@datagrok-libraries/bio 5.33.1 → 5.34.0

package/CHANGELOG.md

@@ -0,0 +1,15 @@
+# `lib` changelog
+
+## 5.34.0 (2023-07-21)
+
+This release focuses on improving feature stability and usability.
+
+*Dependency: datgarok-api >= 1.10.2*
+
+### Features
+
+* Add NotationConverter.getConverter() getting a function to convert a single value  
+
+### Breaking change
+
+* Remove NotationConverter.convertStringToHelm()

package/package.json

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.33.1",
+  "version": "5.34.0",
   "description": "",
   "dependencies": {
     "@datagrok-libraries/gridext": "^1.3.54",

package/src/monomer-works/to-atomic-level.js

@@ -1,6 +1,7 @@
 /* Do not change these import lines to match external modules in webpack configuration */
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
+import { NOTATION } from '../utils/macromolecule/consts';
 import { NotationConverter } from '../utils/notation-converter';
 import { UnitsHandler } from '../utils/units-handler';
 import { getFormattedMonomerLib, keepPrecision } from './to-atomic-level-utils';
@@ -30,7 +31,7 @@ export async function _toAtomicLevel(df, seqCol, monomerLib) {
     // convert 'helm' to 'separator' units
     if (seqUh.isHelm()) {
         const converter = new NotationConverter(seqCol);
-        srcCol = converter.convert("separator" /* NOTATION.SEPARATOR */, '.');
+        srcCol = converter.convert(NOTATION.SEPARATOR, '.');
         srcCol.name = seqCol.name; // Replace converted col name 'separator(<original>)' to '<original>';
     }
     const srcUh = UnitsHandler.getOrCreate(srcCol);

package/src/monomer-works/to-atomic-level.js.map

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

@@ -32,7 +32,7 @@ export class MonomerPlacer {
                 this._rowsProcessed = DG.BitSet.create(this.col.length);
             }));
             this.subs.push(grok.events.onViewRemoved.subscribe((view) => {
-                if (this.grid?.view.id === view.id)
+                if (this.grid?.view?.id === view.id)
                     this.destroy();
             }));
         }

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

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

@@ -1,5 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import { UnitsHandler } from './units-handler';
+import { NOTATION } from './macromolecule/consts';
 /** Class for parsing FASTA files */
 export class FastaFileHandler {
     // private _columnsParsed: boolean = false;
@@ -42,7 +43,7 @@ export class FastaFileHandler {
         const descriptionsArrayCol = DG.Column.fromStrings('description', this.descriptionsArray);
         const sequenceCol = DG.Column.fromStrings('sequence', this.sequencesArray);
         sequenceCol.semType = DG.SEMTYPE.MACROMOLECULE;
-        sequenceCol.setTag(DG.TAGS.UNITS, "fasta" /* NOTATION.FASTA */);
+        sequenceCol.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
         // here should go the code from units handler
         const uh = UnitsHandler.getOrCreate(sequenceCol);
         return [DG.DataFrame.fromColumns([

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

@@ -1 +1 @@
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+{"version":3,"file":"fasta-handler.js","sourceRoot":"","sources":["fasta-handler.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,YAAY,EAAC,MAAM,iBAAiB,CAAC;AAC7C,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAGhD,oCAAoC;AACpC,MAAM,OAAO,gBAAgB;IAI3B,2CAA2C;IAE3C,IAAW,iBAAiB,KAAe,OAAO,IAAI,CAAC,kBAAkB,CAAC,CAAC,CAAC;IAE5E,IAAW,cAAc,KAAe,OAAO,IAAI,CAAC,eAAe,CAAC,CAAC,CAAC;IAEtE;;;;;;;OAOG;IACK,kBAAkB,CACxB,eAAuB,EACvB,aAAqB;QAErB,MAAM,GAAG,GAAG,IAAI,CAAC,YAAY,CAAC,KAAK,CAAC,eAAe,EAAE,aAAa,CAAC,CAAC;QACpE,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;QACjC,OAAO,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IAC3B,CAAC;IAED,2DAA2D;IACnD,YAAY;QAClB,MAAM,KAAK,GAAG,WAAW,CAAC,CAAC,4CAA4C;QAEvE,IAAI,eAAe,GAAG,CAAC,CAAC;QACxB,IAAI,KAAK,CAAC,CAAC,mDAAmD;QAC9D,OAAO,KAAK,GAAG,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,EAAE;YAC5C,MAAM,WAAW,GAAG,IAAI,CAAC,YAAY,CAAC,SAAS,CAAC,KAAK,CAAC,KAAK,GAAG,CAAC,EAAE,KAAK,CAAC,SAAS,CAAC,CAAC;YAClF,IAAI,CAAC,kBAAkB,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC;YAC1C,IAAI,eAAe,KAAK,CAAC;gBACvB,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,IAAI,CAAC,kBAAkB,CAAC,eAAe,EAAE,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC;YACnF,eAAe,GAAG,KAAK,CAAC,SAAS,GAAG,CAAC,CAAC;SACvC;QACD,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,IAAI,CAAC,kBAAkB,CAAC,eAAe,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;QAExE,8BAA8B;IAChC,CAAC;IAED;;;;OAIG;IACI,WAAW;QAChB,MAAM,oBAAoB,GAAG,EAAE,CAAC,MAAM,CAAC,WAAW,CAAC,aAAa,EAAE,IAAI,CAAC,iBAAiB,CAAC,CAAC;QAC1F,MAAM,WAAW,GAAG,EAAE,CAAC,MAAM,CAAC,WAAW,CAAC,UAAU,EAAE,IAAI,CAAC,cAAc,CAAC,CAAC;QAC3E,WAAW,CAAC,OAAO,GAAG,EAAE,CAAC,OAAO,CAAC,aAAa,CAAC;QAC/C,WAAW,CAAC,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC,KAAK,EAAE,QAAQ,CAAC,KAAK,CAAC,CAAC;QAElD,6CAA6C;QAC7C,MAAM,EAAE,GAAG,YAAY,CAAC,WAAW,CAAC,WAAW,CAAC,CAAC;QAEjD,OAAO,CAAC,EAAE,CAAC,SAAS,CAAC,WAAW,CAAC;gBAC/B,oBAAoB;gBACpB,WAAW;aACZ,CAAC,CAAC,CAAC;IACN,CAAC;IAED,YAAY,WAAmB;QA/DvB,uBAAkB,GAAa,EAAE,CAAC,CAAC,4BAA4B;QAC/D,oBAAe,GAAa,EAAE,CAAC,CAAC,wBAAwB;QA+D9D,IAAI,CAAC,YAAY,GAAG,WAAW,CAAC;QAChC,IAAI,CAAC,YAAY,EAAE,CAAC;IACtB,CAAC;CACF"}

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

@@ -1,6 +1,6 @@
 import { CandidateType } from './types';
 /** enum type to simplify setting "user-friendly" notation if necessary */
-export declare const enum NOTATION {
+export declare enum NOTATION {
     FASTA = "fasta",
     SEPARATOR = "separator",
     HELM = "helm"

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

@@ -1 +1 @@
-{"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAKA,OAAO,EAAC,aAAa,EAAC,MAAM,SAAS,CAAC;AAEtC,0EAA0E;AAC1E,0BAAkB,QAAQ;IACxB,KAAK,UAAU;IACf,SAAS,cAAc;IACvB,IAAI,SAAS;CACd;AAED,0BAAkB,SAAS;IACzB,OAAO,YAAY;IACnB,GAAG,QAAQ;CACZ;AAED,0BAAkB,QAAQ;IACxB,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,EAAE,OAAO;IACT,cAAc;IACd,EAAE,OAAO;CACV;AAED,0BAAkB,IAAI;IACpB,OAAO,YAAY;IACnB,QAAQ,aAAa;IACrB,YAAY,kBAAkB;IAC9B,mBAAmB,yBAAyB;IAC5C,SAAS,cAAc;IACvB,gBAAgB,sBAAsB;CACvC;AAED,eAAO,MAAM,SAAS,EAAE,MAAkC,CAAC;AAE3D,eAAO,MAAM,SAAS;;;;;;CASnB,CAAC;AAEJ,eAAO,MAAM,kBAAkB,EAAE,aAAa,EAI7C,CAAC"}
+{"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAKA,OAAO,EAAC,aAAa,EAAC,MAAM,SAAS,CAAC;AAEtC,0EAA0E;AAC1E,oBAAY,QAAQ;IAClB,KAAK,UAAU;IACf,SAAS,cAAc;IACvB,IAAI,SAAS;CACd;AAED,0BAAkB,SAAS;IACzB,OAAO,YAAY;IACnB,GAAG,QAAQ;CACZ;AAED,0BAAkB,QAAQ;IACxB,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,EAAE,OAAO;IACT,cAAc;IACd,EAAE,OAAO;CACV;AAED,0BAAkB,IAAI;IACpB,OAAO,YAAY;IACnB,QAAQ,aAAa;IACrB,YAAY,kBAAkB;IAC9B,mBAAmB,yBAAyB;IAC5C,SAAS,cAAc;IACvB,gBAAgB,sBAAsB;CACvC;AAED,eAAO,MAAM,SAAS,EAAE,MAAkC,CAAC;AAE3D,eAAO,MAAM,SAAS;;;;;;CASnB,CAAC;AAEJ,eAAO,MAAM,kBAAkB,EAAE,aAAa,EAI7C,CAAC"}

package/src/utils/macromolecule/consts.js

@@ -1,4 +1,11 @@
 import { CandidateType } from './types';
+/** enum type to simplify setting "user-friendly" notation if necessary */
+export var NOTATION;
+(function (NOTATION) {
+    NOTATION["FASTA"] = "fasta";
+    NOTATION["SEPARATOR"] = "separator";
+    NOTATION["HELM"] = "helm";
+})(NOTATION || (NOTATION = {}));
 export const monomerRe = /(\[[A-Za-z0-9-_]+\]|.)/g;
 export const Alphabets = new class {
     constructor() {

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

@@ -1 +1 @@
-{"version":3,"file":"consts.js","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAKA,OAAO,EAAC,aAAa,EAAC,MAAM,SAAS,CAAC;AA+BtC,MAAM,CAAC,MAAM,SAAS,GAAW,yBAAyB,CAAC;AAE3D,MAAM,CAAC,MAAM,SAAS,GAAG,IAAI;IAAA;QAC3B,UAAK,GAAG;YACN,OAAO,EAAE,IAAI,GAAG,CAAS;gBACvB,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG;gBAChD,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG;aACjD,CAAC;YACF,GAAG,EAAE,IAAI,GAAG,CAAS,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC;YAC1C,GAAG,EAAE,IAAI,GAAG,CAAS,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC;SAC3C,CAAC;IACJ,CAAC;CAAA,EAAE,CAAC;AAEJ,MAAM,CAAC,MAAM,kBAAkB,GAAoB;IACjD,IAAI,aAAa,yBAAc,SAAS,CAAC,KAAK,CAAC,OAAO,EAAE,IAAI,CAAC;IAC7D,IAAI,aAAa,2BAAe,SAAS,CAAC,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC;IAC1D,IAAI,aAAa,2BAAe,SAAS,CAAC,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC;CAC3D,CAAC"}
+{"version":3,"file":"consts.js","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAKA,OAAO,EAAC,aAAa,EAAC,MAAM,SAAS,CAAC;AAEtC,0EAA0E;AAC1E,MAAM,CAAN,IAAY,QAIX;AAJD,WAAY,QAAQ;IAClB,2BAAe,CAAA;IACf,mCAAuB,CAAA;IACvB,yBAAa,CAAA;AACf,CAAC,EAJW,QAAQ,KAAR,QAAQ,QAInB;AAwBD,MAAM,CAAC,MAAM,SAAS,GAAW,yBAAyB,CAAC;AAE3D,MAAM,CAAC,MAAM,SAAS,GAAG,IAAI;IAAA;QAC3B,UAAK,GAAG;YACN,OAAO,EAAE,IAAI,GAAG,CAAS;gBACvB,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG;gBAChD,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG;aACjD,CAAC;YACF,GAAG,EAAE,IAAI,GAAG,CAAS,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC;YAC1C,GAAG,EAAE,IAAI,GAAG,CAAS,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC;SAC3C,CAAC;IACJ,CAAC;CAAA,EAAE,CAAC;AAEJ,MAAM,CAAC,MAAM,kBAAkB,GAAoB;IACjD,IAAI,aAAa,yBAAc,SAAS,CAAC,KAAK,CAAC,OAAO,EAAE,IAAI,CAAC;IAC7D,IAAI,aAAa,2BAAe,SAAS,CAAC,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC;IAC1D,IAAI,aAAa,2BAAe,SAAS,CAAC,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC;CAC3D,CAAC"}

package/src/utils/macromolecule/index.js

@@ -1,2 +1,3 @@
+export { NOTATION, } from './consts';
 export { getSplitter, splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, getAlphabet, getAlphabetSimilarity, monomerToShort, pickUpPalette, pickUpSeqCol, getPaletteByType, getSplitterForColumn } from './utils';
 //# sourceMappingURL=index.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAgBA,OAAO,EACL,WAAW,EACX,eAAe,EACf,wBAAwB,EACxB,cAAc,EACd,WAAW,EACX,qBAAqB,EACrB,cAAc,EACd,aAAa,EACb,YAAY,EACZ,gBAAgB,EAEhB,oBAAoB,EACrB,MAAM,SAAS,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AASA,OAAO,EAEL,QAAQ,GAGT,MAAM,UAAU,CAAC;AAElB,OAAO,EACL,WAAW,EACX,eAAe,EACf,wBAAwB,EACxB,cAAc,EACd,WAAW,EACX,qBAAqB,EACrB,cAAc,EACd,aAAa,EACb,YAAY,EACZ,gBAAgB,EAEhB,oBAAoB,EACrB,MAAM,SAAS,CAAC"}

package/src/utils/macromolecule/utils.js

@@ -1,7 +1,7 @@
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
 import { CandidateSimType } from './types';
-import { Alphabets, candidateAlphabets, monomerRe } from './consts';
+import { Alphabets, candidateAlphabets, monomerRe, NOTATION } from './consts';
 import { UnitsHandler } from '../units-handler';
 import { Vector } from '@datagrok-libraries/utils/src/type-declarations';
 import { vectorDotProduct, vectorLength } from '@datagrok-libraries/utils/src/vector-operations';
@@ -92,11 +92,11 @@ export function splitterAsHelm(seq) {
  * @return {SplitterFunc}
  */
 export function getSplitter(units, separator, limit = undefined) {
-    if (units.toLowerCase().startsWith("fasta" /* NOTATION.FASTA */))
+    if (units.toLowerCase().startsWith(NOTATION.FASTA))
         return splitterAsFasta;
-    else if (units.toLowerCase().startsWith("separator" /* NOTATION.SEPARATOR */))
+    else if (units.toLowerCase().startsWith(NOTATION.SEPARATOR))
         return getSplitterWithSeparator(separator, limit);
-    else if (units.toLowerCase().startsWith("helm" /* NOTATION.HELM */))
+    else if (units.toLowerCase().startsWith(NOTATION.HELM))
         return splitterAsHelm;
     else
         throw new Error(`Unexpected units ${units} .`);

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

@@ -1 +1 @@
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package/src/utils/notation-converter.d.ts

@@ -2,6 +2,7 @@ import * as DG from 'datagrok-api/dg';
 import { UnitsHandler } from './units-handler';
 import { SplitterFunc } from './macromolecule/types';
 import { NOTATION } from './macromolecule/consts';
+export type ConvertFunc = (src: string) => string;
 /** Class for handling conversion of notation systems in Macromolecule columns */
 export declare class NotationConverter extends UnitsHandler {
     private _splitter;
@@ -9,45 +10,6 @@ export declare class NotationConverter extends UnitsHandler {
     toFasta(targetNotation: NOTATION): boolean;
     toSeparator(targetNotation: NOTATION): boolean;
     toHelm(targetNotation: NOTATION): boolean;
-    /**
-     * Convert a Macromolecule column from FASTA to SEPARATOR notation
-     *
-     * @param {string} separator  A specific separator to be used
-     * @param {string} fastaGapSymbol  Gap symbol in FASTA, '-' by default
-     * @return {DG.Column}        A new column in SEPARATOR notation
-     */
-    private convertFastaToSeparator;
-    /**
-     * Get the wrapper strings for HELM, depending on the type of the
-     * macromolecule (peptide, DNA, RNA)
-     *
-     * @return {string[]} Array of wrappers
-     */
-    private getHelmWrappers;
-    private convertToHelmHelper;
-    /**
-     * Convert a string with SEPARATOR/FASTA notation to HELM
-     *
-     * @param {string} sourcePolymer  A string to be converted
-     * @param {string | null} sourceGapSymbol  An optional gap symbol, set to
-     * default values ('-' for FASTA and '' for SEPARATOR) unless specified
-     * @return {string}  The target HELM string
-     */
-    convertStringToHelm(sourcePolymer: string, sourceGapSymbol?: string | null): string;
-    /**
-     * Convert a column to HELM
-     *
-     * @param {string | null} sourceGapSymbol
-     * @return {DG.Column}
-     */
-    private convertToHelm;
-    /**
-     * Convert SEPARATOR column to FASTA notation
-     *
-     * @param {string | null} fastaGapSymbol Optional gap symbol for FASTA
-     * @return {DG.Column}  Converted column
-     */
-    private convertSeparatorToFasta;
     /**
      *  Convert HELM string to FASTA/SEPARATOR
      *
@@ -59,24 +21,14 @@ export declare class NotationConverter extends UnitsHandler {
      * @return {string} Converted string
      */
     convertHelmToFastaSeparator(helmPolymer: string, tgtNotation: string, tgtSeparator?: string, tgtGapSymbol?: string): string;
-    /**
-     *  Convert HELM column to FASTA/SEPARATOR
-     *
-     * @param {string} tgtNotation    Target notation: FASTA or SEPARATOR
-     * @param {string} tgtSeparator   Optional target separator (for HELM ->
-     * @param {string | null} tgtGapSymbol   Optional target gap symbol
-     * SEPARATOR)
-     * @return {DG.Column} Converted column
-     */
-    private convertHelm;
-    private convertHelmToSeparator;
     /** Dispatcher method for notation conversion
      *
      * @param {NOTATION} tgtNotation   Notation we want to convert to
      * @param {string | null} tgtSeparator   Possible separator
      * @return {DG.Column}                Converted column
      */
-    convert(tgtNotation: NOTATION, tgtSeparator?: string | null): DG.Column;
+    convert(tgtNotation: NOTATION, tgtSeparator?: string): DG.Column;
     constructor(col: DG.Column);
+    getConverter(tgtUnits: NOTATION, tgtSeparator?: string | null): ConvertFunc;
 }
 //# sourceMappingURL=notation-converter.d.ts.map

package/src/utils/notation-converter.d.ts.map

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package/src/utils/notation-converter.js

@@ -1,5 +1,6 @@
-import * as DG from 'datagrok-api/dg';
-import { UnitsHandler } from './units-handler';
+import wu from 'wu';
+import { GapSymbols, UnitsHandler } from './units-handler';
+import { NOTATION } from './macromolecule/consts';
 import { getSplitterForColumn } from './macromolecule/utils';
 /** Class for handling conversion of notation systems in Macromolecule columns */
 export class NotationConverter extends UnitsHandler {
@@ -8,134 +9,9 @@ export class NotationConverter extends UnitsHandler {
             this._splitter = getSplitterForColumn(this.column);
         return this._splitter;
     }
-    toFasta(targetNotation) { return targetNotation === "fasta" /* NOTATION.FASTA */; }
-    toSeparator(targetNotation) { return targetNotation === "separator" /* NOTATION.SEPARATOR */; }
-    toHelm(targetNotation) { return targetNotation === "helm" /* NOTATION.HELM */; }
-    /**
-     * Convert a Macromolecule column from FASTA to SEPARATOR notation
-     *
-     * @param {string} separator  A specific separator to be used
-     * @param {string} fastaGapSymbol  Gap symbol in FASTA, '-' by default
-     * @return {DG.Column}        A new column in SEPARATOR notation
-     */
-    convertFastaToSeparator(separator, fastaGapSymbol = null) {
-        if (fastaGapSymbol === null)
-            fastaGapSymbol = this.defaultGapSymbol;
-        const newColumn = this.getNewColumn("separator" /* NOTATION.SEPARATOR */, separator);
-        // assign the values to the newly created empty column
-        newColumn.init((idx) => {
-            const fastaPolymer = this.column.get(idx);
-            const fastaMonomersArray = this.splitter(fastaPolymer);
-            for (let i = 0; i < fastaMonomersArray.length; i++) {
-                if (fastaMonomersArray[i] === fastaGapSymbol)
-                    fastaMonomersArray[i] = UnitsHandler._defaultGapSymbolsDict.SEPARATOR;
-            }
-            return fastaMonomersArray.join(separator);
-        });
-        newColumn.setTag(DG.TAGS.UNITS, "separator" /* NOTATION.SEPARATOR */);
-        return newColumn;
-    }
-    /**
-     * Get the wrapper strings for HELM, depending on the type of the
-     * macromolecule (peptide, DNA, RNA)
-     *
-     * @return {string[]} Array of wrappers
-     */
-    getHelmWrappers() {
-        const prefix = (this.isDna()) ? 'DNA1{' :
-            (this.isRna() || this.isHelmCompatible()) ? 'RNA1{' : 'PEPTIDE1{';
-        // (this.isPeptide()) ? 'PEPTIDE1{' :
-        // 'Unknown'; // this case should be handled as exceptional
-        // if (prefix === 'Unknown')
-        //   throw new Error('Neither peptide, nor nucleotide');
-        const postfix = '}$$$$';
-        const leftWrapper = (this.isDna()) ? 'D(' :
-            (this.isRna()) ? 'R(' : ''; // no wrapper for peptides
-        const rightWrapper = (this.isDna() || this.isRna()) ? ')P' : ''; // no wrapper for peptides
-        return [prefix, leftWrapper, rightWrapper, postfix];
-    }
-    // A helper function for converting strings to HELM
-    convertToHelmHelper(sourcePolymer, sourceGapSymbol, prefix, leftWrapper, rightWrapper, postfix) {
-        const monomerArray = this.splitter(sourcePolymer);
-        const monomerHelmArray = monomerArray.map((mm) => {
-            if (!mm || mm === sourceGapSymbol) {
-                return UnitsHandler._defaultGapSymbolsDict.HELM;
-            }
-            else {
-                return mm.length == 1 ? `${leftWrapper}${mm}${rightWrapper}` :
-                    `${leftWrapper}[${mm}]${rightWrapper}`;
-            }
-        });
-        return `${prefix}${monomerHelmArray.join('.')}${postfix}`;
-    }
-    /**
-     * Convert a string with SEPARATOR/FASTA notation to HELM
-     *
-     * @param {string} sourcePolymer  A string to be converted
-     * @param {string | null} sourceGapSymbol  An optional gap symbol, set to
-     * default values ('-' for FASTA and '' for SEPARATOR) unless specified
-     * @return {string}  The target HELM string
-     */
-    convertStringToHelm(sourcePolymer, sourceGapSymbol = null) {
-        if (sourceGapSymbol === null)
-            sourceGapSymbol = this.defaultGapSymbol;
-        const [prefix, leftWrapper, rightWrapper, postfix] = this.getHelmWrappers();
-        return this.convertToHelmHelper(sourcePolymer, sourceGapSymbol, prefix, leftWrapper, rightWrapper, postfix);
-    }
-    /**
-     * Convert a column to HELM
-     *
-     * @param {string | null} sourceGapSymbol
-     * @return {DG.Column}
-     */
-    convertToHelm(sourceGapSymbol = null) {
-        if (sourceGapSymbol === null)
-            sourceGapSymbol = this.defaultGapSymbol;
-        const [prefix, leftWrapper, rightWrapper, postfix] = this.getHelmWrappers();
-        const newColumn = this.getNewColumn("helm" /* NOTATION.HELM */);
-        // assign the values to the empty column
-        newColumn.init((idx) => {
-            const sourcePolymer = this.column.get(idx);
-            return this.convertToHelmHelper(sourcePolymer, sourceGapSymbol, prefix, leftWrapper, rightWrapper, postfix);
-        });
-        newColumn.setTag(DG.TAGS.UNITS, "helm" /* NOTATION.HELM */);
-        return newColumn;
-    }
-    /**
-     * Convert SEPARATOR column to FASTA notation
-     *
-     * @param {string | null} fastaGapSymbol Optional gap symbol for FASTA
-     * @return {DG.Column}  Converted column
-     */
-    convertSeparatorToFasta(fastaGapSymbol = null) {
-        if (fastaGapSymbol === null)
-            fastaGapSymbol = UnitsHandler._defaultGapSymbolsDict.FASTA;
-        const newColumn = this.getNewColumn("fasta" /* NOTATION.FASTA */);
-        // assign the values to the empty column
-        newColumn.init((idx) => {
-            const separatorPolymer = this.column.get(idx);
-            // items can be monomers or separators
-            const separatorItemsArray = this.splitter(separatorPolymer);
-            const fastaMonomersArray = [];
-            for (let i = 0; i < separatorItemsArray.length; i++) {
-                const item = separatorItemsArray[i];
-                if (item.length === 0) {
-                    fastaMonomersArray.push(fastaGapSymbol);
-                }
-                else if (item.length > 1) {
-                    // the case of a multi-character monomer
-                    const monomer = '[' + item + ']';
-                    fastaMonomersArray.push(monomer);
-                }
-                else {
-                    fastaMonomersArray.push(item);
-                }
-            }
-            return fastaMonomersArray.join('');
-        });
-        newColumn.setTag(DG.TAGS.UNITS, "fasta" /* NOTATION.FASTA */);
-        return newColumn;
-    }
+    toFasta(targetNotation) { return targetNotation === NOTATION.FASTA; }
+    toSeparator(targetNotation) { return targetNotation === NOTATION.SEPARATOR; }
+    toHelm(targetNotation) { return targetNotation === NOTATION.HELM; }
     /**
      *  Convert HELM string to FASTA/SEPARATOR
      *
@@ -149,8 +25,8 @@ export class NotationConverter extends UnitsHandler {
     convertHelmToFastaSeparator(helmPolymer, tgtNotation, tgtSeparator, tgtGapSymbol) {
         if (!tgtGapSymbol) {
             tgtGapSymbol = (this.toFasta(tgtNotation)) ?
-                UnitsHandler._defaultGapSymbolsDict.FASTA :
-                UnitsHandler._defaultGapSymbolsDict.SEPARATOR;
+                GapSymbols[NOTATION.FASTA] :
+                GapSymbols[NOTATION.SEPARATOR];
         }
         if (!tgtSeparator)
             tgtSeparator = (this.toFasta(tgtNotation)) ? '' : this.separator;
@@ -163,7 +39,7 @@ export class NotationConverter extends UnitsHandler {
             let item = helmItemsArray[i];
             if (isNucleotide)
                 item = item.replace(helmWrappersRe, '');
-            if (item === UnitsHandler._defaultGapSymbolsDict.HELM) {
+            if (item === GapSymbols[NOTATION.HELM]) {
                 tgtMonomersArray.push(tgtGapSymbol);
             }
             else if (this.toFasta(tgtNotation) && item.length > 1) {
@@ -177,72 +53,97 @@ export class NotationConverter extends UnitsHandler {
         }
         return tgtMonomersArray.join(tgtSeparator);
     }
-    /**
-     *  Convert HELM column to FASTA/SEPARATOR
-     *
-     * @param {string} tgtNotation    Target notation: FASTA or SEPARATOR
-     * @param {string} tgtSeparator   Optional target separator (for HELM ->
-     * @param {string | null} tgtGapSymbol   Optional target gap symbol
-     * SEPARATOR)
-     * @return {DG.Column} Converted column
-     */
-    convertHelm(tgtNotation, tgtSeparator, tgtGapSymbol) {
-        // This function must not contain calls of isDna() and isRna(), for
-        // source helm columns may contain RNA, DNA and PT across different rows
-        const newColumn = this.getNewColumn(tgtNotation, tgtSeparator);
-        // assign the values to the empty column
-        newColumn.init((idx) => {
-            const helmPolymer = this.column.get(idx);
-            return this.convertHelmToFastaSeparator(helmPolymer, tgtNotation, tgtSeparator, tgtGapSymbol);
-            // we cannot use isDna() or isRna() because source helm columns can
-            // contain DNA, RNA and PT in different cells, so the corresponding
-            // tags cannot be set for the whole column
-        });
-        // TAGS.aligned is mandatory for columns of NOTATION.FASTA and NOTATION.SEPARATOR
-        const splitter = getSplitterForColumn(newColumn);
-        const aligned = this.stats.sameLength ? 'SEQ.MSA' : 'SEQ';
-        newColumn.setTag("aligned" /* TAGS.aligned */, aligned);
-        return newColumn;
-    }
-    convertHelmToSeparator() {
-        // TODO: implementatioreturn this.getNewColumn();
-        return this.getNewColumn("separator" /* NOTATION.SEPARATOR */);
-    }
     /** Dispatcher method for notation conversion
      *
      * @param {NOTATION} tgtNotation   Notation we want to convert to
      * @param {string | null} tgtSeparator   Possible separator
      * @return {DG.Column}                Converted column
      */
-    convert(tgtNotation, tgtSeparator = null) {
-        // possible exceptions
-        if (this.notation === tgtNotation)
-            throw new Error('tgt notation is invalid');
-        if (this.toSeparator(tgtNotation) && tgtSeparator === null)
-            throw new Error('tgt separator is not specified');
-        if (this.isFasta() && this.toSeparator(tgtNotation) && tgtSeparator !== null) {
-            return this.convertFastaToSeparator(tgtSeparator);
-        }
-        else if ((this.isFasta() || this.isSeparator()) && this.toHelm(tgtNotation)) {
-            return this.convertToHelm();
-        }
-        else if (this.isSeparator() && this.toFasta(tgtNotation)) {
-            return this.convertSeparatorToFasta();
-        }
-        else if (this.isHelm() && this.toFasta(tgtNotation)) { // the case of HELM
-            return this.convertHelm(tgtNotation);
-        }
-        else if (this.isHelm() && this.toSeparator(tgtNotation)) {
-            return this.convertHelm(tgtNotation, tgtSeparator);
-        }
-        else {
-            throw new Error('Not supported conversion ' +
-                `from source notation '${this.notation}' to target notation '${tgtNotation}'.`);
-        }
+    convert(tgtNotation, tgtSeparator) {
+        const convert = this.getConverter(tgtNotation, tgtSeparator);
+        const newColumn = this.getNewColumn(tgtNotation, tgtSeparator);
+        // assign the values to the newly created empty column
+        newColumn.init((rowI) => { return convert(this.column.get(rowI)); });
+        // newColumn.setTag(DG.TAGS.UNITS, NOTATION.SEPARATOR);
+        return newColumn;
     }
     constructor(col) {
         super(col);
         this._splitter = null;
     }
+    getConverter(tgtUnits, tgtSeparator = null) {
+        if (tgtUnits === NOTATION.SEPARATOR && !tgtSeparator)
+            throw new Error(`Target separator is not specified for target units '${NOTATION.SEPARATOR}'.`);
+        const srcUh = this;
+        if (tgtUnits === NOTATION.FASTA)
+            return function (src) { return convertToFasta(srcUh, src); };
+        if (tgtUnits === NOTATION.HELM)
+            return function (src) { return convertToHelm(srcUh, src); };
+        else if (tgtUnits === NOTATION.SEPARATOR)
+            return function (src) { return convertToSeparator(srcUh, src, tgtSeparator); };
+        else
+            throw new Error();
+    }
+}
+const helmWrappersRe = /[RD]\((\w)\)P?/g;
+function convertToFasta(srcUh, src) {
+    const srcMList = srcUh.isHelm() ? splitterAsHelmNucl(srcUh, src) : srcUh.getSplitter()(src);
+    const tgtMList = new Array(srcMList.length);
+    for (const [srcM, mI] of wu.enumerate(srcMList)) {
+        let m = srcM;
+        if (srcUh.isHelm())
+            m = srcM.replace(helmWrappersRe, '$1');
+        if (srcUh.isGap(m))
+            m = GapSymbols[NOTATION.FASTA];
+        else if (m.length > 1)
+            m = '[' + srcMList[mI] + ']';
+        tgtMList[mI] = m;
+    }
+    return tgtMList.join('');
+}
+function convertToSeparator(srcUh, src, tgtSeparator) {
+    const srcMList = srcUh.isHelm() ? splitterAsHelmNucl(srcUh, src) : srcUh.getSplitter()(src);
+    const tgtMList = new Array(srcMList.length);
+    const isPT = src.startsWith('PEPTIDE');
+    for (const [srcM, mI] of wu.enumerate(srcMList)) {
+        let m = srcM;
+        if (srcUh.isGap(m))
+            m = GapSymbols[NOTATION.SEPARATOR];
+        tgtMList[mI] = m;
+    }
+    return tgtMList.filter((m) => m !== null).join(tgtSeparator);
+}
+function convertToHelm(srcUh, src) {
+    const isDna = src.startsWith('DNA');
+    const isRna = src.startsWith('RNA');
+    const [prefix, leftWrapper, rightWrapper, postfix] = srcUh.getHelmWrappers();
+    const srcMList = srcUh.getSplitter()(src);
+    const tgtMList = srcMList.map((srcM) => {
+        let m = srcM;
+        if (srcUh.isGap(m))
+            m = GapSymbols[NOTATION.HELM];
+        else if (isDna || isRna)
+            m = m.replace(helmWrappersRe, '$1');
+        else
+            m = srcM.length == 1 ? `${leftWrapper}${srcM}${rightWrapper}` : `${leftWrapper}[${srcM}]${rightWrapper}`;
+        return m;
+    });
+    return `${prefix}${tgtMList.join('.')}${postfix}`;
+}
+/** Splits Helm sequence adjusting nucleotides to single char symbols. (!) Removes lone phosphorus. */
+function splitterAsHelmNucl(srcUh, src) {
+    const srcMList = srcUh.getSplitter()(src);
+    const tgtMList = new Array(srcMList.length);
+    const isDna = src.startsWith('DNA');
+    const isRna = src.startsWith('RNA');
+    for (const [srcM, mI] of wu.enumerate(srcMList)) {
+        let m = srcM;
+        if (isDna || isRna) {
+            m = m.replace(helmWrappersRe, '$1');
+            m = m === 'P' ? null : m;
+        }
+        tgtMList[mI] = m;
+    }
+    return tgtMList.filter((m) => m !== null);
 }
 //# sourceMappingURL=notation-converter.js.map

package/src/utils/notation-converter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"notation-converter.js","sourceRoot":"","sources":["notation-converter.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,MAAM,IAAI,CAAC;AAEpB,OAAO,EAAC,UAAU,EAAE,YAAY,EAAC,MAAM,iBAAiB,CAAC;AAEzD,OAAO,EAAC,QAAQ,EAAO,MAAM,wBAAwB,CAAC;AACtD,OAAO,EAAC,oBAAoB,EAAiB,MAAM,uBAAuB,CAAC;AAI3E,iFAAiF;AACjF,MAAM,OAAO,iBAAkB,SAAQ,YAAY;IAGjD,IAAc,QAAQ;QACpB,IAAI,IAAI,CAAC,SAAS,KAAK,IAAI;YACzB,IAAI,CAAC,SAAS,GAAG,oBAAoB,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;QACrD,OAAO,IAAI,CAAC,SAAS,CAAC;IACxB,CAAC;IAEM,OAAO,CAAC,cAAwB,IAAa,OAAO,cAAc,KAAK,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC;IAExF,WAAW,CAAC,cAAwB,IAAa,OAAO,cAAc,KAAK,QAAQ,CAAC,SAAS,CAAC,CAAC,CAAC;IAEhG,MAAM,CAAC,cAAwB,IAAa,OAAO,cAAc,KAAK,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC;IAE7F;;;;;;;;;OASG;IACI,2BAA2B,CAChC,WAAmB,EAAE,WAAmB,EAAE,YAAqB,EAAE,YAAqB;QAEtF,IAAI,CAAC,YAAY,EAAE;YACjB,YAAY,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,WAAuB,CAAC,CAAC,CAAC,CAAC;gBACtD,UAAU,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC;gBAC5B,UAAU,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC;SAClC;QAED,IAAI,CAAC,YAAY;YACf,YAAY,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,WAAuB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC;QAE/E,MAAM,cAAc,GAAG,iBAAiB,CAAC;QACzC,MAAM,YAAY,GAAG,WAAW,CAAC,UAAU,CAAC,KAAK,CAAC,IAAI,WAAW,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC;QACpF,iCAAiC;QACjC,MAAM,cAAc,GAAG,IAAI,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAC;QAClD,MAAM,gBAAgB,GAAa,EAAE,CAAC;QACtC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,cAAc,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC9C,IAAI,IAAI,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC;YAC7B,IAAI,YAAY;gBACd,IAAI,GAAG,IAAI,CAAC,OAAO,CAAC,cAAc,EAAE,EAAE,CAAC,CAAC;YAC1C,IAAI,IAAI,KAAK,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE;gBACtC,gBAAgB,CAAC,IAAI,CAAC,YAAa,CAAC,CAAC;aACtC;iBAAM,IAAI,IAAI,CAAC,OAAO,CAAC,WAAuB,CAAC,IAAI,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE;gBACnE,2DAA2D;gBAC3D,MAAM,OAAO,GAAG,GAAG,GAAG,IAAI,GAAG,GAAG,CAAC;gBACjC,gBAAgB,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;aAChC;iBAAM;gBACL,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;aAC7B;SACF;QACD,OAAO,gBAAgB,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;IAC7C,CAAC;IAED;;;;;OAKG;IACI,OAAO,CAAC,WAAqB,EAAE,YAAqB;QAEzD,MAAM,OAAO,GAAgB,IAAI,CAAC,YAAY,CAAC,WAAW,EAAE,YAAY,CAAC,CAAC;QAC1E,MAAM,SAAS,GAAG,IAAI,CAAC,YAAY,CAAC,WAAW,EAAE,YAAY,CAAC,CAAC;QAC/D,sDAAsD;QACtD,SAAS,CAAC,IAAI,CAAC,CAAC,IAAY,EAAE,EAAE,GAAG,OAAO,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QAC7E,uDAAuD;QACvD,OAAO,SAAS,CAAC;IACnB,CAAC;IAED,YAAmB,GAAc;QAC/B,KAAK,CAAC,GAAG,CAAC,CAAC;QA3EL,cAAS,GAAwB,IAAI,CAAC;IA4E9C,CAAC;IAEM,YAAY,CAAC,QAAkB,EAAE,eAA8B,IAAI;QACxE,IAAI,QAAQ,KAAK,QAAQ,CAAC,SAAS,IAAI,CAAC,YAAY;YAClD,MAAM,IAAI,KAAK,CAAC,uDAAuD,QAAQ,CAAC,SAAS,IAAI,CAAC,CAAC;QAEjG,MAAM,KAAK,GAAG,IAAI,CAAC;QACnB,IAAI,QAAQ,KAAK,QAAQ,CAAC,KAAK;YAC7B,OAAO,UAAS,GAAW,IAAI,OAAO,cAAc,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;QACtE,IAAI,QAAQ,KAAK,QAAQ,CAAC,IAAI;YAC5B,OAAO,UAAS,GAAW,IAAI,OAAO,aAAa,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;aAChE,IAAI,QAAQ,KAAK,QAAQ,CAAC,SAAS;YACtC,OAAO,UAAS,GAAW,IAAI,OAAO,kBAAkB,CAAC,KAAK,EAAE,GAAG,EAAE,YAAa,CAAC,CAAC,CAAC,CAAC,CAAC;;YAEvF,MAAM,IAAI,KAAK,EAAE,CAAC;IACtB,CAAC;CACF;AAED,MAAM,cAAc,GAAG,iBAAiB,CAAC;AAGzC,SAAS,cAAc,CAAC,KAAmB,EAAE,GAAW;IACtD,MAAM,QAAQ,GAAa,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,kBAAkB,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,WAAW,EAAE,CAAC,GAAG,CAAC,CAAC;IACtG,MAAM,QAAQ,GAAa,IAAI,KAAK,CAAS,QAAQ,CAAC,MAAM,CAAC,CAAC;IAC9D,KAAK,MAAM,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,EAAE,CAAC,SAAS,CAAC,QAAQ,CAAC,EAAE;QAC/C,IAAI,CAAC,GAAG,IAAI,CAAC;QACb,IAAI,KAAK,CAAC,MAAM,EAAE;YAChB,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,cAAc,EAAE,IAAI,CAAC,CAAC;QAEzC,IAAI,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC;YAChB,CAAC,GAAG,UAAU,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;aAC5B,IAAI,CAAC,CAAC,MAAM,GAAG,CAAC;YACnB,CAAC,GAAG,GAAG,GAAG,QAAQ,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC;QAE/B,QAAQ,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC;KAClB;IACD,OAAO,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;AAC3B,CAAC;AAED,SAAS,kBAAkB,CAAC,KAAmB,EAAE,GAAW,EAAE,YAAoB;IAChF,MAAM,QAAQ,GAAa,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,kBAAkB,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,WAAW,EAAE,CAAC,GAAG,CAAC,CAAC;IACtG,MAAM,QAAQ,GAAa,IAAI,KAAK,CAAS,QAAQ,CAAC,MAAM,CAAC,CAAC;IAC9D,MAAM,IAAI,GAAG,GAAG,CAAC,UAAU,CAAC,SAAS,CAAC,CAAC;IACvC,KAAK,MAAM,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,EAAE,CAAC,SAAS,CAAC,QAAQ,CAAC,EAAE;QAC/C,IAAI,CAAC,GAAkB,IAAI,CAAC;QAC5B,IAAI,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC;YAChB,CAAC,GAAG,UAAU,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC;QACrC,QAAQ,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC;KAClB;IACD,OAAO,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;AAC/D,CAAC;AAED,SAAS,aAAa,CAAC,KAAmB,EAAE,GAAW;IACrD,MAAM,KAAK,GAAG,GAAG,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC;IACpC,MAAM,KAAK,GAAG,GAAG,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC;IACpC,MAAM,CAAC,MAAM,EAAE,WAAW,EAAE,YAAY,EAAE,OAAO,CAAC,GAAG,KAAK,CAAC,eAAe,EAAE,CAAC;IAC7E,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,EAAE,CAAC,GAAG,CAAC,CAAC;IAE1C,MAAM,QAAQ,GAAa,QAAQ,CAAC,GAAG,CAAC,CAAC,IAAY,EAAE,EAAE;QACvD,IAAI,CAAC,GAAW,IAAI,CAAC;QACrB,IAAI,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC;YAChB,CAAC,GAAG,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC;aAC3B,IAAI,KAAK,IAAI,KAAK;YACrB,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,cAAc,EAAE,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package/src/utils/units-handler.d.ts

@@ -7,17 +7,15 @@ export declare const Tags: {
     /** Column's temp slot name for a UnitsHandler object */
     uhTemp: string;
 };
+export declare const GapSymbols: {
+    [units: string]: string;
+};
 /** Class for handling notation units in Macromolecule columns */
 export declare class UnitsHandler {
     protected readonly _column: DG.Column;
     protected _units: string;
     protected _notation: NOTATION;
     protected _defaultGapSymbol: string;
-    protected static readonly _defaultGapSymbolsDict: {
-        HELM: string;
-        SEPARATOR: string;
-        FASTA: string;
-    };
     static setUnitsToFastaColumn(uh: UnitsHandler): void;
     static setUnitsToSeparatorColumn(uh: UnitsHandler, separator?: string): void;
     static setUnitsToHelmColumn(uh: UnitsHandler): void;
@@ -47,19 +45,27 @@ export declare class UnitsHandler {
     isPeptide(): boolean;
     isMsa(): boolean;
     isHelmCompatible(): boolean;
+    isGap(m: string): boolean;
     /** Associate notation types with the corresponding units */
     /**
      * @return {NOTATION}     Notation associated with the units type
      */
     protected getNotation(): NOTATION;
+    /**
+     * Get the wrapper strings for HELM, depending on the type of the
+     * macromolecule (peptide, DNA, RNA)
+     *
+     * @return {string[]} Array of wrappers
+     */
+    getHelmWrappers(): string[];
     /**
      * Create a new empty column of the specified notation type and the same
      * length as column
      *
-     * @param {NOTATION} targetNotation
+     * @param {NOTATION} tgtNotation
      * @return {DG.Column}
      */
-    protected getNewColumn(targetNotation: NOTATION, separator?: string): DG.Column;
+    protected getNewColumn(tgtNotation: NOTATION, tgtSeparator?: string): DG.Column;
     /**
      * Create a new empty column using templateCol as a template
      *

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

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

@@ -1,5 +1,5 @@
 import * as DG from 'datagrok-api/dg';
-import { candidateAlphabets } from './macromolecule/consts';
+import { candidateAlphabets, NOTATION } from './macromolecule/consts';
 import { detectAlphabet, getSplitterForColumn, getSplitterWithSeparator } from './macromolecule/utils';
 import { mmDistanceFunctions, MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import { getMonomerLibHelper } from '../monomer-works/monomer-utils';
@@ -9,27 +9,32 @@ export const Tags = new class {
         this.uhTemp = `units-handler.${DG.SEMTYPE.MACROMOLECULE}`;
     }
 }();
+export const GapSymbols = {
+    [NOTATION.FASTA]: '-',
+    [NOTATION.SEPARATOR]: '',
+    [NOTATION.HELM]: '*',
+};
 /** Class for handling notation units in Macromolecule columns */
 export class UnitsHandler {
     static setUnitsToFastaColumn(uh) {
-        if (uh.column.semType !== DG.SEMTYPE.MACROMOLECULE || uh.column.getTag(DG.TAGS.UNITS) !== "fasta" /* NOTATION.FASTA */)
-            throw new Error(`The column of notation '${"fasta" /* NOTATION.FASTA */}' must be '${DG.SEMTYPE.MACROMOLECULE}'.`);
-        uh.column.setTag(DG.TAGS.UNITS, "fasta" /* NOTATION.FASTA */);
+        if (uh.column.semType !== DG.SEMTYPE.MACROMOLECULE || uh.column.getTag(DG.TAGS.UNITS) !== NOTATION.FASTA)
+            throw new Error(`The column of notation '${NOTATION.FASTA}' must be '${DG.SEMTYPE.MACROMOLECULE}'.`);
+        uh.column.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
         UnitsHandler.setTags(uh);
     }
     static setUnitsToSeparatorColumn(uh, separator) {
-        if (uh.column.semType !== DG.SEMTYPE.MACROMOLECULE || uh.column.getTag(DG.TAGS.UNITS) !== "separator" /* NOTATION.SEPARATOR */)
-            throw new Error(`The column of notation '${"separator" /* NOTATION.SEPARATOR */}' must be '${DG.SEMTYPE.MACROMOLECULE}'.`);
+        if (uh.column.semType !== DG.SEMTYPE.MACROMOLECULE || uh.column.getTag(DG.TAGS.UNITS) !== NOTATION.SEPARATOR)
+            throw new Error(`The column of notation '${NOTATION.SEPARATOR}' must be '${DG.SEMTYPE.MACROMOLECULE}'.`);
         if (!separator)
-            throw new Error(`The column of notation '${"separator" /* NOTATION.SEPARATOR */}' must have the separator tag.`);
-        uh.column.setTag(DG.TAGS.UNITS, "separator" /* NOTATION.SEPARATOR */);
+            throw new Error(`The column of notation '${NOTATION.SEPARATOR}' must have the separator tag.`);
+        uh.column.setTag(DG.TAGS.UNITS, NOTATION.SEPARATOR);
         uh.column.setTag("separator" /* TAGS.separator */, separator);
         UnitsHandler.setTags(uh);
     }
     static setUnitsToHelmColumn(uh) {
         if (uh.column.semType !== DG.SEMTYPE.MACROMOLECULE)
-            throw new Error(`The column of notation '${"helm" /* NOTATION.HELM */}' must be '${DG.SEMTYPE.MACROMOLECULE}'`);
-        uh.column.setTag(DG.TAGS.UNITS, "helm" /* NOTATION.HELM */);
+            throw new Error(`The column of notation '${NOTATION.HELM}' must be '${DG.SEMTYPE.MACROMOLECULE}'`);
+        uh.column.setTag(DG.TAGS.UNITS, NOTATION.HELM);
         UnitsHandler.setTags(uh);
     }
     /** From detectMacromolecule */
@@ -37,7 +42,7 @@ export class UnitsHandler {
         const units = uh.column.getTag(DG.TAGS.UNITS);
         const stats = uh.stats;
         const alphabetIsMultichar = Object.keys(stats.freq).some((m) => m.length > 1);
-        if (["fasta" /* NOTATION.FASTA */, "separator" /* NOTATION.SEPARATOR */].includes(units)) {
+        if ([NOTATION.FASTA, NOTATION.SEPARATOR].includes(units)) {
             // Empty monomer alphabet is not allowed
             if (Object.keys(stats.freq).length === 0)
                 throw new Error('Alphabet is empty');
@@ -59,7 +64,7 @@ export class UnitsHandler {
     get defaultGapSymbol() { return this._defaultGapSymbol; }
     get separator() {
         const separator = this.column.getTag("separator" /* TAGS.separator */) ?? undefined;
-        if (this.notation === "separator" /* NOTATION.SEPARATOR */ && separator === undefined)
+        if (this.notation === NOTATION.SEPARATOR && separator === undefined)
             throw new Error(`Separator is mandatory  for column '${this.column.name}' of notation '${this.notation}'.`);
         return separator;
     }
@@ -82,7 +87,7 @@ export class UnitsHandler {
         return this.column.getTag(".isHelmCompatible" /* TAGS.isHelmCompatible */);
     }
     getAlphabetSize() {
-        if (this.notation == "helm" /* NOTATION.HELM */ || this.alphabet == "UN" /* ALPHABET.UN */) {
+        if (this.notation == NOTATION.HELM || this.alphabet == "UN" /* ALPHABET.UN */) {
             const alphabetSizeStr = this.column.getTag(".alphabetSize" /* TAGS.alphabetSize */);
             let alphabetSize;
             if (alphabetSizeStr) {
@@ -111,7 +116,7 @@ export class UnitsHandler {
         }
     }
     getAlphabetIsMultichar() {
-        if (this.notation === "helm" /* NOTATION.HELM */)
+        if (this.notation === NOTATION.HELM)
             return true;
         else if (this.alphabet !== "UN" /* ALPHABET.UN */)
             return false;
@@ -153,47 +158,66 @@ export class UnitsHandler {
         }
         return this._stats;
     }
-    isFasta() { return this.notation === "fasta" /* NOTATION.FASTA */; }
-    isSeparator() { return this.notation === "separator" /* NOTATION.SEPARATOR */; }
-    isHelm() { return this.notation === "helm" /* NOTATION.HELM */; }
+    isFasta() { return this.notation === NOTATION.FASTA; }
+    isSeparator() { return this.notation === NOTATION.SEPARATOR; }
+    isHelm() { return this.notation === NOTATION.HELM; }
     isRna() { return this.alphabet === "RNA" /* ALPHABET.RNA */; }
     isDna() { return this.alphabet === "DNA" /* ALPHABET.DNA */; }
     isPeptide() { return this.alphabet === "PT" /* ALPHABET.PT */; }
     isMsa() { return this.aligned ? this.aligned.toUpperCase().includes('MSA') : false; }
     isHelmCompatible() { return this.helmCompatible === 'true'; }
+    isGap(m) {
+        return !m || (this.units === NOTATION.FASTA && m === GapSymbols.FASTA) ||
+            (this.units === NOTATION.HELM && m === GapSymbols.HELM);
+    }
     /** Associate notation types with the corresponding units */
     /**
      * @return {NOTATION}     Notation associated with the units type
      */
     getNotation() {
-        if (this.units.toLowerCase().startsWith("fasta" /* NOTATION.FASTA */))
-            return "fasta" /* NOTATION.FASTA */;
-        else if (this.units.toLowerCase().startsWith("separator" /* NOTATION.SEPARATOR */))
-            return "separator" /* NOTATION.SEPARATOR */;
-        else if (this.units.toLowerCase().startsWith("helm" /* NOTATION.HELM */))
-            return "helm" /* NOTATION.HELM */;
+        if (this.units.toLowerCase().startsWith(NOTATION.FASTA))
+            return NOTATION.FASTA;
+        else if (this.units.toLowerCase().startsWith(NOTATION.SEPARATOR))
+            return NOTATION.SEPARATOR;
+        else if (this.units.toLowerCase().startsWith(NOTATION.HELM))
+            return NOTATION.HELM;
         else
             throw new Error(`Column '${this.column.name}' has unexpected notation '${this.units}'.`);
     }
+    /**
+     * Get the wrapper strings for HELM, depending on the type of the
+     * macromolecule (peptide, DNA, RNA)
+     *
+     * @return {string[]} Array of wrappers
+     */
+    getHelmWrappers() {
+        const prefix = (this.isDna()) ? 'DNA1{' :
+            (this.isRna() || this.isHelmCompatible()) ? 'RNA1{' : 'PEPTIDE1{';
+        const postfix = '}$$$$';
+        const leftWrapper = (this.isDna()) ? 'D(' :
+            (this.isRna()) ? 'R(' : ''; // no wrapper for peptides
+        const rightWrapper = (this.isDna() || this.isRna()) ? ')P' : ''; // no wrapper for peptides
+        return [prefix, leftWrapper, rightWrapper, postfix];
+    }
     /**
      * Create a new empty column of the specified notation type and the same
      * length as column
      *
-     * @param {NOTATION} targetNotation
+     * @param {NOTATION} tgtNotation
      * @return {DG.Column}
      */
-    getNewColumn(targetNotation, separator) {
+    getNewColumn(tgtNotation, tgtSeparator) {
         const col = this.column;
         const len = col.length;
-        const name = targetNotation.toLowerCase() + '(' + col.name + ')';
+        const name = tgtNotation.toLowerCase() + '(' + col.name + ')';
         const newColName = col.dataFrame.columns.getUnusedName(name);
         const newColumn = DG.Column.fromList('string', newColName, new Array(len).fill(''));
         newColumn.semType = DG.SEMTYPE.MACROMOLECULE;
-        newColumn.setTag(DG.TAGS.UNITS, targetNotation);
-        if (targetNotation === "separator" /* NOTATION.SEPARATOR */) {
-            if (!separator)
-                throw new Error(`Notation \'${"separator" /* NOTATION.SEPARATOR */}\' requires separator value.`);
-            newColumn.setTag("separator" /* TAGS.separator */, separator);
+        newColumn.setTag(DG.TAGS.UNITS, tgtNotation);
+        if (tgtNotation === NOTATION.SEPARATOR) {
+            if (!tgtSeparator)
+                throw new Error(`Notation \'${NOTATION.SEPARATOR}\' requires separator value.`);
+            newColumn.setTag("separator" /* TAGS.separator */, tgtSeparator);
         }
         newColumn.setTag(DG.TAGS.CELL_RENDERER, 'Macromolecule'); // cell.renderer
         const srcAligned = col.getTag("aligned" /* TAGS.aligned */);
@@ -208,7 +232,7 @@ export class UnitsHandler {
         const srcAlphabetIsMultichar = col.getTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */);
         if (srcAlphabetIsMultichar !== undefined)
             newColumn.setTag(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */, srcAlphabetIsMultichar);
-        if (targetNotation == "helm" /* NOTATION.HELM */) {
+        if (tgtNotation == NOTATION.HELM) {
             srcAlphabetSize = this.getAlphabetSize().toString();
             newColumn.setTag(".alphabetSize" /* TAGS.alphabetSize */, srcAlphabetSize);
         }
@@ -234,7 +258,7 @@ export class UnitsHandler {
      */
     static unitsStringIsValid(units) {
         units = units.toLowerCase();
-        const prefixes = ["fasta" /* NOTATION.FASTA */, "separator" /* NOTATION.SEPARATOR */, "helm" /* NOTATION.HELM */];
+        const prefixes = [NOTATION.FASTA, NOTATION.SEPARATOR, NOTATION.HELM];
         const postfixes = ['rna', 'dna', 'pt'];
         const prefixCriterion = prefixes.some((p) => units.startsWith(p.toLowerCase()));
         return prefixCriterion;
@@ -326,9 +350,9 @@ export class UnitsHandler {
         else
             throw new Error('Units are not specified in column');
         this._notation = this.getNotation();
-        this._defaultGapSymbol = (this.isFasta()) ? UnitsHandler._defaultGapSymbolsDict.FASTA :
-            (this.isHelm()) ? UnitsHandler._defaultGapSymbolsDict.HELM :
-                UnitsHandler._defaultGapSymbolsDict.SEPARATOR;
+        this._defaultGapSymbol = (this.isFasta()) ? GapSymbols[NOTATION.FASTA] :
+            (this.isHelm()) ? GapSymbols[NOTATION.HELM] :
+                GapSymbols[NOTATION.SEPARATOR];
         if (!this.column.tags.has("aligned" /* TAGS.aligned */) || !this.column.tags.has("alphabet" /* TAGS.alphabet */) ||
             (!this.column.tags.has(".alphabetIsMultichar" /* TAGS.alphabetIsMultichar */) && !this.isHelm() && this.alphabet === "UN" /* ALPHABET.UN */)) {
             // The following detectors and setters are to be called because the column is likely
@@ -372,9 +396,4 @@ export class UnitsHandler {
         return col.temp[Tags.uhTemp];
     }
 }
-UnitsHandler._defaultGapSymbolsDict = {
-    HELM: '*',
-    SEPARATOR: '',
-    FASTA: '-',
-};
 //# sourceMappingURL=units-handler.js.map

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

@@ -1 +1 @@
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