@datagrok/peptides 0.4.3 → 0.7.1

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

@@ -3,31 +3,14 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {getSequenceMolecularWeight} from './molecular-measure';
-import {AlignedSequenceEncoder} from '@datagrok-libraries/utils/src/sequence-encoder';
-import {DimensionalityReducer} from '@datagrok-libraries/utils/src/reduce-dimensionality';
-import {Measurer} from '@datagrok-libraries/utils/src/string-measure';
+import {AlignedSequenceEncoder} from '@datagrok-libraries/bio/src/sequence-encoder';
+import {DimensionalityReducer} from '@datagrok-libraries/ml/src/reduce-dimensionality';
+import {
+  createDimensinalityReducingWorker,
+} from '@datagrok-libraries/ml/src/workers/dimensionality-reducing-worker-creator';
+import {StringMeasure} from '@datagrok-libraries/ml/src/string-measure';
 import {Coordinates} from '@datagrok-libraries/utils/src/type-declarations';
 
-function createDimensinalityReducingWorker(
-  columnData: any[],
-  method: string,
-  measure: string,
-  cyclesCount: number,
-): Promise<unknown> {
-  return new Promise(function(resolve) {
-    const worker = new Worker(new URL('../workers/dimensionality-reducer.ts', import.meta.url));
-    worker.postMessage({
-      columnData: columnData,
-      method: method,
-      measure: measure,
-      cyclesCount: cyclesCount,
-    });
-    worker.onmessage = ({data: {embedding}}) => {
-      resolve(embedding);
-    };
-  });
-}
-
 /**
  * Finds a column with an activity.
  *
@@ -38,7 +21,6 @@ function inferActivityColumnsName(table: DG.DataFrame): string | null {
   const re = /activity|ic50/i;
   for (const name of table.columns.names()) {
     if (name.match(re)) {
-      console.log(`${name} found.`);
       return name;
     }
   }
@@ -101,29 +83,27 @@ export async function createPeptideSimilaritySpaceViewer(
   // Add new axes.
   for (const axis of axesNames) {
     const col = table.col(axis);
+    const newCol = edf.getCol(axis);
 
-    if (col == null) {
-      table.columns.insert(edf.getCol(axis));
+    if (col != null) {
+      for (let i = 0; i < newCol.length; ++i) {
+        const v = newCol.get(i);
+        table.set(axis, i, v);
+      }
     } else {
-      table.columns.replace(col, edf.getCol(axis));
+      table.columns.insert(newCol);
     }
   }
 
-  // const viewer = DG.Viewer.scatterPlot(table, {x: '~X', y: '~Y', color: activityColumnName ?? '~MW', size: '~MW'});
   const viewerOptions = {x: '~X', y: '~Y', color: activityColumnName ?? '~MW', size: '~MW'};
-  const viewer = view !== null ?
-    view.addViewer(DG.VIEWER.SCATTER_PLOT, viewerOptions) : DG.Viewer.scatterPlot(table, viewerOptions);
-  // Fit view if needed.
-  /*if (zoom) {
-    viewer.zoom(
-      table.getCol('~X').min,
-      table.getCol('~Y').min,
-      table.getCol('~X').max,
-      table.getCol('~Y').max,
-    );
-  }*/
+  const viewer = DG.Viewer.scatterPlot(table, viewerOptions);
+
+  if (view !== null) {
+    view.addViewer(viewer);
+  }
+
   pi.close();
-  return (viewer as DG.ScatterPlotViewer);
+  return viewer;
 }
 
 /**
@@ -151,7 +131,7 @@ export class PeptideSimilaritySpaceWidget {
    */
   constructor(alignedSequencesColumn: DG.Column, view: DG.TableView) {
     this.availableMethods = DimensionalityReducer.availableMethods;
-    this.availableMetrics = Measurer.availableMeasures;
+    this.availableMetrics = StringMeasure.availableMeasures;
     this.method = this.availableMethods[0];
     this.metrics = this.availableMetrics[0];
     this.currentDf = alignedSequencesColumn.dataFrame;

package/src/utils/split-aligned.ts

@@ -1,5 +1,13 @@
 import * as DG from 'datagrok-api/dg';
 
+/**
+ * Split aligned sequence string into separate parts containing amino acid residues.
+ *
+ * @export
+ * @param {DG.Column} peptideColumn Column containing aligned sequences.
+ * @param {boolean} [filter=true] Filter out columns with all the same residues.
+ * @return {[DG.DataFrame, number[]]} DataFrame containing split sequence and a list of invalid indexes.
+ */
 export function splitAlignedPeptides(peptideColumn: DG.Column, filter: boolean = true): [DG.DataFrame, number[]] {
   const splitPeptidesArray: string[][] = [];
   let currentSplitPeptide: string[];

package/src/viewers/logo-viewer.ts

@@ -7,6 +7,13 @@ import * as logojs from 'logojs-react';
 import {splitAlignedPeptides} from '../utils/split-aligned';
 import {ChemPalette} from '../utils/chem-palette';
 
+/**
+ * Logo viewer.
+ *
+ * @export
+ * @class Logo
+ * @extends {DG.JsViewer}
+ */
 export class Logo extends DG.JsViewer {
   initialized: boolean;
   option: any;
@@ -18,6 +25,11 @@ export class Logo extends DG.JsViewer {
   LET_COLORS: Array<any>;
   target: DG.DataFrame | undefined | null;
 
+  /**
+   * Creates an instance of Logo.
+   *
+   * @memberof Logo
+   */
   constructor() {
     super();
     this.initialized = false;
@@ -59,6 +71,11 @@ export class Logo extends DG.JsViewer {
     ];
   }
 
+  /**
+   * Initializer function.
+   *
+   * @memberof Logo
+   */
   init() {
     this.initialized = true;
     console.log('INIT');
@@ -69,6 +86,11 @@ export class Logo extends DG.JsViewer {
     this.root.style.maxHeight = '200px';
   }
 
+  /**
+   * Function to execute when the table is attached.
+   *
+   * @memberof Logo
+   */
   onTableAttached() {
     if (typeof this.dataFrame !== 'undefined') {
       if (!this.initialized) {
@@ -83,16 +105,32 @@ export class Logo extends DG.JsViewer {
     this.render();
   }
 
+  /**
+   * Function that is executed when the viewer is detached.
+   *
+   * @memberof Logo
+   */
   detach() {
     this.subs.forEach((sub) => sub.unsubscribe());
   }
 
+  /**
+   * Function that is executed when the viewer property is changed.
+   *
+   * @param {DG.Property} property
+   * @memberof Logo
+   */
   onPropertyChanged(property: DG.Property) {
     super.onPropertyChanged(property);
 
     this.render();
   }
 
+  /**
+   * Function that renders the viewer.
+   *
+   * @memberof Logo
+   */
   async render() {
     const bits = this.dataFrame!.selection;
     let selected = false;
@@ -113,11 +151,21 @@ export class Logo extends DG.JsViewer {
     }
   }
 
+  /**
+   * Create logo.
+   *
+   * @memberof Logo
+   */
   async findLogo() {
     this.getInfoFromDf();
     logojs.embedProteinLogo(this.root, {alphabet: this.LET_COLORS, ppm: this.ppm});
   }
 
+  /**
+   * Retrieves information for building logo from the dataframe.
+   *
+   * @memberof Logo
+   */
   getInfoFromDf() {
     let index: number = 0;
     this.ppm = [];