@datagrok/sequence-translator 1.2.6 → 1.2.9

package/src/{view/apps/oligo-structure.ts → apps/structure/view/ui.ts}

@@ -1,19 +1,20 @@
 /* Do not change these import lines to match external modules in webpack configuration */
+import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
-import * as DG from 'datagrok-api/dg';
 
-import * as rxjs from 'rxjs';
-import '../style/structure-app.css';
 import $ from 'cash-dom';
+import * as rxjs from 'rxjs';
+import './style.css';
 
 import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
 
-import {highlightInvalidSubsequence} from '../utils/colored-input/input-painters';
-import {getLinkedMolfile, saveSdf} from '../../model/structure-app/oligo-structure';
-import {ColoredTextInput} from '../utils/colored-input/colored-text-input';
-import {MoleculeImage} from '../utils/molecule-img';
-import {StrandData} from '../../model/structure-app/oligo-structure';
+import {ColoredTextInput} from '../../common/view/components/colored-input/colored-text-input';
+import {highlightInvalidSubsequence} from '../../common/view/components/colored-input/input-painters';
+import {MoleculeImage} from '../../common/view/components/molecule-img';
+import {APP_NAME} from '../../common/view/const';
+import {IsolatedAppUIBase} from '../../common/view/isolated-app-ui';
+import {getLinkedMolfile, saveSdf, StrandData} from '../model/oligo-structure';
 
 const enum DIRECTION {
   STRAIGHT = '5′ → 3′',
@@ -21,7 +22,7 @@ const enum DIRECTION {
 };
 const STRANDS = ['ss', 'as', 'as2'] as const;
 
-export class StructureLayoutHandler {
+class StructureAppLayout {
   constructor() {
     this.onInput = new rxjs.Subject<string>();
     this.onInvalidInput = new rxjs.Subject<string>();
@@ -98,7 +99,7 @@ export class StructureLayoutHandler {
           const selected = (idx === 0) ? DIRECTION.STRAIGHT : DIRECTION.INVERSE;
           return [key, ui.choiceInput(
             `${key.toUpperCase()} direction`, selected, [DIRECTION.STRAIGHT, DIRECTION.INVERSE]
-          )]
+          )];
         }
       )
     );
@@ -106,8 +107,9 @@ export class StructureLayoutHandler {
     STRANDS.forEach((strand, idx) => {
       directionChoiceInput[strand].onChanged(() => {
         let value = directionChoiceInput[strand].value === DIRECTION.INVERSE;
-        // warning: the next line is necessary until the legacy notion of direction used in the molfile generation gets fixed
-        if (idx > 0) { value = !value; }
+        // warning: the next line is necessary
+        // until the legacy notion of direction used in the molfile generation gets fixed
+        if (idx > 0) value = !value;
         this.directionInversion[strand] = value;
         this.onInput.next();
       });
@@ -126,7 +128,7 @@ export class StructureLayoutHandler {
     const clearBlock = Object.fromEntries(
       STRANDS.map(
         (key) => {
-          const clearIcon = ui.icons.delete(() => { coloredInput[key].inputBase.value = '' });
+          const clearIcon = ui.icons.delete(() => { coloredInput[key].inputBase.value = ''; });
           const clearButton = ui.button(clearIcon, () => {});
           ui.tooltip.bind(clearButton, `Clear ${key.toUpperCase()}`);
           return [key, clearIcon];
@@ -163,12 +165,12 @@ export class StructureLayoutHandler {
 
   private getStrandData() {
     return Object.fromEntries(
-      STRANDS.map((strand, idx) => {
-        let invert = this.directionInversion[strand];
+      STRANDS.map((strand) => {
+        const invert = this.directionInversion[strand];
         return [strand, {
           strand: this.inputBase[strand].value.replace(/\s*/g, ''),
           invert: invert
-        }]
+        }];
       })
     );
   }
@@ -192,7 +194,7 @@ export class StructureLayoutHandler {
       const errStr = errorToConsole(err);
       console.error(errStr);
     }
-    // todo: calculate relative numbers
+    // todo: compute relative numbers
     const canvasWidth = 650;
     const canvasHeight = 150;
     const molImgObj = new MoleculeImage(molfile);
@@ -201,3 +203,15 @@ export class StructureLayoutHandler {
     $(this.moleculeImgDiv).find('canvas').css('float', 'inherit');
   }
 }
+
+export class OligoStructureUI extends IsolatedAppUIBase {
+  constructor() {
+    super(APP_NAME.STRUCTURE);
+    this.layout = new StructureAppLayout();
+  }
+  private readonly layout: StructureAppLayout;
+
+  protected getContent(): Promise<HTMLDivElement> {
+    return this.layout.getHtmlDivElement();
+  }
+}

package/src/{model/translator-app → apps/translator/model}/conversion-utils.ts

@@ -1,17 +1,18 @@
-import {DEFAULT_FORMATS, NUCLEOTIDES} from '../const';
+import {DEFAULT_FORMATS, NUCLEOTIDES} from '../../common/model/const';
+import {NUCLEOTIDES_FORMAT} from '../view/const';
 import {UNKNOWN_SYMBOL} from './const';
 import {FormatConverter} from './format-converter';
-import {codesToHelmDictionary} from '../data-loading-utils/json-loader';
-import {MonomerLibWrapper} from '../monomer-lib/lib-wrapper';
+import {CODES_TO_HELM_DICT} from '../../common/model/data-loader/json-loader';
+import {MonomerLibWrapper} from '../../common/model/monomer-lib/lib-wrapper';
 
 export function getTranslatedSequences(sequence: string, indexOfFirstInvalidChar: number, sourceFormat: string): {[key: string]: string} {
-  const supportedFormats = Object.keys(codesToHelmDictionary).concat([DEFAULT_FORMATS.HELM]) as string[];
+  const supportedFormats = Object.keys(CODES_TO_HELM_DICT).concat([DEFAULT_FORMATS.HELM]) as string[];
 
   if (!sequence || (indexOfFirstInvalidChar !== -1 && sourceFormat !== DEFAULT_FORMATS.HELM))
     return {};
 
   if (!supportedFormats.includes(sourceFormat))
-    throw new Error(`${sourceFormat} format is not supported by SequenceTranslator`)
+    throw new Error(`${sourceFormat} format is not supported by SequenceTranslator`);
 
   const outputFormats = supportedFormats.filter((el) => el != sourceFormat)
     .sort((a, b) => a.localeCompare(b));
@@ -25,8 +26,8 @@ export function getTranslatedSequences(sequence: string, indexOfFirstInvalidChar
         translation = null;
       }
       return [format, translation];
-    }).filter(([format, translation]) => translation)
-  )
+    }).filter(([_, translation]) => translation)
+  );
   const helm = (sourceFormat === DEFAULT_FORMATS.HELM) ? sequence : result[DEFAULT_FORMATS.HELM];
   const nucleotides = getNucleotidesSequence(helm, MonomerLibWrapper.getInstance());
   if (nucleotides)
@@ -47,3 +48,20 @@ export function getNucleotidesSequence(helmString: string, monomerLib: MonomerLi
   }).map((el) => el ? el : UNKNOWN_SYMBOL).join('');
   return nucleotides;
 }
+
+// todo: remove after refactoring as a workaround
+export function convert(sequence: string, sourceFormat: string, targetFormat: string): string | null {
+  const converter = new FormatConverter(sequence, sourceFormat);
+  if (targetFormat === NUCLEOTIDES_FORMAT) {
+    const helm = converter.convertTo(DEFAULT_FORMATS.HELM);
+    const nucleotides = getNucleotidesSequence(helm, MonomerLibWrapper.getInstance());
+    return nucleotides;
+  }
+
+  return converter.convertTo(targetFormat);
+}
+
+export function getSupportedTargetFormats(): string[] {
+  const supportedTargetFormats = Object.keys(CODES_TO_HELM_DICT).concat([DEFAULT_FORMATS.HELM, NUCLEOTIDES_FORMAT]).sort() as string[];
+  return supportedTargetFormats;
+}

package/src/{model/translator-app → apps/translator/model}/format-converter.ts

@@ -1,7 +1,7 @@
 import * as DG from 'datagrok-api/dg';
-import {DEFAULT_FORMATS} from '../const';
+import {DEFAULT_FORMATS} from '../../common/model/const';
 import {PHOSPHATE_SYMBOL, UNKNOWN_SYMBOL} from './const';
-import {FormatHandler, getRegExpPattern} from '../parsing-validation/format-handler';
+import {FormatHandler, getRegExpPattern} from '../../common/model/parsing-validation/format-handler';
 
 const HELM_WRAPPER = {
   LEFT: 'RNA1{',
@@ -16,21 +16,16 @@ export class FormatConverter {
   convertTo(targetFormat: string): string {
     const formats = this.formats.getFormatNames();
 
-    if (this.sourceFormat === DEFAULT_FORMATS.HELM && formats.includes(targetFormat))
-      return this.helmToFormat(this.sequence, targetFormat);
-    else if (formats.includes(this.sourceFormat) && targetFormat === DEFAULT_FORMATS.HELM)
-      return this.formatToHelm(this.sequence, this.sourceFormat);
-    else if ([this.sourceFormat, targetFormat].every((el) => formats.includes(el))) {
+    if (this.sourceFormat === DEFAULT_FORMATS.HELM && formats.includes(targetFormat)) { return this.helmToFormat(this.sequence, targetFormat); } else if (formats.includes(this.sourceFormat) && targetFormat === DEFAULT_FORMATS.HELM) { return this.formatToHelm(this.sequence, this.sourceFormat); } else if ([this.sourceFormat, targetFormat].every((el) => formats.includes(el))) {
       const helm = this.formatToHelm(this.sequence, this.sourceFormat);
       return this.helmToFormat(helm, targetFormat);
-    }
-    else {
-      throw new Error (`ST: unsupported translation direction ${this.sourceFormat} -> ${targetFormat}`);
+    } else {
+      throw new Error(`ST: unsupported translation direction ${this.sourceFormat} -> ${targetFormat}`);
     }
   }
 
   private helmToFormat(helmSequence: string, targetFormat: string): string {
-    const wrapperRegExp = new RegExp(getRegExpPattern(Object.values(HELM_WRAPPER)), 'g')
+    const wrapperRegExp = new RegExp(getRegExpPattern(Object.values(HELM_WRAPPER)), 'g');
     let result = helmSequence.replace(wrapperRegExp, '');
 
     const dict = this.formats.getHelmToFormatDict(targetFormat);
@@ -54,7 +49,7 @@ export class FormatConverter {
     const phosphateRegExp = this.formats.getPhosphateHelmCodesRegExp(sourceFormat);
 
     let helm = sequence.replace(formatRegExp, (match) => {
-      const result = formatCodes.includes(match) ?  dict[match] + '.' : '?';
+      const result = formatCodes.includes(match) ? dict[match] + '.' : '?';
       return result;
     });
     helm = helm.replace(/\?+/g, `${UNKNOWN_SYMBOL}.`);

package/src/{view/const/oligo-translator.ts → apps/translator/view/const.ts}

@@ -1,3 +1,5 @@
 export const DEFAULT_INPUT = 'fAmCmGmAmCpsmU';
 export const SEQUENCE_COPIED_MSG = 'Copied';
 export const SEQ_TOOLTIP_MSG = 'Copy sequence';
+
+export const NUCLEOTIDES_FORMAT = 'Nucleotides';