@datagrok/peptides 0.8.13 → 1.0.0

package/src/utils/SAR-multiple-filter.ts

@@ -1,439 +0,0 @@
-import * as DG from 'datagrok-api/dg';
-
-import * as rxjs from 'rxjs';
-
-import {StringDictionary} from '@datagrok-libraries/utils/src/type-declarations';
-import {MultipleSelection} from './SAR-multiple-selection';
-import {FilteringStatistics, Stats as FilterStats} from './filtering-statistics';
-
-import * as C from './constants';
-
-/**
- * Implements multiple filtering callbacks to be used in events subscription.
- */
-export class SARMultipleFilter {
-  protected selection: MultipleSelection;
-  protected resources: Resources;
-  protected filterMode: boolean;
-  protected stats: FilteringStatistics;
-
-  /**
-   * Creates an instance of SARMultipleFilter.
-   * @param {boolean} filterMode Whether to filter or to select.
-   */
-  constructor(filterMode: boolean) {
-    this.filterMode = filterMode;
-    this.resources = new Resources();
-    this.selection = new MultipleSelection();
-    this.stats = new FilteringStatistics();
-  }
-
-  /** Makes label to display filtered residue-positions on accordion. */
-  get filterLabel() {
-    return this.selection.toString();
-  }
-
-  /** Makes query to display data frame statistics on accordion. */
-  get query(): string {
-    this.resources.assert(['residueColumnName']);
-    return this.selection.toQuery(this.resources.residueColumnName);
-  }
-
-  /**
-   * Updates filtering mode.
-   * @param {boolean} value Filtering if true or selection else.
-   */
-  set filteringMode(value: boolean) {
-    this.filterMode = value;
-  }
-
-  /** Returns bit set obtained from selection mask. */
-  get mask() {
-    this.resources.assert(['dataFrame', 'groupMapping']);
-
-    const df = this.resources.dataFrame!;
-    const mask = this.selection.eval(df, this.resources.groupMapping!);
-    return DG.BitSet.create(mask.length, (i) => mask[i]);
-  }
-
-  /** Resets selection mask. */
-  resetSelection() {
-    this.selection = new MultipleSelection();
-  }
-
-  /**
-   * Adds/updates one of objects required.
-   * @param {ResourceKey} key Resource key.
-   * @param {any} value Resource value.
-   */
-  addResource(key: ResourceKey, value: any) {
-    this.resources.add(key, value);
-  }
-
-  /**
-   * Evaluates selection into mask.
-   * @return {boolean[]} List of booleans where a true corresponds to the row selected.
-   */
-  eval(): boolean[] {
-    this.resources.assert(['dataFrame', 'groupMapping']);
-    return this.selection.eval(this.resources.dataFrame!, this.resources.groupMapping!);
-  }
-
-  /**
-   * Reacts on mouse event.
-   * @param {MouseEventType} eventType Mouse event type.
-   * @param {CellType} cellType Type of the grid cell.
-   * @param {(string | null)} colName Name of column the cell from.
-   * @param {(number | null)} rowIdx Index of the row the cell at.
-   * @param {boolean} ctrlPressed Whether CTRL-button was pressed while catching event.
-   */
-  onSARGridMouseEvent(
-    eventType: MouseEventType,
-    cellType: CellType,
-    colName: string | null,
-    rowIdx: number | null,
-    ctrlPressed: boolean,
-  ) {
-    switch (eventType) {
-    case 'mouseout':
-      this.onSARCellMouseOut();
-      break;
-    case 'click':
-      if (colName)
-        this.onSARCellClicked(colName, rowIdx, ctrlPressed);
-      break;
-    case 'mousemove':
-      this.onSARCellHover(colName, rowIdx);
-      break;
-    }
-  }
-
-  /**
-   * Reacts on click to the SAR viewer cell.
-   * @param {string} colName Name of the column which the cell is from.
-   * @param {(number | null)} rowIdx Index of the row at which the cell is.
-   * @param {boolean} ctrlPressed Whether the CTRL button was pressed.
-   */
-  onSARCellClicked(colName: string, rowIdx: number | null, ctrlPressed: boolean) {
-    this.resources.assert(['dataFrame', 'residueColumnName', 'grid']);
-
-    const residueColumnName = this.resources.residueColumnName!;
-    const grid = this.resources.grid!;
-    const isMultiposSel = colName == residueColumnName;
-    const isMultiresSel = rowIdx === null;
-
-    if (isMultiposSel && isMultiresSel)
-      return;
-
-    const changeFilter = ctrlPressed ? this.selection.input : this.selection.set;
-    const df = grid.dataFrame!;
-    const columns = df.columns as DG.ColumnList;
-    let pos: string | undefined;
-    let res: string | undefined;
-
-    if (!isMultiposSel)
-      pos = colName;
-    if (!isMultiresSel)
-      res = df.get(residueColumnName, rowIdx);
-
-    if (isMultiposSel)
-      this.selection.setRes(res!, columns.names().slice(1)); // All except the first residues column.
-    else if (isMultiresSel)
-      this.selection.setPos(pos!, df.col(residueColumnName)!.toList());
-    else
-      changeFilter.bind(this.selection)(pos!, res!);
-
-    // console.warn([ctrlPressed ? 'ctrl+click' : 'click', this.selection.filter]);
-
-    if (this.filterMode)
-      this.resources.dataFrame!.rows.requestFilter();
-    else
-      this.maskRows();
-
-    this.createSplitCol();
-    this.resources.dataFrame!.temp[C.STATS] = this.getStatistics();
-
-    grid.invalidate();
-  }
-
-  createSplitCol() {
-    this.resources.assert(['grid', 'dataFrame']);
-
-    const viewerDf = this.resources.grid!.dataFrame!;
-    const df = this.resources.dataFrame!;
-    let aarLabel = this.filterLabel;
-    if (aarLabel === '') {
-      const currentAAR: string = viewerDf.get(C.COLUMNS_NAMES.AMINO_ACID_RESIDUE, viewerDf.currentRowIdx);
-      const currentPosition = viewerDf.currentCol?.name;
-
-      aarLabel = (currentAAR && currentPosition) ?? true ? 'All' :
-        `${currentAAR === '-' ? 'Gap' : currentAAR} - ${currentPosition}`;
-    }
-
-    const splitCol = df.col(C.COLUMNS_NAMES.SPLIT_COL) ??
-    df.columns.addNew(C.COLUMNS_NAMES.SPLIT_COL, 'string') as DG.Column;
-
-    const bitset = this.filterMode ? df.filter : df.selection;
-    splitCol.init((i) => bitset.get(i) ? aarLabel : C.CATEGORIES.OTHER);
-    splitCol.setCategoryOrder([aarLabel, C.CATEGORIES.OTHER]);
-    splitCol.compact();
-
-    const colorMap: {[index: string]: string | number} = {};
-
-    colorMap[C.CATEGORIES.OTHER] = DG.Color.blue;
-    colorMap[aarLabel] = DG.Color.orange;
-    // colorMap[currentAAR] = cp.getColor(currentAAR);
-    df.getCol(C.COLUMNS_NAMES.SPLIT_COL).colors.setCategorical(colorMap);
-  }
-
-  /**
-   * Reacts on mouse hover over SAR viewer cell.
-   * @param {(string | null)} colName Name of the column which the cell is from.
-   * @param {(number | null)} rowIdx Index of the row at which the cell is.
-   */
-  onSARCellHover(colName: string | null, rowIdx: number | null) {
-    this.resources.assert(['residueColumnName', 'grid', 'dataFrame']);
-
-    const residueColumnName = this.resources.residueColumnName!;
-
-    if (!colName || !rowIdx || colName == residueColumnName)
-      return;
-
-    const df = this.resources.grid?.dataFrame!;
-
-    if (!(df.columns as DG.ColumnList).names().includes(colName))
-      return;
-
-    const res = df.get(residueColumnName, rowIdx);
-
-    this.resources.dataFrame?.rows.match({[colName]: res}).highlight();
-  }
-
-  /** Reacts on mouse out from the SAR viewer */
-  onSARCellMouseOut() {
-    this.resources.assert(['dataFrame']);
-    this.resources.dataFrame?.rows.match({}).highlight();
-  }
-
-  /** Sets up SAR viewer grid visualization. */
-  setupGridVizualization() {
-    this.resources.assert(['grid']);
-    this.resources.grid?.setOptions({
-      'showCurrentRowIndicator': false,
-      'allowBlockSelection': false,
-      'allowColSelection': false,
-      'allowRowSelection': false,
-      'showMouseOverRowIndicator': false,
-    });
-  }
-
-  /**
-   * Custom renderrer to be applied to SAR viewer cell rendering.
-   * @param {DG.GridCellRenderArgs} args Cell rendering arguments.
-   */
-  selectionCellRenderrer(args: DG.GridCellRenderArgs) {
-    if (args.cell.isTableCell) {
-      this.resources.assert(['residueColumnName', 'groupMapping']);
-
-      const residueColumnName = this.resources.residueColumnName!;
-      const cell = args.cell;
-      const pos = cell.gridColumn.name;
-
-      if (pos !== residueColumnName) {
-        const rowIdx = cell.tableRowIndex!;
-        const res = cell.cell.dataFrame.get(residueColumnName, rowIdx);
-
-        if (this.selection.test(pos, res, this.resources.groupMapping!)) {
-          const ctx = args.g;
-          ctx.lineWidth = 1;
-          ctx.strokeStyle = 'black';
-          ctx.strokeRect(args.bounds.x, args.bounds.y, args.bounds.width, args.bounds.height);
-        }
-      }
-    }
-  }
-
-  /** Reacts on SAR grid update/reloading. */
-  onSARGridChanged() {
-    this.resources.assert(['grid']);
-
-    const grid = this.resources.grid!;
-
-    addGridMouseHandler(grid, this.onSARGridMouseEvent.bind(this));
-    this.setupGridVizualization();
-    grid.onCellRender.subscribe(this.selectionCellRenderrer.bind(this));
-  }
-
-  /** Selects or filters rows depending from the filtering mode set. */
-  maskRows() {
-    this.resources.assert(['dataFrame']);
-
-    const df = this.resources.dataFrame!;
-
-    if (this.filterMode) {
-      df.filter.and(this.mask);
-      df.selection.setAll(false, false);
-
-      // console.warn(['onRowsFiltering', this.selection.filter, df.filter.trueCount]);
-    } else {
-      df.selection.copyFrom(this.mask);
-      df.filter.fireChanged();
-
-      // console.warn(['onSelectionChanged', this.selection.filter, df.selection.trueCount]);
-    }
-  }
-
-  /**
-   * Calculates statistics on the activity column.
-   * @return {FilterStats} Statistics.
-   */
-  getStatistics(): FilterStats {
-    this.resources.assert(['activityColumnName', 'dataFrame']);
-
-    const df = this.resources.dataFrame!;
-
-    this.stats.setData(df.col(this.resources.activityColumnName!)?.getRawData() as Float32Array);
-    this.stats.setMask(this.mask);
-    return this.stats.result;
-  }
-}
-
-/** Declares resources needed by the filtering. */
-interface FilterResources {
-  residueColumnName?: string;
-  activityColumnName?: string;
-  grid?: DG.Grid;
-  dataFrame?: DG.DataFrame;
-  groupMapping?: StringDictionary;
-};
-
-type ResourceKey = keyof FilterResources;
-
-/** Resources controlling helper */
-class Resources {
-  protected data: FilterResources;
-
-  /** Creates an instance of Resources. */
-  constructor() {
-    this.data = {};
-  }
-
-  /**
-   * Adds/updates the resource given.
-   * @param {ResourceKey} resource Resource key.
-   * @param {any} value Resource value.
-   */
-  add(resource: ResourceKey, value: any) {
-    this.data[resource] = value;
-  }
-
-  /**
-   * Checks if all requested resources were added previously.
-   * @param {ResourceKey[]} resources Requested resources.
-   * @return {boolean} True if all those resources are initialized.
-   */
-  enough(resources: ResourceKey[]): boolean {
-    return resources.every((k) => this.data[k] !== undefined);
-  }
-
-  /**
-   * Throws an error if one of the resources given was not set.
-   * @param {ResourceKey[]} [resources] Optional set of resources to check.
-   */
-  assert(resources?: ResourceKey[]) {
-    if (resources) {
-      if (!this.enough(resources))
-        throw new Error(`Not enough one of ${resources} or more.`);
-    } else {
-      if (!this.ready())
-        throw new Error(`Resources are not ready.`);
-    }
-  }
-
-  /**
-   * Checks if all resources were initialized.
-   * @return {boolean} True if the test was successful.
-   */
-  ready(): boolean {
-    return Object.values(this.data).every((v) => v !== undefined);
-  }
-
-  /** Data frame resource. */
-  get dataFrame() {
-    return this.data.dataFrame;
-  }
-
-  /** Grid resource. */
-  get grid() {
-    return this.data.grid;
-  }
-
-  /** Group mapping. */
-  get groupMapping() {
-    return this.data.groupMapping;
-  }
-
-  /** Residue column name. */
-  get residueColumnName() {
-    return this.data.residueColumnName;
-  }
-
-  /** Activity column name. */
-  get activityColumnName() {
-    return this.data.activityColumnName;
-  }
-}
-
-const MouseEventsSource = {
-  click: 0,
-  mousemove: 1,
-  mouseout: 2,
-};
-const MouseEvents = Object.keys(MouseEventsSource);
-export type MouseEventType = keyof typeof MouseEventsSource;
-export type CellType = 'isTableCell' | 'isColHeader' | 'unknown';
-
-  type MouseEventHandler = (
-    eventType: MouseEventType,
-    cellType: CellType,
-    colName: string | null,
-    rowIdx: number | null,
-    ctrlPressed: boolean
-  ) => void;
-
-/**
-   * Adds mouse event handler to the click event bus.
-   * @param {DG.Grid} grid Grid to add to.
-   * @param {MouseEventHandler} handler Event handler.
-   */
-export function addGridMouseHandler(grid: DG.Grid, handler: MouseEventHandler) {
-  const onMouseEvent = (mouseEvent: MouseEvent) => {
-    if (!MouseEvents.includes(mouseEvent.type))
-      return;
-
-    const mouseEventType: MouseEventType = mouseEvent.type as MouseEventType;
-    const keyPressed = mouseEvent.ctrlKey || mouseEvent.metaKey;
-    const cell = grid.hitTest(mouseEvent.offsetX, mouseEvent.offsetY);
-    let pos: string | null = null;
-    let rowIdx: number | null = null;
-    let cellType: CellType = 'unknown';
-
-    if (cell) {
-      pos = cell.gridColumn.name;
-
-      if (pos.length == 0)
-        pos = null;
-
-      if (cell.isTableCell) {
-        rowIdx = cell.tableRowIndex!;
-        cellType = 'isTableCell';
-      } else if (cell.isColHeader)
-        cellType = 'isColHeader';
-    }
-
-    handler(mouseEventType, cellType, pos, rowIdx, keyPressed);
-  };
-
-  for (const e of MouseEvents)
-    rxjs.fromEvent<MouseEvent>(grid.overlay, e).subscribe(onMouseEvent);
-}

package/src/utils/SAR-multiple-selection.ts

@@ -1,177 +0,0 @@
-import * as DG from 'datagrok-api/dg';
-
-import {StringDictionary} from '@datagrok-libraries/utils/src/type-declarations';
-
-type Operation = (op1: boolean, op2: boolean) => boolean;
-
-/** Logical operations awailable between selection items. */
-const Operations: {[op: string]: Operation} = {
-  and: (op1: boolean, op2: boolean) => op1 && op2,
-  or: (op1: boolean, op2: boolean) => op1 || op2,
-};
-
-type FilterOperation = 'and' | 'or';
-type PositionFilter = {[pos: string]: Set<string>};
-
-/** Implements multiple selection in position-residue space. */
-export class MultipleSelection {
-  conjunction: boolean;
-  filter: PositionFilter;
-  protected operation: Operation;
-  protected complete: (v: boolean) => boolean;
-
-  /**
-   * Creates an instance of MultipleSelection.
-   * @param {FilterOperation} [operation='and'] Operation to apply to items.
-   */
-  constructor(operation: FilterOperation = 'and') {
-    this.conjunction = operation == 'and';
-    this.filter = {};
-    this.operation = Operations[operation];
-    this.complete = (v: boolean) => (this.conjunction && !v) || (!this.conjunction && v);
-  }
-
-  /**
-   * Adds position-residue entity into selection.
-   * @param {string} pos Position in a sequence.
-   * @param {string} res Residue at the position.
-   */
-  input(pos: string, res: string) {
-    if (!this.filter[pos])
-      this.filter[pos] = new Set([]);
-
-    if (this.filter[pos].has(res))
-      this.remove(pos, res);
-    else
-      this.filter[pos].add(res);
-  }
-
-  /**
-   * Removes position-residue entity from selection.
-   * @param {string} pos Position in a sequence.
-   * @param {string} res Residue at the position.
-   */
-  remove(pos: string, res: string) {
-    if (this.filter[pos]) {
-      this.filter[pos].delete(res);
-
-      if (this.filter[pos].size == 0)
-        delete this.filter[pos];
-    }
-  }
-
-  /**
-   * Sets the particular residue at position into selection.
-   * @param {string} pos Position in a sequence.
-   * @param {string} res Residue at the position.
-   */
-  set(pos: string, res: string) {
-    for (const p of Object.keys(this.filter))
-      delete this.filter[p];
-
-    this.filter[pos] = new Set([res]);
-  }
-
-  /**
-   * Sets the particular position with the given residues into selection.
-   * @param {string} pos Position in a sequence.
-   * @param {string[]} values Residues list at the position.
-   */
-  setPos(pos: string, values: string[]) {
-    this.filter[pos] = new Set(values);
-  }
-
-  /**
-   * Sets the particular residue to be at given positions into selection.
-   * @param {string} res Residue to set.
-   * @param {string[]} values Positions list to assign the residue to.
-   */
-  setRes(res: string, values: string[]) {
-    for (const pos of values) {
-      if (this.filter[pos])
-        this.filter[pos].add(res);
-      else
-        this.filter[pos] = new Set([res]);
-    }
-  }
-
-  /**
-   * Evaluates selection into a list of booleans of the same length as the given data frame.
-   * @param {DG.DataFrame} df Data frame to consider.
-   * @param {StringDictionary} [mapper={}] Optional residues mapper.
-   * @return {boolean[]} List of trues/falses corresponding selection constructed.
-   */
-  eval(df: DG.DataFrame, mapper: StringDictionary = {}): boolean[] {
-    const itemsCount = df.rowCount;
-    const cond = new Array<boolean>(itemsCount).fill(this.conjunction);
-
-    for (let i = 0; i < itemsCount; ++i)
-      cond[i] = this.match(i, df, mapper);
-
-    return cond;
-  }
-
-  /**
-   * Tests if i-th element matches filter.
-   * @param {number} i Element's index
-   * @param {DG.DataFrame} df Data frame to consider.
-   * @param {StringDictionary} [mapper={}] Optional residues mapper.
-   * @return {boolean} Result of the test.
-   */
-  match(i: number, df: DG.DataFrame, mapper: StringDictionary = {}): boolean {
-    let cond: boolean = this.conjunction;
-
-    for (const [posColumnName, resFilter] of Object.entries(this.filter)) {
-      const residue = df.get(posColumnName, i);
-      const isMatched = resFilter.has(mapper[residue] ?? residue);
-      cond = this.operation(cond, isMatched);
-
-      if (this.complete(cond))
-        break;
-    }
-    return cond;
-  }
-
-  /**
-   * Tests if position-residue is selected.
-   * @param {string} pos Position in a sequence.
-   * @param {string} res Residue at the position.
-   * @param {StringDictionary} [mapper={}] Optional residues mapper.
-   * @return {boolean} True if this entity is selected else false.
-   */
-  test(pos: string, res: string, mapper: StringDictionary = {}): boolean {
-    if (this.filter[pos])
-      return this.filter[pos].has(mapper[res] ?? res);
-
-    return false;
-  }
-
-  /**
-   * Make string representation of the selected items.
-   * @return {string} String representation.
-   */
-  toString(): string {
-    let repr = '';
-
-    for (const [pos, res] of Object.entries(this.filter))
-      repr += `${pos}: ${Array.from(res).join(',')}\n`;
-
-    return repr;
-  }
-
-  /**
-   * Turns filter into grouping query string.
-   * @param {string} [residueColumnName='Res'] Optional residues column name.
-   * @return {string} Query-formatted string.
-   */
-  toQuery(residueColumnName: string = 'Res'): string {
-    const alt: string[] = [];
-
-    for (const [pos, residues] of Object.entries(this.filter)) {
-      for (const res of residues)
-        alt.push(`${residueColumnName} = ${res} and Pos = ${pos}`);
-    }
-
-    return alt.join(' or ');
-  }
-}