@datagrok/peptides 1.9.0 → 1.9.2

package/src/utils/misc.ts

@@ -59,8 +59,8 @@ export function calculateSelected(df: DG.DataFrame): type.MonomerSelectionStats
 }
 
 // export function isGridCellInvalid(gc: DG.GridCell | null): boolean {
-//   return !gc || !gc.cell.value || !gc.tableColumn || gc.tableRowIndex == null || gc.tableRowIndex == -1 ||
-//     gc.cell.value == DG.INT_NULL || gc.cell.value == DG.FLOAT_NULL;
+//   return !gc || !gc.cell.value || !gc.tableColumn || gc.tableRowIndex === null || gc.tableRowIndex === -1 ||
+//     gc.cell.value === DG.INT_NULL || gc.cell.value === DG.FLOAT_NULL;
 // }
 
 export function extractColInfo(col: DG.Column<string>): type.RawColumn {

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

@@ -68,7 +68,7 @@ export async function createPeptideSimilaritySpaceViewer(table: DG.DataFrame, me
     const axisCol = table.col(axis);
     const newCol = edf.getCol(axis);
 
-    if (axisCol != null) {
+    if (axisCol !== null) {
       for (let i = 0; i < newCol.length; ++i) {
         const v = newCol.get(i);
         table.set(axis, i, v);
@@ -204,7 +204,7 @@ export class PeptideSimilaritySpaceWidget {
       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')
+        if (opts.type === 'Scatter plot' && opts.look.xColumnName === '~X' && opts.look.yColumnName === '~Y')
           found = true;
       }
 

package/src/viewers/logo-summary.ts

@@ -81,7 +81,7 @@ export class LogoSummaryTable extends DG.JsViewer {
 
   onPropertyChanged(property: DG.Property): void {
     super.onPropertyChanged(property);
-    if (property.name == 'membersRatioThreshold')
+    if (property.name === 'membersRatioThreshold')
       this.updateFilter();
     this.render();
   }
@@ -218,7 +218,7 @@ export class LogoSummaryTable extends DG.JsViewer {
     this.viewerGrid.sort([C.LST_COLUMN_NAMES.MEMBERS], [false]);
     this.updateFilter();
     const gridClustersCol = this.viewerGrid.col(clustersColName)!;
-    gridClustersCol.name = C.LST_COLUMN_NAMES.CLUSTER;
+    gridClustersCol.column!.name = C.LST_COLUMN_NAMES.CLUSTER;
     gridClustersCol.visible = true;
     this.viewerGrid.columns.setOrder([C.LST_COLUMN_NAMES.CLUSTER, C.LST_COLUMN_NAMES.MEMBERS,
       C.LST_COLUMN_NAMES.WEB_LOGO, C.LST_COLUMN_NAMES.DISTRIBUTION, C.LST_COLUMN_NAMES.MEAN_DIFFERENCE,
@@ -227,11 +227,11 @@ export class LogoSummaryTable extends DG.JsViewer {
     this.viewerGrid.props.rowHeight = 55;
     this.viewerGrid.onCellPrepare((cell) => {
       const currentRowIdx = cell.tableRowIndex;
-      if (!cell.isTableCell || currentRowIdx == null || currentRowIdx == -1)
+      if (!cell.isTableCell || currentRowIdx === null || currentRowIdx === -1)
         return;
 
       const height = cell.bounds.height;
-      if (cell.tableColumn?.name == C.LST_COLUMN_NAMES.WEB_LOGO) {
+      if (cell.tableColumn?.name === C.LST_COLUMN_NAMES.WEB_LOGO) {
         const webLogoTable = this.webLogoDfPlot[currentRowIdx];
         const webLogoTableRowCount = webLogoTable.rowCount;
         const webLogoTablePepCol = webLogoTable.getCol(pepCol.name);
@@ -248,7 +248,7 @@ export class LogoSummaryTable extends DG.JsViewer {
           .fromType('WebLogo', {positionHeight: this.webLogoMode, horizontalAlignment: HorizontalAlignments.LEFT,
             maxHeight: 1000, minHeight: height - 2, positionWidth: positionWidth})
           .then((viewer) => cell.element = viewer.root);
-      } else if (cell.tableColumn?.name == C.LST_COLUMN_NAMES.DISTRIBUTION) {
+      } else if (cell.tableColumn?.name === C.LST_COLUMN_NAMES.DISTRIBUTION) {
         const viewerRoot = this.distributionDfPlot[currentRowIdx].plot.histogram({
           filteringEnabled: false,
           valueColumnName: C.COLUMNS_NAMES.ACTIVITY_SCALED,
@@ -269,7 +269,7 @@ export class LogoSummaryTable extends DG.JsViewer {
     });
     this.viewerGrid.root.addEventListener('click', (ev) => {
       const cell = this.viewerGrid.hitTest(ev.offsetX, ev.offsetY);
-      if (!cell || !cell.isTableCell || cell.tableColumn?.name != clustersColName)
+      if (!cell || !cell.isTableCell || cell.tableColumn?.name !== clustersColName)
         return;
 
       summaryTable.currentRowIdx = -1;
@@ -370,13 +370,13 @@ export class LogoSummaryTable extends DG.JsViewer {
 
     for (let i = 0; i < viewerDfColsLength; ++i) {
       const col = viewerDfCols.byIndex(i);
-      newClusterVals[i] = col.name == this.model.settings.clustersColumnName! ? newClusterName :
-        col.name == C.LST_COLUMN_NAMES.MEMBERS ? selection.trueCount :
-          col.name == C.LST_COLUMN_NAMES.WEB_LOGO ? null :
-            col.name == C.LST_COLUMN_NAMES.DISTRIBUTION ? null :
-              col.name == C.LST_COLUMN_NAMES.MEAN_DIFFERENCE ? stats.meanDifference:
-                col.name == C.LST_COLUMN_NAMES.P_VALUE ? stats.pValue:
-                  col.name == C.LST_COLUMN_NAMES.RATIO ? stats.ratio:
+      newClusterVals[i] = col.name === C.LST_COLUMN_NAMES.CLUSTER ? newClusterName :
+        col.name === C.LST_COLUMN_NAMES.MEMBERS ? selection.trueCount :
+          col.name === C.LST_COLUMN_NAMES.WEB_LOGO ? null :
+            col.name === C.LST_COLUMN_NAMES.DISTRIBUTION ? null :
+              col.name === C.LST_COLUMN_NAMES.MEAN_DIFFERENCE ? stats.meanDifference:
+                col.name === C.LST_COLUMN_NAMES.P_VALUE ? stats.pValue:
+                  col.name === C.LST_COLUMN_NAMES.RATIO ? stats.ratio:
                     col.name in aggregatedValues ? aggregatedValues[col.name] :
         console.warn(`PeptidesLSTWarn: value for column ${col.name} is undefined`)! || null;
     }
@@ -388,16 +388,18 @@ export class LogoSummaryTable extends DG.JsViewer {
 
   removeCluster(): void {
     const lss = this.model.clusterSelection;
-    const dfCols = this.dataFrame.columns;
+    const customClusters = wu(this.model.customClusters).map((cluster) => cluster.name).toArray();
 
     // Names of the clusters to remove
-    const clustNames = lss.filter((cluster) => dfCols.contains(cluster));
-    if (clustNames.length == 0)
-      return grok.shell.warning('Only custom clusters can be removed');
+    const clustNames = lss.filter((cluster) => customClusters.includes(cluster));
+    if (clustNames.length === 0)
+      return grok.shell.warning('No custom clusters selected to be removed');
 
     const viewerDf = this.viewerGrid.dataFrame;
     const viewerDfRows = viewerDf.rows;
-    const clustColCat = viewerDf.getCol(this.model.settings.clustersColumnName!).categories;
+    const clustCol = viewerDf.getCol(C.LST_COLUMN_NAMES.CLUSTER);
+    const clustColCat = clustCol.categories;
+    const dfCols = this.dataFrame.columns;
 
     for (const cluster of clustNames) {
       lss.splice(lss.indexOf(cluster), 1);
@@ -409,6 +411,8 @@ export class LogoSummaryTable extends DG.JsViewer {
       this.distributionDfPlot.splice(clustIdx, 1);
     }
 
+    clustCol.compact();
+
     this.model.clusterSelection = lss;
     this.render();
   }
@@ -423,8 +427,8 @@ export class LogoSummaryTable extends DG.JsViewer {
     const activityColData = activityCol.getRawData();
 
 
-    if (clustType == CLUSTER_TYPE.ORIGINAL) {
-      const origClustCol = filteredDf.getCol(this.model.settings.clustersColumnName!);
+    if (clustType === CLUSTER_TYPE.ORIGINAL) {
+      const origClustCol = filteredDf.getCol(C.LST_COLUMN_NAMES.CLUSTER);
       const origClustColData = origClustCol.getRawData();
       const origClustColCategories = origClustCol.categories;
       const seekValue = origClustColCategories.indexOf(clustName);

package/src/viewers/peptide-space-viewer.ts

@@ -47,7 +47,7 @@ export class PeptideSpaceViewer extends DG.JsViewer {
 
   async onPropertyChanged(property: DG.Property | null): Promise<void> {
     super.onPropertyChanged(property);
-    if (this.prevProps[property?.name as 'method' | 'measure' | 'cyclesCount' ?? ''] == property?.get(this))
+    if (this.prevProps[property?.name as 'method' | 'measure' | 'cyclesCount' ?? ''] === property?.get(this))
       return;
 
     if (this.model)
@@ -90,7 +90,7 @@ export class PeptideSpaceViewer extends DG.JsViewer {
 
         viewerRoot.addEventListener('mousemove', (ev) => {
           const idx = scatterPlot.hitTest(ev.offsetX, ev.offsetY);
-          if (idx != -1) {
+          if (idx !== -1) {
             const table = ui.tableFromMap({
               'Activity': colorCol.get(idx),
               'Sequence': alignedSeqCol.get(idx),

package/src/viewers/sar-viewer.ts

@@ -94,7 +94,7 @@ export class MonomerPosition extends DG.JsViewer {
     this.viewerGrid.onCellTooltip((cell: DG.GridCell, x: number, y: number) => showTooltip(cell, x, y, this.model));
     this.viewerGrid.root.addEventListener('click', (ev) => {
       const gridCell = this.viewerGrid.hitTest(ev.offsetX, ev.offsetY);
-      if (!gridCell?.isTableCell || gridCell?.tableColumn?.name == C.COLUMNS_NAMES.MONOMER)
+      if (!gridCell?.isTableCell || gridCell?.tableColumn?.name === C.COLUMNS_NAMES.MONOMER)
         return;
 
       const position = gridCell!.tableColumn!.name;
@@ -112,7 +112,7 @@ export class MonomerPosition extends DG.JsViewer {
     if (!refreshOnly) {
       $(this.root).empty();
       let switchHost = ui.divText(VIEWER_TYPE.MOST_POTENT_RESIDUES, {id: 'pep-viewer-title'});
-      if (this.name == VIEWER_TYPE.MONOMER_POSITION) {
+      if (this.name === VIEWER_TYPE.MONOMER_POSITION) {
         const mutationCliffsMode = ui.boolInput('', this.mode === MONOMER_POSITION_MODE.MUTATION_CLIFFS);
         mutationCliffsMode.root.addEventListener('click', () => {
           invariantMapMode.value = false;
@@ -212,7 +212,7 @@ export class MostPotentResiduesViewer extends DG.JsViewer {
     this.viewerGrid.onCellTooltip((cell: DG.GridCell, x: number, y: number) => showTooltip(cell, x, y, this.model));
     this.viewerGrid.root.addEventListener('click', (ev) => {
       const gridCell = this.viewerGrid.hitTest(ev.offsetX, ev.offsetY);
-      if (!gridCell?.isTableCell || gridCell!.tableColumn!.name != C.COLUMNS_NAMES.MEAN_DIFFERENCE)
+      if (!gridCell?.isTableCell || gridCell!.tableColumn!.name !== C.COLUMNS_NAMES.MEAN_DIFFERENCE)
         return;
 
       const tableRowIdx = gridCell!.tableRowIndex!;
@@ -269,7 +269,7 @@ function renderCell(args: DG.GridCellRenderArgs, model: PeptidesModel, isInvaria
 
   const tableColName = cell.tableColumn?.name;
   const tableRowIndex = cell.tableRowIndex!;
-  if (!cell.isTableCell || renderColNames.indexOf(tableColName!) == -1) {
+  if (!cell.isTableCell || renderColNames.indexOf(tableColName!) === -1) {
     canvasContext.restore();
     return;
   }
@@ -318,11 +318,11 @@ export function showTooltip(cell: DG.GridCell, x: number, y: number, model: Pept
   const tableColName = tableCol?.name;
   const tableRowIndex = cell.tableRowIndex;
 
-  if (!cell.isRowHeader && !cell.isColHeader && tableCol && tableRowIndex != null) {
+  if (!cell.isRowHeader && !cell.isColHeader && tableCol && tableRowIndex !== null) {
     const table = cell.grid.table;
     const currentAAR = table.get(C.COLUMNS_NAMES.MONOMER, tableRowIndex);
 
-    if (tableCol.semType == C.SEM_TYPES.MONOMER)
+    if (tableCol.semType === C.SEM_TYPES.MONOMER)
       model.showMonomerTooltip(currentAAR, x, y);
     else if (renderColNames.includes(tableColName!)) {
       const currentPosition = tableColName !== C.COLUMNS_NAMES.MEAN_DIFFERENCE ? tableColName :

package/src/widgets/mutation-cliffs.ts

@@ -76,7 +76,7 @@ export function mutationCliffsWidget(table: DG.DataFrame, model: PeptidesModel):
 
   const aminoToInput = ui.stringInput('Mutated to:', '', () => {
     const substitutedToAar = aminoToInput.stringValue;
-    if (substitutedToAar != '')
+    if (substitutedToAar !== '')
       substTable.filter.init((idx) => hiddenSubstToAarCol.get(idx) === substitutedToAar);
     else
       substTable.filter.setAll(true);

package/src/widgets/peptides.ts

@@ -30,7 +30,7 @@ export function analyzePeptidesUI(df: DG.DataFrame, col?: DG.Column<string>):
 
     seqColInput = ui.columnInput('Sequence', df, potentialCol, () => {
       const seqCol = seqColInput!.value;
-      if (!(seqCol.getTag(DG.TAGS.SEMTYPE) == DG.SEMTYPE.MACROMOLECULE)) {
+      if (!(seqCol.getTag(DG.TAGS.SEMTYPE) === DG.SEMTYPE.MACROMOLECULE)) {
         grok.shell.warning('Peptides analysis only works with macromolecules');
         seqColInput!.value = potentialCol;
       }
@@ -40,7 +40,7 @@ export function analyzePeptidesUI(df: DG.DataFrame, col?: DG.Column<string>):
         return viewer.root;
       }));
     });
-  } else if (!(col.getTag(bioTAGS.aligned) == ALIGNMENT.SEQ_MSA) &&
+  } else if (!(col.getTag(bioTAGS.aligned) === ALIGNMENT.SEQ_MSA) &&
     col.getTag(DG.TAGS.UNITS) !== NOTATION.HELM) {
     return {
       host: ui.label('Peptides analysis only works with aligned sequences'),
@@ -49,7 +49,7 @@ export function analyzePeptidesUI(df: DG.DataFrame, col?: DG.Column<string>):
   }
 
   let funcs = DG.Func.find({package: 'Bio', name: 'webLogoViewer'});
-  if (funcs.length == 0) {
+  if (funcs.length === 0) {
     return {
       host: ui.label('Bio package is missing or out of date. Please install the latest version.'),
       callback: async (): Promise<boolean> => false,
@@ -57,7 +57,7 @@ export function analyzePeptidesUI(df: DG.DataFrame, col?: DG.Column<string>):
   }
 
   funcs = DG.Func.find({package: 'Bio', name: 'getBioLib'});
-  if (funcs.length == 0) {
+  if (funcs.length === 0) {
     return {
       host: ui.label('Bio package is missing or out of date. Please install the latest version.'),
       callback: async (): Promise<boolean> => false,
@@ -121,7 +121,7 @@ export function analyzePeptidesUI(df: DG.DataFrame, col?: DG.Column<string>):
     if (sequencesCol) {
       const model = await startAnalysis(activityColumnChoice.value!, sequencesCol, clustersColumnChoice.value, df,
         scaledCol, activityScalingMethod.value ?? C.SCALING_METHODS.NONE, targetColumnChoice.value);
-      return model != null;
+      return model !== null;
     }
     return false;
   };
@@ -183,19 +183,19 @@ export async function startAnalysis(activityColumn: DG.Column<number>, peptidesC
 
     if (clustersColumn) {
       const clusterCol = newDf.getCol(clustersColumn.name);
-      if (clusterCol.type != DG.COLUMN_TYPE.STRING)
+      if (clusterCol.type !== DG.COLUMN_TYPE.STRING)
         newDfCols.replace(clusterCol, clusterCol.convertTo(DG.COLUMN_TYPE.STRING));
       settings.clustersColumnName = clustersColumn.name;
     }
     newDf.setTag(C.TAGS.SETTINGS, JSON.stringify(settings));
 
     let monomerType = 'HELM_AA';
-    if (peptidesCol.getTag(DG.TAGS.UNITS) == NOTATION.HELM) {
+    if (peptidesCol.getTag(DG.TAGS.UNITS) === NOTATION.HELM) {
       const sampleSeq = peptidesCol.get(0)!;
       monomerType = sampleSeq.startsWith('PEPTIDE') ? 'HELM_AA' : 'HELM_BASE';
     } else {
       const alphabet = peptidesCol.tags[C.TAGS.ALPHABET];
-      monomerType = alphabet == 'DNA' || alphabet == 'RNA' ? 'HELM_BASE' : 'HELM_AA';
+      monomerType = alphabet === 'DNA' || alphabet === 'RNA' ? 'HELM_BASE' : 'HELM_AA';
     }
     const dfUuid = uuid.v4();
     newDf.setTag(C.TAGS.UUID, dfUuid);

package/src/widgets/settings.ts

@@ -104,7 +104,7 @@ export function getSettingsDialog(model: PeptidesModel): SettingsElements {
   const includedColumnsInputs: DG.InputBase[] = [];
   for (const col of model.df.columns.numerical) {
     const colName = col.name;
-    if (colName == settings.activityColumnName || colName == C.COLUMNS_NAMES.ACTIVITY_SCALED)
+    if (colName === settings.activityColumnName || colName === C.COLUMNS_NAMES.ACTIVITY_SCALED)
       continue;
 
     const isIncludedInput = ui.boolInput(COLUMNS_INPUTS.IS_INCLUDED,
@@ -127,7 +127,7 @@ export function getSettingsDialog(model: PeptidesModel): SettingsElements {
     $(inputsRow).find('div.ui-div').css('display', 'inline-flex');
     inputsRows.push(inputsRow);
   }
-  if (inputsRows.length != 0) {
+  if (inputsRows.length !== 0) {
     accordion.addPane(SETTINGS_PANES.COLUMNS, () => ui.divV(inputsRows), false);
     inputs[SETTINGS_PANES.COLUMNS] = includedColumnsInputs;
   }