@datagrok-libraries/bio 5.40.5 → 5.40.6
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.
- package/CHANGELOG.md +6 -0
- package/package.json +1 -1
- package/src/types/index.d.ts +10 -1
- package/src/types/index.d.ts.map +1 -1
- package/src/types/index.js +6 -1
- package/src/types/index.js.map +1 -1
- package/src/utils/cell-renderer-monomer-placer.d.ts +4 -5
- package/src/utils/cell-renderer-monomer-placer.d.ts.map +1 -1
- package/src/utils/cell-renderer-monomer-placer.js +4 -15
- package/src/utils/cell-renderer-monomer-placer.js.map +1 -1
package/CHANGELOG.md
CHANGED
package/package.json
CHANGED
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@@ -8,7 +8,7 @@
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"access": "public"
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},
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"friendlyName": "Datagrok bio library",
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"version": "5.40.
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"version": "5.40.6",
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"description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
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"dependencies": {
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"@datagrok-libraries/gridext": "^1.3.68",
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package/src/types/index.d.ts
CHANGED
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@@ -1,5 +1,5 @@
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import { Observable } from 'rxjs';
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import { HELM_REQUIRED_FIELD as REQ, HELM_RGROUP_FIELDS as RGP, HELM_OPTIONAL_FIELDS as OPT } from '../utils/const';
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import { HELM_REQUIRED_FIELD as REQ, HELM_RGROUP_FIELDS as RGP, HELM_OPTIONAL_FIELDS as OPT, HELM_POLYMER_TYPE } from '../utils/const';
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export type RGroup = {
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[RGP.CAP_GROUP_SMILES]: string;
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[RGP.ALTERNATE_ID]: string;
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@@ -21,8 +21,10 @@ export type Monomer = {
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[OPT.META]?: {
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[property: string]: any;
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};
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lib?: IMonomerLib;
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};
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export interface IMonomerLib {
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get source(): string | undefined;
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get error(): string | undefined;
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getMonomer(polymerType: string, monomerSymbol: string): Monomer | null;
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getMonomerMolsByPolymerType(polymerType: string): {
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@@ -33,5 +35,12 @@ export interface IMonomerLib {
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getPolymerTypes(): string[];
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update(lib: IMonomerLib): void;
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get onChanged(): Observable<any>;
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getTooltip(polymerType: string, monomerSymbol: string): HTMLElement;
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}
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export declare const alphabetPolymerTypes: {
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DNA: HELM_POLYMER_TYPE;
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RNA: HELM_POLYMER_TYPE;
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PT: HELM_POLYMER_TYPE;
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UN: HELM_POLYMER_TYPE;
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};
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//# sourceMappingURL=index.d.ts.map
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package/src/types/index.d.ts.map
CHANGED
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@@ -1 +1 @@
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-
{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,UAAU,EAAC,MAAM,MAAM,CAAC;AAChC,OAAO,EACL,mBAAmB,IAAI,GAAG,EAC1B,kBAAkB,IAAI,GAAG,EAAE,oBAAoB,IAAI,GAAG,
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+
{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,UAAU,EAAC,MAAM,MAAM,CAAC;AAChC,OAAO,EACL,mBAAmB,IAAI,GAAG,EAC1B,kBAAkB,IAAI,GAAG,EAAE,oBAAoB,IAAI,GAAG,EAAE,iBAAiB,EAC1E,MAAM,gBAAgB,CAAC;AAGxB,MAAM,MAAM,MAAM,GAAG;IACnB,CAAC,GAAG,CAAC,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC/B,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,MAAM,CAAC;IAC3B,CAAC,GAAG,CAAC,cAAc,CAAC,EAAE,MAAM,CAAC;IAC7B,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,MAAM,CAAC;CACrB,CAAA;AACD,MAAM,MAAM,OAAO,GAAG;IACpB,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACrB,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,MAAM,CAAC;IACnB,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,MAAM,CAAC;IACtB,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACrB,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC;IACjB,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACxB,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACrB,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,MAAM,CAAC;IAC3B,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,MAAM,CAAC;IAC3B,CAAC,GAAG,CAAC,WAAW,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACjC,CAAC,GAAG,CAAC,cAAc,CAAC,CAAC,EAAE,MAAM,CAAC;IAC9B,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,EAAE;QAAE,CAAC,QAAQ,EAAE,MAAM,GAAG,GAAG,CAAA;KAAE,CAAC;IACzC,GAAG,CAAC,EAAE,WAAW,CAAC;CACnB,CAAC;AAEF,MAAM,WAAW,WAAW;IAC1B,IAAI,MAAM,IAAI,MAAM,GAAG,SAAS,CAAC;IACjC,IAAI,KAAK,IAAI,MAAM,GAAG,SAAS,CAAC;IAEhC,UAAU,CAAC,WAAW,EAAE,MAAM,EAAE,aAAa,EAAE,MAAM,GAAG,OAAO,GAAG,IAAI,CAAC;IACvE,2BAA2B,CAAC,WAAW,EAAE,MAAM,GAAG;QAAE,CAAC,aAAa,EAAE,MAAM,GAAG,MAAM,CAAA;KAAE,GAAG,IAAI,CAAC;IAC7F,yBAAyB,CAAC,YAAY,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;IACjG,uBAAuB,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;IACvD,eAAe,IAAI,MAAM,EAAE,CAAC;IAC5B,MAAM,CAAC,GAAG,EAAE,WAAW,GAAG,IAAI,CAAC;IAC/B,IAAI,SAAS,IAAI,UAAU,CAAC,GAAG,CAAC,CAAC;IAEjC,UAAU,CAAC,WAAW,EAAE,MAAM,EAAE,aAAa,EAAE,MAAM,GAAG,WAAW,CAAC;CACrE;AAED,eAAO,MAAM,oBAAoB;;;;;CAKhC,CAAC"}
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package/src/types/index.js
CHANGED
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@@ -1,2 +1,7 @@
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export {
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export const alphabetPolymerTypes = {
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["DNA" /* ALPHABET.DNA */]: "RNA" /* HELM_POLYMER_TYPE.RNA */,
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["RNA" /* ALPHABET.RNA */]: "RNA" /* HELM_POLYMER_TYPE.RNA */,
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["PT" /* ALPHABET.PT */]: "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */,
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["UN" /* ALPHABET.UN */]: "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */,
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};
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//# sourceMappingURL=index.js.map
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package/src/types/index.js.map
CHANGED
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@@ -1 +1 @@
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{"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":""}
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{"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAgDA,MAAM,CAAC,MAAM,oBAAoB,GAAG;IAClC,0BAAc,mCAAuB;IACrC,0BAAc,mCAAuB;IACrC,wBAAa,2CAA2B;IACxC,wBAAa,2CAA2B;CACzC,CAAC"}
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import * as DG from 'datagrok-api/dg';
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import { SeqHandler } from './seq-handler';
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import { MonomerToShortFunc } from './macromolecule';
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import { IMonomerLib
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import { IMonomerLib } from '../types';
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type MonomerPlacerProps = {
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seqHandler: SeqHandler;
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monomerLib
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monomerLib: IMonomerLib;
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monomerCharWidth: number;
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separatorWidth: number;
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monomerToShort: MonomerToShortFunc;
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private readonly propsProvider;
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private _monomerLengthList;
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private separatorWidth;
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props: MonomerPlacerProps;
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private _rowsProcessed;
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private _updated;
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get updated(): boolean;
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[key: string]: TextMetrics;
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};
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_monomerStructureMap: {
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[key: string]:
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[key: string]: HTMLElement;
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};
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private readonly subs;
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/** View is required to subscribe and handle for data frame changes */
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private getCellMonomerLengthsForSeqMsa;
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/** Returns seq position for pointer x */
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getPosition(rowIdx: number, x: number): number | null;
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getMonomer(symbol: string): Monomer | null;
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setMonomerLengthLimit(limit: number): void;
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setSeparatorWidth(width: number): void;
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isMsa(): boolean;
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{"version":3,"file":"cell-renderer-monomer-placer.d.ts","sourceRoot":"","sources":["cell-renderer-monomer-placer.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,OAAO,EAAC,UAAU,EAAC,MAAM,eAAe,CAAC;AACzC,OAAO,EAAC,kBAAkB,EAAW,MAAM,iBAAiB,CAAC;AAC7D,OAAO,EAAC,WAAW,
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{"version":3,"file":"cell-renderer-monomer-placer.d.ts","sourceRoot":"","sources":["cell-renderer-monomer-placer.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,OAAO,EAAC,UAAU,EAAC,MAAM,eAAe,CAAC;AACzC,OAAO,EAAC,kBAAkB,EAAW,MAAM,iBAAiB,CAAC;AAC7D,OAAO,EAAC,WAAW,EAAU,MAAM,UAAU,CAAC;AAI9C,KAAK,kBAAkB,GAAG;IACxB,UAAU,EAAE,UAAU,CAAC;IACvB,UAAU,EAAE,WAAW,CAAC;IACxB,gBAAgB,EAAE,MAAM,CAAC;IAAC,cAAc,EAAE,MAAM,CAAC;IACjD,cAAc,EAAE,kBAAkB,CAAC;IAAC,kBAAkB,EAAE,MAAM,CAAC;CAChE,CAAC;AAEF,qBAAa,aAAa;aAiBN,IAAI,EAAE,EAAE,CAAC,IAAI,GAAG,IAAI;aACpB,GAAG,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC;IACtC,OAAO,CAAC,QAAQ,CAAC,aAAa;IAlBhC,OAAO,CAAC,kBAAkB,CAA2B;IAGrD,OAAO,CAAC,cAAc,CAAK;IACpB,KAAK,EAAE,kBAAkB,CAAC;IACjC,OAAO,CAAC,cAAc,CAAY;IAElC,OAAO,CAAC,QAAQ,CAAkB;IAClC,IAAW,OAAO,IAAI,OAAO,CAA0B;IAEhD,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;IACjE,OAAO,CAAC,QAAQ,CAAC,IAAI,CAAwB;IAE7C,sEAAsE;gBAEpD,IAAI,EAAE,EAAE,CAAC,IAAI,GAAG,IAAI,EACpB,GAAG,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EACrB,aAAa,EAAE,MAAM,kBAAkB;IAyB1D,OAAO,CAAC,OAAO;IAIf,qGAAqG;IAC9F,qBAAqB,CAAC,MAAM,EAAE,MAAM,GAAG,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,CAAC;IAWlE,OAAO,CAAC,2BAA2B;IAsBnC,OAAO,CAAC,8BAA8B;IAwCtC,yCAAyC;IAClC,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI;IAkCrD,qBAAqB,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI;IAK1C,iBAAiB,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI;IAKtC,KAAK,IAAI,OAAO;CAGxB"}
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@@ -2,12 +2,6 @@ import * as grok from 'datagrok-api/grok';
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import * as DG from 'datagrok-api/dg';
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import wu from 'wu';
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import { SeqHandler } from './seq-handler';
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const polymerTypeMap = {
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["DNA" /* ALPHABET.DNA */]: "RNA" /* HELM_POLYMER_TYPE.RNA */,
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["RNA" /* ALPHABET.RNA */]: "RNA" /* HELM_POLYMER_TYPE.RNA */,
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["PT" /* ALPHABET.PT */]: "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */,
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["UN" /* ALPHABET.UN */]: "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */,
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};
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export class MonomerPlacer {
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get updated() { return this._updated; }
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/** View is required to subscribe and handle for data frame changes */
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this._monomerLengthList = null;
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this._rowsProcessed = DG.BitSet.create(this.col.length);
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}
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catch (
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console.error(
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catch (err) {
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console.error(err);
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}
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}));
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this.subs.push(grok.events.onViewRemoved.subscribe((view) => {
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if (this.grid?.view?.id === view.id)
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this.destroy();
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}
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catch (
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console.error(
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catch (err) {
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console.error(err);
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}
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}));
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}
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}
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return left;
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}
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getMonomer(symbol) {
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const alphabet = this.props.seqHandler.alphabet ?? "UN" /* ALPHABET.UN */;
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const polymerType = polymerTypeMap[alphabet];
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return this.props.monomerLib?.getMonomer(polymerType, symbol) ?? null;
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}
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setMonomerLengthLimit(limit) {
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this.props.monomerLengthLimit = limit;
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this._updated = true;
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{"version":3,"file":"cell-renderer-monomer-placer.js","sourceRoot":"","sources":["cell-renderer-monomer-placer.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,IAAI,MAAM,mBAAmB,CAAC;AAC1C,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAE,MAAM,IAAI,CAAC;AAEpB,OAAO,EAAC,UAAU,EAAC,MAAM,eAAe,CAAC;AAazC,MAAM,
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