@datagrok/sequence-translator 1.0.11 → 1.0.13

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.0.11",
+  "version": "1.0.13",
   "author": {
     "name": "Vadym Kovadlo",
     "email": "vkovadlo@datagrok.ai"
@@ -13,7 +13,7 @@
     "directory": "packages/SequenceTranslator"
   },
   "dependencies": {
-    "@datagrok-libraries/utils": "^1.11.1",
+    "@datagrok-libraries/utils": "^1.15.5",
     "@types/react": "^18.0.15",
     "datagrok-api": "^1.7.2",
     "datagrok-tools": "^4.1.2",

package/src/__jest__/remote.test.ts

@@ -43,27 +43,35 @@ it('TEST', async () => {
     return new Promise<object>((resolve, reject) => {
       (<any>window).grok.functions.eval(targetPackage + ':test()').then((df: any) => {
         const cStatus = df.columns.byName('success');
+        const cSkipped = df.columns.byName('skipped');
         const cMessage = df.columns.byName('result');
         const cCat = df.columns.byName('category');
         const cName = df.columns.byName('name');
         const cTime = df.columns.byName('ms');
         let failed = false;
+        let skipReport = '';
         let passReport = '';
         let failReport = '';
         for (let i = 0; i < df.rowCount; i++) {
           if (cStatus.get(i)) {
-            passReport += `Test result : Success : ${cTime.get(i)} : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
+            if (cSkipped.get(i)) {
+              skipReport += `Test result : Skipped : ${cTime.get(i)} : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
+            } else {
+              passReport += `Test result : Success : ${cTime.get(i)} : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
+            }
           } else {
             failed = true;
             failReport += `Test result : Failed : ${cTime.get(i)} : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
           }
         }
-        resolve({failReport, passReport, failed});
+        resolve({failReport, skipReport, passReport, failed});
       }).catch((e: any) => reject(e));
     });
   }, targetPackage);
   // @ts-ignore
   console.log(r.passReport);
   // @ts-ignore
+  console.log(r.skipReport);
+  // @ts-ignore
   expect(r.failed).checkOutput(false, r.failReport);
-}, 3600000);
+}, 7200000);

package/src/autostart/calculations.ts

@@ -0,0 +1,37 @@
+import * as DG from 'datagrok-api/dg';
+import {sortByStringLengthInDescendingOrder} from '../helpers';
+import {MODIFICATIONS} from '../structures-works/map';
+
+export function saltMass(
+  saltNames: string[], molWeightCol: DG.Column, equivalentsCol: DG.Column, i: number, saltCol: DG.Column,
+): number {
+  const saltRowIndex = saltNames.indexOf(saltCol.get(i));
+  return (
+    saltRowIndex == -1 || molWeightCol.get(saltRowIndex) == DG.FLOAT_NULL || equivalentsCol.get(i) == DG.INT_NULL
+  ) ?
+    DG.FLOAT_NULL :
+    molWeightCol.get(saltRowIndex) * equivalentsCol.get(i);
+}
+
+export function saltMolWeigth(saltNamesList: string[], saltCol: DG.Column, molWeightCol: DG.Column, i: number): number {
+  const saltRowIndex = saltNamesList.indexOf(saltCol.get(i));
+  return (saltRowIndex == -1) ? DG.FLOAT_NULL : molWeightCol.get(saltRowIndex);
+}
+
+export function batchMolWeight(compoundMolWeightCol: DG.Column, saltMassCol: DG.Column, i: number): number {
+  return (compoundMolWeightCol.getString(i) == '' || saltMassCol.getString(i) == '') ?
+    DG.FLOAT_NULL :
+    compoundMolWeightCol.get(i) + saltMassCol.get(i);
+}
+
+export function molecularWeight(sequence: string, weightsObj: {[index: string]: number}): number {
+  const codes = sortByStringLengthInDescendingOrder(Object.keys(weightsObj)).concat(Object.keys(MODIFICATIONS));
+  let weight = 0;
+  let i = 0;
+  while (i < sequence.length) {
+    const matchedCode = codes.find((s) => s == sequence.slice(i, i + s.length))!;
+    weight += weightsObj[sequence.slice(i, i + matchedCode.length)];
+    i += matchedCode.length;
+  }
+  return weight - 61.97;
+}

package/src/autostart/constants.ts

@@ -0,0 +1,37 @@
+export const SEQUENCE_TYPES = {
+  SENSE_STRAND: 'SS',
+  ANTISENSE_STRAND: 'AS',
+  DUPLEX: 'Duplex',
+  TRIPLEX: 'Triplex',
+  DIMER: 'Dimer',
+};
+
+export const COL_NAMES = {
+  CHEMISTRY: 'Chemistry',
+  NUMBER: 'Number',
+  TYPE: 'Type',
+  CHEMISTRY_NAME: 'Chemistry Name',
+  INTERNAL_COMPOUND_ID: 'Internal compound ID',
+  IDP: 'IDP',
+  SEQUENCE: 'Sequence',
+  COMPOUND_NAME: 'Compound Name',
+  COMPOUND_COMMENTS: 'Compound Comments',
+  SALT: 'Salt',
+  EQUIVALENTS: 'Equivalents',
+  PURITY: 'Purity',
+  COMPOUND_MOL_WEIGHT: 'Cpd MW',
+  SALT_MOL_WEIGHT: 'Salt MW',
+  SALT_MASS: 'Salt mass',
+  BATCH_MOL_WEIGHT: 'Batch MW',
+  SOURCE: 'Source',
+  ICD: 'ICD',
+  OWNER: 'Owner',
+};
+
+export const GENERATED_COL_NAMES = [
+  COL_NAMES.COMPOUND_NAME,
+  COL_NAMES.COMPOUND_COMMENTS,
+  COL_NAMES.COMPOUND_MOL_WEIGHT,
+  COL_NAMES.SALT_MASS,
+  COL_NAMES.BATCH_MOL_WEIGHT,
+];

package/src/autostart/registration.ts

@@ -3,90 +3,59 @@ import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import {siRnaBioSpringToGcrs, siRnaAxolabsToGcrs, gcrsToNucleotides, asoGapmersBioSpringToGcrs, gcrsToMermade12,
   siRnaNucleotidesToGcrs} from '../structures-works/converters';
-import {map, COL_NAMES, MODIFICATIONS} from '../structures-works/map';
+import {weightsObj, SYNTHESIZERS} from '../structures-works/map';
+import {SEQUENCE_TYPES, COL_NAMES, GENERATED_COL_NAMES} from './constants';
+import {saltMass, saltMolWeigth, molecularWeight, batchMolWeight} from './calculations';
 import {isValidSequence} from '../structures-works/sequence-codes-tools';
 import {sequenceToMolV3000} from '../structures-works/from-monomers';
-import {linkV3000} from '../structures-works/mol-transformations';
+import {linkStrandsV3000} from '../structures-works/mol-transformations';
+import {stringify, download, removeEmptyRows, differenceOfTwoArrays} from '../helpers';
 
-import {SALTS_CSV} from '../salts';
-import {USERS_CSV} from '../users';
-import {ICDS} from '../ICDs';
-import {SOURCES} from '../sources';
-import {IDPS} from '../IDPs';
+import {SALTS_CSV} from './salts';
+import {USERS_CSV} from './users';
+import {ICDS} from './ICDs';
+import {SOURCES} from './sources';
+import {IDPS} from './IDPs';
 
 
-function sortByStringLengthInDescendingOrder(array: string[]): string[] {
-  return array.sort(function(a, b) {return b.length - a.length;});
+function parseStrandsFromDuplexCell(s: string): {SS: string, AS: string} {
+  const arr = s.slice(3).split('\r\nAS ');
+  return {SS: arr[0], AS: arr[1]};
 }
 
-function stringify(items: string[]): string {
-  return '["' + items.join('", "') + '"]';
+function parseStrandsFromTriplexOrDimerCell(s: string): {SS: string, AS1: string, AS2: string} {
+  const arr1 = s.slice(3).split('\r\nAS1 ');
+  const arr2 = arr1[1].split('\r\nAS2 ');
+  return {SS: arr1[0], AS1: arr2[0], AS2: arr2[1]};
 }
 
-function saltMass(saltNames: string[], molWeightCol: DG.Column, equivalentsCol: DG.Column, i: number,
-  saltCol: DG.Column) {
-  const saltRowIndex = saltNames.indexOf(saltCol.get(i));
-  return (
-    saltRowIndex == -1 || molWeightCol.get(saltRowIndex) == DG.FLOAT_NULL || equivalentsCol.get(i) == DG.INT_NULL) ?
-    DG.FLOAT_NULL :
-    molWeightCol.get(saltRowIndex) * equivalentsCol.get(i);
-}
-
-function saltMolWeigth(saltNamesList: string[], saltCol: DG.Column, molWeightCol: DG.Column, i: number) {
-  const saltRowIndex = saltNamesList.indexOf(saltCol.get(i));
-  return (saltRowIndex == -1) ? DG.FLOAT_NULL : molWeightCol.get(saltRowIndex);
-}
-
-function batchMolWeight(compoundMolWeightCol: DG.Column, saltMassCol: DG.Column, i: number) {
-  return (compoundMolWeightCol.getString(i) == '' || saltMassCol.getString(i) == '') ?
-    DG.FLOAT_NULL :
-    compoundMolWeightCol.get(i) + saltMassCol.get(i);
-}
-
-function molecularWeight(sequence: string, weightsObj: {[index: string]: number}): number {
-  const codes = sortByStringLengthInDescendingOrder(Object.keys(weightsObj)).concat(Object.keys(MODIFICATIONS));
-  let weight = 0;
-  let i = 0;
-  while (i < sequence.length) {
-    const matchedCode = codes.find((s) => s == sequence.slice(i, i + s.length))!;
-    weight += weightsObj[sequence.slice(i, i + matchedCode.length)];
-    i += matchedCode.length;
+async function saveTableAsSdFile(table: DG.DataFrame) {
+  if (GENERATED_COL_NAMES.some((colName) => !table.columns.contains(colName))) {
+    const absentColNames = differenceOfTwoArrays(GENERATED_COL_NAMES, table.columns.names()).join(`', '`);
+    grok.shell.warning(`File saved without columns '${absentColNames}'`);
   }
-  return weight - 61.97;
-}
 
-function parseStrandsFromDuplexCell(s: string): string[] {
-  return s.slice(3).split('\r\nAS ');
-}
+  const sequenceCol = table.getCol(COL_NAMES.SEQUENCE);
+  const typeCol = table.getCol(COL_NAMES.TYPE);
 
-async function saveTableAsSdFile(table: DG.DataFrame) {
-  if (!table.columns.contains('Compound Name')) {
-    grok.shell.warning(
-      'File saved without columns \'' +
-      [COL_NAMES.COMPOUND_NAME, COL_NAMES.COMPOUND_COMMENTS, COL_NAMES.CPD_MW,
-        COL_NAMES.SALT_MASS, COL_NAMES.BATCH_MW].join('\', \''),
-    );
-  }
-  const structureColumn = table.getCol(COL_NAMES.SEQUENCE);
-  const typeColumn = table.getCol(COL_NAMES.TYPE);
   let result = '';
   for (let i = 0; i < table.rowCount; i++) {
-    const format = 'Janssen GCRS Codes'; //getFormat(structureColumn.get(i))!;
-    if (typeColumn.get(i) == 'Duplex') {
-      const array = parseStrandsFromDuplexCell(structureColumn.get(i));
-      const as = sequenceToMolV3000(array[1], true, true, format) +
-      '\n' + `> <Sequence>\nAnti Sense\n\n`;
-      const ss = sequenceToMolV3000(array[0], false, true, format) +
-      '\n' + `> <Sequence>\nSense Strand\n\n`;
-      result += linkV3000([ss, as], true, true) + '\n\n';
-    } else if (typeColumn.get(i) == 'SS') {
-      const molSS = sequenceToMolV3000(structureColumn.get(i), false, true, format) +
-      '\n' + `> <Sequence>\nSense Strand\n\n`;
-      result += molSS;
-    } else if (typeColumn.get(i) == 'AS') {
-      const molAS = sequenceToMolV3000(structureColumn.get(i), true, true, format) +
-        '\n' + `> <Sequence>\nAnti Sense\n\n`;
-      result += molAS;
+    const format = SYNTHESIZERS.GCRS; //getFormat(sequenceCol.get(i))!;
+    if (typeCol.get(i) == SEQUENCE_TYPES.SENSE_STRAND)
+      result += `${sequenceToMolV3000(sequenceCol.get(i), false, true, format)}\n> <Sequence>\nSense Strand\n\n`;
+    else if (typeCol.get(i) == SEQUENCE_TYPES.ANTISENSE_STRAND)
+      result += `${sequenceToMolV3000(sequenceCol.get(i), true, true, format)}\n> <Sequence>\nAnti Sense\n\n`;
+    else if (typeCol.get(i) == SEQUENCE_TYPES.DUPLEX) {
+      const obj = parseStrandsFromDuplexCell(sequenceCol.get(i));
+      const as = `${sequenceToMolV3000(obj.AS, true, true, format)}\n> <Sequence>\nAnti Sense\n\n`;
+      const ss = `${sequenceToMolV3000(obj.SS, false, true, format)}\n> <Sequence>\nSense Strand\n\n`;
+      result += `${linkStrandsV3000({senseStrands: [ss], antiStrands: [as]}, true)}\n\n`;
+    } else if ([SEQUENCE_TYPES.TRIPLEX, SEQUENCE_TYPES.DIMER].includes(typeCol.get(i))) {
+      const obj = parseStrandsFromTriplexOrDimerCell(sequenceCol.get(i));
+      const as1 = `${sequenceToMolV3000(obj.AS1, true, true, format)}\n> <Sequence>\nAnti Sense\n\n`;
+      const as2 = `${sequenceToMolV3000(obj.AS2, true, true, format)}\n> <Sequence>\nAnti Sense\n\n`;
+      const ss = `${sequenceToMolV3000(obj.SS, false, true, format)}\n> <Sequence>\nSense Strand\n\n`;
+      result += `${linkStrandsV3000({senseStrands: [ss], antiStrands: [as1, as2]}, true)}\n\n`;
     }
 
     for (const col of table.columns) {
@@ -95,17 +64,16 @@ async function saveTableAsSdFile(table: DG.DataFrame) {
     }
     result += '$$$$\n';
   }
-  const element = document.createElement('a');
-  element.setAttribute('href', 'data:text/plain;charset=utf-8,' + encodeURIComponent(result));
-  element.setAttribute('download', table.name + '.sdf');
-  element.click();
+  download(`${table.name}.sdf`, encodeURIComponent(result));
 }
 
 export function autostartOligoSdFileSubscription() {
   grok.events.onViewAdded.subscribe((v: any) => {
-    if (v.type == 'TableView') {
+    if (v.type == DG.VIEW_TYPE.TABLE_VIEW) {
       if (v.dataFrame.columns.contains(COL_NAMES.TYPE))
         oligoSdFile(v.dataFrame);
+
+      // Should be removed after fixing bug https://github.com/datagrok-ai/public/issues/808
       grok.events.onContextMenu.subscribe((args) => {
         const seqCol = args.args.context.table.currentCol; // /^[fsACGUacgu]{6,}$/
         if (DG.Detector.sampleCategories(seqCol,
@@ -166,56 +134,56 @@ export function oligoSdFile(table: DG.DataFrame) {
   const sequenceCol = table.getCol(COL_NAMES.SEQUENCE);
   const saltCol = table.getCol(COL_NAMES.SALT);
   const equivalentsCol = table.getCol(COL_NAMES.EQUIVALENTS);
-  const typeColumn = table.getCol(COL_NAMES.TYPE);
+  const typeCol = table.getCol(COL_NAMES.TYPE);
   const chemistryNameCol = table.getCol(COL_NAMES.CHEMISTRY_NAME);
 
   const molWeightCol = saltsDf.getCol('MOLWEIGHT');
   const saltNamesList = saltsDf.getCol('DISPLAY').toList();
 
+  let newDf: DG.DataFrame;
+  let addColumnsPressed = false;
+
   function addColumns(t: DG.DataFrame) {
-    if (t.columns.contains(COL_NAMES.COMPOUND_NAME))
+    if (GENERATED_COL_NAMES.some((colName) => t.columns.contains(colName)))
       return grok.shell.error('Columns already exist');
 
-    for (let i = t.rowCount - 1; i > -1; i--) {
-      if (sequenceCol.get(i) == '')
-        t.rows.removeAt(i, 1, false);
-    }
+    t = removeEmptyRows(t, sequenceCol);
 
     t.columns.addNewString(COL_NAMES.COMPOUND_NAME).init((i: number) => {
-      return (typeColumn.get(i) == 'Duplex') ? chemistryNameCol.get(i) : sequenceCol.get(i);
+      return ([SEQUENCE_TYPES.DUPLEX, SEQUENCE_TYPES.DIMER, SEQUENCE_TYPES.TRIPLEX].includes(typeCol.get(i))) ?
+        chemistryNameCol.get(i) :
+        sequenceCol.get(i);
     });
 
     t.columns.addNewString(COL_NAMES.COMPOUND_COMMENTS).init((i: number) => {
-      if (typeColumn.get(i) == 'Duplex') {
-        const arr = parseStrandsFromDuplexCell(sequenceCol.get(i));
-        return chemistryNameCol.get(i) + '; duplex of SS: ' + arr[0] + ' and AS: ' + arr[1];
+      if ([SEQUENCE_TYPES.SENSE_STRAND, SEQUENCE_TYPES.ANTISENSE_STRAND].includes(typeCol.get(i)))
+        return sequenceCol.get(i);
+      else if (typeCol.get(i) == SEQUENCE_TYPES.DUPLEX) {
+        const obj = parseStrandsFromDuplexCell(sequenceCol.get(i));
+        return `${chemistryNameCol.get(i)}; duplex of SS: ${obj.SS} and AS: ${obj.AS}`;
+      } else if ([SEQUENCE_TYPES.DIMER, SEQUENCE_TYPES.TRIPLEX].includes(typeCol.get(i))) {
+        const obj = parseStrandsFromTriplexOrDimerCell(sequenceCol.get(i));
+        return `${chemistryNameCol.get(i)}; duplex of SS: ${obj.SS} and AS1: ${obj.AS1} and AS2: ${obj.AS2}`;
       }
-      return sequenceCol.get(i);
     });
 
-    const weightsObj: {[code: string]: number} = {};
-    for (const synthesizer of Object.keys(map)) {
-      for (const technology of Object.keys(map[synthesizer])) {
-        for (const code of Object.keys(map[synthesizer][technology]))
-          weightsObj[code] = map[synthesizer][technology][code].weight!;
-      }
-    }
-    for (const [key, value] of Object.entries(MODIFICATIONS))
-      weightsObj[key] = value.molecularWeight;
-
-    t.columns.addNewFloat(COL_NAMES.CPD_MW).init((i: number) => {
-      if (typeColumn.get(i) == 'Duplex') {
-        const arr = parseStrandsFromDuplexCell(sequenceCol.get(i));
-        return (
-          isValidSequence(arr[0], null).indexOfFirstNotValidChar == -1 &&
-          isValidSequence(arr[1], null).indexOfFirstNotValidChar == -1
-        ) ?
-          molecularWeight(arr[0], weightsObj) + molecularWeight(arr[1], weightsObj) :
+    t.columns.addNewFloat(COL_NAMES.COMPOUND_MOL_WEIGHT).init((i: number) => {
+      if ([SEQUENCE_TYPES.SENSE_STRAND, SEQUENCE_TYPES.ANTISENSE_STRAND].includes(typeCol.get(i))) {
+        return (isValidSequence(sequenceCol.get(i), null).indexOfFirstNotValidChar == -1) ?
+          molecularWeight(sequenceCol.get(i), weightsObj) :
+          DG.FLOAT_NULL;
+      } else if (typeCol.get(i) == SEQUENCE_TYPES.DUPLEX) {
+        const obj = parseStrandsFromDuplexCell(sequenceCol.get(i));
+        return (Object.values(obj).every((seq) => isValidSequence(seq, null).indexOfFirstNotValidChar == -1)) ?
+          molecularWeight(obj.SS, weightsObj) + molecularWeight(obj.AS, weightsObj) :
+          DG.FLOAT_NULL;
+      } else if ([SEQUENCE_TYPES.DIMER, SEQUENCE_TYPES.TRIPLEX].includes(typeCol.get(i))) {
+        const obj = parseStrandsFromTriplexOrDimerCell(sequenceCol.get(i));
+        return (Object.values(obj).every((seq) => isValidSequence(seq, null).indexOfFirstNotValidChar == -1)) ?
+          molecularWeight(obj.SS, weightsObj) + molecularWeight(obj.AS1, weightsObj) +
+          molecularWeight(obj.AS2, weightsObj) :
           DG.FLOAT_NULL;
       }
-      return (isValidSequence(sequenceCol.get(i), null).indexOfFirstNotValidChar == -1) ?
-        molecularWeight(sequenceCol.get(i), weightsObj) :
-        DG.FLOAT_NULL;
     });
 
     t.columns.addNewFloat(COL_NAMES.SALT_MASS).init((i: number) =>
@@ -224,15 +192,24 @@ export function oligoSdFile(table: DG.DataFrame) {
     t.columns.addNewFloat(COL_NAMES.SALT_MOL_WEIGHT).init((i: number) =>
       saltMolWeigth(saltNamesList, saltCol, molWeightCol, i));
 
-    t.columns.addNewFloat(COL_NAMES.BATCH_MW).init((i: number) =>
-      batchMolWeight(t.getCol(COL_NAMES.CPD_MW), t.getCol(COL_NAMES.SALT_MASS), i));
+    const compoundMolWeightCol = t.getCol(COL_NAMES.COMPOUND_MOL_WEIGHT);
+    const saltMassCol = t.getCol(COL_NAMES.SALT_MASS);
+    t.columns.addNewFloat(COL_NAMES.BATCH_MOL_WEIGHT).init((i: number) =>
+      batchMolWeight(compoundMolWeightCol, saltMassCol, i));
 
+    grok.shell.getTableView(table.name).grid.columns.setOrder(Object.values(COL_NAMES));
     addColumnsPressed = true;
     return newDf = t;
   }
 
-  let newDf: DG.DataFrame;
-  let addColumnsPressed = false;
+  function updateCalculatedColumns(t: DG.DataFrame, i: number): void {
+    const smValue = saltMass(saltNamesList, molWeightCol, equivalentsCol, i, saltCol);
+    t.getCol(COL_NAMES.SALT_MASS).set(i, smValue, false);
+    const smwValue = saltMolWeigth(saltNamesList, saltCol, molWeightCol, i);
+    t.getCol(COL_NAMES.SALT_MOL_WEIGHT).set(i, smwValue, false);
+    const bmw = batchMolWeight(t.getCol(COL_NAMES.COMPOUND_MOL_WEIGHT), t.getCol(COL_NAMES.SALT_MASS), i);
+    t.getCol(COL_NAMES.BATCH_MOL_WEIGHT).set(i, bmw, false);
+  }
 
   const d = ui.div([
     ui.icons.edit(() => {
@@ -240,18 +217,15 @@ export function oligoSdFile(table: DG.DataFrame) {
       if (table.getCol(COL_NAMES.IDP).type != DG.COLUMN_TYPE.STRING)
         table.changeColumnType(COL_NAMES.IDP, DG.COLUMN_TYPE.STRING);
       d.append(
-        ui.link('Add Columns', () => {
-          addColumns(table);
-          view.grid.columns.setOrder(Object.values(COL_NAMES));
-        }, 'Add columns: \'' + [COL_NAMES.COMPOUND_NAME, COL_NAMES.COMPOUND_COMMENTS, COL_NAMES.CPD_MW,
-          COL_NAMES.SALT_MASS, COL_NAMES.BATCH_MW].join('\', \''), '',
-        ),
-        ui.button('Save SD file', () => saveTableAsSdFile(addColumnsPressed ? newDf : table)),
+        ui.divH([
+          ui.icons.add(() => addColumns(table), `Add columns: '${GENERATED_COL_NAMES.join(`', '`)}'`),
+          ui.icons.save(() => saveTableAsSdFile(addColumnsPressed ? newDf : table), 'Save SD file'),
+        ]),
       );
 
       const view = grok.shell.getTableView(table.name);
-
-      view.dataFrame.getCol(COL_NAMES.TYPE).setTag(DG.TAGS.CHOICES, '["AS", "SS", "Duplex"]');
+      view.grid.setOptions({rowHeight: 45});
+      view.dataFrame.getCol(COL_NAMES.TYPE).setTag(DG.TAGS.CHOICES, stringify(Object.values(SEQUENCE_TYPES)));
       view.dataFrame.getCol(COL_NAMES.OWNER).setTag(DG.TAGS.CHOICES, stringify(usersDf.columns.byIndex(0).toList()));
       view.dataFrame.getCol(COL_NAMES.SALT).setTag(DG.TAGS.CHOICES, stringify(saltsDf.columns.byIndex(0).toList()));
       view.dataFrame.getCol(COL_NAMES.SOURCE).setTag(DG.TAGS.CHOICES, stringify(sourcesDf.columns.byIndex(0).toList()));
@@ -275,15 +249,6 @@ export function oligoSdFile(table: DG.DataFrame) {
         if ([COL_NAMES.SALT, COL_NAMES.EQUIVALENTS, COL_NAMES.SALT_MOL_WEIGHT].includes(colName))
           updateCalculatedColumns(view.dataFrame, view.dataFrame.currentRowIdx);
       });
-
-      function updateCalculatedColumns(t: DG.DataFrame, i: number): void {
-        const smValue = saltMass(saltNamesList, molWeightCol, equivalentsCol, i, saltCol);
-        t.getCol(COL_NAMES.SALT_MASS).set(i, smValue, false);
-        const smwValue = saltMolWeigth(saltNamesList, saltCol, molWeightCol, i);
-        t.getCol(COL_NAMES.SALT_MOL_WEIGHT).set(i, smwValue, false);
-        const bmw = batchMolWeight(t.getCol(COL_NAMES.CPD_MW), t.getCol(COL_NAMES.SALT_MASS), i);
-        t.getCol(COL_NAMES.BATCH_MW).set(i, bmw, false);
-      }
     }),
   ]);
   grok.shell.v.setRibbonPanels([[d]]);

package/src/axolabs/define-pattern.ts

@@ -131,17 +131,20 @@ export function defineAxolabsPattern() {
       asBases[i] = ui.choiceInput('', asBases[i].value, baseChoices, (v: string) => {
         if (!enumerateModifications.includes(v)) {
           enumerateModifications.push(v);
-          isEnumerateModificationsDiv.append(ui.boolInput(v, true, (boolV: boolean) => {
-            if (boolV) {
-              if (!enumerateModifications.includes(v))
-                enumerateModifications.push(v);
-            } else {
-              const index = enumerateModifications.indexOf(v, 0);
-              if (index > -1)
-                enumerateModifications.splice(index, 1);
-            }
-            updateSvgScheme();
-          }).root);
+          isEnumerateModificationsDiv.append(
+            ui.divText('', {style: {width: '25px'}}),
+            ui.boolInput(v, true, (boolV: boolean) => {
+              if (boolV) {
+                if (!enumerateModifications.includes(v))
+                  enumerateModifications.push(v);
+              } else {
+                const index = enumerateModifications.indexOf(v, 0);
+                if (index > -1)
+                  enumerateModifications.splice(index, 1);
+              }
+              updateSvgScheme();
+            }).root,
+          );
         }
         updateAsModification();
         updateSvgScheme();
@@ -174,17 +177,20 @@ export function defineAxolabsPattern() {
       ssBases[i] = ui.choiceInput('', ssBases[i].value, baseChoices, (v: string) => {
         if (!enumerateModifications.includes(v)) {
           enumerateModifications.push(v);
-          isEnumerateModificationsDiv.append(ui.boolInput(v, true, (boolV: boolean) => {
-            if (boolV) {
-              if (!enumerateModifications.includes(v))
-                enumerateModifications.push(v);
-            } else {
-              const index = enumerateModifications.indexOf(v, 0);
-              if (index > -1)
-                enumerateModifications.splice(index, 1);
-            }
-            updateSvgScheme();
-          }).root);
+          isEnumerateModificationsDiv.append(
+            ui.divText('', {style: {width: '25px'}}),
+            ui.boolInput(v, true, (boolV: boolean) => {
+              if (boolV) {
+                if (!enumerateModifications.includes(v))
+                  enumerateModifications.push(v);
+              } else {
+                const index = enumerateModifications.indexOf(v, 0);
+                if (index > -1)
+                  enumerateModifications.splice(index, 1);
+              }
+              updateSvgScheme();
+            }).root,
+          );
         }
         updateSsModification();
         updateSvgScheme();
@@ -499,18 +505,20 @@ export function defineAxolabsPattern() {
   const loadPatternDiv = ui.div([]);
   const asModificationDiv = ui.div([]);
   const firstAsPtoDiv = ui.div([]);
-  const isEnumerateModificationsDiv = ui.divH([ui.boolInput(defaultBase, true, (v: boolean) => {
-    if (v) {
-      if (!enumerateModifications.includes(defaultBase))
-        enumerateModifications.push(defaultBase);
-    } else {
-      const index = enumerateModifications.indexOf(defaultBase, 0);
-      if (index > -1)
-        enumerateModifications.splice(index, 1);
-    }
-    updateSvgScheme();
-    updateOutputExamples();
-  }).root]);
+  const isEnumerateModificationsDiv = ui.divH([
+    ui.boolInput(defaultBase, true, (v: boolean) => {
+      if (v) {
+        if (!enumerateModifications.includes(defaultBase))
+          enumerateModifications.push(defaultBase);
+      } else {
+        const index = enumerateModifications.indexOf(defaultBase, 0);
+        if (index > -1)
+          enumerateModifications.splice(index, 1);
+      }
+      updateSvgScheme();
+      updateOutputExamples();
+    }).root,
+  ]);
 
   let ssBases = Array(defaultSequenceLength).fill(ui.choiceInput('', defaultBase, baseChoices));
   let asBases = Array(defaultSequenceLength).fill(ui.choiceInput('', defaultBase, baseChoices));

package/src/axolabs/draw-svg.ts

@@ -35,14 +35,8 @@ function getTextWidth(text: string, font: number): number {
   return 2 * context.measureText(text).width;
 }
 
-function getTextInsideCircle(
-  bases: string[], index: number, nucleotideCounter: number,
-  numberOfNucleotides: number, enumerateModifications: string[]): string {
-  return ((bases[index].slice(-3) == '(o)') || !enumerateModifications.includes(bases[index])) ?
-    '' :
-    (['A', 'G', 'C', 'U', 'T'].includes(bases[index])) ?
-      bases[index] :
-      '';//String(numberOfNucleotides - nucleotideCounter);
+function getTextInsideCircle(bases: string[], index: number): string {
+  return (bases[index].slice(-3) == '(o)' || !['A', 'G', 'C', 'U', 'T'].includes(bases[index])) ? '' : bases[index];
 }
 
 function getFontColorVisibleOnBackground(rgbString: string): string {
@@ -160,14 +154,15 @@ export function drawAxolabsPattern(
     Math.max(xOfSsRightModifications, xOfAsRightModifications) +
       widthOfLeftModification + baseDiameter * (Math.max(ssRightOverhangs, asRightOverhangs));
   const yOfTitle = baseRadius;
-  const yOfNumbers = 2 * baseRadius;
+  const yOfSsNumbers = 2 * baseRadius;
+  const yOfAsNumbers = 8.5 * baseRadius;
   const yOfSsTexts = 4 * baseRadius;
   const yOfAsTexts = 7 * baseRadius;
   const yOfComment = asExists ? 11 * baseRadius : 8.5 * baseRadius;
   const yOfSsCircles = 3.5 * baseRadius;
   const yOfAsCircles = 6.5 * baseRadius;
-  const yOfCirclesInLegends = asExists ? 9 * baseRadius : 6 * baseRadius;
-  const yOfTextLegend = asExists ? 9.5 * baseRadius - 3 : yOfAsCircles - 3;
+  const yOfCirclesInLegends = asExists ? 9.5 * baseRadius : 6 * baseRadius;
+  const yOfTextLegend = asExists ? 10 * baseRadius - 3 : yOfAsCircles - 3;
 
   const image = svg.render(width, height);
 
@@ -196,11 +191,13 @@ export function drawAxolabsPattern(
       getShiftToAlignNumberInsideCircle(ssBases, ssBases.length - i, numberOfSsNucleotides - nucleotideCounter);
     if (ssBases[i].slice(-3) != '(o)')
       nucleotideCounter--;
+    const n = (ssBases[i].slice(-3) != '(o)' && enumerateModifications.includes(ssBases[i])) ?
+      String(numberOfSsNucleotides - nucleotideCounter) : '';
     image.append(
-      svg.text(String(numberOfSsNucleotides - nucleotideCounter), xOfNumbers, yOfNumbers, legendFontSize, fontColor),
+      svg.text(n, xOfNumbers, yOfSsNumbers, legendFontSize, fontColor),
       svg.circle(getXOfBaseCircles(i, ssRightOverhangs), yOfSsCircles, baseRadius, getBaseColor(ssBases[i])),
-      svg.text(getTextInsideCircle(ssBases, i, nucleotideCounter, numberOfSsNucleotides, enumerateModifications),
-        xOfNumbers, yOfSsTexts, baseFontSize, getFontColorVisibleOnBackground(axolabsMap[ssBases[i]]['color'])),
+      svg.text(getTextInsideCircle(ssBases, i), xOfNumbers, yOfSsTexts, baseFontSize,
+        getFontColorVisibleOnBackground(getBaseColor(ssBases[i]))),
       ssPtoStatuses[i] ?
         svg.star(getXOfBaseCircles(i, ssRightOverhangs) + baseRadius, yOfSsTexts + psLinkageRadius, psLinkageColor) :
         '',
@@ -222,13 +219,16 @@ export function drawAxolabsPattern(
     for (let i = asBases.length - 1; i > -1; i--) {
       if (asBases[i].slice(-3) != '(o)')
         nucleotideCounter--;
+      const xOfNumbers = getXOfBaseCircles(i, asRightOverhangs) +
+        getShiftToAlignNumberInsideCircle(asBases, i, nucleotideCounter + 1);
+      const n = (asBases[i].slice(-3) != '(o)' && enumerateModifications.includes(asBases[i])) ?
+        String(nucleotideCounter + 1) : '';
       image.append(
+        svg.text(n, xOfNumbers, yOfAsNumbers, legendFontSize, fontColor),
         svg.circle(getXOfBaseCircles(i, asRightOverhangs), yOfAsCircles, baseRadius, getBaseColor(asBases[i])),
-        svg.text(getTextInsideCircle(
-          asBases, i, numberOfAsNucleotides - nucleotideCounter - 1, numberOfAsNucleotides, enumerateModifications),
-        getXOfBaseCircles(i, asRightOverhangs) +
-          getShiftToAlignNumberInsideCircle(asBases, i, nucleotideCounter + 1),
-        yOfAsTexts, baseFontSize, getFontColorVisibleOnBackground(axolabsMap[asBases[i]]['color'])),
+        svg.text(getTextInsideCircle(asBases, i),
+          getXOfBaseCircles(i, asRightOverhangs) + getShiftToAlignNumberInsideCircle(asBases, i, nucleotideCounter + 1),
+          yOfAsTexts, baseFontSize, getFontColorVisibleOnBackground(getBaseColor(asBases[i]))),
         asPtoStatuses[i] ? svg.star(getXOfBaseCircles(i, asRightOverhangs) +
           baseRadius, yOfAsTexts + psLinkageRadius, psLinkageColor) : '',
       );