@datagrok/bio 1.5.10 → 1.7.1

package/src/utils/notation-converter.ts

@@ -3,9 +3,9 @@ import {WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
 
 /** enum type to simplify setting "user-friendly" notation if necessary */
 export const enum NOTATION {
-  FASTA = 'fasta',
-  SEPARATOR = 'separator',
-  HELM = 'helm'
+  FASTA = 'FASTA',
+  SEPARATOR = 'SEPARATOR',
+  HELM = 'HELM'
 }
 
 /** Class for handling conversion of notation systems in Macromolecule columns */
@@ -13,6 +13,12 @@ export class NotationConverter {
   private _sourceColumn: DG.Column; // the column to be converted
   private _sourceUnits: string; // units, of the form fasta:SEQ:NT, etc.
   private _sourceNotation: NOTATION; // current notation (without :SEQ:NT, etc.)
+  private _defaultGapSymbol: string;
+  private _defaultGapSymbolsDict = {
+    helm: '*',
+    separator: '',
+    fasta: '-',
+  };
 
   private get sourceUnits(): string { return this._sourceUnits; }
 
@@ -20,6 +26,16 @@ export class NotationConverter {
 
   public get sourceNotation(): NOTATION { return this._sourceNotation; }
 
+  public get defaultGapSymbol(): string { return this._defaultGapSymbol; }
+
+  public get separator(): string {
+    const separator = this.sourceColumn.getTag('separator');
+    if (separator !== null)
+      return separator;
+    else
+      throw new Error('Separator not set');
+  }
+
   public isFasta(): boolean { return this.sourceNotation === NOTATION.FASTA; }
 
   public isSeparator(): boolean { return this.sourceNotation === NOTATION.SEPARATOR; }
@@ -32,26 +48,34 @@ export class NotationConverter {
 
   public toHelm(targetNotation: NOTATION): boolean { return targetNotation === NOTATION.HELM; }
 
-  // TODO: isRna
-  public isRna(): boolean { return this.sourceUnits.toLowerCase().endsWith('nt'); }
+  public isRna(): boolean { return this.sourceUnits.toLowerCase().endsWith('rna'); }
+
+  public isDna(): boolean { return this.sourceUnits.toLowerCase().endsWith('dna'); }
 
   public isPeptide(): boolean { return this.sourceUnits.toLowerCase().endsWith('pt'); }
 
   /** Associate notation types with the corresponding units */
   /**
-   * @return {NOTATION} notation associated with the units type
+   * @return {NOTATION}     Notation associated with the units type
    */
-  private determineSourceNotation(): NOTATION {
+  private getSourceNotation(): NOTATION {
     if (this.sourceUnits.toLowerCase().startsWith('fasta'))
       return NOTATION.FASTA;
     else if (this.sourceUnits.toLowerCase().startsWith('separator'))
       return NOTATION.SEPARATOR;
-    else
-      // TODO: handle possible exceptions
+    else if (this.sourceUnits.toLowerCase().startsWith('helm'))
       return NOTATION.HELM;
+    else
+      throw new Error('The column has units that do not correspond to any notation');
   }
 
-  // TODO: write doc
+  /**
+   * Create a new empty column of the specified notation type and the same
+   * length as sourceColumn
+   *
+   * @param {NOTATION} targetNotation
+   * @return {DG.Column}
+   */
   private getNewColumn(targetNotation: NOTATION): DG.Column {
     const col = this.sourceColumn;
     const len = col.length;
@@ -59,75 +83,151 @@ export class NotationConverter {
     const newColName = col.dataFrame.columns.getUnusedName(name);
     // dummy code
     const newColumn = DG.Column.fromList('string', newColName, new Array(len).fill(''));
-    newColumn.semType = 'Macromolecule';
-    const newUnits = this.sourceUnits.replace(this.sourceNotation.toString(), targetNotation.toString());
-    newColumn.setTag(DG.TAGS.UNITS, newUnits);
-    // TODO: determine all the qualifiers (units, ...), perhaps, using detectors
+    newColumn.semType = DG.SEMTYPE.MACROMOLECULE;
+    newColumn.setTag(
+      DG.TAGS.UNITS,
+      this.sourceUnits.replace(
+        this.sourceNotation.toLowerCase().toString(),
+        targetNotation.toLowerCase().toString()
+      )
+    );
+    // TODO: specify cell renderers for all cases
+    if (this.toFasta(targetNotation)) {
+      newColumn.setTag(
+        DG.TAGS.CELL_RENDERER,
+        // TODO: replace by the enumeration value
+        'Macromolecule');
+    }
     return newColumn;
   }
 
-  // TODO: write doc
-  private convertFastaToSeparator(separator: string): DG.Column {
-    // TODO: implementation
-    // * specify separator
-    // * fasta gap symbol should NOT be considered '-' only, but set as a parameter
-    // * in fasta every position is a monomer (no multi-char monomers), call splitToMonomers() method
-    // * in the resulting jagged array, every gap symbol is to be replaced by
-    // the empty string, while the monomers, to be separated by the separator
-    // (specified as a parameter)
-    // On splitToMonomers(): /libraries/bio/src/viewers/WebLogo --> getSplitter
-
-    const gapSymbol = '-'; // to be specified as an argument
+  /**
+   * Convert a Macromolecule column from FASTA to SEPARATOR notation
+   *
+   * @param {string} separator  A specific separator to be used
+   * @param {string} gapSymbol  Gap symbol in FASTA, '-' by default
+   * @return {DG.Column}        A new column in SEPARATOR notation
+   */
+  private convertFastaToSeparator(separator: string, gapSymbol: string = '-'): DG.Column {
+    // a function splitting FASTA sequence into an array of monomers:
     const splitterAsFasta = WebLogo.splitterAsFasta;
+
     const newColumn = this.getNewColumn(NOTATION.SEPARATOR);
+    // assign the values to the newly created empty column
     newColumn.init((idx: number) => {
-      const sourcePolymer = this.sourceColumn.get(idx);
-      const monomersArray = splitterAsFasta(sourcePolymer);
-      for (let i = 0; i < monomersArray.length; i++) {
-        if (monomersArray[i] === gapSymbol)
-          monomersArray[i] = '';
+      const fastaPolymer = this.sourceColumn.get(idx);
+      const fastaMonomersArray = splitterAsFasta(fastaPolymer);
+      for (let i = 0; i < fastaMonomersArray.length; i++) {
+        if (fastaMonomersArray[i] === gapSymbol)
+          fastaMonomersArray[i] = '';
       }
-      return monomersArray.join(separator);
+      return fastaMonomersArray.join(separator);
     });
     return newColumn;
   }
 
-  private wrapRnaNucleotideToHelm(monomer: string) {
+  private convertToHelm(sourceGapSymbol: string | null = null) {
+    if (sourceGapSymbol === null)
+      sourceGapSymbol = this.defaultGapSymbol;
+    // A function splitting a sequence into an array of monomers according to
+    // its notation
+    const splitter = WebLogo.getSplitterForColumn(this.sourceColumn);
 
-  }
+    const prefix = (this.isDna()) ? 'DNA1{' :
+      (this.isRna()) ? 'RNA1{' :
+        (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
 
-  private convertFastaToHelm(): DG.Column {
-    const gapSymbol = '-'; // to be specified as an argument
-    const splitterAsFasta = WebLogo.splitterAsFasta;
     const newColumn = this.getNewColumn(NOTATION.HELM);
+    // assign the values to the empty column
     newColumn.init((idx: number) => {
       const sourcePolymer = this.sourceColumn.get(idx);
-      const monomersArray = splitterAsFasta(sourcePolymer);
-      for (let i = 0; i < monomersArray.length; i++) {
-        // // TODO: handle gap symbols -- replace by asterisk
-        // if (monomersArray[i] === gapSymbol)
-        //   monomersArray[i] = '*';
-        // else
+      const sourceMonomersArray = splitter(sourcePolymer);
+      const helmArray = [prefix];
+      let firstIteration = true;
+      for (let i = 0; i < sourceMonomersArray.length; i++) {
+        const dot = firstIteration ? '' : '.';
+        let token = sourceMonomersArray[i];
+        if (token === sourceGapSymbol)
+          token = this._defaultGapSymbolsDict.helm;
+        const item = [dot, leftWrapper, token, rightWrapper];
+        helmArray.push(item.join(''));
+        firstIteration = false;
       }
-      // TODO: determine conditionally (if isDna(), or isRna(), or isPeptide()) the template
-      return monomersArray.join('');
+      helmArray.push(postfix);
+      return helmArray.join('');
     });
     return newColumn;
   }
 
-  private convertSeparatorToFasta(): DG.Column {
+  private handleSeparatorItemForFasta(
+    idx: number,
+    separatorItemsArray: string[],
+    separator: string,
+    gapSymbol: string,
+    fastaMonomersArray: string[]
+  ): void {
+    const item = separatorItemsArray[idx];
+    if (item.length > 1) {
+      // the case of a multi-character monomer
+      const monomer = '[' + item + ']';
+      fastaMonomersArray.push(monomer);
+    }
+    if (item === separator) {
+      if (idx !== 0 && separatorItemsArray[idx - 1] === separator)
+        fastaMonomersArray.push(gapSymbol);
+    }
+  }
+
+  private convertSeparatorToFasta(
+    separator: string | null = null,
+    gapSymbol: string = '-'
+  ): DG.Column {
     // TODO: implementation
     // * similarly to fasta2separator, divide string into monomers
     // * adjacent separators is a gap (symbol to be specified)
     // * the monomers MUST be single-character onles, otherwise forbid
+    // * NO, they can be multi-characters
     // conversion
-    //getSplitterWithSeparator
-    return this.getNewColumn(NOTATION.FASTA);
-  }
+    // * consider automatic determining the separator
 
-  private convertSeparatorToHelm(): DG.Column {
-    // TODO: implementation
-    return this.getNewColumn(NOTATION.HELM);
+    if (separator === null)
+      separator = this.separator;
+
+    // a function splitting FASTA sequence into an array of monomers
+    //const splitterAsSeparator = WebLogo.getSplitterWithSeparator(separator);
+    const splitter = WebLogo.getSplitterForColumn(this.sourceColumn);
+
+    const newColumn = this.getNewColumn(NOTATION.FASTA);
+    // assign the values to the empty column
+    newColumn.init((idx: number) => {
+      const separatorPolymer = this.sourceColumn.get(idx);
+      // items can be monomers or separators
+      const separatorItemsArray = splitter(separatorPolymer);
+      const fastaMonomersArray: string[] = [];
+      for (let i = 0; i < separatorItemsArray.length; i++) {
+        const item = separatorItemsArray[i];
+        if (item.length === 0) {
+          fastaMonomersArray.push(gapSymbol);
+        } 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('');
+    });
+    return newColumn;
   }
 
   private convertHelmToFasta(): DG.Column {
@@ -140,19 +240,25 @@ export class NotationConverter {
     return this.getNewColumn(NOTATION.SEPARATOR);
   }
 
-  /** Dispatcher method for notation conversion */
-  // TODO: write the bodies of converter methods
-  public convert(targetNotation: NOTATION, separator: string | null): DG.Column {
+  /** Dispatcher method for notation conversion
+   *
+   * @param {NOTATION} targetNotation   Notation we want to convert to
+   * @param {string | null} tgtSeparator   Possible separator
+   * @return {DG.Column}                Converted column
+   */
+  public convert(targetNotation: NOTATION, tgtSeparator: string | null = null): DG.Column {
+    // possible exceptions
     if (this.sourceNotation === targetNotation)
-      throw new Error('Target notation is not specified');
-    if (this.isFasta() && this.toSeparator(targetNotation))
-      return this.convertFastaToSeparator(separator!); // there is the only place where a separator is needed
-    else if (this.isFasta() && this.toHelm(targetNotation))
-      return this.convertFastaToHelm();
+      throw new Error('Target notation is invalid');
+    if (this.toSeparator(targetNotation) && tgtSeparator === null)
+      throw new Error('Target separator is not specified');
+
+    if (this.isFasta() && this.toSeparator(targetNotation) && tgtSeparator !== null)
+      return this.convertFastaToSeparator(tgtSeparator);
+    else if ((this.isFasta() || this.isSeparator()) && this.toHelm(targetNotation))
+      return this.convertToHelm();
     else if (this.isSeparator() && this.toFasta(targetNotation))
-      return this.convertSeparatorToFasta();
-    else if (this.isSeparator() && this.toHelm(targetNotation))
-      return this.convertSeparatorToHelm();
+      return this.convertSeparatorToFasta(tgtSeparator!);
     else if (this.isHelm() && this.toFasta(targetNotation))
       return this.convertHelmToFasta();
     else
@@ -161,7 +267,14 @@ export class NotationConverter {
 
   public constructor(col: DG.Column) {
     this._sourceColumn = col;
-    this._sourceUnits = this._sourceColumn.tags[DG.TAGS.UNITS];
-    this._sourceNotation = this.determineSourceNotation();
+    const units = this._sourceColumn.tags[DG.TAGS.UNITS];
+    if (units !== null)
+      this._sourceUnits = units;
+    else
+      throw new Error('Units are not specified in column');
+    this._sourceNotation = this.getSourceNotation();
+    this._defaultGapSymbol = (this.isFasta()) ? this._defaultGapSymbolsDict.fasta :
+      (this.isHelm()) ? this._defaultGapSymbolsDict.helm :
+        this._defaultGapSymbolsDict.separator;
   }
 }

package/{test-Bio-34f75e5127b8-936bf89b.html → test-Bio-34f75e5127b8-726a0649.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 936bf89b.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 726a0649.</title><style type="text/css">html,
 body {
   font-family: Arial, Helvetica, sans-serif;
   font-size: 1rem;
@@ -229,7 +229,7 @@ header {
   font-size: 1rem;
   padding: 0 0.5rem;
 }
-</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 936bf89b.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-11 18:26:55</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts</div><div class="suite-time warn">109.382s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">100.002s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: thrown: "Exceeded timeout of 100000 ms for a test.
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=34f75e5127b8. Commit 726a0649.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-07-13 08:17:30</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts</div><div class="suite-time warn">111.144s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">100.002s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: thrown: "Exceeded timeout of 100000 ms for a test.
 Use jest.setTimeout(newTimeout) to increase the timeout value, if this is a long-running test."
     at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:22:1)
     at Runtime._execModule (/home/runner/work/public/public/packages/Bio/node_modules/jest-runtime/build/index.js:1646:24)

package/src/utils/chem-palette.ts

@@ -1,280 +0,0 @@
-import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
-import * as DG from 'datagrok-api/dg';
-
-import {StringDictionary} from '@datagrok-libraries/utils/src/type-declarations';
-import {MonomerLibrary} from '../monomer-library';
-
-
-export class ChemPalette {
-  cp: StringDictionary = {};
-  isInit: boolean = false;
-  monomerLib: MonomerLibrary | null = null;
-
-  /**
-   * Creates an instance of ChemPalette.
-   *
-   * @param {string} scheme Color scheme to use.
-   * @param {boolean} [grouping=false] Is grouping enabled.
-   * @memberof ChemPalette
-   */
-  private constructor(scheme: string, grouping = false) {
-    if (scheme == 'grok')
-      this.cp = ChemPalette.getDatagrok(grouping);
-  }
-
-  /**
-   * Renders 2D representation of a amino acid residue in a tooltip.
-   *
-   * @param {DG.GridCell} cell Grid cell to show tooltip over.
-   * @param {number} x x coordinate of the mouse pointer.
-   * @param {number} y y coordinate of the mouse pointer.
-   * @param {MonomerLibrary} monomerLib Monomer Library instance
-   */
-  static showTooltip(cell: DG.GridCell, x: number, y: number, monomerLib: MonomerLibrary): void {
-    const s = cell.cell.value as string;
-    let toDisplay = [ui.divText(s)];
-    const [, aarOuter, aarInner] = ChemPalette.getColorAAPivot(s);
-    for (const aar of [aarOuter, aarInner]) {
-      if (monomerLib.monomerNames.includes(aar)) {
-        if (aar in ChemPalette.AANames)
-          toDisplay = [ui.divText(ChemPalette.AANames[aar])];
-
-        if (aar in ChemPalette.AAFullNames)
-          toDisplay = [ui.divText(ChemPalette.AANames[ChemPalette.AAFullNames[aar]])];
-
-        const options = {
-          autoCrop: true,
-          autoCropMargin: 0,
-          suppressChiralText: true,
-        };
-        const sketch = grok.chem.svgMol(monomerLib.getMonomerMol(aar), undefined, undefined, options);
-        if (toDisplay.length == 2)
-          toDisplay.push(ui.divText('Modified'));
-
-        toDisplay.push(sketch);
-      }
-    }
-    ui.tooltip.show(ui.divV(toDisplay), x, y);
-  }
-
-  /**
-   * Retursn divided amino with its content in the bracket, if the conetent is number, then its omitted
-   *
-   * @param {string} c raw amino
-   * @return {[string, string]} outer and inner content
-   */
-  static getInnerOuter(c: string): [string, string] {
-    let isInner = 0;
-    let inner = '';
-    let outer = '';
-
-    for (const char of c) {
-      if (char == '(')
-        isInner++;
-      else if (char == ')')
-        isInner--;
-      else if (isInner)
-        inner += char;
-      else
-        outer += char;
-    }
-
-    return !isNaN(parseInt(inner)) ? [outer, ''] : [outer, inner];
-  }
-
-  static getColorAAPivot(monomer: string = '', scheme: 'grok' = 'grok'): [string, string, string, number] {
-    const chemPaletteInstance = ChemPalette.getPalette(scheme);
-    let [outerMonomer, innerMonomer] = ChemPalette.getInnerOuter(monomer);
-    outerMonomer = (outerMonomer.length > 6 ? `${outerMonomer.slice(0, 3)}...` : outerMonomer);
-    innerMonomer = (innerMonomer.length > 6 ? `${innerMonomer.slice(0, 3)}...` : innerMonomer);
-
-    if (monomer.length == 1 || monomer[1] == '(') {
-      const amino = monomer[0]?.toUpperCase()!;
-      return amino in chemPaletteInstance ?
-        [chemPaletteInstance[amino], amino, innerMonomer, 1]:
-        [ChemPalette.undefinedColor, outerMonomer, innerMonomer, 1];
-    }
-
-    if (monomer[0] == 'd' && monomer[1]! in chemPaletteInstance) {
-      if (monomer.length == 2 || monomer[2] == '(') {
-        const amino = monomer[1]?.toUpperCase()!;
-        return amino in chemPaletteInstance ?
-          [chemPaletteInstance[amino], amino, innerMonomer, 2]:
-          [ChemPalette.undefinedColor, outerMonomer, innerMonomer, 2];
-      }
-    }
-
-    if (monomer.substring(0, 3) in ChemPalette.AAFullNames) {
-      if (monomer.length == 3 || monomer[3] == '(') {
-        const amino = ChemPalette.AAFullNames[monomer.substring(0, 3)];
-        return amino in chemPaletteInstance ?
-          [chemPaletteInstance[amino], amino, innerMonomer, 3]:
-          [ChemPalette.undefinedColor, outerMonomer, innerMonomer, 3];
-      }
-    }
-
-    if (monomer[0]?.toLowerCase() == monomer[0]) {
-      if (monomer.substring(1, 3) in ChemPalette.AAFullNames) {
-        if (monomer.length == 4 || monomer[4] == '(') {
-          const amino = ChemPalette.AAFullNames[monomer.substring(1, 3)];
-          return amino in chemPaletteInstance ?
-            [chemPaletteInstance[amino], amino, innerMonomer, 4]:
-            [ChemPalette.undefinedColor, outerMonomer, innerMonomer, 4];
-        }
-      }
-    }
-
-    return [ChemPalette.undefinedColor, outerMonomer, innerMonomer, 0];
-  }
-
-  static colourPalette: {[key: string]: string[]} = {
-    'orange': ['rgb(255,187,120)', 'rgb(245,167,100)', 'rgb(235,137,70)', 'rgb(205, 111, 71)'],
-    'all_green': ['rgb(44,160,44)', 'rgb(74,160,74)', 'rgb(23,103,57)', 'rgb(30,110,96)', 'rgb(60,131,95)',
-      'rgb(24,110,79)', 'rgb(152,223,138)', 'rgb(182, 223, 138)', 'rgb(152, 193, 138)'],
-    'all_blue': ['rgb(31,119,180)', 'rgb(23,190,207)', 'rgb(122, 102, 189)', 'rgb(158,218,229)', 'rgb(141, 124, 217)',
-      'rgb(31, 120, 150)'],
-    'magenta': ['rgb(162,106,192)', 'rgb(197,165,224)', 'rgb(208,113,218)'],
-    'red': ['rgb(214,39,40)', 'rgb(255,152,150)'],
-    'st_blue': ['rgb(23,190,207)', 'rgb(158,218,229)', 'rgb(31,119,180)'],
-    'dark_blue': ['rgb(31,119,180)', 'rgb(31, 120, 150)'],
-    'light_blue': ['rgb(23,190,207)', 'rgb(158,218,229)', 'rgb(108, 218, 229)', 'rgb(23,190,227)'],
-    'lilac_blue': ['rgb(124,102,211)', 'rgb(149,134,217)', 'rgb(97, 81, 150)'],
-    'dark_green': ['rgb(23,103,57)', 'rgb(30,110,96)', 'rgb(60,131,95)', 'rgb(24,110,79)'],
-    'green': ['rgb(44,160,44)', 'rgb(74,160,74)'],
-    'light_green': ['rgb(152,223,138)', 'rgb(182, 223, 138)', 'rgb(152, 193, 138)'],
-    'st_green': ['rgb(44,160,44)', 'rgb(152,223,138)', 'rgb(39, 174, 96)', 'rgb(74,160,74)'],
-    'pink': ['rgb(247,182,210)'],
-    'brown': ['rgb(140,86,75)', 'rgb(102, 62, 54)'],
-    'gray': ['rgb(127,127,127)', 'rgb(199,199,199)', 'rgb(196,156,148)', 'rgb(222, 222, 180)'],
-    'yellow': ['rgb(188,189,34)'],
-    'white': ['rgb(230,230,230)'],
-  };
-
-  static grokGroups: {[key: string]: string[]} = {
-    'yellow': ['C', 'U'],
-    'red': ['G', 'P'],
-    'all_green': ['A', 'V', 'I', 'L', 'M', 'F', 'Y', 'W'],
-    'light_blue': ['R', 'H', 'K'],
-    'dark_blue': ['D', 'E'],
-    'orange': ['S', 'T', 'N', 'Q'],
-  };
-
-  static undefinedColor = 'rgb(100,100,100)';
-
-  static makePalette(dt: {[key: string]: string[]}, simplified = false, grouping = false): StringDictionary {
-    const palette: { [key: string]: string } = {};
-    const groups = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ';
-    let currentGroup = 0;
-    for (const [color, monomers] of Object.entries(dt)) {
-      monomers.forEach((monomer, index) => {
-        palette[grouping ? groups[currentGroup] : monomer] = ChemPalette.colourPalette[color][simplified ? 0 : index];
-      });
-      currentGroup++;
-    }
-    return palette;
-  }
-
-  static AANames: StringDictionary = {
-    'G': 'Glycine',
-    'L': 'Leucine',
-    'Y': 'Tyrosine',
-    'S': 'Serine',
-    'E': 'Glutamic acid',
-    'Q': 'Glutamine',
-    'D': 'Aspartic acid',
-    'N': 'Asparagine',
-    'F': 'Phenylalanine',
-    'A': 'Alanine',
-    'K': 'Lysine',
-    'R': 'Arginine',
-    'H': 'Histidine',
-    'C': 'Cysteine',
-    'V': 'Valine',
-    'P': 'Proline',
-    'W': 'Tryptophan',
-    'I': 'Isoleucine',
-    'M': 'Methionine',
-    'T': 'Threonine',
-  };
-
-  static AASmiles: StringDictionary = {
-    'G': 'NCC(=O)O',
-    'L': 'N[C@H](CC(C)C)C(=O)O',
-    'Y': 'NC(CC1=CC=C(O)C=C1)C(=O)O',
-    'S': 'NC(CO)C(=O)O',
-    'E': 'N[C@@H](CCC(O)=O)C(=O)O',
-    'Q': 'N[C@@H](CCC(N)=O)C(=O)O',
-    'D': 'N[C@@H](CC(O)=O)C(=O)O',
-    'N': 'N[C@@H](CC(N)=O)C(=O)O',
-    'F': 'NC(CC1=CC=CC=C1)C(=O)O',
-    'A': 'N[C@H](C)C(=O)O',
-    'K': 'NC(CCCCN)C(=O)O',
-    'R': 'N[C@H](CCCNC(=N)C)C(=O)O',
-    'H': 'NC(CC1=CN=C[N]1)C(=O)O',
-    'C': 'N[C@@H](CS)C(=O)O',
-    'V': 'NC(C(C)C)C(=O)O',
-    'P': 'N(CCC1)C1C(=O)O',
-    'W': 'N[C@@H](Cc1c2ccccc2n([H])c1)C(=O)O',
-    'I': 'N[C@H]([C@H](C)CC)C(=O)O',
-    'M': 'NC(CCSC)C(=O)O',
-    'T': 'NC(C(O)C)C(=O)O',
-  };
-
-  static AASmilesTruncated: StringDictionary = {
-    'G': '*C*',
-    'L': 'CC(C)C[C@H](*)*',
-    'Y': 'C1=CC(=CC=C1CC(*)*)O',
-    'S': 'OCC(*)C*',
-    'E': '*[C@@H](CCC(O)=O)*',
-    'Q': '*N[C@@H](CCC(N)=O)*',
-    'D': '*[C@@H](CC(O)=O)*',
-    'N': '*[C@@H](CC(N)=O)*',
-    'F': 'C1=CC=C(C=C1)CC(*)*',
-    'A': 'C[C@H](*)*',
-    'K': 'C(CCN)CC(*)*',
-    'R': '*[C@H](CCCNC(=N)C)*',
-    'H': 'C1=C(NC=N1)CC(*)*',
-    'C': 'C([C@@H](*)*)S',
-    'V': 'CC(C)C(*)*',
-    'P': 'C1CCN(*)C1*',
-    'W': '*[C@@H](Cc1c2ccccc2n([H])c1)*',
-    'I': 'CC[C@H](C)[C@H](*)*',
-    'M': 'CSCCC(*)*',
-    'T': 'CC(O)C(*)*',
-  };
-
-  static AAFullNames: StringDictionary = {
-    'Ala': 'A',
-    'Arg': 'R',
-    'Asn': 'N',
-    'Asp': 'D',
-    'Cys': 'C',
-    'Gln': 'Q',
-    'Glu': 'E',
-    'Gly': 'G',
-    'His': 'H',
-    'Ile': 'I',
-    'Leu': 'L',
-    'Lys': 'K',
-    'Met': 'M',
-    'Phe': 'F',
-    'Pro': 'P',
-    'Ser': 'S',
-    'Thr': 'T',
-    'Trp': 'W',
-    'Tyr': 'Y',
-    'Val': 'V',
-  };
-
-  static getDatagrok(grouping = false): StringDictionary {
-    return ChemPalette.makePalette(ChemPalette.grokGroups, false, grouping);
-  }
-
-  static getPalette(scheme: 'grok'): StringDictionary {
-    if (scheme == 'grok')
-      return ChemPalette.getDatagrok();
-    else
-      throw new Error(`ChemPalette: scheme \`${scheme}\` does not exist`);
-  }
-}

package/src/utils/misc.ts

@@ -1,29 +0,0 @@
-import * as DG from 'datagrok-api/dg';
-
-import * as C from './constants';
-
-export function stringToBool(str: string): boolean {
-  return str === 'true' ? true : false;
-}
-
-export function getSeparator(col: DG.Column<string>): string {
-  const separator = col.tags[C.TAGS.SEPARATOR];
-  if (separator)
-    return separator as string;
-
-  const defaultSeparators = ['.', '-', ' '];
-  const categories = col.categories;
-  const catLen = categories.length;
-  for (const potentialSeparator of defaultSeparators) {
-    if (categories.filter((sequence) => sequence.includes(potentialSeparator)).length == catLen)
-      return potentialSeparator;
-  }
-  return separator as string ?? '';
-}
-
-export function getTypedArrayConstructor(
-  maxNum: number): Uint8ArrayConstructor | Uint16ArrayConstructor | Uint32ArrayConstructor {
-  return maxNum < 256 ? Uint8Array :
-    maxNum < 65536 ? Uint16Array :
-      Uint32Array;
-}