@datagrok/bio 2.0.17 → 2.0.18

package/src/utils/cell-renderer.ts

@@ -1,31 +1,26 @@
-import * as C from './constants';
-import * as DG from 'datagrok-api/dg';
-import {AminoacidsPalettes} from '@datagrok-libraries/bio/src/aminoacids';
-import {NucleotidesPalettes} from '@datagrok-libraries/bio/src/nucleotides';
-import {UnknownSeqPalettes} from '@datagrok-libraries/bio/src/unknown';
-import {SplitterFunc, WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
-import {SeqPalette} from '@datagrok-libraries/bio/src/seq-palettes';
+import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
-import {printLeftOrCentered, DrawStyle} from '@datagrok-libraries/bio/src/utils/cell-renderer';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import * as DG from 'datagrok-api/dg';
+import * as bio from '@datagrok-libraries/bio';
+import * as C from './constants';
 
 const undefinedColor = 'rgb(100,100,100)';
-const monomerToShortFunction: (amino: string, maxLengthOfMonomer: number) => string = WebLogo.monomerToShort;
+const monomerToShortFunction: (amino: string, maxLengthOfMonomer: number) => string = bio.monomerToShort;
 
 
-function getPaletteByType(paletteType: string): SeqPalette {
+function getPaletteByType(paletteType: string): bio.SeqPalette {
   switch (paletteType) {
   case 'PT':
-    return AminoacidsPalettes.GrokGroups;
+    return bio.AminoacidsPalettes.GrokGroups;
   case 'NT':
-    return NucleotidesPalettes.Chromatogram;
+    return bio.NucleotidesPalettes.Chromatogram;
   case 'DNA':
-    return NucleotidesPalettes.Chromatogram;
+    return bio.NucleotidesPalettes.Chromatogram;
   case 'RNA':
-    return NucleotidesPalettes.Chromatogram;
+    return bio.NucleotidesPalettes.Chromatogram;
     // other
   default:
-    return UnknownSeqPalettes.Color;
+    return bio.UnknownSeqPalettes.Color;
   }
 }
 
@@ -66,7 +61,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
   }
 
   onMouseMove(gridCell: DG.GridCell, e: MouseEvent): void {
-    if (gridCell.cell.column.getTag(UnitsHandler.TAGS.aligned) !== 'SEQ.MSA')
+    if (gridCell.cell.column.getTag(bio.UnitsHandler.TAGS.aligned) !== 'SEQ.MSA')
       return;
 
     const maxLengthWordsSum = gridCell.cell.column.temp['bio-sum-maxLengthWords'];
@@ -94,7 +89,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     }
     left = (argsX >= maxLengthWordsSum[left]) ? left + 1 : left;
     const separator = gridCell.cell.column.getTag('separator') ?? '';
-    const splitterFunc: SplitterFunc = WebLogo.getSplitter('separator', separator);
+    const splitterFunc: bio.SplitterFunc = bio.getSplitter('separator', separator);
     const subParts: string[] = splitterFunc(gridCell.cell.value);
     (((subParts[left]?.length ?? 0) > 0)) ?
       ui.tooltip.show(ui.div(subParts[left]), e.x + 16, e.y + 16) : ui.tooltip.hide();
@@ -135,7 +130,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
 
     const separator = gridCell.cell.column.getTag('separator') ?? '';
     const splitLimit = gridCell.bounds.width / 5;
-    const splitterFunc: SplitterFunc = WebLogo.getSplitter(units, separator, splitLimit);
+    const splitterFunc: bio.SplitterFunc = bio.getSplitter(units, separator, splitLimit);
     const referenceSequence: string[] = splitterFunc(((gridCell.cell.column?.temp['reference-sequence'] != null) && (gridCell.cell.column?.temp['reference-sequence'] != ''))
       ? gridCell.cell.column.temp['reference-sequence'] : gridCell.cell.column.temp['current-word'] ?? '');
     const monomerWidth = (gridCell.cell.column?.temp['monomer-width'] != null) ? gridCell.cell.column.temp['monomer-width'] : 'short';
@@ -188,15 +183,15 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     const subParts: string[] = splitterFunc(cell.value);
     let x1 = x;
     let color = undefinedColor;
-    let drawStyle = DrawStyle.classic;
+    let drawStyle = bio.DrawStyle.classic;
     if (gridCell.cell.column.getTag('aligned').includes('MSA') && gridCell.cell.column.getTag('units') === 'separator')
-      drawStyle = DrawStyle.MSA;
+      drawStyle = bio.DrawStyle.MSA;
 
     subParts.every((amino, index) => {
       color = palette.get(amino);
       g.fillStyle = undefinedColor;
       let last = index === subParts.length - 1;
-      x1 = printLeftOrCentered(x1, y, w, h, g, amino, color, 0, true, 1.0, separator, last, drawStyle, maxLengthWords, index, gridCell, referenceSequence, maxLengthOfMonomer);
+      x1 = bio.printLeftOrCentered(x1, y, w, h, g, amino, color, 0, true, 1.0, separator, last, drawStyle, maxLengthWords, index, gridCell, referenceSequence, maxLengthOfMonomer);
       return x1 - minDistanceRenderer - gridCell.gridColumn.left + (gridCell.gridColumn.left - gridCell.bounds.x) <= gridCell.bounds.width;
     });
 
@@ -273,7 +268,7 @@ export class MacromoleculeDifferenceCellRenderer extends DG.GridCellRenderer {
     w = getUpdatedWidth(grid, g, x, w);
     //TODO: can this be replaced/merged with splitSequence?
     const [s1, s2] = s.split('#');
-    const splitter = WebLogo.getSplitter(units, separator);
+    const splitter = bio.getSplitter(units, separator);
     const subParts1 = splitter(s1);
     const subParts2 = splitter(s2);
     drawMoleculeDifferenceOnCanvas(g, x, y, w, h, subParts1, subParts2, units, separator);
@@ -315,7 +310,7 @@ export function drawMoleculeDifferenceOnCanvas(
   g.font = '12px monospace';
   g.textBaseline = 'top';
 
-  let palette: SeqPalette = UnknownSeqPalettes.Color;
+  let palette: bio.SeqPalette = bio.UnknownSeqPalettes.Color;
   if (units != 'HELM')
     palette = getPaletteByType(units.substring(units.length - 2));
 
@@ -327,12 +322,12 @@ export function drawMoleculeDifferenceOnCanvas(
 
     if (amino1 != amino2) {
       const color2 = palette.get(amino2);
-      const subX0 = printLeftOrCentered(updatedX, updatedY - vShift, w, h, g, amino1, color1, 0, true);
-      const subX1 = printLeftOrCentered(updatedX, updatedY + vShift, w, h, g, amino2, color2, 0, true);
+      const subX0 = bio.printLeftOrCentered(updatedX, updatedY - vShift, w, h, g, amino1, color1, 0, true);
+      const subX1 = bio.printLeftOrCentered(updatedX, updatedY + vShift, w, h, g, amino2, color2, 0, true);
       updatedX = Math.max(subX1, subX0);
       if (molDifferences)
         molDifferences[i] = createDifferenceCanvas(amino1, amino2, color1, color2, updatedY, vShift, h);
-    } else { updatedX = printLeftOrCentered(updatedX, updatedY, w, h, g, amino1, color1, 0, true, 0.5); }
+    } else { updatedX = bio.printLeftOrCentered(updatedX, updatedY, w, h, g, amino1, color1, 0, true, 0.5); }
     updatedX += 4;
   }
   g.restore();
@@ -356,7 +351,7 @@ function createDifferenceCanvas(
   canvas.width = width + 4;
   context.font = '12px monospace';
   context.textBaseline = 'top';
-  printLeftOrCentered(0, y - shift, width, h, context, amino1, color1, 0, true);
-  printLeftOrCentered(0, y + shift, width, h, context, amino2, color2, 0, true);
+  bio.printLeftOrCentered(0, y - shift, width, h, context, amino1, color1, 0, true);
+  bio.printLeftOrCentered(0, y + shift, width, h, context, amino2, color2, 0, true);
   return canvas;
 }

package/src/utils/convert.ts

@@ -1,11 +1,10 @@
 import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 import * as grok from 'datagrok-api/grok';
+import * as bio from '@datagrok-libraries/bio';
 
 import $ from 'cash-dom';
 import {Subscription} from 'rxjs';
-import {NotationConverter} from '@datagrok-libraries/bio/src/utils/notation-converter';
-import {NOTATION, UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 
 
 let convertDialog: DG.Dialog | null = null;
@@ -17,13 +16,13 @@ let convertDialogSubs: Subscription[] = [];
  * @param {DG.column} col Column with 'Macromolecule' semantic type
  */
 export function convert(col: DG.Column): void {
-  const converter = new NotationConverter(col);
-  const currentNotation: NOTATION = converter.notation;
+  const converter = new bio.NotationConverter(col);
+  const currentNotation: bio.NOTATION = converter.notation;
   //TODO: read all notations
   const notations = [
-    NOTATION.FASTA,
-    NOTATION.SEPARATOR,
-    NOTATION.HELM
+    bio.NOTATION.FASTA,
+    bio.NOTATION.SEPARATOR,
+    bio.NOTATION.HELM
   ];
   const separatorArray = ['-', '.', '/'];
   const filteredNotations = notations.filter((e) => e !== currentNotation);
@@ -33,7 +32,7 @@ export function convert(col: DG.Column): void {
 
   // hide the separator input for non-SEPARATOR target notations
   const toggleSeparator = () => {
-    if (targetNotationInput.value !== NOTATION.SEPARATOR)
+    if (targetNotationInput.value !== bio.NOTATION.SEPARATOR)
       $(separatorInput.root).hide();
     else
       $(separatorInput.root).show();
@@ -64,7 +63,7 @@ export function convert(col: DG.Column): void {
         separatorInput.root
       ]))
       .onOK(async () => {
-        const targetNotation = targetNotationInput.value as NOTATION;
+        const targetNotation = targetNotationInput.value as bio.NOTATION;
         const separator: string | null = separatorInput.value;
 
         await convertDo(col, targetNotation, separator);
@@ -81,9 +80,9 @@ export function convert(col: DG.Column): void {
 
 /** Creates a new column with converted sequences and detects its semantic type */
 export async function convertDo(
-  srcCol: DG.Column, targetNotation: NOTATION, separator: string | null
+  srcCol: DG.Column, targetNotation: bio.NOTATION, separator: string | null
 ): Promise<DG.Column> {
-  const converter = new NotationConverter(srcCol);
+  const converter = new bio.NotationConverter(srcCol);
   const newColumn = converter.convert(targetNotation, separator);
   srcCol.dataFrame.columns.add(newColumn);
 

package/src/utils/save-as-fasta.ts

@@ -1,9 +1,9 @@
 import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 import * as grok from 'datagrok-api/grok';
-import {SplitterFunc, WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
+import * as bio from '@datagrok-libraries/bio';
+
 import wu from 'wu';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 
 const FASTA_LINE_WIDTH = 60;
 
@@ -27,7 +27,7 @@ export function saveAsFastaUI() {
     .filter((gc: DG.GridColumn) => {
       const col: DG.Column | null = gc.column;
       if (col && col.semType === DG.SEMTYPE.MACROMOLECULE) {
-        const uh = new UnitsHandler(col);
+        const uh = new bio.UnitsHandler(col);
         return uh.isFasta();
       }
       return false;
@@ -69,7 +69,7 @@ export function saveAsFastaUI() {
 export function saveAsFastaDo(
   idColList: DG.Column[], seqCol: DG.Column, lineWidth: number = FASTA_LINE_WIDTH, lineSeparator: string = '\n'
 ): string {
-  const splitter: SplitterFunc = WebLogo.splitterAsFasta;
+  const splitter: bio.SplitterFunc = bio.splitterAsFasta;
 
   const fastaLines: string[] = [];
 
@@ -91,7 +91,7 @@ export function saveAsFastaDo(
 }
 
 /* split sequence for monomers to prevent wrapping monomer partially */
-export function wrapSequence(seq: string, splitter: SplitterFunc, lineWidth: number = FASTA_LINE_WIDTH): string[] {
+export function wrapSequence(seq: string, splitter: bio.SplitterFunc, lineWidth: number = FASTA_LINE_WIDTH): string[] {
   const seqMonomerList = splitter(seq);
   let seqPos: number = 0;
   const seqLength: number = seqMonomerList.length;

package/src/utils/utils.ts

@@ -1,6 +1,8 @@
-import * as DG from 'datagrok-api/dg';
-import {WebLogo, SplitterFunc} from '@datagrok-libraries/bio/src/viewers/web-logo';
 import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+import * as bio from '@datagrok-libraries/bio';
+
 import {
   CAP_GROUP_NAME, CAP_GROUP_SMILES, jsonSdfMonomerLibDict, MONOMER_ENCODE_MAX, MONOMER_ENCODE_MIN, MONOMER_SYMBOL,
   RGROUP_ALTER_ID, RGROUP_FIELD, RGROUP_LABEL, SDF_MONOMER_NAME
@@ -18,7 +20,7 @@ export function encodeMonomers(col: DG.Column): DG.Column | null {
   const monomerSymbolDict: { [key: string]: number } = {};
   const units = col.tags[DG.TAGS.UNITS];
   const sep = col.getTag(UnitsHandler.TAGS.separator);
-  const splitterFunc: SplitterFunc = WebLogo.getSplitter(units, sep);
+  const splitterFunc: bio.SplitterFunc = bio.getSplitter(units, sep);
   const encodedStringArray = [];
   for (let i = 0; i < col.length; ++i) {
     let encodedMonomerStr = '';
@@ -42,7 +44,7 @@ export function encodeMonomers(col: DG.Column): DG.Column | null {
 export function getMolfilesFromSeq(col: DG.Column, monomersLibObject: any[]): any[][] | null {
   const units = col.tags[DG.TAGS.UNITS];
   const sep = col.getTag('separator');
-  const splitterFunc: SplitterFunc = WebLogo.getSplitter(units, sep);
+  const splitterFunc: bio.SplitterFunc = bio.getSplitter(units, sep);
   const monomersDict = createMomomersMolDict(monomersLibObject);
   const molFiles = [];
   for (let i = 0; i < col.length; ++i) {
@@ -66,7 +68,7 @@ export function getMolfilesFromSeq(col: DG.Column, monomersLibObject: any[]): an
 export function getMolfilesFromSingleSeq(cell: DG.Cell, monomersLibObject: any[]): any[][] | null {
   const units = cell.column.tags[DG.TAGS.UNITS];
   const sep = cell.column!.getTag('separator');
-  const splitterFunc: SplitterFunc = WebLogo.getSplitter(units, sep);
+  const splitterFunc: bio.SplitterFunc = bio.getSplitter(units, sep);
   const monomersDict = createMomomersMolDict(monomersLibObject);
   const molFiles = [];
   const macroMolecule = cell.value;

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

@@ -1,12 +1,9 @@
 import * as ui from 'datagrok-api/ui';
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
+import * as bio from '@datagrok-libraries/bio';
 
-import {VdRegionType, VdRegion} from '@datagrok-libraries/bio/src/vd-regions';
-import {IVdRegionsViewer} from '@datagrok-libraries/bio/src/viewers/vd-regions-viewer';
-import {WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
-
-const vrt = VdRegionType;
+const vrt = bio.VdRegionType;
 
 // Positions of regions for numbering schemes
 // http://www.bioinf.org.uk/abs/info.html
@@ -37,7 +34,7 @@ const vrt = VdRegionType;
 /** Viewer with tabs based on description of chain regions.
  *  Used to define regions of an immunoglobulin LC.
  */
-export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
+export class VdRegionsViewer extends DG.JsViewer implements bio.IVdRegionsViewer {
   // private regionsDf: DG.DataFrame;
   private regionsFg: DG.FilterGroup | null = null;
   // private regionsTV: DG.TableView;
@@ -46,7 +43,7 @@ export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
   private isOpened: boolean = false;
   private panelNode: DG.DockNode | null = null;
 
-  public regions: VdRegion[] = [];
+  public regions: bio.VdRegion[] = [];
   public regionTypes: string[];
   public chains: string[];
   public sequenceColumnNamePostfix: string;
@@ -60,7 +57,7 @@ export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
   }
 
   // TODO: .onTableAttached is not calling on dataFrame set, onPropertyChanged  also not calling
-  public async setDf(value: DG.DataFrame, regions: VdRegion[]) {
+  public async setDf(value: DG.DataFrame, regions: bio.VdRegion[]) {
     console.debug('VdRegionsViewer.setDf()');
     await this.destroyView();
     this.regions = regions;
@@ -177,7 +174,7 @@ export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
   //#region -- View --
   private host: HTMLElement | null = null;
   private mainLayout: HTMLTableElement | null = null;
-  private logos: { [chain: string]: WebLogo }[] = [];
+  private logos: { [chain: string]: bio.WebLogo }[] = [];
 
   private async destroyView(): Promise<void> {
     // TODO: Unsubscribe from and remove all view elements
@@ -197,16 +194,16 @@ export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
     const colNames: { [chain: string]: string } = Object.assign({},
       ...this.chains.map((chain) => ({[chain]: `${chain} ${this.sequenceColumnNamePostfix}`})));
 
-    const regionsFiltered: VdRegion[] = this.regions.filter((r: VdRegion) => this.regionTypes.includes(r.type));
+    const regionsFiltered: bio.VdRegion[] = this.regions.filter((r: bio.VdRegion) => this.regionTypes.includes(r.type));
 
     const orderList: number[] = Array.from(new Set(regionsFiltered.map((r) => r.order))).sort();
 
     this.logos = [];
 
     for (let orderI = 0; orderI < orderList.length; orderI++) {
-      const regionChains: { [chain: string]: WebLogo } = {};
+      const regionChains: { [chain: string]: bio.WebLogo } = {};
       for (const chain of this.chains) {
-        const region: VdRegion | undefined = regionsFiltered
+        const region: bio.VdRegion | undefined = regionsFiltered
           .find((r) => r.order == orderList[orderI] && r.chain == chain);
         regionChains[chain] = (await this.dataFrame.plot.fromType('WebLogo', {
           sequenceColumnName: colNames[chain],
@@ -215,7 +212,7 @@ export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
           fixWidth: true,
           skipEmptyPositions: this.skipEmptyPositions,
           positionWidth: this.positionWidth,
-        })) as unknown as WebLogo;
+        })) as unknown as bio.WebLogo;
       }
       // WebLogo creation fires onRootSizeChanged event even before control being added to this.logos
       this.logos[orderI] = regionChains;
@@ -240,7 +237,7 @@ export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
           })] : []),
           // List with controls for regions
           ...[...Array(orderList.length).keys()].map((orderI) => {
-            const wl: WebLogo = this.logos[orderI][chain];
+            const wl: bio.WebLogo = this.logos[orderI][chain];
             wl.root.style.height = '100%';
 
             const resDiv = ui.div([wl.root]/*`${chain} ${regionsFiltered[rI]}`*/, {
@@ -257,7 +254,7 @@ export class VdRegionsViewer extends DG.JsViewer implements IVdRegionsViewer {
       },
       ['', ...[...Array(orderList.length).keys()].map(
         (orderI: number) => regionsFiltered.find(
-          (r: VdRegion) => r.order == orderList[orderI] && r.chain == this.chains[0]
+          (r: bio.VdRegion) => r.order == orderList[orderI] && r.chain == this.chains[0]
         )!.name || 'Name')]
     );
     this.mainLayout.className = 'mlb-vd-regions-viewer-table2';