@datagrok-libraries/bio 5.39.29 → 5.40.1

package/src/utils/macromolecule/types.js

@@ -1,3 +1,5 @@
+/** Canonical gap symbol */
+export const GAP_SYMBOL = '';
 /** Alphabet candidate type */
 export class CandidateType {
     constructor(name, alphabet, cutoff) {

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

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

@@ -1,22 +1,44 @@
 import * as DG from 'datagrok-api/dg';
-import { CandidateType, MonomerFreqs, SeqColStats, SplitterFunc } from './types';
+import { CandidateType, ISeqSplitted, MonomerFreqs, SeqColStats, SeqSplittedBase, SplitterFunc } from './types';
 import { ALPHABET } from './consts';
 import { SeqPalette } from '../../seq-palettes';
+export declare class StringListSeqSplitted implements ISeqSplitted {
+    private readonly mList;
+    private readonly gapOriginalMonomer;
+    get length(): number;
+    get canonicals(): SeqSplittedBase;
+    get originals(): SeqSplittedBase;
+    isGap(posIdx: number): boolean;
+    getCanonical(posIdx: number): string;
+    getOriginal(posIdx: number): string;
+    constructor(mList: SeqSplittedBase, gapOriginalMonomer: string);
+}
+export declare class FastaSimpleSeqSplitted implements ISeqSplitted {
+    private readonly seqS;
+    get length(): number;
+    get canonicals(): string;
+    get originals(): string;
+    isGap(posIdx: number): boolean;
+    getCanonical(posIdx: number): string;
+    getOriginal(posIdx: number): string;
+    constructor(seqS: string);
+}
 /** Stats of sequences with specified splitter func, returns { freq, sameLength }.
  * @param {DG.Column} seqCol
  * @param {number} minLength
  * @param {SplitterFunc} splitter
  * @return { SeqColStats }, sameLength: boolean } stats of column sequences
  */
-export declare function getStatsForCol(seqCol: DG.Column, minLength: number, splitter: SplitterFunc): SeqColStats;
+export declare function getStatsForCol(seqCol: DG.Column<string>, minLength: number, splitter: SplitterFunc): SeqColStats;
 /** Split sequence for single character monomers, square brackets multichar monomer names or gap symbol.
- * @param {any} seq object with sequence
+ * @param seq object with sequence
+ * @param getMonomer Source of the {@link seq} string
  * @return {string[]} array of monomers
  */
-export declare function splitterAsFasta(seq: any): string[];
-export declare function splitterAsFastaSimple(seq: any): string[];
+export declare const splitterAsFasta: SplitterFunc;
+export declare const splitterAsFastaSimple: SplitterFunc;
 /** Gets method to split sequence by separator
- * @param {string} separator
+ * @param separator Monomer separator
  * @param limit
  * @return {SplitterFunc}
  */
@@ -24,9 +46,10 @@ export declare function getSplitterWithSeparator(separator: string, limit?: numb
 /** Splits Helm string to monomers, but does not replace monomer names to other notation (e.g. for RNA).
  * Only for linear polymers, does not split RNA for ribose and phosphate monomers.
  * @param {string} seq Source string of HELM notation
+ * @param {ISeqSource} src Source of the {@link seq} string
  * @return {string[]}
  */
-export declare function splitterAsHelm(seq: any): string[];
+export declare const splitterAsHelm: SplitterFunc;
 /** Func type to shorten a {@link monomerLabel} with length {@link limit} */
 export type MonomerToShortFunc = (monomerLabel: string, limit: number) => string;
 /** Get splitter method to split sequences to monomers (required for MacromoleculeDifferenceCellRenderer)
@@ -36,11 +59,6 @@ export type MonomerToShortFunc = (monomerLabel: string, limit: number) => string
  * @return {SplitterFunc}
  */
 export declare function getSplitter(units: string, separator: string, limit?: number | undefined): SplitterFunc;
-/** Generate splitter function for sequence column
- * @param {DG.Column} col
- * @return {SplitterFunc} Splitter function
- */
-export declare function getSplitterForColumn(col: DG.Column): SplitterFunc;
 /** Convert long monomer names to short ones */
 export declare function monomerToShort(amino: string, maxLengthOfMonomer: number): string;
 /** */

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

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

@@ -1,13 +1,58 @@
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
-import { CandidateSimType } from './types';
+import { CandidateSimType, GAP_SYMBOL } from './types';
 import { Alphabets, candidateAlphabets, monomerRe, NOTATION } from './consts';
-import { UnitsHandler } from '../units-handler';
+import { GapOriginals, SeqHandler } from '../seq-handler';
 import { Vector } from '@datagrok-libraries/utils/src/type-declarations';
 import { vectorDotProduct, vectorLength } from '@datagrok-libraries/utils/src/vector-operations';
 import { AminoacidsPalettes } from '../../aminoacids';
 import { NucleotidesPalettes } from '../../nucleotides';
 import { UnknownSeqPalettes } from '../../unknown';
+export class StringListSeqSplitted {
+    get length() { return this.mList.length; }
+    get canonicals() { return this.mList; }
+    get originals() { return this.mList; }
+    isGap(posIdx) {
+        return this.getOriginal(posIdx) === this.gapOriginalMonomer;
+    }
+    getCanonical(posIdx) {
+        if (this.length <= posIdx)
+            throw new Error('Index out of bounds');
+        return this.mList[posIdx];
+    }
+    getOriginal(posIdx) {
+        if (this.length <= posIdx)
+            throw new Error('Index out of bounds');
+        return this.mList[posIdx];
+    }
+    constructor(mList, gapOriginalMonomer) {
+        this.mList = mList;
+        this.gapOriginalMonomer = gapOriginalMonomer;
+    }
+}
+export class FastaSimpleSeqSplitted {
+    get length() { return this.seqS.length; }
+    get canonicals() { return this.seqS; }
+    get originals() { return this.seqS; }
+    isGap(posIdx) {
+        return this.getOriginal(posIdx) === GapOriginals[NOTATION.FASTA];
+    }
+    getCanonical(posIdx) {
+        if (this.length <= posIdx)
+            throw new Error('Index out of bounds');
+        if (this.isGap(posIdx))
+            return GAP_SYMBOL;
+        return this.seqS[posIdx];
+    }
+    getOriginal(posIdx) {
+        if (this.length <= posIdx)
+            throw new Error('Index out of bounds');
+        return this.seqS[posIdx];
+    }
+    constructor(seqS) {
+        this.seqS = seqS;
+    }
+}
 /** Stats of sequences with specified splitter func, returns { freq, sameLength }.
  * @param {DG.Column} seqCol
  * @param {number} minLength
@@ -16,8 +61,8 @@ import { UnknownSeqPalettes } from '../../unknown';
  */
 export function getStatsForCol(seqCol, minLength, splitter) {
     const cats = seqCol.categories;
-    const splitted = wu(seqCol.getRawData())
-        .map((catI) => splitter(seqCol.categories[catI]));
+    const splitted = wu.enumerate(seqCol.getRawData())
+        .map(([catI, rowIdx]) => splitter(cats[catI]));
     return getStats(splitted, minLength);
 }
 function getStats(splitted, minLength) {
@@ -30,44 +75,48 @@ function getStats(splitted, minLength) {
         else if (mSeq.length !== firstLength)
             sameLength = false;
         if (mSeq.length >= minLength) {
-            for (const m of mSeq) {
-                if (!(m in freq))
-                    freq[m] = 0;
-                freq[m] += 1;
+            for (const cm of mSeq.canonicals) {
+                if (!(cm in freq))
+                    freq[cm] = 0;
+                freq[cm] += 1;
             }
         }
     }
     return { freq: freq, sameLength: sameLength };
 }
 /** Split sequence for single character monomers, square brackets multichar monomer names or gap symbol.
- * @param {any} seq object with sequence
+ * @param seq object with sequence
+ * @param getMonomer Source of the {@link seq} string
  * @return {string[]} array of monomers
  */
-export function splitterAsFasta(seq) {
-    // return seq.toString().replace(monomerRe, '.$1').slice(1).split('.').map((monomer: string) => {
-    //   if (monomer.startsWith('[') && monomer.endsWith(']'))
-    //     return monomer.slice(1, -1);
-    //   else if (monomer === '-')
-    //     return '';
-    //   else
-    //     return monomer;
-    // });
-    return wu(seq.toString().matchAll(monomerRe))
+export const splitterAsFasta = (seq) => {
+    const mmList = wu(seq.toString().matchAll(monomerRe))
         .map((ma) => {
         return ma[2] ?? ma[1]; // preserve '-' as gap symbol for compatibility with simpleAsFastaSimple
     }).toArray();
-}
-export function splitterAsFastaSimple(seq) {
-    return !seq ? [] : seq;
-}
+    return new StringListSeqSplitted(mmList, GapOriginals[NOTATION.FASTA]);
+    // return new Proxy(splittedList as object, {
+    //   get(target: string[], p: string | symbol, receiver: any): any {
+    //     const k = 11;
+    //   }
+    // }) as ISeqSplitted;
+};
+export const splitterAsFastaSimple = (seq) => {
+    return !!seq ? new FastaSimpleSeqSplitted(seq) : new StringListSeqSplitted([], GapOriginals[NOTATION.FASTA]);
+};
 /** Gets method to split sequence by separator
- * @param {string} separator
+ * @param separator Monomer separator
  * @param limit
  * @return {SplitterFunc}
  */
 export function getSplitterWithSeparator(separator, limit = undefined) {
     return (seq) => {
-        return !seq ? [] : seq.replaceAll('\"-\"', '').replaceAll('\'-\'', '').split(separator, limit);
+        if (!seq)
+            return new StringListSeqSplitted([], GapOriginals[NOTATION.SEPARATOR]);
+        else {
+            const mmList = seq.replaceAll('\"-\"', '').replaceAll('\'-\'', '').split(separator, limit);
+            return new StringListSeqSplitted(mmList, GapOriginals[NOTATION.SEPARATOR]);
+        }
     };
 }
 const helmRe = /(PEPTIDE1|DNA1|RNA1)\{([^}]+)}/g;
@@ -75,9 +124,10 @@ const helmPp1Re = /\[([^\[\]]+)]/g;
 /** Splits Helm string to monomers, but does not replace monomer names to other notation (e.g. for RNA).
  * Only for linear polymers, does not split RNA for ribose and phosphate monomers.
  * @param {string} seq Source string of HELM notation
+ * @param {ISeqSource} src Source of the {@link seq} string
  * @return {string[]}
  */
-export function splitterAsHelm(seq) {
+export const splitterAsHelm = (seq) => {
     helmRe.lastIndex = 0;
     const ea = helmRe.exec(seq.toString());
     const inSeq = ea ? ea[2] : null;
@@ -90,8 +140,8 @@ export function splitterAsHelm(seq) {
             return mm;
     };
     const mmList = inSeq ? inSeq.split('.') : [];
-    return mmList.map(mmPostProcess);
-}
+    return new StringListSeqSplitted(mmList.map(mmPostProcess), GapOriginals[NOTATION.HELM]);
+};
 /** Get splitter method to split sequences to monomers (required for MacromoleculeDifferenceCellRenderer)
  * @param {string} units
  * @param {string} separator
@@ -109,14 +159,6 @@ export function getSplitter(units, separator, limit = undefined) {
         throw new Error(`Unexpected units ${units} .`);
     // TODO: Splitter for HELM
 }
-/** Generate splitter function for sequence column
- * @param {DG.Column} col
- * @return {SplitterFunc} Splitter function
- */
-export function getSplitterForColumn(col) {
-    const uh = UnitsHandler.getOrCreate(col);
-    return uh.getSplitter();
-}
 const longMonomerPartRe = /([^\W_]+)/g;
 /** Convert long monomer names to short ones */
 export function monomerToShort(amino, maxLengthOfMonomer) {
@@ -173,9 +215,8 @@ export function detectAlphabet(freq, candidates, gapSymbol = '-') {
         const sim = candidatesSims.find((cs) => cs.similarity === maxSim);
         alphabetName = sim.name;
     }
-    else {
+    else
         alphabetName = "UN" /* ALPHABET.UN */;
-    }
     return alphabetName;
 }
 /** Selects a suitable palette based on column data
@@ -186,8 +227,8 @@ export function detectAlphabet(freq, candidates, gapSymbol = '-') {
 export function pickUpPalette(seqCol, minLength = 5) {
     let alphabet;
     if (seqCol.semType == DG.SEMTYPE.MACROMOLECULE) {
-        const uh = UnitsHandler.getOrCreate(seqCol);
-        alphabet = uh.alphabet;
+        const sh = SeqHandler.forColumn(seqCol);
+        alphabet = sh.alphabet;
     }
     else {
         const stats = getStatsForCol(seqCol, minLength, splitterAsFasta);

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

@@ -1 +1 @@
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package/src/utils/{units-handler.d.ts → seq-handler.d.ts}

@@ -1,13 +1,14 @@
 import * as DG from 'datagrok-api/dg';
 import { NOTATION } from './macromolecule';
-import { ISeqSplitted, SeqColStats, SplitterFunc } from './macromolecule/types';
+import { ISeqSplitted, SeqColStats, SplitterFunc, INotationProvider } from './macromolecule/types';
 import { MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import { mmDistanceFunctionType } from '@datagrok-libraries/ml/src/macromolecule-distance-functions/types';
-export declare const Temps: {
-    /** Column's temp slot name for a UnitsHandler object */
-    uh: string;
+export declare const SeqTemps: {
+    /** Column's temp slot name for a SeqHandler object */
+    seqHandler: string;
+    notationProvider: string;
 };
-export declare const GapSymbols: {
+export declare const GapOriginals: {
     [units: string]: string;
 };
 export type ConvertFunc = (src: string) => string;
@@ -15,21 +16,25 @@ export type JoinerFunc = (src: ISeqSplitted) => string;
 /** Class for handling notation units in Macromolecule columns and
  * conversion of notation systems in Macromolecule columns
  */
-export declare class UnitsHandler {
+export declare class SeqHandler {
     protected readonly _column: DG.Column;
+    protected readonly _columnVersion: number;
     protected readonly _units: string;
     protected readonly _notation: NOTATION;
-    protected readonly _defaultGapSymbol: string;
+    protected readonly _defaultGapOriginal: string;
+    protected readonly notationProvider: INotationProvider | null;
     private _splitter;
-    static setUnitsToFastaColumn(uh: UnitsHandler): void;
-    static setUnitsToSeparatorColumn(uh: UnitsHandler, separator?: string): void;
-    static setUnitsToHelmColumn(uh: UnitsHandler): void;
+    protected constructor(col: DG.Column<string>);
+    static setUnitsToFastaColumn(uh: SeqHandler): void;
+    static setUnitsToSeparatorColumn(uh: SeqHandler, separator?: string): void;
+    static setUnitsToHelmColumn(uh: SeqHandler): void;
     /** From detectMacromolecule */
-    static setTags(uh: UnitsHandler): void;
+    static setTags(uh: SeqHandler): void;
     protected get column(): DG.Column;
+    get length(): number;
     get units(): string;
     get notation(): NOTATION;
-    get defaultGapSymbol(): string;
+    get defaultGapOriginal(): string;
     get separator(): string | undefined;
     get aligned(): string;
     /** Alphabet name (upper case) */
@@ -37,9 +42,10 @@ export declare class UnitsHandler {
     protected get helmCompatible(): string | undefined;
     getAlphabetSize(): number;
     getAlphabetIsMultichar(): boolean;
+    private cached;
     private _splitted;
-    /** */
-    get splitted(): ISeqSplitted[];
+    private columnVersion;
+    getSplitted(rowIdx: number): ISeqSplitted;
     private _stats;
     get stats(): SeqColStats;
     private _maxLength;
@@ -54,7 +60,11 @@ export declare class UnitsHandler {
     isPeptide(): boolean;
     isMsa(): boolean;
     isHelmCompatible(): boolean;
-    isGap(m: string): boolean;
+    /** Checks {@link om} for being a gap
+     * @param {string} om Original monomer of sequence symbol
+     * @return {boolean}
+     */
+    isGap(om: string): boolean;
     /** Associate notation types with the corresponding units */
     /**
      * @return {NOTATION}     Notation associated with the units type
@@ -75,7 +85,8 @@ export declare class UnitsHandler {
      * @return {DG.Column}
      */
     protected getNewColumn(tgtNotation: NOTATION, tgtSeparator?: string, colName?: string, data?: string[]): DG.Column<string>;
-    getNewColumnFromList(name: string, list: string[]): DG.Column<string>;
+    /** Creates a new column on data of {@link seqList} with the same tags */
+    getNewColumnFromList(name: string, seqList: string[]): DG.Column<string>;
     /**
      * Create a new empty column using templateCol as a template
      *
@@ -102,7 +113,8 @@ export declare class UnitsHandler {
      */
     static getNewColumnFromParams(len: number, name: string, units: string): DG.Column;
     /** Gets function to split seq value to monomers */
-    getSplitter(limit?: number): SplitterFunc;
+    protected getSplitter(limit?: number): SplitterFunc;
+    split(seq: string): ISeqSplitted;
     getDistanceFunctionName(): MmDistanceFunctionsNames;
     getDistanceFunction(): mmDistanceFunctionType;
     checkHelmCompatibility(): Promise<boolean>;
@@ -113,14 +125,14 @@ export declare class UnitsHandler {
     /**
      *  Convert HELM string to FASTA/SEPARATOR
      *
-     * @param {string} helmPolymer    A string to be converted
+     * @param {string} srcSeq    A string to be converted
      * @param {string} tgtNotation    Target notation: FASTA or SEPARATOR
      * @param {string} tgtSeparator   Optional target separator (for HELM ->
-     * @param {string | null} tgtGapSymbol   Optional target gap symbol
+     * @param {string | null} tgtGapOriginal   Optional target gap symbol
      * SEPARATOR)
      * @return {string} Converted string
      */
-    convertHelmToFastaSeparator(helmPolymer: string, tgtNotation: string, tgtSeparator?: string, tgtGapSymbol?: string): string;
+    convertHelmToFastaSeparator(srcSeq: string, tgtNotation: string, tgtSeparator?: string, tgtGapOriginal?: string): string;
     /** Dispatcher method for notation conversion
      *
      * @param {NOTATION} tgtNotation   Notation we want to convert to
@@ -135,10 +147,19 @@ export declare class UnitsHandler {
      */
     getRegion(startIdx: number | null, endIdx: number | null, name: string): DG.Column<string>;
     private _joiner?;
-    getJoiner(): JoinerFunc;
+    get joiner(): JoinerFunc;
+    getJoiner(opts?: {
+        notation: NOTATION;
+        separator?: string;
+    }): JoinerFunc;
     getConverter(tgtUnits: NOTATION, tgtSeparator?: string | undefined): ConvertFunc;
-    protected constructor(col: DG.Column<string>);
     /** Gets a column's UnitsHandler object from temp slot or creates a new and stores it to the temp slot. */
-    static getOrCreate(col: DG.Column<string>): UnitsHandler;
+    static forColumn(col: DG.Column<string>): SeqHandler;
+    private joinToFasta;
+    private convertToFasta;
+    private convertToSeparator;
+    private convertToHelm;
+    /** Splits Helm sequence adjusting nucleotides to single char symbols. (!) Removes lone phosphorus. */
+    private splitterAsHelmNucl;
 }
-//# sourceMappingURL=units-handler.d.ts.map
+//# sourceMappingURL=seq-handler.d.ts.map

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

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