@teselagen/ove 0.3.31 → 0.3.43

package/index.umd.js

@@ -45029,25 +45029,16 @@ ${latestSubscriptionCallbackError.current.stack}
   var _cof = /* @__PURE__ */ __name(function(it) {
     return toString$4.call(it).slice(8, -1);
   }, "_cof");
-  var _iobject;
-  var hasRequired_iobject;
-  function require_iobject() {
-    if (hasRequired_iobject)
-      return _iobject;
-    hasRequired_iobject = 1;
-    var cof2 = _cof;
-    _iobject = Object("z").propertyIsEnumerable(0) ? Object : function(it) {
-      return cof2(it) == "String" ? it.split("") : Object(it);
-    };
-    return _iobject;
-  }
-  __name(require_iobject, "require_iobject");
+  var cof$2 = _cof;
+  var _iobject = Object("z").propertyIsEnumerable(0) ? Object : function(it) {
+    return cof$2(it) == "String" ? it.split("") : Object(it);
+  };
   var _defined = /* @__PURE__ */ __name(function(it) {
     if (it == void 0)
       throw TypeError("Can't call method on  " + it);
     return it;
   }, "_defined");
-  var IObject = require_iobject();
+  var IObject = _iobject;
   var defined$2 = _defined;
   var _toIobject = /* @__PURE__ */ __name(function(it) {
     return IObject(defined$2(it));
@@ -45144,15 +45135,7 @@ ${latestSubscriptionCallbackError.current.stack}
   var _objectGops = {};
   _objectGops.f = Object.getOwnPropertySymbols;
   var _objectPie = {};
-  var hasRequired_objectPie;
-  function require_objectPie() {
-    if (hasRequired_objectPie)
-      return _objectPie;
-    hasRequired_objectPie = 1;
-    _objectPie.f = {}.propertyIsEnumerable;
-    return _objectPie;
-  }
-  __name(require_objectPie, "require_objectPie");
+  _objectPie.f = {}.propertyIsEnumerable;
   var defined$1 = _defined;
   var _toObject = /* @__PURE__ */ __name(function(it) {
     return Object(defined$1(it));
@@ -45166,9 +45149,9 @@ ${latestSubscriptionCallbackError.current.stack}
     var DESCRIPTORS2 = require_descriptors();
     var getKeys2 = _objectKeys;
     var gOPS2 = _objectGops;
-    var pIE2 = require_objectPie();
+    var pIE2 = _objectPie;
     var toObject2 = _toObject;
-    var IObject2 = require_iobject();
+    var IObject2 = _iobject;
     var $assign = Object.assign;
     _objectAssign = !$assign || _fails(function() {
       var A2 = {};
@@ -45803,7 +45786,7 @@ ${latestSubscriptionCallbackError.current.stack}
   }, "_wksDefine");
   var getKeys = _objectKeys;
   var gOPS$1 = _objectGops;
-  var pIE$1 = require_objectPie();
+  var pIE$1 = _objectPie;
   var _enumKeys = /* @__PURE__ */ __name(function(it) {
     var result = getKeys(it);
     var getSymbols2 = gOPS$1.f;
@@ -45844,7 +45827,7 @@ ${latestSubscriptionCallbackError.current.stack}
     return windowNames && toString$3.call(it) == "[object Window]" ? getWindowNames(it) : gOPN$1(toIObject$2(it));
   }, "getOwnPropertyNames");
   var _objectGopd = {};
-  var pIE = require_objectPie();
+  var pIE = _objectPie;
   var createDesc$1 = _propertyDesc;
   var toIObject$1 = _toIobject;
   var toPrimitive$1 = _toPrimitive$1;
@@ -46024,7 +46007,7 @@ ${latestSubscriptionCallbackError.current.stack}
     $GOPD.f = $getOwnPropertyDescriptor;
     $DP.f = $defineProperty;
     _objectGopn.f = gOPNExt.f = $getOwnPropertyNames;
-    require_objectPie().f = $propertyIsEnumerable;
+    _objectPie.f = $propertyIsEnumerable;
     $GOPS.f = $getOwnPropertySymbols;
     if (DESCRIPTORS && !_library) {
       redefine(ObjectProto, "propertyIsEnumerable", $propertyIsEnumerable);
@@ -107748,6 +107731,7 @@ ${latestSubscriptionCallbackError.current.stack}
     minimumOrfSizeUpdate
   }, Symbol.toStringTag, { value: "Module" }));
   const protein_letters = "ACDEFGHIKLMNPQRSTVWY";
+  const protein_letters_withUandX = "ACDEFGHIKLMNPQRSTVWYUX";
   const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO.*-";
   const ambiguous_dna_letters = "GATCRYWSMKHBVDN";
   const unambiguous_dna_letters = "GATC";
@@ -107816,6 +107800,7 @@ ${latestSubscriptionCallbackError.current.stack}
     extended_protein_letters,
     extended_protein_values,
     protein_letters,
+    protein_letters_withUandX,
     unambiguous_dna_letters,
     unambiguous_rna_letters
   }, Symbol.toStringTag, { value: "Module" }));
@@ -113834,20 +113819,91 @@ ${latestSubscriptionCallbackError.current.stack}
     "primers",
     "guides"
   ];
-  function filterSequenceString(sequenceString, additionalValidChars = "", charOverrides) {
-    if (sequenceString) {
-      return sequenceString.replace(
-        new RegExp(
-          `[^${charOverrides || `atgcyrswkmbvdhnu${additionalValidChars.split("").join("\\")}`}]`,
-          "gi"
-        ),
-        ""
+  function filterSequenceString(sequenceString, {
+    additionalValidChars = "",
+    isOligo: isOligo2,
+    name: name2,
+    isProtein: isProtein2,
+    isRna: isRna2,
+    isMixedRnaAndDna,
+    includeStopCodon
+  } = {}) {
+    const acceptedChars = getAcceptedChars({
+      isOligo: isOligo2,
+      isProtein: isProtein2,
+      isRna: isRna2,
+      isMixedRnaAndDna,
+      includeStopCodon
+    });
+    const replaceChars = getReplaceChars({
+      isOligo: isOligo2,
+      isProtein: isProtein2,
+      isRna: isRna2,
+      isMixedRnaAndDna
+    });
+    let sanitizedVal = "";
+    const invalidChars = [];
+    const chars2 = `${acceptedChars}${additionalValidChars.split("").join("\\")}`;
+    const warnings = [];
+    const replaceCount = {};
+    sequenceString.split("").forEach((letter) => {
+      const lowerLetter = letter.toLowerCase();
+      if (replaceChars && replaceChars[lowerLetter]) {
+        if (!replaceCount[lowerLetter]) {
+          replaceCount[lowerLetter] = 0;
+        }
+        replaceCount[lowerLetter]++;
+        const isUpper = lowerLetter !== letter;
+        sanitizedVal += isUpper ? replaceChars[lowerLetter].toUpperCase() : replaceChars[lowerLetter];
+      } else if (chars2.includes(lowerLetter)) {
+        sanitizedVal += letter;
+      } else {
+        invalidChars.push(letter);
+      }
+    });
+    Object.keys(replaceCount).forEach((letter) => {
+      warnings.push(
+        `Replaced "${letter}" with "${replaceChars[letter]}"${replaceCount[letter] > 1 ? ` ${replaceCount[letter]} times` : ""}`
       );
-    } else {
-      return sequenceString;
+    });
+    if (sequenceString.length !== sanitizedVal.length) {
+      warnings.push(
+        `${name2 ? `Sequence ${name2}: ` : ""}Invalid character(s) detected and removed: ${invalidChars.slice(0, 100).join(", ")} `
+      );
+    }
+    if (typeof window !== "undefined" && window.toastr && warnings.length) {
+      warnings.forEach((warning2) => {
+        window.toastr.warning(warning2);
+      });
     }
+    return [sanitizedVal, warnings];
   }
   __name(filterSequenceString, "filterSequenceString");
+  function getAcceptedChars({
+    isOligo: isOligo2,
+    isProtein: isProtein2,
+    isRna: isRna2,
+    isMixedRnaAndDna,
+    includeStopCodon
+  } = {}) {
+    return isProtein2 ? `${protein_letters_withUandX.toLowerCase()}${includeStopCodon ? "*." : ""}}` : isOligo2 ? ambiguous_rna_letters.toLowerCase() + "t" : isRna2 ? ambiguous_rna_letters.toLowerCase() + "t" : isMixedRnaAndDna ? ambiguous_rna_letters.toLowerCase() + ambiguous_dna_letters.toLowerCase() : (
+      //just plain old dna
+      ambiguous_rna_letters.toLowerCase() + ambiguous_dna_letters.toLowerCase()
+    );
+  }
+  __name(getAcceptedChars, "getAcceptedChars");
+  function getReplaceChars({
+    isOligo: isOligo2,
+    isProtein: isProtein2,
+    isRna: isRna2,
+    isMixedRnaAndDna
+  } = {}) {
+    return isProtein2 ? {} : isOligo2 ? {} : isRna2 ? { t: "u" } : isMixedRnaAndDna ? {} : (
+      //just plain old dna
+      {}
+    );
+  }
+  __name(getReplaceChars, "getReplaceChars");
   function tidyUpAnnotation(_annotation, {
     sequenceData: sequenceData2 = {},
     convertAnnotationsFromAAIndices,
@@ -113976,14 +114032,6 @@ ${latestSubscriptionCallbackError.current.stack}
     }
   }
   __name(coerceLocation, "coerceLocation");
-  function filterAminoAcidSequenceString(sequenceString, options) {
-    options = options || {};
-    if (options.includeStopCodon) {
-      return sequenceString == null ? void 0 : sequenceString.replace(/[^xtgalmfwkqespvicyhrndu.*]/gi, "");
-    }
-    return sequenceString == null ? void 0 : sequenceString.replace(/[^xtgalmfwkqespvicyhrndu]/gi, "");
-  }
-  __name(filterAminoAcidSequenceString, "filterAminoAcidSequenceString");
   function getDegenerateDnaStringFromAAString(aaString) {
     return aaString.split("").map((char2) => aminoAcidToDegenerateDnaMap[char2.toLowerCase()] || "nnn").join("");
   }
@@ -113995,11 +114043,10 @@ ${latestSubscriptionCallbackError.current.stack}
       removeUnwantedChars,
       additionalValidChars,
       noTranslationData,
-      charOverrides,
       doNotProvideIdsForAnnotations,
-      proteinFilterOptions,
       noCdsTranslations,
-      convertAnnotationsFromAAIndices
+      convertAnnotationsFromAAIndices,
+      topLevelSeqData
     } = options;
     let seqData = lodashExports.cloneDeep(pSeqData);
     const response = {
@@ -114029,16 +114076,15 @@ ${latestSubscriptionCallbackError.current.stack}
     }
     if (removeUnwantedChars) {
       if (seqData.isProtein) {
-        seqData.proteinSequence = filterAminoAcidSequenceString(
-          seqData.proteinSequence,
-          __spreadValues({ includeStopCodon: true }, proteinFilterOptions)
-        );
+        const [newSeq] = filterSequenceString(seqData.proteinSequence, __spreadValues({
+          includeStopCodon: true
+        }, topLevelSeqData || seqData));
+        seqData.proteinSequence = newSeq;
       } else {
-        seqData.sequence = filterSequenceString(
-          seqData.sequence,
-          `${additionalValidChars || ""}${seqData.isRna || seqData.isMixedRnaAndDna ? "u" : ""}`,
-          charOverrides
-        );
+        const [newSeq] = filterSequenceString(seqData.sequence, __spreadValues({
+          additionalValidChars
+        }, topLevelSeqData || seqData));
+        seqData.sequence = newSeq;
       }
     }
     if (seqData.isProtein) {
@@ -123385,7 +123431,8 @@ ${latestSubscriptionCallbackError.current.stack}
       inclusive1BasedEnd,
       additionalValidChars,
       allowOverflowAnnotations,
-      coerceFeatureTypes
+      coerceFeatureTypes,
+      includeStopCodon
     } = options;
     [
       "isDNA",
@@ -123435,7 +123482,6 @@ ${latestSubscriptionCallbackError.current.stack}
       response.messages.push("No sequence detected");
       sequence2.sequence = "";
     }
-    let validChars;
     if (sequence2.isProtein === void 0 && guessIfProtein) {
       sequence2.isProtein = !guessIfSequenceIsDnaAndNotProtein(
         sequence2.sequence,
@@ -123443,12 +123489,15 @@ ${latestSubscriptionCallbackError.current.stack}
       );
     }
     if (sequence2.isProtein) {
-      validChars = filterAminoAcidSequenceString(sequence2.sequence);
+      const [validChars, warnings] = filterSequenceString(sequence2.sequence, {
+        name: sequence2.name,
+        isProtein: true,
+        additionalValidChars,
+        includeStopCodon
+      });
       if (validChars !== sequence2.sequence) {
         sequence2.sequence = validChars;
-        response.messages.push(
-          "Import Error: Illegal character(s) detected and removed from amino acid sequence. Allowed characters are: xtgalmfwkqespvicyhrndu"
-        );
+        response.messages.push(...warnings);
       }
       sequence2.type = "PROTEIN";
       sequence2.isProtein = true;
@@ -123470,12 +123519,12 @@ ${latestSubscriptionCallbackError.current.stack}
       } else {
         sequence2.type = "DNA";
       }
-      validChars = filterSequenceString(sequence2.sequence, additionalValidChars);
+      const [validChars, warnings] = filterSequenceString(sequence2.sequence, __spreadValues({
+        additionalValidChars
+      }, sequence2));
       if (validChars !== sequence2.sequence) {
         sequence2.sequence = validChars;
-        response.messages.push(
-          "Import Error: Illegal character(s) detected and removed from sequence. Allowed characters are: atgcyrswkmbvdhn"
-        );
+        response.messages.push(...warnings);
       }
     }
     if (!sequence2.size) {
@@ -138363,18 +138412,6 @@ ${seq.sequence}
     return selToUse;
   }
   __name(getSelFromWrappedAddon, "getSelFromWrappedAddon");
-  function getAcceptedChars({
-    isOligo: isOligo2,
-    isProtein: isProtein2,
-    isRna: isRna2,
-    isMixedRnaAndDna
-  } = {}) {
-    return isProtein2 ? extended_protein_letters.toLowerCase() : isOligo2 ? ambiguous_rna_letters.toLowerCase() + "t" : isRna2 ? ambiguous_rna_letters.toLowerCase() : isMixedRnaAndDna ? ambiguous_rna_letters.toLowerCase() + ambiguous_dna_letters.toLowerCase() : (
-      //just plain old dna
-      ambiguous_dna_letters.toLowerCase()
-    );
-  }
-  __name(getAcceptedChars, "getAcceptedChars");
   function getStripedPattern({ color: color2 }) {
     return /* @__PURE__ */ React$2.createElement(
       "pattern",
@@ -154960,7 +154997,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
   }
   __name(showFileDialog, "showFileDialog");
   const name = "@teselagen/ove";
-  const version = "0.3.30";
+  const version = "0.3.42";
   const main = "./src/index.js";
   const exports$1 = {
     ".": {
@@ -157107,9 +157144,8 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
         selectionLayer: selectionLayer2,
         sequenceLength,
         isProtein: isProtein2,
-        replaceChars,
         caretPosition: caretPosition2,
-        acceptedChars,
+        sequenceData: sequenceData2,
         maxInsertSize
       } = this.props;
       const { charsToInsert, hasTempError } = this.state;
@@ -157142,17 +157178,13 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
           autoFocus: true,
           style: hasTempError ? { borderColor: "red" } : {},
           onChange: (e2) => {
-            let sanitizedVal = "";
-            e2.target.value.split("").forEach((letter) => {
-              const lowerLetter = letter.toLowerCase();
-              if (replaceChars && replaceChars[lowerLetter]) {
-                const isUpper = lowerLetter !== letter;
-                sanitizedVal += isUpper ? replaceChars[lowerLetter].toUpperCase() : replaceChars[lowerLetter];
-              } else if (acceptedChars.includes(lowerLetter)) {
-                sanitizedVal += letter;
-              }
-            });
-            if (e2.target.value.length !== sanitizedVal.length) {
+            const [sanitizedVal, warnings] = filterSequenceString(
+              e2.target.value,
+              __spreadProps(__spreadValues({}, sequenceData2), {
+                name: void 0
+              })
+            );
+            if (warnings.length) {
               this.setState({
                 hasTempError: true
               });
@@ -158027,7 +158059,8 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
             selectionLayer: selectionLayer2 = { start: -1, end: -1 },
             readOnly: readOnly2,
             onPaste,
-            disableBpEditing
+            disableBpEditing,
+            sequenceData: sequenceData2
           } = this.props;
           if (disableBpEditing) {
             return window.toastr.warning("Sorry the underlying sequence is locked");
@@ -158052,6 +158085,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
             };
           }
           seqDataToInsert = tidyUpSequenceData(seqDataToInsert, {
+            topLevelSeqData: sequenceData2,
             provideNewIdsForAnnotations: true,
             annotationsAsObjects: true,
             removeUnwantedChars: true,
@@ -158147,8 +158181,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
             createSequenceInputPopup({
               useEventPositioning,
               isReplace,
-              replaceChars: sequenceData2.isRna ? { t: "u" } : void 0,
-              acceptedChars: getAcceptedChars(sequenceData2),
+              sequenceData: sequenceData2,
               isProtein: sequenceData2.isProtein,
               selectionLayer: selectionLayer2,
               sequenceLength,
@@ -169641,14 +169674,8 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
       const newVal2 = e2.target.innerText;
       const savedCaretPosition = EditCaretPositioning.saveSelection(e2.currentTarget);
       setCaretPosition(savedCaretPosition);
-      const acceptedChars = getAcceptedChars(sequenceData2);
-      let newBases = "";
-      newVal2.split("").forEach((letter) => {
-        if (acceptedChars.includes(letter.toLowerCase())) {
-          newBases += letter;
-        }
-      });
-      if (newVal2.length !== newBases.length) {
+      const [newBases, warnings] = filterSequenceString(newVal2, sequenceData2);
+      if (warnings.length) {
         setTempError(true);
         setTimeout(() => {
           setTempError(false);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.3.31",
+  "version": "0.3.43",
   "main": "./src/index.js",
   "exports": {
     ".": {
@@ -13,12 +13,12 @@
     "node": "16.20.2"
   },
   "dependencies": {
-    "@teselagen/sequence-utils": "0.3.8",
+    "@teselagen/sequence-utils": "0.3.9",
     "@teselagen/range-utils": "0.3.7",
-    "@teselagen/ui": "0.3.30",
+    "@teselagen/ui": "0.3.32",
     "@teselagen/file-utils": "0.3.9",
     "@teselagen/bounce-loader": "0.3.11",
-    "@teselagen/bio-parsers": "0.3.10",
+    "@teselagen/bio-parsers": "0.4.1",
     "@blueprintjs/core": "3.52.0",
     "@blueprintjs/datetime": "3.23.19",
     "@blueprintjs/icons": "3.33.0",

package/src/helperComponents/AddOrEditPrimerDialog/index.js

@@ -6,11 +6,13 @@ import {
   generateField,
   RadioGroupField
 } from "@teselagen/ui";
-import { getReverseComplementSequenceString } from "@teselagen/sequence-utils";
+import {
+  filterSequenceString,
+  getReverseComplementSequenceString
+} from "@teselagen/sequence-utils";
 
 import AddOrEditAnnotationDialog from "../AddOrEditAnnotationDialog";
 import { convertRangeTo0Based } from "@teselagen/range-utils";
-import { getAcceptedChars } from "../../utils/editorUtils";
 import classNames from "classnames";
 import "./style.css";
 import { getSequenceWithinRange } from "@teselagen/range-utils";
@@ -42,14 +44,9 @@ const CustomContentEditable = generateField(function CustomContentEditable({
     const newVal = e.target.innerText;
     const savedCaretPosition = CaretPositioning.saveSelection(e.currentTarget);
     setCaretPosition(savedCaretPosition);
-    const acceptedChars = getAcceptedChars(sequenceData);
-    let newBases = "";
-    newVal.split("").forEach(letter => {
-      if (acceptedChars.includes(letter.toLowerCase())) {
-        newBases += letter;
-      }
-    });
-    if (newVal.length !== newBases.length) {
+    const [newBases, warnings] = filterSequenceString(newVal, sequenceData);
+
+    if (warnings.length) {
       setTempError(true);
       setTimeout(() => {
         setTempError(false);

package/src/utils/editorUtils.js

@@ -4,7 +4,6 @@ import { divideBy3 } from "./proteinUtils";
 import {
   getInsertBetweenVals,
   calculatePercentGC,
-  bioData,
   aliasedEnzymesByName
 } from "@teselagen/sequence-utils";
 import { get, sortBy } from "lodash";
@@ -172,24 +171,6 @@ export function getSelFromWrappedAddon(selectionLayer, sequenceLength) {
   return selToUse;
 }
 
-export function getAcceptedChars({
-  isOligo,
-  isProtein,
-  isRna,
-  isMixedRnaAndDna
-} = {}) {
-  return isProtein
-    ? bioData.extended_protein_letters.toLowerCase()
-    : isOligo
-    ? bioData.ambiguous_rna_letters.toLowerCase() + "t"
-    : isRna
-    ? bioData.ambiguous_rna_letters.toLowerCase()
-    : isMixedRnaAndDna
-    ? bioData.ambiguous_rna_letters.toLowerCase() +
-      bioData.ambiguous_dna_letters.toLowerCase()
-    : //just plain old dna
-      bioData.ambiguous_dna_letters.toLowerCase();
-}
 export function getStripedPattern({ color }) {
   return (
     <pattern

package/src/withEditorInteractions/createSequenceInputPopup.js

@@ -6,7 +6,8 @@ import Popper from "popper.js";
 
 import {
   getInsertBetweenVals,
-  convertDnaCaretPositionOrRangeToAA
+  convertDnaCaretPositionOrRangeToAA,
+  filterSequenceString
 } from "@teselagen/sequence-utils";
 import React from "react";
 import { divideBy3 } from "../utils/proteinUtils";
@@ -77,9 +78,8 @@ class SequenceInputNoHotkeys extends React.Component {
       selectionLayer,
       sequenceLength,
       isProtein,
-      replaceChars,
       caretPosition,
-      acceptedChars,
+      sequenceData,
       maxInsertSize
     } = this.props;
     const { charsToInsert, hasTempError } = this.state;
@@ -136,19 +136,14 @@ class SequenceInputNoHotkeys extends React.Component {
           autoFocus
           style={hasTempError ? { borderColor: "red" } : {}}
           onChange={e => {
-            let sanitizedVal = "";
-            e.target.value.split("").forEach(letter => {
-              const lowerLetter = letter.toLowerCase();
-              if (replaceChars && replaceChars[lowerLetter]) {
-                const isUpper = lowerLetter !== letter;
-                sanitizedVal += isUpper
-                  ? replaceChars[lowerLetter].toUpperCase()
-                  : replaceChars[lowerLetter];
-              } else if (acceptedChars.includes(lowerLetter)) {
-                sanitizedVal += letter;
+            const [sanitizedVal, warnings] = filterSequenceString(
+              e.target.value,
+              {
+                ...sequenceData,
+                name: undefined
               }
-            });
-            if (e.target.value.length !== sanitizedVal.length) {
+            );
+            if (warnings.length) {
               this.setState({
                 hasTempError: true
               });
@@ -165,7 +160,6 @@ class SequenceInputNoHotkeys extends React.Component {
               );
             }
             e.target.value = sanitizedVal;
-
             this.setState({ charsToInsert: sanitizedVal });
           }}
         />

package/src/withEditorInteractions/index.js

@@ -41,11 +41,7 @@ import {
   createNewAnnotationMenu
 } from "../MenuBar/defaultConfig";
 import { fullSequenceTranslationMenu } from "../MenuBar/viewSubmenu";
-import {
-  getAcceptedChars,
-  getNodeToRefocus,
-  getSelFromWrappedAddon
-} from "../utils/editorUtils";
+import { getNodeToRefocus, getSelFromWrappedAddon } from "../utils/editorUtils";
 
 import {
   showAddOrEditAnnotationDialog,
@@ -212,7 +208,8 @@ function VectorInteractionHOC(Component /* options */) {
         selectionLayer = { start: -1, end: -1 },
         readOnly,
         onPaste,
-        disableBpEditing
+        disableBpEditing,
+        sequenceData
       } = this.props;
 
       if (disableBpEditing) {
@@ -240,6 +237,7 @@ function VectorInteractionHOC(Component /* options */) {
       }
 
       seqDataToInsert = tidyUpSequenceData(seqDataToInsert, {
+        topLevelSeqData: sequenceData,
         provideNewIdsForAnnotations: true,
         annotationsAsObjects: true,
         removeUnwantedChars: true,
@@ -360,8 +358,7 @@ function VectorInteractionHOC(Component /* options */) {
         createSequenceInputPopup({
           useEventPositioning,
           isReplace,
-          replaceChars: sequenceData.isRna ? { t: "u" } : undefined,
-          acceptedChars: getAcceptedChars(sequenceData),
+          sequenceData,
           isProtein: sequenceData.isProtein,
           selectionLayer,
           sequenceLength,