@teselagen/ove 0.3.4 → 0.3.5

package/index.umd.js

@@ -23996,7 +23996,7 @@
   var ownKeys$9 = typeof Reflect !== "undefined" && Reflect.ownKeys ? Reflect.ownKeys : hasGetOwnPropertySymbols ? function (obj) {
     return Object.getOwnPropertyNames(obj).concat(Object.getOwnPropertySymbols(obj));
   } : /* istanbul ignore next */Object.getOwnPropertyNames;
-  function toPrimitive$2(value) {
+  function toPrimitive$3(value) {
     return value === null ? null : typeof value === "object" ? "" + value : value;
   }
   function hasProp(target, prop) {
@@ -24925,7 +24925,7 @@
       return this.name_ + "[" + this.value_ + "]";
     };
     _proto.valueOf = function valueOf() {
-      return toPrimitive$2(this.get());
+      return toPrimitive$3(this.get());
     };
     _proto[_Symbol$toPrimitive] = function () {
       return this.valueOf();
@@ -25153,7 +25153,7 @@
       return this.name_ + "[" + this.derivation.toString() + "]";
     };
     _proto.valueOf = function valueOf() {
-      return toPrimitive$2(this.get());
+      return toPrimitive$3(this.get());
     };
     _proto[_Symbol$toPrimitive$1] = function () {
       return this.valueOf();
@@ -57050,18 +57050,10 @@
     }
   };
 
-  var _descriptors;
-  var hasRequired_descriptors;
-
-  function require_descriptors () {
-  	if (hasRequired_descriptors) return _descriptors;
-  	hasRequired_descriptors = 1;
-  	// Thank's IE8 for his funny defineProperty
-  	_descriptors = !_fails(function () {
-  	  return Object.defineProperty({}, 'a', { get: function () { return 7; } }).a != 7;
-  	});
-  	return _descriptors;
-  }
+  // Thank's IE8 for his funny defineProperty
+  var _descriptors = !_fails(function () {
+    return Object.defineProperty({}, 'a', { get: function () { return 7; } }).a != 7;
+  });
 
   var _domCreate;
   var hasRequired_domCreate;
@@ -57079,17 +57071,9 @@
   	return _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;
-  }
+  var _ie8DomDefine = !_descriptors && !_fails(function () {
+    return Object.defineProperty(require_domCreate()('div'), 'a', { get: function () { return 7; } }).a != 7;
+  });
 
   // 7.1.1 ToPrimitive(input [, PreferredType])
   var isObject$6 = _isObject;
@@ -57104,29 +57088,22 @@
     throw TypeError("Can't convert object to primitive value");
   };
 
-  var hasRequired_objectDp;
+  var anObject$3 = _anObject;
+  var IE8_DOM_DEFINE$1 = _ie8DomDefine;
+  var toPrimitive$2 = _toPrimitive$1;
+  var dP$2 = Object.defineProperty;
 
-  function require_objectDp () {
-  	if (hasRequired_objectDp) return _objectDp;
-  	hasRequired_objectDp = 1;
-  	var anObject = _anObject;
-  	var IE8_DOM_DEFINE = require_ie8DomDefine();
-  	var toPrimitive = _toPrimitive$1;
-  	var dP = Object.defineProperty;
-
-  	_objectDp.f = require_descriptors() ? Object.defineProperty : function defineProperty(O, P, Attributes) {
-  	  anObject(O);
-  	  P = toPrimitive(P, true);
-  	  anObject(Attributes);
-  	  if (IE8_DOM_DEFINE) try {
-  	    return dP(O, P, Attributes);
-  	  } catch (e) { /* empty */ }
-  	  if ('get' in Attributes || 'set' in Attributes) throw TypeError('Accessors not supported!');
-  	  if ('value' in Attributes) O[P] = Attributes.value;
-  	  return O;
-  	};
-  	return _objectDp;
-  }
+  _objectDp.f = _descriptors ? Object.defineProperty : function defineProperty(O, P, Attributes) {
+    anObject$3(O);
+    P = toPrimitive$2(P, true);
+    anObject$3(Attributes);
+    if (IE8_DOM_DEFINE$1) try {
+      return dP$2(O, P, Attributes);
+    } catch (e) { /* empty */ }
+    if ('get' in Attributes || 'set' in Attributes) throw TypeError('Accessors not supported!');
+    if ('value' in Attributes) O[P] = Attributes.value;
+    return O;
+  };
 
   var _propertyDesc = function (bitmap, value) {
     return {
@@ -57137,9 +57114,9 @@
     };
   };
 
-  var dP$1 = require_objectDp();
+  var dP$1 = _objectDp;
   var createDesc$3 = _propertyDesc;
-  var _hide = require_descriptors() ? function (object, key, value) {
+  var _hide = _descriptors ? function (object, key, value) {
     return dP$1.f(object, key, createDesc$3(1, value));
   } : function (object, key, value) {
     object[key] = value;
@@ -57220,12 +57197,20 @@
     return toString$4.call(it).slice(8, -1);
   };
 
-  // fallback for non-array-like ES3 and non-enumerable old V8 strings
-  var cof$2 = _cof;
-  // eslint-disable-next-line no-prototype-builtins
-  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;
+  	// fallback for non-array-like ES3 and non-enumerable old V8 strings
+  	var cof = _cof;
+  	// eslint-disable-next-line no-prototype-builtins
+  	_iobject = Object('z').propertyIsEnumerable(0) ? Object : function (it) {
+  	  return cof(it) == 'String' ? it.split('') : Object(it);
+  	};
+  	return _iobject;
+  }
 
   // 7.2.1 RequireObjectCoercible(argument)
   var _defined = function (it) {
@@ -57234,7 +57219,7 @@
   };
 
   // to indexed object, toObject with fallback for non-array-like ES3 strings
-  var IObject = _iobject;
+  var IObject = require_iobject();
   var defined$2 = _defined;
   var _toIobject = function (it) {
     return IObject(defined$2(it));
@@ -57354,7 +57339,14 @@
 
   var _objectPie = {};
 
-  _objectPie.f = {}.propertyIsEnumerable;
+  var hasRequired_objectPie;
+
+  function require_objectPie () {
+  	if (hasRequired_objectPie) return _objectPie;
+  	hasRequired_objectPie = 1;
+  	_objectPie.f = {}.propertyIsEnumerable;
+  	return _objectPie;
+  }
 
   // 7.1.13 ToObject(argument)
   var defined$1 = _defined;
@@ -57369,12 +57361,12 @@
   	if (hasRequired_objectAssign) return _objectAssign;
   	hasRequired_objectAssign = 1;
   	// 19.1.2.1 Object.assign(target, source, ...)
-  	var DESCRIPTORS = require_descriptors();
+  	var DESCRIPTORS = _descriptors;
   	var getKeys = _objectKeys;
   	var gOPS = _objectGops;
-  	var pIE = _objectPie;
+  	var pIE = require_objectPie();
   	var toObject = _toObject;
-  	var IObject = _iobject;
+  	var IObject = require_iobject();
   	var $assign = Object.assign;
 
   	// should work with symbols and should have deterministic property order (V8 bug)
@@ -57451,11 +57443,11 @@
   function require_objectDps () {
   	if (hasRequired_objectDps) return _objectDps;
   	hasRequired_objectDps = 1;
-  	var dP = require_objectDp();
+  	var dP = _objectDp;
   	var anObject = _anObject;
   	var getKeys = _objectKeys;
 
-  	_objectDps = require_descriptors() ? Object.defineProperties : function defineProperties(O, Properties) {
+  	_objectDps = _descriptors ? Object.defineProperties : function defineProperties(O, Properties) {
   	  anObject(O);
   	  var keys = getKeys(Properties);
   	  var length = keys.length;
@@ -57544,7 +57536,7 @@
 
   var _wksExports = _wks.exports;
 
-  var def = require_objectDp().f;
+  var def = _objectDp.f;
   var has$b = _has;
   var TAG$1 = _wksExports('toStringTag');
 
@@ -57858,7 +57850,7 @@
     return it !== undefined && (Iterators.Array === it || ArrayProto[ITERATOR] === it);
   };
 
-  var $defineProperty$1 = require_objectDp();
+  var $defineProperty$1 = _objectDp;
   var createDesc$2 = _propertyDesc;
 
   var _createProperty = function (object, index, value) {
@@ -57991,7 +57983,7 @@
 
   var $export$3 = _export;
   // 19.1.2.4 / 15.2.3.6 Object.defineProperty(O, P, Attributes)
-  $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 = function defineProperty(it, key, desc) {
@@ -58039,7 +58031,7 @@
   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;
@@ -58094,7 +58086,7 @@
 
   var core = _coreExports;
   var wksExt$1 = _wksExt;
-  var defineProperty$4 = require_objectDp().f;
+  var defineProperty$4 = _objectDp.f;
   var _wksDefine = function (name) {
     var $Symbol = core.Symbol || (core.Symbol = {} );
     if (name.charAt(0) != '_' && !(name in $Symbol)) defineProperty$4($Symbol, name, { value: wksExt$1.f(name) });
@@ -58103,7 +58095,7 @@
   // all enumerable object keys, includes symbols
   var getKeys = _objectKeys;
   var gOPS$1 = _objectGops;
-  var pIE$1 = _objectPie;
+  var pIE$1 = require_objectPie();
   var _enumKeys = function (it) {
     var result = getKeys(it);
     var getSymbols = gOPS$1.f;
@@ -58156,15 +58148,15 @@
 
   var _objectGopd = {};
 
-  var pIE = _objectPie;
+  var pIE = require_objectPie();
   var createDesc$1 = _propertyDesc;
   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 : function getOwnPropertyDescriptor(O, P) {
+  _objectGopd.f = _descriptors ? gOPD$2 : function getOwnPropertyDescriptor(O, P) {
     O = toIObject$1(O);
     P = toPrimitive$1(P, true);
     if (IE8_DOM_DEFINE) try {
@@ -58176,7 +58168,7 @@
   // ECMAScript 6 symbols shim
   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;
@@ -58199,7 +58191,7 @@
   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;
@@ -58324,7 +58316,7 @@
     $GOPD.f = $getOwnPropertyDescriptor;
     $DP.f = $defineProperty;
     _objectGopn.f = gOPNExt.f = $getOwnPropertyNames;
-    _objectPie.f = $propertyIsEnumerable;
+    require_objectPie().f = $propertyIsEnumerable;
     $GOPS.f = $getOwnPropertySymbols;
 
     if (DESCRIPTORS && !_library) {
@@ -151686,9 +151678,7 @@
   };
 
   function validateSequence(sequence, options = {}) {
-    let {
-      isProtein,
-      isOligo,
+    const {
       guessIfProtein,
       guessIfProteinOptions,
       reformatSeqName,
@@ -151698,6 +151688,19 @@
       allowOverflowAnnotations,
       coerceFeatureTypes
     } = options;
+    [
+      "isDNA",
+      "isOligo",
+      "isRNA",
+      "isDoubleStrandedDNA",
+      "isSingleStrandedDNA",
+      "isDoubleStrandedRNA",
+      "isProtein"
+    ].forEach((k) => {
+      if (options[k] !== void 0 && sequence[k] === void 0) {
+        sequence[k] = options[k];
+      }
+    });
     const response = {
       validatedAndCleanedSequence: {},
       messages: []
@@ -151734,13 +151737,13 @@
       sequence.sequence = "";
     }
     let validChars;
-    if (isProtein === void 0 && guessIfProtein) {
-      isProtein = !guessIfSequenceIsDnaAndNotProtein(
+    if (sequence.isProtein === void 0 && guessIfProtein) {
+      sequence.isProtein = !guessIfSequenceIsDnaAndNotProtein(
         sequence.sequence,
         guessIfProteinOptions
       );
     }
-    if (isProtein) {
+    if (sequence.isProtein) {
       validChars = filterAminoAcidSequenceString(sequence.sequence);
       if (validChars !== sequence.sequence) {
         sequence.sequence = validChars;
@@ -151756,13 +151759,13 @@
       sequence.proteinSize = sequence.proteinSequence.length;
     } else {
       const temp = sequence.sequence;
-      if (!isOligo) {
+      if (!sequence.isOligo) {
         sequence.sequence = sequence.sequence.replace(
           /u/gi,
           (u) => u === "U" ? "T" : "t"
         );
       }
-      if (temp !== sequence.sequence) {
+      if (temp !== sequence.sequence && !sequence.isDNA && !sequence.isProtein) {
         sequence.type = "RNA";
         sequence.sequence = temp;
       } else {
@@ -151777,7 +151780,7 @@
       }
     }
     if (!sequence.size) {
-      sequence.size = isProtein ? sequence.proteinSequence.length * 3 : sequence.sequence.length;
+      sequence.size = sequence.isProtein ? sequence.proteinSequence.length * 3 : sequence.sequence.length;
     }
     let circularityExplicitlyDefined;
     if (sequence.circular === false || sequence.circular === "false" || sequence.circular === -1) {
@@ -152342,10 +152345,13 @@
           }
           options.sequenceTypeFromLocus = item;
           if (item.match(/ss-dna/i)) {
+            options.isDNA = true;
             options.isSingleStrandedDNA = true;
-          }
-          if (item.match(/rna/i)) {
+          } else if (item.match(/rna/i)) {
             options.isRna = true;
+          } else if (item.match(/ds-dna/i) || item.match(/dna/i)) {
+            options.isDNA = true;
+            options.isDoubleStrandedDNA = true;
           }
           if (item.match(/rna/i) && !item.match(/ss-rna/i)) {
             options.isDoubleStrandedRNA = true;
@@ -152360,6 +152366,8 @@
       }
       result.parsedSequence.gbDivision = gbDivision;
       result.parsedSequence.sequenceTypeFromLocus = options.sequenceTypeFromLocus;
+      result.parsedSequence.isDNA = options.isDNA;
+      result.parsedSequence.isDoubleStrandedDNA = options.isDoubleStrandedDNA;
       result.parsedSequence.isSingleStrandedDNA = options.isSingleStrandedDNA;
       result.parsedSequence.isRna = options.isRna;
       result.parsedSequence.isDoubleStrandedRNA = options.isDoubleStrandedRNA;
@@ -188655,7 +188663,7 @@ double click --> edit`}`;
   }
 
   const name = "@teselagen/ove";
-  const version = "0.3.3";
+  const version = "0.3.4";
   const main = "./src/index.js";
   const packageJson = {
   	name: name,

package/package.json

@@ -1,14 +1,14 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.3.4",
+  "version": "0.3.5",
   "main": "./src/index.js",
   "dependencies": {
-    "@teselagen/sequence-utils": "0.3.4",
-    "@teselagen/range-utils": "0.3.4",
-    "@teselagen/ui": "0.3.4",
-    "@teselagen/file-utils": "0.3.4",
-    "@teselagen/bounce-loader": "0.3.4",
-    "@teselagen/bio-parsers": "0.3.4",
+    "@teselagen/sequence-utils": "0.3.5",
+    "@teselagen/range-utils": "0.3.5",
+    "@teselagen/ui": "0.3.5",
+    "@teselagen/file-utils": "0.3.5",
+    "@teselagen/bounce-loader": "0.3.5",
+    "@teselagen/bio-parsers": "0.3.5",
     "@blueprintjs/core": "3.52.0",
     "@blueprintjs/datetime": "3.23.19",
     "@blueprintjs/icons": "3.33.0",