npm - @datagrok-libraries/bio - Versions diffs - 5.33.2 → 5.34.1 - Mend

@datagrok-libraries/bio 5.33.2 → 5.34.1

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.

Files changed (23) hide show

package/CHANGELOG.md +25 -0
package/package.json +2 -2
package/src/monomer-works/to-atomic-level.js +2 -1
package/src/monomer-works/to-atomic-level.js.map +1 -1
package/src/utils/fasta-handler.js +2 -1
package/src/utils/fasta-handler.js.map +1 -1
package/src/utils/macromolecule/consts.d.ts +1 -1
package/src/utils/macromolecule/consts.d.ts.map +1 -1
package/src/utils/macromolecule/consts.js +7 -0
package/src/utils/macromolecule/consts.js.map +1 -1
package/src/utils/macromolecule/index.js +1 -0
package/src/utils/macromolecule/index.js.map +1 -1
package/src/utils/macromolecule/utils.d.ts.map +1 -1
package/src/utils/macromolecule/utils.js +7 -6
package/src/utils/macromolecule/utils.js.map +1 -1
package/src/utils/notation-converter.d.ts +3 -51
package/src/utils/notation-converter.d.ts.map +1 -1
package/src/utils/notation-converter.js +90 -189
package/src/utils/notation-converter.js.map +1 -1
package/src/utils/units-handler.d.ts +13 -7
package/src/utils/units-handler.d.ts.map +1 -1
package/src/utils/units-handler.js +60 -41
package/src/utils/units-handler.js.map +1 -1

package/CHANGELOG.md ADDED Viewed

@@ -0,0 +1,25 @@
+# bio changelog
+## 5.34.1 (2023-08-01)
+Patch release for a small fix for Macromolecule cell renderer
+*Dependency: datgarok-api >= 1.10.2*
+### Bug fixes
+* GROK-13659: Bio | Tools: Fix MaxMonomerLength Macromolecule cell renderer
+## 5.34.0 (2023-07-21)
+This release focuses on improving usability.
+*Dependency: datgarok-api >= 1.10.2*
+### Features
+* Added `NotationConverter.getConverter()` getting a function to convert a single value.
+### Breaking change
+* Removed `NotationConverter.convertStringToHelm()`.

package/package.json CHANGED Viewed

@@ -8,10 +8,10 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.33.2",
+  "version": "5.34.1",
   "description": "",
   "dependencies": {
-    "@datagrok-libraries/gridext": "^1.3.54",
+    "@datagrok-libraries/gridext": "^1.3.64",
     "@datagrok-libraries/utils": "^2.5.0",
     "@datagrok-libraries/ml": "^6.3.28",
     "@deck.gl/core": "8.8.12",

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

@@ -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 CHANGED Viewed

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

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/macromolecule/consts.d.ts CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/macromolecule/consts.js CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/macromolecule/index.js CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"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.d.ts.map CHANGED Viewed

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

@@ -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 ${units} .`);
@@ -113,15 +113,16 @@ export function getSplitterForColumn(col) {
     const separator = col.getTag("separator" /* TAGS.separator */);
     return getSplitter(units, separator);
 }
-const longMonomerPartRe = /(\w+)/g;
+const longMonomerPartRe = /([^\W_]+)/g;
 /** Convert long monomer names to short ones */
 export function monomerToShort(amino, maxLengthOfMonomer) {
     if (amino.length <= maxLengthOfMonomer)
         return amino;
+    //const kebabAmino = amino.replace(/[A-Z]+(?![a-z])|[A-Z]/g, ($, ofs) => (ofs ? '-' : '') + $);
     const shortAminoMatch = amino.match(longMonomerPartRe);
     const needAddDots = amino.length > maxLengthOfMonomer || (shortAminoMatch?.length ?? 0) > 1;
     const shortAmino = shortAminoMatch?.[0] ?? ' ';
-    return !needAddDots ? shortAmino : shortAmino.substring(0, maxLengthOfMonomer) + '…';
+    return !needAddDots ? shortAmino : shortAmino.substring(0, maxLengthOfMonomer - 1) + '…';
 }
 /** */
 export function getAlphabet(alphabet) {

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

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

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/notation-converter.js CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/src/utils/units-handler.d.ts CHANGED Viewed

@@ -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 CHANGED Viewed

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

@@ -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

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