@datagrok-libraries/bio 5.44.4 → 5.45.0

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

@@ -1,12 +1,13 @@
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
-import { SeqHandler } from './seq-handler';
+import { getSeqHelper } from './seq-helper';
 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)';
@@ -43,7 +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.sysMonomerLib = null;
         this.padding = 5;
         this.props = this.propsProvider();
         this._processedRows = DG.BitSet.create(this.tableCol.length);
@@ -59,21 +60,29 @@ export class MonomerPlacer extends CellRendererBackBase {
                 if (df.currentRowIdx === -1) {
                     this.tableCol.temp["reference-sequence" /* tempTAGS.referenceSequence */] = null;
                     this.tableCol.temp["current-word" /* tempTAGS.currentWord */] = null;
-                    grid.invalidate();
+                    this.invalidateGrid();
                 }
             }));
         }
-        getMonomerLibHelper().then((libHelper) => {
-            if (this.destroyed)
-                return;
-            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();
-            }));
-        });
+    }
+    async init() {
+        await Promise.all([
+            (async () => {
+                this.seqHelper = await getSeqHelper();
+                this.invalidateGrid();
+            })(),
+            (async () => {
+                const libHelper = await getMonomerLibHelper();
+                this.sysMonomerLib = libHelper.getMonomerLib();
+            })(),
+        ]);
+        this.subs.push(this.sysMonomerLib.onChanged.subscribe(() => {
+            this.reset();
+        }));
+        this.reset();
+    }
+    getMonomerLib() {
+        return this.tableCol.temp[".mm.cellRenderer.overriddenLibrary" /* MmcrTemps.overriddenLibrary */] ?? this.sysMonomerLib;
     }
     reset() {
         if (this.propsProvider)
@@ -83,9 +92,15 @@ export class MonomerPlacer extends CellRendererBackBase {
         this._monomerLengthMap = {};
         this._monomerStructureMap = {};
         super.reset();
+        this.invalidateGrid();
+    }
+    invalidateGrid() {
+        if (this.gridCol && this.gridCol.dart)
+            this.gridCol.grid?.invalidate();
     }
     /** Returns monomers lengths of the {@link rowIdx} and cumulative sums for borders, monomer places */
     getCellMonomerLengths(rowIdx, newWidth) {
+        const sh = this.seqHelper.getSeqHandler(this.tableCol);
         if (this.colWidth < newWidth) {
             this.colWidth = newWidth;
             this.dirty = true;
@@ -99,7 +114,7 @@ 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 +127,10 @@ 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 = this.seqHelper.getSeqHandler(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 +139,7 @@ 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;
@@ -164,7 +180,7 @@ export class MonomerPlacer extends CellRendererBackBase {
         for (let seqIdx = startIdx; seqIdx < endIdx; seqIdx++) {
             if (this._processedRows.get(seqIdx) && maxVisibleSeqLength <= this._processedMaxVisibleSeqLength)
                 continue;
-            const seqSS = SeqHandler.forColumn(this.tableCol)
+            const seqSS = this.seqHelper.getSeqHandler(this.tableCol)
                 .getSplitted(seqIdx, maxVisibleSeqLength);
             const visibleSeqLength = Math.min(maxVisibleSeqLength, seqSS.length);
             if (visibleSeqLength > res.length)
@@ -186,7 +202,7 @@ export class MonomerPlacer extends CellRendererBackBase {
     /** Returns seq position for pointer x */
     getPosition(rowIdx, x, width) {
         const [_monomerMaxLengthList, monomerMaxLengthSumList] = this.getCellMonomerLengths(rowIdx, width);
-        const sh = SeqHandler.forColumn(this.tableCol);
+        const sh = this.seqHelper.getSeqHandler(this.tableCol);
         const seqSS = sh.getSplitted(rowIdx);
         if (seqSS.length === 0)
             return null;
@@ -204,14 +220,12 @@ export class MonomerPlacer extends CellRendererBackBase {
             this.dirty = true;
         }
     }
-    isMsa() {
-        return this.props.seqHandler.isMsa();
-    }
     render(g, x, y, w, h, gridCell, _cellStyle) {
+        if (!this.seqHelper)
+            return;
         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 +238,18 @@ 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 = this.seqHelper.getSeqHandler(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 +268,6 @@ 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 +280,19 @@ 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; */
-            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 monomerLib = this.getMonomerLib();
+                if (monomerLib) {
                     const biotype = sh.defaultBiotype;
                     //this.logger.debug(`${logPrefix}, biotype: ${biotype}, amino: ${amino}`);
-                    const wem = this.monomerLib.getWebEditorMonomer(biotype, cm);
-                    color = wem.backgroundcolor;
+                    color = monomerLib.getMonomerTextColor(biotype, cm);
                 }
                 g.fillStyle = undefinedColor;
                 const last = posIdx === subParts.length - 1;
@@ -291,7 +303,7 @@ 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;
             }
@@ -307,7 +319,7 @@ export class MonomerPlacer extends CellRendererBackBase {
         }
     }
     onMouseMove(gridCell, e) {
-        if (gridCell.tableRowIndex == null)
+        if (!this.seqHelper || gridCell.tableRowIndex == null)
             return;
         // if (gridCell.cell.column.getTag(bioTAGS.aligned) !== ALIGNMENT.SEQ_MSA)
         //   return;
@@ -325,10 +337,9 @@ export class MonomerPlacer extends CellRendererBackBase {
         // 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);
+        const sh = this.seqHelper.getSeqHandler(tableCol);
+        const seqSS = sh.getSplitted(gridCell.tableRowIndex);
         if (left !== null && left < seqSS.length) {
-            const sh = SeqHandler.forColumn(tableCol);
             const alphabet = sh.alphabet ?? ALPHABET.UN;
             const seqMonomer = {
                 position: left,
@@ -338,8 +349,9 @@ export class MonomerPlacer extends CellRendererBackBase {
             const tooltipElements = [];
             let monomerDiv = seqColTemp._monomerStructureMap[seqMonomer.symbol];
             if (!monomerDiv || true) {
+                const monomerLib = this.getMonomerLib();
                 monomerDiv = seqColTemp._monomerStructureMap[seqMonomer.symbol] = (() => {
-                    return this.monomerLib ? this.monomerLib.getTooltip(seqMonomer.biotype, seqMonomer.symbol) :
+                    return monomerLib ? monomerLib.getTooltip(seqMonomer.biotype, seqMonomer.symbol) :
                         ui.divText('Monomer library is not available');
                 })();
             }

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

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

@@ -1 +1 @@
-{"version":3,"file":"fasta-handler.d.ts","sourceRoot":"","sources":["fasta-handler.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,oCAAoC;AACpC,qBAAa,gBAAgB;IAC3B,OAAO,CAAC,YAAY,CAAS;IAC7B,OAAO,CAAC,kBAAkB,CAAgB;IAC1C,OAAO,CAAC,eAAe,CAAgB;IAGvC,IAAW,iBAAiB,IAAI,MAAM,EAAE,CAAoC;IAE5E,IAAW,cAAc,IAAI,MAAM,EAAE,CAAiC;IAEtE;;;;;;;OAOG;IACH,OAAO,CAAC,kBAAkB;IAS1B,2DAA2D;IAC3D,OAAO,CAAC,YAAY;IAiBpB;;;;OAIG;IACI,WAAW,IAAI,EAAE,CAAC,SAAS,EAAG;gBAezB,WAAW,EAAE,MAAM;CAIhC"}
+{"version":3,"file":"fasta-handler.d.ts","sourceRoot":"","sources":["fasta-handler.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,oCAAoC;AACpC,qBAAa,gBAAgB;IAC3B,OAAO,CAAC,YAAY,CAAS;IAC7B,OAAO,CAAC,kBAAkB,CAAgB;IAC1C,OAAO,CAAC,eAAe,CAAgB;IAGvC,IAAW,iBAAiB,IAAI,MAAM,EAAE,CAAoC;IAE5E,IAAW,cAAc,IAAI,MAAM,EAAE,CAAiC;IAEtE;;;;;;;OAOG;IACH,OAAO,CAAC,kBAAkB;IAS1B,2DAA2D;IAC3D,OAAO,CAAC,YAAY;IAiBpB;;;;OAIG;IACI,WAAW,IAAI,EAAE,CAAC,SAAS,EAAG;gBAYzB,WAAW,EAAE,MAAM;CAIhC"}

package/src/utils/fasta-handler.js

@@ -1,5 +1,4 @@
 import * as DG from 'datagrok-api/dg';
-import { SeqHandler } from './seq-handler';
 import { NOTATION } from './macromolecule/consts';
 /** Class for parsing FASTA files */
 export class FastaFileHandler {
@@ -44,8 +43,6 @@ export class FastaFileHandler {
         const sequenceCol = DG.Column.fromStrings('sequence', this.sequencesArray);
         sequenceCol.semType = DG.SEMTYPE.MACROMOLECULE;
         sequenceCol.meta.units = NOTATION.FASTA;
-        // here should go the code from units handler
-        const sh = SeqHandler.forColumn(sequenceCol);
         return [DG.DataFrame.fromColumns([
                 descriptionsArrayCol,
                 sequenceCol,

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

@@ -1 +1 @@
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package/src/utils/generator.d.ts

@@ -1,8 +1,9 @@
 import * as DG from 'datagrok-api/dg';
 import { ALPHABET, NOTATION } from './macromolecule';
+import { ISeqHelper } from './seq-helper';
 import { IMonomerLib } from '../types/index';
 export declare function generateManySequences(): DG.Column[];
 /** Generates the column 'MSA' with sequences length of order 10^6 and the 'Activity' float column. */
 export declare function generateLongSequence(length?: number): DG.Column[];
-export declare function generateLongSequence2(notation?: NOTATION, alphabet?: ALPHABET, separator?: string | undefined, monomerLib?: IMonomerLib | undefined, colName?: string, rowCount?: number, seqLength?: number): DG.Column;
+export declare function generateLongSequence2(seqHelper: ISeqHelper, notation?: NOTATION, alphabet?: ALPHABET, separator?: string | undefined, monomerLib?: IMonomerLib | undefined, colName?: string, rowCount?: number, seqLength?: number): DG.Column;
 //# sourceMappingURL=generator.d.ts.map

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

@@ -1 +1 @@
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+{"version":3,"file":"generator.d.ts","sourceRoot":"","sources":["generator.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAC,QAAQ,EAAe,QAAQ,EAAO,MAAM,iBAAiB,CAAC;AACtE,OAAO,EAAC,UAAU,EAAC,MAAM,cAAc,CAAC;AAExC,OAAO,EAAC,WAAW,EAAC,MAAM,gBAAgB,CAAC;AAI3C,wBAAgB,qBAAqB,IAAI,EAAE,CAAC,MAAM,EAAE,CAQnD;AAED,sGAAsG;AACtG,wBAAgB,oBAAoB,CAAC,MAAM,GAAE,MAAgB,GAAG,EAAE,CAAC,MAAM,EAAE,CAc1E;AAED,wBAAgB,qBAAqB,CAAC,SAAS,EAAE,UAAU,EACzD,QAAQ,GAAE,QAA6B,EAAE,QAAQ,GAAE,QAAsB,EACzE,SAAS,GAAE,MAAM,GAAG,SAA+D,EACnF,UAAU,GAAE,WAAW,GAAG,SAAqB,EAC/C,OAAO,GAAE,MAAc,EAAE,QAAQ,GAAE,MAAY,EAAE,SAAS,GAAE,MAAgB,GAC3E,EAAE,CAAC,MAAM,CAqBX"}

package/src/utils/generator.js

@@ -1,7 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
 import { ALPHABET, getAlphabet, NOTATION, TAGS } from './macromolecule';
-import { SeqHandler } from './seq-handler';
 import { StringListSeqSplitted } from './macromolecule/utils';
 import { GapOriginals } from './macromolecule/consts';
 export function generateManySequences() {
@@ -24,7 +23,7 @@ export function generateLongSequence(length = 10 ** 5) {
     columns.push(DG.Column.fromList(DG.COLUMN_TYPE.FLOAT, 'Activity', new Array(10 ** 2).fill(7.30751)));
     return columns;
 }
-export function generateLongSequence2(notation = NOTATION.SEPARATOR, alphabet = ALPHABET.PT, separator = (notation === NOTATION.SEPARATOR ? '-' : undefined), monomerLib = undefined, colName = 'seq', rowCount = 100, seqLength = 10 ** 6) {
+export function generateLongSequence2(seqHelper, notation = NOTATION.SEPARATOR, alphabet = ALPHABET.PT, separator = (notation === NOTATION.SEPARATOR ? '-' : undefined), monomerLib = undefined, colName = 'seq', rowCount = 100, seqLength = 10 ** 6) {
     const alphabetSet = alphabet === ALPHABET.UN ?
         monomerLib?.getMonomerSymbolsByType("PEPTIDE" /* PolymerTypes.PEPTIDE */) ?? [] : Array.from(getAlphabet(alphabet));
     const alphabetSize = alphabetSet.length;
@@ -34,7 +33,7 @@ export function generateLongSequence2(notation = NOTATION.SEPARATOR, alphabet =
     col.setTag(TAGS.alphabet, alphabet);
     if (notation == NOTATION.SEPARATOR)
         col.setTag(TAGS.separator, separator);
-    const sh = SeqHandler.forColumn(col);
+    const sh = seqHelper.getSeqHandler(col);
     for (let rowI = 0; rowI < rowCount; rowI++) {
         const seqMList = wu.count(0).take(seqLength)
             .map((i) => { return alphabetSet[Math.floor(Math.random() * alphabetSize)]; })

package/src/utils/generator.js.map

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

@@ -28,6 +28,7 @@ export declare enum TAGS {
     positionLabels = ".positionLabels",
     regions = ".regions"
 }
+export { TAGS as BioTags };
 export declare const positionSeparator: string;
 export declare const monomerRe: RegExp;
 export declare const helmRe: RegExp;

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

@@ -1 +1 @@
-{"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,aAAa,EAAC,MAAM,SAAS,CAAC;AAEtC,0EAA0E;AAC1E,oBAAY,QAAQ;IAClB,KAAK,UAAU;IACf,SAAS,cAAc;IACvB,IAAI,SAAS;IACmB,MAAM,WAAW;CAClD;AAED,0BAAkB,SAAS;IACzB,OAAO,YAAY;IACnB,GAAG,QAAQ;CACZ;AAED,oBAAY,QAAQ;IAClB,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,EAAE,OAAO;IACT,cAAc;IACd,EAAE,OAAO;CACV;AAED,oBAAY,IAAI;IACd,OAAO,YAAY;IACnB,QAAQ,aAAa;IACrB,YAAY,kBAAkB;IAC9B,mBAAmB,yBAAyB;IAC5C,SAAS,cAAc;IACvB,gBAAgB,sBAAsB;IACtC,aAAa,mBAAmB;IAChC,cAAc,oBAAoB;IAClC,OAAO,aAAa;CACrB;AAED,eAAO,MAAM,iBAAiB,EAAE,MAAa,CAAC;AAE9C,eAAO,MAAM,SAAS,EAAE,MAAqD,CAAC;AAE9E,eAAO,MAAM,MAAM,EAAE,MAA0C,CAAC;AAChE,eAAO,MAAM,SAAS,EAAE,MAAyB,CAAC;AAElD,eAAO,MAAM,SAAS;;;;;;CASnB,CAAC;AAEJ,eAAO,MAAM,kBAAkB,EAAE,aAAa,EAI7C,CAAC;AAEF,2BAA2B;AAC3B,eAAO,MAAM,UAAU,EAAE,MAAW,CAAC;AAErC,eAAO,MAAM,YAAY,EAAE;IACzB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAAA;CAKxB,CAAC"}
+{"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,aAAa,EAAC,MAAM,SAAS,CAAC;AAEtC,0EAA0E;AAC1E,oBAAY,QAAQ;IAClB,KAAK,UAAU;IACf,SAAS,cAAc;IACvB,IAAI,SAAS;IACmB,MAAM,WAAW;CAClD;AAED,0BAAkB,SAAS;IACzB,OAAO,YAAY;IACnB,GAAG,QAAQ;CACZ;AAED,oBAAY,QAAQ;IAClB,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,EAAE,OAAO;IACT,cAAc;IACd,EAAE,OAAO;CACV;AAED,oBAAY,IAAI;IACd,OAAO,YAAY;IACnB,QAAQ,aAAa;IACrB,YAAY,kBAAkB;IAC9B,mBAAmB,yBAAyB;IAC5C,SAAS,cAAc;IACvB,gBAAgB,sBAAsB;IACtC,aAAa,mBAAmB;IAChC,cAAc,oBAAoB;IAClC,OAAO,aAAa;CACrB;AAED,OAAO,EAAC,IAAI,IAAI,OAAO,EAAC,CAAC;AAEzB,eAAO,MAAM,iBAAiB,EAAE,MAAa,CAAC;AAE9C,eAAO,MAAM,SAAS,EAAE,MAAqD,CAAC;AAE9E,eAAO,MAAM,MAAM,EAAE,MAA0C,CAAC;AAChE,eAAO,MAAM,SAAS,EAAE,MAAyB,CAAC;AAElD,eAAO,MAAM,SAAS;;;;;;CASnB,CAAC;AAEJ,eAAO,MAAM,kBAAkB,EAAE,aAAa,EAI7C,CAAC;AAEF,2BAA2B;AAC3B,eAAO,MAAM,UAAU,EAAE,MAAW,CAAC;AAErC,eAAO,MAAM,YAAY,EAAE;IACzB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAAA;CAKxB,CAAC"}

package/src/utils/macromolecule/consts.js

@@ -27,6 +27,7 @@ export var TAGS;
     TAGS["positionLabels"] = ".positionLabels";
     TAGS["regions"] = ".regions";
 })(TAGS || (TAGS = {}));
+export { TAGS as BioTags };
 export const positionSeparator = ', ';
 export const monomerRe = /(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g;
 export const helmRe = /(PEPTIDE1|DNA1|RNA1)\{([^}]+)}/g;

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

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

@@ -1,5 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import { ISeqSplitted } from '../../utils/macromolecule/types';
+import { ISeqHelper } from '../seq-helper';
 export declare enum SCORE {
     IDENTITY = "identity",
     SIMILARITY = "similarity"
@@ -9,8 +10,9 @@ export declare enum SCORE {
  * @param {DG.Column<string>} col Sequences column to score. Must have Macromolecule semantic type.
  * @param {string} ref Reference sequence to score against.
  * @param {SCORE} scoring Scoring method.
+ * @param {ISeqHelper} seqHelper Helper for sequence operations.
  * @returns {DG.Column<number>} Scores column. */
-export declare function calculateScores(table: DG.DataFrame, col: DG.Column<string>, ref: string, scoring: SCORE): Promise<DG.Column<number>>;
+export declare function calculateScores(table: DG.DataFrame, col: DG.Column<string>, ref: string, scoring: SCORE, seqHelper: ISeqHelper): Promise<DG.Column<number>>;
 /** Calculates identity scores as fraction of matching monomers on the same position.
  * @param {ISeqSplitted} reference Splitted reference sequence.
  * @param {DG.DataFrame} positionsDf Table which only contains position columns with semantic type Monomer.
@@ -20,5 +22,5 @@ export declare function calculateIdentity(reference: ISeqSplitted, positionsDf:
  * @param {ISeqSplitted} reference Splitted reference sequence.
  * @param {DG.DataFrame} positionsDf Table which only contains position columns with semantic type Monomer.
  * @return {DG.Column<number>} Scores column. */
-export declare function calculateSimilarity(reference: ISeqSplitted, positionsDf: DG.DataFrame): Promise<DG.Column<number>>;
+export declare function calculateSimilarity(reference: ISeqSplitted, positionsDf: DG.DataFrame, seqHelper: ISeqHelper): Promise<DG.Column<number>>;
 //# sourceMappingURL=scoring.d.ts.map

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

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package/src/utils/macromolecule/scoring.js

@@ -1,7 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import { sequenceChemSimilarity } from '../../monomer-works/monomer-utils';
 import { splitAlignedSequences } from '../splitter';
-import { SeqHandler } from '../seq-handler';
 import { GAP_SYMBOL } from './consts';
 export var SCORE;
 (function (SCORE) {
@@ -13,15 +12,16 @@ export var SCORE;
  * @param {DG.Column<string>} col Sequences column to score. Must have Macromolecule semantic type.
  * @param {string} ref Reference sequence to score against.
  * @param {SCORE} scoring Scoring method.
+ * @param {ISeqHelper} seqHelper Helper for sequence operations.
  * @returns {DG.Column<number>} Scores column. */
-export async function calculateScores(table, col, ref, scoring) {
-    const splitSeqDf = splitAlignedSequences(col);
-    const srcSh = SeqHandler.forColumn(col);
+export async function calculateScores(table, col, ref, scoring, seqHelper) {
+    const splitSeqDf = splitAlignedSequences(col, seqHelper);
+    const srcSh = seqHelper.getSeqHandler(col);
     const refCol = srcSh.getNewColumnFromList('ref', [ref]);
-    const refUh = SeqHandler.forColumn(refCol);
+    const refUh = seqHelper.getSeqHandler(refCol);
     const refSplitted = refUh.getSplitted(0); // ref is at 0
     const scoresCol = scoring === SCORE.IDENTITY ? calculateIdentity(refSplitted, splitSeqDf) :
-        scoring === SCORE.SIMILARITY ? await calculateSimilarity(refSplitted, splitSeqDf) : null;
+        scoring === SCORE.SIMILARITY ? await calculateSimilarity(refSplitted, splitSeqDf, seqHelper) : null;
     if (scoresCol === null)
         throw new Error(`In bio library: Unknown sequence scoring method: ${scoring}`);
     scoresCol.name = table.columns.getUnusedName(scoresCol.name);
@@ -62,9 +62,9 @@ export function calculateIdentity(reference, positionsDf) {
  * @param {ISeqSplitted} reference Splitted reference sequence.
  * @param {DG.DataFrame} positionsDf Table which only contains position columns with semantic type Monomer.
  * @return {DG.Column<number>} Scores column. */
-export async function calculateSimilarity(reference, positionsDf) {
+export async function calculateSimilarity(reference, positionsDf, seqHelper) {
     const monomerColumns = positionsDf.columns.toList();
-    const scoresCol = await sequenceChemSimilarity(monomerColumns, reference);
+    const scoresCol = await sequenceChemSimilarity(monomerColumns, reference, seqHelper);
     return scoresCol;
 }
 //# sourceMappingURL=scoring.js.map

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

@@ -0,0 +1,47 @@
+import * as DG from 'datagrok-api/dg';
+import { MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
+import { ISeqSplitted, SeqColStats } from './types';
+import { NOTATION } from './consts';
+import { HelmType } from '../../helm/types';
+import { CellRendererBackBase } from '../cell-renderer-back-base';
+export declare const SeqTemps: {
+    /** Column's temp slot name for a SeqHandler object */
+    seqHandler: string;
+    notationProvider: string;
+};
+export type ConvertFunc = (src: string) => string;
+export type JoinerFunc = (src: ISeqSplitted) => string;
+export interface ISeqHandler {
+    get alphabet(): string;
+    get notation(): NOTATION;
+    get separator(): string | undefined;
+    get aligned(): string;
+    get units(): string;
+    get defaultBiotype(): HelmType;
+    get maxLength(): number;
+    get length(): number;
+    get defaultGapOriginal(): string;
+    get stats(): SeqColStats;
+    get joiner(): JoinerFunc;
+    get posList(): string[];
+    isFasta(): boolean;
+    isMsa(): boolean;
+    isHelm(): boolean;
+    isSeparator(): boolean;
+    getSplitted(rowIdx: number, limit?: number): ISeqSplitted;
+    getHelm(rowIdx: number, options?: any): Promise<DG.SemanticValue<string>>;
+    getAlphabetSize(): number;
+    getAlphabetIsMultichar(): boolean;
+    getNewColumnFromList(name: string, seqList: string[]): DG.Column<string>;
+    convert(tgtNotation: NOTATION, tgtSeparator?: string): DG.Column<string>;
+    convertHelmToFastaSeparator(srcSeq: string, tgtNotation: string, tgtSeparator?: string, tgtGapOriginal?: string): string;
+    getRegion(startIdx: number | null, endIdx: number | null, name: string): DG.Column<string>;
+    getJoiner(opts?: {
+        notation: NOTATION;
+        separator?: string;
+    }): JoinerFunc;
+    getDistanceFunctionName(): MmDistanceFunctionsNames;
+    getConverter(tgtUnits: NOTATION, tgtSeparator?: string): ConvertFunc;
+    getRendererBack(gridCol: DG.GridColumn | null, tableCol: DG.Column<string>): CellRendererBackBase<string>;
+}
+//# sourceMappingURL=seq-handler.d.ts.map

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

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