@datagrok/sequence-translator 0.0.4 → 0.0.8

package/src/defineAxolabsPattern.ts

@@ -4,10 +4,10 @@ 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 $ from 'cash-dom';
 
-import {drawAxolabsPattern} from "./drawAxolabsPattern";
-import {axolabsMap} from "./axolabsMap";
+import {drawAxolabsPattern} from './drawAxolabsPattern';
+import {axolabsMap} from './axolabsMap';
 
 const baseChoices: string[] = Object.keys(axolabsMap);
 const defaultBase: string = baseChoices[0];
@@ -28,37 +28,45 @@ function findDuplicates(data: Int32Array | Float32Array | Float64Array | Uint32A
 
 async function isCurrentUserCreatedThisPattern(patternName: string): Promise<boolean> {
   return await grok.dapi.users.current().then((user) => {
-    let [firstName, lastName] = getUserName(patternName);
+    const [firstName, lastName] = getUserName(patternName);
     return (user.firstName != firstName || user.lastName != lastName);
   });
 }
 
 function getShortName(patternName: string): string {
   let first = patternName.length + 1;
-  for (let i = 0; i < patternName.length; i++)
+  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++)
+  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);
 }
 
-function translateSequence(sequence: string, bases: any, ptoLinkages: any, startModification: any, endModification: any, firstPtoExist: boolean) {
+function translateSequence(
+  sequence: string,
+  bases: any,
+  ptoLinkages: any,
+  startModification: any,
+  endModification: any,
+  firstPtoExist: boolean): string {
   let counter: number = -1;
-  let mainSequence = sequence.replace(/[AUGC]/g, function (x: string) {
+  let mainSequence = sequence.replace(/[AUGC]/g, function(x: string) {
     counter++;
-    let indexOfSymbol = axolabsMap["RNA"]["symbols"].indexOf(x);
-    let symbol = axolabsMap[bases[counter].value]["symbols"][indexOfSymbol];
+    const indexOfSymbol = axolabsMap['RNA']['symbols'].indexOf(x);
+    const symbol = axolabsMap[bases[counter].value]['symbols'][indexOfSymbol];
     return (ptoLinkages[counter].value) ? symbol + 's' : symbol;
   });
   if (mainSequence.slice(0, 5).split('mU').length == 3)
@@ -70,27 +78,34 @@ function translateSequence(sequence: string, bases: any, ptoLinkages: any, start
 
 function addColumnWithIds(tableName: string, columnName: string, patternName: string) {
   const nameOfNewColumn = 'ID ' + patternName;
-  let columns = grok.shell.table(tableName).columns;
+  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) => columnWithIds.get(i) + '_' + patternName);
 }
 
-function addColumnWithTranslatedSequences(tableName: string, columnName: string, bases: any, ptoLinkages: any, startModification: any, endModification: any, firstPtoExist: boolean) {
+function addColumnWithTranslatedSequences(
+  tableName: string,
+  columnName: string,
+  bases: any,
+  ptoLinkages: any,
+  startModification: any,
+  endModification: any,
+  firstPtoExist: boolean) {
   const nameOfNewColumn = 'Axolabs ' + columnName;
-  let columns = grok.shell.table(tableName).columns;
+  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 translateSequence(columnWithInputSequences.getString(i), bases, ptoLinkages, startModification, endModification, firstPtoExist);
+    return translateSequence(columnWithInputSequences.getString(i),
+      bases, ptoLinkages, startModification, endModification, firstPtoExist);
   });
 }
 
 export function defineAxolabsPattern() {
-
-  let enumerateModifications = [defaultBase];
+  const enumerateModifications = [defaultBase];
   let maximalSsLength = defaultSequenceLength;
   let maximalAsLength = defaultSequenceLength;
 
@@ -123,18 +138,16 @@ export function defineAxolabsPattern() {
         updateSvgScheme();
         updateOutputExamples();
       });
-      let isOverhang = false;
-      if (asBases[i].value.slice(-3) == '(o)') {
-        isOverhang = true;
-      } else {
+      if (asBases[i].value.slice(-3) != '(o)')
         nucleotideCounter++;
-      }
+
       asModificationItems.append(
         ui.divH([
-          ui.div([ui.label(asBases[i].value.slice(-3) == '(o)' ? '' : String(nucleotideCounter))], {style: {width: '20px'}})!,
+          ui.div([ui.label(asBases[i].value.slice(-3) == '(o)' ? '' : String(nucleotideCounter))],
+            {style: {width: '20px'}})!,
           ui.block75([asBases[i]])!,
-          ui.div([asPtoLinkages[i]])!
-        ], {style: {alignItems: "center"}})
+          ui.div([asPtoLinkages[i]])!,
+        ], {style: {alignItems: 'center'}}),
       );
     }
   }
@@ -168,18 +181,16 @@ export function defineAxolabsPattern() {
         updateSvgScheme();
         updateOutputExamples();
       });
-      let isOverhang = false;
-      if (ssBases[i].value.slice(-3) == '(o)') {
-        isOverhang = true;
-      } else {
+      if (ssBases[i].value.slice(-3) != '(o)')
         nucleotideCounter++;
-      }
+
       ssModificationItems.append(
         ui.divH([
-          ui.div([ui.label(ssBases[i].value.slice(-3) == '(o)' ? '' : String(nucleotideCounter))], {style: {width: '20px'}})!,
+          ui.div([ui.label(ssBases[i].value.slice(-3) == '(o)' ? '' : String(nucleotideCounter))],
+            {style: {width: '20px'}})!,
           ui.block75([ssBases[i]])!,
-          ui.div([ssPtoLinkages[i]])!
-        ], {style: {alignItems: "center"}})
+          ui.div([ssPtoLinkages[i]])!,
+        ], {style: {alignItems: 'center'}}),
       );
     }
   }
@@ -197,29 +208,30 @@ export function defineAxolabsPattern() {
       updateOutputExamples();
     } else {
       ui.dialog('Sequence length is out of range')
-        .add(ui.divText('Sequence length should be less than ' + maximalValidSequenceLength.toString() + ' due to UI constrains.'))
+        .add(ui.divText('Sequence length should be less than ' +
+          maximalValidSequenceLength.toString() + ' due to UI constrains.'))
         .add(ui.divText('Please change sequence length in order to define new pattern.'))
         .show();
     }
   }
 
-  function updatePto(newPtoValue: boolean) {
-    for (let i = 0; i < ssPtoLinkages.length; i++) {
+  function updatePto(newPtoValue: boolean): void {
+    for (let i = 0; i < ssPtoLinkages.length; i++)
       ssPtoLinkages[i].value = newPtoValue;
-    }
-    for (let i = 0; i < asPtoLinkages.length; i++) {
+
+    for (let i = 0; i < asPtoLinkages.length; i++)
       asPtoLinkages[i].value = newPtoValue;
-    }
+
     updateSvgScheme();
   }
 
-  function updateBases(newBasisValue: string) {
-    for (let i = 0; i < ssBases.length; i++) {
+  function updateBases(newBasisValue: string): void {
+    for (let i = 0; i < ssBases.length; i++)
       ssBases[i].value = newBasisValue;
-    }
-    for (let i = 0; i < asBases.length; i++) {
+
+    for (let i = 0; i < asBases.length; i++)
       asBases[i].value = newBasisValue;
-    }
+
     updateSvgScheme();
   }
 
@@ -230,9 +242,12 @@ export function defineAxolabsPattern() {
   }
 
   function updateOutputExamples() {
-    ssOutputExample.value = translateSequence(ssInputExample.value, ssBases, ssPtoLinkages, ssFiveModification, ssThreeModification, firstSsPto.value);
-    if (createAsStrand.value)
-      asOutputExample.value = translateSequence(asInputExample.value, asBases, asPtoLinkages, asFiveModification, asThreeModification, firstAsPto.value);
+    ssOutputExample.value = translateSequence(
+      ssInputExample.value, ssBases, ssPtoLinkages, ssFiveModification, ssThreeModification, firstSsPto.value);
+    if (createAsStrand.value) {
+      asOutputExample.value = translateSequence(
+        asInputExample.value, asBases, asPtoLinkages, asFiveModification, asThreeModification, firstAsPto.value);
+    }
   }
 
   function updateSvgScheme() {
@@ -251,17 +266,18 @@ export function defineAxolabsPattern() {
           asThreeModification.value,
           asFiveModification.value,
           comment.value,
-          enumerateModifications
-        )
-      ])
+          enumerateModifications,
+        ),
+      ]),
     );
   }
 
   function detectDefaultBasis(array: string[]) {
-    let modeMap: {[index: string]: number} = {};
-    let maxEl = array[0], maxCount = 1;
-    for(let i = 0; i < array.length; i++) {
-      let el = array[i];
+    const modeMap: {[index: string]: number} = {};
+    let maxEl = array[0];
+    let maxCount = 1;
+    for (let i = 0; i < array.length; i++) {
+      const el = array[i];
       if (modeMap[el] == null)
         modeMap[el] = 1;
       else
@@ -275,9 +291,9 @@ export function defineAxolabsPattern() {
   }
 
   async function parsePatternAndUpdateUi(newName: string) {
-    let pi = DG.TaskBarProgressIndicator.create('Loading pattern...');
+    const pi = DG.TaskBarProgressIndicator.create('Loading pattern...');
     await grok.dapi.userDataStorage.get(userStorageKey, false).then((entities) => {
-      let obj = JSON.parse(entities[newName]);
+      const obj = JSON.parse(entities[newName]);
       sequenceBase.value = detectDefaultBasis(obj['asBases'].concat(obj['ssBases']));
       createAsStrand.value = (obj['asBases'].length > 0);
       saveAs.value = newName;
@@ -313,7 +329,7 @@ export function defineAxolabsPattern() {
   }
 
   function checkWhetherAllValuesInColumnHaveTheSameLength(colName: string): boolean {
-    let col = tables.value.columns.byName(colName);
+    const col = tables.value.columns.byName(colName);
     let allLengthsAreTheSame = true;
     for (let i = 1; i < col.length; i++) {
       if (col.get(i - 1).length != col.get(i).length) {
@@ -322,14 +338,14 @@ export function defineAxolabsPattern() {
       }
     }
     if (!allLengthsAreTheSame) {
-      let dialog = ui.dialog('Sequences lengths mismatch');
+      const dialog = ui.dialog('Sequences lengths mismatch');
       $(dialog.getButton('OK')).hide();
       dialog
         .add(ui.divText('The sequence length should match the number of Raw sequences in the input file'))
-        .add(ui.divText("'ADD COLUMN' to see sequences lengths"))
+        .add(ui.divText('\'ADD COLUMN\' to see sequences lengths'))
         .addButton('ADD COLUMN', () => {
           tables.value.columns.addNewInt('Sequences lengths in ' + colName).init((j: number) => col.get(j).length);
-          grok.shell.info("Column with lengths added to '" + tables.value.name + "'");
+          grok.shell.info('Column with lengths added to \'' + tables.value.name + '\'');
           dialog.close();
           grok.shell.v = grok.shell.getTableView(tables.value.name);
         })
@@ -339,47 +355,50 @@ export function defineAxolabsPattern() {
   }
 
   async function getCurrentUserName(): Promise<string> {
-    return await grok.dapi.users.current().then((user) => {return ' (created by ' + user.firstName + ' ' + user.lastName + ')'});
+    return await grok.dapi.users.current().then((user) => {
+      return ' (created by ' + user.firstName + ' ' + user.lastName + ')';
+    });
   }
 
   async function postPatternToUserStorage() {
-    let author = await getCurrentUserName();
+    const author = await getCurrentUserName();
     if (!saveAs.stringValue.includes('(created by '))
       saveAs.value = saveAs.stringValue + author;
     return grok.dapi.userDataStorage.postValue(
       userStorageKey,
       saveAs.stringValue,
       JSON.stringify({
-        "ssBases": ssBases.slice(0, ssLength.value).map((e) => e.value),
-        "asBases": asBases.slice(0, asLength.value).map((e) => e.value),
-        "ssPtoLinkages": [firstSsPto.value].concat(ssPtoLinkages.slice(0, ssLength.value).map((e) => e.value)),
-        "asPtoLinkages": [firstAsPto.value].concat(asPtoLinkages.slice(0, asLength.value).map((e) => e.value)),
-        "ssThreeModification": ssThreeModification.value,
-        "ssFiveModification": ssFiveModification.value,
-        "asThreeModification": asThreeModification.value,
-        "asFiveModification": asFiveModification.value,
-        "comment": comment.value
+        'ssBases': ssBases.slice(0, ssLength.value).map((e) => e.value),
+        'asBases': asBases.slice(0, asLength.value).map((e) => e.value),
+        'ssPtoLinkages': [firstSsPto.value].concat(ssPtoLinkages.slice(0, ssLength.value).map((e) => e.value)),
+        'asPtoLinkages': [firstAsPto.value].concat(asPtoLinkages.slice(0, asLength.value).map((e) => e.value)),
+        'ssThreeModification': ssThreeModification.value,
+        'ssFiveModification': ssFiveModification.value,
+        'asThreeModification': asThreeModification.value,
+        'asFiveModification': asFiveModification.value,
+        'comment': comment.value,
       }),
-      false
-    ).then(() => grok.shell.info("Pattern '" + saveAs.value + "' was successfully uploaded!"));
+      false,
+    ).then(() => grok.shell.info('Pattern \'' + saveAs.value + '\' was successfully uploaded!'));
   }
 
   async function updatePatternsList() {
     grok.dapi.userDataStorage.get(userStorageKey, false).then(async (entities) => {
-      let lstMy: string[] = [],
-        lstOthers: string[] = [];
+      const lstMy: string[] = [];
+      const lstOthers: string[] = [];
 
-      for (let ent of Object.keys(entities))
+      for (const ent of Object.keys(entities)) {
         if (await isCurrentUserCreatedThisPattern(ent))
           lstOthers.push(ent);
         else
           lstMy.push(getShortName(ent));
+      }
 
       let loadPattern = ui.choiceInput('Load Pattern', '', lstMy, (v: string) => parsePatternAndUpdateUi(v));
 
-      let myOrOthersPatternList = ui.choiceInput('', 'Mine', ['Mine', 'Others'], (v: string) => {
-        let currentList = v == 'Mine' ? lstMy : lstOthers;
-        loadPattern = ui.choiceInput('Load Pattern', '', currentList, (v: string) => parsePatternAndUpdateUi(v))
+      const myOrOthersPatternList = ui.choiceInput('', 'Mine', ['Mine', 'Others'], (v: string) => {
+        const currentList = v == 'Mine' ? lstMy : lstOthers;
+        loadPattern = ui.choiceInput('Load Pattern', '', currentList, (v: string) => parsePatternAndUpdateUi(v));
 
         loadPattern.root.append(myOrOthersPatternList.input);
         loadPattern.root.append(loadPattern.input);
@@ -392,17 +411,17 @@ export function defineAxolabsPattern() {
         loadPattern.root.append(
           ui.div([
             ui.button(ui.iconFA('trash-alt', () => {}), async () => {
-              if (loadPattern.value == null) {
+              if (loadPattern.value == null)
                 grok.shell.warning('Choose pattern to delete');
-              } else if (await isCurrentUserCreatedThisPattern(saveAs.value)) {
+              else if (await isCurrentUserCreatedThisPattern(saveAs.value))
                 grok.shell.warning('Cannot delete pattern, created by other user');
-              } else {
+              else {
                 await grok.dapi.userDataStorage.remove(userStorageKey, loadPattern.value, false)
-                  .then(() => grok.shell.info("Pattern '" + loadPattern.value + "' deleted"));
+                  .then(() => grok.shell.info('Pattern \'' + loadPattern.value + '\' deleted'));
               }
               await updatePatternsList();
-            })
-          ], 'ui-input-options')
+            }),
+          ], 'ui-input-options'),
         );
       });
       loadPattern.root.append(myOrOthersPatternList.input);
@@ -416,17 +435,17 @@ export function defineAxolabsPattern() {
       loadPattern.root.append(
         ui.div([
           ui.button(ui.iconFA('trash-alt', () => {}), async () => {
-            if (loadPattern.value == null) {
+            if (loadPattern.value == null)
               grok.shell.warning('Choose pattern to delete');
-            } else if (await isCurrentUserCreatedThisPattern(saveAs.value)) {
+            else if (await isCurrentUserCreatedThisPattern(saveAs.value))
               grok.shell.warning('Cannot delete pattern, created by other user');
-            } else {
+            else {
               await grok.dapi.userDataStorage.remove(userStorageKey, loadPattern.value, false)
-                .then(() => grok.shell.info("Pattern '" + loadPattern.value + "' deleted"));
+                .then(() => grok.shell.info('Pattern \'' + loadPattern.value + '\' deleted'));
             }
             await updatePatternsList();
-          })
-        ], 'ui-input-options')
+          }),
+        ], 'ui-input-options'),
       );
     });
   }
@@ -435,10 +454,10 @@ export function defineAxolabsPattern() {
     await grok.dapi.userDataStorage.get(userStorageKey, false)
       .then((entities) => {
         if (Object.keys(entities).includes(saveAs.value)) {
-          let dialog = ui.dialog('Pattern already exists');
+          const dialog = ui.dialog('Pattern already exists');
           $(dialog.getButton('OK')).hide();
           dialog
-            .add(ui.divText("Pattern name '" + saveAs.value + "' already exists."))
+            .add(ui.divText('Pattern name \'' + saveAs.value + '\' already exists.'))
             .add(ui.divText('Replace pattern?'))
             .addButton('YES', async () => {
               await grok.dapi.userDataStorage.remove(userStorageKey, saveAs.value, false)
@@ -446,48 +465,47 @@ export function defineAxolabsPattern() {
               dialog.close();
             })
             .show();
-        } else {
+        } else
           postPatternToUserStorage();
-        }
       });
     await updatePatternsList();
   }
 
-  let inputSsColumnDiv = ui.div([]),
-    inputAsColumnDiv = ui.div([]),
-    inputIdColumnDiv = ui.div([]),
-    ssModificationItems = ui.div([]),
-    asModificationItems = ui.div([]),
-    svgDiv = ui.div([]),
-    asExampleDiv = ui.div([]),
-    appAxolabsDescription = ui.div([]),
-    loadPatternDiv = ui.div([]),
-    asModificationDiv = ui.div([]),
-    firstAsPtoDiv = ui.div([]),
-    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 inputSsColumnDiv = ui.div([]);
+  const inputAsColumnDiv = ui.div([]);
+  const inputIdColumnDiv = ui.div([]);
+  const ssModificationItems = ui.div([]);
+  const asModificationItems = ui.div([]);
+  const svgDiv = ui.div([]);
+  const asExampleDiv = ui.div([]);
+  const appAxolabsDescription = ui.div([]);
+  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]);
 
-  let ssBases = Array(defaultSequenceLength).fill(ui.choiceInput('', defaultBase, baseChoices)),
-    asBases = Array(defaultSequenceLength).fill(ui.choiceInput('', defaultBase, baseChoices)),
-    ssPtoLinkages = Array(defaultSequenceLength).fill(ui.boolInput('', defaultPto)),
-    asPtoLinkages = Array(defaultSequenceLength).fill(ui.boolInput('', defaultPto));
+  let ssBases = Array(defaultSequenceLength).fill(ui.choiceInput('', defaultBase, baseChoices));
+  let asBases = Array(defaultSequenceLength).fill(ui.choiceInput('', defaultBase, baseChoices));
+  let ssPtoLinkages = Array(defaultSequenceLength).fill(ui.boolInput('', defaultPto));
+  let asPtoLinkages = Array(defaultSequenceLength).fill(ui.boolInput('', defaultPto));
 
-  let ssLength = ui.intInput('SS Length', defaultSequenceLength, () => updateUiForNewSequenceLength());
-  let asLength = ui.intInput('AS Length', defaultSequenceLength, () => updateUiForNewSequenceLength());
-  let asLengthDiv = ui.div([asLength.root]);
+  const ssLength = ui.intInput('SS Length', defaultSequenceLength, () => updateUiForNewSequenceLength());
+  const asLength = ui.intInput('AS Length', defaultSequenceLength, () => updateUiForNewSequenceLength());
+  const asLengthDiv = ui.div([asLength.root]);
 
   function validateSsColumn(colName: string) {
-    let allLengthsAreTheSame: boolean = checkWhetherAllValuesInColumnHaveTheSameLength(colName);
+    const allLengthsAreTheSame: boolean = checkWhetherAllValuesInColumnHaveTheSameLength(colName);
     const firstSequence = tables.value.columns.byName(colName).get(0);
     if (allLengthsAreTheSame && firstSequence.length != ssLength.value)
       ssLength.value = tables.value.columns.byName(colName).get(0).length;
@@ -495,7 +513,7 @@ export function defineAxolabsPattern() {
   }
 
   function validateAsColumn(colName: string) {
-    let allLengthsAreTheSame: boolean = checkWhetherAllValuesInColumnHaveTheSameLength(colName);
+    const allLengthsAreTheSame: boolean = checkWhetherAllValuesInColumnHaveTheSameLength(colName);
     const firstSequence = tables.value.columns.byName(colName).get(0);
     if (allLengthsAreTheSame && firstSequence.length != asLength.value)
       asLength.value = tables.value.columns.byName(colName).get(0).length;
@@ -511,18 +529,18 @@ export function defineAxolabsPattern() {
     else if (col.categories.length < col.length) {
       const duplicates = findDuplicates(col.getRawData());
       ui.dialog('Non-unique IDs')
-        .add(ui.divText("Press 'OK' to select rows with non-unique values"))
+        .add(ui.divText('Press \'OK\' to select rows with non-unique values'))
         .onOK(() => {
-          let selection = tables.value.selection;
+          const selection = tables.value.selection;
           selection.init((i: number) => duplicates.indexOf(col.get(i)) > -1);
           grok.shell.v = grok.shell.getTableView(tables.value.name);
-          grok.shell.info("Rows are selected in table '" + tables.value.name + "'");
+          grok.shell.info('Rows are selected in table \'' + tables.value.name + '\'');
         })
         .show();
     }
   }
 
-  let tables = ui.tableInput('Tables', grok.shell.tables[0], grok.shell.tables, (t: DG.DataFrame) => {
+  const tables = ui.tableInput('Tables', grok.shell.tables[0], grok.shell.tables, (t: DG.DataFrame) => {
     inputSsColumn = ui.choiceInput('SS Column', '', t.columns.names(), (colName: string) => validateSsColumn(colName));
     inputSsColumnDiv.innerHTML = '';
     inputSsColumnDiv.append(inputSsColumn.root);
@@ -543,23 +561,23 @@ export function defineAxolabsPattern() {
 
   updatePatternsList();
 
-  let sequenceBase = ui.choiceInput('Sequence Basis', defaultBase, baseChoices, (v: string) => {
+  const sequenceBase = ui.choiceInput('Sequence Basis', defaultBase, baseChoices, (v: string) => {
     updateBases(v);
     updateOutputExamples();
   });
 
-  let fullyPto = ui.boolInput('Fully PTO', defaultPto, (v: boolean) => {
+  const fullyPto = ui.boolInput('Fully PTO', defaultPto, (v: boolean) => {
     firstSsPto.value = v;
     firstAsPto.value = v;
     updatePto(v);
     updateOutputExamples();
   });
 
-  let firstSsPto = ui.boolInput('First SS PTO', fullyPto.value, () => updateSvgScheme());
-  let firstAsPto = ui.boolInput('First AS PTO', fullyPto.value, () => updateSvgScheme());
+  const firstSsPto = ui.boolInput('First SS PTO', fullyPto.value, () => updateSvgScheme());
+  const firstAsPto = ui.boolInput('First AS PTO', fullyPto.value, () => updateSvgScheme());
   firstAsPtoDiv.append(firstAsPto.root);
 
-  let createAsStrand = ui.boolInput('Create AS Strand', true, (v: boolean) => {
+  const createAsStrand = ui.boolInput('Create AS Strand', true, (v: boolean) => {
     asModificationSection.hidden = (!v);
     inputAsColumnDiv.hidden = (!v);
     asLengthDiv.hidden = (!v);
@@ -569,62 +587,61 @@ export function defineAxolabsPattern() {
     updateSvgScheme();
   });
 
-  let saveAs = ui.textInput('Save As', 'Pattern Name', () => updateSvgScheme());
+  const saveAs = ui.textInput('Save As', 'Pattern Name', () => updateSvgScheme());
   saveAs.setTooltip('Name Of New Pattern');
 
-  let ssThreeModification = ui.stringInput("SS 3' Modification", "", () => {
+  const ssThreeModification = ui.stringInput('SS 3\' Modification', '', () => {
     updateSvgScheme();
     updateOutputExamples();
   });
-  ssThreeModification.setTooltip("Additional SS 3' Modification");
+  ssThreeModification.setTooltip('Additional SS 3\' Modification');
 
-  let ssFiveModification = ui.stringInput("SS 5' Modification", "", () => {
+  const ssFiveModification = ui.stringInput('SS 5\' Modification', '', () => {
     updateSvgScheme();
     updateOutputExamples();
   });
-  ssFiveModification.setTooltip("Additional SS 5' Modification");
+  ssFiveModification.setTooltip('Additional SS 5\' Modification');
 
-  let asThreeModification = ui.stringInput("AS 3' Modification", "", () => {
+  const asThreeModification = ui.stringInput('AS 3\' Modification', '', () => {
     updateSvgScheme();
     updateOutputExamples();
   });
-  asThreeModification.setTooltip("Additional AS 3' Modification");
+  asThreeModification.setTooltip('Additional AS 3\' Modification');
 
-  let asFiveModification = ui.stringInput("AS 5' Modification", "", () => {
+  const asFiveModification = ui.stringInput('AS 5\' Modification', '', () => {
     updateSvgScheme();
     updateOutputExamples();
   });
-  asFiveModification.setTooltip("Additional AS 5' Modification");
+  asFiveModification.setTooltip('Additional AS 5\' Modification');
 
   asModificationDiv.append(asThreeModification.root);
   asModificationDiv.append(asFiveModification.root);
 
-  let comment = ui.textInput('Comment', '', () => updateSvgScheme());
+  const comment = ui.textInput('Comment', '', () => updateSvgScheme());
 
-  let savePatternButton = ui.button('Save', () => {
-    if (saveAs.value != '') {
-      savePattern().then(r => grok.shell.info('Pattern saved'));
-    } else {
-      let name = ui.stringInput('Enter Name', '');
+  const savePatternButton = ui.button('Save', () => {
+    if (saveAs.value != '')
+      savePattern().then((r) => grok.shell.info('Pattern saved'));
+    else {
+      const name = ui.stringInput('Enter Name', '');
       ui.dialog('Pattern Name')
         .add(name.root)
         .onOK(() => {
           saveAs.value = name.value;
-          savePattern().then(r => grok.shell.info('Pattern saved'));
+          savePattern().then((r) => grok.shell.info('Pattern saved'));
         })
         .show();
     }
   });
 
-  let convertSequenceButton = ui.button('Convert Sequences', () => {
-    if (inputSsColumn.value == null || (createAsStrand.value && inputAsColumn.value == null)) {
-      grok.shell.info("Please select table and columns on which to apply pattern");
-    }
+  const convertSequenceButton = ui.button('Convert Sequences', () => {
+    if (inputSsColumn.value == null || (createAsStrand.value && inputAsColumn.value == null))
+      grok.shell.info('Please select table and columns on which to apply pattern');
     else if (ssLength.value != ssInputExample.value.length || asLength.value != asInputExample.value.length) {
-      let dialog = ui.dialog("Length Mismatch")
+      const dialog = ui.dialog('Length Mismatch');
       $(dialog.getButton('OK')).hide();
       dialog
-        .add(ui.divText("Length of sequences in columns doesn't match entered length. Update length value?"))
+        .add(ui.divText('Length of sequences in columns doesn\'t match entered length. Update length value?'))
         .addButton('YES', () => {
           ssLength.value = tables.value.columns.byName(inputSsColumn.value).getString(0).length;
           asLength.value = tables.value.columns.byName(inputAsColumn.value).getString(0).length;
@@ -634,18 +651,26 @@ export function defineAxolabsPattern() {
     } else {
       if (inputIdColumn.value != null)
         addColumnWithIds(tables.value.name, inputIdColumn.value, getShortName(saveAs.value));
-      addColumnWithTranslatedSequences(tables.value.name, inputSsColumn.value, ssBases, ssPtoLinkages, ssFiveModification, ssThreeModification, firstSsPto.value);
-      if (createAsStrand.value)
-        addColumnWithTranslatedSequences(tables.value.name, inputAsColumn.value, asBases, asPtoLinkages, asFiveModification, asThreeModification, firstAsPto.value);
+      addColumnWithTranslatedSequences(
+        tables.value.name, inputSsColumn.value, ssBases, ssPtoLinkages,
+        ssFiveModification, ssThreeModification, firstSsPto.value);
+      if (createAsStrand.value) {
+        addColumnWithTranslatedSequences(
+          tables.value.name, inputAsColumn.value, asBases, asPtoLinkages,
+          asFiveModification, asThreeModification, firstAsPto.value);
+      }
       grok.shell.v = grok.shell.getTableView(tables.value.name);
-      grok.shell.info(((createAsStrand.value) ? "Columns were" : "Column was") + " added to table '" + tables.value.name + "'");
+      grok.shell.info(((createAsStrand.value) ? 'Columns were' : 'Column was') +
+      ' added to table \'' + tables.value.name + '\'');
     }
   });
 
-  let ssInputExample = ui.textInput('Sense Strand', generateExample(ssLength.value, sequenceBase.value),() => {
-    ssOutputExample.value = translateSequence(ssInputExample.value, ssBases, ssPtoLinkages, ssFiveModification, ssThreeModification, firstSsPto.value)
+  const ssInputExample = ui.textInput('Sense Strand', generateExample(ssLength.value, sequenceBase.value), () => {
+    ssOutputExample.value = translateSequence(ssInputExample.value, ssBases, ssPtoLinkages,
+      ssFiveModification, ssThreeModification, firstSsPto.value);
   });
-  let ssOutputExample = ui.textInput(' ', translateSequence(ssInputExample.value, ssBases, ssPtoLinkages, ssThreeModification, ssFiveModification, firstSsPto.value));
+  const ssOutputExample = ui.textInput(' ', translateSequence(
+    ssInputExample.value, ssBases, ssPtoLinkages, ssThreeModification, ssFiveModification, firstSsPto.value));
   (ssInputExample.input as HTMLElement).style.resize = 'none';
   (ssInputExample.input as HTMLElement).style.minWidth = exampleMinWidth;
   (ssOutputExample.input as HTMLElement).style.resize = 'none';
@@ -655,15 +680,18 @@ export function defineAxolabsPattern() {
   ssOutputExample.root.append(
     ui.div([
       ui.button(ui.iconFA('copy', () => {}), () => {
-        navigator.clipboard.writeText(ssOutputExample.value).then(() => grok.shell.info('Sequence was copied to clipboard'));
-      })
-    ], 'ui-input-options')
+        navigator.clipboard.writeText(ssOutputExample.value).then(() =>
+          grok.shell.info('Sequence was copied to clipboard'));
+      }),
+    ], 'ui-input-options'),
   );
 
-  let asInputExample = ui.textInput('Antisense Strand', generateExample(asLength.value, sequenceBase.value),() => {
-    asOutputExample.value = translateSequence(asInputExample.value, asBases, asPtoLinkages, asFiveModification, asThreeModification, firstSsPto.value);
+  const asInputExample = ui.textInput('Antisense Strand', generateExample(asLength.value, sequenceBase.value), () => {
+    asOutputExample.value = translateSequence(
+      asInputExample.value, asBases, asPtoLinkages, asFiveModification, asThreeModification, firstSsPto.value);
   });
-  let asOutputExample = ui.textInput(' ', translateSequence(asInputExample.value, asBases, asPtoLinkages, asFiveModification, asThreeModification, firstSsPto.value));
+  const asOutputExample = ui.textInput(' ', translateSequence(
+    asInputExample.value, asBases, asPtoLinkages, asFiveModification, asThreeModification, firstSsPto.value));
   (asInputExample.input as HTMLElement).style.resize = 'none';
   (asInputExample.input as HTMLElement).style.minWidth = exampleMinWidth;
   (asOutputExample.input as HTMLElement).style.resize = 'none';
@@ -673,40 +701,41 @@ export function defineAxolabsPattern() {
   asOutputExample.root.append(
     ui.div([
       ui.button(ui.iconFA('copy', () => {}), () => {
-        navigator.clipboard.writeText(asOutputExample.value).then(() => grok.shell.info('Sequence was copied to clipboard'));
-      })
-    ], 'ui-input-options')
+        navigator.clipboard.writeText(asOutputExample.value).then(() =>
+          grok.shell.info('Sequence was copied to clipboard'));
+      }),
+    ], 'ui-input-options'),
   );
   asExampleDiv.append(asInputExample.root);
   asExampleDiv.append(asOutputExample.root);
 
   updateUiForNewSequenceLength();
 
-  let exampleSection = ui.div([
+  const exampleSection = ui.div([
     ui.h1('Example'),
     ssInputExample.root,
     ssOutputExample.root,
-    asExampleDiv
+    asExampleDiv,
   ], 'ui-form');
 
-  let inputsSection = ui.div([
+  const inputsSection = ui.div([
     ui.h1('Inputs'),
     ui.divH([
       tables.root,
-      inputSsColumnDiv
+      inputSsColumnDiv,
     ]),
     ui.divH([
       inputAsColumnDiv,
-      inputIdColumnDiv
+      inputIdColumnDiv,
     ]),
     ui.buttonsInput([
-      convertSequenceButton
-    ])
+      convertSequenceButton,
+    ]),
   ], 'ui-form');
 
-  let mainSection = ui.panel([
+  const mainSection = ui.panel([
     ui.block([
-      svgDiv
+      svgDiv,
     ], {style: {overflowX: 'scroll'}}),
     ui.button('Download', () => svg.saveSvgAsPng(document.getElementById('mySvg'), saveAs.value)),
     isEnumerateModificationsDiv,
@@ -715,11 +744,11 @@ export function defineAxolabsPattern() {
         ui.divH([
           ui.h1('Pattern'),
           ui.div([
-            ui.iconFA('question-circle',() => {
+            ui.iconFA('question-circle', () => {
               appAxolabsDescription.innerHTML = '';
               appAxolabsDescription.append(info);
-            })
-          ], {style: {padding: '2px'}})
+            }),
+          ], {style: {padding: '2px'}}),
         ]),
         ui.divH([
           ui.div([
@@ -730,8 +759,8 @@ export function defineAxolabsPattern() {
             loadPatternDiv,
             saveAs.root,
             ui.buttonsInput([
-              savePatternButton
-            ])
+              savePatternButton,
+            ]),
           ], 'ui-form'),
           ui.div([
             createAsStrand.root,
@@ -741,56 +770,56 @@ export function defineAxolabsPattern() {
             ssFiveModification.root,
             ssThreeModification.root,
             asModificationDiv,
-          ], 'ui-form')
-        ], 'ui-form')
+          ], 'ui-form'),
+        ], 'ui-form'),
       ], 'ui-form'),
       inputsSection,
-      exampleSection
-    ], {style: {flexWrap: 'wrap'}})
+      exampleSection,
+    ], {style: {flexWrap: 'wrap'}}),
   ]);
 
-  let ssModificationSection = ui.panel([
+  const ssModificationSection = ui.panel([
     ui.h1('Sense Strand'),
     ui.divH([
       ui.div([ui.divText('#')], {style: {width: '20px'}})!,
       ui.block75([ui.divText('Modification')])!,
-      ui.div([ui.divText('PTO')], {style: {paddingRight: '8px'}})!
+      ui.div([ui.divText('PTO')], {style: {paddingRight: '8px'}})!,
     ]),
-    ssModificationItems
+    ssModificationItems,
   ])!;
 
-  let asModificationSection = ui.panel([
+  const asModificationSection = ui.panel([
     ui.h1('Antisense Strand'),
     ui.divH([
       ui.div([ui.divText('#')], {style: {width: '20px'}})!,
       ui.block75([ui.divText('Modification')])!,
-      ui.div([ui.divText('PTO')], {style: {paddingRight: '8px'}})!
+      ui.div([ui.divText('PTO')], {style: {paddingRight: '8px'}})!,
     ]),
-    asModificationItems
+    asModificationItems,
   ])!;
 
-  let info = ui.info(
+  const info = ui.info(
     [
-      ui.divText("\n How to define new pattern:",{style: {'font-weight': 'bolder'}}),
-      ui.divText("1. Choose table and columns with sense and antisense strands"),
-      ui.divText("2. Choose lengths of both strands by editing checkboxes below"),
-      ui.divText("3. Choose basis and PTO status for each nucleotide"),
-      ui.divText("4. Set additional modifications for sequence edges"),
-      ui.divText("5. Press 'Convert Sequences' button"),
-      ui.divText("This will add the result column(s) to the right of the table"),
-    ], 'Create and apply Axolabs translation patterns.'
+      ui.divText('\n How to define new pattern:', {style: {'font-weight': 'bolder'}}),
+      ui.divText('1. Choose table and columns with sense and antisense strands'),
+      ui.divText('2. Choose lengths of both strands by editing checkboxes below'),
+      ui.divText('3. Choose basis and PTO status for each nucleotide'),
+      ui.divText('4. Set additional modifications for sequence edges'),
+      ui.divText('5. Press \'Convert Sequences\' button'),
+      ui.divText('This will add the result column(s) to the right of the table'),
+    ], 'Create and apply Axolabs translation patterns.',
   );
 
   return ui.splitH([
     ui.div([
       appAxolabsDescription,
-      mainSection!
+      mainSection!,
     ])!,
     ui.box(
       ui.divH([
         ssModificationSection,
-        asModificationSection
-      ]), {style: {maxWidth: '360px'}}
-    )
+        asModificationSection,
+      ]), {style: {maxWidth: '360px'}},
+    ),
   ]);
-}
+}