@teselagen/ove 0.4.2 → 0.4.4

package/index.umd.js

@@ -25840,10 +25840,10 @@ var __async = (__this, __arguments, generator) => {
     /* istanbul ignore next */
     Object.getOwnPropertyNames
   );
-  function toPrimitive$2(value) {
+  function toPrimitive$3(value) {
     return value === null ? null : typeof value === "object" ? "" + value : value;
   }
-  __name(toPrimitive$2, "toPrimitive$2");
+  __name(toPrimitive$3, "toPrimitive$3");
   function hasProp(target, prop2) {
     return objectPrototype$2.hasOwnProperty.call(target, prop2);
   }
@@ -26740,7 +26740,7 @@ var __async = (__this, __arguments, generator) => {
       return this.name_ + "[" + this.value_ + "]";
     }, "toString");
     _proto.valueOf = /* @__PURE__ */ __name(function valueOf() {
-      return toPrimitive$2(this.get());
+      return toPrimitive$3(this.get());
     }, "valueOf");
     _proto[_Symbol$toPrimitive] = function() {
       return this.valueOf();
@@ -26925,7 +26925,7 @@ var __async = (__this, __arguments, generator) => {
       return this.name_ + "[" + this.derivation.toString() + "]";
     }, "toString");
     _proto.valueOf = /* @__PURE__ */ __name(function valueOf() {
-      return toPrimitive$2(this.get());
+      return toPrimitive$3(this.get());
     }, "valueOf");
     _proto[_Symbol$toPrimitive$1] = function() {
       return this.valueOf();
@@ -43595,20 +43595,11 @@ ${latestSubscriptionCallbackError.current.stack}
       return true;
     }
   }, "_fails");
-  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 _descriptors = !_fails(function() {
+    return Object.defineProperty({}, "a", { get: function() {
+      return 7;
+    } }).a != 7;
+  });
   var _domCreate;
   var hasRequired_domCreate;
   function require_domCreate() {
@@ -43624,20 +43615,11 @@ ${latestSubscriptionCallbackError.current.stack}
     return _domCreate;
   }
   __name(require_domCreate, "require_domCreate");
-  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 _ie8DomDefine = !_descriptors && !_fails(function() {
+    return Object.defineProperty(require_domCreate()("div"), "a", { get: function() {
+      return 7;
+    } }).a != 7;
+  });
   var isObject$6 = _isObject;
   var _toPrimitive$1 = /* @__PURE__ */ __name(function(it, S2) {
     if (!isObject$6(it))
@@ -43651,33 +43633,25 @@ ${latestSubscriptionCallbackError.current.stack}
       return val2;
     throw TypeError("Can't convert object to primitive value");
   }, "_toPrimitive$1");
-  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 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 _propertyDesc = /* @__PURE__ */ __name(function(bitmap, value) {
     return {
       enumerable: !(bitmap & 1),
@@ -43686,9 +43660,9 @@ ${latestSubscriptionCallbackError.current.stack}
       value
     };
   }, "_propertyDesc");
-  var dP$2 = require_objectDp();
+  var dP$2 = _objectDp;
   var createDesc$3 = _propertyDesc;
-  var _hide = require_descriptors() ? function(object2, key2, value) {
+  var _hide = _descriptors ? function(object2, key2, value) {
     return dP$2.f(object2, key2, createDesc$3(1, value));
   } : function(object2, key2, value) {
     object2[key2] = value;
@@ -43894,7 +43868,7 @@ ${latestSubscriptionCallbackError.current.stack}
     if (hasRequired_objectAssign)
       return _objectAssign;
     hasRequired_objectAssign = 1;
-    var DESCRIPTORS2 = require_descriptors();
+    var DESCRIPTORS2 = _descriptors;
     var getKeys2 = _objectKeys;
     var gOPS2 = _objectGops;
     var pIE2 = require_objectPie();
@@ -43960,10 +43934,10 @@ ${latestSubscriptionCallbackError.current.stack}
   }, "_iterStep");
   var _iterators = {};
   var _redefine = _hide;
-  var dP$1 = require_objectDp();
+  var dP$1 = _objectDp;
   var anObject$4 = _anObject;
   var getKeys$1 = _objectKeys;
-  var _objectDps = require_descriptors() ? Object.defineProperties : /* @__PURE__ */ __name(function defineProperties2(O2, Properties2) {
+  var _objectDps = _descriptors ? Object.defineProperties : /* @__PURE__ */ __name(function defineProperties2(O2, Properties2) {
     anObject$4(O2);
     var keys2 = getKeys$1(Properties2);
     var length = keys2.length;
@@ -44030,7 +44004,7 @@ ${latestSubscriptionCallbackError.current.stack}
   };
   $exports.store = store$2;
   var _wksExports = _wks.exports;
-  var def = require_objectDp().f;
+  var def = _objectDp.f;
   var has$b = _has;
   var TAG$1 = _wksExports("toStringTag");
   var _setToStringTag = /* @__PURE__ */ __name(function(it, tag, stat) {
@@ -44303,7 +44277,7 @@ ${latestSubscriptionCallbackError.current.stack}
   var _isArrayIter = /* @__PURE__ */ __name(function(it) {
     return it !== void 0 && (Iterators.Array === it || ArrayProto[ITERATOR] === it);
   }, "_isArrayIter");
-  var $defineProperty$1 = require_objectDp();
+  var $defineProperty$1 = _objectDp;
   var createDesc$2 = _propertyDesc;
   var _createProperty = /* @__PURE__ */ __name(function(object2, index2, value) {
     if (index2 in object2)
@@ -44432,7 +44406,7 @@ ${latestSubscriptionCallbackError.current.stack}
     }
   }, "_default$8");
   var $export$3 = _export;
-  $export$3($export$3.S + $export$3.F * !require_descriptors(), "Object", { defineProperty: require_objectDp().f });
+  $export$3($export$3.S + $export$3.F * !_descriptors, "Object", { defineProperty: _objectDp.f });
   var $Object$1 = _coreExports.Object;
   var defineProperty$6 = /* @__PURE__ */ __name(function defineProperty2(it, key2, desc) {
     return $Object$1.defineProperty(it, key2, desc);
@@ -44473,7 +44447,7 @@ ${latestSubscriptionCallbackError.current.stack}
   var META$1 = _uid("meta");
   var isObject$5 = _isObject;
   var has$9 = _has;
-  var setDesc = require_objectDp().f;
+  var setDesc = _objectDp.f;
   var id$1 = 0;
   var isExtensible = Object.isExtensible || function() {
     return true;
@@ -44526,7 +44500,7 @@ ${latestSubscriptionCallbackError.current.stack}
   var _metaExports = _meta.exports;
   var core = _coreExports;
   var wksExt$1 = _wksExt;
-  var defineProperty$4 = require_objectDp().f;
+  var defineProperty$4 = _objectDp.f;
   var _wksDefine = /* @__PURE__ */ __name(function(name2) {
     var $Symbol2 = core.Symbol || (core.Symbol = {});
     if (name2.charAt(0) != "_" && !(name2 in $Symbol2))
@@ -44588,9 +44562,9 @@ ${latestSubscriptionCallbackError.current.stack}
   var toIObject$1 = _toIobject;
   var toPrimitive$1 = _toPrimitive$1;
   var has$8 = _has;
-  var IE8_DOM_DEFINE = require_ie8DomDefine();
+  var IE8_DOM_DEFINE = _ie8DomDefine;
   var gOPD$2 = Object.getOwnPropertyDescriptor;
-  _objectGopd.f = require_descriptors() ? gOPD$2 : /* @__PURE__ */ __name(function getOwnPropertyDescriptor2(O2, P2) {
+  _objectGopd.f = _descriptors ? gOPD$2 : /* @__PURE__ */ __name(function getOwnPropertyDescriptor2(O2, P2) {
     O2 = toIObject$1(O2);
     P2 = toPrimitive$1(P2, true);
     if (IE8_DOM_DEFINE)
@@ -44603,7 +44577,7 @@ ${latestSubscriptionCallbackError.current.stack}
   }, "getOwnPropertyDescriptor");
   var global$1 = _globalExports;
   var has$7 = _has;
-  var DESCRIPTORS = require_descriptors();
+  var DESCRIPTORS = _descriptors;
   var $export$2 = _export;
   var redefine = _redefine;
   var META = _metaExports.KEY;
@@ -44626,7 +44600,7 @@ ${latestSubscriptionCallbackError.current.stack}
   var gOPNExt = _objectGopnExt;
   var $GOPD = _objectGopd;
   var $GOPS = _objectGops;
-  var $DP = require_objectDp();
+  var $DP = _objectDp;
   var $keys$1 = _objectKeys;
   var gOPD$1 = $GOPD.f;
   var dP = $DP.f;
@@ -113552,12 +113526,12 @@ ${latestSubscriptionCallbackError.current.stack}
     // 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, C2, Na2) {
       if (typeof type === "undefined") {
@@ -135589,13 +135563,12 @@ ${seq.sequence}
       proteinSize,
       proteinSequence
     } = cleanedData;
-    options = options || {};
-    let seqToUse = sequence2;
-    let sizeToUse = size;
-    if (isProtein2 && proteinSequence) {
-      seqToUse = proteinSequence;
-      sizeToUse = proteinSize;
-    }
+    options = __spreadValues({
+      sequence: isProtein2 && proteinSequence ? proteinSequence : sequence2,
+      size: isProtein2 && proteinSequence ? proteinSize : size
+    }, options);
+    const seqToUse = options.sequence;
+    const sizeToUse = options.size;
     let fastaString = "";
     fastaString += `>${name2 || "Untitled Sequence"}|`;
     fastaString += "|" + sizeToUse;
@@ -139310,7 +139283,7 @@ ${seq.sequence}
     }
     __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") {
@@ -139329,7 +139302,9 @@ ${seq.sequence}
       console.error(`Invalid export format: '${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");
@@ -154268,7 +154243,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
   }
   __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 = {
     ".": {
@@ -155190,9 +155165,21 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
       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",
@@ -155272,7 +155259,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
   const noSelection = /* @__PURE__ */ __name(({ selectionLayer: selectionLayer2 = {} }) => !(selectionLayer2.start > -1 && selectionLayer2.end > -1) && "Selection Required", "noSelection");
   const triggerClipboardCommand = /* @__PURE__ */ __name((type, props) => {
     const wrapper2 = document.querySelector(
-      `#${props.editorName} .veVectorInteractionWrapper`
+      `.${props.editorName} .veVectorInteractionWrapper`
     );
     if (!wrapper2) {
       return window.toastr.info(`Cannot trigger a ${type} in the current view`);
@@ -157180,7 +157167,8 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
           showInSearchMenu: true,
           submenu: [
             { cmd: "exportSequenceAsGenbank" },
-            { cmd: "exportSequenceAsFasta" },
+            { cmd: "exportDNASequenceAsFasta" },
+            { cmd: "exportProteinSequenceAsFasta" },
             { cmd: "exportSequenceAsTeselagenJson" }
           ]
         },
@@ -165528,7 +165516,8 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
         onClick: (event) => showContextMenu(
           [
             "exportSequenceAsGenbank",
-            "exportSequenceAsFasta",
+            "exportDNASequenceAsFasta",
+            "exportProteinSequenceAsFasta",
             "exportSequenceAsTeselagenJson"
           ],
           [
@@ -172438,7 +172427,8 @@ ${seqDataToCopy}\r
     return /* @__PURE__ */ React$2.createElement(Menu, null, createCommandMenu(
       [
         "exportSequenceAsGenbank",
-        "exportSequenceAsFasta",
+        "exportDNASequenceAsFasta",
+        "exportProteinSequenceAsFasta",
         "exportSequenceAsTeselagenJson"
       ],
       getCommands({ props })

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.4.2",
+  "version": "0.4.4",
   "main": "./src/index.js",
   "exports": {
     ".": {
@@ -13,7 +13,7 @@
     "node": "16.20.2"
   },
   "dependencies": {
-    "@teselagen/sequence-utils": "0.3.18",
+    "@teselagen/sequence-utils": "0.3.19",
     "@teselagen/range-utils": "0.3.7",
     "@teselagen/ui": "0.3.75",
     "@teselagen/file-utils": "0.3.16",

package/src/MenuBar/defaultConfig.js

@@ -41,7 +41,8 @@ export default [
         showInSearchMenu: true,
         submenu: [
           { cmd: "exportSequenceAsGenbank" },
-          { cmd: "exportSequenceAsFasta" },
+          { cmd: "exportDNASequenceAsFasta" },
+          { cmd: "exportProteinSequenceAsFasta" },
           { cmd: "exportSequenceAsTeselagenJson" }
         ]
       },

package/src/SimpleCircularOrLinearView.js

@@ -102,8 +102,8 @@ export default props => {
   )
     ? CircularView
     : _sequenceData.isOligo && _sequenceData.sequence
-    ? SimpleOligoPreview
-    : LinearView;
+      ? SimpleOligoPreview
+      : LinearView;
   if (withChoosePreviewType && previewType === "row") {
     Component = RowView;
     tickSpacing = undefined;
@@ -291,7 +291,8 @@ const DownloadBtn = withHandlers({ exportSequenceToFile })(props => {
           showContextMenu(
             [
               "exportSequenceAsGenbank",
-              "exportSequenceAsFasta",
+              "exportDNASequenceAsFasta",
+              "exportProteinSequenceAsFasta",
               "exportSequenceAsTeselagenJson"
             ],
             [

package/src/ToolBar/downloadTool.js

@@ -28,7 +28,8 @@ const Dropdown = withEditorProps(props => {
       {createCommandMenu(
         [
           "exportSequenceAsGenbank",
-          "exportSequenceAsFasta",
+          "exportDNASequenceAsFasta",
+          "exportProteinSequenceAsFasta",
           "exportSequenceAsTeselagenJson"
         ],
         getCommands({ props })

package/src/commands/index.js

@@ -264,9 +264,24 @@ const fileCommandDefs = {
     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",
@@ -360,7 +375,7 @@ const noSelection = ({ selectionLayer = {} }) =>
 
 const triggerClipboardCommand = (type, props) => {
   const wrapper = document.querySelector(
-    `#${props.editorName} .veVectorInteractionWrapper`
+    `.${props.editorName} .veVectorInteractionWrapper`
   );
   if (!wrapper) {
     return window.toastr.info(`Cannot trigger a ${type} in the current view`);

package/src/withEditorProps/index.js

@@ -50,8 +50,8 @@ const getUpperOrLowerSeq = defaultMemoize(
     uppercaseSequenceMapFont === "uppercase"
       ? sequence.toUpperCase()
       : uppercaseSequenceMapFont === "lowercase"
-      ? sequence.toLowerCase()
-      : sequence
+        ? sequence.toLowerCase()
+        : sequence
 );
 
 const getTypesToOmit = annotationsToSupport => {
@@ -284,7 +284,7 @@ export const importSequenceFromFile =
     }
   };
 
-export const exportSequenceToFile = props => format => {
+export const exportSequenceToFile = props => (format, options) => {
   const { sequenceData } = props;
   let convert, fileExt;
 
@@ -304,7 +304,9 @@ export const exportSequenceToFile = props => format => {
     console.error(`Invalid export format: '${format}'`); // dev error
     return;
   }
-  const blob = new Blob([convert(sequenceData)], { type: "text/plain" });
+  const blob = new Blob([convert(sequenceData, options)], {
+    type: "text/plain"
+  });
   const filename = `${sequenceData.name || "Untitled_Sequence"}.${fileExt}`;
   FileSaver.saveAs(blob, filename);
   window.toastr.success("File Downloaded Successfully");
@@ -441,16 +443,16 @@ export default compose(
             selectionLayer.start > -1
               ? { ...selectionLayer, id: undefined }
               : caretPosition > -1
-              ? {
-                  start: caretPosition,
-                  end: sequenceData.isProtein
-                    ? caretPosition + 2
-                    : caretPosition
-                }
-              : {
-                  start: 0,
-                  end: sequenceData.isProtein ? 2 : 0
-                };
+                ? {
+                    start: caretPosition,
+                    end: sequenceData.isProtein
+                      ? caretPosition + 2
+                      : caretPosition
+                  }
+                : {
+                    start: 0,
+                    end: sequenceData.isProtein ? 2 : 0
+                  };
           showAddOrEditAnnotationDialog({
             type: key.toLowerCase(),
             annotation: {