@datagrok-libraries/bio 5.51.2 → 5.52.0

package/CHANGELOG.md

@@ -1,5 +1,9 @@
 # bio changelog
 
+## 5.52.0 (2025-05-12)
+
+Sequence rendering with shift configuration. MSA improvements
+
 ## 5.51.1 (2025-04-22)
 
 Update weblogo defaults 

package/package.json

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.51.2",
+  "version": "5.52.0",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/chem-meta": "^1.2.7",

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

@@ -50,6 +50,7 @@ export declare class MonomerPlacer extends CellRendererBackBase<string> {
     setMonomerLengthLimit(value: number): void;
     setSeparatorWidth(value: number): void;
     private padding;
+    get positionShift(): number;
     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;
 }

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

@@ -1 +1 @@
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+{"version":3,"file":"cell-renderer-monomer-placer.d.ts","sourceRoot":"","sources":["cell-renderer-monomer-placer.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,OAAO,EAAW,kBAAkB,EAA0C,MAAM,iBAAiB,CAAC;AAEtG,OAAO,EAAC,oBAAoB,EAAqB,MAAM,2BAA2B,CAAC;AACnF,OAAO,EAAC,OAAO,EAAC,MAAM,UAAU,CAAC;AAKjC,OAAO,EAAC,eAAe,EAAC,MAAM,gBAAgB,CAAC;AAM/C,KAAK,kBAAkB,GAAG;IACxB,cAAc,EAAE,MAAM,CAAC;IACvB,cAAc,EAAE,kBAAkB,CAAC;IACnC,IAAI,EAAE,MAAM,CAAC;IAAC,aAAa,EAAE,MAAM,CAAC;CACrC,CAAC;AAEF,eAAO,MAAM,cAAc,qBAAqB,CAAC;AAEjD,wBAAgB,SAAS,CAAC,MAAM,EAAE,MAAM,EAAE,EAAE,CAAC,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAoBpE;AAED,qBAAa,aAAc,SAAQ,oBAAoB,CAAC,MAAM,CAAC;IAsBpD,kBAAkB,EAAE,MAAM;IACjC,OAAO,CAAC,QAAQ,CAAC,aAAa;IAtBhC,OAAO,CAAC,QAAQ,CAAa;IAC7B,OAAO,CAAC,kBAAkB,CAA2B;IAGrD,OAAO,KAAK,cAAc,GAAwE;IAC3F,KAAK,EAAE,kBAAkB,CAAC;IACjC,OAAO,CAAC,cAAc,CAAY;IAClC,OAAO,CAAC,6BAA6B,CAAa;IAE3C,iBAAiB,EAAE;QAAE,CAAC,GAAG,EAAE,MAAM,GAAG,WAAW,CAAA;KAAE,CAAM;IACvD,oBAAoB,EAAE;QAAE,CAAC,GAAG,EAAE,MAAM,GAAG,WAAW,CAAA;KAAE,CAAM;IAEjE,OAAO,CAAC,SAAS,CAAc;IAE/B,OAAO,CAAC,aAAa,CAAgC;IAErD,sEAAsE;gBAEpE,OAAO,EAAE,EAAE,CAAC,UAAU,GAAG,IAAI,EAC7B,QAAQ,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAC3B,MAAM,EAAE,OAAO,EACR,kBAAkB,EAAE,MAAM,EAChB,aAAa,EAAE,MAAM,kBAAkB;IA+B7C,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC;WAmBpB,eAAe,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC,MAAM;;;;IAWzC,KAAK,IAAI,MAAM;IAIxB,SAAS,CAAC,aAAa,IAAI,eAAe,GAAG,IAAI;cAI9B,KAAK,IAAI,IAAI;IAWhC,SAAS,CAAC,cAAc,IAAI,IAAI;IAIhC,qGAAqG;IAC9F,qBAAqB,CAAC,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,CAAC;IAmBpF,OAAO,CAAC,uBAAuB;IAgB/B,OAAO,CAAC,2BAA2B;IAgCnC,OAAO,CAAC,gCAAgC;IAqBxC,OAAO,CAAC,8BAA8B;IAoDtC,yCAAyC;IAClC,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI;IASpE,qBAAqB,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI;IAO1C,iBAAiB,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI;IAO7C,OAAO,CAAC,OAAO,CAAa;IAE5B,IAAI,aAAa,IAAI,MAAM,CAE1B;IAED,MAAM,CAAC,CAAC,EAAE,wBAAwB,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAC5E,QAAQ,EAAE,EAAE,CAAC,QAAQ,EAAE,UAAU,EAAE,EAAE,CAAC,aAAa;IA4H5C,WAAW,CAAC,QAAQ,EAAE,EAAE,CAAC,QAAQ,EAAE,CAAC,EAAE,UAAU,GAAG,IAAI;CA+CjE;AAED,wBAAgB,eAAe,CAC7B,IAAI,EAAE,EAAE,CAAC,IAAI,GAAG,IAAI,GAAG,SAAS,EAAE,CAAC,EAAE,wBAAwB,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,GAC/F,MAAM,CAER"}

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

@@ -10,6 +10,7 @@ import { DrawStyle, printLeftOrCentered, TAGS as mmcrTAGS } from './cell-rendere
 import { rendererSettingsChangedState } from './cell-renderer-consts';
 import { HelmTypes } from '../helm/consts';
 import { execMonomerHoverLinks } from '../monomer-works/monomer-hover';
+import * as operators from 'rxjs/operators';
 export const undefinedColor = 'rgb(100,100,100)';
 export function hitBounds(bounds, x) {
     let iterationCount = 100;
@@ -63,6 +64,9 @@ export class MonomerPlacer extends CellRendererBackBase {
                     this.invalidateGrid();
                 }
             }));
+            this.subs.push(DG.debounce(this.tableCol.dataFrame.onMetadataChanged.pipe(operators.filter((a) => a.args.source === this.tableCol && a.args.key === bioTAGS.positionShift)), 200).subscribe((_) => {
+                this.reset();
+            }));
         }
     }
     async init() {
@@ -147,25 +151,26 @@ export class MonomerPlacer extends CellRendererBackBase {
         return resSum;
     }
     getCellMonomerLengthsForSeq(rowIdx) {
-        const logPrefix = `${this.toLog()}.getCellMonomerLengthsForSeqMsa()`;
+        const logPrefix = `${this.toLog()}.getCellMonomerLengthsForSeq()`;
         // this.logger.debug(`${logPrefix}, start`);
         if (this._monomerLengthList === null)
             this._monomerLengthList = new Array(this.tableCol.length).fill(null);
+        const visibleSeqStart = this.positionShift;
         const sh = this.seqHelper.getSeqHandler(this.tableCol);
         const minMonWidth = this.props.separatorWidth + 1 * this.props.fontCharWidth;
-        const maxVisibleSeqLength = Math.ceil(this.colWidth / minMonWidth);
+        const maxVisibleSeqLength = Math.ceil(this.colWidth / minMonWidth) + visibleSeqStart;
         const seqSS = sh.getSplitted(rowIdx);
-        const visibleSeqLength = Math.min(maxVisibleSeqLength, seqSS.length);
+        const visibleSeqEnd = Math.min(maxVisibleSeqLength, seqSS.length);
         let res = this._monomerLengthList[rowIdx];
-        if (res === null || res.length < visibleSeqLength) {
+        if (res === null || res.length != visibleSeqEnd - visibleSeqStart) {
             res = this._monomerLengthList[rowIdx] = new Array(seqSS.length);
             let seqWidth = 0;
-            for (let seqMonI = 0; seqMonI < visibleSeqLength; ++seqMonI) {
+            for (let seqMonI = visibleSeqStart; seqMonI < visibleSeqEnd; ++seqMonI) {
                 const seqMonLabel = seqSS.getOriginal(seqMonI);
                 const shortMon = this.props.monomerToShort(seqMonLabel, this.monomerLengthLimit);
                 const separatorWidth = sh.isSeparator() ? this.separatorWidth : this.props.separatorWidth;
                 const seqMonWidth = separatorWidth + shortMon.length * this.props.fontCharWidth;
-                res[seqMonI] = seqMonWidth;
+                res[seqMonI - visibleSeqStart] = seqMonWidth;
                 seqWidth += seqMonWidth;
                 if (seqWidth > this.colWidth)
                     break;
@@ -176,17 +181,18 @@ export class MonomerPlacer extends CellRendererBackBase {
     getCellMonomerLengthsForSeqValue(value, width) {
         const sh = this.seqHelper.getSeqHandler(this.tableCol);
         const minMonWidth = this.props.separatorWidth + 1 * this.props.fontCharWidth;
-        const maxVisibleSeqLength = Math.ceil(width / minMonWidth);
+        const visibleSeqStart = this.positionShift;
+        const maxVisibleSeqLength = Math.ceil(width / minMonWidth) + visibleSeqStart;
         const seqSS = sh.splitter(value);
-        const visibleSeqLength = Math.min(maxVisibleSeqLength, seqSS.length);
-        const res = new Array(visibleSeqLength);
+        const visibleSeqEnd = Math.min(maxVisibleSeqLength, seqSS.length);
+        const res = new Array(visibleSeqEnd - visibleSeqStart);
         let seqWidth = 0;
-        for (let seqMonI = 0; seqMonI < visibleSeqLength; ++seqMonI) {
+        for (let seqMonI = visibleSeqStart; seqMonI < visibleSeqEnd; ++seqMonI) {
             const seqMonLabel = seqSS.getOriginal(seqMonI);
             const shortMon = this.props.monomerToShort(seqMonLabel, this.monomerLengthLimit);
             const separatorWidth = sh.isSeparator() ? this.separatorWidth : this.props.separatorWidth;
             const seqMonWidth = separatorWidth + shortMon.length * this.props.fontCharWidth;
-            res[seqMonI] = seqMonWidth;
+            res[seqMonI - visibleSeqStart] = seqMonWidth;
             seqWidth += seqMonWidth;
             if (seqWidth > width)
                 break;
@@ -220,26 +226,28 @@ export class MonomerPlacer extends CellRendererBackBase {
             }
         })();
         const minMonWidth = this.props.separatorWidth + 1 * this.props.fontCharWidth;
-        const maxVisibleSeqLength = Math.ceil(this.colWidth / minMonWidth);
+        const visibleSequenceStart = this.positionShift;
+        const maxVisibleSeqLength = Math.ceil(this.colWidth / minMonWidth) + visibleSequenceStart;
         for (let seqIdx = startIdx; seqIdx < endIdx; seqIdx++) {
             if (this._processedRows.get(seqIdx) && maxVisibleSeqLength <= this._processedMaxVisibleSeqLength)
                 continue;
             const sh = this.seqHelper.getSeqHandler(this.tableCol);
             const seqSS = sh.getSplitted(seqIdx, maxVisibleSeqLength);
-            const visibleSeqLength = Math.min(maxVisibleSeqLength, seqSS.length);
-            if (visibleSeqLength > res.length)
-                res.push(...new Array(visibleSeqLength - res.length).fill(minMonWidth));
+            const visibleSeqEnd = Math.min(maxVisibleSeqLength, seqSS.length);
+            if (visibleSeqEnd - visibleSequenceStart > res.length)
+                res.push(...new Array(visibleSeqEnd - visibleSequenceStart - res.length).fill(minMonWidth));
             let seqWidth = 0;
-            for (let seqMonI = 0; seqMonI < visibleSeqLength; ++seqMonI) {
+            for (let seqMonI = visibleSequenceStart; seqMonI < visibleSeqEnd; ++seqMonI) {
                 const seqMonLabel = seqSS.getOriginal(seqMonI);
                 const shortMon = this.props.monomerToShort(seqMonLabel, this.monomerLengthLimit);
                 const seqMonWidth = this.props.separatorWidth + shortMon.length * this.props.fontCharWidth;
-                res[seqMonI] = Math.max(res[seqMonI] ?? 0, seqMonWidth);
+                res[seqMonI - visibleSequenceStart] = Math.max(res[seqMonI - visibleSequenceStart] ?? 0, seqMonWidth);
                 seqWidth += seqMonWidth;
                 if (seqWidth >= this.colWidth)
                     break;
             }
             this._processedMaxVisibleSeqLength = Math.max(this._processedMaxVisibleSeqLength, maxVisibleSeqLength);
+            this._processedRows.set(seqIdx, true);
         }
         return res; // first (and single) row of data
     }
@@ -264,6 +272,9 @@ export class MonomerPlacer extends CellRendererBackBase {
             this.dirty = true;
         }
     }
+    get positionShift() {
+        return Number.parseInt(this.tableCol?.tags[bioTAGS.positionShift] ?? '0') ?? 0;
+    }
     render(g, x, y, w, h, gridCell, _cellStyle) {
         // for cases when we render it on somewhere other than grid, gridRow might be null or incorrect (set to 0).
         //for this case we can just recalculate split sequence without caching
@@ -273,6 +284,7 @@ export class MonomerPlacer extends CellRendererBackBase {
         const gridCol = this.gridCol;
         const tableCol = this.tableCol;
         const dpr = window.devicePixelRatio;
+        const positionShift = this.positionShift;
         const logPrefix = `${this.toLog()}.render()`;
         this.logger.debug(`${logPrefix}, start`);
         // Cell renderer settings
@@ -317,7 +329,7 @@ export class MonomerPlacer extends CellRendererBackBase {
             const aligned = tableCol.getTag(bioTAGS.aligned);
             const separator = tableCol.getTag(bioTAGS.separator) ?? '';
             const minMonWidth = this.props.separatorWidth + 1 * this.props.fontCharWidth;
-            const splitLimit = Math.ceil(w / minMonWidth);
+            const splitLimit = Math.ceil(w / minMonWidth) + positionShift;
             const tempReferenceSequence = tableCol.temp["reference-sequence" /* tempTAGS.referenceSequence */];
             const tempCurrentWord = this.tableCol.temp["current-word" /* tempTAGS.currentWord */];
             if (tempCurrentWord && tableCol?.dataFrame?.currentRowIdx === -1)
@@ -336,9 +348,9 @@ export class MonomerPlacer extends CellRendererBackBase {
             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);
+            for (let posIdx = positionShift; posIdx < visibleSeqLength; ++posIdx) {
+                const om = posIdx < subParts.length ? subParts.getOriginal(posIdx) : sh.defaultGapOriginal;
+                const cm = posIdx < subParts.length ? subParts.getCanonical(posIdx) : sh.defaultGapOriginal;
                 let color = undefinedColor;
                 const monomerLib = this.getMonomerLib();
                 if (monomerLib) {
@@ -351,7 +363,7 @@ export class MonomerPlacer extends CellRendererBackBase {
                 /*x1 = */
                 const opts = {
                     color: color, pivot: 0, left: true, transparencyRate: 1.0, separator: separator, last: last,
-                    drawStyle: drawStyle, maxWord: maxLengthWordsSum, wordIdx: posIdx, gridCell: gridCell,
+                    drawStyle: drawStyle, maxWord: maxLengthWordsSum, wordIdx: posIdx - positionShift, gridCell: gridCell,
                     referenceSequence: referenceSequence, maxLengthOfMonomer: maxLengthOfMonomer,
                     monomerTextSizeMap: this._monomerLengthMap, logger: this.logger
                 };
@@ -389,12 +401,12 @@ export class MonomerPlacer extends CellRendererBackBase {
         this.logger.debug(`${logPrefix}, start, argsX: ${argsX}, left: ${left}`);
         const sh = this.seqHelper.getSeqHandler(this.tableCol);
         const seqSS = sh.getSplitted(gridCell.tableRowIndex);
-        if (left !== null && left < seqSS.length) {
+        if (left !== null && left + this.positionShift < seqSS.length) {
             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),
+                symbol: seqSS.getCanonical(left + this.positionShift),
             };
             const tooltipElements = [];
             let monomerDiv = this._monomerStructureMap[seqMonomer.symbol];

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

@@ -1 +1 @@
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package/src/utils/macromolecule/consts.d.ts

@@ -26,7 +26,8 @@ export declare enum TAGS {
     isHelmCompatible = ".isHelmCompatible",
     positionNames = ".positionNames",
     positionLabels = ".positionLabels",
-    regions = ".regions"
+    regions = ".regions",
+    positionShift = ".positionShift"
 }
 export { TAGS as BioTags };
 export declare const positionSeparator: string;

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

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

@@ -26,6 +26,7 @@ export var TAGS;
     TAGS["positionNames"] = ".positionNames";
     TAGS["positionLabels"] = ".positionLabels";
     TAGS["regions"] = ".regions";
+    TAGS["positionShift"] = ".positionShift";
 })(TAGS || (TAGS = {}));
 export { TAGS as BioTags };
 export const positionSeparator = ', ';

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

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