@datagrok-libraries/bio 5.30.3 → 5.31.0
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/package.json
CHANGED
package/src/types/index.d.ts
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@@ -23,6 +23,7 @@ export type Monomer = {
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};
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};
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export interface IMonomerLib {
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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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[monomerSymbol: string]: string;
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package/src/types/index.d.ts.map
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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,
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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,oBAAoB,IAAI,GAAG,EAC3B,kBAAkB,IAAI,GAAG,EAAE,oBAAoB,IAAI,GAAG,EACvD,MAAM,gBAAgB,CAAC;AAExB,KAAK,MAAM,GAAG;IACZ,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,CAAA;CACzC,CAAC;AAEF,MAAM,WAAW,WAAW;IAC1B,IAAI,KAAK,IAAI,MAAM,GAAG,SAAS,CAAC;IAChC,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,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;CAClC"}
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@@ -1,25 +0,0 @@
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/** Distance matrix class compatible with data structure of scipy.spatial.distance.pdist */
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export declare class DistanceMatrix {
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_data: Float32Array;
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_size: number;
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get data(): Float32Array;
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get size(): number;
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/**
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* @param {Float32Array} data Distance data
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* @param {number} size Number of original observations
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*/
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constructor(data?: Float32Array, size?: number);
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private _linearizeIJ;
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get(i: number, j: number): number;
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set(i: number, j: number, value: number): void;
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static calc<TObj>(list: Indexable<TObj>, method: (a: TObj, b: TObj) => number): DistanceMatrix;
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square(): void;
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add(other: DistanceMatrix): void;
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sqrt(): void;
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normalize(): void;
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}
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export interface Indexable<TObj> {
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[index: number]: TObj;
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get length(): number;
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}
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//# sourceMappingURL=distance-matrix.d.ts.map
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{"version":3,"file":"distance-matrix.d.ts","sourceRoot":"","sources":["distance-matrix.ts"],"names":[],"mappings":"AAIA,2FAA2F;AAC3F,qBAAa,cAAc;IACzB,KAAK,EAAE,YAAY,CAAC;IACpB,KAAK,EAAE,MAAM,CAAC;IAEd,IAAI,IAAI,IAAI,YAAY,CAAuB;IAE/C,IAAI,IAAI,IAAI,MAAM,CAAuB;IAEzC;;;OAGG;gBACS,IAAI,CAAC,EAAE,YAAY,EAAE,IAAI,CAAC,EAAE,MAAM;IAqB9C,OAAO,CAAC,YAAY;IAKpB,GAAG,CAAC,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM;IASxB,GAAG,CAAC,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM;IAIvC,MAAM,CAAC,IAAI,CAAC,IAAI,EAAE,IAAI,EAAE,SAAS,CAAC,IAAI,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,IAAI,KAAK,MAAM,GAAG,cAAc;IAWvF,MAAM;IAMN,GAAG,CAAC,KAAK,EAAE,cAAc;IAQzB,IAAI;IAMJ,SAAS;CAajB;AAED,MAAM,WAAW,SAAS,CAAC,IAAI;IAC7B,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,IAAI,MAAM,IAAI,MAAM,CAAC;CACtB"}
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@@ -1,88 +0,0 @@
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/** Distance matrix class compatible with data structure of scipy.spatial.distance.pdist */
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export class DistanceMatrix {
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get data() { return this._data; }
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get size() { return this._size; }
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/**
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* @param {Float32Array} data Distance data
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* @param {number} size Number of original observations
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*/
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constructor(data, size) {
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if (size == undefined) {
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if (data == undefined)
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throw new Error('Arguments error: data or size is required.');
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this._data = data;
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this._size = (1 + Math.sqrt(1 + 4 * 2 * this._data.length)) / 2;
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if (this._size != Math.floor(this._size))
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throw new Error(`Invalid data length ${this._data.length} leads to non integer size ${this._size}`);
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}
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else {
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this._size = size;
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const dataLength = size * (size - 1) / 2;
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if (data) {
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if (data.length != dataLength)
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throw new Error(`Invalid data length. Observations size ${size} requires data length ${dataLength}.`);
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this._data = data;
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}
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else {
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this._data = new Float32Array(dataLength);
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}
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}
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}
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_linearizeIJ(i, j) {
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if (!(i < j))
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throw new Error('i must be less than j');
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return this._size * i + j - Math.floor(((i + 2) * (i + 1)) / 2);
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}
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get(i, j) {
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if (i == j)
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return 0;
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else if (i < j)
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return this._data[this._linearizeIJ(i, j)];
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else
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return this._data[this._linearizeIJ(j, i)];
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}
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set(i, j, value) {
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this._data[this._linearizeIJ(i, j)] = value;
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}
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static calc(list, method) {
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const size = list.length;
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const res = new DistanceMatrix(undefined, size);
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for (let i = 0; i < size; i++) {
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for (let j = i + 1; j < size; j++)
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res.set(i, j, method(list[i], list[j]));
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}
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return res;
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}
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// squares each value in matrix in place
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square() {
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for (let i = 0; i < this._data.length; i++)
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this._data[i] = Math.pow(this._data[i], 2);
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}
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// adds another matrix to this one in place
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add(other) {
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if (this._size !== other._size)
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throw new Error(`Matrices must have the same size. This size: ${this._size}, other size: ${other._size}`);
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for (let i = 0; i < this._data.length; i++)
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this._data[i] += other._data[i];
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}
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// square root each value in matrix in place
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sqrt() {
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for (let i = 0; i < this._data.length; i++)
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this._data[i] = Math.sqrt(this._data[i]);
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}
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//normilze distance matrix in place
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normalize() {
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let min = this._data[0];
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let max = this._data[0];
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for (let i = 0; i < this._data.length; i++) {
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if (this._data[i] < min)
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min = this._data[i];
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if (this._data[i] > max)
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max = this._data[i];
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}
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const range = max - min;
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for (let i = 0; i < this._data.length; i++)
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this._data[i] = range === 0 ? this._data[i] - min : (this._data[i] - min) / (max - min);
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}
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}
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//# sourceMappingURL=distance-matrix.js.map
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{"version":3,"file":"distance-matrix.js","sourceRoot":"","sources":["distance-matrix.ts"],"names":[],"mappings":"AAIA,2FAA2F;AAC3F,MAAM,OAAO,cAAc;IAIzB,IAAI,IAAI,KAAmB,OAAO,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC;IAE/C,IAAI,IAAI,KAAa,OAAO,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC;IAEzC;;;OAGG;IACH,YAAY,IAAmB,EAAE,IAAa;QAC5C,IAAI,IAAI,IAAI,SAAS,EAAE;YACrB,IAAI,IAAI,IAAI,SAAS;gBAAE,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAC;YAErF,IAAI,CAAC,KAAK,GAAG,IAAK,CAAC;YACnB,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC;YAChE,IAAI,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC;gBACtC,MAAM,IAAI,KAAK,CAAC,uBAAuB,IAAI,CAAC,KAAK,CAAC,MAAM,8BAA8B,IAAI,CAAC,KAAK,EAAE,CAAC,CAAC;SACvG;aAAM;YACL,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC;YAClB,MAAM,UAAU,GAAW,IAAI,GAAG,CAAC,IAAI,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC;YACjD,IAAI,IAAI,EAAE;gBACR,IAAI,IAAI,CAAC,MAAM,IAAI,UAAU;oBAC3B,MAAM,IAAI,KAAK,CAAC,0CAA0C,IAAI,yBAAyB,UAAU,GAAG,CAAC,CAAC;gBACxG,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC;aACnB;iBAAM;gBACL,IAAI,CAAC,KAAK,GAAG,IAAI,YAAY,CAAC,UAAU,CAAC,CAAC;aAC3C;SACF;IACH,CAAC;IAEO,YAAY,CAAC,CAAS,EAAE,CAAS;QACvC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;YAAE,MAAM,IAAI,KAAK,CAAC,uBAAuB,CAAC,CAAC;QACvD,OAAO,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;IAClE,CAAC;IAED,GAAG,CAAC,CAAS,EAAE,CAAS;QACtB,IAAI,CAAC,IAAI,CAAC;YACR,OAAO,CAAC,CAAC;aACN,IAAI,CAAC,GAAG,CAAC;YACZ,OAAO,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;;YAE3C,OAAO,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;IAC/C,CAAC;IAED,GAAG,CAAC,CAAS,EAAE,CAAS,EAAE,KAAa;QACrC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC;IAC9C,CAAC;IAED,MAAM,CAAC,IAAI,CAAO,IAAqB,EAAE,MAAoC;QAC3E,MAAM,IAAI,GAAW,IAAI,CAAC,MAAM,CAAC;QACjC,MAAM,GAAG,GAAG,IAAI,cAAc,CAAC,SAAS,EAAE,IAAI,CAAC,CAAC;QAChD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE;YAC7B,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE;gBAC/B,GAAG,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;SAC3C;QACD,OAAO,GAAG,CAAC;IACb,CAAC;IAED,wCAAwC;IACjC,MAAM;QACX,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE;YACxC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,SAAA,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAI,CAAC,CAAA,CAAC;IACvC,CAAC;IAED,2CAA2C;IACpC,GAAG,CAAC,KAAqB;QAC9B,IAAI,IAAI,CAAC,KAAK,KAAK,KAAK,CAAC,KAAK;YAC5B,MAAM,IAAI,KAAK,CAAC,gDAAgD,IAAI,CAAC,KAAK,iBAAiB,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC;QAC5G,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE;YACxC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;IACpC,CAAC;IAED,4CAA4C;IACrC,IAAI;QACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE;YACxC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC;IAC7C,CAAC;IAED,mCAAmC;IAC5B,SAAS;QACd,IAAI,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;QACxB,IAAI,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;QACxB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC1C,IAAI,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,GAAG;gBACrB,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;YACtB,IAAI,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,GAAG;gBACrB,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;SACvB;QACD,MAAM,KAAK,GAAG,GAAG,GAAG,GAAG,CAAC;QACxB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE;YACxC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,CAAC,GAAG,GAAG,GAAG,CAAC,CAAC;IAC5F,CAAC;CACF"}
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