@datagrok-libraries/bio 5.44.3 → 5.44.5

package/src/utils/cell-renderer-monomer-placer.js

@@ -1,11 +1,15 @@
+import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
 import { SeqHandler } from './seq-handler';
-import { getPaletteByType, NOTATION, TAGS as bioTAGS } from './macromolecule';
-import { CellRendererBackBase } from './cell-renderer-back-base';
+import { ALPHABET, NOTATION, TAGS as bioTAGS } from './macromolecule';
+import { CellRendererBackBase, getGridCellColTemp } from './cell-renderer-back-base';
 import { getMonomerLibHelper } from '../monomer-works/monomer-utils';
 import { errInfo } from './err-info';
 import { DrawStyle, printLeftOrCentered, TAGS as mmcrTAGS } from './cell-renderer';
+import { rendererSettingsChangedState } from './cell-renderer-consts';
+import { HelmTypes } from '../helm/consts';
+import { execMonomerHoverLinks } from '../monomer-works/monomer-hover';
 export const undefinedColor = 'rgb(100,100,100)';
 export function hitBounds(bounds, x) {
     let iterationCount = 100;
@@ -40,6 +44,7 @@ export class MonomerPlacer extends CellRendererBackBase {
         this._processedMaxVisibleSeqLength = 0;
         this._monomerLengthMap = {}; // caches the lengths to save time on g.measureText
         this._monomerStructureMap = {}; // caches the atomic structures of monomers
+        this.monomerLib = null;
         this.padding = 5;
         this.props = this.propsProvider();
         this._processedRows = DG.BitSet.create(this.tableCol.length);
@@ -62,8 +67,10 @@ export class MonomerPlacer extends CellRendererBackBase {
         getMonomerLibHelper().then((libHelper) => {
             if (this.destroyed)
                 return;
-            const monomerLib = libHelper.getMonomerLib();
-            this.subs.push(monomerLib.onChanged.subscribe(() => {
+            this.monomerLib = libHelper.getMonomerLib();
+            this.dirty = true;
+            this.gridCol?.grid?.invalidate();
+            this.subs.push(this.monomerLib.onChanged.subscribe(() => {
                 this.dirty = true;
                 this.gridCol?.grid?.invalidate();
             }));
@@ -80,6 +87,7 @@ export class MonomerPlacer extends CellRendererBackBase {
     }
     /** Returns monomers lengths of the {@link rowIdx} and cumulative sums for borders, monomer places */
     getCellMonomerLengths(rowIdx, newWidth) {
+        const sh = SeqHandler.forColumn(this.tableCol);
         if (this.colWidth < newWidth) {
             this.colWidth = newWidth;
             this.dirty = true;
@@ -93,7 +101,7 @@ export class MonomerPlacer extends CellRendererBackBase {
                 this.logger.error(errMsg, undefined, errStack);
             }
         }
-        const res = this.props.seqHandler.isMsa() ? this.getCellMonomerLengthsForSeqMsa() :
+        const res = sh.isMsa() ? this.getCellMonomerLengthsForSeqMsa() :
             this.getCellMonomerLengthsForSeq(rowIdx);
         const resSum = new Array(res.length + 1);
         resSum[0] = 5; // padding
@@ -104,12 +112,12 @@ export class MonomerPlacer extends CellRendererBackBase {
     getCellMonomerLengthsForSeq(rowIdx) {
         const logPrefix = `${this.toLog()}.getCellMonomerLengthsForSeqMsa()`;
         // this.logger.debug(`${logPrefix}, start`);
-        if (this._monomerLengthList === null) {
+        if (this._monomerLengthList === null)
             this._monomerLengthList = new Array(this.tableCol.length).fill(null);
-        }
+        const sh = SeqHandler.forColumn(this.tableCol);
         const minMonWidth = this.props.separatorWidth + 1 * this.props.monomerCharWidth;
         const maxVisibleSeqLength = Math.ceil(this.colWidth / minMonWidth);
-        const seqSS = SeqHandler.forColumn(this.tableCol).getSplitted(rowIdx);
+        const seqSS = sh.getSplitted(rowIdx);
         const visibleSeqLength = Math.min(maxVisibleSeqLength, seqSS.length);
         let res = this._monomerLengthList[rowIdx];
         if (res === null || res.length < visibleSeqLength) {
@@ -118,7 +126,7 @@ export class MonomerPlacer extends CellRendererBackBase {
             for (let seqMonI = 0; seqMonI < visibleSeqLength; ++seqMonI) {
                 const seqMonLabel = seqSS.getOriginal(seqMonI);
                 const shortMon = this.props.monomerToShort(seqMonLabel, this.monomerLengthLimit);
-                const separatorWidth = this.props.seqHandler.isSeparator() ? this.separatorWidth : this.props.separatorWidth;
+                const separatorWidth = sh.isSeparator() ? this.separatorWidth : this.props.separatorWidth;
                 const seqMonWidth = separatorWidth + shortMon.length * this.props.monomerCharWidth;
                 res[seqMonI] = seqMonWidth;
                 seqWidth += seqMonWidth;
@@ -132,9 +140,8 @@ export class MonomerPlacer extends CellRendererBackBase {
         var _a;
         const logPrefix = `${this.toLog()}.getCellMonomerLengthsForSeqMsa()`;
         // this.logger.debug(`${logPrefix}, start`);
-        if (this._monomerLengthList === null) {
+        if (this._monomerLengthList === null)
             this._monomerLengthList = new Array(1).fill(null);
-        }
         (_a = this._monomerLengthList)[0] ?? (_a[0] = new Array(0));
         const res = this._monomerLengthList[0];
         // const startIdx = Math.max(Math.floor((this.grid?.vertScroll.min ?? 0) - 10), 0);
@@ -200,14 +207,10 @@ export class MonomerPlacer extends CellRendererBackBase {
             this.dirty = true;
         }
     }
-    isMsa() {
-        return this.props.seqHandler.isMsa();
-    }
     render(g, x, y, w, h, gridCell, _cellStyle) {
         const gridCol = this.gridCol;
         const tableCol = this.tableCol;
         const dpr = window.devicePixelRatio;
-        let separatorWidth = this.props.separatorWidth;
         // Cell renderer settings
         let maxLengthOfMonomer = this.monomerLengthLimit;
         if (mmcrTAGS.maxMonomerLength in tableCol.tags) {
@@ -220,17 +223,18 @@ export class MonomerPlacer extends CellRendererBackBase {
         }
         g.save();
         try {
-            // if (
-            //   tableCol.temp[MmcrTemps.rendererSettingsChanged] === rendererSettingsChangedState.true ||
-            //   this.monomerLengthLimit != maxLengthOfMonomer
-            // ) {
-            //   gapLength = tableCol.temp[MmcrTemps.gapLength] as number ?? gapLength;
-            //   // this event means that the mm renderer settings have changed,
-            //   // particularly monomer representation and max width.
-            //   this.setMonomerLengthLimit(maxLengthOfMonomer);
-            //   this.setSeparatorWidth(this.isMsa() ? msaGapLength : gapLength);
-            //   tableCol.temp[MmcrTemps.rendererSettingsChanged] = rendererSettingsChangedState.false;
-            // }
+            const sh = SeqHandler.forColumn(tableCol);
+            if (tableCol.temp[".mm.cellRenderer.settingsChanged" /* MmcrTemps.rendererSettingsChanged */] === rendererSettingsChangedState.true ||
+                this.monomerLengthLimit != maxLengthOfMonomer) {
+                let gapLength = 0;
+                const msaGapLength = 8;
+                gapLength = tableCol.temp[".mm.cellRenderer.gapLength" /* MmcrTemps.gapLength */] ?? gapLength;
+                // this event means that the mm renderer settings have changed,
+                // particularly monomer representation and max width.
+                this.setMonomerLengthLimit(maxLengthOfMonomer);
+                this.setSeparatorWidth(sh.isMsa() ? msaGapLength : gapLength);
+                tableCol.temp[".mm.cellRenderer.settingsChanged" /* MmcrTemps.rendererSettingsChanged */] = rendererSettingsChangedState.false;
+            }
             const [maxLengthWords, maxLengthWordsSum] = this.getCellMonomerLengths(gridCell.tableRowIndex, w);
             const _maxIndex = maxLengthWords.length;
             const value = gridCell.cell.value;
@@ -246,11 +250,9 @@ export class MonomerPlacer extends CellRendererBackBase {
             //TODO: can this be replaced/merged with splitSequence?
             const units = tableCol.meta.units;
             const aligned = tableCol.getTag(bioTAGS.aligned);
-            const palette = getPaletteByType(paletteType);
             const separator = tableCol.getTag(bioTAGS.separator) ?? '';
             const minMonWidth = this.props.separatorWidth + 1 * this.props.monomerCharWidth;
             const splitLimit = Math.ceil(w / minMonWidth);
-            const sh = SeqHandler.forColumn(tableCol);
             const tempReferenceSequence = tableCol.temp["reference-sequence" /* tempTAGS.referenceSequence */];
             const tempCurrentWord = this.tableCol.temp["current-word" /* tempTAGS.currentWord */];
             if (tempCurrentWord && tableCol?.dataFrame?.currentRowIdx === -1)
@@ -263,15 +265,19 @@ export class MonomerPlacer extends CellRendererBackBase {
                 return wu.count(0).take(seqSS.length).map((posIdx) => seqSS.getOriginal(posIdx)).toArray();
             })();
             const subParts = sh.getSplitted(rowIdx);
-            /* let x1 = x; */
-            let color = undefinedColor;
             let drawStyle = DrawStyle.classic;
             if (aligned && aligned.includes('MSA') && units == NOTATION.SEPARATOR)
                 drawStyle = DrawStyle.MSA;
             const visibleSeqLength = Math.min(subParts.length, splitLimit);
             for (let posIdx = 0; posIdx < visibleSeqLength; ++posIdx) {
-                const amino = subParts.getOriginal(posIdx);
-                color = palette.get(amino);
+                const om = subParts.getOriginal(posIdx);
+                const cm = subParts.getCanonical(posIdx);
+                let color = undefinedColor;
+                if (this.monomerLib) {
+                    const biotype = sh.defaultBiotype;
+                    //this.logger.debug(`${logPrefix}, biotype: ${biotype}, amino: ${amino}`);
+                    color = this.monomerLib.getMonomerTextColor(biotype, cm);
+                }
                 g.fillStyle = undefinedColor;
                 const last = posIdx === subParts.length - 1;
                 /*x1 = */
@@ -281,7 +287,7 @@ export class MonomerPlacer extends CellRendererBackBase {
                     referenceSequence: referenceSequence, maxLengthOfMonomer: maxLengthOfMonomer,
                     monomerTextSizeMap: this._monomerLengthMap, logger: this.logger
                 };
-                printLeftOrCentered(g, amino, x + this.padding, y, w, h, opts);
+                printLeftOrCentered(g, om, x + this.padding, y, w, h, opts);
                 if (minDistanceRenderer > w)
                     break;
             }
@@ -296,6 +302,53 @@ export class MonomerPlacer extends CellRendererBackBase {
             g.restore();
         }
     }
+    onMouseMove(gridCell, e) {
+        if (gridCell.tableRowIndex == null)
+            return;
+        // if (gridCell.cell.column.getTag(bioTAGS.aligned) !== ALIGNMENT.SEQ_MSA)
+        //   return;
+        const [_gridCol, tableCol, temp] = getGridCellColTemp(gridCell);
+        const seqColTemp = temp.rendererBack;
+        if (!seqColTemp)
+            return; // Can do nothing without precalculated data
+        const gridCellBounds = gridCell.bounds;
+        // const value: any = gridCell.cell.value;
+        //
+        // const maxLengthWords: number[] = seqColTemp.getCellMonomerLengths(gridCell.tableRowIndex!);
+        // const maxLengthWordsSum: number[] = new Array<number>(maxLengthWords.length).fill(0);
+        // for (let posI: number = 1; posI < maxLengthWords.length; posI++)
+        //   maxLengthWordsSum[posI] = maxLengthWordsSum[posI - 1] + maxLengthWords[posI];
+        // const maxIndex = maxLengthWords.length;
+        const argsX = e.offsetX - gridCell.gridColumn.left + (gridCell.gridColumn.left - gridCellBounds.x);
+        const left = seqColTemp.getPosition(gridCell.tableRowIndex, argsX, gridCellBounds.width);
+        const seqSS = SeqHandler.forColumn(tableCol)
+            .getSplitted(gridCell.tableRowIndex);
+        if (left !== null && left < seqSS.length) {
+            const sh = SeqHandler.forColumn(tableCol);
+            const alphabet = sh.alphabet ?? ALPHABET.UN;
+            const seqMonomer = {
+                position: left,
+                biotype: alphabet === ALPHABET.RNA || alphabet === ALPHABET.DNA ? HelmTypes.NUCLEOTIDE : HelmTypes.AA,
+                symbol: seqSS.getCanonical(left),
+            };
+            const tooltipElements = [];
+            let monomerDiv = seqColTemp._monomerStructureMap[seqMonomer.symbol];
+            if (!monomerDiv || true) {
+                monomerDiv = seqColTemp._monomerStructureMap[seqMonomer.symbol] = (() => {
+                    return this.monomerLib ? this.monomerLib.getTooltip(seqMonomer.biotype, seqMonomer.symbol) :
+                        ui.divText('Monomer library is not available');
+                })();
+            }
+            tooltipElements.push(monomerDiv);
+            ui.tooltip.show(ui.divV(tooltipElements), e.x + 16, e.y + 16);
+            execMonomerHoverLinks(gridCell, seqMonomer);
+        }
+        else {
+            //
+            ui.tooltip.hide();
+            execMonomerHoverLinks(gridCell, null);
+        }
+    }
 }
 export function getUpdatedWidth(grid, g, x, w, dpr) {
     return !!grid ? Math.max(Math.min(grid.canvas.width / dpr - x, w)) : Math.max(g.canvas.width / dpr - x, 0);

package/src/utils/cell-renderer-monomer-placer.js.map

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package/src/utils/macromolecule/utils.d.ts.map

@@ -1 +1 @@
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package/src/utils/macromolecule/utils.js

@@ -119,9 +119,8 @@ export function getSplitterWithSeparator(separator, limit = undefined) {
                 mmList = new Array(Math.ceil(limit));
                 let mEa = null;
                 let mI = 0;
-                while ((mEa = mRe.exec(seq)) !== null && mI < limit) {
+                while ((mEa = mRe.exec(seq)) !== null && mI < limit)
                     mmList[mI++] = mEa[0].replace(`"-"`, '').replace(`'-'`, '');
-                }
                 mmList.splice(mI);
             }
             else

package/src/utils/macromolecule/utils.js.map

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package/src/utils/monomer-ui.d.ts.map

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package/src/utils/monomer-ui.js.map

@@ -1 +1 @@
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package/src/utils/seq-handler.d.ts

@@ -4,6 +4,7 @@ import { INotationProvider, ISeqSplitted, SeqColStats, SplitterFunc } from './ma
 import { MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import { mmDistanceFunctionType } from '@datagrok-libraries/ml/src/macromolecule-distance-functions/types';
 import { CellRendererBackBase } from './cell-renderer-back-base';
+import { HelmType } from '../helm/types';
 export declare const SeqTemps: {
     /** Column's temp slot name for a SeqHandler object */
     seqHandler: string;
@@ -36,6 +37,7 @@ export declare class SeqHandler {
     get aligned(): string;
     /** Alphabet name (upper case) */
     get alphabet(): string;
+    get defaultBiotype(): HelmType;
     protected get helmCompatible(): string | undefined;
     getAlphabetSize(): number;
     getAlphabetIsMultichar(): boolean;

package/src/utils/seq-handler.d.ts.map

@@ -1 +1 @@
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package/src/utils/seq-handler.js

@@ -1,11 +1,14 @@
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
+/* eslint-disable max-len */
 import { ALPHABET, candidateAlphabets, getSplitterWithSeparator, NOTATION, positionSeparator, splitterAsFasta, splitterAsHelm, TAGS } from './macromolecule';
 import { detectAlphabet, splitterAsFastaSimple, StringListSeqSplitted } from './macromolecule/utils';
 import { mmDistanceFunctions, MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import { getMonomerLibHelper } from '../monomer-works/monomer-utils';
 import { HELM_WRAPPERS_REGEXP, PHOSPHATE_SYMBOL } from './const';
 import { GAP_SYMBOL, GapOriginals } from './macromolecule/consts';
+import { HelmTypes } from '../helm/consts';
+/* eslint-enable max-len */
 export const SeqTemps = new class {
     constructor() {
         /** Column's temp slot name for a SeqHandler object */
@@ -148,6 +151,9 @@ export class SeqHandler {
             throw new Error('Tag alphabet not set');
         return alphabet;
     }
+    get defaultBiotype() {
+        return this.alphabet === ALPHABET.RNA || this.alphabet === ALPHABET.DNA ? HelmTypes.NUCLEOTIDE : HelmTypes.AA;
+    }
     get helmCompatible() {
         return this.column.getTag(TAGS.isHelmCompatible);
     }
@@ -271,7 +277,7 @@ export class SeqHandler {
         return this._posList;
     }
     isFasta() { return this.notation === NOTATION.FASTA; }
-    isSeparator() { return this.notation === NOTATION.SEPARATOR; }
+    isSeparator() { return this.notation === NOTATION.SEPARATOR || !!this.separator; }
     isHelm() { return this.notation === NOTATION.HELM; }
     isRna() { return this.alphabet === ALPHABET.RNA; }
     isDna() { return this.alphabet === ALPHABET.DNA; }

package/src/utils/seq-handler.js.map

@@ -1 +1 @@
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