@datagrok/peptides 0.8.6 → 0.8.7

package/src/tests/utils.ts

@@ -5,6 +5,17 @@ import {PeptideSimilaritySpaceWidget, createPeptideSimilaritySpaceViewer} from '
 import {
   createDimensinalityReducingWorker,
 } from '@datagrok-libraries/ml/src/workers/dimensionality-reducing-worker-creator';
+import {runKalign} from '../utils/multiple-sequence-alignment';
+import { StringMetrics } from '@datagrok-libraries/ml/src/typed-metrics';
+
+/**
+ * Tests if a table has non zero rows and columns.
+ *
+ * @param {DG.DataFrame} table Target table.
+ */
+export function _testTableIsNotEmpty(table: DG.DataFrame) {
+  expect(table.columns.length > 0 && table.rowCount > 0, true);
+}
 
 /**
  * Tests if peptide space viewer is drawing without exceptions.
@@ -31,9 +42,18 @@ export async function _testViewerIsDrawing(table: DG.DataFrame, view: DG.TableVi
  * @param {string} method Embedding method.
  * @param {string} measure Measure to apply to a pair of strings.
  */
-export async function _testDimensionalityReducer(columnData: Array<string>, method: string, measure: string) {
+export async function _testDimensionalityReducer(columnData: Array<string>, method: StringMetrics, measure: string) {
+  let noException = true;
   const cyclesCount = 100;
-  const embcols = await createDimensinalityReducingWorker(columnData, method, measure, cyclesCount);
+  let embcols;
+
+  try {
+    embcols = await createDimensinalityReducingWorker({data: columnData, metric: measure as StringMetrics}, method, cyclesCount);
+  } catch (error) {
+    noException = false;
+  }
+  expect(noException, true);
+
   const [X, Y] = embcols as Array<Float32Array>;
 
   expect(X.every((v) => v !== null && v !== NaN), true);
@@ -58,20 +78,28 @@ export async function _testPeptideSimilaritySpaceViewer(
   method: string,
   measure: string,
   cyclesCount: number,
-  //view: DG.TableView | null,
-  //activityColumnName?: string | null,
 ) {
-  const viewer = await createPeptideSimilaritySpaceViewer(
-    table,
-    alignedSequencesColumn,
-    method,
-    measure,
-    cyclesCount,
-    null, //    view,
-    //    activityColumnName,
-  );
-  const df = viewer.dataFrame;
   let noException = true;
+  let viewer;
+  let df: DG.DataFrame;
+
+  try {
+    viewer = await createPeptideSimilaritySpaceViewer(
+      table,
+      alignedSequencesColumn,
+      method,
+      measure,
+      cyclesCount,
+      null,
+    );
+    df = viewer.dataFrame!;
+  } catch (error) {
+    noException = false;
+  }
+
+  expect(noException, true);
+
+  noException = true;
 
   try {
     const axesNames = ['~X', '~Y', '~MW'];
@@ -84,3 +112,15 @@ export async function _testPeptideSimilaritySpaceViewer(
   }
   expect(noException, true);
 }
+
+/**
+ * Tests if MSA works and returns consistent result.
+ *
+ * @export
+ * @param {DG.Column} col Aligned sequences column.
+ */
+export async function _testMSAIsCorrect(col: DG.Column) {
+  const msaCol = await runKalign(col, true);
+  expect(msaCol.toList().every((v, i) => v == col.get(i)), true);
+}
+

package/src/utils/cell-renderer.ts

@@ -301,3 +301,105 @@ export function processSequence(subParts: string[]): [string[], boolean] {
   });
   return [text, simplified];
 }
+
+/**
+ * Aligned sequence difference cell renderer.
+ *
+ * @export
+ * @class AlignedSequenceDifferenceCellRenderer
+ * @extends {DG.GridCellRenderer}
+ */
+ export class AlignedSequenceDifferenceCellRenderer extends DG.GridCellRenderer {
+  /**
+   * Renderer name.
+   *
+   * @readonly
+   * @memberof AlignedSequenceDifferenceCellRenderer
+   */
+  get name() {
+    return 'alignedSequenceDifferenceCR';
+  }
+
+  /**
+   * Cell type.
+   *
+   * @readonly
+   * @memberof AlignedSequenceDifferenceCellRenderer
+   */
+  get cellType() {
+    return 'alignedSequenceDifference';
+  }
+
+  /**
+   * Cell height.
+   *
+   * @readonly
+   * @memberof AlignedSequenceDifferenceCellRenderer
+   */
+  get defaultHeight() {
+    return 35;
+  }
+
+  /**
+   * Cell renderer function.
+   *
+   * @param {CanvasRenderingContext2D} g Canvas rendering context.
+   * @param {number} x x coordinate on the canvas.
+   * @param {number} y y coordinate on the canvas.
+   * @param {number} w width of the cell.
+   * @param {number} h height of the cell.
+   * @param {DG.GridCell} gridCell Grid cell.
+   * @param {DG.GridCellStyle} cellStyle Cell style.
+   * @memberof AlignedSequenceDifferenceCellRenderer
+   */
+  render(
+    g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number,
+    gridCell: DG.GridCell, cellStyle: DG.GridCellStyle,
+  ) {
+    const grid = gridCell.dart.grid ? gridCell.grid : gridCell.dart.grid;
+    const cell = gridCell.cell;
+
+    w = grid ? Math.min(grid.canvas.width - x, w) : g.canvas.width - x;
+    y += 3;
+    g.save();
+    g.beginPath();
+    g.rect(x, y, w, h);
+    g.clip();
+    g.font = '14px monospace';
+    g.textBaseline = 'top';
+    const s: string = cell.value ?? '';
+
+    //TODO: can this be replaced/merged with splitSequence?
+    const [s1, s2] = s.split('#');
+    const subParts1 = s1.split('-');
+    const subParts2 = s2.split('-');
+    const [text, simplified] = processSequence(subParts1);
+    const textSize = g.measureText(text.join(''));
+    x = Math.max(x, x + (w - textSize.width) / 2);
+
+    subParts1.forEach((amino1: string, index) => {
+      let color, pivot;
+      let amino2 = subParts2[index];
+
+      if (amino1 != '')
+        [color, pivot] = cp.getColorPivot(amino1);
+      else
+        [color, pivot] = cp.getColorPivot(amino2);
+      
+      if (amino1 != amino2) {
+        const verticalShift = 10;
+
+        if (amino1 == '') 
+          amino1 = '-';
+        if (amino2 == '') 
+          amino2 = '-';
+
+        printLeftOrCentered(x, y - verticalShift, w, h, g, amino1, 'red', pivot, true);
+        x = printLeftOrCentered(x, y + verticalShift, w, h, g, amino2, 'red', pivot, true);
+      } else {
+        x = printLeftOrCentered(x, y, w, h, g, amino1, color, pivot, true);
+      } 
+    });
+    g.restore();
+  }
+}

package/src/utils/chem-palette.ts

@@ -2,6 +2,8 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
+import {StringDictionary} from '@datagrok-libraries/utils/src/type-declarations';
+
 /**
  * Chem palette class.
  *
@@ -9,7 +11,7 @@ import * as DG from 'datagrok-api/dg';
  * @class ChemPalette
  */
 export class ChemPalette {
-  cp: {[key: string]: string} = {};
+  cp: StringDictionary = {};
 
   /**
    * Creates an instance of ChemPalette.
@@ -213,10 +215,10 @@ export class ChemPalette {
    * Amino acid residue names.
    *
    * @static
-   * @type {{[key: string]: string}}
+   * @type {StringDictionary}
    * @memberof ChemPalette
    */
-  static AANames: {[key: string]: string} = {
+  static AANames: StringDictionary = {
     'G': 'Glycine',
     'L': 'Leucine',
     'Y': 'Tyrosine',
@@ -243,10 +245,10 @@ export class ChemPalette {
    * Amino acid residue SMILES.
    *
    * @static
-   * @type {{[key: string]: string}}
+   * @type {StringDictionary}
    * @memberof ChemPalette
    */
-  static AASmiles: {[key: string]: string} = {
+  static AASmiles: StringDictionary = {
     'G': 'NCC(=O)O',
     'L': 'N[C@H](CC(C)C)C(=O)O',
     'Y': 'NC(CC1=CC=C(O)C=C1)C(=O)O',
@@ -273,10 +275,10 @@ export class ChemPalette {
    * Amino acid residue truncated SMILES.
    *
    * @static
-   * @type {{[key: string]: string}}
+   * @type {StringDictionary}
    * @memberof ChemPalette
    */
-  static AASmilesTruncated: {[key: string]: string} = {
+  static AASmilesTruncated: StringDictionary = {
     'G': '*C*',
     'L': 'CC(C)C[C@H](*)*',
     'Y': 'C1=CC(=CC=C1CC(*)*)O',
@@ -303,10 +305,10 @@ export class ChemPalette {
    * Amino acid residue full names.
    *
    * @static
-   * @type {{[key: string]: string}}
+   * @type {StringDictionary}
    * @memberof ChemPalette
    */
-  static AAFullNames: {[key: string]: string} = {
+  static AAFullNames: StringDictionary = {
     'Ala': 'A',
     'Arg': 'R',
     'Asn': 'N',

package/src/utils/multiple-sequence-alignment.ts

@@ -72,7 +72,6 @@ export async function runKalign(col: DG.Column, isAligned = false) : Promise<DG.
   if (isAligned)
     sequences = sequences.map((v: string, _) => AlignedSequenceEncoder.clean(v).replace(/\-/g, ''));
 
-
   const fasta = _stringsToFasta(sequences);
 
   const CLI = await new Aioli('kalign/3.3.1');

package/src/utils/peptide-similarity-space.ts

@@ -8,7 +8,7 @@ import {DimensionalityReducer} from '@datagrok-libraries/ml/src/reduce-dimension
 import {
   createDimensinalityReducingWorker,
 } from '@datagrok-libraries/ml/src/workers/dimensionality-reducing-worker-creator';
-import {StringMeasure} from '@datagrok-libraries/ml/src/string-measure';
+import {Measure, StringMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 import {Coordinates} from '@datagrok-libraries/utils/src/type-declarations';
 
 /**
@@ -67,7 +67,7 @@ export async function createPeptideSimilaritySpaceViewer(
   const axesNames = ['~X', '~Y', '~MW'];
   const columnData = alignedSequencesColumn.toList().map((v, _) => AlignedSequenceEncoder.clean(v));
 
-  const embcols = await createDimensinalityReducingWorker(columnData, method, measure, cyclesCount);
+  const embcols = await createDimensinalityReducingWorker({data: columnData, metric: measure as StringMetrics}, method, cyclesCount);
 
   const columns = Array.from(
     embcols as Coordinates,
@@ -109,7 +109,6 @@ export async function createPeptideSimilaritySpaceViewer(
   if (view !== null)
     view.addViewer(viewer);
 
-
   pi.close();
   return viewer;
 }
@@ -139,7 +138,7 @@ export class PeptideSimilaritySpaceWidget {
    */
   constructor(alignedSequencesColumn: DG.Column, view: DG.TableView) {
     this.availableMethods = DimensionalityReducer.availableMethods;
-    this.availableMetrics = StringMeasure.availableMeasures;
+    this.availableMetrics = Measure.getMetricByDataType('String');
     this.method = this.availableMethods[0];
     this.metrics = this.availableMetrics[0];
     this.currentDf = alignedSequencesColumn.dataFrame;
@@ -175,9 +174,10 @@ export class PeptideSimilaritySpaceWidget {
    * @memberof PeptideSimilaritySpaceWidget
    */
   protected async updateViewer() {
-    this.viewer.lastChild?.remove();
     const viewer = await this.drawViewer();
+    this.viewer.lastChild?.remove();
     this.viewer.appendChild(viewer.root);
+    viewer.dataFrame?.fireValuesChanged();
   }
 
   /**
@@ -222,6 +222,25 @@ export class PeptideSimilaritySpaceWidget {
    * @memberof PeptideSimilaritySpaceWidget
    */
   public async draw(): Promise<DG.Widget> {
-    return new DG.Widget(ui.divV([(await this.drawViewer()).root, await this.drawInputs()]));
+    const plot = await this.drawViewer();
+    const inputs = await this.drawInputs();
+    const elements = ui.divV([plot.root, inputs]);
+
+    // Move detaching scatterplot to the grid.
+    plot.onEvent('d4-viewer-detached').subscribe((args) => {
+      let found = false;
+
+      for (const v of this.view.viewers) {
+        const opts = v.getOptions() as {[name: string]: any};
+
+        if (opts.type == 'Scatter plot' && opts.look.xColumnName == '~X' && opts.look.yColumnName == '~Y')
+          found = true;
+      }
+
+      if (!found)
+        this.view.addViewer(plot);
+    });
+
+    return new DG.Widget(elements);
   }
 }

package/src/viewers/sar-viewer.ts

@@ -3,6 +3,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import $ from 'cash-dom';
+import {StringDictionary} from '@datagrok-libraries/utils/src/type-declarations';
 
 import {model} from '../model';
 
@@ -28,7 +29,7 @@ export class SARViewer extends DG.JsViewer {
   protected viewerVGrid: DG.Grid | null;
   protected currentBitset: DG.BitSet | null;
   grouping: boolean;
-  groupMapping: {[key: string]: string} | null;
+  groupMapping: StringDictionary | null;
   // protected pValueThreshold: number;
   // protected amountOfBestAARs: number;
   // duplicatesHandingMethod: string;
@@ -289,7 +290,7 @@ function applyBitset(
   dataFrame: DG.DataFrame,
   viewerGrid: DG.Grid,
   aminoAcidResidue: string,
-  groupMapping: {[key: string]: string},
+  groupMapping: StringDictionary,
   initialBitset: DG.BitSet,
   filterMode: boolean,
 ) {
@@ -378,7 +379,7 @@ function accordionFunc(
         hist.style.width = 'auto';
         elements.push(hist);
 
-        const tableMap: {[key: string]: string} = {'Statistics:': ''};
+        const tableMap: StringDictionary = {'Statistics:': ''};
         for (const colName of new Set(['Count', 'pValue', 'Mean difference'])) {
           const query = `${aminoAcidResidue} = ${currentAAR} and Position = ${currentPosition}`;
           const textNum = statsDf.groupBy([colName]).where(query).aggregate().get(colName, 0);

package/src/viewers/subst-viewer.ts

@@ -1,4 +1,4 @@
-// import * as grok from 'datagrok-api/grok';
+import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
@@ -6,6 +6,7 @@ import $ from 'cash-dom';
 
 // import {aarGroups} from '../describe';
 import {setAARRenderer} from '../utils/cell-renderer';
+import { SemanticValue } from 'datagrok-api/dg';
 
 export class SubstViewer extends DG.JsViewer {
   viewerGrid: DG.Grid | null;
@@ -35,7 +36,7 @@ export class SubstViewer extends DG.JsViewer {
     const df: DG.DataFrame = this.dataFrame!;
     const col: DG.Column = df.columns.bySemType('alignedSequence');
     // let values: number[] = df.columns.byName('IC50').toList();
-    const values = df.getCol(this.activityColumnName).toList().map((x) => -Math.log10(x));
+    const values = df.getCol(this.activityColumnName).toList();
     // values = values;
     const splitedMatrix = this.split(col);
 
@@ -123,6 +124,7 @@ export class SubstViewer extends DG.JsViewer {
     const tableValuesKeys = Object.keys(tableValues);
     const dfLength = tableValuesKeys.length;
     const cols = [...nColsArray.keys()].map((v) => DG.Column.int(v.toString(), dfLength));
+    cols.forEach((col: DG.Column) => col.semType = 'Substitution');
     const aarCol = DG.Column.string(aarColName, dfLength);
     cols.splice(0, 1, aarCol);
     const table = DG.DataFrame.fromColumns(cols);
@@ -200,8 +202,11 @@ export class SubstViewer extends DG.JsViewer {
 
         this.casesGrid = tempDf.plot.grid();
         this.casesGrid.props.allowEdit = false;
-      } else
+        grok.shell.o = SemanticValue.fromValueType(tempDf, 'Substitution');
+      } else {
+        grok.shell.o = SemanticValue.fromValueType(null, 'Substitution');
         this.casesGrid = null;
+      }
 
       this.render();
     });
@@ -211,9 +216,7 @@ export class SubstViewer extends DG.JsViewer {
 
   render() {
     $(this.root).empty();
-    this.root.appendChild(this.casesGrid === null ?
-      this.viewerGrid!.root : ui.splitH([this.viewerGrid!.root, this.casesGrid.root]),
-    );
+    this.root.appendChild(this.viewerGrid!.root);
   }
 
   split(peptideColumn: DG.Column, filter: boolean = true): string[][] {

package/src/widgets/analyze-peptides.ts

@@ -3,6 +3,7 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import {Peptides} from '../peptides';
 import '../styles.css';
+import {StringDictionary} from '@datagrok-libraries/utils/src/type-declarations';
 
 /**
  * Peptide analysis widget.
@@ -77,7 +78,7 @@ export async function analyzePeptidesWidget(
   const startBtn = ui.button('Launch SAR', async () => {
     if (activityColumnChoice.value.type === DG.TYPE.FLOAT) {
       const progress = DG.TaskBarProgressIndicator.create('Loading SAR...');
-      const options: {[key: string]: string} = {
+      const options: StringDictionary = {
         'activityColumnName': activityColumnChoice.value.name,
         'scaling': activityScalingMethod.value,
       };

package/src/workers/dimensionality-reducer.ts

@@ -1,4 +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';
 
 /**
@@ -10,7 +11,7 @@ import {Coordinates} from '@datagrok-libraries/utils/src/type-declarations';
  * @param {number} cyclesCount Number of cycles to repeat.
  * @return {Coordinates} Embedding.
  */
-function onMessage(columnData: [], method: KnownMethods, measure: string, cyclesCount: number): Coordinates {
+function onMessage(columnData: any[], method: KnownMethods, measure: KnownMetrics, cyclesCount: number): Coordinates {
   const reducer = new DimensionalityReducer(
     columnData,
     method,