@teselagen/ove 0.3.61 → 0.3.63

package/index.es.js

@@ -5497,10 +5497,10 @@ var ownKeys$7 = typeof Reflect !== "undefined" && Reflect.ownKeys ? Reflect.ownK
   /* 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$1.hasOwnProperty.call(target, prop2);
 }
@@ -6397,7 +6397,7 @@ var ObservableValue = /* @__PURE__ */ function(_Atom) {
     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();
@@ -6582,7 +6582,7 @@ var ComputedValue = /* @__PURE__ */ function() {
     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$1] = function() {
     return this.valueOf();
@@ -11216,7 +11216,7 @@ lodash.exports;
         "^" + funcToString2.call(hasOwnProperty2).replace(reRegExpChar2, "\\$&").replace(/hasOwnProperty|(function).*?(?=\\\()| for .+?(?=\\\])/g, "$1.*?") + "$"
       );
       var Buffer2 = moduleExports2 ? context.Buffer : undefined$12, Symbol2 = context.Symbol, Uint8Array2 = context.Uint8Array, allocUnsafe2 = Buffer2 ? Buffer2.allocUnsafe : undefined$12, getPrototype2 = overArg2(Object2.getPrototypeOf, Object2), objectCreate2 = Object2.create, propertyIsEnumerable3 = objectProto2.propertyIsEnumerable, splice3 = arrayProto2.splice, spreadableSymbol2 = Symbol2 ? Symbol2.isConcatSpreadable : undefined$12, symIterator = Symbol2 ? Symbol2.iterator : undefined$12, symToStringTag2 = Symbol2 ? Symbol2.toStringTag : undefined$12;
-      var defineProperty6 = function() {
+      var defineProperty5 = function() {
         try {
           var func = getNative2(Object2, "defineProperty");
           func({}, "", {});
@@ -11656,8 +11656,8 @@ lodash.exports;
       }
       __name(baseAssignIn2, "baseAssignIn");
       function baseAssignValue2(object3, key, value) {
-        if (key == "__proto__" && defineProperty6) {
-          defineProperty6(object3, key, {
+        if (key == "__proto__" && defineProperty5) {
+          defineProperty5(object3, key, {
             "configurable": true,
             "enumerable": true,
             "value": value,
@@ -12390,8 +12390,8 @@ lodash.exports;
         metaMap.set(func, data);
         return func;
       };
-      var baseSetToString2 = !defineProperty6 ? identity4 : function(func, string2) {
-        return defineProperty6(func, "toString", {
+      var baseSetToString2 = !defineProperty5 ? identity4 : function(func, string2) {
+        return defineProperty5(func, "toString", {
           "configurable": true,
           "enumerable": false,
           "value": constant2(string2),
@@ -16915,11 +16915,20 @@ 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() {
@@ -16935,11 +16944,20 @@ function require_domCreate() {
   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$d = _isObject;
 var _toPrimitive$1 = /* @__PURE__ */ __name(function(it, S2) {
   if (!isObject$d(it))
@@ -16953,25 +16971,33 @@ var _toPrimitive$1 = /* @__PURE__ */ __name(function(it, S2) {
     return val2;
   throw TypeError("Can't convert object to primitive value");
 }, "_toPrimitive$1");
-var anObject$3 = _anObject;
-var IE8_DOM_DEFINE$1 = _ie8DomDefine;
-var toPrimitive$2 = _toPrimitive$1;
-var dP$2 = Object.defineProperty;
-_objectDp.f = _descriptors ? Object.defineProperty : /* @__PURE__ */ __name(function defineProperty2(O2, P2, Attributes) {
-  anObject$3(O2);
-  P2 = toPrimitive$2(P2, true);
-  anObject$3(Attributes);
-  if (IE8_DOM_DEFINE$1)
-    try {
-      return dP$2(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 defineProperty5(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),
@@ -16980,9 +17006,9 @@ var _propertyDesc = /* @__PURE__ */ __name(function(bitmap, value) {
     value
   };
 }, "_propertyDesc");
-var dP$1 = _objectDp;
+var dP$1 = require_objectDp();
 var createDesc$3 = _propertyDesc;
-var _hide = _descriptors ? function(object3, key, value) {
+var _hide = require_descriptors() ? function(object3, key, value) {
   return dP$1.f(object3, key, createDesc$3(1, value));
 } : function(object3, key, value) {
   object3[key] = value;
@@ -17054,16 +17080,25 @@ var toString$6 = {}.toString;
 var _cof = /* @__PURE__ */ __name(function(it) {
   return toString$6.call(it).slice(8, -1);
 }, "_cof");
-var cof$2 = _cof;
-var _iobject = Object("z").propertyIsEnumerable(0) ? Object : function(it) {
-  return cof$2(it) == "String" ? it.split("") : Object(it);
-};
+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 _defined = /* @__PURE__ */ __name(function(it) {
   if (it == void 0)
     throw TypeError("Can't call method on  " + it);
   return it;
 }, "_defined");
-var IObject = _iobject;
+var IObject = require_iobject();
 var defined$2 = _defined;
 var _toIobject = /* @__PURE__ */ __name(function(it) {
   return IObject(defined$2(it));
@@ -17179,12 +17214,12 @@ 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 = require_objectPie();
   var toObject2 = _toObject;
-  var IObject2 = _iobject;
+  var IObject2 = require_iobject();
   var $assign = Object.assign;
   _objectAssign = !$assign || _fails(function() {
     var A2 = {};
@@ -17251,10 +17286,10 @@ function require_objectDps() {
   if (hasRequired_objectDps)
     return _objectDps;
   hasRequired_objectDps = 1;
-  var dP2 = _objectDp;
+  var dP2 = require_objectDp();
   var anObject2 = _anObject;
   var getKeys2 = _objectKeys;
-  _objectDps = _descriptors ? Object.defineProperties : /* @__PURE__ */ __name(function defineProperties3(O2, Properties2) {
+  _objectDps = require_descriptors() ? Object.defineProperties : /* @__PURE__ */ __name(function defineProperties3(O2, Properties2) {
     anObject2(O2);
     var keys5 = getKeys2(Properties2);
     var length = keys5.length;
@@ -17333,7 +17368,7 @@ var $exports = _wks.exports = function(name2) {
 };
 $exports.store = store$2;
 var _wksExports = _wks.exports;
-var def = _objectDp.f;
+var def = require_objectDp().f;
 var has$c = _has;
 var TAG$1 = _wksExports("toStringTag");
 var _setToStringTag = /* @__PURE__ */ __name(function(it, tag, stat) {
@@ -17606,7 +17641,7 @@ var ArrayProto = Array.prototype;
 var _isArrayIter = /* @__PURE__ */ __name(function(it) {
   return it !== void 0 && (Iterators.Array === it || ArrayProto[ITERATOR] === it);
 }, "_isArrayIter");
-var $defineProperty$2 = _objectDp;
+var $defineProperty$2 = require_objectDp();
 var createDesc$2 = _propertyDesc;
 var _createProperty = /* @__PURE__ */ __name(function(object3, index2, value) {
   if (index2 in object3)
@@ -17735,9 +17770,9 @@ 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: require_objectDp().f });
 var $Object$2 = _coreExports.Object;
-var defineProperty$c = /* @__PURE__ */ __name(function defineProperty3(it, key, desc) {
+var defineProperty$c = /* @__PURE__ */ __name(function defineProperty2(it, key, desc) {
   return $Object$2.defineProperty(it, key, desc);
 }, "defineProperty");
 var defineProperty$b = { "default": defineProperty$c, __esModule: true };
@@ -17776,7 +17811,7 @@ var _meta = { exports: {} };
 var META$1 = _uid("meta");
 var isObject$c = _isObject;
 var has$a = _has;
-var setDesc = _objectDp.f;
+var setDesc = require_objectDp().f;
 var id$1 = 0;
 var isExtensible = Object.isExtensible || function() {
   return true;
@@ -17829,7 +17864,7 @@ var meta = _meta.exports = {
 var _metaExports = _meta.exports;
 var core = _coreExports;
 var wksExt$1 = _wksExt;
-var defineProperty$a = _objectDp.f;
+var defineProperty$a = require_objectDp().f;
 var _wksDefine = /* @__PURE__ */ __name(function(name2) {
   var $Symbol2 = core.Symbol || (core.Symbol = {});
   if (name2.charAt(0) != "_" && !(name2 in $Symbol2))
@@ -17883,9 +17918,9 @@ var createDesc$1 = _propertyDesc;
 var toIObject$1 = _toIobject;
 var toPrimitive$1 = _toPrimitive$1;
 var has$9 = _has;
-var IE8_DOM_DEFINE = _ie8DomDefine;
+var IE8_DOM_DEFINE = require_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)
@@ -17898,7 +17933,7 @@ _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;
@@ -17921,7 +17956,7 @@ var _create$1 = require_objectCreate();
 var gOPNExt = _objectGopnExt;
 var $GOPD = _objectGopd;
 var $GOPS = _objectGops;
-var $DP = _objectDp;
+var $DP = require_objectDp();
 var $keys$1 = _objectKeys;
 var gOPD$4 = $GOPD.f;
 var dP = $DP.f;
@@ -17964,7 +17999,7 @@ var isSymbol$8 = USE_NATIVE && typeof $Symbol.iterator == "symbol" ? function(it
 } : function(it) {
   return it instanceof $Symbol;
 };
-var $defineProperty$1 = /* @__PURE__ */ __name(function defineProperty4(it, key, D2) {
+var $defineProperty$1 = /* @__PURE__ */ __name(function defineProperty3(it, key, D2) {
   if (it === ObjectProto)
     $defineProperty$1(OPSymbols, key, D2);
   anObject(it);
@@ -42367,14 +42402,14 @@ const generateToast = /* @__PURE__ */ __name((intent) => (message, options) => {
       updatedTimeout = ++counter$1;
     }
   }
-  if (window.Cypress && intent === Intent.DANGER) {
-    console.error("toastr error message: ", message);
+  if (intent === Intent.DANGER) {
+    console.error("Toastr error message: ", message);
   }
   const uniqKey = toastToUse.show(
     {
       intent,
       message,
-      timeout: options.timeout || updatedTimeout,
+      timeout: options.timeout || updatedTimeout || intent === Intent.DANGER ? 6e4 : void 0,
       action: options.action,
       icon: options.icon,
       className: options.className
@@ -70545,11 +70580,11 @@ function UploaderInner({
             {
               description: "Download Example CSV File",
               exampleFile: () => {
-                var _a3;
+                var _a3, _b3;
                 const rows = [];
                 const schemaToUse = [
                   ...a2.validateAgainstSchema.fields,
-                  ...a2.validateAgainstSchema.exampleDownloadFields
+                  ...(_a3 = a2.validateAgainstSchema.exampleDownloadFields) != null ? _a3 : []
                 ];
                 rows.push(
                   schemaToUse.map((f2) => {
@@ -70562,7 +70597,7 @@ function UploaderInner({
                   })
                 );
                 const csv = papaparse_minExports.unparse(rows);
-                const downloadFn = ((_a3 = window.Cypress) == null ? void 0 : _a3.downloadTest) || downloadjs;
+                const downloadFn = ((_b3 = window.Cypress) == null ? void 0 : _b3.downloadTest) || downloadjs;
                 downloadFn(csv, `${nameToUse}.csv`, "csv");
               }
             },
@@ -91648,7 +91683,7 @@ function escapeStringRegexp(string2) {
   return string2.replace(/[|\\{}()[\]^$+*?.]/g, "\\$&").replace(/-/g, "\\x2d");
 }
 __name(escapeStringRegexp, "escapeStringRegexp");
-function getAminoAcidStringFromSequenceString(sequenceString) {
+function getAminoAcidStringFromSequenceString(sequenceString, { doNotExcludeAsterisk } = {}) {
   const aminoAcidsPerBase = getAminoAcidDataForEachBaseOfDna(
     sequenceString,
     true
@@ -91659,7 +91694,7 @@ function getAminoAcidStringFromSequenceString(sequenceString) {
     if (!aa.fullCodon) {
       return;
     }
-    if (index2 === aminoAcidsPerBase.length - 1 && aa.aminoAcid.value === "*") {
+    if (!doNotExcludeAsterisk && index2 >= aminoAcidsPerBase.length - 3 && aa.aminoAcid.value === "*") {
       return;
     }
     aaArray[aa.aminoAcidIndex] = aa.aminoAcid.value;
@@ -91716,18 +91751,22 @@ function findSequenceMatchesTopStrand(sequence2, searchString, options = {}) {
   if (isProteinSearch) {
     sequencesToCheck = [
       {
-        seqToCheck: getAminoAcidStringFromSequenceString(sequenceToUse),
+        seqToCheck: getAminoAcidStringFromSequenceString(sequenceToUse, {
+          doNotExcludeAsterisk: true
+        }),
         offset: 0
       },
       {
         seqToCheck: getAminoAcidStringFromSequenceString(
-          sequenceToUse.substr(1)
+          sequenceToUse.substr(1),
+          { doNotExcludeAsterisk: true }
         ),
         offset: 1
       },
       {
         seqToCheck: getAminoAcidStringFromSequenceString(
-          sequenceToUse.substr(2)
+          sequenceToUse.substr(2),
+          { doNotExcludeAsterisk: true }
         ),
         offset: 2
       }
@@ -92913,7 +92952,7 @@ function flattenSequenceArray(parsingResultArray, opts2) {
   return parsingResultArray;
 }
 __name(flattenSequenceArray, "flattenSequenceArray");
-function parseFeatureLocation(locStr, isProtein2, inclusive1BasedStart, inclusive1BasedEnd) {
+function parseFeatureLocation(locStr, isProtein2, inclusive1BasedStart, inclusive1BasedEnd, isCircular, sequenceLength) {
   locStr = locStr.trim();
   const locArr = [];
   locStr.replace(/(\d+)/g, function(string2, match2) {
@@ -92934,6 +92973,19 @@ function parseFeatureLocation(locStr, isProtein2, inclusive1BasedStart, inclusiv
       isProtein2 ? convertAACaretPositionOrRangeToDna(location2) : location2
     );
   }
+  if (isCircular) {
+    for (let i = 0; i < locArray.length; i += 2) {
+      const firstFeature = locArray[i];
+      const secondFeature = locArray[i + 1];
+      if (firstFeature.end === sequenceLength - (inclusive1BasedEnd ? 0 : 1) && secondFeature.start === 1 - (inclusive1BasedStart ? 0 : 1)) {
+        locArray[i] = {
+          start: firstFeature.start,
+          end: secondFeature.end
+        };
+        locArray.splice(i + 1, 1);
+      }
+    }
+  }
   return locArray;
 }
 __name(parseFeatureLocation, "parseFeatureLocation");
@@ -93267,7 +93319,9 @@ function genbankToJson(string2, options = {}) {
             line.trim(),
             options.isProtein,
             inclusive1BasedStart,
-            inclusive1BasedEnd
+            inclusive1BasedEnd,
+            result.parsedSequence.circular,
+            result.parsedSequence.sequence.length
           )
         );
         lastLineWasLocation = true;
@@ -93300,7 +93354,9 @@ function genbankToJson(string2, options = {}) {
             val2,
             options.isProtein,
             inclusive1BasedStart,
-            inclusive1BasedEnd
+            inclusive1BasedEnd,
+            result.parsedSequence.circular,
+            result.parsedSequence.sequence.length
           )
         );
         lastLineWasLocation = true;
@@ -124735,7 +124791,7 @@ function showFileDialog({ multiple = false, onSelect }) {
 }
 __name(showFileDialog, "showFileDialog");
 const name = "@teselagen/ove";
-const version = "0.3.60";
+const version = "0.3.62";
 const main = "./src/index.js";
 const exports$1 = {
   ".": {
@@ -127062,7 +127118,7 @@ var createClass = function() {
     return Constructor;
   };
 }();
-var defineProperty5 = /* @__PURE__ */ __name(function(obj, key, value) {
+var defineProperty4 = /* @__PURE__ */ __name(function(obj, key, value) {
   if (key in obj) {
     Object.defineProperty(obj, key, {
       value,
@@ -127673,7 +127729,7 @@ function arrow(data, options) {
   var sideValue = center - data.offsets.popper[side] - popperMarginSide - popperBorderSide;
   sideValue = Math.max(Math.min(popper2[len] - arrowElementSize, sideValue), 0);
   data.arrowElement = arrowElement;
-  data.offsets.arrow = (_data$offsets$arrow = {}, defineProperty5(_data$offsets$arrow, side, Math.round(sideValue)), defineProperty5(_data$offsets$arrow, altSide, ""), _data$offsets$arrow);
+  data.offsets.arrow = (_data$offsets$arrow = {}, defineProperty4(_data$offsets$arrow, side, Math.round(sideValue)), defineProperty4(_data$offsets$arrow, altSide, ""), _data$offsets$arrow);
   return data;
 }
 __name(arrow, "arrow");
@@ -127904,7 +127960,7 @@ function preventOverflow(data, options) {
       if (popper2[placement] < boundaries[placement] && !options.escapeWithReference) {
         value = Math.max(popper2[placement], boundaries[placement]);
       }
-      return defineProperty5({}, placement, value);
+      return defineProperty4({}, placement, value);
     }, "primary"),
     secondary: /* @__PURE__ */ __name(function secondary(placement) {
       var mainSide = placement === "right" ? "left" : "top";
@@ -127912,7 +127968,7 @@ function preventOverflow(data, options) {
       if (popper2[placement] > boundaries[placement] && !options.escapeWithReference) {
         value = Math.min(popper2[mainSide], boundaries[placement] - (placement === "right" ? popper2.width : popper2.height));
       }
-      return defineProperty5({}, mainSide, value);
+      return defineProperty4({}, mainSide, value);
     }, "secondary")
   };
   order2.forEach(function(placement) {
@@ -127933,8 +127989,8 @@ function shift3(data) {
     var side = isVertical ? "left" : "top";
     var measurement = isVertical ? "width" : "height";
     var shiftOffsets = {
-      start: defineProperty5({}, side, reference2[side]),
-      end: defineProperty5({}, side, reference2[side] + reference2[measurement] - popper2[measurement])
+      start: defineProperty4({}, side, reference2[side]),
+      end: defineProperty4({}, side, reference2[side] + reference2[measurement] - popper2[measurement])
     };
     data.offsets.popper = _extends$1({}, popper2, shiftOffsets[shiftvariation]);
   }