@teselagen/ove 0.3.61 → 0.3.63

package/index.umd.js

@@ -25818,10 +25818,10 @@ 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);
   }
@@ -26718,7 +26718,7 @@ 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();
@@ -26903,7 +26903,7 @@ 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();
@@ -43573,11 +43573,20 @@ ${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() {
@@ -43593,11 +43602,20 @@ ${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))
@@ -43611,25 +43629,33 @@ ${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),
@@ -43638,9 +43664,9 @@ ${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;
@@ -43819,10 +43845,10 @@ ${latestSubscriptionCallbackError.current.stack}
     return result;
   }, "_objectKeysInternal");
   var _enumBugKeys = "constructor,hasOwnProperty,isPrototypeOf,propertyIsEnumerable,toLocaleString,toString,valueOf".split(",");
-  var $keys$2 = _objectKeysInternal;
+  var $keys$3 = _objectKeysInternal;
   var enumBugKeys$1 = _enumBugKeys;
   var _objectKeys = Object.keys || /* @__PURE__ */ __name(function keys2(O2) {
-    return $keys$2(O2, enumBugKeys$1);
+    return $keys$3(O2, enumBugKeys$1);
   }, "keys");
   var _objectGops = {};
   _objectGops.f = Object.getOwnPropertySymbols;
@@ -43846,7 +43872,7 @@ ${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();
@@ -43912,10 +43938,10 @@ ${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;
@@ -43982,7 +44008,7 @@ ${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) {
@@ -44255,7 +44281,7 @@ ${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)
@@ -44384,7 +44410,7 @@ ${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);
@@ -44425,7 +44451,7 @@ ${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;
@@ -44478,7 +44504,7 @@ ${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))
@@ -44507,21 +44533,13 @@ ${latestSubscriptionCallbackError.current.stack}
   }, "isArray");
   var _objectGopnExt = {};
   var _objectGopn = {};
-  var hasRequired_objectGopn;
-  function require_objectGopn() {
-    if (hasRequired_objectGopn)
-      return _objectGopn;
-    hasRequired_objectGopn = 1;
-    var $keys2 = _objectKeysInternal;
-    var hiddenKeys = _enumBugKeys.concat("length", "prototype");
-    _objectGopn.f = Object.getOwnPropertyNames || /* @__PURE__ */ __name(function getOwnPropertyNames2(O2) {
-      return $keys2(O2, hiddenKeys);
-    }, "getOwnPropertyNames");
-    return _objectGopn;
-  }
-  __name(require_objectGopn, "require_objectGopn");
+  var $keys$2 = _objectKeysInternal;
+  var hiddenKeys = _enumBugKeys.concat("length", "prototype");
+  _objectGopn.f = Object.getOwnPropertyNames || /* @__PURE__ */ __name(function getOwnPropertyNames2(O2) {
+    return $keys$2(O2, hiddenKeys);
+  }, "getOwnPropertyNames");
   var toIObject$2 = _toIobject;
-  var gOPN$1 = require_objectGopn().f;
+  var gOPN$1 = _objectGopn.f;
   var toString$3 = {}.toString;
   var windowNames = typeof window == "object" && window && Object.getOwnPropertyNames ? Object.getOwnPropertyNames(window) : [];
   var getWindowNames = /* @__PURE__ */ __name(function(it) {
@@ -44540,9 +44558,9 @@ ${latestSubscriptionCallbackError.current.stack}
   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)
@@ -44555,7 +44573,7 @@ ${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;
@@ -44578,7 +44596,7 @@ ${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;
@@ -44714,7 +44732,7 @@ ${latestSubscriptionCallbackError.current.stack}
     }, "toString"));
     $GOPD.f = $getOwnPropertyDescriptor;
     $DP.f = $defineProperty;
-    require_objectGopn().f = gOPNExt.f = $getOwnPropertyNames;
+    _objectGopn.f = gOPNExt.f = $getOwnPropertyNames;
     require_objectPie().f = $propertyIsEnumerable;
     $GOPS.f = $getOwnPropertySymbols;
     if (DESCRIPTORS && !_library) {
@@ -72454,14 +72472,14 @@ ${latestSubscriptionCallbackError.current.stack}
         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
@@ -100450,11 +100468,11 @@ ${latestSubscriptionCallbackError.current.stack}
               {
                 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) => {
@@ -100467,7 +100485,7 @@ ${latestSubscriptionCallbackError.current.stack}
                     })
                   );
                   const csv = papaparse_minExports.unparse(rows);
-                  const downloadFn = ((_a3 = window.Cypress) == null ? void 0 : _a3.downloadTest) || downloadjs;
+                  const downloadFn = ((_b3 = window.Cypress) == null ? void 0 : _b3.downloadTest) || downloadjs;
                   downloadFn(csv, `${nameToUse}.csv`, "csv");
                 }
               },
@@ -121547,7 +121565,7 @@ ${latestSubscriptionCallbackError.current.stack}
     return string2.replace(/[|\\{}()[\]^$+*?.]/g, "\\$&").replace(/-/g, "\\x2d");
   }
   __name(escapeStringRegexp, "escapeStringRegexp");
-  function getAminoAcidStringFromSequenceString(sequenceString) {
+  function getAminoAcidStringFromSequenceString(sequenceString, { doNotExcludeAsterisk } = {}) {
     const aminoAcidsPerBase = getAminoAcidDataForEachBaseOfDna(
       sequenceString,
       true
@@ -121558,7 +121576,7 @@ ${latestSubscriptionCallbackError.current.stack}
       if (!aa2.fullCodon) {
         return;
       }
-      if (index2 === aminoAcidsPerBase.length - 1 && aa2.aminoAcid.value === "*") {
+      if (!doNotExcludeAsterisk && index2 >= aminoAcidsPerBase.length - 3 && aa2.aminoAcid.value === "*") {
         return;
       }
       aaArray[aa2.aminoAcidIndex] = aa2.aminoAcid.value;
@@ -121615,18 +121633,22 @@ ${latestSubscriptionCallbackError.current.stack}
     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
         }
@@ -122812,7 +122834,7 @@ ${latestSubscriptionCallbackError.current.stack}
     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) {
@@ -122833,6 +122855,19 @@ ${latestSubscriptionCallbackError.current.stack}
         isProtein2 ? convertAACaretPositionOrRangeToDna(location2) : location2
       );
     }
+    if (isCircular) {
+      for (let i2 = 0; i2 < locArray.length; i2 += 2) {
+        const firstFeature = locArray[i2];
+        const secondFeature = locArray[i2 + 1];
+        if (firstFeature.end === sequenceLength - (inclusive1BasedEnd ? 0 : 1) && secondFeature.start === 1 - (inclusive1BasedStart ? 0 : 1)) {
+          locArray[i2] = {
+            start: firstFeature.start,
+            end: secondFeature.end
+          };
+          locArray.splice(i2 + 1, 1);
+        }
+      }
+    }
     return locArray;
   }
   __name(parseFeatureLocation, "parseFeatureLocation");
@@ -123166,7 +123201,9 @@ ${latestSubscriptionCallbackError.current.stack}
               line.trim(),
               options.isProtein,
               inclusive1BasedStart,
-              inclusive1BasedEnd
+              inclusive1BasedEnd,
+              result.parsedSequence.circular,
+              result.parsedSequence.sequence.length
             )
           );
           lastLineWasLocation = true;
@@ -123199,7 +123236,9 @@ ${latestSubscriptionCallbackError.current.stack}
               val2,
               options.isProtein,
               inclusive1BasedStart,
-              inclusive1BasedEnd
+              inclusive1BasedEnd,
+              result.parsedSequence.circular,
+              result.parsedSequence.sequence.length
             )
           );
           lastLineWasLocation = true;
@@ -154017,7 +154056,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
   }
   __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 = {
     ".": {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.3.61",
+  "version": "0.3.63",
   "main": "./src/index.js",
   "exports": {
     ".": {
@@ -13,12 +13,12 @@
     "node": "16.20.2"
   },
   "dependencies": {
-    "@teselagen/sequence-utils": "0.3.14",
+    "@teselagen/sequence-utils": "0.3.15",
     "@teselagen/range-utils": "0.3.7",
-    "@teselagen/ui": "0.3.51",
+    "@teselagen/ui": "0.3.55",
     "@teselagen/file-utils": "0.3.11",
     "@teselagen/bounce-loader": "0.3.11",
-    "@teselagen/bio-parsers": "0.4.8",
+    "@teselagen/bio-parsers": "0.4.10",
     "@blueprintjs/core": "3.52.0",
     "@blueprintjs/datetime": "3.23.19",
     "@blueprintjs/icons": "3.33.0",