npm - @datagrok-libraries/bio - Versions diffs - 5.44.4 → 5.44.5 - Mend

@datagrok-libraries/bio 5.44.4 → 5.44.5

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (10) hide show

package/CHANGELOG.md +9 -0
package/package.json +1 -1
package/src/types/index.d.ts +3 -1
package/src/types/index.d.ts.map +1 -1
package/src/utils/cell-renderer-monomer-placer.d.ts +0 -3
package/src/utils/cell-renderer-monomer-placer.d.ts.map +1 -1
package/src/utils/cell-renderer-monomer-placer.js +21 -25
package/src/utils/cell-renderer-monomer-placer.js.map +1 -1
package/src/utils/seq-handler.js +1 -1
package/src/utils/seq-handler.js.map +1 -1

package/CHANGELOG.md CHANGED Viewed

@@ -1,5 +1,14 @@
 # bio changelog
+## 5.44.5 (2024-10-03)
+### Bug fixes
+* Fix MonomerPlacer to use IMonomerLibBase.getMonomerTextColor
+* Fix MonomerPlacer for changed column settings
+* Fix MonomerPlacer for original monomer symbol
+* Fix SeqHandler .isSeparator to account column tag
 ## 5.44.4 (2024-10-02)
 ### New features

package/package.json CHANGED Viewed

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.44.4",
+  "version": "5.44.5",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/chem-meta": "^1.2.7",

package/src/types/index.d.ts CHANGED Viewed

@@ -1,7 +1,7 @@
 import * as DG from 'datagrok-api/dg';
 import { Observable } from 'rxjs';
 import { HelmAtom } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
-import { HelmType, IWebEditorMonomer, MonomerSetType, MonomerType, PolymerType } from '../helm/types';
+import { HelmType, IMonomerColors, IWebEditorMonomer, MonomerSetType, MonomerType, PolymerType } from '../helm/types';
 import { HELM_REQUIRED_FIELD as REQ, HELM_RGROUP_FIELDS as RGP, HELM_OPTIONAL_FIELDS as OPT } from '../utils/const';
 export type RGroup = {
     [RGP.CAP_GROUP_SMILES]: string;
@@ -69,6 +69,8 @@ export interface IMonomerLibBase {
         [r: string]: string;
     };
     getTooltip(biotype: HelmType, monomerSymbol: string): HTMLElement;
+    getMonomerColors(biotype: HelmType, symbol: string): IMonomerColors;
+    getMonomerTextColor(biotype: HelmType, symbol: string): string;
 }
 export interface IMonomerLib extends IMonomerLibBase {
     get source(): string | undefined;

package/src/types/index.d.ts.map CHANGED Viewed

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package/src/utils/cell-renderer-monomer-placer.d.ts CHANGED Viewed

@@ -1,10 +1,8 @@
 import * as DG from 'datagrok-api/dg';
-import { SeqHandler } from './seq-handler';
 import { MonomerToShortFunc } from './macromolecule';
 import { CellRendererBackBase } from './cell-renderer-back-base';
 import { ILogger } from './logger';
 type MonomerPlacerProps = {
-    seqHandler: SeqHandler;
     monomerCharWidth: number;
     separatorWidth: number;
     monomerToShort: MonomerToShortFunc;
@@ -38,7 +36,6 @@ export declare class MonomerPlacer extends CellRendererBackBase<string> {
     getPosition(rowIdx: number, x: number, width: number): number | null;
     setMonomerLengthLimit(value: number): void;
     setSeparatorWidth(value: number): void;
-    isMsa(): boolean;
     private padding;
     render(g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell, _cellStyle: DG.GridCellStyle): void;
     onMouseMove(gridCell: DG.GridCell, e: MouseEvent): void;

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

@@ -7,6 +7,7 @@ import { CellRendererBackBase, getGridCellColTemp } from './cell-renderer-back-b
 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)';
@@ -86,6 +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;
@@ -99,7 +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
@@ -112,9 +114,10 @@ export class MonomerPlacer extends CellRendererBackBase {
         // this.logger.debug(`${logPrefix}, start`);
         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) {
@@ -123,7 +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;
@@ -204,14 +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;
-        const separatorWidth = this.props.separatorWidth;
         // Cell renderer settings
         let maxLengthOfMonomer = this.monomerLengthLimit;
         if (mmcrTAGS.maxMonomerLength in tableCol.tags) {
@@ -224,17 +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;
@@ -253,7 +253,6 @@ export class MonomerPlacer extends CellRendererBackBase {
             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)
@@ -266,21 +265,18 @@ 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; */
-            const 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 om = subParts.getOriginal(posIdx);
                 const cm = subParts.getCanonical(posIdx);
                 let color = undefinedColor;
                 if (this.monomerLib) {
-                    const sh = SeqHandler.forColumn(this.tableCol);
                     const biotype = sh.defaultBiotype;
                     //this.logger.debug(`${logPrefix}, biotype: ${biotype}, amino: ${amino}`);
-                    const wem = this.monomerLib.getWebEditorMonomer(biotype, cm);
-                    color = wem.backgroundcolor;
+                    color = this.monomerLib.getMonomerTextColor(biotype, cm);
                 }
                 g.fillStyle = undefinedColor;
                 const last = posIdx === subParts.length - 1;
@@ -291,7 +287,7 @@ export class MonomerPlacer extends CellRendererBackBase {
                     referenceSequence: referenceSequence, maxLengthOfMonomer: maxLengthOfMonomer,
                     monomerTextSizeMap: this._monomerLengthMap, logger: this.logger
                 };
-                printLeftOrCentered(g, cm, x + this.padding, y, w, h, opts);
+                printLeftOrCentered(g, om, x + this.padding, y, w, h, opts);
                 if (minDistanceRenderer > w)
                     break;
             }

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

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

@@ -277,7 +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 CHANGED Viewed

	@@ -1 +1 @@
1	- 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