@teselagen/ove 0.4.2 → 0.4.4

package/index.es.js

@@ -5519,10 +5519,10 @@ var ownKeys$7 = typeof Reflect !== "undefined" && Reflect.ownKeys ? Reflect.ownK
   /* istanbul ignore next */
   Object.getOwnPropertyNames
 );
-function toPrimitive$3(value) {
+function toPrimitive$2(value) {
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 }
-__name(toPrimitive$3, "toPrimitive$3");
+__name(toPrimitive$2, "toPrimitive$2");
 function hasProp(target, prop2) {
   return objectPrototype$1.hasOwnProperty.call(target, prop2);
 }
@@ -6419,7 +6419,7 @@ 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();
@@ -6604,7 +6604,7 @@ 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$1] = function() {
     return this.valueOf();
@@ -11238,7 +11238,7 @@ lodash.exports;
         "^" + funcToString2.call(hasOwnProperty2).replace(reRegExpChar2, "\\$&").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$12;
-      var defineProperty6 = function() {
+      var defineProperty5 = function() {
         try {
           var func = getNative2(Object2, "defineProperty");
           func({}, "", {});
@@ -11678,8 +11678,8 @@ lodash.exports;
       }
       __name(baseAssignIn2, "baseAssignIn");
       function baseAssignValue2(object3, key, value) {
-        if (key == "__proto__" && defineProperty6) {
-          defineProperty6(object3, key, {
+        if (key == "__proto__" && defineProperty5) {
+          defineProperty5(object3, key, {
             "configurable": true,
             "enumerable": true,
             "value": value,
@@ -12412,8 +12412,8 @@ lodash.exports;
         metaMap.set(func, data);
         return func;
       };
-      var baseSetToString2 = !defineProperty6 ? identity4 : function(func, string2) {
-        return defineProperty6(func, "toString", {
+      var baseSetToString2 = !defineProperty5 ? identity4 : function(func, string2) {
+        return defineProperty5(func, "toString", {
           "configurable": true,
           "enumerable": false,
           "value": constant2(string2),
@@ -16966,11 +16966,20 @@ function require_domCreate() {
   return _domCreate;
 }
 __name(require_domCreate, "require_domCreate");
-var _ie8DomDefine = !require_descriptors() && !_fails(function() {
-  return Object.defineProperty(require_domCreate()("div"), "a", { get: function() {
-    return 7;
-  } }).a != 7;
-});
+var _ie8DomDefine;
+var hasRequired_ie8DomDefine;
+function require_ie8DomDefine() {
+  if (hasRequired_ie8DomDefine)
+    return _ie8DomDefine;
+  hasRequired_ie8DomDefine = 1;
+  _ie8DomDefine = !require_descriptors() && !_fails(function() {
+    return Object.defineProperty(require_domCreate()("div"), "a", { get: function() {
+      return 7;
+    } }).a != 7;
+  });
+  return _ie8DomDefine;
+}
+__name(require_ie8DomDefine, "require_ie8DomDefine");
 var isObject$d = _isObject;
 var _toPrimitive$1 = /* @__PURE__ */ __name(function(it, S2) {
   if (!isObject$d(it))
@@ -16984,25 +16993,33 @@ 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;
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-var dP$2 = Object.defineProperty;
-_objectDp.f = require_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),
@@ -17011,7 +17028,7 @@ var _propertyDesc = /* @__PURE__ */ __name(function(bitmap, value) {
     value
   };
 }, "_propertyDesc");
-var dP$1 = _objectDp;
+var dP$1 = require_objectDp();
 var createDesc$3 = _propertyDesc;
 var _hide = require_descriptors() ? function(object3, key, value) {
   return dP$1.f(object3, key, createDesc$3(1, value));
@@ -17085,25 +17102,16 @@ var toString$6 = {}.toString;
 var _cof = /* @__PURE__ */ __name(function(it) {
   return toString$6.call(it).slice(8, -1);
 }, "_cof");
-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 cof$2 = _cof;
+var _iobject = Object("z").propertyIsEnumerable(0) ? Object : function(it) {
+  return cof$2(it) == "String" ? it.split("") : Object(it);
+};
 var _defined = /* @__PURE__ */ __name(function(it) {
   if (it == void 0)
     throw TypeError("Can't call method on  " + it);
   return it;
 }, "_defined");
-var IObject = require_iobject();
+var IObject = _iobject;
 var defined$2 = _defined;
 var _toIobject = /* @__PURE__ */ __name(function(it) {
   return IObject(defined$2(it));
@@ -17224,7 +17232,7 @@ function require_objectAssign() {
   var gOPS2 = _objectGops;
   var pIE2 = require_objectPie();
   var toObject2 = _toObject;
-  var IObject2 = require_iobject();
+  var IObject2 = _iobject;
   var $assign = Object.assign;
   _objectAssign = !$assign || _fails(function() {
     var A2 = {};
@@ -17291,7 +17299,7 @@ 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 = require_descriptors() ? Object.defineProperties : /* @__PURE__ */ __name(function defineProperties3(O2, Properties2) {
@@ -17373,7 +17381,7 @@ 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) {
@@ -17646,7 +17654,7 @@ 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)
@@ -17775,9 +17783,9 @@ var _default$8 = /* @__PURE__ */ __name(function(instance, Constructor) {
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 }, "_default$8");
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-$export$3($export$3.S + $export$3.F * !require_descriptors(), "Object", { defineProperty: _objectDp.f });
+$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 };
@@ -17816,7 +17824,7 @@ 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;
@@ -17869,7 +17877,7 @@ 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))
@@ -17923,7 +17931,7 @@ 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 = require_descriptors() ? gOPD$5 : /* @__PURE__ */ __name(function getOwnPropertyDescriptor(O2, P2) {
   O2 = toIObject$1(O2);
@@ -17961,7 +17969,7 @@ 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;
@@ -18004,7 +18012,7 @@ 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$1(OPSymbols, key, D2);
   anObject(it);
@@ -83645,12 +83653,12 @@ const calcTmMethods = {
   // Monovalent salt concentration. 50mM is typical for PCR.
   /**
    * Calculates temperature for DNA sequence using a given algorithm.
-   * @param  {String} sequence The DNA sequence to use.
-   * @param  {String} type Either Teselagen.bio.tools.TemperatureCalculator.TABLE_BRESLAUER, TABLE_SUGIMOTO, or TABLE_UNIFIED
-   * @param  {Double} A Helix initation for deltaS. Defaults to -10.8.
-   * @param  {Double} R The gas constant, in cal/(K*mol). Defaults to 0.5e-6M.
-   * @param  {Double} Na THe monovalent salt concentration. Defaults to 50e-3M.
-   * @return {Double} Temperature for the given sequence, in Celsius.
+   * sequence - The DNA sequence to use.
+   * type - Either Teselagen.bio.tools.TemperatureCalculator.TABLE_BRESLAUER, TABLE_SUGIMOTO, or TABLE_UNIFIED
+   * A - Helix initation for deltaS. Defaults to -10.8.
+   * R - The gas constant, in cal/(K*mol). Defaults to 0.5e-6M.
+   * Na - THe monovalent salt concentration. Defaults to 50e-3M.
+   * return - Temperature for the given sequence, in Celsius.
    */
   calculateTemperature: function(sequence2, type, A2, R2, C, Na) {
     if (typeof type === "undefined") {
@@ -105684,13 +105692,12 @@ function jsonToFasta(jsonSequence, options) {
     proteinSize,
     proteinSequence
   } = cleanedData;
-  options = options || {};
-  let seqToUse = sequence2;
-  let sizeToUse = size;
-  if (isProtein2 && proteinSequence) {
-    seqToUse = proteinSequence;
-    sizeToUse = proteinSize;
-  }
+  options = __spreadValues({
+    sequence: isProtein2 && proteinSequence ? proteinSequence : sequence2,
+    size: isProtein2 && proteinSequence ? proteinSize : size
+  }, options);
+  const seqToUse = options.sequence;
+  const sizeToUse = options.size;
   let fastaString = "";
   fastaString += `>${name2 || "Untitled Sequence"}|`;
   fastaString += "|" + sizeToUse;
@@ -109999,7 +110006,7 @@ const importSequenceFromFile = /* @__PURE__ */ __name((props) => (_0, ..._1) =>
   }
   __name(finishDisplayingSeq, "finishDisplayingSeq");
 }), "importSequenceFromFile");
-const exportSequenceToFile = /* @__PURE__ */ __name((props) => (format2) => {
+const exportSequenceToFile = /* @__PURE__ */ __name((props) => (format2, options) => {
   const { sequenceData: sequenceData2 } = props;
   let convert2, fileExt;
   if (format2 === "genbank") {
@@ -110018,7 +110025,9 @@ const exportSequenceToFile = /* @__PURE__ */ __name((props) => (format2) => {
     console.error(`Invalid export format: '${format2}'`);
     return;
   }
-  const blob = new Blob([convert2(sequenceData2)], { type: "text/plain" });
+  const blob = new Blob([convert2(sequenceData2, options)], {
+    type: "text/plain"
+  });
   const filename = `${sequenceData2.name || "Untitled_Sequence"}.${fileExt}`;
   FileSaver.saveAs(blob, filename);
   window.toastr.success("File Downloaded Successfully");
@@ -124978,7 +124987,7 @@ function showFileDialog({ multiple = false, onSelect }) {
 }
 __name(showFileDialog, "showFileDialog");
 const name = "@teselagen/ove";
-const version = "0.4.1";
+const version = "0.4.3";
 const main = "./src/index.js";
 const exports$1 = {
   ".": {
@@ -125900,9 +125909,21 @@ const fileCommandDefs = __spreadValues(__spreadProps(__spreadValues({
     name: (props) => isProtein(props) ? "Download GenPept File" : "Download Genbank File",
     handler: (props) => props.exportSequenceToFile(isProtein(props) ? "genpept" : "genbank")
   },
-  exportSequenceAsFasta: {
-    name: "Download FASTA File",
-    handler: (props) => props.exportSequenceToFile("fasta")
+  exportDNASequenceAsFasta: {
+    name: (props) => `Download ${props.sequenceData.isProtein ? "DNA " : ""}FASTA File`,
+    isHidden: (props) => !props.sequenceData.sequence,
+    handler: (props) => props.exportSequenceToFile("fasta", {
+      sequence: props.sequenceData.sequence,
+      size: props.sequenceData.size
+    })
+  },
+  exportProteinSequenceAsFasta: {
+    name: "Download AA FASTA File",
+    isHidden: (props) => !props.sequenceData.proteinSequence,
+    handler: (props) => props.exportSequenceToFile("fasta", {
+      sequence: props.sequenceData.proteinSequence,
+      size: props.sequenceData.proteinSize
+    })
   },
   exportSequenceAsTeselagenJson: {
     name: "Download Teselagen JSON File",
@@ -125982,7 +126003,7 @@ const bpEditingDisabledTooltip = "Sequence Editing Disabled";
 const noSelection = /* @__PURE__ */ __name(({ selectionLayer: selectionLayer2 = {} }) => !(selectionLayer2.start > -1 && selectionLayer2.end > -1) && "Selection Required", "noSelection");
 const triggerClipboardCommand = /* @__PURE__ */ __name((type, props) => {
   const wrapper2 = document.querySelector(
-    `#${props.editorName} .veVectorInteractionWrapper`
+    `.${props.editorName} .veVectorInteractionWrapper`
   );
   if (!wrapper2) {
     return window.toastr.info(`Cannot trigger a ${type} in the current view`);
@@ -127307,7 +127328,7 @@ var createClass = function() {
     return Constructor;
   };
 }();
-var defineProperty5 = /* @__PURE__ */ __name(function(obj, key, value) {
+var defineProperty4 = /* @__PURE__ */ __name(function(obj, key, value) {
   if (key in obj) {
     Object.defineProperty(obj, key, {
       value,
@@ -127918,7 +127939,7 @@ function arrow(data, options) {
   var sideValue = center - data.offsets.popper[side] - popperMarginSide - popperBorderSide;
   sideValue = Math.max(Math.min(popper2[len] - arrowElementSize, sideValue), 0);
   data.arrowElement = arrowElement;
-  data.offsets.arrow = (_data$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");
@@ -128149,7 +128170,7 @@ 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";
@@ -128157,7 +128178,7 @@ 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) {
@@ -128178,8 +128199,8 @@ 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]);
   }
@@ -129496,7 +129517,8 @@ const menuDef = [
         showInSearchMenu: true,
         submenu: [
           { cmd: "exportSequenceAsGenbank" },
-          { cmd: "exportSequenceAsFasta" },
+          { cmd: "exportDNASequenceAsFasta" },
+          { cmd: "exportProteinSequenceAsFasta" },
           { cmd: "exportSequenceAsTeselagenJson" }
         ]
       },
@@ -137844,7 +137866,8 @@ const DownloadBtn = withHandlers({ exportSequenceToFile })((props) => {
       onClick: (event) => showContextMenu(
         [
           "exportSequenceAsGenbank",
-          "exportSequenceAsFasta",
+          "exportDNASequenceAsFasta",
+          "exportProteinSequenceAsFasta",
           "exportSequenceAsTeselagenJson"
         ],
         [
@@ -145266,7 +145289,8 @@ const Dropdown = withEditorProps((props) => {
   return /* @__PURE__ */ React__default$1.createElement(Menu, null, createCommandMenu(
     [
       "exportSequenceAsGenbank",
-      "exportSequenceAsFasta",
+      "exportDNASequenceAsFasta",
+      "exportProteinSequenceAsFasta",
       "exportSequenceAsTeselagenJson"
     ],
     getCommands({ props })