@datagrok-libraries/bio 5.55.0 → 5.60.0

package/src/types/monomer-library.d.ts

@@ -0,0 +1,181 @@
+import * as DG from 'datagrok-api/dg';
+import { HelmAtom, HelmType, IMonomerColors, IWebEditorMonomer, MonomerSetType, MonomerType, PolymerType } from '../helm/types';
+import { Observable } from 'rxjs';
+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;
+    [RGP.ALTERNATE_ID]: string;
+    [RGP.CAP_GROUP_NAME]: string;
+    [RGP.LABEL]: string;
+};
+/** https://github.com/PistoiaHELM/HELMMonomerSets/blob/master/HELMmonomerSchema.json */
+export type Monomer = {
+    [REQ.SYMBOL]: string;
+    [REQ.NAME]: string;
+    [REQ.MOLFILE]: string;
+    [REQ.AUTHOR]: string;
+    [REQ.ID]: number;
+    [REQ.RGROUPS]: RGroup[];
+    [REQ.SMILES]: string;
+    [REQ.POLYMER_TYPE]: PolymerType;
+    [REQ.MONOMER_TYPE]: MonomerType;
+    [REQ.CREATE_DATE]: string | null;
+    [OPT.NATURAL_ANALOG]?: string;
+    [OPT.META]?: {
+        [property: string]: any;
+    };
+    lib?: IMonomerLibBase;
+    wem?: IWebEditorMonomer;
+};
+export interface IMonomerLibBase {
+    get source(): string;
+    get isEmpty(): boolean;
+    get onChanged(): Observable<any>;
+    getMonomerSymbolsByType(polymerType: PolymerType): string[];
+    addMissingMonomer(polymerType: PolymerType, monomerSymbol: string): Monomer;
+    getMonomer(polymerType: PolymerType | null, monomerSymbol: string): Monomer | null;
+    /** HELMWebEditor expects null for HelmTypes.LINKER and R-Group count != 2 */
+    getWebEditorMonomer(a: HelmAtom | HelmType, symbol?: string): IWebEditorMonomer | null;
+    /** Get R groups from smiles and returns as object. CCC[OH:1] would return {[R1]: 'OH'} */
+    getRS(smiles: string): {
+        [r: string]: string;
+    };
+    getTooltip(biotype: HelmType, monomerSymbol: string): HTMLElement;
+    getMonomerColors(biotype: HelmType, symbol: string): IMonomerColors;
+    getMonomerTextColor(biotype: HelmType, symbol: string): string;
+}
+export interface IMonomerSetPlaceholder {
+    get symbol(): string;
+    get polymerType(): PolymerType;
+    get monomerType(): MonomerType;
+    get monomerLinks(): IMonomerLinkData[];
+    get monomers(): Monomer[];
+}
+export interface IMonomerSet {
+    get source(): string | undefined;
+    get error(): string | undefined;
+    get description(): string;
+    get placeholders(): IMonomerSetPlaceholder[];
+}
+export type MonomerLibSummaryType = {
+    [polymerType: string]: number;
+};
+export type MonomerLibData = {
+    [polymerType: string]: {
+        [symbol: string]: Monomer;
+    };
+};
+export interface IMonomerLib extends IMonomerLibBase {
+    get error(): string | undefined;
+    getMonomerMolsByPolymerType(polymerType: PolymerType): {
+        [monomerSymbol: string]: string;
+    } | null;
+    getMonomerSymbolsByRGroup(rGroupNumber: number, polymerType: PolymerType, element?: string): string[];
+    getPolymerTypes(): PolymerType[];
+    toJSON(): Monomer[];
+    toString(): string;
+    /** Summary string with lib monomer count by type
+     * @deprecated Keep for backward compatibility */
+    getSummary(): string;
+    /** Summary with lib monomer count by type */
+    getSummaryObj(): MonomerLibSummaryType;
+    /** Gets dataframe with columns 'polymerType', 'count'. */
+    getSummaryDf(): DG.DataFrame;
+    getMonomerSet(biotype: HelmType): MonomerSetType | null;
+    override(overrideData: MonomerLibData, source: string): IMonomerLibBase;
+}
+export interface IMonomerLinkData {
+    source: string;
+    symbol: string;
+    notes: string;
+}
+export interface IMonomerLink {
+    get lib(): IMonomerLib;
+    get symbol(): string;
+}
+export declare const DEFAULT_FILES_LIB_PROVIDER_NAME = "Files";
+export interface IMonomerLibProvider {
+    name: string;
+    listLibraries(): Promise<string[]>;
+    refreshLists(): Promise<void>;
+    get loadPromise(): Promise<void>;
+    loadLibraries(names: string[]): Promise<MonomerLibData[]>;
+    deleteLibrary(name: string): Promise<void>;
+    addOrUpdateLibraryString(name: string, contentString: string): Promise<void>;
+    addOrUpdateLibrary(libraryName: string, monomers: Monomer[]): Promise<void>;
+    updateOrAddMonomersInLibrary(libraryName: string, monomers: Monomer[]): Promise<void>;
+    getSingleLibrary(name: string): Promise<MonomerLibData | null>;
+    getLibraryAsString(libName: string): Promise<string>;
+    listSets(): Promise<string[]>;
+    loadSets(names: string[]): Promise<IMonomerSet[]>;
+    deleteSet(name: string): Promise<void>;
+    addOrUpdateSetString(name: string, contentString: string): Promise<void>;
+    addOrUpdateSet(setName: string, monomerSet: IMonomerSet): Promise<void>;
+    deleteMonomersFromLibrary(libraryName: string, monomers: ({
+        polymerType: PolymerType;
+        symbol: string;
+    }[])): Promise<void>;
+    get onChanged(): Observable<void>;
+}
+export declare function findProviderWithLibraryName(providers: IMonomerLibProvider[], libraryName: string): Promise<IMonomerLibProvider | null>;
+export interface IMonomerLibHelper {
+    get providersDataChanged(): Observable<void>;
+    /** Returns list of monomer library providers. can be files, DBs, etc */
+    getProviders(): Promise<IMonomerLibProvider[]>;
+    /** Ensures files are loaded and validated, throws error after timeout */
+    awaitLoaded(timeout?: number): Promise<void>;
+    /** Singleton monomer library collected from various sources */
+    getMonomerLib(): IMonomerLib;
+    getAvaliableLibraryNames(): Promise<string[]>;
+    refreshValidLibraryLists(): Promise<void>;
+    getAvailableLibrariesPerProvider(): Promise<Map<string, string[]>>;
+    /**  @deprecated Use {@link getMonomerLib} */
+    getBioLib(): IMonomerLib;
+    /** Singleton monomer set collected from various sources */
+    getMonomerSets(): IMonomerSet;
+    /** (Re)Loads libraries based on settings in user storage {@link LIB_STORAGE_NAME} to singleton.
+     * @param {boolean} reload Clean {@link monomerLib} before load libraries [false]
+     */
+    loadMonomerLib(reload?: boolean): Promise<void>;
+    /** @deprecated Use {@link loadMonomerLib} */
+    loadLibraries(reload?: boolean): Promise<void>;
+    /** (Re)loads monomer sets based on settings in user storage {@link SETS_STORAGE_NAME} to singleton.
+     * @param {boolean} reload Clean {@link monomerSets} before load sets [false]
+     */
+    loadMonomerSets(reload?: boolean): Promise<void>;
+    /** Read single library from given provider */
+    readSingleLibrary(providerName: string, libraryName: string): Promise<IMonomerLib | null>;
+    /** Reads single library by finding suitable provider itself. Condition must be met that there are no overlapping library names */
+    readSingleLibraryByName(libraryName: string): Promise<IMonomerLib | null>;
+    readSingleSet(providerName: string, setName: string): Promise<IMonomerSet | null>;
+    refreshValidLibraryLists(): Promise<void>;
+    /** Changes user lib settings. */
+    loadMonomerLibForTests(): Promise<void>;
+    get fileUploadRequested(): Observable<void>;
+    requestFileUpload(): void;
+    get librarySelectionChanged(): Observable<void>;
+    notifyLibrarySelectionChanged(): void;
+    /** Use default file provider to read monomer library. just a shorthand */
+    readLibraryFromFilePath(filePath: string): Promise<IMonomerLib>;
+}
+export declare function getMonomerLibHelper(): Promise<IMonomerLibHelper>;
+export declare class MonomerSetPlaceholder implements IMonomerSetPlaceholder {
+    private readonly monomerLib;
+    symbol: string;
+    readonly polymerType: PolymerType;
+    readonly monomerType: MonomerType;
+    readonly monomerLinks: IMonomerLinkData[];
+    readonly monomers: Monomer[];
+    readonly error: string | null;
+    constructor(monomerLib: IMonomerLib, symbol: string, polymerType: PolymerType, monomerType: MonomerType, monomerLinks: IMonomerLinkData[]);
+}
+export declare class MonomerSet implements IMonomerSet {
+    readonly description: string;
+    placeholders: IMonomerSetPlaceholder[];
+    readonly source: string | undefined;
+    readonly error: string | undefined;
+    constructor(description: string, placeholders: IMonomerSetPlaceholder[], source?: string | undefined, error?: string | undefined);
+    updateSets(setList: IMonomerSet[], reload?: boolean): void;
+    private _updateSetInt;
+}
+//# sourceMappingURL=monomer-library.d.ts.map

package/src/types/monomer-library.d.ts.map

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package/src/types/monomer-library.js

@@ -0,0 +1,65 @@
+/* eslint-disable max-len */
+import * as DG from 'datagrok-api/dg';
+import { errInfo } from '../utils/err-info';
+export const DEFAULT_FILES_LIB_PROVIDER_NAME = 'Files';
+export async function findProviderWithLibraryName(providers, libraryName) {
+    for (const provider of providers) {
+        const libNames = await provider.listLibraries();
+        if (libNames.includes(libraryName) || libNames.includes(`${libraryName}.json`))
+            return provider;
+    }
+    return null;
+}
+export async function getMonomerLibHelper() {
+    const funcList = DG.Func.find({ package: 'Bio', name: 'getMonomerLibHelper' });
+    if (funcList.length === 0)
+        throw new Error('Package "Bio" must be installed for MonomerLibHelper.');
+    const res = (await funcList[0].prepare().call()).getOutputParamValue();
+    return res;
+}
+export class MonomerSetPlaceholder {
+    constructor(monomerLib, symbol, polymerType, monomerType, monomerLinks) {
+        this.monomerLib = monomerLib;
+        this.symbol = symbol;
+        this.polymerType = polymerType;
+        this.monomerType = monomerType;
+        this.monomerLinks = monomerLinks;
+        this.error = null;
+        try {
+            this.monomers = this.monomerLinks.map((mLink) => {
+                const resM = this.monomerLib.getMonomer(this.polymerType, mLink.symbol);
+                if (!resM)
+                    throw new Error('Monomer not found: ');
+                if (resM.lib?.source != mLink.source)
+                    throw new Error(`Monomer '${symbol}' found in different library.`);
+                return resM;
+            });
+        }
+        catch (err) {
+            const [errMsg, _errStack] = errInfo(err);
+            this.error = errMsg;
+            this.monomers = [];
+        }
+    }
+}
+export class MonomerSet {
+    constructor(description, placeholders, source = undefined, error = undefined) {
+        this.description = description;
+        this.placeholders = placeholders;
+        this.source = source;
+        this.error = error;
+    }
+    updateSets(setList, reload = false) {
+        if (reload)
+            this.placeholders = [];
+        for (const _set of setList)
+            if (!_set.error)
+                this._updateSetInt(_set);
+        // TODO: File onChanged
+    }
+    _updateSetInt(set) {
+        for (const setPh of set.placeholders)
+            this.placeholders.push(setPh);
+    }
+}
+//# sourceMappingURL=monomer-library.js.map

package/src/types/monomer-library.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"monomer-library.js","sourceRoot":"","sources":["monomer-library.ts"],"names":[],"mappings":"AAAA,4BAA4B;AAC5B,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAQtC,OAAO,EAAC,OAAO,EAAC,MAAM,mBAAmB,CAAC;AA+G1C,MAAM,CAAC,MAAM,+BAA+B,GAAG,OAAO,CAAC;AAsBvD,MAAM,CAAC,KAAK,UAAU,2BAA2B,CAAC,SAAgC,EAAE,WAAmB;IACrG,KAAK,MAAM,QAAQ,IAAI,SAAS,EAAE,CAAC;QACjC,MAAM,QAAQ,GAAG,MAAM,QAAQ,CAAC,aAAa,EAAE,CAAC;QAChD,IAAI,QAAQ,CAAC,QAAQ,CAAC,WAAW,CAAC,IAAI,QAAQ,CAAC,QAAQ,CAAC,GAAG,WAAW,OAAO,CAAC;YAC5E,OAAO,QAAQ,CAAC;IACpB,CAAC;IACD,OAAO,IAAI,CAAC;AACd,CAAC;AA+DD,MAAM,CAAC,KAAK,UAAU,mBAAmB;IACvC,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,KAAK,EAAE,IAAI,EAAE,qBAAqB,EAAC,CAAC,CAAC;IAC7E,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,uDAAuD,CAAC,CAAC;IAE3E,MAAM,GAAG,GAAsB,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAuB,CAAC;IAC/G,OAAO,GAAG,CAAC;AACb,CAAC;AAGD,MAAM,OAAO,qBAAqB;IAKhC,YACmB,UAAuB,EACjC,MAAc,EACL,WAAwB,EACxB,WAAwB,EACxB,YAAgC;QAJ/B,eAAU,GAAV,UAAU,CAAa;QACjC,WAAM,GAAN,MAAM,CAAQ;QACL,gBAAW,GAAX,WAAW,CAAa;QACxB,gBAAW,GAAX,WAAW,CAAa;QACxB,iBAAY,GAAZ,YAAY,CAAoB;QAPlC,UAAK,GAAkB,IAAI,CAAC;QAS1C,IAAI,CAAC;YACH,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE;gBAC9C,MAAM,IAAI,GAAG,IAAI,CAAC,UAAU,CAAC,UAAU,CAAC,IAAI,CAAC,WAAW,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC;gBACxE,IAAI,CAAC,IAAI;oBACP,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAC;gBACzC,IAAI,IAAI,CAAC,GAAG,EAAE,MAAM,IAAI,KAAK,CAAC,MAAM;oBAClC,MAAM,IAAI,KAAK,CAAC,YAAY,MAAM,+BAA+B,CAAC,CAAC;gBACrE,OAAO,IAAI,CAAC;YACd,CAAC,CAAC,CAAC;QACL,CAAC;QAAC,OAAO,GAAQ,EAAE,CAAC;YAClB,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC;YACzC,IAAI,CAAC,KAAK,GAAG,MAAM,CAAC;YACpB,IAAI,CAAC,QAAQ,GAAG,EAAE,CAAC;QACrB,CAAC;IACH,CAAC;CACF;AAED,MAAM,OAAO,UAAU;IACrB,YACkB,WAAmB,EAC5B,YAAsC,EAC7B,SAA6B,SAAS,EACtC,QAA4B,SAAS;QAHrC,gBAAW,GAAX,WAAW,CAAQ;QAC5B,iBAAY,GAAZ,YAAY,CAA0B;QAC7B,WAAM,GAAN,MAAM,CAAgC;QACtC,UAAK,GAAL,KAAK,CAAgC;IACpD,CAAC;IAEJ,UAAU,CAAC,OAAsB,EAAE,SAAkB,KAAK;QACxD,IAAI,MAAM;YACR,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC;QACzB,KAAK,MAAM,IAAI,IAAI,OAAO;YACxB,IAAI,CAAC,IAAI,CAAC,KAAK;gBAAE,IAAI,CAAC,aAAa,CAAC,IAAI,CAAC,CAAC;QAE5C,uBAAuB;IACzB,CAAC;IAEO,aAAa,CAAC,GAAgB;QACpC,KAAK,MAAM,KAAK,IAAI,GAAG,CAAC,YAAY;YAClC,IAAI,CAAC,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IAClC,CAAC;CACF"}

package/src/unknown.js

@@ -1,6 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import { SeqPaletteBase } from './seq-palettes';
-import { getMonomerLibHelper } from './monomer-works/monomer-utils';
+import { getMonomerLibHelper } from './types/monomer-library';
 /** makes the color less white, makes the transparency effect always perceptible
  * @param {string} color color in string format either hex or rgb.
  * @param {boolean} scale if scale is needed to 210 brightness.

package/src/unknown.js.map

@@ -1 +1 @@
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package/src/utils/cell-renderer-monomer-placer.d.ts

@@ -2,7 +2,7 @@ import * as DG from 'datagrok-api/dg';
 import { MonomerToShortFunc } from './macromolecule';
 import { CellRendererBackBase } from './cell-renderer-back-base';
 import { ILogger } from './logger';
-import { IMonomerLibBase } from '../types/index';
+import { IMonomerLibBase } from '../types/monomer-library';
 type MonomerPlacerProps = {
     separatorWidth: number;
     monomerToShort: MonomerToShortFunc;

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

@@ -1 +1 @@
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package/src/utils/cell-renderer-monomer-placer.js

@@ -4,7 +4,7 @@ import wu from 'wu';
 import { getSeqHelper } from './seq-helper';
 import { ALPHABET, NOTATION, TAGS as bioTAGS } from './macromolecule';
 import { CellRendererBackBase } from './cell-renderer-back-base';
-import { getMonomerLibHelper } from '../monomer-works/monomer-utils';
+import { getMonomerLibHelper } from '../types/monomer-library';
 import { errInfo } from './err-info';
 import { DrawStyle, printLeftOrCentered, TAGS as mmcrTAGS } from './cell-renderer';
 import { rendererSettingsChangedState } from './cell-renderer-consts';

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

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package/src/utils/composition-table.d.ts

@@ -1,6 +1,8 @@
-import { IMonomerLibBase } from './../types';
+import { IMonomerLibBase } from './../types/monomer-library';
 import { HelmType } from './../helm/types';
 export declare function buildCompositionTable(counts: {
     [m: string]: number;
-}, biotype: HelmType, monomerLib: IMonomerLibBase): HTMLTableElement;
+}, biotype: HelmType, monomerLib: IMonomerLibBase, monomerBioTypes?: {
+    [m: string]: HelmType;
+}): HTMLTableElement;
 //# sourceMappingURL=composition-table.d.ts.map

package/src/utils/composition-table.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"composition-table.d.ts","sourceRoot":"","sources":["composition-table.ts"],"names":[],"mappings":"AAKA,OAAO,EAAC,eAAe,EAAC,MAAM,YAAY,CAAC;AAC3C,OAAO,EAAC,QAAQ,EAAC,MAAM,iBAAiB,CAAC;AAEzC,wBAAgB,qBAAqB,CACnC,MAAM,EAAE;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,EAAE,OAAO,EAAE,QAAQ,EAAE,UAAU,EAAE,eAAe,GAC9E,gBAAgB,CA0ClB"}
+{"version":3,"file":"composition-table.d.ts","sourceRoot":"","sources":["composition-table.ts"],"names":[],"mappings":"AAKA,OAAO,EAAC,eAAe,EAAC,MAAM,4BAA4B,CAAC;AAC3D,OAAO,EAAC,QAAQ,EAAC,MAAM,iBAAiB,CAAC;AAEzC,wBAAgB,qBAAqB,CACnC,MAAM,EAAE;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,EAAE,OAAO,EAAE,QAAQ,EAAE,UAAU,EAAE,eAAe,EAC/E,eAAe,CAAC,EAAE;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,QAAQ,CAAA;CAAE,GAC1C,gBAAgB,CA2ClB"}

package/src/utils/composition-table.js

@@ -1,7 +1,7 @@
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import { GAP_SYMBOL } from './macromolecule/consts';
-export function buildCompositionTable(counts, biotype, monomerLib) {
+export function buildCompositionTable(counts, biotype, monomerLib, monomerBioTypes) {
     let sumValue = 0;
     let maxValue = null;
     for (const value of Object.values(counts)) {
@@ -15,7 +15,8 @@ export function buildCompositionTable(counts, biotype, monomerLib) {
         const ratio = value / sumValue;
         let color;
         try {
-            const colors = monomerLib.getMonomerColors(biotype, cm);
+            const actBioType = monomerBioTypes ? (monomerBioTypes[cm] || biotype) : biotype;
+            const colors = monomerLib.getMonomerColors(actBioType, cm);
             color = colors?.backgroundcolor || '#CCCCCC';
         }
         catch (error) {

package/src/utils/composition-table.js.map

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

@@ -2,7 +2,7 @@ import { MonomerType, PolymerType } from '../helm/types';
 import { MonomerTypes, PolymerTypes } from '../helm/consts';
 import HELM_POLYMER_TYPE = PolymerTypes;
 import HELM_MONOMER_TYPE = MonomerTypes;
-import { RGroup } from '../types';
+import { RGroup } from '../types/monomer-library';
 export { HELM_POLYMER_TYPE, HELM_MONOMER_TYPE };
 /** Required HELM library monomer fields:
  * https://github.com/PistoiaHELM/HELMMonomerSets/blob/master/HELMmonomerSchema.json */

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

@@ -1 +1 @@
-{"version":3,"file":"const.d.ts","sourceRoot":"","sources":["const.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,WAAW,EAAE,WAAW,EAAC,MAAM,eAAe,CAAC;AACvD,OAAO,EAAC,YAAY,EAAE,YAAY,EAAC,MAAM,gBAAgB,CAAC;AAE1D,OAAO,iBAAiB,GAAG,YAAY,CAAC;AACxC,OAAO,iBAAiB,GAAG,YAAY,CAAC;AACxC,OAAO,EAAC,MAAM,EAAC,MAAM,UAAU,CAAC;AAEhC,OAAO,EAAC,iBAAiB,EAAE,iBAAiB,EAAC,CAAC;AAE9C;uFACuF;AACvF,0BAAkB,mBAAmB;IACnC,MAAM,WAAW;IACjB,IAAI,SAAS;IACb,OAAO,YAAY;IACnB,MAAM,WAAW;IACjB,EAAE,OAAO;IACT,OAAO,YAAY;IACnB,MAAM,WAAW;IACjB,YAAY,gBAAgB;IAC5B,YAAY,gBAAgB;IAC5B,WAAW,eAAe;CAC3B;AAGD,0BAAkB,kBAAkB;IAClC,gBAAgB,mBAAmB;IAEnC,0BAA0B,mBAAmB;IAC7C,YAAY,gBAAgB;IAC5B,cAAc,iBAAiB;IAC/B,KAAK,UAAU;CAChB;AAED,0BAAkB,oBAAoB;IACpC,cAAc,kBAAkB;IAChC,IAAI,SAAS;CACd;AAGD,0BAAkB,WAAW;IAC3B,YAAY,gBAAgB;IAC5B,MAAM,WAAW;IACjB,IAAI,SAAS;IACb,MAAM,WAAW;IACjB,OAAO,YAAY;IACnB,cAAc,kBAAkB;IAChC,OAAO,YAAY;IACnB,WAAW,eAAe;IAC1B,EAAE,OAAO;IACT,YAAY,gBAAgB;IAC5B,MAAM,WAAW;CAClB;AAGD,eAAO,MAAM,gBAAgB,eAO5B,CAAC;AAEF,eAAO,MAAM,gBAAgB,gBAAgB,CAAC;AAG9C,eAAO,MAAM,qBAAqB;;;;;;;;;;;;CAYjC,CAAC;AAEF,eAAO,MAAM,aAAa;0BACK,WAAW;;;;;;sBAMvB,MAAM,EAAE;;;0BAGG,WAAW;;CAE/B,CAAC;AAGX,eAAO,MAAM,kBAAkB,MAAQ,CAAC;AACxC,eAAO,MAAM,kBAAkB,OAAQ,CAAC;AAExC,eAAO,MAAM,aAAa,MAAM,CAAC;AACjC,eAAO,MAAM,kBAAkB,MAAM,CAAC;AACtC,eAAO,MAAM,gBAAgB,MAAM,CAAC;AACpC,eAAO,MAAM,oBAAoB,QAGhC,CAAC"}
+{"version":3,"file":"const.d.ts","sourceRoot":"","sources":["const.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,WAAW,EAAE,WAAW,EAAC,MAAM,eAAe,CAAC;AACvD,OAAO,EAAC,YAAY,EAAE,YAAY,EAAC,MAAM,gBAAgB,CAAC;AAE1D,OAAO,iBAAiB,GAAG,YAAY,CAAC;AACxC,OAAO,iBAAiB,GAAG,YAAY,CAAC;AACxC,OAAO,EAAC,MAAM,EAAC,MAAM,0BAA0B,CAAC;AAEhD,OAAO,EAAC,iBAAiB,EAAE,iBAAiB,EAAC,CAAC;AAE9C;uFACuF;AACvF,0BAAkB,mBAAmB;IACnC,MAAM,WAAW;IACjB,IAAI,SAAS;IACb,OAAO,YAAY;IACnB,MAAM,WAAW;IACjB,EAAE,OAAO;IACT,OAAO,YAAY;IACnB,MAAM,WAAW;IACjB,YAAY,gBAAgB;IAC5B,YAAY,gBAAgB;IAC5B,WAAW,eAAe;CAC3B;AAGD,0BAAkB,kBAAkB;IAClC,gBAAgB,mBAAmB;IAEnC,0BAA0B,mBAAmB;IAC7C,YAAY,gBAAgB;IAC5B,cAAc,iBAAiB;IAC/B,KAAK,UAAU;CAChB;AAED,0BAAkB,oBAAoB;IACpC,cAAc,kBAAkB;IAChC,IAAI,SAAS;CACd;AAGD,0BAAkB,WAAW;IAC3B,YAAY,gBAAgB;IAC5B,MAAM,WAAW;IACjB,IAAI,SAAS;IACb,MAAM,WAAW;IACjB,OAAO,YAAY;IACnB,cAAc,kBAAkB;IAChC,OAAO,YAAY;IACnB,WAAW,eAAe;IAC1B,EAAE,OAAO;IACT,YAAY,gBAAgB;IAC5B,MAAM,WAAW;CAClB;AAGD,eAAO,MAAM,gBAAgB,eAO5B,CAAC;AAEF,eAAO,MAAM,gBAAgB,gBAAgB,CAAC;AAG9C,eAAO,MAAM,qBAAqB;;;;;;;;;;;;CAYjC,CAAC;AAEF,eAAO,MAAM,aAAa;0BACK,WAAW;;;;;;sBAMvB,MAAM,EAAE;;;0BAGG,WAAW;;CAE/B,CAAC;AAGX,eAAO,MAAM,kBAAkB,MAAQ,CAAC;AACxC,eAAO,MAAM,kBAAkB,OAAQ,CAAC;AAExC,eAAO,MAAM,aAAa,MAAM,CAAC;AACjC,eAAO,MAAM,kBAAkB,MAAM,CAAC;AACtC,eAAO,MAAM,gBAAgB,MAAM,CAAC;AACpC,eAAO,MAAM,oBAAoB,QAGhC,CAAC"}

package/src/utils/generator.d.ts

@@ -1,7 +1,7 @@
 import * as DG from 'datagrok-api/dg';
 import { ALPHABET, NOTATION } from './macromolecule';
 import { ISeqHelper } from './seq-helper';
-import { IMonomerLib } from '../types/index';
+import { IMonomerLib } from '../types/monomer-library';
 export declare function generateManySequences(): DG.Column[];
 /** Generates the column 'MSA' with sequences length of order 10^5 and the 'Activity' float column. */
 export declare function generateLongSequence(length?: number): DG.Column[];

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

@@ -1 +1 @@
-{"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"}
+{"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,0BAA0B,CAAC;AAIrD,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/macromolecule/consts.d.ts

@@ -29,7 +29,8 @@ export declare enum TAGS {
     positionLabels = ".positionLabels",
     regions = ".regions",
     positionShift = ".positionShift",
-    selectedPosition = ".selectedPosition"
+    selectedPosition = ".selectedPosition",
+    polymerTypeColumnName = ".polymerTypeColumnName"
 }
 export { TAGS as BioTags };
 export declare const positionSeparator: string;

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;IACjB,IAAI,SAAS;CAC9C;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;IACpB,aAAa,mBAAmB;IAChC,gBAAgB,sBAAsB;CACvC;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;CAMxB,CAAC;AAEF,eAAO,MAAM,sBAAsB,QAAQ,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;IACjB,IAAI,SAAS;CAC9C;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;IACpB,aAAa,mBAAmB;IAChC,gBAAgB,sBAAsB;IACtC,qBAAqB,2BAA2B;CACjD;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;CAMxB,CAAC;AAEF,eAAO,MAAM,sBAAsB,QAAQ,CAAC"}

package/src/utils/macromolecule/consts.js

@@ -29,6 +29,7 @@ export var TAGS;
     TAGS["regions"] = ".regions";
     TAGS["positionShift"] = ".positionShift";
     TAGS["selectedPosition"] = ".selectedPosition";
+    TAGS["polymerTypeColumnName"] = ".polymerTypeColumnName";
 })(TAGS || (TAGS = {}));
 export { TAGS as BioTags };
 export const positionSeparator = ', ';

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

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