@datagrok/sequence-translator 1.3.5 → 1.3.10

package/webpack.config.js

@@ -2,9 +2,7 @@ const path = require('path');
 const packageName = path.parse(require('./package.json').name).name.toLowerCase().replace(/-/g, '');
 
 module.exports = {
-  cache: {
-    type: 'filesystem',
-  },
+  cache: {type: 'filesystem'},
   mode: 'development',
   entry: {
     package: ['./src/package.ts'],
@@ -12,7 +10,7 @@ module.exports = {
       filename: 'package-test.js',
       library: {type: 'var', name: `${packageName}_test`},
       import: './src/package-test.ts',
-    }
+    },
   },
   resolve: {
     extensions: ['.ts', '.tsx', '.wasm', '.mjs', '.js', '.json'],

package/src/polytool/pt-enumeration.ts

@@ -1,141 +0,0 @@
-import * as ui from 'datagrok-api/ui';
-import * as grok from 'datagrok-api/grok';
-import * as DG from 'datagrok-api/dg';
-
-import {IHelmHelper, getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
-import {IHelmWebEditor} from '@datagrok-libraries/bio/src/helm/types';
-import '@datagrok-libraries/bio/src/types/helm';
-import '@datagrok-libraries/bio/src/types/jsdraw2';
-import * as org from 'org';
-import $ from 'cash-dom';
-import {Unsubscribable, fromEvent} from 'rxjs';
-import {IMonomerLibFileManager, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
-import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
-
-import {Chain} from './pt-conversion';
-
-const LIB_PATH = 'System:AppData/Bio/monomer-libraries/';
-const PT_HELM_EXAMPLE = 'PEPTIDE1{[R].[F].[T].[G].[H].[F].[G].[A].[A].[Y].[P].[E].[NH2]}$$$$';
-
-export async function getLibrariesList(): Promise<string[]> {
-  const monomerLibHelper: IMonomerLibHelper = await grok.functions.call('Bio:getMonomerLibHelper', {});
-  const monomerFileManager: IMonomerLibFileManager = await monomerLibHelper.getFileManager();
-  return monomerFileManager.getValidLibraryPaths();
-}
-
-export async function getEnumeration(helmString: string, helmSelections: number[], screenLibrary: string):
-  Promise<string[]> {
-  const variableMonomers = await getAvaialableMonomers(screenLibrary);
-  const chain: Chain = Chain.fromHelm(helmString);
-  const size = helmSelections.length*variableMonomers.length;
-  const enumerations = new Array<string>(size);
-
-  for (let i = 0; i < helmSelections.length; i++) {
-    for (let j = 0; j < variableMonomers.length; j++)
-      enumerations[i*variableMonomers.length + j] = chain.getHelmChanged(helmSelections[i], variableMonomers[j]);
-  }
-
-  return enumerations;
-}
-
-export class HelmInput {
-  webEditorHost: HTMLDivElement | null;
-  webEditorApp: org.helm.IWebEditorApp | null;
-  helmHelper: IHelmHelper;
-  editor: IHelmWebEditor;
-  subs: Unsubscribable[];
-
-  helmString: string = PT_HELM_EXAMPLE;
-  helmSelection: number[];
-
-  constructor(
-    helmHelper: IHelmHelper, editor: IHelmWebEditor) {
-    this.helmHelper = helmHelper;
-    this.editor = editor;
-
-    this.webEditorHost = null;
-    this.webEditorApp = null;
-    const subs: Unsubscribable[] = [];
-
-    subs.push(fromEvent<MouseEvent>(editor.host, 'click').subscribe(() => {
-      this.webEditorHost = ui.div();
-      //TODO: use not hh, but anything from editor.getHelm(true)
-      this.webEditorApp = helmHelper.createWebEditorApp(this.webEditorHost, this.getHelmString());
-      const dlg = ui.dialog({showHeader: false, showFooter: true})
-        .add(this.webEditorHost!)
-        .onOK(() => {
-          try {
-            const webEditorValue = this.webEditorApp!.canvas.getHelm(true)
-              .replace(/<\/span>/g, '').replace(/<span style='background:#bbf;'>/g, '');
-            editor.editor.setHelm(webEditorValue);
-            this.helmString = webEditorValue;
-            this.helmSelection = [];
-
-            //@ts-ignore
-            const selection = this.webEditorApp?.canvas.helm.jsd.m.atoms;
-            for (let i = 0; i < selection.length; i++) {
-              if (selection[i].selected)
-                this.helmSelection.push(i);
-            }
-          } catch (err: any) {
-            //this.logger.error(err);
-          } finally {
-            $(this.webEditorHost).empty();
-            this.webEditorHost = null;
-            this.webEditorApp = null;
-          }
-        })
-        .onCancel(() => {
-          $(this.webEditorHost).empty();
-          this.webEditorHost = null;
-          this.webEditorApp = null;
-        })
-        .show({modal: true, fullScreen: true});
-    }));
-  }
-
-  static async init() {
-    const helmHelper = await getHelmHelper();
-
-    const editor = helmHelper.createHelmWebEditor();
-    editor.host.style.width = '200px';
-    editor.host.style.height = '100px';
-    editor.host.style.paddingLeft = '40px';
-
-    const cell = grok.shell.tv.dataFrame.currentCell;
-
-    if (cell.column.semType === DG.SEMTYPE.MACROMOLECULE && cell.column.tags[DG.TAGS.UNITS] === NOTATION.HELM)
-      editor.editor.setHelm(cell.value);
-    else
-      editor.editor.setHelm(PT_HELM_EXAMPLE);
-
-    return new HelmInput(helmHelper, editor);
-  }
-
-  getHelmString(): string {
-    return this.helmString;
-  }
-
-  getHelmSelections() {
-    return this.helmSelection;
-  }
-
-  setHelmString(helm: string): void {
-    this.helmString = helm;
-    this.editor.editor.setHelm(helm);
-    this.helmSelection = [];
-  }
-
-  getDiv(): HTMLDivElement {
-    const title = ui.divText('Macromolecule', {style: {paddingTop: '43px', color: 'var(--grey-4)'}});
-
-    return ui.divH([title, this.editor.host], {style: {paddingLeft: '48px'}});
-  }
-}
-
-async function getAvaialableMonomers(screenLibrary: string): Promise<string[]> {
-  const monomerLibHelper: IMonomerLibHelper = await grok.functions.call('Bio:getMonomerLibHelper', {});
-  const monomerLib = await monomerLibHelper.readLibrary(LIB_PATH, screenLibrary);
-  //NOTICE: works with Peptides only
-  return monomerLib.getMonomerSymbolsByType('PEPTIDE');
-}