@datagrok/peptides 0.8.9 → 0.8.13

package/src/describe.ts

@@ -1,534 +0,0 @@
-import * as ui from 'datagrok-api/ui';
-import * as DG from 'datagrok-api/dg';
-// import {splitAlignedPeptides} from './utils/split-aligned';
-import {tTest} from '@datagrok-libraries/statistics/src/tests';
-import {fdrcorrection} from '@datagrok-libraries/statistics/src/multiple-tests';
-import {StringDictionary} from '@datagrok-libraries/utils/src/type-declarations';
-import {ChemPalette} from './utils/chem-palette';
-import {setAARRenderer} from './utils/cell-renderer';
-import {PeptidesController} from './peptides';
-
-const cp = new ChemPalette('grok');
-
-export const aarGroups = {
-  'R': 'PC',
-  'H': 'PC',
-  'K': 'PC',
-  'D': 'NC',
-  'E': 'NC',
-  'S': 'U',
-  'T': 'U',
-  'N': 'U',
-  'Q': 'U',
-  'C': 'SC',
-  'U': 'SC',
-  'G': 'SC',
-  'P': 'SC',
-  'A': 'H',
-  'V': 'H',
-  'I': 'H',
-  'L': 'H',
-  'M': 'H',
-  'F': 'H',
-  'Y': 'H',
-  'W': 'H',
-  '-': '-',
-};
-
-const groupDescription: {[key: string]: {'description': string, 'aminoAcids': string[]}} = {
-  'PC': {'description': 'Positive Amino Acids, with Electrically Charged Side Chains', 'aminoAcids': ['R', 'H', 'K']},
-  'NC': {'description': 'Negative Amino Acids, with Electrically Charged Side Chains', 'aminoAcids': ['D', 'E']},
-  'U': {'description': 'Amino Acids with Polar Uncharged Side Chains', 'aminoAcids': ['S', 'T', 'N', 'Q']},
-  'SC': {'description': 'Special Cases', 'aminoAcids': ['C', 'U', 'G', 'P']},
-  'H': {
-    'description': 'Amino Acids with Hydrophobic Side Chain',
-    'aminoAcids': ['A', 'V', 'I', 'L', 'M', 'F', 'Y', 'W'],
-  },
-  '-': {'description': 'Unknown Amino Acid', 'aminoAcids': ['-']},
-};
-
-/*function customGridColumnHeader(cell: DG.GridCell) {
-  if (cell.isColHeader && cell.tableColumn != null) {
-    if (highlightedColumns.includes(parseInt(cell.tableColumn.name))) {
-      cell.style.backColor = 0xff1f77b4;
-    }
-  }
-}*/
-
-function joinDataFrames(df: DG.DataFrame, positionColumns: string[], splitSeqDf: DG.DataFrame, activityColumn: string) {
-  // if (df.col(activityColumnScaled))
-  //   (df.columns as DG.ColumnList).remove(activityColumnScaled);
-
-
-  //FIXME: this column usually duplicates, so remove it then
-  // if (df.col(`${activityColumnScaled} (2)`))
-  //   (df.columns as DG.ColumnList).remove(`${activityColumnScaled} (2)`);
-
-
-  // append splitSeqDf columns to source table and make sure columns are not added more than once
-  const dfColsSet = new Set((df.columns as DG.ColumnList).names());
-  if (!positionColumns.every((col: string) => dfColsSet.has(col))) {
-    df.join(
-      splitSeqDf, [activityColumn], [activityColumn], (df.columns as DG.ColumnList).names(), positionColumns, 'inner',
-      true);
-  }
-}
-
-function sortSourceGrid(sourceGrid: DG.Grid) {
-  if (sourceGrid) {
-    const colNames: DG.GridColumn[] = [];
-    for (let i = 1; i < sourceGrid.columns.length; i++)
-      colNames.push(sourceGrid.columns.byIndex(i)!);
-
-    colNames.sort((a, b)=>{
-      if (a.column!.semType == 'aminoAcids') {
-        if (b.column!.semType == 'aminoAcids')
-          return 0;
-        return -1;
-      }
-      if (b.column!.semType == 'aminoAcids')
-        return 1;
-      return 0;
-    });
-    sourceGrid.columns.setOrder(colNames.map((v) => v.name));
-  }
-}
-
-// export async function scaleActivity(
-//   activityScaling: string, activityColumn: string, activityColumnScaled: string, df: DG.DataFrame,
-// ): Promise<[DG.DataFrame, string]> {
-//   // const df = sourceGrid.dataFrame!;
-//   const tempDf = df.clone(null, [activityColumn]);
-
-//   let formula = '${' + activityColumn + '}';
-//   let newColName = activityColumn;
-//   switch (activityScaling) {
-//   case 'none':
-//     break;
-//   case 'lg':
-//     formula = `Log10(${formula})`;
-//     newColName = `Log10(${newColName})`;
-//     break;
-//   case '-lg':
-//     formula = `-1*Log10(${formula})`;
-//     newColName = `-Log10(${newColName})`;
-//     break;
-//   default:
-//     throw new Error(`ScalingError: method \`${activityScaling}\` is not available.`);
-//   }
-
-//   await (tempDf.columns as DG.ColumnList).addNewCalculated(activityColumnScaled, formula);
-
-//   return [tempDf, newColName];
-// }
-
-async function calculateStatistics(
-  matrixDf: DG.DataFrame,
-  positionColName: string,
-  aminoAcidResidue: string,
-  activityColumnScaled: string,
-  peptidesCount: number,
-  splitSeqDf: DG.DataFrame,
-  groupMapping: StringDictionary,
-) {
-  matrixDf = matrixDf.groupBy([positionColName, aminoAcidResidue])
-    .add('count', activityColumnScaled, 'Count')
-    .aggregate();
-
-  const countThreshold = 4;
-  //@ts-ignore: never gets old
-  matrixDf.rows.filter((row) => row.Count >= countThreshold && row.Count <= peptidesCount - countThreshold);
-  matrixDf = matrixDf.clone(matrixDf.filter);
-
-  // calculate additional stats
-  await (matrixDf.columns as DG.ColumnList).addNewCalculated('Ratio', '${count}/'.concat(`${peptidesCount}`));
-
-  //calculate p-values based on t-test
-  let pvalues: Float32Array = new Float32Array(matrixDf.rowCount).fill(1);
-  const mdCol: DG.Column = (matrixDf.columns as DG.ColumnList).addNewFloat('Mean difference');
-  const pValCol: DG.Column = (matrixDf.columns as DG.ColumnList).addNewFloat('pValue');
-  for (let i = 0; i < matrixDf.rowCount; i++) {
-    const position = matrixDf.get(positionColName, i);
-    const aar = matrixDf.get(aminoAcidResidue, i);
-
-    //@ts-ignore
-    splitSeqDf.rows.select((row) => groupMapping[row[position]] === aar);
-    const currentActivity: number[] = splitSeqDf
-      .clone(splitSeqDf.selection, [activityColumnScaled])
-      .getCol(activityColumnScaled)
-      .toList();
-
-    //@ts-ignore
-    splitSeqDf.rows.select((row) => groupMapping[row[position]] !== aar);
-    const otherActivity: number[] = splitSeqDf
-      .clone(splitSeqDf.selection, [activityColumnScaled])
-      .getCol(activityColumnScaled)
-      .toList();
-
-    const testResult = tTest(currentActivity, otherActivity);
-    // testResult = uTest(currentActivity, otherActivity);
-    const currentMeanDiff = testResult['Mean difference']!;
-    const pvalue = testResult[currentMeanDiff >= 0 ? 'p-value more' : 'p-value less'];
-
-    mdCol.set(i, currentMeanDiff);
-    pvalues[i] = pvalue;
-  }
-
-  if (true)
-    pvalues = fdrcorrection(pvalues)[1];
-
-
-  for (let i = 0; i < pvalues.length; ++i)
-    pValCol.set(i, pvalues[i]);
-
-
-  return matrixDf.clone();
-}
-
-async function setCategoryOrder(
-  twoColorMode: boolean, statsDf: DG.DataFrame, aminoAcidResidue: string, matrixDf: DG.DataFrame,
-) {
-  const sortArgument = twoColorMode ? 'Absolute Mean difference' : 'Mean difference';
-  if (twoColorMode)
-    await (statsDf.columns as DG.ColumnList).addNewCalculated('Absolute Mean difference', 'Abs(${Mean difference})');
-
-  const aarWeightsDf = statsDf.groupBy([aminoAcidResidue]).sum(sortArgument, 'weight').aggregate();
-  const aarList = aarWeightsDf.getCol(aminoAcidResidue).toList();
-  const getWeight = (aar: string) => aarWeightsDf
-    .groupBy(['weight'])
-    .where(`${aminoAcidResidue} = ${aar}`)
-    .aggregate()
-    .get('weight', 0);
-  aarList.sort((first, second) => getWeight(second) - getWeight(first));
-
-  matrixDf.getCol(aminoAcidResidue).setCategoryOrder(aarList);
-}
-
-function createVerticalTable(
-  statsDf: DG.DataFrame,
-  aminoAcidResidue: string,
-  positionColName: string,
-  twoColorMode: boolean,
-) {
-  // TODO: aquire ALL of the positions
-  let sequenceDf = statsDf.groupBy(['Mean difference', aminoAcidResidue, positionColName, 'Count', 'Ratio', 'pValue'])
-    .where('pValue <= 0.1')
-    .aggregate();
-
-  let tempStats: DG.Stats;
-  const maxAtPos: {[index: string]: number} = {};
-  for (const pos of sequenceDf.getCol(positionColName).categories) {
-    tempStats = DG.Stats.fromColumn(
-      sequenceDf.getCol('Mean difference'),
-      DG.BitSet.create(sequenceDf.rowCount, (i) => sequenceDf.get(positionColName, i) === pos),
-    );
-    maxAtPos[pos] = twoColorMode ?
-      (tempStats.max > Math.abs(tempStats.min) ? tempStats.max : tempStats.min) : tempStats.max;
-  }
-  sequenceDf = sequenceDf.clone(DG.BitSet.create(sequenceDf.rowCount, (i) => {
-    return sequenceDf.get('Mean difference', i) === maxAtPos[sequenceDf.get(positionColName, i)];
-  }));
-
-  return sequenceDf;
-}
-
-function createGrids(
-  matrixDf: DG.DataFrame,
-  aminoAcidResidue: string,
-  positionColumns: string[],
-  sequenceDf: DG.DataFrame,
-  positionColName: string,
-  grouping: boolean,
-) {
-  const sarGrid = matrixDf.plot.grid();
-  sarGrid.sort([aminoAcidResidue]);
-  sarGrid.columns.setOrder([aminoAcidResidue].concat(positionColumns));
-
-  const sarVGrid = sequenceDf.plot.grid();
-  sarVGrid.sort([positionColName]);
-  sarVGrid.col('pValue')!.format = 'four digits after comma';
-  sarVGrid.col('pValue')!.name = 'P-Value';
-
-  if (!grouping) {
-    let tempCol = (matrixDf.columns as DG.ColumnList).byName(aminoAcidResidue);
-    if (tempCol)
-      setAARRenderer(tempCol, sarGrid);
-
-    tempCol = (sequenceDf.columns as DG.ColumnList).byName(aminoAcidResidue);
-    if (tempCol)
-      setAARRenderer(tempCol, sarGrid);
-  }
-
-  return [sarGrid, sarVGrid];
-}
-
-function setCellRendererFunc(
-    renderColNames: string[], positionColName: string, aminoAcidResidue: string, statsDf: DG.DataFrame,
-    twoColorMode: boolean, sarGrid: DG.Grid, sarVGrid: DG.Grid) {
-  const mdCol = statsDf.getCol('Mean difference');
-  const cellRendererFunc = function(args: DG.GridCellRenderArgs) {
-    args.g.save();
-    args.g.beginPath();
-    args.g.rect(args.bounds.x, args.bounds.y, args.bounds.width, args.bounds.height);
-    args.g.clip();
-
-    if (args.cell.isRowHeader && args.cell.gridColumn.visible) {
-      args.cell.gridColumn.visible = false;
-      args.preventDefault();
-      return;
-    }
-
-    if (
-      args.cell.isTableCell &&
-      args.cell.tableRowIndex !== null &&
-      args.cell.tableColumn !== null &&
-      args.cell.cell.value !== null
-    ) {
-      if (renderColNames.indexOf(args.cell.tableColumn.name) !== -1) {
-        const currentPosition = args.cell.tableColumn.name !== 'Mean difference' ?
-          args.cell.tableColumn.name : args.cell.grid.table.get(positionColName, args.cell.tableRowIndex);
-        const query =
-          `${aminoAcidResidue} = ${args.cell.grid.table.get(aminoAcidResidue, args.cell.tableRowIndex)} ` +
-          `and ${positionColName} = ${currentPosition}`;
-
-        const pVal: number = statsDf.groupBy(['pValue']).where(query).aggregate().get('pValue', 0);
-
-        let coef;
-        const variant = args.cell.cell.value < 0;
-        if (pVal < 0.01)
-          coef = variant && twoColorMode ? '#FF7900' : '#299617';
-        else if (pVal < 0.05)
-          coef = variant && twoColorMode ? '#FFA500' : '#32CD32';
-        else if (pVal < 0.1)
-          coef = variant && twoColorMode ? '#FBCEB1' : '#98FF98';
-        else
-          coef = DG.Color.toHtml(DG.Color.lightLightGray);
-
-
-        const chooseMin = () => twoColorMode ? 0 : mdCol.min;
-        const chooseMax = () => twoColorMode ? Math.max(Math.abs(mdCol.min), mdCol.max) : mdCol.max;
-        const chooseCurrent = () => twoColorMode ? Math.abs(args.cell.cell.value) : args.cell.cell.value;
-
-        const rCoef = (chooseCurrent() - chooseMin()) / (chooseMax() - chooseMin());
-
-        const maxRadius = 0.9 * (args.bounds.width > args.bounds.height ? args.bounds.height : args.bounds.width) / 2;
-        const radius = Math.floor(maxRadius * rCoef);
-
-        args.g.beginPath();
-        args.g.fillStyle = coef;
-        args.g.arc(
-          args.bounds.x + args.bounds.width / 2, args.bounds.y + args.bounds.height / 2, radius < 3 ? 3 : radius, 0,
-          Math.PI * 2, true,
-        );
-        args.g.closePath();
-
-        args.g.fill();
-        args.preventDefault();
-      }
-    }
-    args.g.restore();
-  };
-  sarGrid.onCellRender.subscribe(cellRendererFunc);
-  sarVGrid.onCellRender.subscribe(cellRendererFunc);
-}
-
-function setTooltipFunc(
-    renderColNames: string[], statsDf: DG.DataFrame, aminoAcidResidue: string, positionColName: string,
-    peptidesCount: number, grouping: boolean, sarGrid: DG.Grid, sarVGrid: DG.Grid) {
-  const onCellTooltipFunc = async function(cell: DG.GridCell, x: number, y: number) {
-    if (
-        !cell.isRowHeader && !cell.isColHeader && cell.tableColumn !== null && cell.cell.value !== null &&
-        cell.tableRowIndex !== null && renderColNames.indexOf(cell.tableColumn.name) !== -1) {
-      const tooltipMap: { [index: string]: string } = {};
-
-      for (const col of (statsDf.columns as DG.ColumnList).names()) {
-        if (col !== aminoAcidResidue && col !== positionColName) {
-          const currentPosition = cell.tableColumn.name !== 'Mean difference' ?
-            cell.tableColumn.name : cell.grid.table.get(positionColName, cell.tableRowIndex);
-          const query =
-            `${aminoAcidResidue} = ${cell.grid.table.get(aminoAcidResidue, cell.tableRowIndex)} ` +
-            `and ${positionColName} = ${currentPosition}`;
-          const textNum = statsDf.groupBy([col]).where(query).aggregate().get(col, 0);
-          let text = `${col === 'Count' ? textNum : textNum.toFixed(5)}`;
-
-          if (col === 'Count')
-            text += ` / ${peptidesCount}`;
-          else if (col === 'pValue')
-            text = parseFloat(text) !== 0 ? text : '<0.01';
-
-
-          tooltipMap[col === 'pValue' ? 'p-value' : col] = text;
-        }
-      }
-
-      ui.tooltip.show(ui.tableFromMap(tooltipMap), x, y);
-    }
-    if (
-      !cell.isColHeader &&
-      cell.tableColumn !== null &&
-      cell.tableColumn.name == aminoAcidResidue &&
-      cell.cell.value !== null &&
-      cell.tableRowIndex !== null
-    ) {
-      if (grouping) {
-        const currentGroup = groupDescription[cell.cell.value];
-        const divText = ui.divText('Amino Acids in this group: ' + currentGroup['aminoAcids'].join(', '));
-        ui.tooltip.show(ui.divV([ui.h3(currentGroup['description']), divText]), x, y);
-      } else
-        await cp.showTooltip(cell, x, y);
-    }
-    return true;
-  };
-  sarGrid.onCellTooltip(onCellTooltipFunc);
-  sarVGrid.onCellTooltip(onCellTooltipFunc);
-}
-
-function postProcessGrids(
-  sourceGrid: DG.Grid,
-  invalidIndexes: number[],
-  grouping: boolean,
-  aminoAcidResidue: string,
-  sarGrid: DG.Grid,
-  sarVGrid: DG.Grid,
-) {
-  sourceGrid.onCellPrepare((cell: DG.GridCell) => {
-    const currentRowIndex = cell.tableRowIndex;
-    if (currentRowIndex && invalidIndexes.includes(currentRowIndex) && !cell.isRowHeader)
-      cell.style.backColor = DG.Color.lightLightGray;
-  });
-
-  const mdCol: DG.GridColumn = sarVGrid.col('Mean difference')!;
-  mdCol.name = 'Diff';
-
-  for (const grid of [sarGrid, sarVGrid]) {
-    grid.props.rowHeight = 20;
-    grid.columns.rowHeader!.width = 20;
-    for (let i = 0; i < grid.columns.length; ++i) {
-      const col = grid.columns.byIndex(i)!;
-      if (grid == sarVGrid && col.name !== 'Diff' && col.name !== 'AAR')
-        col.width = 45;
-      else
-        col.width = grid.props.rowHeight;
-    }
-  }
-
-  if (grouping) {
-    sarGrid.col(aminoAcidResidue)!.name = 'Groups';
-    sarVGrid.col(aminoAcidResidue)!.name = 'Groups';
-  }
-
-  sarGrid.props.allowEdit = false;
-  sarVGrid.props.allowEdit = false;
-}
-
-export async function describe(
-  df: DG.DataFrame,
-  activityColumn: string,
-  activityScaling: string,
-  sourceGrid: DG.Grid,
-  twoColorMode: boolean,
-  initialBitset: DG.BitSet | null,
-  grouping: boolean,
-): Promise<[DG.Grid, DG.Grid, DG.DataFrame, StringDictionary]> {
-  //Split the aligned sequence into separate AARs
-  let splitSeqDf: DG.DataFrame | undefined;
-  let invalidIndexes: number[];
-  const col: DG.Column = (df.columns as DG.ColumnList).bySemType('alignedSequence')!;
-  [splitSeqDf, invalidIndexes] = PeptidesController.splitAlignedPeptides(col);
-  splitSeqDf.name = 'Split sequence';
-
-  const positionColumns = (splitSeqDf.columns as DG.ColumnList).names();
-  const activityColumnScaled = `${activityColumn}Scaled`;
-  const renderColNames: string[] = (splitSeqDf.columns as DG.ColumnList).names();
-  const positionColName = 'Pos';
-  const aminoAcidResidue = 'AAR';
-
-  (splitSeqDf.columns as DG.ColumnList).add(df.getCol(activityColumn));
-
-  joinDataFrames(df, positionColumns, splitSeqDf, activityColumn);
-
-  for (const col of (df.columns as DG.ColumnList)) {
-    if (splitSeqDf.col(col.name) && col.name != activityColumn)
-      setAARRenderer(col, sourceGrid);
-  }
-
-  sortSourceGrid(sourceGrid);
-
-  const [scaledDf, newColName] = await PeptidesController.scaleActivity(
-    activityScaling, activityColumn, activityColumnScaled, df);
-  //TODO: make another func
-  const scaledCol = scaledDf.getCol(activityColumnScaled);
-  const oldScaledCol = df.getCol(activityColumnScaled);
-  const oldScaledColGridName = oldScaledCol.temp['gridName'];
-  const oldScaledGridCol = sourceGrid.col(oldScaledColGridName);
-
-  (splitSeqDf.columns as DG.ColumnList).add(scaledCol);
-  (df.columns as DG.ColumnList).replace(oldScaledCol, scaledCol);
-  if (newColName === activityColumn)
-    sourceGrid.col(activityColumn)!.name = `~${activityColumn}`;
-  if (oldScaledGridCol !== null) {
-    oldScaledGridCol.name = newColName;
-    oldScaledGridCol.visible = true;
-  }
-  sourceGrid.columns.setOrder([newColName]);
-
-  splitSeqDf = splitSeqDf.clone(initialBitset);
-
-  //unpivot a table and handle duplicates
-  splitSeqDf = splitSeqDf.groupBy(positionColumns)
-    .add('med', activityColumnScaled, activityColumnScaled)
-    .aggregate();
-
-  const peptidesCount = splitSeqDf.getCol(activityColumnScaled).length;
-
-  let matrixDf = splitSeqDf.unpivot([activityColumnScaled], positionColumns, positionColName, aminoAcidResidue);
-
-  //TODO: move to chem palette
-  let groupMapping: StringDictionary = {};
-  if (grouping) {
-    groupMapping = aarGroups;
-    const aarCol = matrixDf.getCol(aminoAcidResidue);
-    aarCol.init((index) => groupMapping[aarCol.get(index)[0]] ?? '-');
-    aarCol.compact();
-  } else
-    Object.keys(aarGroups).forEach((value) => groupMapping[value] = value);
-
-
-  //statistics for specific AAR at a specific position
-  const statsDf = await calculateStatistics(
-    matrixDf, positionColName, aminoAcidResidue, activityColumnScaled, peptidesCount, splitSeqDf, groupMapping,
-  );
-
-  // SAR matrix table
-  //pivot a table to make it matrix-like
-  matrixDf = statsDf.groupBy([aminoAcidResidue])
-    .pivot(positionColName)
-    .add('first', 'Mean difference', '')
-    .aggregate();
-  matrixDf.name = 'SAR';
-
-  // Setting category order
-  await setCategoryOrder(twoColorMode, statsDf, aminoAcidResidue, matrixDf);
-
-  // SAR vertical table (naive, choose best Mean difference from pVals <= 0.01)
-  const sequenceDf = createVerticalTable(statsDf, aminoAcidResidue, positionColName, twoColorMode);
-  renderColNames.push('Mean difference');
-
-  const [sarGrid, sarVGrid] = createGrids(
-    matrixDf, aminoAcidResidue, positionColumns, sequenceDf, positionColName, grouping,
-  );
-
-  setCellRendererFunc(
-    renderColNames, positionColName, aminoAcidResidue, statsDf, twoColorMode, sarGrid, sarVGrid,
-  );
-
-  // show all the statistics in a tooltip over cell
-  setTooltipFunc(
-    renderColNames, statsDf, aminoAcidResidue, positionColName, peptidesCount, grouping, sarGrid, sarVGrid,
-  );
-
-  postProcessGrids(sourceGrid, invalidIndexes, grouping, aminoAcidResidue, sarGrid, sarVGrid);
-
-  //TODO: return class instead
-  return [sarGrid, sarVGrid, statsDf, groupMapping];
-}

package/src/utils/split-aligned.ts

@@ -1,72 +0,0 @@
-// import * as DG from 'datagrok-api/dg';
-
-/**
- * Split aligned sequence string into separate parts containing amino acid residues.
- *
- * @export
- * @param {DG.Column} peptideColumn Column containing aligned sequences.
- * @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;
-
-//   // 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
-
-//   //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,
-//   ];
-// }