@datagrok/peptides 0.4.2 → 0.4.3

package/package.json

@@ -1,6 +1,6 @@
 {
 	"name": "@datagrok/peptides",
-	"version": "0.4.2",
+	"version": "0.4.3",
 	"description": "",
 	"dependencies": {
 		"@keckelt/tsne": "^1.0.2",

package/src/describe.ts

@@ -1,5 +1,3 @@
-// eslint-disable-next-line no-unused-vars
-import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import {splitAlignedPeptides} from './utils/split-aligned';
@@ -240,11 +238,9 @@ export async function describe(
   aarList.sort((first, second) => getWeight(second) - getWeight(first));
 
   matrixDf.getCol(aminoAcidResidue).setCategoryOrder(aarList);
-  //const sequenceDf = segregateBestAtAllCateg(statsDf, twoColorMode);
 
   // SAR vertical table (naive, choose best Mean difference from pVals <= 0.01)
   // TODO: aquire ALL of the positions
-
   let sequenceDf = statsDf.groupBy(['Mean difference', aminoAcidResidue, positionColName, 'Count', 'Ratio', 'pValue'])
     .where('pValue <= 0.1')
     .aggregate();
@@ -298,19 +294,6 @@ export async function describe(
       return;
     }
 
-    // if (args.cell.isColHeader) {
-    //   if (args.cell.gridColumn.name != aminoAcidResidue) {
-    //     const textSize = args.g.measureText(args.cell.gridColumn.name);
-    //     args.g.fillStyle = '#4b4b4a';
-    //     args.g.fillText(
-    //       args.cell.gridColumn.name,
-    //       args.bounds.x + (args.bounds.width - textSize.width) / 2,
-    //       args.bounds.y + (textSize.actualBoundingBoxAscent + textSize.actualBoundingBoxDescent),
-    //     );
-    //   }
-    //   args.preventDefault();
-    // }
-
     if (
       args.cell.isTableCell &&
       args.cell.tableRowIndex !== null &&

package/src/package.ts

@@ -25,35 +25,13 @@ let view: DG.TableView;
 
 async function main(chosenFile: string) {
   const pi = DG.TaskBarProgressIndicator.create('Loading Peptides');
-  //let peptides =
-  //  await grok.data.loadTable('https://datagrok.jnj.com/p/ejaeger.il23peptideidp5562/il-23_peptide_idp-5562');
   const path = _package.webRoot + 'files/' + chosenFile;
   const peptides = (await grok.data.loadTable(path));
   peptides.name = 'Peptides';
   peptides.setTag('dataType', 'peptides');
   const view = grok.shell.addTableView(peptides);
   tableGrid = view.grid;
-  // peptides.onSemanticTypeDetecting.subscribe((_: any) => {
-  //   const regexp = new RegExp(/^([^-^\n]*-){2,49}(\w|\(|\))+$/);
-  //   for (const col of peptides.columns) {
-  //     col.semType = DG.Detector.sampleCategories(col, (s: any) => regexp.test(s.trim())) ? 'alignedSequence' : null;
-  //     if (col.semType == 'alignedSequence') {
-  //       expandColumn(col, tableGrid, (ent)=>{
-  //         const subParts:string[] = ent.split('-');
-  //         // eslint-disable-next-line no-unused-vars
-  //         const [text, _] = processSequence(subParts);
-  //         let textSize = 0;
-  //         text.forEach((aar)=>{
-  //           textSize += aar.length;
-  //         });
-  //         return textSize;
-  //       });
-  //     }
-  //   }
-  // });
-
   view.name = 'PeptidesView';
-
   grok.shell.windows.showProperties = true;
 
   pi.close();
@@ -67,7 +45,6 @@ export function Peptides() {
 
   const appDescription = ui.info(
     [
-      // ui.divText('\n To start the application :', {style: {'font-weight': 'bolder'}}),
       ui.list([
         '- automatic recognition of peptide sequences',
         '- native integration with tons of Datagrok out-of-the box features (visualization, filtering, clustering, ' +

package/src/utils/chem-palette.ts

@@ -107,14 +107,6 @@ export class ChemPalette {
       'white': ['rgb(230,230,230)'],
     }
 
-    // static grokGroups: [string[], string][] = [
-    //   [['C', 'U'], 'yellow'],
-    //   [['G', 'P'], 'red'],
-    //   [['A', 'V', 'I', 'L', 'M', 'F', 'Y', 'W'], 'all_green'],
-    //   [['R', 'H', 'K'], 'light_blue'],
-    //   [['D', 'E'], 'dark_blue'],
-    //   [['S', 'T', 'N', 'Q'], 'orange'],
-    // ];
     static grokGroups: {[key: string]: string[]} = {
       'yellow': ['C', 'U'],
       'red': ['G', 'P'],

package/src/utils/correlation-analysis.ts

@@ -1,6 +1,4 @@
 /* Do not change these import lines. Datagrok will import API library in exactly the same manner */
-//import * as grok from 'datagrok-api/grok';
-//import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import {AlignedSequenceEncoder} from '@datagrok-libraries/utils/src/sequence-encoder';
@@ -59,7 +57,6 @@ function melt(df: DG.DataFrame): DG.DataFrame {
  * @param {DG.DataFrame} df A data frame to process.
  * @return {DG.DataFrame} The correlation matrix.
  */
-// eslint-disable-next-line no-unused-vars
 function calcSpearmanRhoMatrix(df: DG.DataFrame): DG.DataFrame {
   const nItems = df.columns.length;
   const rho = new Array(nItems).fill(0).map((_) => new Float32Array(nItems).fill(0));

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

@@ -1,6 +1,4 @@
 /* Do not change these import lines. Datagrok will import API library in exactly the same manner */
-// eslint-disable-next-line no-unused-vars
-import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 

package/src/utils/split-aligned.ts

@@ -45,7 +45,6 @@ export function splitAlignedPeptides(peptideColumn: DG.Column, filter: boolean =
   columnNames.push('C-terminal');
 
   // filter out the columns with the same values
-
   if (filter) {
     splitColumns = splitColumns.filter((positionArray, index) => {
       const isRetained = new Set(positionArray).size > 1;

package/src/viewers/logo-viewer.ts

@@ -61,7 +61,6 @@ export class Logo extends DG.JsViewer {
 
   init() {
     this.initialized = true;
-    // this.reactHost = ui.div([]);
     console.log('INIT');
     this.target = this.dataFrame;
     [this.splitted] = splitAlignedPeptides(this.dataFrame!.columns.bySemType(this.colSemType));
@@ -111,10 +110,6 @@ export class Logo extends DG.JsViewer {
 
     if (typeof this.dataFrame !== 'undefined') {
       this.findLogo();
-
-      // if (this.reactHost !== null) {
-      //   this.root.appendChild(this.reactHost);
-      // }
     }
   }
 

package/src/viewers/sar-viewer.ts

@@ -22,7 +22,6 @@ export class SARViewer extends DG.JsViewer {
   protected currentBitset: DG.BitSet | null;
   grouping: boolean;
   groupMapping: {[key: string]: string} | null;
-  // private df: DG.DataFrame | null;
   // protected pValueThreshold: number;
   // protected amountOfBestAARs: number;
   // duplicatesHandingMethod: string;
@@ -123,21 +122,9 @@ export class SARViewer extends DG.JsViewer {
       splitCol!.init((i) => isChosen(i) ? aarLabel : otherLabel);
 
       //TODO: use column.compact
-
-      // if (this.filterMode) {
-      //   this.dataFrame.selection.setAll(false, false);
-      //   this.dataFrame.filter.init(isChosen).and(this._initialBitset!, false);
-      // } else {
-      //   this.dataFrame.filter.copyFrom(this._initialBitset!);
-      //   this.dataFrame.selection.init(isChosen).and(this._initialBitset!, false);
-      // }
       this.currentBitset = DG.BitSet.create(this.dataFrame.rowCount, isChosen).and(this._initialBitset!);
-      // (this.filterMode ? this.dataFrame.selection.setAll(false) :
-      // this.dataFrame.filter.copyFrom(this._initialBitset!)).fireChanged();
       this.sourceFilteringFunc();
 
-
-      // df.getCol(splitColName).setCategoryOrder([otherLabel, aarLabel]);
       const colorMap: {[index: string]: string | number} = {};
       colorMap[otherLabel] = DG.Color.blue;
       colorMap[aarLabel] = DG.Color.orange;
@@ -267,14 +254,6 @@ export class SARViewer extends DG.JsViewer {
     //TODO: optimize. Don't calculate everything again if only view changes
     if (computeData) {
       if (typeof this.dataFrame !== 'undefined' && this.activityColumnColumnName && this.sourceGrid) {
-        // [this.viewerGrid, this.viewerVGrid, this.statsDf] = await describe(
-        //   this.dataFrame,
-        //   this.activityColumnColumnName,
-        //   this.activityScalingMethod,
-        //   this.sourceGrid,
-        //   this.bidirectionalAnalysis,
-        //   this._initialBitset,
-        // );
         await model?.updateData(
           this.dataFrame!,
           this.activityColumnColumnName,

package/src/viewers/stacked-barchart-viewer.ts

@@ -287,8 +287,7 @@ export class StackedBarChart extends DG.JsViewer {
         if (h * margin / 2 <= sBarHeight - gapSize && h * margin / 2 <= w) {
           g.fillStyle = 'rgb(0,0,0)';
           g.font = `${h * margin / 2}px`;
-          // eslint-disable-next-line no-unused-vars
-          const [_c, aar, _p] = cp.getColorAAPivot(obj['name']);
+          const [, aar] = cp.getColorAAPivot(obj['name']);
           g.fillText(aar,
             x + w / 2 - h * margin / 8,
             y + h * (this.max - sum + curSum) / this.max + gapSize / 2 + (sBarHeight - gapSize)/2 - h * margin / 8);
@@ -398,11 +397,8 @@ export class StackedBarChart extends DG.JsViewer {
         return;
       }
       this.dataFrame!.selection.handleClick((i) => {
-        //let selected = true;
         // @ts-ignore
         return this.highlighted!['aaName'] === (this.dataFrame.getCol(this.highlighted!['colName']).get(i));
-
-        //&& (scope.dataFrame.selection.get(i) === selected);
       }, event);
     }
 }