@datagrok/peptides 0.8.13 → 1.0.0

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',
-};
-
-

package/src/tests/peptides-tests.ts

@@ -1,60 +0,0 @@
-import {after, before, category, test} from '@datagrok-libraries/utils/src/test';
-import {StringDictionary} from '@datagrok-libraries/utils/src/type-declarations';
-import * as DG from 'datagrok-api/dg';
-import * as grok from 'datagrok-api/grok';
-import {PeptidesController} from '../peptides';
-import {analyzePeptidesWidget} from '../widgets/analyze-peptides';
-import {manualAlignmentWidget} from '../widgets/manual-alignment';
-import {peptideMoleculeWidget} from '../widgets/peptide-molecule';
-import {_packageTest} from '../package-test';
-
-category('peptides', async () => {
-  let peptidesDf: DG.DataFrame;
-  let options: StringDictionary;
-  // let peptidesGrid: DG.Grid;
-  let asCol: DG.Column;
-  // let pepView: DG.TableView;
-
-  before(async () => {
-    peptidesDf = DG.DataFrame.fromCsv(await _packageTest.files.readAsText('aligned.csv'));
-    options = {
-      activityColumnName: 'IC50',
-      scaling: '-lg',
-    };
-    asCol = peptidesDf.getCol('AlignedSequence');
-    // pepView = grok.shell.addTableView(peptidesDf);
-    // peptidesGrid = pepView.grid;
-  });
-
-  test('utils.split-sequence', async () => {
-    PeptidesController.splitAlignedPeptides(peptidesDf.getCol('AlignedSequence'));
-  });
-
-  // test('describe', async () => {
-  //   await describe(
-  //     peptidesDf, options['activityColumnName'], options['scaling'], peptidesGrid, true,
-  //     DG.BitSet.create(peptidesDf.rowCount, (i) => i % 2 === 0), true);
-  // });
-
-  test('Peptides-controller', async () => {
-    const peptides = await PeptidesController.getInstance(peptidesDf);
-    peptides.init(peptidesDf); //, peptidesDf.columns.names());
-  });
-
-  test('widgets.analyze-peptides', async () => {
-    await analyzePeptidesWidget(peptidesDf, asCol);
-  });
-
-  test('widgets.manual-alignment', async () => {
-    manualAlignmentWidget(asCol, peptidesDf);
-  });
-
-  test('widgets.peptide-molecule', async () => {
-    await peptideMoleculeWidget('NH2--A-N-T-T-Y-K-N-Y-R-S-N-L-L--COOH');
-  });
-
-  after(async () => {
-    // pepView.close();
-    grok.shell.closeTable(peptidesDf);
-  });
-});