Commit 2f1c6575.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-04-29 11:32:43</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts</div><div class="suite-time warn">119.379s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">100.001s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: thrown: "Exceeded timeout of 100000 ms for a test.
-Use jest.setTimeout(newTimeout) to increase the timeout value, if this is a long-running test."
-    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:22:1)
-    at Runtime._execModule (/home/runner/work/public/public/packages/Peptides/node_modules/jest-runtime/build/index.js:1646:24)
-    at Runtime._loadModule (/home/runner/work/public/public/packages/Peptides/node_modules/jest-runtime/build/index.js:1185:12)
-    at Runtime.requireModule (/home/runner/work/public/public/packages/Peptides/node_modules/jest-runtime/build/index.js:1009:12)
-    at jestAdapter (/home/runner/work/public/public/packages/Peptides/node_modules/jest-circus/build/legacy-code-todo-rewrite/jestAdapter.js:79:13)
-    at runTestInternal (/home/runner/work/public/public/packages/Peptides/node_modules/jest-runner/build/runTest.js:389:16)
-    at runTest (/home/runner/work/public/public/packages/Peptides/node_modules/jest-runner/build/runTest.js:475:34)
-    at TestRunner.runTests (/home/runner/work/public/public/packages/Peptides/node_modules/jest-runner/build/index.js:101:12)
-    at TestScheduler.scheduleTests (/home/runner/work/public/public/packages/Peptides/node_modules/@jest/core/build/TestScheduler.js:333:13)
-    at runJest (/home/runner/work/public/public/packages/Peptides/node_modules/@jest/core/build/runJest.js:404:19)
-    at _run10000 (/home/runner/work/public/public/packages/Peptides/node_modules/@jest/core/build/cli/index.js:320:7)
-    at runCLI (/home/runner/work/public/public/packages/Peptides/node_modules/@jest/core/build/cli/index.js:173:3)
-    at Object.run (/home/runner/work/public/public/packages/Peptides/node_modules/jest-cli/build/cli/index.js:155:37)</pre></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Peptides/src/__jest__/test-node.ts:62:11)
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=e702a345ac13. Commit 2a8c8b59.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-06-06 21:05:18</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts</div><div class="suite-time warn">105.848s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">95.396s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: expect(received).toBe(expected) // Object.is equality
+
+Expected: false
+Received: true
+    at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:49:20
+    at Generator.next (&lt;anonymous&gt;)
+    at fulfilled (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:24:58)
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Peptides/src/__jest__/test-node.ts:62:11)
     at Generator.next (&lt;anonymous&gt;)
     at fulfilled (/home/runner/work/public/public/packages/Peptides/src/__jest__/test-node.ts:24:58)
     at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Using web root: http://localhost:8080</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:24:11
@@ -253,4 +246,9 @@ Use jest.setTimeout(newTimeout) to increase the timeout value, if this is a long
     at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:23:12)
     at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:22:23)
     at Promise.then.completed (/home/runner/work/public/public/packages/Peptides/node_modules/jest-circus/build/utils.js:391:28)
-    at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing Peptides package</pre></div></div></div></div></body></html>
+    at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing Peptides package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:47:11
+    at Generator.next (&lt;anonymous&gt;)
+    at fulfilled (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:24:58)
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Core.Start analysis: simple: Operation caused an exception (FileSystemException: Cannot open file, path = '/home/grok/data/prod/packages/data/Peptides/HELMMonomers_June10.sdf' (OS Error: No such file or directory, errno = 2))
+Core.Start analysis: сomplex: Operation caused an exception (FileSystemException: Cannot open file, path = '/home/grok/data/prod/packages/data/Peptides/HELMMonomers_June10.sdf' (OS Error: No such file or directory, errno = 2))
+</pre></div></div></div></div></body></html>

package/src/peptides.ts

@@ -1,327 +0,0 @@
-import * as grok from 'datagrok-api/grok';
-import * as DG from 'datagrok-api/dg';
-import {PeptidesModel} from './model';
-import {SARViewer, SARViewerVertical} from './viewers/sar-viewer';
-import {ChemPalette} from './utils/chem-palette';
-import {Observable} from 'rxjs';
-import {MonomerLibrary} from './monomer-library';
-import {_package} from './package';
-import {setAARRenderer} from './utils/cell-renderer';
-import * as C from './utils/constants';
-import {PeptideSpaceViewer} from './viewers/peptide-space-viewer';
-import { FilteringStatistics } from './utils/filtering-statistics';
-
-type viewerTypes = SARViewer | SARViewerVertical;
-export class PeptidesController {
-  private static _controllerName: string = 'peptidesController';
-  private helpUrl = '/help/domains/bio/peptides.md';
-
-  private _model: PeptidesModel;
-  sarViewer!: SARViewer;
-  sarViewerVertical!: SARViewerVertical;
-  isInitialized = false;
-
-  private constructor(dataFrame: DG.DataFrame) {
-    this._model = PeptidesModel.getInstance(dataFrame);
-  }
-
-  static async getInstance(dataFrame: DG.DataFrame): Promise<PeptidesController> {
-    dataFrame.temp[PeptidesController.controllerName] ??= new PeptidesController(dataFrame);
-    if (dataFrame.temp[MonomerLibrary.id] === null) {
-      const sdf = await _package.files.readAsText('HELMMonomers_June10.sdf');
-      dataFrame.temp[MonomerLibrary.id] ??= new MonomerLibrary(sdf);
-    }
-    return dataFrame.temp[PeptidesController.controllerName];
-  }
-
-  static get controllerName() {return PeptidesController._controllerName;}
-
-  get dataFrame() {return this._model.dataFrame;}
-
-  static setAARRenderer(col: DG.Column, grid: DG.Grid) {
-    return setAARRenderer(col, grid);
-  }
-
-  get onStatsDataFrameChanged(): Observable<DG.DataFrame> {return this._model.onStatsDataFrameChanged;}
-
-  get onSARGridChanged(): Observable<DG.Grid> {return this._model.onSARGridChanged;}
-
-  get onSARVGridChanged(): Observable<DG.Grid> {return this._model.onSARVGridChanged;}
-
-  // get onGroupMappingChanged(): Observable<StringDictionary> {return this._model.onGroupMappingChanged;}
-
-  get onSubstTableChanged(): Observable<DG.DataFrame> {return this._model.onSubstTableChanged;}
-
-  async updateDefault() {await this._model.updateDefault();}
-
-  get sarGrid() {return this._model._sarGrid;}
-
-  get sarVGrid() {return this._model._sarVGrid;}
-
-  get sourceGrid() {return this._model._sourceGrid!; }
-
-  async updateData(
-    activityScaling?: string, sourceGrid?: DG.Grid, twoColorMode?: boolean, activityLimit?: number,
-    maxSubstitutions?: number, isSubstitutionOn?: boolean, filterMode?: boolean,
-  ) {
-    filterMode ??= false;
-    await this._model.updateData(
-      activityScaling, sourceGrid, twoColorMode, activityLimit, maxSubstitutions, isSubstitutionOn, filterMode);
-  }
-
-  getSubstitutions() {
-    return this._model.getSubstitutionTable();
-  }
-
-  static async scaleActivity(
-    activityScaling: string, df: DG.DataFrame, originalActivityName?: string, cloneBitset = false,
-  ): Promise<[DG.DataFrame, string]> {
-    // const df = sourceGrid.dataFrame!;
-    let currentActivityColName = originalActivityName ?? C.COLUMNS_NAMES.ACTIVITY;
-    const flag = (df.columns as DG.ColumnList).names().includes(currentActivityColName) &&
-      currentActivityColName === originalActivityName;
-    currentActivityColName = flag ? currentActivityColName : C.COLUMNS_NAMES.ACTIVITY;
-    const tempDf = df.clone(cloneBitset ? df.filter : null, [currentActivityColName]);
-
-    let formula = '${' + currentActivityColName + '}';
-    let newColName = 'activity'; //originalActivityName ?? df.temp[C.COLUMNS_NAMES.ACTIVITY] ?? currentActivityColName;
-    switch (activityScaling) {
-    case 'none':
-      break;
-    case 'lg':
-      formula = `Log10(${formula})`;
-      newColName = `Log10(${newColName})`;
-      break;
-    case '-lg':
-      formula = `-1*Log10(${formula})`;
-      newColName = `-Log10(${newColName})`;
-      break;
-    default:
-      throw new Error(`ScalingError: method \`${activityScaling}\` is not available.`);
-    }
-
-    await (tempDf.columns as DG.ColumnList).addNewCalculated(C.COLUMNS_NAMES.ACTIVITY_SCALED, formula);
-    df.tags['scaling'] = activityScaling;
-
-    return [tempDf, newColName];
-  }
-
-  get originalActivityColumnName(): string {return this.dataFrame.temp[C.COLUMNS_NAMES.ACTIVITY];}
-
-  get substTooltipData() {return this._model.substTooltipData;}
-
-  static splitAlignedPeptides(peptideColumn: DG.Column, filter: boolean = true): [DG.DataFrame, number[]] {
-    const splitPeptidesArray: string[][] = [];
-    let currentSplitPeptide: string[];
-    let modeMonomerCount = 0;
-    let currentLength;
-    const colLength = peptideColumn.length;
-
-    // splitting data
-    const monomerLengths: {[index: string]: number} = {};
-    for (let i = 0; i < colLength; i++) {
-      currentSplitPeptide = peptideColumn.get(i).split('-').map((value: string) => value ? value : '-');
-      splitPeptidesArray.push(currentSplitPeptide);
-      currentLength = currentSplitPeptide.length;
-      monomerLengths[currentLength + ''] =
-        monomerLengths[currentLength + ''] ? monomerLengths[currentLength + ''] + 1 : 1;
-    }
-    //@ts-ignore: what I do here is converting string to number the most effective way I could find. parseInt is slow
-    modeMonomerCount = 1 * Object.keys(monomerLengths).reduce((a, b) => monomerLengths[a] > monomerLengths[b] ? a : b);
-
-    // making sure all of the sequences are of the same size
-    // and marking invalid sequences
-    let nTerminal: string;
-    const invalidIndexes: number[] = [];
-    let splitColumns: string[][] = Array.from({length: modeMonomerCount}, (_) => []);
-    modeMonomerCount--; // minus N-terminal
-    for (let i = 0; i < colLength; i++) {
-      currentSplitPeptide = splitPeptidesArray[i];
-      nTerminal = currentSplitPeptide.pop()!; // it is guaranteed that there will be at least one element
-      currentLength = currentSplitPeptide.length;
-      if (currentLength !== modeMonomerCount)
-        invalidIndexes.push(i);
-
-      for (let j = 0; j < modeMonomerCount; j++)
-        splitColumns[j].push(j < currentLength ? currentSplitPeptide[j] : '-');
-
-      splitColumns[modeMonomerCount].push(nTerminal);
-    }
-    modeMonomerCount--; // minus C-terminal
-
-    //create column names list
-    const columnNames = Array.from({length: modeMonomerCount}, (_, index) => `${index + 1 < 10 ? 0 : ''}${index + 1 }`);
-    columnNames.splice(0, 0, 'Nterminal');
-    columnNames.push('Cterminal');
-
-    // filter out the columns with the same values
-    if (filter) {
-      splitColumns = splitColumns.filter((positionArray, index) => {
-        const isRetained = new Set(positionArray).size > 1;
-        if (!isRetained)
-          columnNames.splice(index, 1);
-
-        return isRetained;
-      });
-    }
-
-    return [
-      DG.DataFrame.fromColumns(splitColumns.map((positionArray, index) => {
-        return DG.Column.fromList('string', columnNames[index], positionArray);
-      })),
-      invalidIndexes,
-    ];
-  }
-
-  static get chemPalette() { return ChemPalette; }
-
-  assertVar(variable: string, init = false): boolean {
-    //@ts-ignore
-    let foundVariable: any = this[variable];
-    if (!foundVariable && init) {
-      //@ts-ignore
-      this[variable] = foundVariable = this.dataFrame.temp[variable];
-    }
-
-    const assertionResult = foundVariable ? true : false
-    if (init && !assertionResult)
-      throw new Error(`Variable assertion error: variable '${variable}' is not found in dataFrame`);
-      
-    return assertionResult;
-  }
-
-  assertVariables(variables: string[], init = false) {
-    let result = true;
-    for (const variable of variables)
-      result &&= this.assertVar(variable, init);
-
-    return result;
-  }
-
-  syncProperties(isSourceSAR = true) {
-    this.assertVariables(['sarViewer', 'sarViewerVertical'], true);
-    const sourceViewer = isSourceSAR ? this.sarViewer : this.sarViewerVertical;
-    const targetViewer = isSourceSAR ? this.sarViewerVertical : this.sarViewer;
-    const properties = sourceViewer.props.getProperties();
-    for (const property of properties)
-      targetViewer.props.set(property.name, property.get(sourceViewer));
-  }
-
-  modifyOrCreateSplitCol(aar: string, position: string, notify: boolean = true) {
-    this._model.modifyOrCreateSplitCol(aar, position);
-    if (notify)
-      this._model.fireBitsetChanged();
-  }
-
-  setSARGridCellAt(aar: string, position: string) {
-    const sarDf = this.sarGrid.dataFrame;
-    const aarCol = sarDf.getCol(C.COLUMNS_NAMES.AMINO_ACID_RESIDUE);
-    const aarColLen = aarCol.length;
-    let index = -1;
-    for (let i = 0; i < aarColLen; i++) {
-      if (aarCol.get(i) === aar) {
-        index = i;
-        break;
-      }
-    }
-    position = position === C.CATEGORIES.ALL ? C.COLUMNS_NAMES.AMINO_ACID_RESIDUE : position;
-    sarDf.currentCell = sarDf.cell(index, position);
-  }
-
-  /**
-   * Class initializer
-   *
-   * @param {DG.Grid} sourceGrid Working talbe grid.
-   * @param {DG.TableView} currentView Working view.
-   * @param {DG.DataFrame} currentDf Working table.
-   * @param {StringDictionary} options SAR viewer options
-   * @param {DG.Column} col Aligned sequences column.
-   * @memberof Peptides
-   */
-  async init(table: DG.DataFrame) {
-    if (this.isInitialized)
-      return;
-    this.isInitialized = true;
-    //calculate initial stats
-    const stats = new FilteringStatistics();
-    const activityScaledCol = table.getCol(C.COLUMNS_NAMES.ACTIVITY_SCALED);
-    stats.setData(activityScaledCol.getRawData() as Float32Array);
-    stats.setMask(table.selection);
-    table.temp[C.STATS] = stats;
-
-    //set up views
-    let currentView = grok.shell.v as DG.TableView ;
-    if (currentView.dataFrame.tags['isPeptidesAnalysis'] !== 'true')
-      currentView = grok.shell.addTableView(table);
-    const sourceGrid = currentView.grid;
-    sourceGrid.col(C.COLUMNS_NAMES.ACTIVITY_SCALED)!.name = table.temp[C.COLUMNS_NAMES.ACTIVITY_SCALED];
-    sourceGrid.columns.setOrder([table.temp[C.COLUMNS_NAMES.ACTIVITY_SCALED]]);
-    
-    this.dataFrame.temp[C.EMBEDDING_STATUS] = false;
-    function adjustCellSize(grid: DG.Grid) {
-      const colNum = grid.columns.length;
-      for (let i = 0; i < colNum; ++i) {
-        const iCol = grid.columns.byIndex(i)!;
-        iCol.width = isNaN(parseInt(iCol.name)) ? 50 : 40;
-      }
-      grid.props.rowHeight = 20;
-    }
-
-    for (let i = 0; i < sourceGrid.columns.length; i++) {
-      const aarCol = sourceGrid.columns.byIndex(i);
-      if (aarCol && aarCol.name && aarCol.column?.semType !== C.SEM_TYPES.AMINO_ACIDS &&
-        aarCol.name !== this.dataFrame.temp[C.COLUMNS_NAMES.ACTIVITY_SCALED]
-      )
-        sourceGrid.columns.byIndex(i)!.visible = false;
-    }
-
-    const options = {scaling: table.tags['scaling']};
-    await this.updateData(table.tags['scaling'], sourceGrid, false, 1, 2, false, false);
-
-    const dockManager = currentView.dockManager;
-
-    this.dataFrame.temp['sarViewer'] = this.sarViewer =
-      await this.dataFrame.plot.fromType('peptide-sar-viewer', options) as SARViewer;
-    this.sarViewer.helpUrl = this.helpUrl;
-
-    this.dataFrame.temp['sarViewerVertical'] = this.sarViewerVertical =
-      await this.dataFrame.plot.fromType('peptide-sar-viewer-vertical', options) as SARViewerVertical;
-      this.sarViewerVertical.helpUrl = this.helpUrl;
-
-    const sarViewersGroup: viewerTypes[] = [this.sarViewer, this.sarViewerVertical];
-
-    const peptideSpaceViewerOptions = {method: 't-SNE', measure: 'Levenshtein', cyclesCount: 100};
-    const peptideSpaceViewer =
-      await this.dataFrame.plot.fromType('peptide-space-viewer', peptideSpaceViewerOptions) as PeptideSpaceViewer;
-    dockManager.dock(peptideSpaceViewer, DG.DOCK_TYPE.RIGHT, null, 'Peptide Space Viewer');
-
-    dockViewers(sarViewersGroup, DG.DOCK_TYPE.RIGHT, dockManager, DG.DOCK_TYPE.DOWN);
-
-    sourceGrid.props.allowEdit = false;
-    adjustCellSize(sourceGrid);
-
-    // this._model._sarGrid.invalidate();
-    // this._model._sarVGrid.invalidate();
-    this._model.invalidateGrids();
-  }
-
-  invalidateSourceGrid() { this.sourceGrid.invalidate(); }
-}
-
-function dockViewers(
-  viewerList: viewerTypes[], attachDirection: DG.DockType, dockManager: DG.DockManager,
-  initialAttachDirection?: DG.DockType): DG.DockNode[] | null {
-  const viewerListLength = viewerList.length;
-  if (viewerListLength === 0)
-    return null;
-
-  let currentViewer = viewerList[0];
-  const nodeList = [dockManager.dock(currentViewer, initialAttachDirection, null, currentViewer.name ?? '')];
-  const ratio = 1 / viewerListLength;
-
-  for (let i = 1; i < viewerListLength; i++) {
-    currentViewer = viewerList[i];
-    nodeList.push(dockManager.dock(currentViewer, attachDirection, nodeList[i - 1], currentViewer.name ?? '', ratio));
-  }
-  return nodeList;
-}

package/src/semantics.ts

@@ -1,5 +0,0 @@
-export const SEMTYPE = {
-  ALIGNED: 'alignedSequence',
-};
-
-