@teselagen/ove 0.0.16 → 0.0.18

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;
-
-  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;
+  var anObject$5 = _anObject;
+  var IE8_DOM_DEFINE$1 = _ie8DomDefine;
+  var toPrimitive$2 = _toPrimitive$1;
+  var dP$3 = 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$5(O);
+    P = toPrimitive$2(P, true);
+    anObject$5(Attributes);
+    if (IE8_DOM_DEFINE$1) try {
+      return dP$3(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 {
@@ -57137,10 +57114,10 @@
     };
   };
 
-  var dP$1 = require_objectDp();
+  var dP$2 = _objectDp;
   var createDesc$3 = _propertyDesc;
-  var _hide = require_descriptors() ? function (object, key, value) {
-    return dP$1.f(object, key, createDesc$3(1, value));
+  var _hide = _descriptors ? function (object, key, value) {
+    return dP$2.f(object, key, createDesc$3(1, value));
   } : function (object, key, value) {
     object[key] = value;
     return object;
@@ -57156,7 +57133,7 @@
   var ctx$1 = _ctx;
   var hide$2 = _hide;
   var has$d = _has;
-  var PROTOTYPE$1 = 'prototype';
+  var PROTOTYPE$2 = 'prototype';
 
   var $export$8 = function (type, name, source) {
     var IS_FORCED = type & $export$8.F;
@@ -57166,8 +57143,8 @@
     var IS_BIND = type & $export$8.B;
     var IS_WRAP = type & $export$8.W;
     var exports = IS_GLOBAL ? core$3 : core$3[name] || (core$3[name] = {});
-    var expProto = exports[PROTOTYPE$1];
-    var target = IS_GLOBAL ? global$4 : IS_STATIC ? global$4[name] : (global$4[name] || {})[PROTOTYPE$1];
+    var expProto = exports[PROTOTYPE$2];
+    var target = IS_GLOBAL ? global$4 : IS_STATIC ? global$4[name] : (global$4[name] || {})[PROTOTYPE$2];
     var key, own, out;
     if (IS_GLOBAL) source = name;
     for (key in source) {
@@ -57191,7 +57168,7 @@
             } return new C(a, b, c);
           } return C.apply(this, arguments);
         };
-        F[PROTOTYPE$1] = C[PROTOTYPE$1];
+        F[PROTOTYPE$2] = C[PROTOTYPE$2];
         return F;
       // make static versions for prototype methods
       })(out) : IS_PROTO && typeof out == 'function' ? ctx$1(Function.call, out) : out;
@@ -57328,14 +57305,14 @@
   var has$c = _has;
   var toIObject$4 = _toIobject;
   var arrayIndexOf$1 = _arrayIncludes$1(false);
-  var IE_PROTO$1 = _sharedKey('IE_PROTO');
+  var IE_PROTO$2 = _sharedKey('IE_PROTO');
 
   var _objectKeysInternal = function (object, names) {
     var O = toIObject$4(object);
     var i = 0;
     var result = [];
     var key;
-    for (key in O) if (key != IE_PROTO$1) has$c(O, key) && result.push(key);
+    for (key in O) if (key != IE_PROTO$2) has$c(O, key) && result.push(key);
     // Don't enum bug & hidden keys
     while (names.length > i) if (has$c(O, key = names[i++])) {
       ~arrayIndexOf$1(result, key) || result.push(key);
@@ -57350,10 +57327,10 @@
 
   // 19.1.2.14 / 15.2.3.14 Object.keys(O)
   var $keys$3 = _objectKeysInternal;
-  var enumBugKeys = _enumBugKeys;
+  var enumBugKeys$1 = _enumBugKeys;
 
   var _objectKeys = Object.keys || function keys(O) {
-    return $keys$3(O, enumBugKeys);
+    return $keys$3(O, enumBugKeys$1);
   };
 
   var _objectGops = {};
@@ -57362,7 +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;
@@ -57377,10 +57361,10 @@
   	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 = require_iobject();
   	var $assign = Object.assign;
@@ -57453,27 +57437,19 @@
 
   var _redefine = _hide;
 
-  var _objectDps;
-  var hasRequired_objectDps;
+  var dP$1 = _objectDp;
+  var anObject$4 = _anObject;
+  var getKeys$1 = _objectKeys;
 
-  function require_objectDps () {
-  	if (hasRequired_objectDps) return _objectDps;
-  	hasRequired_objectDps = 1;
-  	var dP = require_objectDp();
-  	var anObject = _anObject;
-  	var getKeys = _objectKeys;
-
-  	_objectDps = require_descriptors() ? Object.defineProperties : function defineProperties(O, Properties) {
-  	  anObject(O);
-  	  var keys = getKeys(Properties);
-  	  var length = keys.length;
-  	  var i = 0;
-  	  var P;
-  	  while (length > i) dP.f(O, P = keys[i++], Properties[P]);
-  	  return O;
-  	};
-  	return _objectDps;
-  }
+  var _objectDps = _descriptors ? Object.defineProperties : function defineProperties(O, Properties) {
+    anObject$4(O);
+    var keys = getKeys$1(Properties);
+    var length = keys.length;
+    var i = 0;
+    var P;
+    while (length > i) dP$1.f(O, P = keys[i++], Properties[P]);
+    return O;
+  };
 
   var _html;
   var hasRequired_html;
@@ -57486,55 +57462,47 @@
   	return _html;
   }
 
-  var _objectCreate;
-  var hasRequired_objectCreate;
+  // 19.1.2.2 / 15.2.3.5 Object.create(O [, Properties])
+  var anObject$3 = _anObject;
+  var dPs = _objectDps;
+  var enumBugKeys = _enumBugKeys;
+  var IE_PROTO$1 = _sharedKey('IE_PROTO');
+  var Empty = function () { /* empty */ };
+  var PROTOTYPE$1 = 'prototype';
 
-  function require_objectCreate () {
-  	if (hasRequired_objectCreate) return _objectCreate;
-  	hasRequired_objectCreate = 1;
-  	// 19.1.2.2 / 15.2.3.5 Object.create(O [, Properties])
-  	var anObject = _anObject;
-  	var dPs = require_objectDps();
-  	var enumBugKeys = _enumBugKeys;
-  	var IE_PROTO = _sharedKey('IE_PROTO');
-  	var Empty = function () { /* empty */ };
-  	var PROTOTYPE = 'prototype';
-
-  	// Create object with fake `null` prototype: use iframe Object with cleared prototype
-  	var createDict = function () {
-  	  // Thrash, waste and sodomy: IE GC bug
-  	  var iframe = require_domCreate()('iframe');
-  	  var i = enumBugKeys.length;
-  	  var lt = '<';
-  	  var gt = '>';
-  	  var iframeDocument;
-  	  iframe.style.display = 'none';
-  	  require_html().appendChild(iframe);
-  	  iframe.src = 'javascript:'; // eslint-disable-line no-script-url
-  	  // createDict = iframe.contentWindow.Object;
-  	  // html.removeChild(iframe);
-  	  iframeDocument = iframe.contentWindow.document;
-  	  iframeDocument.open();
-  	  iframeDocument.write(lt + 'script' + gt + 'document.F=Object' + lt + '/script' + gt);
-  	  iframeDocument.close();
-  	  createDict = iframeDocument.F;
-  	  while (i--) delete createDict[PROTOTYPE][enumBugKeys[i]];
-  	  return createDict();
-  	};
-
-  	_objectCreate = Object.create || function create(O, Properties) {
-  	  var result;
-  	  if (O !== null) {
-  	    Empty[PROTOTYPE] = anObject(O);
-  	    result = new Empty();
-  	    Empty[PROTOTYPE] = null;
-  	    // add "__proto__" for Object.getPrototypeOf polyfill
-  	    result[IE_PROTO] = O;
-  	  } else result = createDict();
-  	  return Properties === undefined ? result : dPs(result, Properties);
-  	};
-  	return _objectCreate;
-  }
+  // Create object with fake `null` prototype: use iframe Object with cleared prototype
+  var createDict = function () {
+    // Thrash, waste and sodomy: IE GC bug
+    var iframe = require_domCreate()('iframe');
+    var i = enumBugKeys.length;
+    var lt = '<';
+    var gt = '>';
+    var iframeDocument;
+    iframe.style.display = 'none';
+    require_html().appendChild(iframe);
+    iframe.src = 'javascript:'; // eslint-disable-line no-script-url
+    // createDict = iframe.contentWindow.Object;
+    // html.removeChild(iframe);
+    iframeDocument = iframe.contentWindow.document;
+    iframeDocument.open();
+    iframeDocument.write(lt + 'script' + gt + 'document.F=Object' + lt + '/script' + gt);
+    iframeDocument.close();
+    createDict = iframeDocument.F;
+    while (i--) delete createDict[PROTOTYPE$1][enumBugKeys[i]];
+    return createDict();
+  };
+
+  var _objectCreate = Object.create || function create(O, Properties) {
+    var result;
+    if (O !== null) {
+      Empty[PROTOTYPE$1] = anObject$3(O);
+      result = new Empty();
+      Empty[PROTOTYPE$1] = null;
+      // add "__proto__" for Object.getPrototypeOf polyfill
+      result[IE_PROTO$1] = O;
+    } else result = createDict();
+    return Properties === undefined ? result : dPs(result, Properties);
+  };
 
   var _wks = {exports: {}};
 
@@ -57552,7 +57520,7 @@
 
   var _wksExports = _wks.exports;
 
-  var def = require_objectDp().f;
+  var def = _objectDp.f;
   var has$b = _has;
   var TAG$1 = _wksExports('toStringTag');
 
@@ -57560,7 +57528,7 @@
     if (it && !has$b(it = stat ? it : it.prototype, TAG$1)) def(it, TAG$1, { configurable: true, value: tag });
   };
 
-  var create$4 = require_objectCreate();
+  var create$4 = _objectCreate;
   var descriptor = _propertyDesc;
   var setToStringTag$2 = _setToStringTag;
   var IteratorPrototype = {};
@@ -57866,7 +57834,7 @@
     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) {
@@ -57999,7 +57967,7 @@
 
   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) {
@@ -58047,7 +58015,7 @@
   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;
@@ -58102,7 +58070,7 @@
 
   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) });
@@ -58111,7 +58079,7 @@
   // 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;
@@ -58164,15 +58132,15 @@
 
   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 {
@@ -58184,7 +58152,7 @@
   // 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;
@@ -58203,11 +58171,11 @@
   var toIObject = _toIobject;
   var toPrimitive = _toPrimitive$1;
   var createDesc = _propertyDesc;
-  var _create$1 = require_objectCreate();
+  var _create$1 = _objectCreate;
   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;
@@ -58332,7 +58300,7 @@
     $GOPD.f = $getOwnPropertyDescriptor;
     $DP.f = $defineProperty;
     _objectGopn.f = gOPNExt.f = $getOwnPropertyNames;
-    _objectPie.f = $propertyIsEnumerable;
+    require_objectPie().f = $propertyIsEnumerable;
     $GOPS.f = $getOwnPropertySymbols;
 
     if (DESCRIPTORS && !_library) {
@@ -58513,7 +58481,7 @@
 
   var $export = _export;
   // 19.1.2.2 / 15.2.3.5 Object.create(O [, Properties])
-  $export($export.S, 'Object', { create: require_objectCreate() });
+  $export($export.S, 'Object', { create: _objectCreate });
 
   var $Object = _coreExports.Object;
   var create$3 = function create(P, D) {
@@ -126254,8 +126222,7 @@
     const zipExtracted = await extractZipFiles(file);
     const acceptedFiles = [];
     for (const extFile of zipExtracted) {
-      const extension = "." + getExt(extFile);
-      if (accepted.some((ext) => ext === extension)) {
+      if (accepted.some((ext) => ext?.replace(".", "") === getExt(extFile))) {
         acceptedFiles.push(extFile);
       }
     }
@@ -152118,10 +152085,11 @@
     );
   }
 
-  function getComplementSequenceString(sequence) {
+  function getComplementSequenceString(sequence, isRna) {
     let complementSeqString = "";
+    const complementMap = lodashExports.merge(DNAComplementMap, isRna ? { a: "u", A: "U" } : { a: "t", A: "T" });
     for (let i = 0; i < sequence.length; i++) {
-      let complementChar = DNAComplementMap[sequence[i]];
+      let complementChar = complementMap[sequence[i]];
       if (!complementChar) {
         complementChar = sequence[i];
       }
@@ -152231,7 +152199,7 @@
       options
     );
     const newSeqObj = Object.assign({}, seqObj, {
-      sequence: getComplementSequenceString(seqObj.sequence)
+      sequence: getComplementSequenceString(seqObj.sequence, seqObj.isRna)
     });
     return tidyUpSequenceData(newSeqObj, options);
   }
@@ -153654,7 +153622,7 @@
           options.sequenceTypeFromLocus = item;
           options.isProtein = true;
         }
-        if (j === 4 && (item.match(/ds-dna/i) || item.match(/ss-dna/i) || item.match(/dna/i))) {
+        if (j === 4 && (item.match(/ds-dna/i) || item.match(/ss-dna/i) || item.match(/dna/i) || item.match(/rna/i))) {
           if (options.isProtein === void 0) {
             options.isProtein = false;
           }
@@ -153662,6 +153630,9 @@
           if (item.match(/ss-dna/i)) {
             options.isSingleStrandedDNA = true;
           }
+          if (item.match(/rna/i) && !item.match(/ss-rna/i)) {
+            options.isDoubleStrandedRNA = true;
+          }
         }
         if (typeof lineArr[j] === "string" && gbDivisions[lineArr[j].toUpperCase()]) {
           gbDivision = lineArr[j].toUpperCase();
@@ -153673,6 +153644,7 @@
       result.parsedSequence.gbDivision = gbDivision;
       result.parsedSequence.sequenceTypeFromLocus = options.sequenceTypeFromLocus;
       result.parsedSequence.isSingleStrandedDNA = options.isSingleStrandedDNA;
+      result.parsedSequence.isDoubleStrandedRNA = options.isDoubleStrandedRNA;
       result.parsedSequence.date = date;
       result.parsedSequence.circular = circular;
     }
@@ -167247,9 +167219,9 @@
     if (serSeq.isProtein) {
       dnaType = "";
     } else if (serSeq.type === "RNA") {
-      dnaType = "RNA";
+      dnaType = serSeq?.doubleStranded ? "RNA" : serSeq?.sequenceTypeFromLocus ?? "ss-RNA";
     } else {
-      dnaType = serSeq?.sequenceTypeFromLocus ?? "DNA";
+      dnaType = serSeq?.doubleStranded ? "DNA" : serSeq?.sequenceTypeFromLocus ?? "DNA";
     }
     const date = getCurrentDateString();
     let line = StringUtil.rpad("LOCUS", " ", 12);
@@ -189952,7 +189924,7 @@ double click --> edit`}`;
   }
 
   const name = "@teselagen/ove";
-  const version = "0.0.15";
+  const version = "0.0.17";
   const main = "./src/index.js";
   const type = "commonjs";
   const packageJson = {

package/package.json

@@ -1,9 +1,15 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.0.16",
+  "version": "0.0.18",
   "main": "./src/index.js",
   "type": "module",
   "dependencies": {
+    "@teselagen/sequence-utils": "0.1.19",
+    "@teselagen/range-utils": "0.1.18",
+    "@teselagen/ui": "0.0.23",
+    "@teselagen/file-utils": "0.2.25",
+    "@teselagen/bounce-loader": "0.0.12",
+    "@teselagen/bio-parsers": "0.1.24",
     "@blueprintjs/core": "3.52.0",
     "@blueprintjs/datetime": "3.23.19",
     "@blueprintjs/icons": "3.33.0",
@@ -42,6 +48,7 @@
     "math-expression-evaluator": "^1.3.7",
     "mobx": "^6.9.0",
     "mobx-react": "^7.6.0",
+    "mock-fs": "5.2.0",
     "nanoid": "^4.0.0",
     "node-interval-tree": "^1.3.3",
     "papaparse": "^5.3.2",