@datagrok/peptides 1.24.0 → 1.25.0

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/peptides",
   "friendlyName": "Peptides",
-  "version": "1.24.0",
+  "version": "1.25.0",
   "author": {
     "name": "Davit Rizhinashvili",
     "email": "drizhinashvili@datagrok.ai"
@@ -13,9 +13,9 @@
     "directory": "packages/Peptides"
   },
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.60.0",
+    "@datagrok-libraries/bio": "^5.61.3",
     "@datagrok-libraries/math": "^1.2.6",
-    "@datagrok-libraries/ml": "^6.10.6",
+    "@datagrok-libraries/ml": "^6.10.7",
     "@datagrok-libraries/statistics": "^1.2.12",
     "@datagrok-libraries/tutorials": "^1.7.4",
     "@datagrok-libraries/utils": "^4.6.9",

package/src/model.ts

@@ -312,9 +312,7 @@ export class PeptidesModel {
    * @return {type.Selection} - Current Monomer-Position selection that came from WebLogo in header
    */
   get webLogoSelection(): type.Selection {
-    const tagSelection = this.df.getTag(`${C.SUFFIXES.WL}${C.TAGS.INVARIANT_MAP_SELECTION}`);
-    this._webLogoSelection ??= tagSelection === null && this.positionColumns !== null ?
-      initSelection(this.positionColumns) : JSON.parse(tagSelection ?? `{}`);
+    this._webLogoSelection ??= initSelection(this.positionColumns ?? []);
     return this._webLogoSelection!;
   }
 
@@ -323,7 +321,6 @@ export class PeptidesModel {
    */
   set webLogoSelection(selection: type.Selection) {
     this._webLogoSelection = selection;
-    this.df.setTag(`${C.SUFFIXES.WL}${C.TAGS.INVARIANT_MAP_SELECTION}`, JSON.stringify(selection));
     this.fireBitsetChanged(null);
     this.analysisView.grid.invalidate();
   }

package/src/tests/misc.ts

@@ -6,6 +6,7 @@ import {findMutations, MutationCliffsOptions} from '../utils/algorithms';
 import * as type from '../utils/types';
 import {extractColInfo} from '../utils/misc';
 import {PeptideUtils} from '../peptideUtils';
+import BitArray from '@datagrok-libraries/utils/src/bit-array';
 
 category('Algorithms', () => {
   let activityCol: type.RawData;
@@ -53,8 +54,9 @@ category('Algorithms', () => {
     expect(d32[0], 1, `MutationCliffsInfo['D']['3'][2] should have value 1`);
 
     // Check with target
-    settings.targetCol = targetCol;
-    settings.currentTarget = '1';
+    const filter = new BitArray(3, false);
+    filter.setBit(0, true);
+    settings.filter = filter.buffer;
     mutationCliffsInfo = await findMutations(activityCol, monomerColumns, settings);
     expect(mutationCliffsInfo.size, 0, `MutationCliffsInfo should be empty for target '1'`);
   });

package/src/utils/algorithms.ts

@@ -18,8 +18,7 @@ import {
 export type MutationCliffsOptions = {
   maxMutations?: number,
   minActivityDelta?: number,
-  targetCol?: type.RawColumn | null,
-  currentTarget?: string | null
+  filter?: Uint32Array
 };
 
 /**
@@ -98,10 +97,6 @@ export function calculateMonomerPositionStatistics(activityCol: DG.Column<number
   positionColumns: DG.Column<string>[], options: {
     isFiltered?: boolean,
     columns?: string[],
-    target?: {
-      col: DG.Column<string>,
-      cat: string,
-    },
     aggValue?: {
       col: DG.Column,
       type: DG.AGG
@@ -109,27 +104,23 @@ export function calculateMonomerPositionStatistics(activityCol: DG.Column<number
   } = {}): MonomerPositionStats {
   options.isFiltered ??= false;
   const monomerPositionObject = {general: {}} as MonomerPositionStats & { general: SummaryStats };
-  let activityColData: Float64Array = activityCol.getRawData() as Float64Array;
-  let sourceDfLen = activityCol.length;
+  const activityColData: Float64Array = activityCol.getRawData() as Float64Array;
+  const sourceDfLen = activityCol.length;
   options.columns ??= positionColumns.map((col) => col.name);
-  if (options.isFiltered) {
-    sourceDfLen = filter.trueCount;
-    const tempActivityData = new Float64Array(sourceDfLen);
-    const selectedIndexes = filter.getSelectedIndexes();
-    for (let i = 0; i < sourceDfLen; ++i)
-      tempActivityData[i] = activityColData[selectedIndexes[i]];
-
-
-    activityColData = tempActivityData;
-    positionColumns = DG.DataFrame.fromColumns(positionColumns).clone(filter, options.columns).columns.toList();
-    if (options.target)
-      options.target.col = options.target.col.clone(filter);
-    if (options.aggValue)
-      options.aggValue.col = options.aggValue.col.clone(filter);
-  }
-  const targetColIndexes = options.target?.col?.getRawData();
-  const targetColCat = options.target?.col.categories;
-  const targetIndex = options.target?.cat ? targetColCat?.indexOf(options.target.cat) : -1;
+  // if (options.isFiltered) {
+  //   sourceDfLen = filter.trueCount;
+  //   const tempActivityData = new Float64Array(sourceDfLen);
+  //   const selectedIndexes = filter.getSelectedIndexes();
+  //   for (let i = 0; i < sourceDfLen; ++i)
+  //     tempActivityData[i] = activityColData[selectedIndexes[i]];
+
+
+  //   activityColData = tempActivityData;
+  //   positionColumns = DG.DataFrame.fromColumns(positionColumns).clone(filter, options.columns).columns.toList();
+  //   if (options.aggValue)
+  //     options.aggValue.col = options.aggValue.col.clone(filter);
+  // }
+
   for (const posCol of positionColumns) {
     if (!options.columns.includes(posCol.name))
       continue;
@@ -147,7 +138,7 @@ export function calculateMonomerPositionStatistics(activityCol: DG.Column<number
 
       const boolArray: boolean[] = new Array(sourceDfLen).fill(false);
       for (let i = 0; i < sourceDfLen; ++i) {
-        if (posColData[i] === categoryIndex && (!targetColIndexes || targetIndex === -1 || targetColIndexes[i] === targetIndex))
+        if (posColData[i] === categoryIndex && (!options.isFiltered || filter.get(i)))
           boolArray[i] = true;
       }
       const bitArray = BitArray.fromValues(boolArray);

package/src/utils/cell-renderer.ts

@@ -127,7 +127,7 @@ export function renderMutationCliffCell(canvasContext: CanvasRenderingContext2D,
   } else if (viewer instanceof MostPotentResidues) {
     // in case of most potent residues viewer, we render the invariant of monomer-position. i.e. how many sequences there are with that monomer at that position
     // same as in invariant map viewer
-    const positionStats = viewer.monomerPositionStats ?? viewer?.model?.monomerPositionStats;
+    const positionStats = viewer.monomerPositionStats;
     const count = positionStats?.[currentPosition]?.[currentMonomer]?.count;
     if (count)
       canvasContext.fillText(count.toString(), midX + halfWidth - 5, midY, halfWidth - 5);

package/src/utils/constants.ts

@@ -12,6 +12,7 @@ export enum COLUMNS_NAMES {
   COUNT = 'Count',
   RATIO = 'Ratio',
   MEAN = 'Mean',
+  TOTAL_COUNT = '∑'
 }
 
 export enum LST_COLUMN_NAMES {
@@ -28,13 +29,9 @@ export enum TAGS {
   MONOMER = 'monomer',
   POSITION = 'pos',
   SEPARATOR = 'separator',
-  SELECTION = 'selection',
-  MUTATION_CLIFFS_SELECTION = 'mutationCliffsSelection',
   ALPHABET = 'alphabet',
   FILTER = 'filter',
-  INVARIANT_MAP_SELECTION = 'invariantMapSelection',
   SAR_MODE = 'sarMode',
-  CLUSTER_SELECTION = 'clusterSelection',
   VISIBLE = 'visible',
   SETTINGS = 'settings',
   CUSTOM_CLUSTER = 'customCluster',

package/src/utils/misc.ts

@@ -388,7 +388,8 @@ export function getSelectionBitset(selection: type.Selection, stats: MasksInfo):
     }
   }
 
-  return (combinedBitset != null) ? DG.BitSet.fromBytes(combinedBitset!.buffer.buffer, combinedBitset!.length) : null;
+  return (combinedBitset != null) ?
+    DG.BitSet.fromBytes(combinedBitset!.buffer.buffer as ArrayBuffer, combinedBitset!.length) : null;
 }
 
 /**

package/src/utils/parallel-mutation-cliffs.ts

@@ -22,8 +22,6 @@ export class ParallelMutationCliffs {
     options: MutationCliffsOptions = {}): Promise<type.MutationCliffs> {
     const substitutionsInfo: type.MutationCliffs = new Map();
     try {
-      const currentTargetIdx = options.targetCol?.cat!.indexOf(options.currentTarget!) ?? -1;
-
       const len = activityArray.length;
       const promises = new Array<Promise<ParallelMutationReturnType>>(this._workerCount);
       const matSize = len * (len - 1) / 2; // size of reduced upper triangular matrix
@@ -34,13 +32,12 @@ export class ParallelMutationCliffs {
       monomerInfoArray.forEach((monomerInfo) => {
         monomerInfo.cat = monomerInfo.cat?.slice();
       });
-      options.targetCol?.cat && (options.targetCol.cat = options.targetCol.cat.slice());
       for (let idx = 0; idx < this._workerCount; idx++) {
         promises[idx] = new Promise((resolveWorker, rejectWorker) => {
           const startIdx = Math.floor(idx * chunkSize);
           const endIdx = idx === this._workerCount - 1 ? matSize : Math.floor((idx + 1) * chunkSize);
           this._workers[idx].postMessage(
-            {startIdx, endIdx, activityArray, monomerInfoArray, settings: options, currentTargetIdx});
+            {startIdx, endIdx, activityArray, monomerInfoArray, settings: options});
           this._workers[idx].onmessage = ({data: {pos, seq1Idxs, seq2Idxs, error}}): void => {
             if (error) {
               this._workers[idx]?.terminate();

package/src/viewers/logo-summary.ts

@@ -195,9 +195,7 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
    * @return - cluster selection.
    */
   get clusterSelection(): type.Selection {
-    const tagSelection = this.dataFrame.getTag(C.TAGS.CLUSTER_SELECTION);
-    this._clusterSelection ??= tagSelection === null ? this.initClusterSelection({notify: false}) :
-      JSON.parse(tagSelection);
+    this._clusterSelection ??= this.initClusterSelection({notify: false});
     return this._clusterSelection!;
   }
 
@@ -207,7 +205,6 @@ export class LogoSummaryTable extends DG.JsViewer implements ILogoSummaryTable {
    */
   set clusterSelection(selection: type.Selection) {
     this._clusterSelection = selection;
-    this.dataFrame.setTag(C.TAGS.CLUSTER_SELECTION, JSON.stringify(selection));
     this.model.fireBitsetChanged(VIEWER_TYPE.LOGO_SUMMARY_TABLE);
     this.model.analysisView.grid.invalidate();
   }