@teselagen/ove 0.3.31 → 0.3.44

package/index.cjs.js

@@ -77896,6 +77896,7 @@ const minimumOrfSize$1 = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.de
   minimumOrfSizeUpdate
 }, Symbol.toStringTag, { value: "Module" }));
 const protein_letters = "ACDEFGHIKLMNPQRSTVWY";
+const protein_letters_withUandX = "ACDEFGHIKLMNPQRSTVWYUX";
 const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO.*-";
 const ambiguous_dna_letters = "GATCRYWSMKHBVDN";
 const unambiguous_dna_letters = "GATC";
@@ -77964,6 +77965,7 @@ const bioData = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.definePrope
   extended_protein_letters,
   extended_protein_values,
   protein_letters,
+  protein_letters_withUandX,
   unambiguous_dna_letters,
   unambiguous_rna_letters
 }, Symbol.toStringTag, { value: "Module" }));
@@ -83982,20 +83984,91 @@ const modifiableTypes = [
   "primers",
   "guides"
 ];
-function filterSequenceString(sequenceString, additionalValidChars = "", charOverrides) {
-  if (sequenceString) {
-    return sequenceString.replace(
-      new RegExp(
-        `[^${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,
@@ -84124,14 +84197,6 @@ function coerceLocation({
   }
 }
 __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((char) => aminoAcidToDegenerateDnaMap[char.toLowerCase()] || "nnn").join("");
 }
@@ -84143,11 +84208,10 @@ function tidyUpSequenceData(pSeqData, options = {}) {
     removeUnwantedChars,
     additionalValidChars,
     noTranslationData,
-    charOverrides,
     doNotProvideIdsForAnnotations,
-    proteinFilterOptions,
     noCdsTranslations,
-    convertAnnotationsFromAAIndices
+    convertAnnotationsFromAAIndices,
+    topLevelSeqData
   } = options;
   let seqData = lodashExports.cloneDeep(pSeqData);
   const response = {
@@ -84177,16 +84241,15 @@ function tidyUpSequenceData(pSeqData, options = {}) {
   }
   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) {
@@ -93533,7 +93596,8 @@ function validateSequence(sequence2, options = {}) {
     inclusive1BasedEnd,
     additionalValidChars,
     allowOverflowAnnotations,
-    coerceFeatureTypes
+    coerceFeatureTypes,
+    includeStopCodon
   } = options;
   [
     "isDNA",
@@ -93583,7 +93647,6 @@ function validateSequence(sequence2, options = {}) {
     response.messages.push("No sequence detected");
     sequence2.sequence = "";
   }
-  let validChars;
   if (sequence2.isProtein === void 0 && guessIfProtein) {
     sequence2.isProtein = !guessIfSequenceIsDnaAndNotProtein(
       sequence2.sequence,
@@ -93591,12 +93654,15 @@ function validateSequence(sequence2, options = {}) {
     );
   }
   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;
@@ -93618,12 +93684,12 @@ function validateSequence(sequence2, options = {}) {
     } 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) {
@@ -109105,18 +109171,6 @@ function getSelFromWrappedAddon(selectionLayer2, sequenceLength) {
   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",
@@ -125723,7 +125777,7 @@ function showFileDialog({ multiple = false, onSelect }) {
 }
 __name(showFileDialog, "showFileDialog");
 const name = "@teselagen/ove";
-const version = "0.3.30";
+const version = "0.3.43";
 const main = "./src/index.js";
 const exports$1 = {
   ".": {
@@ -129476,9 +129530,8 @@ const _SequenceInputNoHotkeys = class _SequenceInputNoHotkeys extends React$2.Co
       selectionLayer: selectionLayer2,
       sequenceLength,
       isProtein: isProtein2,
-      replaceChars,
       caretPosition: caretPosition2,
-      acceptedChars,
+      sequenceData: sequenceData2,
       maxInsertSize
     } = this.props;
     const { charsToInsert, hasTempError } = this.state;
@@ -129511,17 +129564,13 @@ const _SequenceInputNoHotkeys = class _SequenceInputNoHotkeys extends React$2.Co
         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
             });
@@ -130396,7 +130445,8 @@ function VectorInteractionHOC(Component) {
           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");
@@ -130421,6 +130471,7 @@ function VectorInteractionHOC(Component) {
           };
         }
         seqDataToInsert = tidyUpSequenceData(seqDataToInsert, {
+          topLevelSeqData: sequenceData2,
           provideNewIdsForAnnotations: true,
           annotationsAsObjects: true,
           removeUnwantedChars: true,
@@ -130516,8 +130567,7 @@ function VectorInteractionHOC(Component) {
           createSequenceInputPopup({
             useEventPositioning,
             isReplace,
-            replaceChars: sequenceData2.isRna ? { t: "u" } : void 0,
-            acceptedChars: getAcceptedChars(sequenceData2),
+            sequenceData: sequenceData2,
             isProtein: sequenceData2.isProtein,
             selectionLayer: selectionLayer2,
             sequenceLength,
@@ -142010,14 +142060,8 @@ const CustomContentEditable = generateField(/* @__PURE__ */ __name(function Cust
     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/index.es.js

@@ -77878,6 +77878,7 @@ const minimumOrfSize$1 = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.de
   minimumOrfSizeUpdate
 }, Symbol.toStringTag, { value: "Module" }));
 const protein_letters = "ACDEFGHIKLMNPQRSTVWY";
+const protein_letters_withUandX = "ACDEFGHIKLMNPQRSTVWYUX";
 const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO.*-";
 const ambiguous_dna_letters = "GATCRYWSMKHBVDN";
 const unambiguous_dna_letters = "GATC";
@@ -77946,6 +77947,7 @@ const bioData = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.definePrope
   extended_protein_letters,
   extended_protein_values,
   protein_letters,
+  protein_letters_withUandX,
   unambiguous_dna_letters,
   unambiguous_rna_letters
 }, Symbol.toStringTag, { value: "Module" }));
@@ -83964,20 +83966,91 @@ const modifiableTypes = [
   "primers",
   "guides"
 ];
-function filterSequenceString(sequenceString, additionalValidChars = "", charOverrides) {
-  if (sequenceString) {
-    return sequenceString.replace(
-      new RegExp(
-        `[^${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,
@@ -84106,14 +84179,6 @@ function coerceLocation({
   }
 }
 __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((char) => aminoAcidToDegenerateDnaMap[char.toLowerCase()] || "nnn").join("");
 }
@@ -84125,11 +84190,10 @@ function tidyUpSequenceData(pSeqData, options = {}) {
     removeUnwantedChars,
     additionalValidChars,
     noTranslationData,
-    charOverrides,
     doNotProvideIdsForAnnotations,
-    proteinFilterOptions,
     noCdsTranslations,
-    convertAnnotationsFromAAIndices
+    convertAnnotationsFromAAIndices,
+    topLevelSeqData
   } = options;
   let seqData = lodashExports.cloneDeep(pSeqData);
   const response = {
@@ -84159,16 +84223,15 @@ function tidyUpSequenceData(pSeqData, options = {}) {
   }
   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) {
@@ -93515,7 +93578,8 @@ function validateSequence(sequence2, options = {}) {
     inclusive1BasedEnd,
     additionalValidChars,
     allowOverflowAnnotations,
-    coerceFeatureTypes
+    coerceFeatureTypes,
+    includeStopCodon
   } = options;
   [
     "isDNA",
@@ -93565,7 +93629,6 @@ function validateSequence(sequence2, options = {}) {
     response.messages.push("No sequence detected");
     sequence2.sequence = "";
   }
-  let validChars;
   if (sequence2.isProtein === void 0 && guessIfProtein) {
     sequence2.isProtein = !guessIfSequenceIsDnaAndNotProtein(
       sequence2.sequence,
@@ -93573,12 +93636,15 @@ function validateSequence(sequence2, options = {}) {
     );
   }
   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;
@@ -93600,12 +93666,12 @@ function validateSequence(sequence2, options = {}) {
     } 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) {
@@ -109087,18 +109153,6 @@ function getSelFromWrappedAddon(selectionLayer2, sequenceLength) {
   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__default$1.createElement(
     "pattern",
@@ -125705,7 +125759,7 @@ function showFileDialog({ multiple = false, onSelect }) {
 }
 __name(showFileDialog, "showFileDialog");
 const name = "@teselagen/ove";
-const version = "0.3.30";
+const version = "0.3.43";
 const main = "./src/index.js";
 const exports$1 = {
   ".": {
@@ -129458,9 +129512,8 @@ const _SequenceInputNoHotkeys = class _SequenceInputNoHotkeys extends React__def
       selectionLayer: selectionLayer2,
       sequenceLength,
       isProtein: isProtein2,
-      replaceChars,
       caretPosition: caretPosition2,
-      acceptedChars,
+      sequenceData: sequenceData2,
       maxInsertSize
     } = this.props;
     const { charsToInsert, hasTempError } = this.state;
@@ -129493,17 +129546,13 @@ const _SequenceInputNoHotkeys = class _SequenceInputNoHotkeys extends React__def
         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
             });
@@ -130378,7 +130427,8 @@ function VectorInteractionHOC(Component2) {
           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");
@@ -130403,6 +130453,7 @@ function VectorInteractionHOC(Component2) {
           };
         }
         seqDataToInsert = tidyUpSequenceData(seqDataToInsert, {
+          topLevelSeqData: sequenceData2,
           provideNewIdsForAnnotations: true,
           annotationsAsObjects: true,
           removeUnwantedChars: true,
@@ -130498,8 +130549,7 @@ function VectorInteractionHOC(Component2) {
           createSequenceInputPopup({
             useEventPositioning,
             isReplace,
-            replaceChars: sequenceData2.isRna ? { t: "u" } : void 0,
-            acceptedChars: getAcceptedChars(sequenceData2),
+            sequenceData: sequenceData2,
             isProtein: sequenceData2.isProtein,
             selectionLayer: selectionLayer2,
             sequenceLength,
@@ -141992,14 +142042,8 @@ const CustomContentEditable = generateField(/* @__PURE__ */ __name(function Cust
     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);