@datagrok-libraries/bio 5.43.1 → 5.44.1

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

@@ -1 +1 @@
-{"version":3,"file":"scoring.js","sourceRoot":"","sources":["scoring.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,sBAAsB,EAAC,MAAM,mCAAmC,CAAC;AACzE,OAAO,EAAC,UAAU,EAAe,MAAM,iCAAiC,CAAC;AACzE,OAAO,EAAC,qBAAqB,EAAC,MAAM,aAAa,CAAC;AAClD,OAAO,EAAC,UAAU,EAAC,MAAM,gBAAgB,CAAC;AAE1C,MAAM,CAAN,IAAY,KAGX;AAHD,WAAY,KAAK;IACf,8BAAqB,CAAA;IACrB,kCAAyB,CAAA;AAC3B,CAAC,EAHW,KAAK,KAAL,KAAK,QAGhB;AAED;;;;;iDAKiD;AACjD,MAAM,CAAC,KAAK,UAAU,eAAe,CACnC,KAAmB,EAAE,GAAsB,EAAE,GAAW,EAAE,OAAc;IAExE,MAAM,UAAU,GAAG,qBAAqB,CAAC,GAAG,CAAC,CAAC;IAC9C,MAAM,KAAK,GAAG,UAAU,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC;IACxC,MAAM,MAAM,GAAG,KAAK,CAAC,oBAAoB,CAAC,KAAK,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC;IACxD,MAAM,KAAK,GAAG,UAAU,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC;IAC3C,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,cAAc;IAExD,MAAM,SAAS,GAAG,OAAO,KAAK,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,WAAW,EAAE,UAAU,CAAC,CAAC,CAAC;QACzF,OAAO,KAAK,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,MAAM,mBAAmB,CAAC,WAAW,EAAE,UAAU,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IAC3F,IAAI,SAAS,KAAK,IAAI;QACpB,MAAM,IAAI,KAAK,CAAC,oDAAoD,OAAO,EAAE,CAAC,CAAC;IACjF,SAAS,CAAC,IAAI,GAAG,KAAK,CAAC,OAAO,CAAC,aAAa,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC;IAC7D,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC;IAC7B,OAAO,SAAS,CAAC;AACnB,CAAC;AAED;;;iDAGiD;AACjD,MAAM,UAAU,iBAAiB,CAAC,SAAuB,EAAE,WAAyB;IAClF,MAAM,YAAY,GAAG,WAAW,CAAC,OAAO,CAAC,MAAM,CAAC;IAChD,MAAM,YAAY,GAAkB,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC;IAC5D,MAAM,uBAAuB,GAAa,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC;IAClE,MAAM,uBAAuB,GAAa,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC;IAElE,KAAK,IAAI,MAAM,GAAG,CAAC,EAAE,MAAM,GAAG,YAAY,EAAE,EAAE,MAAM,EAAE,CAAC;QACrD,MAAM,MAAM,GAAG,WAAW,CAAC,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC;QACnD,YAAY,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,UAAU,EAAiB,CAAC;QAC1D,uBAAuB,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;QAChE,MAAM,IAAI,GAAG,MAAM,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC;QACpF,uBAAuB,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,UAAU,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC;IACpE,CAAC;IAED,MAAM,iBAAiB,GAAG,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,UAAU,EAAE,WAAW,CAAC,QAAQ,CAAC,CAAC;IAC5E,MAAM,kBAAkB,GAAG,iBAAiB,CAAC,UAAU,EAAE,CAAC;IAC1D,KAAK,IAAI,QAAQ,GAAG,CAAC,EAAE,QAAQ,GAAG,WAAW,CAAC,QAAQ,EAAE,EAAE,QAAQ,EAAE,CAAC;QACnE,kBAAkB,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC;QACjC,KAAK,IAAI,MAAM,GAAG,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,CAAC;YACzD,MAAM,WAAW,GAAG,YAAY,CAAC,MAAM,CAAC,CAAC;YACzC,MAAM,aAAa,GAAW,WAAW,CAAC,CAAC,CAAC,YAAY,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YAC/E,IAAI,aAAa,KAAK,uBAAuB,CAAC,MAAM,CAAC;gBACnD,EAAE,kBAAkB,CAAC,QAAQ,CAAC,CAAC;QACnC,CAAC;QACD,kBAAkB,CAAC,QAAQ,CAAC,IAAI,SAAS,CAAC,MAAM,CAAC;IACnD,CAAC;IAED,OAAO,iBAAiB,CAAC;AAC3B,CAAC;AAED;;;gDAGgD;AAChD,MAAM,CAAC,KAAK,UAAU,mBAAmB,CACvC,SAAuB,EAAE,WAAyB;IAElD,MAAM,cAAc,GAAG,WAAW,CAAC,OAAO,CAAC,MAAM,EAAyB,CAAC;IAC3E,MAAM,SAAS,GAAG,MAAM,sBAAsB,CAAC,cAAc,EAAE,SAAS,CAAC,CAAC;IAC1E,OAAO,SAAS,CAAC;AACnB,CAAC"}
+{"version":3,"file":"scoring.js","sourceRoot":"","sources":["scoring.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,sBAAsB,EAAC,MAAM,mCAAmC,CAAC;AAEzE,OAAO,EAAC,qBAAqB,EAAC,MAAM,aAAa,CAAC;AAClD,OAAO,EAAC,UAAU,EAAC,MAAM,gBAAgB,CAAC;AAC1C,OAAO,EAAC,UAAU,EAAC,MAAM,UAAU,CAAC;AAEpC,MAAM,CAAN,IAAY,KAGX;AAHD,WAAY,KAAK;IACf,8BAAqB,CAAA;IACrB,kCAAyB,CAAA;AAC3B,CAAC,EAHW,KAAK,KAAL,KAAK,QAGhB;AAED;;;;;iDAKiD;AACjD,MAAM,CAAC,KAAK,UAAU,eAAe,CACnC,KAAmB,EAAE,GAAsB,EAAE,GAAW,EAAE,OAAc;IAExE,MAAM,UAAU,GAAG,qBAAqB,CAAC,GAAG,CAAC,CAAC;IAC9C,MAAM,KAAK,GAAG,UAAU,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC;IACxC,MAAM,MAAM,GAAG,KAAK,CAAC,oBAAoB,CAAC,KAAK,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC;IACxD,MAAM,KAAK,GAAG,UAAU,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC;IAC3C,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,cAAc;IAExD,MAAM,SAAS,GAAG,OAAO,KAAK,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,WAAW,EAAE,UAAU,CAAC,CAAC,CAAC;QACzF,OAAO,KAAK,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,MAAM,mBAAmB,CAAC,WAAW,EAAE,UAAU,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IAC3F,IAAI,SAAS,KAAK,IAAI;QACpB,MAAM,IAAI,KAAK,CAAC,oDAAoD,OAAO,EAAE,CAAC,CAAC;IACjF,SAAS,CAAC,IAAI,GAAG,KAAK,CAAC,OAAO,CAAC,aAAa,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC;IAC7D,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC;IAC7B,OAAO,SAAS,CAAC;AACnB,CAAC;AAED;;;iDAGiD;AACjD,MAAM,UAAU,iBAAiB,CAAC,SAAuB,EAAE,WAAyB;IAClF,MAAM,YAAY,GAAG,WAAW,CAAC,OAAO,CAAC,MAAM,CAAC;IAChD,MAAM,YAAY,GAAkB,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC;IAC5D,MAAM,uBAAuB,GAAa,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC;IAClE,MAAM,uBAAuB,GAAa,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC;IAElE,KAAK,IAAI,MAAM,GAAG,CAAC,EAAE,MAAM,GAAG,YAAY,EAAE,EAAE,MAAM,EAAE,CAAC;QACrD,MAAM,MAAM,GAAG,WAAW,CAAC,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC;QACnD,YAAY,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,UAAU,EAAiB,CAAC;QAC1D,uBAAuB,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;QAChE,MAAM,IAAI,GAAG,MAAM,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC;QACpF,uBAAuB,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,UAAU,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC;IACpE,CAAC;IAED,MAAM,iBAAiB,GAAG,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,UAAU,EAAE,WAAW,CAAC,QAAQ,CAAC,CAAC;IAC5E,MAAM,kBAAkB,GAAG,iBAAiB,CAAC,UAAU,EAAE,CAAC;IAC1D,KAAK,IAAI,QAAQ,GAAG,CAAC,EAAE,QAAQ,GAAG,WAAW,CAAC,QAAQ,EAAE,EAAE,QAAQ,EAAE,CAAC;QACnE,kBAAkB,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC;QACjC,KAAK,IAAI,MAAM,GAAG,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,CAAC;YACzD,MAAM,WAAW,GAAG,YAAY,CAAC,MAAM,CAAC,CAAC;YACzC,MAAM,aAAa,GAAW,WAAW,CAAC,CAAC,CAAC,YAAY,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YAC/E,IAAI,aAAa,KAAK,uBAAuB,CAAC,MAAM,CAAC;gBACnD,EAAE,kBAAkB,CAAC,QAAQ,CAAC,CAAC;QACnC,CAAC;QACD,kBAAkB,CAAC,QAAQ,CAAC,IAAI,SAAS,CAAC,MAAM,CAAC;IACnD,CAAC;IAED,OAAO,iBAAiB,CAAC;AAC3B,CAAC;AAED;;;gDAGgD;AAChD,MAAM,CAAC,KAAK,UAAU,mBAAmB,CACvC,SAAuB,EAAE,WAAyB;IAElD,MAAM,cAAc,GAAG,WAAW,CAAC,OAAO,CAAC,MAAM,EAAyB,CAAC;IAC3E,MAAM,SAAS,GAAG,MAAM,sBAAsB,CAAC,cAAc,EAAE,SAAS,CAAC,CAAC;IAC1E,OAAO,SAAS,CAAC;AACnB,CAAC"}

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

@@ -1,10 +1,7 @@
 import * as DG from 'datagrok-api/dg';
-/** Canonical gap symbol */
-export declare const GAP_SYMBOL: string;
+import { CellRendererBackBase } from '../cell-renderer-back-base';
 export type SeqSplittedBase = ArrayLike<string> & Iterable<string>;
 export interface ISeqSplitted {
-    get canonicals(): SeqSplittedBase;
-    get originals(): SeqSplittedBase;
     isGap(posIdx: number): boolean;
     /** */
     getCanonical(posIdx: number): string;
@@ -15,6 +12,7 @@ export interface ISeqSplitted {
 export interface INotationProvider {
     get splitter(): SplitterFunc;
     getHelm(seqCol: DG.Column<string>, options?: any): Promise<DG.Column<string>>;
+    createCellRendererBack(gridCol: DG.GridColumn | null, tableCol: DG.Column<string>): CellRendererBackBase<string>;
 }
 export type SeqColStats = {
     freq: MonomerFreqs;

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

@@ -1 +1 @@
-{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,2BAA2B;AAC3B,eAAO,MAAM,UAAU,EAAE,MAAW,CAAC;AAErC,MAAM,MAAM,eAAe,GAAG,SAAS,CAAC,MAAM,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC;AAEnE,MAAM,WAAW,YAAY;IAC3B,IAAI,UAAU,IAAI,eAAe,CAAC;IAClC,IAAI,SAAS,IAAI,eAAe,CAAC;IAEjC,KAAK,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC;IAE/B,MAAM;IACN,YAAY,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAAC;IAErC,uEAAuE;IACvE,WAAW,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAAC;IAEpC,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,QAAQ,IAAI,YAAY,CAAC;IAE7B,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,OAAO,CAAC,EAAE,GAAG,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;CAC/E;AAED,MAAM,MAAM,WAAW,GAAG;IAAE,IAAI,EAAE,YAAY,CAAC;IAAC,UAAU,EAAE,OAAO,CAAA;CAAE,CAAA;AACrE,MAAM,MAAM,YAAY,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,YAAY,CAAC;AACzD,MAAM,MAAM,YAAY,GAAG;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,CAAC;AAEnD,8BAA8B;AAC9B,qBAAa,aAAa;IACxB,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC;IACtB,MAAM,EAAE,MAAM,CAAC;gBAEH,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,EAAE,MAAM;CAKhE;AAED,yCAAyC;AACzC,qBAAa,gBAAiB,SAAQ,aAAa;IACjD,IAAI,EAAE,YAAY,CAAC;IACnB,4BAA4B;IAC5B,UAAU,EAAE,MAAM,CAAC;gBAEP,SAAS,EAAE,aAAa,EAAE,IAAI,EAAE,YAAY,EAAE,UAAU,EAAE,MAAM;CAK7E"}
+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,oBAAoB,EAAC,MAAM,4BAA4B,CAAC;AAEhE,MAAM,MAAM,eAAe,GAAG,SAAS,CAAC,MAAM,CAAC,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC;AAEnE,MAAM,WAAW,YAAY;IAC3B,KAAK,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC;IAE/B,MAAM;IACN,YAAY,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAAC;IAErC,uEAAuE;IACvE,WAAW,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAAC;IAEpC,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,QAAQ,IAAI,YAAY,CAAC;IAE7B,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,OAAO,CAAC,EAAE,GAAG,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;IAE9E,sBAAsB,CAAC,OAAO,EAAE,EAAE,CAAC,UAAU,GAAG,IAAI,EAAE,QAAQ,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,oBAAoB,CAAC,MAAM,CAAC,CAAC;CAClH;AAED,MAAM,MAAM,WAAW,GAAG;IAAE,IAAI,EAAE,YAAY,CAAC;IAAC,UAAU,EAAE,OAAO,CAAA;CAAE,CAAA;AACrE,MAAM,MAAM,YAAY,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,YAAY,CAAC;AACzD,MAAM,MAAM,YAAY,GAAG;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,CAAC;AAEnD,8BAA8B;AAC9B,qBAAa,aAAa;IACxB,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC;IACtB,MAAM,EAAE,MAAM,CAAC;gBAEH,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,EAAE,MAAM;CAKhE;AAED,yCAAyC;AACzC,qBAAa,gBAAiB,SAAQ,aAAa;IACjD,IAAI,EAAE,YAAY,CAAC;IACnB,4BAA4B;IAC5B,UAAU,EAAE,MAAM,CAAC;gBAEP,SAAS,EAAE,aAAa,EAAE,IAAI,EAAE,YAAY,EAAE,UAAU,EAAE,MAAM;CAK7E"}

package/src/utils/macromolecule/types.js

@@ -1,5 +1,3 @@
-/** 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 @@
-{"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAOA,2BAA2B;AAC3B,MAAM,CAAC,MAAM,UAAU,GAAW,EAAE,CAAC;AA6BrC,8BAA8B;AAC9B,MAAM,OAAO,aAAa;IAKxB,YAAY,IAAY,EAAE,QAAqB,EAAE,MAAc;QAC7D,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC;QACzB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC;IACvB,CAAC;CACF;AAED,yCAAyC;AACzC,MAAM,OAAO,gBAAiB,SAAQ,aAAa;IAKjD,YAAY,SAAwB,EAAE,IAAkB,EAAE,UAAkB;QAC1E,KAAK,CAAC,SAAS,CAAC,IAAI,EAAE,SAAS,CAAC,QAAQ,EAAE,SAAS,CAAC,MAAM,CAAC,CAAC;QAC5D,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,UAAU,GAAG,UAAU,CAAC;IAC/B,CAAC;CACF"}
+{"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAgCA,8BAA8B;AAC9B,MAAM,OAAO,aAAa;IAKxB,YAAY,IAAY,EAAE,QAAqB,EAAE,MAAc;QAC7D,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC;QACzB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC;IACvB,CAAC;CACF;AAED,yCAAyC;AACzC,MAAM,OAAO,gBAAiB,SAAQ,aAAa;IAKjD,YAAY,SAAwB,EAAE,IAAkB,EAAE,UAAkB;QAC1E,KAAK,CAAC,SAAS,CAAC,IAAI,EAAE,SAAS,CAAC,QAAQ,EAAE,SAAS,CAAC,MAAM,CAAC,CAAC;QAC5D,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,UAAU,GAAG,UAAU,CAAC;IAC/B,CAAC;CACF"}

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

@@ -6,8 +6,6 @@ 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;
@@ -16,8 +14,6 @@ export declare class StringListSeqSplitted implements ISeqSplitted {
 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;

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

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

@@ -1,8 +1,8 @@
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
-import { CandidateSimType, GAP_SYMBOL } from './types';
-import { ALPHABET, Alphabets, candidateAlphabets, monomerRe, NOTATION } from './consts';
-import { GapOriginals, SeqHandler } from '../seq-handler';
+import { CandidateSimType } from './types';
+import { ALPHABET, Alphabets, candidateAlphabets, GAP_SYMBOL, GapOriginals, monomerRe, NOTATION } from './consts';
+import { 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';
@@ -10,15 +10,14 @@ 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];
+        const om = this.mList[posIdx];
+        return om !== this.gapOriginalMonomer ? om : GAP_SYMBOL;
     }
     getOriginal(posIdx) {
         if (this.length <= posIdx)
@@ -32,8 +31,6 @@ export class StringListSeqSplitted {
 }
 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];
     }
@@ -69,13 +66,14 @@ function getStats(splitted, minLength) {
     const freq = {};
     let sameLength = true;
     let firstLength = null;
-    for (const mSeq of splitted) {
+    for (const seqSS of splitted) {
         if (firstLength == null)
-            firstLength = mSeq.length;
-        else if (mSeq.length !== firstLength)
+            firstLength = seqSS.length;
+        else if (seqSS.length !== firstLength)
             sameLength = false;
-        if (mSeq.length >= minLength) {
-            for (const cm of mSeq.canonicals) {
+        if (seqSS.length >= minLength) {
+            for (let posIdx = 0; posIdx < seqSS.length; ++posIdx) {
+                const cm = seqSS.getCanonical(posIdx);
                 if (!(cm in freq))
                     freq[cm] = 0;
                 freq[cm] += 1;

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

@@ -3,14 +3,12 @@ import { NOTATION } from './macromolecule';
 import { INotationProvider, ISeqSplitted, SeqColStats, SplitterFunc } from './macromolecule/types';
 import { MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import { mmDistanceFunctionType } from '@datagrok-libraries/ml/src/macromolecule-distance-functions/types';
+import { CellRendererBackBase } from './cell-renderer-back-base';
 export declare const SeqTemps: {
     /** Column's temp slot name for a SeqHandler object */
     seqHandler: string;
     notationProvider: string;
 };
-export declare const GapOriginals: {
-    [units: string]: string;
-};
 export type ConvertFunc = (src: string) => string;
 export type JoinerFunc = (src: ISeqSplitted) => string;
 /** Class for handling notation units in Macromolecule columns and
@@ -162,5 +160,6 @@ export declare class SeqHandler {
     private convertToHelm;
     /** Splits Helm sequence adjusting nucleotides to single char symbols. (!) Removes lone phosphorus. */
     private splitterAsHelmNucl;
+    getRendererBack(gridCol: DG.GridColumn | null, tableCol: DG.Column<string>): CellRendererBackBase<string>;
 }
 //# sourceMappingURL=seq-handler.d.ts.map

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

@@ -1 +1 @@
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package/src/utils/seq-handler.js

@@ -1,11 +1,11 @@
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
 import { ALPHABET, candidateAlphabets, getSplitterWithSeparator, NOTATION, positionSeparator, splitterAsFasta, splitterAsHelm, TAGS } from './macromolecule';
-import { GAP_SYMBOL, } from './macromolecule/types';
 import { detectAlphabet, splitterAsFastaSimple, StringListSeqSplitted } from './macromolecule/utils';
 import { mmDistanceFunctions, MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import { getMonomerLibHelper } from '../monomer-works/monomer-utils';
 import { HELM_WRAPPERS_REGEXP, PHOSPHATE_SYMBOL } from './const';
+import { GAP_SYMBOL, GapOriginals } from './macromolecule/consts';
 export const SeqTemps = new class {
     constructor() {
         /** Column's temp slot name for a SeqHandler object */
@@ -13,16 +13,12 @@ export const SeqTemps = new class {
         this.notationProvider = `seq-handler.notation-provider`;
     }
 }();
-export const GapOriginals = {
-    [NOTATION.FASTA]: '-',
-    [NOTATION.SEPARATOR]: '',
-    [NOTATION.HELM]: '*',
-};
 /** Class for handling notation units in Macromolecule columns and
  * conversion of notation systems in Macromolecule columns
  */
 export class SeqHandler {
     constructor(col) {
+        this.notationProvider = null;
         this._splitter = null;
         this.cached = true;
         this._splitted = null;
@@ -74,7 +70,10 @@ export class SeqHandler {
                     `tag '${TAGS.alphabetIsMultichar}' is mandatory.`);
             }
         }
-        this.notationProvider = this.column.temp[SeqTemps.notationProvider] ?? null;
+        if (this.column.meta.units === NOTATION.CUSTOM) {
+            // this.column.temp[SeqTemps.notationProvider] must be set at detector stage
+            this.notationProvider = this.column.temp[SeqTemps.notationProvider] ?? null;
+        }
         this.columnVersion = this.column.version;
     }
     static setUnitsToFastaColumn(uh) {
@@ -245,7 +244,8 @@ export class SeqHandler {
                     firstLength = mSeq.length;
                 else if (mSeq.length !== firstLength)
                     sameLength = false;
-                for (const cm of mSeq.canonicals) {
+                for (let posIdx = 0; posIdx < mSeq.length; ++posIdx) {
+                    const cm = mSeq.getCanonical(posIdx);
                     if (!(cm in freq))
                         freq[cm] = 0;
                     freq[cm] += 1;
@@ -296,6 +296,8 @@ export class SeqHandler {
             return NOTATION.SEPARATOR;
         else if (this.units.toLowerCase().startsWith(NOTATION.HELM))
             return NOTATION.HELM;
+        else if (this.units.toLowerCase().startsWith(NOTATION.CUSTOM))
+            return NOTATION.CUSTOM;
         else
             throw new Error(`Column '${this.column.name}' has unexpected notation '${this.units}'.`);
     }
@@ -324,7 +326,7 @@ export class SeqHandler {
     getNewColumn(tgtNotation, tgtSeparator, colName, data) {
         const col = this.column;
         const name = tgtNotation.toLowerCase() + '(' + col.name + ')';
-        const newColName = colName ?? col.dataFrame.columns.getUnusedName(name);
+        const newColName = colName ?? col.dataFrame?.columns.getUnusedName(name) ?? name;
         const newColumn = DG.Column.fromList('string', newColName, data ?? new Array(this.column.length).fill(''));
         newColumn.semType = DG.SEMTYPE.MACROMOLECULE;
         newColumn.meta.units = tgtNotation;
@@ -473,8 +475,9 @@ export class SeqHandler {
             const catI = colRawData[rowIdx];
             if (!(catI in catIdxSet)) {
                 catIdxSet.add(catI);
-                const monomers = this.getSplitted(rowIdx);
-                for (const cm of monomers.canonicals) {
+                const seqSS = this.getSplitted(rowIdx);
+                for (let posIdx = 0; posIdx < seqSS.length; ++posIdx) {
+                    const cm = seqSS.getCanonical(posIdx);
                     if (!peptidesSet.has(cm)) {
                         this.column.setTag(TAGS.isHelmCompatible, 'false');
                         return false;
@@ -694,6 +697,14 @@ export class SeqHandler {
         }
         return new StringListSeqSplitted(tgtMList.filter((om) => !!om), GapOriginals[NOTATION.HELM]);
     }
+    // Custom notation provider
+    getRendererBack(gridCol, tableCol) {
+        const temp = this.column.temp;
+        let res = temp.rendererBack;
+        if (!res)
+            res = temp.rendererBack = this.notationProvider.createCellRendererBack(gridCol, tableCol);
+        return res;
+    }
 }
 // -- joiners --
 function joinToSeparator(seqS, tgtSeparator, isHelm) {

package/src/utils/seq-handler.js.map

@@ -1 +1 @@
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package/src/utils/seq-helper.d.ts

@@ -1,26 +1,17 @@
 import * as DG from 'datagrok-api/dg';
-export declare const SUBSTRUCT_COL = "substruct-col";
-export interface ISubstruct {
-    atoms?: number[];
-    bonds?: number[];
-    highlightAtomColors?: {
-        [key: number]: number[] | null;
-    };
-    highlightBondColors?: {
-        [key: number]: number[] | null;
-    };
-}
-export type ToAtomicLevelResType = {
-    molCol: DG.Column<string>;
-    molHighlightCol: DG.Column<object>;
+import { IMonomerLibBase } from '../types';
+export type ToAtomicLevelRes = {
+    molCol: DG.Column<string> | null;
+    warnings: string[];
 };
 export interface ISeqHelper {
     /**
      * @param helmCol {DG.Column<string>} Macromolecules in Helm format
      * @param chiralityEngine {boolean} [true] Use chirality engine for molecule visualization
      * @param highlight {boolean} [true] Generates molHighlightCol of result
+     * @param overrideMonomerLib {IMonomerLibBase} [null] Override monomer library for monomers from reactions
      **/
-    helmToAtomicLevel(helmCol: DG.Column<string>, chiralityEngine?: boolean, highlight?: boolean): Promise<ToAtomicLevelResType>;
+    helmToAtomicLevel(helmCol: DG.Column<string>, chiralityEngine?: boolean, highlight?: boolean, overrideMonomerLib?: IMonomerLibBase): Promise<ToAtomicLevelRes>;
 }
 export declare function getSeqHelper(): Promise<ISeqHelper>;
 //# sourceMappingURL=seq-helper.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"seq-helper.d.ts","sourceRoot":"","sources":["seq-helper.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,eAAO,MAAM,aAAa,kBAAkB,CAAC;AAE7C,MAAM,WAAW,UAAU;IACzB,KAAK,CAAC,EAAE,MAAM,EAAE,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,EAAE,CAAC;IACjB,mBAAmB,CAAC,EAAE;QAAE,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,IAAI,CAAA;KAAE,CAAC;IACzD,mBAAmB,CAAC,EAAE;QAAE,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,IAAI,CAAA;KAAE,CAAA;CACzD;AAED,MAAM,MAAM,oBAAoB,GAAG;IACjC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;IAC1B,eAAe,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;CACpC,CAAA;AAED,MAAM,WAAW,UAAU;IACzB;;;;QAII;IACJ,iBAAiB,CACf,OAAO,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,eAAe,CAAC,EAAE,OAAO,EAAE,SAAS,CAAC,EAAE,OAAO,GACzE,OAAO,CAAC,oBAAoB,CAAC,CAAC;CAClC;AAED,wBAAsB,YAAY,IAAI,OAAO,CAAC,UAAU,CAAC,CAOxD"}
+{"version":3,"file":"seq-helper.d.ts","sourceRoot":"","sources":["seq-helper.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AACtC,OAAO,EAAC,eAAe,EAAC,MAAM,UAAU,CAAC;AAEzC,MAAM,MAAM,gBAAgB,GAAG;IAC7B,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,IAAI,CAAC;IACjC,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB,CAAA;AAED,MAAM,WAAW,UAAU;IACzB;;;;;QAKI;IACJ,iBAAiB,CACf,OAAO,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,eAAe,CAAC,EAAE,OAAO,EAAE,SAAS,CAAC,EAAE,OAAO,EAAE,kBAAkB,CAAC,EAAE,eAAe,GAC/G,OAAO,CAAC,gBAAgB,CAAC,CAAC;CAC9B;AAED,wBAAsB,YAAY,IAAI,OAAO,CAAC,UAAU,CAAC,CAOxD"}

package/src/utils/seq-helper.js

@@ -1,5 +1,4 @@
 import * as DG from 'datagrok-api/dg';
-export const SUBSTRUCT_COL = 'substruct-col';
 export async function getSeqHelper() {
     const packageName = 'Bio';
     const funcList = DG.Func.find({ package: packageName, name: `getSeqHelper` });

package/src/utils/seq-helper.js.map

@@ -1 +1 @@
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