@teselagen/ove 0.3.30 → 0.3.43

package/index.es.js

@@ -18218,11 +18218,20 @@ var _fails = /* @__PURE__ */ __name(function(exec) {
     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() {
@@ -18238,7 +18247,7 @@ function require_domCreate() {
   return _domCreate;
 }
 __name(require_domCreate, "require_domCreate");
-var _ie8DomDefine = !_descriptors && !_fails(function() {
+var _ie8DomDefine = !require_descriptors() && !_fails(function() {
   return Object.defineProperty(require_domCreate()("div"), "a", { get: function() {
     return 7;
   } }).a != 7;
@@ -18260,7 +18269,7 @@ 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) {
+_objectDp.f = require_descriptors() ? Object.defineProperty : /* @__PURE__ */ __name(function defineProperty2(O2, P2, Attributes) {
   anObject$5(O2);
   P2 = toPrimitive$2(P2, true);
   anObject$5(Attributes);
@@ -18285,7 +18294,7 @@ var _propertyDesc = /* @__PURE__ */ __name(function(bitmap, value) {
 }, "_propertyDesc");
 var dP$2 = _objectDp;
 var createDesc$3 = _propertyDesc;
-var _hide = _descriptors ? function(object3, key, value) {
+var _hide = require_descriptors() ? function(object3, key, value) {
   return dP$2.f(object3, key, createDesc$3(1, value));
 } : function(object3, key, value) {
   object3[key] = value;
@@ -18474,7 +18483,7 @@ function require_objectAssign() {
   if (hasRequired_objectAssign)
     return _objectAssign;
   hasRequired_objectAssign = 1;
-  var DESCRIPTORS2 = _descriptors;
+  var DESCRIPTORS2 = require_descriptors();
   var getKeys2 = _objectKeys;
   var gOPS2 = _objectGops;
   var pIE2 = _objectPie;
@@ -18543,7 +18552,7 @@ var _redefine = _hide;
 var dP$1 = _objectDp;
 var anObject$4 = _anObject;
 var getKeys$1 = _objectKeys;
-var _objectDps = _descriptors ? Object.defineProperties : /* @__PURE__ */ __name(function defineProperties(O2, Properties2) {
+var _objectDps = require_descriptors() ? Object.defineProperties : /* @__PURE__ */ __name(function defineProperties(O2, Properties2) {
   anObject$4(O2);
   var keys5 = getKeys$1(Properties2);
   var length = keys5.length;
@@ -19012,7 +19021,7 @@ var _default$8 = /* @__PURE__ */ __name(function(instance, Constructor) {
   }
 }, "_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: _objectDp.f });
 var $Object$2 = _coreExports.Object;
 var defineProperty$c = /* @__PURE__ */ __name(function defineProperty3(it, key, desc) {
   return $Object$2.defineProperty(it, key, desc);
@@ -19162,7 +19171,7 @@ var toPrimitive$1 = _toPrimitive$1;
 var has$9 = _has;
 var IE8_DOM_DEFINE = _ie8DomDefine;
 var gOPD$5 = Object.getOwnPropertyDescriptor;
-_objectGopd.f = _descriptors ? gOPD$5 : /* @__PURE__ */ __name(function getOwnPropertyDescriptor(O2, P2) {
+_objectGopd.f = require_descriptors() ? gOPD$5 : /* @__PURE__ */ __name(function getOwnPropertyDescriptor(O2, P2) {
   O2 = toIObject$1(O2);
   P2 = toPrimitive$1(P2, true);
   if (IE8_DOM_DEFINE)
@@ -19175,7 +19184,7 @@ _objectGopd.f = _descriptors ? gOPD$5 : /* @__PURE__ */ __name(function getOwnPr
 }, "getOwnPropertyDescriptor");
 var global$2 = _globalExports;
 var has$8 = _has;
-var DESCRIPTORS = _descriptors;
+var DESCRIPTORS = require_descriptors();
 var $export$2 = _export;
 var redefine = _redefine;
 var META = _metaExports.KEY;
@@ -57072,7 +57081,7 @@ const _DataTable = class _DataTable extends React__default$1.Component {
         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]) {
@@ -59268,6 +59277,21 @@ function stripNumberAtEnd(str) {
   return str.replace(getNumberStrAtEnd(str), "");
 }
 __name(stripNumberAtEnd, "stripNumberAtEnd");
+function isEntityClean(e2) {
+  let isClean = true;
+  lodashExports.some(e2, (val2, key) => {
+    if (key === "id")
+      return;
+    if (key === "_isClean")
+      return;
+    if (val2) {
+      isClean = false;
+      return true;
+    }
+  });
+  return isClean;
+}
+__name(isEntityClean, "isEntityClean");
 const wrapDialog = /* @__PURE__ */ __name((topLevelDialogProps = {}) => (Component2) => (props) => {
   const r2 = useRef();
   const memoedHotkeys = useMemo$1(
@@ -61782,7 +61806,7 @@ __name(asyncValidateHelper, "asyncValidateHelper");
 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;
@@ -76747,7 +76771,9 @@ ptIconWrapper(
   ))),
   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) {
@@ -77800,6 +77826,7 @@ const minimumOrfSize$1 = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.de
   minimumOrfSizeUpdate
 }, Symbol.toStringTag, { value: "Module" }));
 const protein_letters = "ACDEFGHIKLMNPQRSTVWY";
+const protein_letters_withUandX = "ACDEFGHIKLMNPQRSTVWYUX";
 const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO.*-";
 const ambiguous_dna_letters = "GATCRYWSMKHBVDN";
 const unambiguous_dna_letters = "GATC";
@@ -77868,6 +77895,7 @@ const bioData = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.definePrope
   extended_protein_letters,
   extended_protein_values,
   protein_letters,
+  protein_letters_withUandX,
   unambiguous_dna_letters,
   unambiguous_rna_letters
 }, Symbol.toStringTag, { value: "Module" }));
@@ -83886,20 +83914,91 @@ const modifiableTypes = [
   "primers",
   "guides"
 ];
-function filterSequenceString(sequenceString, additionalValidChars = "", charOverrides) {
-  if (sequenceString) {
-    return sequenceString.replace(
-      new RegExp(
-        `[^${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 ? ` ${replaceCount[letter]} times` : ""}`
     );
-  } else {
-    return sequenceString;
+  });
+  if (sequenceString.length !== sanitizedVal.length) {
+    warnings.push(
+      `${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,
@@ -84028,14 +84127,6 @@ 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("");
 }
@@ -84047,11 +84138,10 @@ function tidyUpSequenceData(pSeqData, options = {}) {
     removeUnwantedChars,
     additionalValidChars,
     noTranslationData,
-    charOverrides,
     doNotProvideIdsForAnnotations,
-    proteinFilterOptions,
     noCdsTranslations,
-    convertAnnotationsFromAAIndices
+    convertAnnotationsFromAAIndices,
+    topLevelSeqData
   } = options;
   let seqData = lodashExports.cloneDeep(pSeqData);
   const response = {
@@ -84081,16 +84171,15 @@ 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) {
@@ -93437,7 +93526,8 @@ function validateSequence(sequence2, options = {}) {
     inclusive1BasedEnd,
     additionalValidChars,
     allowOverflowAnnotations,
-    coerceFeatureTypes
+    coerceFeatureTypes,
+    includeStopCodon
   } = options;
   [
     "isDNA",
@@ -93487,7 +93577,6 @@ 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,
@@ -93495,12 +93584,15 @@ 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;
@@ -93522,12 +93614,12 @@ 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) {
@@ -109009,18 +109101,6 @@ 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",
@@ -125627,7 +125707,7 @@ function showFileDialog({ multiple = false, onSelect }) {
 }
 __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 = {
   ".": {
@@ -129380,9 +129460,8 @@ 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;
@@ -129415,17 +129494,13 @@ 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
             });
@@ -130300,7 +130375,8 @@ 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");
@@ -130325,6 +130401,7 @@ function VectorInteractionHOC(Component2) {
           };
         }
         seqDataToInsert = tidyUpSequenceData(seqDataToInsert, {
+          topLevelSeqData: sequenceData2,
           provideNewIdsForAnnotations: true,
           annotationsAsObjects: true,
           removeUnwantedChars: true,
@@ -130420,8 +130497,7 @@ function VectorInteractionHOC(Component2) {
           createSequenceInputPopup({
             useEventPositioning,
             isReplace,
-            replaceChars: sequenceData2.isRna ? { t: "u" } : void 0,
-            acceptedChars: getAcceptedChars(sequenceData2),
+            sequenceData: sequenceData2,
             isProtein: sequenceData2.isProtein,
             selectionLayer: selectionLayer2,
             sequenceLength,
@@ -141914,14 +141990,8 @@ 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);