@datagrok/sequence-translator 1.2.7 → 1.3.0

package/src/model/pattern-app/oligo-pattern.ts

@@ -1,111 +0,0 @@
-import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
-import * as DG from 'datagrok-api/dg';
-// @ts-ignore
-import * as svg from 'save-svg-as-png';
-import $ from 'cash-dom';
-
-import {isOverhang} from './helpers';
-import {axolabsStyleMap} from '../data-loading-utils/json-loader';
-
-export function generateExample(sequenceLength: number, sequenceBasis: string): string {
-  const AXOLABS_MAP = axolabsStyleMap;
-  const uniqueSymbols = AXOLABS_MAP[sequenceBasis].symbols.join('');
-  return uniqueSymbols.repeat(Math.floor(sequenceLength / 4)) + uniqueSymbols.slice(0, sequenceLength % 4);
-}
-
-export function findDuplicates(data: Int32Array | Float32Array | Float64Array | Uint32Array): number[] {
-  return Array.from(new Set(data)).filter((value) => data.indexOf(value) !== data.lastIndexOf(value));
-}
-
-export async function isCurrentUserCreatedThisPattern(patternName: string): Promise<boolean> {
-  return await grok.dapi.users.current().then((user) => {
-    const [firstName, lastName] = getUserName(patternName);
-    return (user.firstName !== firstName || user.lastName !== lastName);
-  });
-}
-
-export function getShortName(patternName: string): string {
-  let first = patternName.length + 1;
-  for (let i = 0; i < patternName.length; i++) {
-    if (patternName[i] === '(') {
-      first = i;
-      break;
-    }
-  }
-  return patternName.slice(0, first - 1);
-}
-
-function getUserName(patternName: string): string[] {
-  let first = -1;
-  for (let i = 0; i < patternName.length; i++) {
-    if (patternName[i] === '(') {
-      first = i;
-      break;
-    }
-  }
-  return (first === -1) ? ['', ''] : patternName.slice(first + 9, patternName.length - 1).split(' ').slice(1);
-}
-
-export function translateSequence(
-  sequence: string,
-  bases: DG.InputBase[],
-  ptoLinkages: DG.InputBase[],
-  startModification: DG.InputBase,
-  endModification: DG.InputBase,
-  firstPtoExist: boolean): string {
-  let i: number = -1;
-  let mainSequence = sequence.replace(/[AUGC]/g, function(x: string) {
-    i++;
-    const AXOLABS_MAP = axolabsStyleMap;
-
-    const baseChoices: string[] = Object.keys(AXOLABS_MAP);
-    // const defaultBase: string = baseChoices[0];
-    const indexOfSymbol = AXOLABS_MAP['RNA']['symbols'].indexOf(x);
-    let symbol = AXOLABS_MAP[bases[i].value]['symbols'][indexOfSymbol];
-    if (isOverhang(bases[i].value)) {
-      if (i < sequence.length / 2 && !isOverhang(bases[i + 1].value))
-        symbol = symbol + x + 'f';
-      else if (i > sequence.length / 2 && !isOverhang(bases[i - 1].value))
-        symbol = x + 'f' + symbol;
-    }
-    return (ptoLinkages[i].value) ? symbol + 's' : symbol;
-  });
-  if (mainSequence.slice(0, 5).split('mU').length === 3)
-    mainSequence = '(uu)' + mainSequence.slice(4);
-  if (mainSequence.slice(mainSequence.length - 7).split('mU').length === 3)
-    mainSequence = mainSequence.slice(0, mainSequence.length - 4) + '(uu)';
-  return startModification.value + (firstPtoExist ? 's' : '') + mainSequence + endModification.value;
-}
-
-export function addColumnWithIds(tableName: string, columnName: string, patternName: string) {
-  const nameOfNewColumn = 'ID ' + patternName;
-  const columns = grok.shell.table(tableName).columns;
-  if (columns.contains(nameOfNewColumn))
-    columns.remove(nameOfNewColumn);
-  const columnWithIds = columns.byName(columnName);
-  return columns.addNewString(nameOfNewColumn).init((i: number) => {
-    return (columnWithIds.getString(i) === '') ? '' : columnWithIds.get(i) + '_' + patternName;
-  });
-}
-
-export function addColumnWithTranslatedSequences(
-  tableName: string,
-  columnName: string,
-  bases: DG.InputBase[],
-  ptoLinkages: DG.InputBase[],
-  startModification: DG.InputBase,
-  endModification: DG.InputBase,
-  firstPtoExist: boolean) {
-  const nameOfNewColumn = 'Axolabs ' + columnName;
-  const columns = grok.shell.table(tableName).columns;
-  if (columns.contains(nameOfNewColumn))
-    columns.remove(nameOfNewColumn);
-  const columnWithInputSequences = columns.byName(columnName);
-  return columns.addNewString(nameOfNewColumn).init((i: number) => {
-    return columnWithInputSequences.getString(i) === '' ?
-      '' :
-      translateSequence(columnWithInputSequences.getString(i), bases, ptoLinkages, startModification, endModification,
-        firstPtoExist);
-  });
-}

package/src/view/app-ui.ts

@@ -1,193 +0,0 @@
-/* Do not change these import lines to match external modules in webpack configuration */
-import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
-import * as DG from 'datagrok-api/dg';
-
-import {TAB, APP} from './const/ui';
-import {TranslatorLayoutHandler} from './apps/oligo-translator';
-import {StructureLayoutHandler} from './apps/oligo-structure';
-import {PatternLayoutHandler} from './apps/oligo-pattern';
-import {MonomerLibViewer} from './monomer-lib-viewer/viewer';
-import {_package} from '../package';
-import {tryCatch} from '../model/helpers';
-
-type ViewFactories = {[name: string]: () => DG.View};
-
-export abstract class AppUIBase {
-  constructor(protected appName: string, protected parentAppName?: string) { }
-  abstract addView(): Promise<void>;
-
-  async createAppLayout(): Promise<void> {
-    const pi: DG.TaskBarProgressIndicator = DG.TaskBarProgressIndicator.create(`Loading ${this.appName}...`);
-
-    let currentView = grok.shell.v?.root;
-    if (currentView)
-      ui.setUpdateIndicator(currentView, true);
-
-    await tryCatch(async () => {
-      await this.addView();
-    }, () => pi.close());
-
-    if (currentView)
-      ui.setUpdateIndicator(currentView, false);
-  }
-}
-
-abstract class SimpleAppUIBase extends AppUIBase {
-  constructor(appName: string) {
-    super(appName);
-    this.view = DG.View.create();
-    this.setupView();
-  }
-
-  protected view: DG.View;
-  async addView(): Promise<void> {
-    await this.initView();
-    const name = this.parentAppName ? this.parentAppName + '/' + this.appName : this.appName;
-    this.view.path = `/apps/${_package.name}/${name.replace(/\s/g, '')}/`;
-    grok.shell.addView(this.view);
-  }
-
-  protected abstract getHtml(): Promise<HTMLDivElement>;
-  async initView(): Promise<void> {
-    const html = await this.getHtml();
-    this.view.append(html);
-  }
-
-  protected setupView(): void {
-    this.view.box = true;
-    this.view.name = this.appName;
-
-    const windows = grok.shell.windows;
-    windows.showProperties = false;
-    windows.showToolbox = false;
-    windows.showHelp = false;
-  }
-
-  getView(): DG.View {
-    return this.view;
-  }
-}
-
-export class CombinedAppUI extends AppUIBase {
-  constructor(externalViewFactories: ViewFactories) {
-    super(APP.COMBINED)
-    this.externalViewFactories = externalViewFactories;
-    const factories = this.getViewFactories();
-    this.multiView = new DG.MultiView({viewFactories: factories}); 
-  }
-
-  private multiView: DG.MultiView;
-  private externalViewFactories?: ViewFactories;
-
-  private getViewFactories(): ViewFactories {
-    function viewFactory(uiConstructor: new (view: DG.View) => SimpleAppUIBase): () => DG.View {
-      const view = DG.View.create();
-      const translateUI = new uiConstructor(view);
-      // intentonally don't await for the promise
-      translateUI.initView();
-      return () => translateUI.getView();
-    }
-
-    let result: {[key: string]: () => DG.View } = {
-      [TAB.TRANSLATOR]: viewFactory(OligoTranslatorUI),
-      [TAB.PATTERN]: viewFactory(OligoPatternUI),
-      [TAB.STRUCTRE]: viewFactory(OligoStructureUI),
-    }
-
-    if (this.externalViewFactories)
-      result = Object.assign({}, result, this.externalViewFactories);
-
-    return result
-  }
-
-  private getPath(): string {
-    let name = this.multiView.tabs.currentPane.name;
-    name = name.charAt(0).toUpperCase() + name.substring(1).toLowerCase();
-    const path = `/apps/${_package.name}/OligoToolkit/${name}`;
-    return path;
-  }
-
-  private setUrl(): void {
-    this.multiView.path = this.getPath();
-  }
-
-  async addView(): Promise<void> {
-    this.multiView.tabs.onTabChanged.subscribe(() => this.setUrl());
-    this.setUrl();
-    grok.shell.addView(this.multiView);
-  }
-}
-
-/** For plugins from external packages */
-export class ExternalPluginUI extends SimpleAppUIBase {
-  constructor(viewName: string, layout: HTMLDivElement) {
-    super(viewName);
-    this.layout = layout;
-  }
-  private layout: HTMLDivElement;
-
-  protected getHtml(): Promise<HTMLDivElement> {
-    return Promise.resolve(this.layout);
-  }
-}
-
-export class AppUIFactory {
-  private constructor() {}
-
-  static getUI(appName: string): SimpleAppUIBase {
-    switch (appName) {
-      case APP.TRANSLATOR:
-        return new OligoTranslatorUI();
-      case APP.PATTERN:
-        return new OligoPatternUI();
-      case APP.STRUCTRE:
-        return new OligoStructureUI();
-      default:
-        throw new Error(`Unknown app name: ${appName}`);
-    }
-  }
-}
-
-class OligoTranslatorUI extends SimpleAppUIBase {
-  constructor() {
-    super(APP.TRANSLATOR);
-
-    const viewMonomerLibIcon = ui.iconFA('book', MonomerLibViewer.view, 'View monomer library');
-    this.topPanel = [
-      viewMonomerLibIcon,
-    ];
-    this.view.setRibbonPanels([this.topPanel]);
-    this.ui = new TranslatorLayoutHandler();
-  }
-
-  private readonly topPanel: HTMLElement[];
-  private readonly ui: TranslatorLayoutHandler;
-
-  protected getHtml(): Promise<HTMLDivElement> {
-    return this.ui.getHtmlElement();
-  };
-}
-
-class OligoPatternUI extends SimpleAppUIBase {
-  constructor() {
-    super(APP.PATTERN);
-    this.ui = new PatternLayoutHandler();
-  }
-  private readonly ui: PatternLayoutHandler;
-  protected getHtml(): Promise<HTMLDivElement> {
-    return Promise.resolve(this.ui.htmlDivElement);
-  }
-}
-
-class OligoStructureUI extends SimpleAppUIBase {
-  constructor() {
-    super(APP.STRUCTRE)
-    this.ui = new StructureLayoutHandler();
-  }
-  private readonly ui: StructureLayoutHandler;
-
-  protected getHtml(): Promise<HTMLDivElement> {
-    return this.ui.getHtmlDivElement();
-  }
-}