@datagrok-libraries/bio 5.42.15 → 5.43.0
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 +4 -0
- package/package.json +5 -5
- package/src/seq-palettes.d.ts +2 -2
- package/src/seq-palettes.d.ts.map +1 -1
- package/src/seq-palettes.js +1 -1
- package/src/seq-palettes.js.map +1 -1
- package/src/unknown.d.ts +10 -4
- package/src/unknown.d.ts.map +1 -1
- package/src/unknown.js +34 -5
- package/src/unknown.js.map +1 -1
package/CHANGELOG.md
CHANGED
package/package.json
CHANGED
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@@ -8,12 +8,12 @@
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"access": "public"
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},
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"friendlyName": "Datagrok bio library",
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"version": "5.
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"version": "5.43.0",
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"description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
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"dependencies": {
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"@datagrok-libraries/chem-meta": "^1.2.5",
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"@datagrok-libraries/gridext": "^1.3.71",
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"@datagrok-libraries/ml": "^6.7.
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"@datagrok-libraries/ml": "^6.7.1",
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"@datagrok-libraries/utils": "^4.3.0",
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"@deck.gl/core": "8.8.12",
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"cash-dom": "latest",
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@@ -45,11 +45,11 @@
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"link": "npm link",
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"link-api": "npm link datagrok-api",
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"link-utils": "npm link @datagrok-libraries/utils",
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"link-all": "npm link datagrok-api @datagrok-libraries/gridext @datagrok-libraries/utils @datagrok-libraries/ml",
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"link-all": "npm link @datagrok-libraries/chem-meta datagrok-api @datagrok-libraries/gridext @datagrok-libraries/utils @datagrok-libraries/ml",
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"build-bio": "git clean -f -X -d ./src && tsc",
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"build": "tsc",
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-
"build-all": "npm --prefix ./../../js-api run build && npm --prefix ./../../libraries/gridext run build && npm --prefix ./../../libraries/utils run build && npm --prefix ./../../libraries/ml run build && npm run build",
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"build-all": "npm --prefix ./../../libraries/chem-meta run build && npm --prefix ./../../js-api run build && npm --prefix ./../../libraries/gridext run build && npm --prefix ./../../libraries/utils run build && npm --prefix ./../../libraries/ml run build && npm run build",
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"lint": "eslint \"./src/**/*.ts\"",
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"lint-fix": "eslint \"./src/**/*.ts\" --fix"
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}
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-
}
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}
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package/src/seq-palettes.d.ts
CHANGED
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@@ -2,7 +2,7 @@ export interface SeqPalette {
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/** Monomer color
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* @param {string} m Monomer
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*/
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get(m: string): string;
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get(m: string, polymerType?: string): string;
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}
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export declare class SeqPaletteBase implements SeqPalette {
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static undefinedColor: string;
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@@ -15,6 +15,6 @@ export declare class SeqPaletteBase implements SeqPalette {
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constructor(palette: {
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[m: string]: string;
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});
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get(m: string): string;
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get(m: string, polymerType?: string): string;
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}
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//# sourceMappingURL=seq-palettes.d.ts.map
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@@ -1 +1 @@
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-
{"version":3,"file":"seq-palettes.d.ts","sourceRoot":"","sources":["seq-palettes.ts"],"names":[],"mappings":"AAIA,MAAM,WAAW,UAAU;IAOzB;;OAEG;IACH,GAAG,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;
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{"version":3,"file":"seq-palettes.d.ts","sourceRoot":"","sources":["seq-palettes.ts"],"names":[],"mappings":"AAIA,MAAM,WAAW,UAAU;IAOzB;;OAEG;IACH,GAAG,CAAC,CAAC,EAAE,MAAM,EAAE,WAAW,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;CAC9C;AAED,qBAAa,cAAe,YAAW,UAAU;IAC/C,OAAc,cAAc,SAAsB;IAElD,4CAA4C;IAC5C,OAAc,aAAa,EAAE;QAAE,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,EAAE,CAAA;KAAE,CAqBtD;IAEF,SAAS,CAAC,MAAM,CAAC,WAAW,CAAC,EAAE,EAAE,CAAC,MAAM,EAAE,EAAE,MAAM,CAAC,EAAE,EACnD,UAAU,UAAQ,EAAE,WAAW,GAAE,OAAO,cAA+B;IAazE,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAA0B;gBAEvC,OAAO,EAAE;QAAE,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAA;KAAE;IAIrC,GAAG,CAAC,CAAC,EAAE,MAAM,EAAE,WAAW,CAAC,EAAE,MAAM,GAAG,MAAM;CAGpD"}
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package/src/seq-palettes.js
CHANGED
package/src/seq-palettes.js.map
CHANGED
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@@ -1 +1 @@
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{"version":3,"file":"seq-palettes.js","sourceRoot":"","sources":["seq-palettes.ts"],"names":[],"mappings":"AAiBA,MAAM,OAAO,cAAc;IA2Bf,MAAM,CAAC,WAAW,CAAC,EAAwB,EACnD,UAAU,GAAG,KAAK,EAAE,cAAqC,cAAc;QAEvE,MAAM,OAAO,GAA8B,EAAE,CAAC;QAC9C,EAAE,CAAC,OAAO,CAAC,CAAC,EAAE,EAAE,EAAE;YAChB,MAAM,OAAO,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC;YACtB,MAAM,MAAM,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC;YACrB,OAAO,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE;gBAC3B,OAAO,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;YAClE,CAAC,CAAC,CAAC;QACL,CAAC,CAAC,CAAC;QACH,OAAO,IAAI,WAAW,CAAC,OAAO,CAAC,CAAC;IAClC,CAAC;IAID,YAAY,OAAgC;QAC1C,IAAI,CAAC,QAAQ,GAAG,OAAO,CAAC;IAC1B,CAAC;IAEM,GAAG,CAAC,CAAS;
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{"version":3,"file":"seq-palettes.js","sourceRoot":"","sources":["seq-palettes.ts"],"names":[],"mappings":"AAiBA,MAAM,OAAO,cAAc;IA2Bf,MAAM,CAAC,WAAW,CAAC,EAAwB,EACnD,UAAU,GAAG,KAAK,EAAE,cAAqC,cAAc;QAEvE,MAAM,OAAO,GAA8B,EAAE,CAAC;QAC9C,EAAE,CAAC,OAAO,CAAC,CAAC,EAAE,EAAE,EAAE;YAChB,MAAM,OAAO,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC;YACtB,MAAM,MAAM,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC;YACrB,OAAO,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE;gBAC3B,OAAO,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;YAClE,CAAC,CAAC,CAAC;QACL,CAAC,CAAC,CAAC;QACH,OAAO,IAAI,WAAW,CAAC,OAAO,CAAC,CAAC;IAClC,CAAC;IAID,YAAY,OAAgC;QAC1C,IAAI,CAAC,QAAQ,GAAG,OAAO,CAAC;IAC1B,CAAC;IAEM,GAAG,CAAC,CAAS,EAAE,WAAoB;QACxC,OAAO,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC;IAC1B,CAAC;;AAhDa,6BAAc,GAAG,kBAAkB,CAAC;AAElD,4CAA4C;AAC9B,4BAAa,GAAgC;IACzD,QAAQ,EAAE,CAAC,kBAAkB,EAAE,kBAAkB,EAAE,iBAAiB,EAAE,mBAAmB,CAAC;IAC1F,WAAW,EAAE,CAAC,gBAAgB,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,gBAAgB;QACpG,gBAAgB,EAAE,kBAAkB,EAAE,oBAAoB,EAAE,oBAAoB,CAAC;IACnF,UAAU,EAAE,CAAC,iBAAiB,EAAE,iBAAiB,EAAE,oBAAoB,EAAE,kBAAkB,EAAE,oBAAoB;QAC/G,mBAAmB,CAAC;IACtB,SAAS,EAAE,CAAC,kBAAkB,EAAE,kBAAkB,EAAE,kBAAkB,CAAC;IACvE,KAAK,EAAE,CAAC,gBAAgB,EAAE,kBAAkB,CAAC;IAC7C,SAAS,EAAE,CAAC,iBAAiB,EAAE,kBAAkB,EAAE,iBAAiB,CAAC;IACrE,WAAW,EAAE,CAAC,iBAAiB,EAAE,mBAAmB,CAAC;IACrD,YAAY,EAAE,CAAC,iBAAiB,EAAE,kBAAkB,EAAE,oBAAoB,EAAE,iBAAiB,CAAC;IAC9F,YAAY,EAAE,CAAC,kBAAkB,EAAE,kBAAkB,EAAE,kBAAkB,CAAC;IAC1E,YAAY,EAAE,CAAC,gBAAgB,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,gBAAgB,CAAC;IACtF,OAAO,EAAE,CAAC,gBAAgB,EAAE,gBAAgB,CAAC;IAC7C,aAAa,EAAE,CAAC,kBAAkB,EAAE,oBAAoB,EAAE,oBAAoB,CAAC;IAC/E,UAAU,EAAE,CAAC,gBAAgB,EAAE,kBAAkB,EAAE,kBAAkB,EAAE,gBAAgB,CAAC;IACxF,MAAM,EAAE,CAAC,kBAAkB,CAAC;IAC5B,OAAO,EAAE,CAAC,gBAAgB,EAAE,kBAAkB,CAAC;IAC/C,MAAM,EAAE,CAAC,kBAAkB,EAAE,kBAAkB,EAAE,kBAAkB,EAAE,oBAAoB,CAAC;IAC1F,QAAQ,EAAE,CAAC,iBAAiB,CAAC;IAC7B,OAAO,EAAE,CAAC,kBAAkB,CAAC;CAC9B,CAAC"}
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package/src/unknown.d.ts
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import { SeqPalette, SeqPaletteBase } from './seq-palettes';
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export declare class StringUtils {
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static hashCode(s: string): number;
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}
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import { SeqPalette, SeqPaletteBase } from './seq-palettes';
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export declare abstract class UnknownSeqPalette implements SeqPalette {
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abstract get(m: string): string;
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abstract get(m: string, polymerType?: string): string;
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}
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export declare class GrayAllPalette extends UnknownSeqPalette {
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get(
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get(_m: string, _polymerType?: string): string;
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}
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export declare class UnknownColorPalette extends UnknownSeqPalette {
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static palette: string[];
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static customMonomerColors: {
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[symbol: string]: {
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[polymerType: string]: string;
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};
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};
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static polymerTypes: string[];
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private static buildPalette;
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get(m: string): string;
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get(m: string, polymerType?: string): string;
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}
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export declare class UnknownSeqPalettes extends SeqPaletteBase {
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private static gray;
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package/src/unknown.d.ts.map
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{"version":3,"file":"unknown.d.ts","sourceRoot":"","sources":["unknown.ts"],"names":[],"mappings":"
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{"version":3,"file":"unknown.d.ts","sourceRoot":"","sources":["unknown.ts"],"names":[],"mappings":"AAGA,OAAO,EAAC,UAAU,EAAE,cAAc,EAAC,MAAM,gBAAgB,CAAC;AA4B1D,qBAAa,WAAW;WACR,QAAQ,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM;CAW1C;AAED,8BAAsB,iBAAkB,YAAW,UAAU;aAC3C,GAAG,CAAC,CAAC,EAAE,MAAM,EAAE,WAAW,CAAC,EAAE,MAAM,GAAG,MAAM;CAC7D;AAED,qBAAa,cAAe,SAAQ,iBAAiB;IAC5C,GAAG,CAAC,EAAE,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,MAAM,GAAG,MAAM;CAGtD;AAGD,qBAAa,mBAAoB,SAAQ,iBAAiB;IACxD,OAAc,OAAO,EAAE,MAAM,EAAE,CAAsC;IAGrE,OAAc,mBAAmB,EAAE;QAAC,CAAC,MAAM,EAAE,MAAM,GAAG;YAAC,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,CAAA;SAAC,CAAA;KAAC,CAAM;IAC5F,OAAc,YAAY,EAAE,MAAM,EAAE,CAAM;IAC1C,OAAO,CAAC,MAAM,CAAC,YAAY;IA2BpB,GAAG,CAAC,CAAC,EAAE,MAAM,EAAE,WAAW,CAAC,EAAE,MAAM,GAAG,MAAM;CASpD;AAED,qBAAa,kBAAmB,SAAQ,cAAc;IACpD,OAAO,CAAC,MAAM,CAAC,IAAI,CAAa;IAEhC,WAAkB,IAAI,IAAI,UAAU,CAInC;IAED,OAAO,CAAC,MAAM,CAAC,KAAK,CAAa;IAEjC,WAAkB,KAAK,IAAI,UAAU,CAIpC;CACF"}
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package/src/unknown.js
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import * as DG from 'datagrok-api/dg';
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import { SeqPaletteBase } from './seq-palettes';
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import { getMonomerLibHelper } from './monomer-works/monomer-utils';
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/** makes the color less white, makes the transparency effect always perceptible
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* */
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const normR = r / distToBlack;
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const normG = g / distToBlack;
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const normB = b / distToBlack;
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if (distToBlack > 210)
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if (distToBlack > 210)
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return `rgb(${normR * 210},${normG * 210},${normB * 210})`;
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}
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return DG.Color.toRgb(dgColor);
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}
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export class StringUtils {
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return hash;
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}
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}
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import { SeqPaletteBase } from './seq-palettes';
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export class UnknownSeqPalette {
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}
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export class GrayAllPalette extends UnknownSeqPalette {
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get(
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get(_m, _polymerType) {
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return '#666666';
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}
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}
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export class UnknownColorPalette extends UnknownSeqPalette {
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static buildPalette() {
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getMonomerLibHelper().then((lh) => {
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lh.awaitLoaded().then(() => {
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const monLib = lh.getMonomerLib();
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monLib.onChanged.subscribe(() => {
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UnknownColorPalette.customMonomerColors = {};
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UnknownColorPalette.polymerTypes = monLib.getPolymerTypes();
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for (const polymerType of this.polymerTypes) {
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const monomerSymbols = monLib.getMonomerSymbolsByType(polymerType);
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for (const monomerSymbol of monomerSymbols) {
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const monomer = monLib.getMonomer(polymerType, monomerSymbol);
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if (monomer?.meta?.colors?.default?.background) {
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if (!this.customMonomerColors[monomerSymbol])
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this.customMonomerColors[monomerSymbol] = {};
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this.customMonomerColors[monomerSymbol][polymerType] =
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correctColor(monomer.meta.colors.default.background);
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}
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}
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}
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});
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});
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});
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const res = [].concat(...Object.values(SeqPaletteBase.colourPalette));
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return res;
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}
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get(m) {
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get(m, polymerType) {
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const colorObj = UnknownColorPalette.customMonomerColors[m];
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const polType = polymerType ?? "PEPTIDE" /* PolymerTypes.PEPTIDE */;
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if (colorObj && colorObj[polType])
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return colorObj[polType];
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const hash = StringUtils.hashCode(m);
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const pI = hash % UnknownColorPalette.palette.length;
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return correctColor(UnknownColorPalette.palette[pI]);
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}
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}
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UnknownColorPalette.palette = UnknownColorPalette.buildPalette();
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// this way is just more futureproof, when we start distinguishing
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// between different polymer types for coloring of non natural aa's or nucleotides
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UnknownColorPalette.customMonomerColors = {};
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UnknownColorPalette.polymerTypes = [];
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export class UnknownSeqPalettes extends SeqPaletteBase {
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static get Gray() {
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if (this.gray === void 0)
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package/src/unknown.js.map
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{"version":3,"file":"unknown.js","sourceRoot":"","sources":["unknown.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;
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