@datagrok/bio 2.4.7 → 2.4.9

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.4.7",
+  "version": "2.4.9",
   "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",
@@ -14,7 +14,7 @@
   },
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.27.0",
+    "@datagrok-libraries/bio": "^5.28.0",
     "@datagrok-libraries/chem-meta": "^1.0.1",
     "@datagrok-libraries/ml": "^6.3.16",
     "@datagrok-libraries/utils": "^2.1.3",

package/src/demo/bio05-helm-msa-sequence-space.ts

@@ -35,6 +35,7 @@ export async function demoBio05UI(funcPath: string): Promise<void> {
       const gapExtend: number = 0;
       msaHelmCol = await runPepsea(helmCol, msaHelmColName, method, gapOpen, gapExtend, undefined);
       df.columns.add(msaHelmCol);
+      await grok.data.detectSemanticTypes(df);
     })();
 
     await step('Composition analysis on MSA results', async () => {

package/src/tests/WebLogo-positions-test.ts

@@ -5,7 +5,6 @@ import {after, before, category, expect, expectArray, test} from '@datagrok-libr
 import {ALPHABET, NOTATION, SplitterFunc, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {
   countForMonomerAtPosition,
-  FilterSources,
   PositionInfo as PI,
   PositionMonomerInfo as PMI,
   WebLogoViewer
@@ -81,7 +80,7 @@ ATC-G-TTGC--
   });
 
   test('positions with shrinkEmptyTail option true (filtered)', async () => {
-    const csvDf2 = `seq 
+    const csvDf2 = `seq
 -TC-G-TTGC--
 -TC-GCTTGC--
 -T--C-GT-

package/src/viewers/vd-regions-viewer.ts

@@ -2,12 +2,12 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
 import * as rxjs from 'rxjs';
-import {FilterSources, WebLogoViewer, PROPS as wlPROPS} from '../viewers/web-logo-viewer';
+import {WebLogoViewer, PROPS as wlPROPS} from '../viewers/web-logo-viewer';
 import {
   VdRegionsPropsDefault, VdRegionsProps, IVdRegionsViewer,
   VdRegion, VdRegionType
 } from '@datagrok-libraries/bio/src/viewers/vd-regions';
-import {PositionHeight} from '@datagrok-libraries/bio/src/viewers/web-logo';
+import {FilterSources, PositionHeight} from '@datagrok-libraries/bio/src/viewers/web-logo';
 import {Unsubscribable} from 'rxjs';
 
 const vrt = VdRegionType;

package/src/viewers/web-logo-viewer.ts

@@ -16,6 +16,10 @@ import {
   WebLogoPropsDefault, WebLogoProps, IWebLogoViewer,
   PositionHeight,
   positionSeparator,
+  VerticalAlignments,
+  HorizontalAlignments,
+  PositionMarginStates,
+  FilterSources,
 } from '@datagrok-libraries/bio/src/viewers/web-logo';
 import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
 import {TAGS as wlTAGS} from '@datagrok-libraries/bio/src/viewers/web-logo';
@@ -80,29 +84,6 @@ export class PositionInfo {
   }
 }
 
-export enum VerticalAlignments {
-  TOP = 'top',
-  MIDDLE = 'middle',
-  BOTTOM = 'bottom',
-}
-
-export enum HorizontalAlignments {
-  LEFT = 'left',
-  CENTER = 'center',
-  RIGHT = 'right',
-}
-
-export enum PositionMarginStates {
-  AUTO = 'auto',
-  ON = 'on',
-  OFF = 'off',
-}
-
-export enum FilterSources {
-  Filtered = 'Filtered',
-  Selected = 'Selected',
-}
-
 export enum PROPS_CATS {
   STYLE = 'Style',
   BEHAVIOR = 'Behavior',
@@ -138,6 +119,8 @@ export enum PROPS {
   filterSource = 'filterSource',
 }
 
+const defaults: WebLogoProps = WebLogoPropsDefault;
+
 export class WebLogoViewer extends DG.JsViewer {
   public static residuesSet = 'nucleotides';
   private static viewerCount: number = -1;
@@ -270,43 +253,41 @@ export class WebLogoViewer extends DG.JsViewer {
     this.unitsHandler = null;
 
     // -- Data --
-    this.sequenceColumnName = this.string(PROPS.sequenceColumnName, null,
+    this.sequenceColumnName = this.string(PROPS.sequenceColumnName, defaults.sequenceColumnName,
       {category: PROPS_CATS.DATA});
-    this.startPositionName = this.string(PROPS.startPositionName, null,
+    this.startPositionName = this.string(PROPS.startPositionName, defaults.startPositionName,
       {category: PROPS_CATS.DATA});
-    this.endPositionName = this.string(PROPS.endPositionName, null,
+    this.endPositionName = this.string(PROPS.endPositionName, defaults.endPositionName,
       {category: PROPS_CATS.DATA});
-    this.skipEmptySequences = this.bool(PROPS.skipEmptySequences, true,
+    this.skipEmptySequences = this.bool(PROPS.skipEmptySequences, defaults.skipEmptySequences,
       {category: PROPS_CATS.DATA});
-    this.skipEmptyPositions = this.bool(PROPS.skipEmptyPositions, false,
+    this.skipEmptyPositions = this.bool(PROPS.skipEmptyPositions, defaults.skipEmptyPositions,
       {category: PROPS_CATS.DATA});
-    this.shrinkEmptyTail = this.bool(PROPS.shrinkEmptyTail, true,
+    this.shrinkEmptyTail = this.bool(PROPS.shrinkEmptyTail, defaults.shrinkEmptyTail,
       {category: PROPS_CATS.DATA});
 
-
     // -- Style --
-    this.backgroundColor = this.int(PROPS.backgroundColor, 0xFFFFFFFF,
+    this.backgroundColor = this.int(PROPS.backgroundColor, defaults.backgroundColor,
       {category: PROPS_CATS.STYLE});
-    this.positionHeight = this.string(PROPS.positionHeight, PositionHeight.full,
+    this.positionHeight = this.string(PROPS.positionHeight, defaults.positionHeight,
       {category: PROPS_CATS.STYLE, choices: Object.values(PositionHeight)});
-    this._positionWidth = this.positionWidth = this.float(PROPS.positionWidth, 16,
+    this._positionWidth = this.positionWidth = this.float(PROPS.positionWidth, defaults.positionWidth,
       {category: PROPS_CATS.STYLE/* editor: 'slider', min: 4, max: 64, postfix: 'px' */});
 
-
     // -- Layout --
-    this.verticalAlignment = this.string(PROPS.verticalAlignment, VerticalAlignments.MIDDLE,
+    this.verticalAlignment = this.string(PROPS.verticalAlignment, defaults.verticalAlignment,
       {category: PROPS_CATS.LAYOUT, choices: Object.values(VerticalAlignments)});
-    this.horizontalAlignment = this.string(PROPS.horizontalAlignment, HorizontalAlignments.CENTER,
+    this.horizontalAlignment = this.string(PROPS.horizontalAlignment, defaults.horizontalAlignment,
       {category: PROPS_CATS.LAYOUT, choices: Object.values(HorizontalAlignments)});
-    this.fixWidth = this.bool(PROPS.fixWidth, false,
+    this.fixWidth = this.bool(PROPS.fixWidth, defaults.fixWidth,
       {category: PROPS_CATS.LAYOUT});
-    this.fitArea = this.bool(PROPS.fitArea, true,
+    this.fitArea = this.bool(PROPS.fitArea, defaults.fitArea,
       {category: PROPS_CATS.LAYOUT});
-    this.minHeight = this.float(PROPS.minHeight, 50,
+    this.minHeight = this.float(PROPS.minHeight, defaults.minHeight,
       {category: PROPS_CATS.LAYOUT/*, editor: 'slider', min: 25, max: 250, postfix: 'px'*/});
-    this.maxHeight = this.float(PROPS.maxHeight, 100,
+    this.maxHeight = this.float(PROPS.maxHeight, defaults.maxHeight,
       {category: PROPS_CATS.LAYOUT/*, editor: 'slider', min: 25, max: 500, postfix: 'px'*/});
-    this.positionMarginState = this.string(PROPS.positionMarginState, PositionMarginStates.AUTO,
+    this.positionMarginState = this.string(PROPS.positionMarginState, defaults.positionMarginState,
       {category: PROPS_CATS.LAYOUT, choices: Object.values(PositionMarginStates)});
     let defaultValueForPositionMargin = 0;
     if (this.positionMarginState === 'auto') defaultValueForPositionMargin = 4;
@@ -314,7 +295,7 @@ export class WebLogoViewer extends DG.JsViewer {
       {category: PROPS_CATS.LAYOUT, min: 0, max: 16});
 
     // -- Behavior --
-    this.filterSource = this.string(PROPS.filterSource, FilterSources.Filtered,
+    this.filterSource = this.string(PROPS.filterSource, defaults.filterSource,
       {category: PROPS_CATS.BEHAVIOR, choices: Object.values(FilterSources)}) as FilterSources;
 
     const style: SliderOptions = {style: 'barbell'};