@datagrok/bio - npm Package Compare versions

Comparing version 1.7.22 to 1.7.23

package.json

@@ -5,3 +5,7 @@ {
   "friendlyName": "Bio",
-  "version": "1.7.22",
+  "author": {
+    "name": "Leonid Stolbov",
+    "email": "[e-mail]"
+  },
+  "version": "1.7.23",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
@@ -15,3 +19,3 @@ "repository": {
     "@biowasm/aioli": ">=2.4.0",
-    "@datagrok-libraries/bio": "^3.0.0",
+    "@datagrok-libraries/bio": "^3.0.2",
     "@datagrok-libraries/ml": "^3.0.0",
@@ -18,0 +22,0 @@ "@datagrok-libraries/utils": "^1.4.0",

src/package-test.ts

@@ -14,2 +14,3 @@ import * as DG from 'datagrok-api/dg';
 import './tests/convert-test';
+import './tests/fasta-handler-test';
 import './tests/WebLogo-positions-test';
@@ -16,0 +17,0 @@

src/package.ts

@@ -8,3 +8,3 @@ /* Do not change these import lines to match external modules in webpack configuration */
 
-import {AlignedSequenceDifferenceCellRenderer, AminoAcidsCellRenderer} from './utils/cell-renderer';
+import {MacromoleculeDifferenceCellRenderer, MonomerCellRenderer} from './utils/cell-renderer';
 import {WebLogo, SeqColStats} from '@datagrok-libraries/bio/src/viewers/web-logo';
@@ -245,2 +245,10 @@ import {VdRegionsViewer} from './viewers/vd-regions-viewer';
 
+//name: Bio | MSA
+//tags: bio, panel
+//input: column sequence { semType: Macromolecule }
+//output: column result
+export async function panelMSA(col: DG.Column): Promise<DG.Column | null> {
+  return multipleSequenceAlignmentAny(col.dataFrame, col);
+}
+
 //name: Composition Analysis
@@ -339,16 +347,16 @@ //top-menu: Bio | Composition Analysis
 
-//name: aminoAcidsCellRenderer
+//name: monomerCellRenderer
 //tags: cellRenderer
-//meta.cellType: aminoAcids
+//meta.cellType: Monomer
 //output: grid_cell_renderer result
-export function aminoAcidsCellRenderer(): AminoAcidsCellRenderer {
-  return new AminoAcidsCellRenderer();
+export function monomerCellRenderer(): MonomerCellRenderer {
+  return new MonomerCellRenderer();
 }
 
-//name: alignedSequenceDifferenceCellRenderer
+//name: MacromoleculeDifferenceCellRenderer
 //tags: cellRenderer
-//meta.cellType: alignedSequenceDifference
+//meta.cellType: MacromoleculeDifference
 //output: grid_cell_renderer result
-export function alignedSequenceDifferenceCellRenderer(): AlignedSequenceDifferenceCellRenderer {
-  return new AlignedSequenceDifferenceCellRenderer();
+export function macromoleculeDifferenceCellRenderer(): MacromoleculeDifferenceCellRenderer {
+  return new MacromoleculeDifferenceCellRenderer();
 }
@@ -355,0 +363,0 @@

src/tests/WebLogo-positions-test.ts

@@ -0,1 +1,2 @@
+
 import {after, before, category, test, expect, expectObject} from '@datagrok-libraries/utils/src/test';
@@ -7,6 +8,6 @@
 import {PositionInfo, PositionMonomerInfo, WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
-
 category('WebLogo-positions', () => {
   let tvList: DG.TableView[];
   let dfList: DG.DataFrame[];
+  let currentView: DG.View;
 
@@ -26,9 +27,10 @@ const csvDf1 = `seq
     dfList = [];
+    currentView = grok.shell.tv;
   });
 
   after(async () => {
-    dfList.forEach((df: DG.DataFrame) => { grok.shell.closeTable(df); });
+    dfList.forEach((df: DG.DataFrame) => { grok.shell.closeTable(df);});
     tvList.forEach((tv: DG.TableView) => tv.close());
+    currentView = grok.shell.tv;
   });
-
   test('allPositions', async () => {
@@ -60,12 +62,82 @@ const df: DG.DataFrame = DG.DataFrame.fromCsv(csvDf1);
     ];
+    console.log(positions);
+    expect(positions.length,resAllDf1.length);
     // check all positions are equal resAllDf1
     for (let i = 0; i < positions.length; i++) {
       expect(positions[i].name, resAllDf1[i].name);
-        for (const key in positions[i].freq) {
-          expect(positions[i].freq[key].count, resAllDf1[i].freq[key].count);
-        }
+      for (const key in positions[i].freq) {
+        expect(positions[i].freq[key].count, resAllDf1[i].freq[key].count);
+      }
     }
 
   });
+  test('positions with shrinkEmptyTail option', async () => {
+    const df: DG.DataFrame = DG.DataFrame.fromCsv(csvDf1);
+    const tv: DG.TableView = grok.shell.addTableView(df);
 
+    const wlViewer: WebLogo = await df.plot.fromType('WebLogo', {'shrinkEmptyTail': true}) as unknown as WebLogo;
+    tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
+
+    tvList.push(tv);
+    dfList.push(df);
+
+    const positions: PositionInfo[] = wlViewer['positions'];
+
+    const resAllDf1: PositionInfo[] = [
+      new PositionInfo('1', {'A': new PositionMonomerInfo(2), '-': new PositionMonomerInfo(3)}),
+      new PositionInfo('2', {'T': new PositionMonomerInfo(5)}),
+      new PositionInfo('3', {'C': new PositionMonomerInfo(5)}),
+      new PositionInfo('4', {'-': new PositionMonomerInfo(5)}),
+      new PositionInfo('5', {'G': new PositionMonomerInfo(5)}),
+      new PositionInfo('6', {'-': new PositionMonomerInfo(3), 'C': new PositionMonomerInfo(2)}),
+      new PositionInfo('7', {'T': new PositionMonomerInfo(5)}),
+      new PositionInfo('8', {'T': new PositionMonomerInfo(5)}),
+      new PositionInfo('9', {'G': new PositionMonomerInfo(5)}),
+      new PositionInfo('10', {'C': new PositionMonomerInfo(5)})
+    ];
+
+    console.log(positions);
+    for (let i = 0; i < positions.length; i++) {
+      expect(positions[i].name, resAllDf1[i].name);
+      for (const key in positions[i].freq) {
+        expect(positions[i].freq[key].count, resAllDf1[i].freq[key].count);
+      }
+    }
+
+  });
+
+  test('positions with skipEmptyPositions option', async () => {
+    const df: DG.DataFrame = DG.DataFrame.fromCsv(csvDf1);
+    const tv: DG.TableView = grok.shell.addTableView(df);
+
+    const wlViewer: WebLogo = await df.plot.fromType('WebLogo', {'skipEmptyPositions': false}) as unknown as WebLogo;
+    tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
+
+    tvList.push(tv);
+    dfList.push(df);
+
+    const positions: PositionInfo[] = wlViewer['positions'];
+
+    const resAllDf1: PositionInfo[] = [
+      new PositionInfo('1', {'A': new PositionMonomerInfo(2), '-': new PositionMonomerInfo(3)}),
+      new PositionInfo('2', {'T': new PositionMonomerInfo(5)}),
+      new PositionInfo('3', {'C': new PositionMonomerInfo(5)}),
+      new PositionInfo('5', {'G': new PositionMonomerInfo(5)}),
+      new PositionInfo('6', {'-': new PositionMonomerInfo(3), 'C': new PositionMonomerInfo(2)}),
+      new PositionInfo('7', {'T': new PositionMonomerInfo(5)}),
+      new PositionInfo('8', {'T': new PositionMonomerInfo(5)}),
+      new PositionInfo('9', {'G': new PositionMonomerInfo(5)}),
+      new PositionInfo('10', {'C': new PositionMonomerInfo(5)})
+    ];
+    console.log(positions);
+
+    for (let i = 0; i < positions.length; i++) {
+      expect(positions[i].name, resAllDf1[i].name);
+      for (const key in positions[i].freq) {
+        expect(positions[i].freq[key].count, resAllDf1[i].freq[key].count);
+      }
+    }
+
+  });
+
 });

src/tests/WebLogo-test.ts

@@ -149,1 +149,2 @@ import {after, before, category, test, expect, expectObject} from '@datagrok-libraries/utils/src/test';
 }
+

src/utils/cell-renderer.ts

@@ -5,3 +5,3 @@ import * as C from './constants';
 import {NucleotidesPalettes} from '@datagrok-libraries/bio/src/nucleotides';
-import {UnknownSeqPalettes} from '@datagrok-libraries/bio/src/unknown';
+import {UnknownSeqPalette, UnknownSeqPalettes} from '@datagrok-libraries/bio/src/unknown';
 import {SplitterFunc, WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
@@ -48,2 +48,3 @@ import {SeqPalette} from '@datagrok-libraries/bio/src/seq-palettes';
 
+
 /**
@@ -70,12 +71,24 @@ * A function that prints a string aligned to left or centered.
   pivot: number = 0, left = false, transparencyRate: number = 1.0,
-  separator: string = '', last: boolean = false): number {
+  separator: string = '', last: boolean = false, drawStyle: string = 'classic', maxWord:any={}, maxWordIdx:number=0, gridCell:any = {}): number {
   g.textAlign = 'start';
   const colorPart = s.substring(0);
-  let grayPart =  last ? '' : separator;
+  let grayPart = last ? '' : separator;
+  if (drawStyle === 'msa') {
+    grayPart = ' ';
+  }
 
-  const textSize = g.measureText(colorPart + grayPart);
+  let textSize: any = g.measureText(colorPart + grayPart);
   const indent = 5;
 
-  const colorTextSize = g.measureText(colorPart);
+  let colorTextSize = g.measureText(colorPart).width;
   const dy = (textSize.fontBoundingBoxAscent + textSize.fontBoundingBoxDescent) / 2;
+  textSize = textSize.width;
+  if (drawStyle === 'msa') {
+    if (colorTextSize > maxWord) {
+      maxWord[maxWordIdx] = colorTextSize;
+      gridCell.cell.column.temp = maxWord;
+    }
+    colorTextSize = maxWord[maxWordIdx];
+    textSize = maxWord[maxWordIdx];
+  }
 
@@ -86,14 +99,15 @@ function draw(dx1: number, dx2: number): void {
     g.fillText(colorPart, x + dx1, y + dy);
-    g.fillStyle = grayColor;
-    g.fillText(grayPart, x + dx2, y + dy);
+    if (drawStyle === 'classic') {
+      g.fillStyle = grayColor;
+      g.fillText(grayPart, x + dx2, y + dy);
+    }
   }
 
-
-  if (left || textSize.width > w) {
-    draw(indent, indent + colorTextSize.width);
-    return x + colorTextSize.width + g.measureText(grayPart).width;
+  if (left || textSize > w) {
+    draw(indent, indent + colorTextSize);
+    return x + colorTextSize + g.measureText(grayPart).width;
   } else {
-    const dx = (w - textSize.width) / 2;
-    draw(dx, dx + colorTextSize.width);
-    return x + dx + colorTextSize.width;
+    const dx = (w - textSize) / 2;
+    draw(dx, dx + colorTextSize);
+    return x + dx + colorTextSize;
   }
@@ -121,3 +135,3 @@ }
 
-  get cellType(): string { return C.SEM_TYPES.Macro_Molecule; }
+  get cellType(): string { return C.SEM_TYPES.MACROMOLECULE; }
 
@@ -206,6 +220,42 @@ get defaultHeight(): number { return 30; }
 
+      // обработка новых елементов
+      const columns = gridCell.cell.column.categories;
+      let maxLengthWords = {};
+      // check if gridCell.cell.column.temp is array
+      if (gridCell.cell.column.getTag('.calculatedCellRender') !== 'exist') {
+        for (let i = 0; i < columns.length; i++) {
+          let subParts: string[] = splitterFunc(columns[i]);
+          subParts.forEach((amino, index) => {
+            //@ts-ignore
+            let textSizeWidth = g.measureText(WebLogo.monomerToText(amino) + ' ');
+            //@ts-ignore
+            if (textSizeWidth.width > (maxLengthWords[index] ?? 0)) {
+              //@ts-ignore
+              maxLengthWords[index] = textSizeWidth.width;
+            }
+          });
+        }
+        gridCell.cell.column.temp = maxLengthWords;
+        gridCell.cell.column.setTag('.calculatedCellRender', 'exist');
+      } else {
+        maxLengthWords = gridCell.cell.column.temp;
+      }
+
       const subParts: string[] = splitterFunc(cell.value);
-      // console.log(subParts);
       let x1 = x;
       let color = undefinedColor;
+      // get max length word in subParts
+      let tagUnits = gridCell.cell.column.getTag(DG.TAGS.UNITS);
+      let maxLength = 0;
+      let maxWord = '';
+      let drawStyle = 'classic';
+      if (tagUnits.includes('MSA')) {
+        subParts.forEach(part => {
+          if (part.length > maxLength) {
+            maxLength = part.length;
+            maxWord = part;
+            drawStyle = 'msa';
+          }
+        });
+      }
       subParts.forEach((amino, index) => {
@@ -215,3 +265,3 @@ color = palette.get(amino);
         let last = index === subParts.length - 1;
-        x1 = printLeftOrCentered(x1, y, w, h, g, amino, color, 0, true, 1.0, separator, last);
+        x1 = printLeftOrCentered(x1, y, w, h, g, WebLogo.monomerToText(amino), color, 0, true, 1.0, separator, last, drawStyle, maxLengthWords, index, gridCell);
       });
@@ -225,8 +275,7 @@
 
+export class MonomerCellRenderer extends DG.GridCellRenderer {
+  get name(): string {return 'MonomerCR';}
 
-export class AminoAcidsCellRenderer extends DG.GridCellRenderer {
-  get name(): string {return 'aminoAcidsCR';}
+  get cellType(): string {return C.SEM_TYPES.MONOMER;}
 
-  get cellType(): string {return C.SEM_TYPES.AMINO_ACIDS;}
-
   get defaultHeight(): number {return 15;}
@@ -267,6 +316,6 @@
 
-export class AlignedSequenceDifferenceCellRenderer extends DG.GridCellRenderer {
-  get name(): string {return 'alignedSequenceDifferenceCR';}
+export class MacromoleculeDifferenceCellRenderer extends DG.GridCellRenderer {
+  get name(): string {return 'MacromoleculeDifferenceCR';}
 
-  get cellType(): string {return C.SEM_TYPES.ALIGNED_SEQUENCE_DIFFERENCE;}
+  get cellType(): string {return C.SEM_TYPES.MACROMOLECULE_DIFFERENCE;}
 
@@ -307,4 +356,6 @@ get defaultHeight(): number {return 30;}
     const separator = gridCell.tableColumn!.tags[C.TAGS.SEPARATOR];
-    const subParts1 = s1.split(separator);
-    const subParts2 = s2.split(separator);
+    const units: string = gridCell.tableColumn!.tags[DG.TAGS.UNITS];
+    const splitter = WebLogo.getSplitter(units, separator);
+    const subParts1 = splitter(s1);
+    const subParts2 = splitter(s2);
     const [text] = processSequence(subParts1);
@@ -316,3 +367,7 @@ const textSize = g.measureText(text.join(''));
 
-    const palette = getPalleteByType(gridCell.tableColumn!.tags[C.TAGS.ALPHABET]);
+    let palette: SeqPalette = UnknownSeqPalettes.Color;
+    if (units != 'HELM')
+      palette = getPalleteByType(units.substring(units.length - 2));
+
+    const vShift = 7;
     for (let i = 0; i < subParts1.length; i++) {
@@ -322,6 +377,5 @@ const amino1 = subParts1[i];
       const color1 = palette.get(amino1);
-      const color2 = palette.get(amino2);
 
       if (amino1 != amino2) {
-        const vShift = 7;
+        const color2 = palette.get(amino2);
         const subX0 = printLeftOrCentered(updatedX, updatedY - vShift, w, h, g, amino1, color1, 0, true);
@@ -328,0 +382,0 @@ const subX1 = printLeftOrCentered(updatedX, updatedY + vShift, w, h, g, amino2, color2, 0, true);

src/utils/constants.ts

@@ -26,8 +26,7 @@ export enum COLUMNS_NAMES {
 export enum SEM_TYPES {
-  AMINO_ACIDS = 'aminoAcids',
-  ALIGNED_SEQUENCE = 'alignedSequence',
-  ALIGNED_SEQUENCE_DIFFERENCE = 'alignedSequenceDifference',
+  MONOMER = 'Monomer',
+  MACROMOLECULE_DIFFERENCE = 'MacromoleculeDifference',
   ACTIVITY = 'activity',
   ACTIVITY_SCALED = 'activityScaled',
-  Macro_Molecule = 'Macromolecule',
+  MACROMOLECULE = 'Macromolecule',
 }
@@ -34,0 +33,0 @@

src/viewers/vd-regions-viewer.ts

@@ -53,2 +53,5 @@ import * as ui from 'datagrok-api/ui';
 
+  public skipEmptyPositions: boolean;
+
+
   public get df(): DG.DataFrame {
@@ -76,2 +79,4 @@ return this.dataFrame;
     this.sequenceColumnNamePostfix = this.string('sequenceColumnNamePostfix', 'chain sequence');
+
+    this.skipEmptyPositions = this.bool('skipEmptyPositions', false);
   }
@@ -124,2 +129,13 @@
         break;
+      case 'skipEmptyPositions':
+        // for (let orderI = 0; orderI < this.logos.length; orderI++) {
+        //   for (let chainI = 0; chainI < this.chains.length; chainI++) {
+        //     const chain: string = this.chains[chainI];
+        //     this.logos[orderI][chain].setOptions({skipEmptyPositions: this.skipEmptyPositions});
+        //   }
+        // }
+        // this.calcSize();
+        await this.destroyView();
+        await this.buildView();
+        break;
       }
@@ -194,2 +210,3 @@ }
           fixWidth: true,
+          skipEmptyPositions: this.skipEmptyPositions,
         })) as unknown as WebLogo;
@@ -196,0 +213,0 @@ }

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Found 1 instance in 1 package

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Improved metrics

Total package byte prevSize

14187049

increased by0.5%

Number of package files

84

increased by1.2%

Lines of code

99592

increased by0.64%

Number of low maintenance alerts

1

decreased by-50%

Dependency changes

• Updated@datagrok-libraries/bio@^3.0.2