@datagrok/bio 2.11.15 → 2.11.18

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.11.15",
+  "version": "2.11.18",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
@@ -30,15 +30,22 @@
       "propertyType": "string",
       "defaultValue": ".",
       "nullable": false
+    },
+    {
+      "name": "Debug",
+      "propertyType": "string_list",
+      "choices": ["detectors", "WebLogo"],
+      "defaultValue": [],
+      "nullable": false
     }
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.39.10",
+    "@datagrok-libraries/bio": "^5.39.13",
     "@datagrok-libraries/chem-meta": "^1.2.1",
-    "@datagrok-libraries/ml": "^6.3.62",
+    "@datagrok-libraries/ml": "^6.3.67",
     "@datagrok-libraries/tutorials": "^1.3.11",
-    "@datagrok-libraries/utils": "^4.1.34",
+    "@datagrok-libraries/utils": "^4.1.36",
     "cash-dom": "^8.0.0",
     "css-loader": "^6.7.3",
     "datagrok-api": "^1.16.0",
@@ -64,9 +71,9 @@
     "webpack": "^5.76.3",
     "webpack-bundle-analyzer": "latest",
     "webpack-cli": "^4.9.1",
-    "@datagrok/chem": "^1.8.6",
+    "@datagrok/chem": "^1.8.8",
     "@datagrok/helm": "^2.1.22",
-    "@datagrok/dendrogram": "^1.2.21"
+    "@datagrok/dendrogram": "^1.2.22"
   },
   "scripts": {
     "link-api": "npm link datagrok-api",

package/src/analysis/sequence-activity-cliffs.ts

@@ -60,7 +60,7 @@ export async function getChemSimilaritiesMatrix(dim: number, seqCol: DG.Column,
 }
 
 export function createTooltipElement(params: ITooltipAndPanelParams): HTMLDivElement {
-  const tooltipElement = ui.divH([]);
+  const tooltipElement = ui.divH([], {style: {gap: '10px'}});
   const columnNames = ui.divV([
     ui.divText(params.seqCol.name),
     ui.divText(params.activityCol.name),
@@ -69,7 +69,7 @@ export function createTooltipElement(params: ITooltipAndPanelParams): HTMLDivEle
   columnNames.style.display = 'flex';
   columnNames.style.justifyContent = 'space-between';
   tooltipElement.append(columnNames);
-  params.line.mols.forEach((molIdx: number, _idx: number) => {
+  params.points.forEach((molIdx: number) => {
     const activity = ui.divText(params.activityCol.get(molIdx).toFixed(2));
     activity.style.display = 'flex';
     activity.style.justifyContent = 'left';
@@ -99,7 +99,7 @@ export function createPropPanelElement(params: ITooltipAndPanelParams): HTMLDivE
 
   const sequencesArray = new Array<string>(2);
   const activitiesArray = new Array<number>(2);
-  params.line.mols.forEach((molIdx, idx) => {
+  params.points.forEach((molIdx, idx) => {
     sequencesArray[idx] = params.seqCol.get(molIdx);
     activitiesArray[idx] = params.activityCol.get(molIdx);
   });

package/src/demo/bio01a-hierarchical-clustering-and-sequence-space.ts

@@ -22,6 +22,7 @@ export async function demoBio01aUI() {
   let _spViewer: DG.ScatterPlotViewer;
 
   const dimRedMethod: string = 'UMAP';
+  const activityColName = 'activity';
 
   try {
     const demoScript = new DemoScript(
@@ -48,6 +49,7 @@ export async function demoBio01aUI() {
       })
       .step('Build sequence space', async () => {
         _spViewer = await demoSequenceSpace(view, df, seqColName, dimRedMethod);
+        _spViewer.setOptions({color: activityColName});
       }, {
         description: `Reduce sequence space dimensionality to display on 2D representation.`,
         delay: 2000,
@@ -66,16 +68,13 @@ export async function demoBio01aUI() {
         delay: 2000,
       })
       .step('Select a sequence', async () => {
-        df.selection.init((idx: number) => [15].includes(idx));
+        df.selection.set(65, true);
       }, {
         description: `Handling selection of data frame row reflecting on linked viewers.`,
         delay: 2000,
       })
       .step('Select a bunch of sequences', async () => {
-        const seqIdCol: DG.Column<string> = df.getCol('sequence_id');
-        df.selection.init((rowI: number) => {
-          return ['c0_seq120', 'c0_seq105', 'c0_seq121', 'c0_seq93'].includes(seqIdCol.get(rowI)!);
-        });
+        [67, 72, 77, 82, 83, 84, 85, 91, 93].forEach((idx) => df.selection.set(idx, true));
         df.currentRowIdx = 27;
       }, {
         // eslint-disable-next-line max-len

package/src/package-types.ts

@@ -3,7 +3,7 @@ import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 
 import {Observable, Subject} from 'rxjs';
-import {ObjectPropertyBag} from 'datagrok-api/dg';
+import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 
 /** Names of package properties/settings declared in properties section of {@link './package.json'} */
 export const enum BioPackagePropertiesNames {
@@ -60,13 +60,12 @@ export class BioPackage extends DG.Package {
 
   private _initialized: boolean = false;
 
-  public get initialized(): boolean { return this._initialized;}
+  public get initialized(): boolean { return this._initialized; }
 
-  public completeInit(): void { this._initialized = true;}
+  public completeInit(): void { this._initialized = true; }
 
   handleErrorUI(err: any) {
-    const errMsg = err instanceof Error ? err.message : err.toString();
-    const errStack = err instanceof Error ? err.stack : undefined;
+    const [errMsg, errStack] = errInfo(err);
     grok.shell.error(errMsg);
     this.logger.error(errMsg, undefined, errStack);
   }

package/src/package.ts

@@ -68,7 +68,7 @@ import {SplitToMonomersFunctionEditor} from './function-edtiors/split-to-monomer
 import {splitToMonomersUI} from './utils/split-to-monomers';
 import {MonomerCellRenderer} from './utils/monomer-cell-renderer';
 import {BioPackage, BioPackageProperties} from './package-types';
-import {PackageSettingsEditorWidget} from './widgets/package-settings-editor-widget';
+// import {PackageSettingsEditorWidget} from './widgets/package-settings-editor-widget';
 import {getCompositionAnalysisWidget} from './widgets/composition-analysis-widget';
 import {MacromoleculeColumnWidget} from './utils/macromolecule-column-widget';
 import {addCopyMenuUI} from './utils/context-menu';
@@ -268,16 +268,16 @@ export function SeqActivityCliffsEditor(call: DG.FuncCall) {
 
 // -- Package settings editor --
 
-//name: packageSettingsEditor
-//description: The database connection
-//tags: packageSettingsEditor
-//input: object propList
-//output: widget result
-export function packageSettingsEditor(propList: DG.Property[]): DG.Widget {
-  const widget = new PackageSettingsEditorWidget(propList);
-  widget.init().then(); // Ignore promise returned
-  return widget as DG.Widget;
-}
+// //name: packageSettingsEditor
+// //description: The database connection
+// //tags: packageSettingsEditor
+// //input: object propList
+// //output: widget result
+// export function packageSettingsEditor(propList: DG.Property[]): DG.Widget {
+//   const widget = new PackageSettingsEditorWidget(propList);
+//   widget.init().then(); // Ignore promise returned
+//   return widget as DG.Widget;
+// }
 
 // -- Cell renderers --
 
@@ -498,11 +498,14 @@ export async function activityCliffs(df: DG.DataFrame, macroMolecule: DG.Column<
 //meta.supportedDistanceFunctions: Hamming,Levenshtein,Monomer chemical distance,Needlemann-Wunsch
 //input: column col {semType: Macromolecule}
 //input: string metric
+//input: double gapOpen = 1 {caption: Gap open penalty; default: 1; optional: true}
+//input: double gapExtend = 0.6 {caption: Gap extension penalty; default: 0.6; optional: true}
 //output: object result
 export async function macromoleculePreprocessingFunction(
-  col: DG.Column, metric: MmDistanceFunctionsNames): Promise<PreprocessFunctionReturnType> {
+  col: DG.Column, metric: MmDistanceFunctionsNames, gapOpen: number = 1, gapExtend: number = 0.6
+): Promise<PreprocessFunctionReturnType> {
   const {seqList, options} = await getEncodedSeqSpaceCol(col, metric);
-  return {entries: seqList, options};
+  return {entries: seqList, options: {...options, gapOpen, gapExtend}};
 }
 
 //name: Helm Fingerprints

package/src/utils/get-region-func-editor.ts

@@ -235,7 +235,7 @@ export class GetRegionFuncEditor {
     const inputsForm = ui.inputs(Object.values(this.inputs), {style: {minWidth: '320px'}});
     ui.dialog({title: 'Get Region'})
       .add(inputsForm)
-      .onOK(async () => {
+      .onOK(() => {
         (async () => {
           const callParams = this.getParams();
           await this.call.func.prepare(callParams).call(true);
@@ -247,8 +247,8 @@ export class GetRegionFuncEditor {
 
   public widget(): DG.Widget {
     const inputsForm = ui.inputs(Object.entries(this.inputs)
-      .filter(([inputName, input]) => !['table', 'sequence'].includes(inputName))
-      .map(([inputName, input]) => input));
+      .filter(([inputName, _input]) => !['table', 'sequence'].includes(inputName))
+      .map(([_inputName, input]) => input));
     const doBtn = ui.button('Get Region', () => {
       (async () => {
         const callParams = this.getParams();