@datagrok/peptides 1.17.2 → 1.17.4

package/src/package.ts

@@ -88,9 +88,8 @@ export function peptidesDialog(): DG.Dialog {
   const analyzeObject = analyzePeptidesUI(grok.shell.t);
   const dialog = ui.dialog('Analyze Peptides').add(analyzeObject.host).onOK(async () => {
     const startSuccess = analyzeObject.callback();
-    if (!startSuccess) {
+    if (!startSuccess)
       dialog.show();
-    }
   });
   return dialog.show();
 }
@@ -138,9 +137,8 @@ export function manualAlignment(_monomer: string): DG.Widget {
   //TODO: recalculate Molfile and Molecule panels on sequence update
   const df = grok.shell.t;
   const model: PeptidesModel | null = df?.temp[PeptidesModel.modelName];
-  if (!model) {
+  if (!model)
     return new DG.Widget(ui.divText('Manual alignment works with peptides analysis'));
-  }
 
 
   const col = df.getCol(model.settings!.sequenceColumnName!);

package/src/tests/benchmarks.ts

@@ -15,25 +15,23 @@ import * as C from '../utils/constants';
 const benchmarkDatasetSizes = [5, 50, 100, 200];
 
 category('Benchmarks: Mutation Cliffs', () => {
-  for (const size of benchmarkDatasetSizes) {
-    test(`${size}k sequences`, async () => await mutationCliffsBenchmark(size), {timeout: 150000});
-  }
+  for (const size of benchmarkDatasetSizes)
+    test(`${size}k sequences`, async () => await mutationCliffsBenchmark(size), {timeout: 180000});
 });
 
 category('Benchmarks: Cluster stats', () => {
   for (const size of benchmarkDatasetSizes) {
     test(`${size}k sequences`, async () => {
-      if (!DG.Test.isInBenchmark) {
+      if (!DG.Test.isInBenchmark)
         return null;
-      }
 
 
       const df = (await _package.files.readBinaryDataFrames(`tests/${size}k.d42`))[0];
       const clustersColumnName = 'cluster';
       const scaledActivity = scaleActivity(df.getCol('activity'), C.SCALING_METHODS.NONE);
-      if (df.columns.names().map((s) => s.toLowerCase()).includes(scaledActivity.name.toLowerCase())) {
+      if (df.columns.names().map((s) => s.toLowerCase()).includes(scaledActivity.name.toLowerCase()))
         df.columns.remove(scaledActivity.name);
-      }
+
 
       df.columns.add(scaledActivity);
       DG.time(`Cluster stats benchmark - ${size}k`,
@@ -45,9 +43,8 @@ category('Benchmarks: Cluster stats', () => {
 category('Benchmarks: Monomer-Position stats', () => {
   for (const size of benchmarkDatasetSizes) {
     test(`${size}k sequences`, async () => {
-      if (!DG.Test.isInBenchmark) {
+      if (!DG.Test.isInBenchmark)
         return null;
-      }
 
 
       const df = (await _package.files.readBinaryDataFrames(`tests/${size}k.d42`))[0];
@@ -58,9 +55,9 @@ category('Benchmarks: Monomer-Position stats', () => {
         ++i;
       }
       const scaledActivity = scaleActivity(df.getCol('activity'), C.SCALING_METHODS.NONE);
-      if (df.columns.names().map((s) => s.toLowerCase()).includes(scaledActivity.name.toLowerCase())) {
+      if (df.columns.names().map((s) => s.toLowerCase()).includes(scaledActivity.name.toLowerCase()))
         df.columns.remove(scaledActivity.name);
-      }
+
 
       df.columns.add(scaledActivity);
       DG.time(`Monomer-Position stats benchmark - ${size}k`,
@@ -72,9 +69,8 @@ category('Benchmarks: Monomer-Position stats', () => {
 category('Benchmarks: Analysis start', () => {
   for (const size of benchmarkDatasetSizes) {
     test(`${size}k sequences`, async () => {
-      if (!DG.Test.isInBenchmark) {
+      if (!DG.Test.isInBenchmark)
         return;
-      }
 
 
       const df = (await _package.files.readBinaryDataFrames(`tests/${size}k.d42`))[0];
@@ -88,18 +84,16 @@ category('Benchmarks: Analysis start', () => {
       await DG.timeAsync('Analysis start', async () => {
         const model = await startAnalysis(activityCol, sequenceCol, clustersCol, df, scaledActivityCol,
           C.SCALING_METHODS.NONE);
-        if (model) {
+        if (model)
           grok.shell.closeTable(model.df);
-        }
       });
     }, {timeout: 100000});
   }
 });
 
 async function mutationCliffsBenchmark(size: number): Promise<void> {
-  if (!DG.Test.isInBenchmark) {
+  if (!DG.Test.isInBenchmark)
     return;
-  }
 
 
   const df = (await _package.files.readBinaryDataFrames(`tests/${size}k.d42`))[0];

package/src/tests/core.ts

@@ -105,5 +105,5 @@ category('Core', () => {
     await grok.dapi.layouts.delete(sl);
     await grok.dapi.tables.delete(sti);
     await grok.dapi.projects.delete(sp);
-  });
+  }, {skipReason: 'ViewLayout should become ViewInfo in 1.18.'});
 });

package/src/utils/algorithms.ts

@@ -31,9 +31,8 @@ export type MutationCliffsOptions = {
 export async function findMutations(activityArray: type.RawData, monomerInfoArray: type.RawColumn[],
   options: MutationCliffsOptions = {}): Promise<type.MutationCliffs> {
   const nCols = monomerInfoArray.length;
-  if (nCols === 0) {
+  if (nCols === 0)
     throw new Error(`PepAlgorithmError: Couldn't find any column of semType '${C.SEM_TYPES.MONOMER}'`);
-  }
 
 
   options.minActivityDelta ??= 0;
@@ -68,9 +67,8 @@ export function calculateMonomerPositionStatistics(activityCol: DG.Column<number
     sourceDfLen = filter.trueCount;
     const tempActivityData = new Float64Array(sourceDfLen);
     const selectedIndexes = filter.getSelectedIndexes();
-    for (let i = 0; i < sourceDfLen; ++i) {
+    for (let i = 0; i < sourceDfLen; ++i)
       tempActivityData[i] = activityColData[selectedIndexes[i]];
-    }
 
 
     activityColData = tempActivityData;
@@ -79,9 +77,8 @@ export function calculateMonomerPositionStatistics(activityCol: DG.Column<number
   options.columns ??= positionColumns.map((col) => col.name);
 
   for (const posCol of positionColumns) {
-    if (!options.columns.includes(posCol.name)) {
+    if (!options.columns.includes(posCol.name))
       continue;
-    }
 
 
     const posColData = posCol.getRawData();
@@ -90,16 +87,14 @@ export function calculateMonomerPositionStatistics(activityCol: DG.Column<number
 
     for (let categoryIndex = 0; categoryIndex < posColCateogries.length; ++categoryIndex) {
       const monomer = posColCateogries[categoryIndex];
-      if (monomer === '') {
+      if (monomer === '')
         continue;
-      }
 
 
       const boolArray: boolean[] = new Array(sourceDfLen).fill(false);
       for (let i = 0; i < sourceDfLen; ++i) {
-        if (posColData[i] === categoryIndex) {
+        if (posColData[i] === categoryIndex)
           boolArray[i] = true;
-        }
       }
       const bitArray = BitArray.fromValues(boolArray);
       const stats = bitArray.allFalse || bitArray.allTrue ?
@@ -123,66 +118,57 @@ export function calculateMonomerPositionStatistics(activityCol: DG.Column<number
  */
 export function getSummaryStats(genObj: SummaryStats, stats: StatsItem | null = null,
   summaryStats: SummaryStats | null = null): void {
-  if (stats === null && summaryStats === null) {
+  if (stats === null && summaryStats === null)
     throw new Error(`MonomerPositionStatsError: either stats or summaryStats must be present`);
-  }
 
 
   const possibleMaxCount = stats?.count ?? summaryStats!.maxCount;
   genObj.maxCount ??= possibleMaxCount;
-  if (genObj.maxCount < possibleMaxCount) {
+  if (genObj.maxCount < possibleMaxCount)
     genObj.maxCount = possibleMaxCount;
-  }
 
 
   const possibleMinCount = stats?.count ?? summaryStats!.minCount;
   genObj.minCount ??= possibleMinCount;
-  if (genObj.minCount > possibleMinCount) {
+  if (genObj.minCount > possibleMinCount)
     genObj.minCount = possibleMinCount;
-  }
 
 
   const possibleMaxMeanDifference = stats?.meanDifference ?? summaryStats!.maxMeanDifference;
   genObj.maxMeanDifference ??= possibleMaxMeanDifference;
-  if (genObj.maxMeanDifference < possibleMaxMeanDifference) {
+  if (genObj.maxMeanDifference < possibleMaxMeanDifference)
     genObj.maxMeanDifference = possibleMaxMeanDifference;
-  }
 
 
   const possibleMinMeanDifference = stats?.meanDifference ?? summaryStats!.minMeanDifference;
   genObj.minMeanDifference ??= possibleMinMeanDifference;
-  if (genObj.minMeanDifference > possibleMinMeanDifference) {
+  if (genObj.minMeanDifference > possibleMinMeanDifference)
     genObj.minMeanDifference = possibleMinMeanDifference;
-  }
 
 
   if (!isNaN(stats?.pValue ?? NaN)) {
     const possibleMaxPValue = stats?.pValue ?? summaryStats!.maxPValue;
     genObj.maxPValue ??= possibleMaxPValue;
-    if (genObj.maxPValue < possibleMaxPValue) {
+    if (genObj.maxPValue < possibleMaxPValue)
       genObj.maxPValue = possibleMaxPValue;
-    }
 
 
     const possibleMinPValue = stats?.pValue ?? summaryStats!.minPValue;
     genObj.minPValue ??= possibleMinPValue;
-    if (genObj.minPValue > possibleMinPValue) {
+    if (genObj.minPValue > possibleMinPValue)
       genObj.minPValue = possibleMinPValue;
-    }
   }
 
   const possibleMaxRatio = stats?.ratio ?? summaryStats!.maxRatio;
   genObj.maxRatio ??= possibleMaxRatio;
-  if (genObj.maxRatio < possibleMaxRatio) {
+  if (genObj.maxRatio < possibleMaxRatio)
     genObj.maxRatio = possibleMaxRatio;
-  }
 
 
   const possibleMinRatio = stats?.ratio ?? summaryStats!.minRatio;
   genObj.minRatio ??= possibleMinRatio;
-  if (genObj.minRatio > possibleMinRatio) {
+  if (genObj.minRatio > possibleMinRatio)
     genObj.minRatio = possibleMinRatio;
-  }
 }
 
 /**
@@ -201,9 +187,8 @@ export function calculateClusterStatistics(df: DG.DataFrame, clustersColumnName:
   const origClustColCat = origClustCol.categories;
   const origClustMasks: BitArray[] = Array.from({length: origClustColCat.length},
     () => new BitArray(rowCount, false));
-  for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx) {
+  for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx)
     origClustMasks[origClustColData[rowIdx]].setTrue(rowIdx);
-  }
 
 
   const customClustMasks = customClusters.map(

package/src/utils/misc.ts

@@ -210,9 +210,8 @@ export function setGridProps(grid: DG.Grid, autosize: boolean = true): void {
   grid.props.showCurrentRowIndicator = false;
   grid.root.style.width = '100%';
   grid.root.style.maxWidth = '100%';
-  if (autosize) {
+  if (autosize)
     grid.autoSize(1000, 175, 0, 0, true);
-  }
 }
 
 /**

package/src/utils/types.ts

@@ -2,7 +2,7 @@ import * as DG from 'datagrok-api/dg';
 import {ClusterType} from '../viewers/logo-summary';
 import {SCALING_METHODS} from './constants';
 import {AggregationColumns} from './statistics';
-import { MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
+import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 
 export type RawData = Int32Array | Uint32Array | Float32Array | Float64Array;
 export type UTypedArray = Uint8Array | Uint16Array | Uint32Array;
@@ -25,13 +25,16 @@ export interface PeptidesSettings {
 }
 
 export class SequenceSpaceParams {
-  distanceF:  MmDistanceFunctionsNames = MmDistanceFunctionsNames.NEEDLEMANN_WUNSCH;
+  distanceF: MmDistanceFunctionsNames = MmDistanceFunctionsNames.NEEDLEMANN_WUNSCH;
   gapOpen: number = 1;
   gapExtend: number = 0.6;
   clusterEmbeddings: boolean = true;
   epsilon: number = 0.01;
   minPts: number = 4;
   fingerprintType: string = 'Morgan';
+  constructor(clusterEmbeddings?: boolean) {
+    this.clusterEmbeddings = !!clusterEmbeddings;
+  }
 }
 
 export type PartialPeptidesSettings = Partial<PeptidesSettings>;

package/src/viewers/logo-summary.ts

@@ -109,7 +109,7 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
         choices: [PositionHeight.full, PositionHeight.Entropy],
         category: LST_CATEGORIES.STYLE,
       });
-    this.membersRatioThreshold = this.float(LST_PROPERTIES.MEMBERS_RATIO_THRESHOLD, 0.3,
+    this.membersRatioThreshold = this.float(LST_PROPERTIES.MEMBERS_RATIO_THRESHOLD, 0.1,
       {
         min: 0,
         max: 1.0,
@@ -206,24 +206,21 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
    * @return - position columns.
    */
   get positionColumns(): DG.Column<string>[] {
-    if (this._positionColumns != null) {
+    if (this._positionColumns != null)
       return this._positionColumns;
-    }
 
 
     const getSharedPositionColumns = (viewerType: VIEWER_TYPE): DG.Column<string>[] | null => {
       const viewer = this.model.findViewer(viewerType) as SARViewer | null;
-      if (this.sequenceColumnName === viewer?.sequenceColumnName) {
+      if (this.sequenceColumnName === viewer?.sequenceColumnName)
         return viewer._positionColumns;
-      }
 
 
       return null;
     };
 
-    if (this.model.positionColumns != null && this.sequenceColumnName === this.model.settings?.sequenceColumnName) {
+    if (this.model.positionColumns != null && this.sequenceColumnName === this.model.settings?.sequenceColumnName)
       this._positionColumns = this.model.positionColumns;
-    }
 
 
     this._positionColumns ??= getSharedPositionColumns(VIEWER_TYPE.MONOMER_POSITION) ??
@@ -261,9 +258,8 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
    */
   getScaledActivityColumn(isFiltered: boolean = false): DG.Column<number> {
     if (this.model.settings?.activityColumnName === this.activityColumnName &&
-      this.model.settings?.activityScaling === this.activityScaling) {
+      this.model.settings?.activityScaling === this.activityScaling)
       this._scaledActivityColumn = this.model.getScaledActivityColumn(isFiltered);
-    }
 
 
     this._scaledActivityColumn ??= scaleActivity(this.dataFrame.getCol(this.activityColumnName),
@@ -380,9 +376,8 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
       doRender = true;
       break;
     }
-    if (doRender) {
+    if (doRender)
       this.render();
-    }
   }
 
   /**
@@ -399,11 +394,10 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
     const newClusterSelection = {} as type.Selection;
     newClusterSelection[CLUSTER_TYPE.ORIGINAL] = [];
     newClusterSelection[CLUSTER_TYPE.CUSTOM] = [];
-    if (options.notify) {
+    if (options.notify)
       this.clusterSelection = newClusterSelection;
-    } else {
+    else
       this._clusterSelection = newClusterSelection;
-    }
 
 
     return this.clusterSelection;
@@ -473,9 +467,8 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
       const customClustCol = customClustColList[rowIdx];
       customLSTClustCol.set(rowIdx, customClustCol.name);
       const bitArray = BitArray.fromUint32Array(filteredDfRowCount, customClustCol.getRawData() as Uint32Array);
-      if (bitArray.allFalse || bitArray.allTrue) {
+      if (bitArray.allFalse || bitArray.allTrue)
         continue;
-      }
 
 
       const bsMask = DG.BitSet.fromBytes(bitArray.buffer.buffer, filteredDfRowCount);
@@ -504,9 +497,8 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
     const origLSTCols = origLST.columns;
     const origLSTClustCol: DG.Column<string> = origLST.getCol(clustersColName);
     origLSTClustCol.name = C.LST_COLUMN_NAMES.CLUSTER;
-    if (origLSTClustCol.type !== DG.COLUMN_TYPE.STRING) {
+    if (origLSTClustCol.type !== DG.COLUMN_TYPE.STRING)
       origLST.columns.replace(origLSTClustCol, origLSTClustCol.convertTo(DG.COLUMN_TYPE.STRING));
-    }
 
 
     const origLSTClustColCat = origLSTClustCol.categories;
@@ -528,9 +520,8 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
 
     for (let rowIdx = 0; rowIdx < origLSTLen; ++rowIdx) {
       const mask = origClustMasks[rowIdx];
-      if (mask.allFalse || mask.allTrue) {
+      if (mask.allFalse || mask.allTrue)
         continue;
-      }
 
 
       const bsMask = DG.BitSet.fromBytes(mask.buffer.buffer, filteredDfRowCount);
@@ -586,9 +577,8 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
     grid.onCellRender.subscribe(async (gridCellArgs) => {
       const gridCell = gridCellArgs.cell;
       const currentRowIdx = gridCell.tableRowIndex;
-      if (!gridCell.isTableCell || currentRowIdx === null || currentRowIdx === -1) {
+      if (!gridCell.isTableCell || currentRowIdx === null || currentRowIdx === -1)
         return;
-      }
 
 
       const canvasContext = gridCellArgs.g;
@@ -613,13 +603,12 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
             const viewerProps = viewer.getProperties();
 
             for (const prop of viewerProps) {
-              if (prop.name === 'positionHeight' && prop.get(viewer) !== this.webLogoMode) {
+              if (prop.name === 'positionHeight' && prop.get(viewer) !== this.webLogoMode)
                 prop.set(viewer, this.webLogoMode);
-              } else if (prop.name === 'positionWidth' && prop.get(viewer) !== positionWidth) {
+              else if (prop.name === 'positionWidth' && prop.get(viewer) !== positionWidth)
                 prop.set(viewer, positionWidth);
-              } else if (prop.name === 'minHeight' && prop.get(viewer) !== height) {
+              else if (prop.name === 'minHeight' && prop.get(viewer) !== height)
                 prop.set(viewer, height);
-              }
             }
             const viewerRoot = $(viewer.root).css('height', `${height}px`);//;
             viewerRoot.children().first().css('overflow-y', 'hidden !important');
@@ -667,15 +656,13 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
     });
     grid.root.addEventListener('mouseleave', (_ev) => this.model.unhighlight());
     DG.debounce(grid.onCurrentCellChanged, 500).subscribe((gridCell) => {
-      if (!gridCell.isTableCell) {
+      if (!gridCell.isTableCell)
         return;
-      }
 
 
       try {
-        if (!this.keyPress || gridCell.tableColumn?.name !== C.LST_COLUMN_NAMES.CLUSTER) {
+        if (!this.keyPress || gridCell.tableColumn?.name !== C.LST_COLUMN_NAMES.CLUSTER)
           return;
-        }
 
 
         if (this.currentRowIndex !== null && this.currentRowIndex !== -1) {
@@ -698,14 +685,13 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
     });
     grid.root.addEventListener('keydown', (ev) => {
       this.keyPress = ev.key.startsWith('Arrow');
-      if (this.keyPress) {
+      if (this.keyPress)
         return;
-      }
 
 
-      if (ev.key === 'Escape' || (ev.code === 'KeyA' && ev.shiftKey && ev.ctrlKey)) {
+      if (ev.key === 'Escape' || (ev.code === 'KeyA' && ev.shiftKey && ev.ctrlKey))
         this.initClusterSelection({notify: false});
-      } else if (ev.code === 'KeyA' && ev.ctrlKey) {
+      else if (ev.code === 'KeyA' && ev.ctrlKey) {
         for (let rowIdx = 0; rowIdx < this.logoSummaryTable.rowCount; ++rowIdx) {
           this.modifyClusterSelection(this.getCluster(grid.cell(C.LST_COLUMN_NAMES.CLUSTER, rowIdx)),
             {
@@ -719,9 +705,8 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
     });
     grid.root.addEventListener('click', (ev) => {
       const gridCell = grid.hitTest(ev.offsetX, ev.offsetY);
-      if (!gridCell || !gridCell.isTableCell || gridCell.tableColumn?.name !== C.LST_COLUMN_NAMES.CLUSTER) {
+      if (!gridCell || !gridCell.isTableCell || gridCell.tableColumn?.name !== C.LST_COLUMN_NAMES.CLUSTER)
         return;
-      }
 
 
       const selection = this.getCluster(gridCell);
@@ -743,9 +728,8 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
 
       const cluster = this.getCluster(gridCell);
       this.highlightCluster(cluster);
-      if (gridCell.tableColumn?.name === C.LST_COLUMN_NAMES.CLUSTER) {
+      if (gridCell.tableColumn?.name === C.LST_COLUMN_NAMES.CLUSTER)
         this.showTooltip(cluster, x, y);
-      }
 
 
       return true;
@@ -829,9 +813,8 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
                   col.name === C.LST_COLUMN_NAMES.RATIO ? stats.ratio :
                     col.name in aggregatedValues ? aggregatedValues[col.name] :
                       undefined;
-      if (typeof newClusterVals[i] === 'undefined') {
+      if (typeof newClusterVals[i] === 'undefined')
         _package.logger.warning(`PeptidesLSTWarn: value for column ${col.name} is undefined`);
-      }
     }
     this.logoSummaryTable.rows.addNew(newClusterVals);
 
@@ -893,11 +876,10 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
     shiftPressed: false,
     ctrlPressed: false,
   }, notify: boolean = true): void {
-    if (notify) {
+    if (notify)
       this.clusterSelection = modifySelection(this.clusterSelection, cluster, options);
-    } else {
+    else
       this._clusterSelection = modifySelection(this.clusterSelection, cluster, options);
-    }
   }
 
   /**
@@ -922,9 +904,8 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
       const seekValue = origClustColCategories.indexOf(cluster.monomerOrCluster);
 
       for (let i = 0; i < rowCount; ++i) {
-        if (origClustColData[i] === seekValue) {
+        if (origClustColData[i] === seekValue)
           bitArray.setTrue(i);
-        }
       }
       bitArray.incrementVersion();
     } else {
@@ -935,9 +916,8 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
     const stats = bs.anyFalse ? getStats(activityColData, bitArray) :
       this.clusterStats[cluster.positionOrClusterType as ClusterType][cluster.monomerOrCluster];
 
-    if (!stats.count) {
+    if (!stats.count)
       return null;
-    }
 
 
     const mask = DG.BitSet.fromBytes(bitArray.buffer.buffer, rowCount);