@datagrok/peptides 0.8.5 → 0.8.9

package/src/utils/chem-palette.ts

@@ -2,6 +2,10 @@ 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 {_package} from '../package';
+import {MonomerLibrary} from '../monomer-library';
+
 /**
  * Chem palette class.
  *
@@ -9,8 +13,9 @@ import * as DG from 'datagrok-api/dg';
  * @class ChemPalette
  */
 export class ChemPalette {
-  cp: {[key: string]: string} = {};
-
+  cp: StringDictionary = {};
+  isInit: boolean = false;
+  monomerLib: MonomerLibrary | null = null;
   /**
    * Creates an instance of ChemPalette.
    *
@@ -19,9 +24,8 @@ export class ChemPalette {
    * @memberof ChemPalette
    */
   constructor(scheme: string, grouping = false) {
-    if (scheme == 'grok') {
+    if (scheme == 'grok')
       this.cp = ChemPalette.getDatagrok(grouping);
-    }
   }
 
   /**
@@ -31,24 +35,32 @@ export class ChemPalette {
    * @param {number} x x coordinate of the mouse pointer.
    * @param {number} y y coordinate of the mouse pointer.
    */
-  showTooltip(cell: DG.GridCell, x: number, y: number) {
+  async showTooltip(cell: DG.GridCell, x: number, y: number) {
+    if (!this.isInit)
+      this.monomerLib = new MonomerLibrary(await _package.files.readAsText(`HELMMonomers_June10.sdf`));
+
     const s = cell.cell.value as string;
     let toDisplay = [ui.divText(s)];
-    const [, aar] = this.getColorAAPivot(s);
-    if (aar in ChemPalette.AASmiles) {
-      if (s in ChemPalette.AANames) {
-        toDisplay = [ui.divText(ChemPalette.AANames[s])];
-      }
-      if (s in ChemPalette.AAFullNames) {
-        toDisplay = [ui.divText(ChemPalette.AANames[ChemPalette.AAFullNames[s]])];
+    const [, aarOuter, aarInner] = this.getColorAAPivot(s);
+    for (const aar of [aarOuter, aarInner]) {
+      if (this.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(this.monomerLib!.getMonomerMol(aar), undefined, undefined, options);
+        if (toDisplay.length == 2)
+          toDisplay.push(ui.divText('Modified'));
+
+        toDisplay.push(sketch);
       }
-      const options = {
-        autoCrop: true,
-        autoCropMargin: 0,
-        suppressChiralText: true,
-      };
-      const sketch = grok.chem.svgMol(ChemPalette.AASmiles[aar], undefined, undefined, options);
-      toDisplay.push(sketch);
     }
     ui.tooltip.show(ui.divV(toDisplay), x, y);
   }
@@ -63,25 +75,54 @@ export class ChemPalette {
     return color;
   }
 
+  /**
+   * 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
+   */
+  private getInnerOuter(c: string): [string, string] {
+    let isInner = 0;
+    let inner = '';
+    let outer = '';
+
+    for (let i = 0; i < c.length; ++i) {
+      if (c[i] == '(')
+        isInner++;
+      else if (c[i] == ')')
+        isInner--;
+      else if (isInner)
+        inner += c[i];
+      else
+        outer += c[i];
+    }
+
+    return !isNaN(parseInt(inner)) ? [outer, ''] : [outer, inner];
+  }
+
   /**
    * Get color for the provided amino acid residue pivot
    * @param {string} [c=''] Amino acid residue string.
    * @return {[string, string, number]}
    */
-  getColorAAPivot(c: string = ''): [string, string, number] {
+  getColorAAPivot(c: string = ''): [string, string, string, number] {
+    let [outerC, innerC] = this.getInnerOuter(c);
+    outerC = (outerC.length > 6 ? outerC.slice(0, 3) + '...' : outerC);
+    innerC = (innerC.length > 6 ? innerC.slice(0, 3) + '...' : innerC);
+
     if (c.length == 1 || c[1] == '(') {
       const amino = c[0]?.toUpperCase()!;
       return amino in this.cp?
-        [this.cp[amino], amino, 1]:
-        [ChemPalette.undefinedColor, '', 1];
+        [this.cp[amino], amino, innerC, 1]:
+        [ChemPalette.undefinedColor, outerC, innerC, 1];
     }
 
     if (c[0] == 'd' && c[1]! in this.cp) {
       if (c.length == 2 || c[2] == '(') {
         const amino = c[1]?.toUpperCase()!;
         return amino in this.cp?
-          [this.cp[amino], amino, 2]:
-          [ChemPalette.undefinedColor, '', 2];
+          [this.cp[amino], amino, innerC, 2]:
+          [ChemPalette.undefinedColor, outerC, innerC, 2];
       }
     }
 
@@ -89,8 +130,8 @@ export class ChemPalette {
       if (c.length == 3 || c[3] == '(') {
         const amino = ChemPalette.AAFullNames[c.substr(0, 3)];
         return amino in this.cp?
-          [this.cp[amino], amino, 3]:
-          [ChemPalette.undefinedColor, '', 3];
+          [this.cp[amino], amino, innerC, 3]:
+          [ChemPalette.undefinedColor, outerC, innerC, 3];
       }
     }
 
@@ -99,13 +140,13 @@ export class ChemPalette {
         if (c.length == 4 || c[4] == '(') {
           const amino = ChemPalette.AAFullNames[c.substr(1, 3)];
           return amino in this.cp?
-            [this.cp[amino], amino, 4]:
-            [ChemPalette.undefinedColor, '', 4];
+            [this.cp[amino], amino, innerC, 4]:
+            [ChemPalette.undefinedColor, outerC, innerC, 4];
         }
       }
     }
 
-    return [ChemPalette.undefinedColor, '', 0];
+    return [ChemPalette.undefinedColor, outerC, innerC, 0];
   }
 
   /**
@@ -116,7 +157,7 @@ export class ChemPalette {
    */
   getColorPivot(c = ''): [string, number] {
     //TODO: merge with getColorAAPivot?
-    const [color,, pivot] = this.getColorAAPivot(c);
+    const [color,,, pivot] = this.getColorAAPivot(c);
     return [color, pivot];
   };
 
@@ -148,7 +189,7 @@ export class ChemPalette {
     '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)'],
-  }
+  };
 
   /**
    * Grok color scheme groups.
@@ -164,7 +205,7 @@ export class ChemPalette {
     'light_blue': ['R', 'H', 'K'],
     'dark_blue': ['D', 'E'],
     'orange': ['S', 'T', 'N', 'Q'],
-  }
+  };
 
   /**
    * Lesk color scheme groups.
@@ -179,7 +220,7 @@ export class ChemPalette {
     'magenta': ['N', 'Q', 'H'],
     'red': ['D', 'E'],
     'all_blue': ['K', 'R'],
-  }
+  };
 
   /**
    * Undefined color.
@@ -214,10 +255,10 @@ export class ChemPalette {
    * Amino acid residue names.
    *
    * @static
-   * @type {{[key: string]: string}}
+   * @type {StringDictionary}
    * @memberof ChemPalette
    */
-  static AANames: {[key: string]: string} = {
+  static AANames: StringDictionary = {
     'G': 'Glycine',
     'L': 'Leucine',
     'Y': 'Tyrosine',
@@ -238,16 +279,16 @@ export class ChemPalette {
     'I': 'Isoleucine',
     'M': 'Methionine',
     'T': 'Threonine',
-  }
+  };
 
   /**
    * Amino acid residue SMILES.
    *
    * @static
-   * @type {{[key: string]: string}}
+   * @type {StringDictionary}
    * @memberof ChemPalette
    */
-  static AASmiles: {[key: string]: string} = {
+  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',
@@ -268,16 +309,16 @@ export class ChemPalette {
     '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',
-  }
+  };
 
   /**
    * Amino acid residue truncated SMILES.
    *
    * @static
-   * @type {{[key: string]: string}}
+   * @type {StringDictionary}
    * @memberof ChemPalette
    */
-  static AASmilesTruncated: {[key: string]: string} = {
+  static AASmilesTruncated: StringDictionary = {
     'G': '*C*',
     'L': 'CC(C)C[C@H](*)*',
     'Y': 'C1=CC(=CC=C1CC(*)*)O',
@@ -298,16 +339,16 @@ export class ChemPalette {
     'I': 'CC[C@H](C)[C@H](*)*',
     'M': 'CSCCC(*)*',
     'T': 'CC(O)C(*)*',
-  }
+  };
 
   /**
    * Amino acid residue full names.
    *
    * @static
-   * @type {{[key: string]: string}}
+   * @type {StringDictionary}
    * @memberof ChemPalette
    */
-  static AAFullNames: {[key: string]: string} = {
+  static AAFullNames: StringDictionary = {
     'Ala': 'A',
     'Arg': 'R',
     'Asn': 'N',
@@ -328,7 +369,7 @@ export class ChemPalette {
     'Trp': 'W',
     'Tyr': 'Y',
     'Val': 'V',
-  }
+  };
 
   /**
    * Get Datagrok palette.

package/src/utils/molecular-measure.ts

@@ -142,9 +142,9 @@ const _lib = [
 const weightsLib : {[name: string]: number} = {};
 
 // Create a dictionary linking one-letter code with the corresponding residues weight.
-for (const d of _lib) {
+for (const d of _lib)
   weightsLib[d['One-letter']] = parseFloat(d.Weight.substring(0, d.Weight.length-2));
-}
+
 
 /**
  * Calculates molecular weight of the given peptide in daltons.
@@ -167,9 +167,8 @@ export function getSequenceMolecularWeight(sequence: string): number {
   }
 
   for (const i of sequence) {
-    if (i in weightsLib) {
+    if (i in weightsLib)
       sum += weightsLib[i];
-    }
   }
   return sum;
 }

package/src/utils/multiple-sequence-alignment.ts

@@ -53,9 +53,9 @@ function _stringsToAligned(alignment: string[]): string[] {
   const nItems = alignment.length;
   const aligned = new Array<string>(nItems);
 
-  for (let i = 0; i < nItems; ++i) {
+  for (let i = 0; i < nItems; ++i)
     aligned[i] = _castAligned(alignment[i]);
-  }
+
   return aligned;
 }
 
@@ -69,9 +69,8 @@ function _stringsToAligned(alignment: string[]): string[] {
 export async function runKalign(col: DG.Column, isAligned = false) : Promise<DG.Column> {
   let sequences = col.toList();
 
-  if (isAligned) {
+  if (isAligned)
     sequences = sequences.map((v: string, _) => AlignedSequenceEncoder.clean(v).replace(/\-/g, ''));
-  }
 
   const fasta = _stringsToFasta(sequences);
 

package/src/utils/peptide-similarity-space.ts

@@ -8,7 +8,7 @@ import {DimensionalityReducer} from '@datagrok-libraries/ml/src/reduce-dimension
 import {
   createDimensinalityReducingWorker,
 } from '@datagrok-libraries/ml/src/workers/dimensionality-reducing-worker-creator';
-import {StringMeasure} from '@datagrok-libraries/ml/src/string-measure';
+import {Measure, StringMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 import {Coordinates} from '@datagrok-libraries/utils/src/type-declarations';
 
 /**
@@ -20,9 +20,8 @@ import {Coordinates} from '@datagrok-libraries/utils/src/type-declarations';
 function inferActivityColumnsName(table: DG.DataFrame): string | null {
   const re = /activity|ic50/i;
   for (const name of table.columns.names()) {
-    if (name.match(re)) {
+    if (name.match(re))
       return name;
-    }
   }
   return null;
 }
@@ -53,40 +52,30 @@ export function cleanAlignedSequencesColumn(col: DG.Column): Array<string> {
  * @return {Promise<DG.ScatterPlotViewer>} A viewer.
  */
 export async function createPeptideSimilaritySpaceViewer(
-  table: DG.DataFrame,
-  alignedSequencesColumn: DG.Column,
-  method: string,
-  measure: string,
-  cyclesCount: number,
-  view: DG.TableView | null,
-  activityColumnName?: string | null,
-): Promise<DG.ScatterPlotViewer> {
-  const pi = DG.TaskBarProgressIndicator.create('Creating embedding.');
+  table: DG.DataFrame, alignedSequencesColumn: DG.Column, method: string, measure: string, cyclesCount: number,
+  view: DG.TableView | null, activityColumnName?: string | null): Promise<DG.ScatterPlotViewer> {
+  const pi = DG.TaskBarProgressIndicator.create('Creating embedding...');
 
   activityColumnName = activityColumnName ?? inferActivityColumnsName(table);
 
   const axesNames = ['~X', '~Y', '~MW'];
   const columnData = alignedSequencesColumn.toList().map((v, _) => AlignedSequenceEncoder.clean(v));
 
-  const embcols = await createDimensinalityReducingWorker(columnData, method, measure, cyclesCount);
+  const embcols = await createDimensinalityReducingWorker(
+    {data: columnData, metric: measure as StringMetrics}, method, cyclesCount);
 
   const columns = Array.from(
-    embcols as Coordinates,
-    (v: Float32Array, k) => (DG.Column.fromFloat32Array(axesNames[k], v)),
-  );
-
-  function _getMW(sequences = columnData) {
-    const mw: Float32Array = new Float32Array(sequences.length).fill(0);
-    let currentSequence;
-
-    for (let i = 0; i < sequences.length; ++i) {
-      currentSequence = sequences[i];
-      mw[i] = currentSequence == null ? 0 : getSequenceMolecularWeight(currentSequence);
-    }
+    embcols as Coordinates, (v: Float32Array, k) => DG.Column.fromFloat32Array(axesNames[k], v));
+
+  function _getMW(sequences: string[]) {
+    const mw: Float32Array = new Float32Array(sequences.length);
+
+    mw.map((_, index) => getSequenceMolecularWeight(sequences[index] ?? ''));
+
     return mw;
   }
 
-  columns.push(DG.Column.fromFloat32Array('~MW', _getMW()));
+  columns.push(DG.Column.fromFloat32Array('~MW', _getMW(columnData)));
 
   const edf = DG.DataFrame.fromColumns(columns);
 
@@ -100,17 +89,15 @@ export async function createPeptideSimilaritySpaceViewer(
         const v = newCol.get(i);
         table.set(axis, i, v);
       }
-    } else {
+    } else
       table.columns.insert(newCol);
-    }
   }
 
-  const viewerOptions = {x: '~X', y: '~Y', color: activityColumnName ?? '~MW', size: '~MW'};
-  const viewer = DG.Viewer.scatterPlot(table, viewerOptions);
-
-  if (view !== null) {
-    view.addViewer(viewer);
-  }
+  const viewerOptions = {
+    x: '~X', y: '~Y', color: activityColumnName ?? '~MW', size: '~MW', title: 'Peptide Space', showYSelector: false,
+    showXSelector: false, showColorSelector: false, showSizeSelector: false,
+  };
+  const viewer = table.plot.scatter(viewerOptions);
 
   pi.close();
   return viewer;
@@ -141,7 +128,7 @@ export class PeptideSimilaritySpaceWidget {
    */
   constructor(alignedSequencesColumn: DG.Column, view: DG.TableView) {
     this.availableMethods = DimensionalityReducer.availableMethods;
-    this.availableMetrics = StringMeasure.availableMeasures;
+    this.availableMetrics = Measure.getMetricByDataType('String');
     this.method = this.availableMethods[0];
     this.metrics = this.availableMetrics[0];
     this.currentDf = alignedSequencesColumn.dataFrame;
@@ -177,9 +164,10 @@ export class PeptideSimilaritySpaceWidget {
    * @memberof PeptideSimilaritySpaceWidget
    */
   protected async updateViewer() {
-    this.viewer.lastChild?.remove();
     const viewer = await this.drawViewer();
+    this.viewer.lastChild?.remove();
     this.viewer.appendChild(viewer.root);
+    viewer.dataFrame?.fireValuesChanged();
   }
 
   /**
@@ -224,6 +212,25 @@ export class PeptideSimilaritySpaceWidget {
    * @memberof PeptideSimilaritySpaceWidget
    */
   public async draw(): Promise<DG.Widget> {
-    return new DG.Widget(ui.divV([(await this.drawViewer()).root, await this.drawInputs()]));
+    const plot = await this.drawViewer();
+    const inputs = await this.drawInputs();
+    const elements = ui.divV([plot.root, inputs]);
+
+    // Move detaching scatterplot to the grid.
+    plot.onEvent('d4-viewer-detached').subscribe((args) => {
+      let found = false;
+
+      for (const v of this.view.viewers) {
+        const opts = v.getOptions() as {[name: string]: any};
+
+        if (opts.type == 'Scatter plot' && opts.look.xColumnName == '~X' && opts.look.yColumnName == '~Y')
+          found = true;
+      }
+
+      if (!found)
+        this.view.addViewer(plot);
+    });
+
+    return new DG.Widget(elements);
   }
 }

package/src/utils/split-aligned.ts

@@ -1,4 +1,4 @@
-import * as DG from 'datagrok-api/dg';
+// import * as DG from 'datagrok-api/dg';
 
 /**
  * Split aligned sequence string into separate parts containing amino acid residues.
@@ -8,65 +8,65 @@ import * as DG from 'datagrok-api/dg';
  * @param {boolean} [filter=true] Filter out columns with all the same residues.
  * @return {[DG.DataFrame, number[]]} DataFrame containing split sequence and a list of invalid indexes.
  */
-export function splitAlignedPeptides(peptideColumn: DG.Column, filter: boolean = true): [DG.DataFrame, number[]] {
-  const splitPeptidesArray: string[][] = [];
-  let currentSplitPeptide: string[];
-  let modeMonomerCount = 0;
-  let currentLength;
-  const colLength = peptideColumn.length;
+// export function splitAlignedPeptides(peptideColumn: DG.Column, filter: boolean = true): [DG.DataFrame, number[]] {
+//   const splitPeptidesArray: string[][] = [];
+//   let currentSplitPeptide: string[];
+//   let modeMonomerCount = 0;
+//   let currentLength;
+//   const colLength = peptideColumn.length;
 
-  // splitting data
-  const monomerLengths: {[index: string]: number} = {};
-  for (let i = 0; i < colLength; i++) {
-    currentSplitPeptide = peptideColumn.get(i).split('-').map((value: string) => value ? value : '-');
-    splitPeptidesArray.push(currentSplitPeptide);
-    currentLength = currentSplitPeptide.length;
-    monomerLengths[currentLength + ''] =
-      monomerLengths[currentLength + ''] ? monomerLengths[currentLength + ''] + 1 : 1;
-  }
-  //@ts-ignore: what I do here is converting string to number the most effective way I could find. parseInt is slow
-  modeMonomerCount = 1 * Object.keys(monomerLengths).reduce((a, b) => monomerLengths[a] > monomerLengths[b] ? a : b);
+//   // splitting data
+//   const monomerLengths: {[index: string]: number} = {};
+//   for (let i = 0; i < colLength; i++) {
+//     currentSplitPeptide = peptideColumn.get(i).split('-').map((value: string) => value ? value : '-');
+//     splitPeptidesArray.push(currentSplitPeptide);
+//     currentLength = currentSplitPeptide.length;
+//     monomerLengths[currentLength + ''] =
+//       monomerLengths[currentLength + ''] ? monomerLengths[currentLength + ''] + 1 : 1;
+//   }
+//   //@ts-ignore: what I do here is converting string to number the most effective way I could find. parseInt is slow
+//   modeMonomerCount = 1 * Object.keys(monomerLengths).reduce((a, b) => monomerLengths[a] > monomerLengths[b] ? a : b);
 
-  // making sure all of the sequences are of the same size
-  // and marking invalid sequences
-  let nTerminal: string;
-  const invalidIndexes: number[] = [];
-  let splitColumns: string[][] = Array.from({length: modeMonomerCount}, (_) => []);
-  modeMonomerCount--; // minus N-terminal
-  for (let i = 0; i < colLength; i++) {
-    currentSplitPeptide = splitPeptidesArray[i];
-    nTerminal = currentSplitPeptide.pop()!; // it is guaranteed that there will be at least one element
-    currentLength = currentSplitPeptide.length;
-    if (currentLength !== modeMonomerCount) {
-      invalidIndexes.push(i);
-    }
-    for (let j = 0; j < modeMonomerCount; j++) {
-      splitColumns[j].push(j < currentLength ? currentSplitPeptide[j] : '-');
-    }
-    splitColumns[modeMonomerCount].push(nTerminal);
-  }
-  modeMonomerCount--; // minus C-terminal
+//   // making sure all of the sequences are of the same size
+//   // and marking invalid sequences
+//   let nTerminal: string;
+//   const invalidIndexes: number[] = [];
+//   let splitColumns: string[][] = Array.from({length: modeMonomerCount}, (_) => []);
+//   modeMonomerCount--; // minus N-terminal
+//   for (let i = 0; i < colLength; i++) {
+//     currentSplitPeptide = splitPeptidesArray[i];
+//     nTerminal = currentSplitPeptide.pop()!; // it is guaranteed that there will be at least one element
+//     currentLength = currentSplitPeptide.length;
+//     if (currentLength !== modeMonomerCount)
+//       invalidIndexes.push(i);
 
-  //create column names list
-  const columnNames = Array.from({length: modeMonomerCount}, (_, index) => `${index + 1 < 10 ? 0 : ''}${index + 1 }`);
-  columnNames.splice(0, 0, 'N-terminal');
-  columnNames.push('C-terminal');
+//     for (let j = 0; j < modeMonomerCount; j++)
+//       splitColumns[j].push(j < currentLength ? currentSplitPeptide[j] : '-');
 
-  // filter out the columns with the same values
-  if (filter) {
-    splitColumns = splitColumns.filter((positionArray, index) => {
-      const isRetained = new Set(positionArray).size > 1;
-      if (!isRetained) {
-        columnNames.splice(index, 1);
-      }
-      return isRetained;
-    });
-  }
+//     splitColumns[modeMonomerCount].push(nTerminal);
+//   }
+//   modeMonomerCount--; // minus C-terminal
 
-  return [
-    DG.DataFrame.fromColumns(splitColumns.map((positionArray, index) => {
-      return DG.Column.fromList('string', columnNames[index], positionArray);
-    })),
-    invalidIndexes,
-  ];
-}
+//   //create column names list
+//   const columnNames = Array.from({length: modeMonomerCount}, (, index) => `${index + 1 < 10 ? 0 : ''}${index + 1 }`);
+//   columnNames.splice(0, 0, 'N-terminal');
+//   columnNames.push('C-terminal');
+
+//   // filter out the columns with the same values
+//   if (filter) {
+//     splitColumns = splitColumns.filter((positionArray, index) => {
+//       const isRetained = new Set(positionArray).size > 1;
+//       if (!isRetained)
+//         columnNames.splice(index, 1);
+
+//       return isRetained;
+//     });
+//   }
+
+//   return [
+//     DG.DataFrame.fromColumns(splitColumns.map((positionArray, index) => {
+//       return DG.Column.fromList('string', columnNames[index], positionArray);
+//     })),
+//     invalidIndexes,
+//   ];
+// }

package/src/viewers/logo-viewer.ts

@@ -4,8 +4,9 @@ import * as DG from 'datagrok-api/dg';
 import $ from 'cash-dom';
 
 import * as logojs from 'logojs-react';
-import {splitAlignedPeptides} from '../utils/split-aligned';
+// import {splitAlignedPeptides} from '../utils/split-aligned';
 import {ChemPalette} from '../utils/chem-palette';
+import {PeptidesController} from '../peptides';
 
 /**
  * Logo viewer.
@@ -80,7 +81,7 @@ export class Logo extends DG.JsViewer {
     this.initialized = true;
     console.log('INIT');
     this.target = this.dataFrame;
-    [this.splitted] = splitAlignedPeptides(this.dataFrame!.columns.bySemType(this.colSemType));
+    [this.splitted] = PeptidesController.splitAlignedPeptides(this.dataFrame!.columns.bySemType(this.colSemType));
     this.root.style.width = 'auto';
     this.root.style.height = 'auto';
     this.root.style.maxHeight = '200px';
@@ -93,9 +94,9 @@ export class Logo extends DG.JsViewer {
    */
   onTableAttached() {
     if (typeof this.dataFrame !== 'undefined') {
-      if (!this.initialized) {
+      if (!this.initialized)
         this.init();
-      }
+
 
       this.subs.push(DG.debounce(this.dataFrame.selection.onChanged, 50).subscribe((_: any) => this.render()));
       this.subs.push(DG.debounce(this.dataFrame.filter.onChanged, 50).subscribe((_: any) => this.render()));
@@ -141,14 +142,13 @@ export class Logo extends DG.JsViewer {
         .whereRowMask(this.dataFrame!.selection)
         .aggregate();
     }
-    if (selected) {
-      [this.splitted] = splitAlignedPeptides(this.target!.columns.bySemType(this.colSemType));
-    } else [this.splitted] = splitAlignedPeptides(this.dataFrame!.columns.bySemType(this.colSemType));
+    if (selected)
+      [this.splitted] = PeptidesController.splitAlignedPeptides(this.target!.columns.bySemType(this.colSemType));
+    else [this.splitted] = PeptidesController.splitAlignedPeptides(this.dataFrame!.columns.bySemType(this.colSemType));
     $(this.root).empty();
 
-    if (typeof this.dataFrame !== 'undefined') {
+    if (typeof this.dataFrame !== 'undefined')
       this.findLogo();
-    }
   }
 
   /**
@@ -176,17 +176,16 @@ export class Logo extends DG.JsViewer {
       for (let i = 0; i < col.length; i++) {
         const c = col.get(i);
         if (c != '-') {
-          if (c[1] == '(') {
+          if (c[1] == '(')
             this.ppm[index][this.PROT_NUMS[c.substr(0, 1).toUpperCase()]] += 1 / size;
-          } else if (c.substr(0, 3) in ChemPalette.AAFullNames && (c.length == 3 || c.at(3) == '(')) {
+          else if (c.substr(0, 3) in ChemPalette.AAFullNames && (c.length == 3 || c.at(3) == '('))
             this.ppm[index][this.PROT_NUMS[ChemPalette.AAFullNames[c.substr(0, 3)]]] += 1 / size;
-          } else if (c.at(0)?.toLowerCase() == c.at(0) && c.substr(1, 3) in ChemPalette.AAFullNames &&
+          else if (c.at(0)?.toLowerCase() == c.at(0) && c.substr(1, 3) in ChemPalette.AAFullNames &&
             (c.length == 4 || c.at(4) == '(')
-          ) {
+          )
             this.ppm[index][this.PROT_NUMS[ChemPalette.AAFullNames[c.substr(1, 3)]]] += 1 / size;
-          } else {
+          else
             this.ppm[index][this.PROT_NUMS[c]] += 1 / size;
-          }
         }
       }
       index++;