@teselagen/ove 0.3.30 → 0.3.43

package/index.umd.js

@@ -27120,10 +27120,10 @@ var __async = (__this, __arguments, generator) => {
     /* istanbul ignore next */
     Object.getOwnPropertyNames
   );
-  function toPrimitive$3(value) {
+  function toPrimitive$2(value) {
     return value === null ? null : typeof value === "object" ? "" + value : value;
   }
-  __name(toPrimitive$3, "toPrimitive$3");
+  __name(toPrimitive$2, "toPrimitive$2");
   function hasProp(target, prop2) {
     return objectPrototype$2.hasOwnProperty.call(target, prop2);
   }
@@ -28020,7 +28020,7 @@ var __async = (__this, __arguments, generator) => {
       return this.name_ + "[" + this.value_ + "]";
     }, "toString");
     _proto.valueOf = /* @__PURE__ */ __name(function valueOf() {
-      return toPrimitive$3(this.get());
+      return toPrimitive$2(this.get());
     }, "valueOf");
     _proto[_Symbol$toPrimitive] = function() {
       return this.valueOf();
@@ -28205,7 +28205,7 @@ var __async = (__this, __arguments, generator) => {
       return this.name_ + "[" + this.derivation.toString() + "]";
     }, "toString");
     _proto.valueOf = /* @__PURE__ */ __name(function valueOf() {
-      return toPrimitive$3(this.get());
+      return toPrimitive$2(this.get());
     }, "valueOf");
     _proto[_Symbol$toPrimitive$1] = function() {
       return this.valueOf();
@@ -44864,11 +44864,20 @@ ${latestSubscriptionCallbackError.current.stack}
       return true;
     }
   }, "_fails");
-  var _descriptors = !_fails(function() {
-    return Object.defineProperty({}, "a", { get: function() {
-      return 7;
-    } }).a != 7;
-  });
+  var _descriptors;
+  var hasRequired_descriptors;
+  function require_descriptors() {
+    if (hasRequired_descriptors)
+      return _descriptors;
+    hasRequired_descriptors = 1;
+    _descriptors = !_fails(function() {
+      return Object.defineProperty({}, "a", { get: function() {
+        return 7;
+      } }).a != 7;
+    });
+    return _descriptors;
+  }
+  __name(require_descriptors, "require_descriptors");
   var _domCreate;
   var hasRequired_domCreate;
   function require_domCreate() {
@@ -44884,11 +44893,20 @@ ${latestSubscriptionCallbackError.current.stack}
     return _domCreate;
   }
   __name(require_domCreate, "require_domCreate");
-  var _ie8DomDefine = !_descriptors && !_fails(function() {
-    return Object.defineProperty(require_domCreate()("div"), "a", { get: function() {
-      return 7;
-    } }).a != 7;
-  });
+  var _ie8DomDefine;
+  var hasRequired_ie8DomDefine;
+  function require_ie8DomDefine() {
+    if (hasRequired_ie8DomDefine)
+      return _ie8DomDefine;
+    hasRequired_ie8DomDefine = 1;
+    _ie8DomDefine = !require_descriptors() && !_fails(function() {
+      return Object.defineProperty(require_domCreate()("div"), "a", { get: function() {
+        return 7;
+      } }).a != 7;
+    });
+    return _ie8DomDefine;
+  }
+  __name(require_ie8DomDefine, "require_ie8DomDefine");
   var isObject$6 = _isObject;
   var _toPrimitive$1 = /* @__PURE__ */ __name(function(it, S2) {
     if (!isObject$6(it))
@@ -44902,25 +44920,33 @@ ${latestSubscriptionCallbackError.current.stack}
       return val2;
     throw TypeError("Can't convert object to primitive value");
   }, "_toPrimitive$1");
-  var anObject$5 = _anObject;
-  var IE8_DOM_DEFINE$1 = _ie8DomDefine;
-  var toPrimitive$2 = _toPrimitive$1;
-  var dP$3 = Object.defineProperty;
-  _objectDp.f = _descriptors ? Object.defineProperty : /* @__PURE__ */ __name(function defineProperty2(O2, P2, Attributes) {
-    anObject$5(O2);
-    P2 = toPrimitive$2(P2, true);
-    anObject$5(Attributes);
-    if (IE8_DOM_DEFINE$1)
-      try {
-        return dP$3(O2, P2, Attributes);
-      } catch (e2) {
-      }
-    if ("get" in Attributes || "set" in Attributes)
-      throw TypeError("Accessors not supported!");
-    if ("value" in Attributes)
-      O2[P2] = Attributes.value;
-    return O2;
-  }, "defineProperty");
+  var hasRequired_objectDp;
+  function require_objectDp() {
+    if (hasRequired_objectDp)
+      return _objectDp;
+    hasRequired_objectDp = 1;
+    var anObject2 = _anObject;
+    var IE8_DOM_DEFINE2 = require_ie8DomDefine();
+    var toPrimitive2 = _toPrimitive$1;
+    var dP2 = Object.defineProperty;
+    _objectDp.f = require_descriptors() ? Object.defineProperty : /* @__PURE__ */ __name(function defineProperty2(O2, P2, Attributes) {
+      anObject2(O2);
+      P2 = toPrimitive2(P2, true);
+      anObject2(Attributes);
+      if (IE8_DOM_DEFINE2)
+        try {
+          return dP2(O2, P2, Attributes);
+        } catch (e2) {
+        }
+      if ("get" in Attributes || "set" in Attributes)
+        throw TypeError("Accessors not supported!");
+      if ("value" in Attributes)
+        O2[P2] = Attributes.value;
+      return O2;
+    }, "defineProperty");
+    return _objectDp;
+  }
+  __name(require_objectDp, "require_objectDp");
   var _propertyDesc = /* @__PURE__ */ __name(function(bitmap, value) {
     return {
       enumerable: !(bitmap & 1),
@@ -44929,9 +44955,9 @@ ${latestSubscriptionCallbackError.current.stack}
       value
     };
   }, "_propertyDesc");
-  var dP$2 = _objectDp;
+  var dP$2 = require_objectDp();
   var createDesc$3 = _propertyDesc;
-  var _hide = _descriptors ? function(object2, key2, value) {
+  var _hide = require_descriptors() ? function(object2, key2, value) {
     return dP$2.f(object2, key2, createDesc$3(1, value));
   } : function(object2, key2, value) {
     object2[key2] = value;
@@ -45109,15 +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));
@@ -45128,10 +45146,10 @@ ${latestSubscriptionCallbackError.current.stack}
     if (hasRequired_objectAssign)
       return _objectAssign;
     hasRequired_objectAssign = 1;
-    var DESCRIPTORS2 = _descriptors;
+    var DESCRIPTORS2 = require_descriptors();
     var getKeys2 = _objectKeys;
     var gOPS2 = _objectGops;
-    var pIE2 = require_objectPie();
+    var pIE2 = _objectPie;
     var toObject2 = _toObject;
     var IObject2 = _iobject;
     var $assign = Object.assign;
@@ -45194,10 +45212,10 @@ ${latestSubscriptionCallbackError.current.stack}
   }, "_iterStep");
   var _iterators = {};
   var _redefine = _hide;
-  var dP$1 = _objectDp;
+  var dP$1 = require_objectDp();
   var anObject$4 = _anObject;
   var getKeys$1 = _objectKeys;
-  var _objectDps = _descriptors ? Object.defineProperties : /* @__PURE__ */ __name(function defineProperties2(O2, Properties2) {
+  var _objectDps = require_descriptors() ? Object.defineProperties : /* @__PURE__ */ __name(function defineProperties2(O2, Properties2) {
     anObject$4(O2);
     var keys2 = getKeys$1(Properties2);
     var length = keys2.length;
@@ -45264,7 +45282,7 @@ ${latestSubscriptionCallbackError.current.stack}
   };
   $exports.store = store$2;
   var _wksExports = _wks.exports;
-  var def = _objectDp.f;
+  var def = require_objectDp().f;
   var has$b = _has;
   var TAG$1 = _wksExports("toStringTag");
   var _setToStringTag = /* @__PURE__ */ __name(function(it, tag, stat) {
@@ -45537,7 +45555,7 @@ ${latestSubscriptionCallbackError.current.stack}
   var _isArrayIter = /* @__PURE__ */ __name(function(it) {
     return it !== void 0 && (Iterators.Array === it || ArrayProto[ITERATOR] === it);
   }, "_isArrayIter");
-  var $defineProperty$1 = _objectDp;
+  var $defineProperty$1 = require_objectDp();
   var createDesc$2 = _propertyDesc;
   var _createProperty = /* @__PURE__ */ __name(function(object2, index2, value) {
     if (index2 in object2)
@@ -45666,7 +45684,7 @@ ${latestSubscriptionCallbackError.current.stack}
     }
   }, "_default$8");
   var $export$3 = _export;
-  $export$3($export$3.S + $export$3.F * !_descriptors, "Object", { defineProperty: _objectDp.f });
+  $export$3($export$3.S + $export$3.F * !require_descriptors(), "Object", { defineProperty: require_objectDp().f });
   var $Object$1 = _coreExports.Object;
   var defineProperty$6 = /* @__PURE__ */ __name(function defineProperty2(it, key2, desc) {
     return $Object$1.defineProperty(it, key2, desc);
@@ -45707,7 +45725,7 @@ ${latestSubscriptionCallbackError.current.stack}
   var META$1 = _uid("meta");
   var isObject$5 = _isObject;
   var has$9 = _has;
-  var setDesc = _objectDp.f;
+  var setDesc = require_objectDp().f;
   var id$1 = 0;
   var isExtensible = Object.isExtensible || function() {
     return true;
@@ -45760,7 +45778,7 @@ ${latestSubscriptionCallbackError.current.stack}
   var _metaExports = _meta.exports;
   var core = _coreExports;
   var wksExt$1 = _wksExt;
-  var defineProperty$4 = _objectDp.f;
+  var defineProperty$4 = require_objectDp().f;
   var _wksDefine = /* @__PURE__ */ __name(function(name2) {
     var $Symbol2 = core.Symbol || (core.Symbol = {});
     if (name2.charAt(0) != "_" && !(name2 in $Symbol2))
@@ -45768,7 +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;
@@ -45809,14 +45827,14 @@ ${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;
   var has$8 = _has;
-  var IE8_DOM_DEFINE = _ie8DomDefine;
+  var IE8_DOM_DEFINE = require_ie8DomDefine();
   var gOPD$2 = Object.getOwnPropertyDescriptor;
-  _objectGopd.f = _descriptors ? gOPD$2 : /* @__PURE__ */ __name(function getOwnPropertyDescriptor2(O2, P2) {
+  _objectGopd.f = require_descriptors() ? gOPD$2 : /* @__PURE__ */ __name(function getOwnPropertyDescriptor2(O2, P2) {
     O2 = toIObject$1(O2);
     P2 = toPrimitive$1(P2, true);
     if (IE8_DOM_DEFINE)
@@ -45829,7 +45847,7 @@ ${latestSubscriptionCallbackError.current.stack}
   }, "getOwnPropertyDescriptor");
   var global$1 = _globalExports;
   var has$7 = _has;
-  var DESCRIPTORS = _descriptors;
+  var DESCRIPTORS = require_descriptors();
   var $export$2 = _export;
   var redefine = _redefine;
   var META = _metaExports.KEY;
@@ -45852,7 +45870,7 @@ ${latestSubscriptionCallbackError.current.stack}
   var gOPNExt = _objectGopnExt;
   var $GOPD = _objectGopd;
   var $GOPS = _objectGops;
-  var $DP = _objectDp;
+  var $DP = require_objectDp();
   var $keys$1 = _objectKeys;
   var gOPD$1 = $GOPD.f;
   var dP = $DP.f;
@@ -45989,7 +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);
@@ -86978,7 +86996,7 @@ ${latestSubscriptionCallbackError.current.stack}
           isEntityDisabled,
           entity
         });
-        const _isClean = entity._isClean && doNotValidateUntouchedRows;
+        const _isClean = entity._isClean && doNotValidateUntouchedRows || isEntityClean(entity);
         const err2 = !_isClean && reduxFormCellValidation[cellId];
         let selectedTopBorder, selectedRightBorder, selectedBottomBorder, selectedLeftBorder;
         if (reduxFormSelectedCells[cellId]) {
@@ -89174,6 +89192,21 @@ ${latestSubscriptionCallbackError.current.stack}
     return str.replace(getNumberStrAtEnd(str), "");
   }
   __name(stripNumberAtEnd, "stripNumberAtEnd");
+  function isEntityClean(e2) {
+    let isClean = true;
+    lodashExports.some(e2, (val2, key2) => {
+      if (key2 === "id")
+        return;
+      if (key2 === "_isClean")
+        return;
+      if (val2) {
+        isClean = false;
+        return true;
+      }
+    });
+    return isClean;
+  }
+  __name(isEntityClean, "isEntityClean");
   const wrapDialog = /* @__PURE__ */ __name((topLevelDialogProps = {}) => (Component) => (props) => {
     const r2 = reactExports.useRef();
     const memoedHotkeys = reactExports.useMemo(
@@ -91688,7 +91721,7 @@ ${latestSubscriptionCallbackError.current.stack}
   function removeCleanRows(reduxFormEntities, reduxFormCellValidation) {
     const toFilterOut = {};
     const entsToUse = (reduxFormEntities || []).filter((e2) => {
-      if (!e2._isClean)
+      if (!(e2._isClean || isEntityClean(e2)))
         return true;
       else {
         toFilterOut[getIdOrCodeOrIndex(e2)] = true;
@@ -106643,7 +106676,9 @@ ${latestSubscriptionCallbackError.current.stack}
     ))),
     400
   );
-  const isSafari = /^((?!chrome|android).)*safari/i.test(navigator.userAgent);
+  const isSafari = /^((?!chrome|android).)*safari/i.test(
+    navigator.userAgent
+  );
   function genericCommandFactory(config) {
     const out = {};
     for (const cmdId in config.commandDefs) {
@@ -107696,6 +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";
@@ -107764,6 +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" }));
@@ -113782,20 +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 ? ` ${replaceCount[letter]} times` : ""}`
+      );
+    });
+    if (sequenceString.length !== sanitizedVal.length) {
+      warnings.push(
+        `${name2 ? `Sequence ${name2}: ` : ""}Invalid character(s) detected and removed: ${invalidChars.slice(0, 100).join(", ")} `
       );
-    } else {
-      return sequenceString;
     }
+    if (typeof window !== "undefined" && window.toastr && warnings.length) {
+      warnings.forEach((warning2) => {
+        window.toastr.warning(warning2);
+      });
+    }
+    return [sanitizedVal, warnings];
   }
   __name(filterSequenceString, "filterSequenceString");
+  function getAcceptedChars({
+    isOligo: isOligo2,
+    isProtein: isProtein2,
+    isRna: isRna2,
+    isMixedRnaAndDna,
+    includeStopCodon
+  } = {}) {
+    return isProtein2 ? `${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,
@@ -113924,14 +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("");
   }
@@ -113943,11 +114043,10 @@ ${latestSubscriptionCallbackError.current.stack}
       removeUnwantedChars,
       additionalValidChars,
       noTranslationData,
-      charOverrides,
       doNotProvideIdsForAnnotations,
-      proteinFilterOptions,
       noCdsTranslations,
-      convertAnnotationsFromAAIndices
+      convertAnnotationsFromAAIndices,
+      topLevelSeqData
     } = options;
     let seqData = lodashExports.cloneDeep(pSeqData);
     const response = {
@@ -113977,16 +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) {
@@ -123333,7 +123431,8 @@ ${latestSubscriptionCallbackError.current.stack}
       inclusive1BasedEnd,
       additionalValidChars,
       allowOverflowAnnotations,
-      coerceFeatureTypes
+      coerceFeatureTypes,
+      includeStopCodon
     } = options;
     [
       "isDNA",
@@ -123383,7 +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,
@@ -123391,12 +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;
@@ -123418,12 +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) {
@@ -138311,18 +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",
@@ -154908,7 +154997,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
   }
   __name(showFileDialog, "showFileDialog");
   const name = "@teselagen/ove";
-  const version = "0.3.29";
+  const version = "0.3.42";
   const main = "./src/index.js";
   const exports$1 = {
     ".": {
@@ -157055,9 +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;
@@ -157090,17 +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
               });
@@ -157975,7 +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");
@@ -158000,6 +158085,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
             };
           }
           seqDataToInsert = tidyUpSequenceData(seqDataToInsert, {
+            topLevelSeqData: sequenceData2,
             provideNewIdsForAnnotations: true,
             annotationsAsObjects: true,
             removeUnwantedChars: true,
@@ -158095,8 +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,
@@ -169589,14 +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);