@teselagen/ove 0.5.12 → 0.5.14
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/AlignmentTool/index.d.ts +4 -6
- package/index.cjs.js +399 -351
- package/index.es.js +399 -351
- package/index.umd.js +437 -363
- package/package.json +2 -2
- package/src/AlignmentTool/index.js +7 -11
- package/src/RowItem/Translations/AASliver.js +12 -11
- package/src/RowItem/Translations/Translation.js +41 -9
package/index.umd.js
CHANGED
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@@ -59,7 +59,7 @@ var __async = (__this, __arguments, generator) => {
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});
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};
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-
var
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var _s, _t, _u, _v, _w, _x, _A, _D, _K;
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function _mergeNamespaces(n2, m2) {
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for (var i2 = 0; i2 < m2.length; i2++) {
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const e2 = m2[i2];
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@@ -10047,7 +10047,7 @@ var __async = (__this, __arguments, generator) => {
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}, _typeof$7(o2);
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}
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__name(_typeof$7, "_typeof$7");
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-
function toPrimitive$
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function toPrimitive$3(t2, r2) {
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if ("object" != _typeof$7(t2) || !t2)
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return t2;
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var e2 = t2[Symbol.toPrimitive];
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@@ -10059,9 +10059,9 @@ var __async = (__this, __arguments, generator) => {
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}
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return ("string" === r2 ? String : Number)(t2);
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}
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__name(toPrimitive$
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__name(toPrimitive$3, "toPrimitive$3");
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function toPropertyKey(t2) {
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-
var i2 = toPrimitive$
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var i2 = toPrimitive$3(t2, "string");
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return "symbol" == _typeof$7(i2) ? i2 : String(i2);
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}
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__name(toPropertyKey, "toPropertyKey");
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@@ -25997,10 +25997,10 @@ var __async = (__this, __arguments, generator) => {
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/* istanbul ignore next */
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Object.getOwnPropertyNames
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);
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function toPrimitive$
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function toPrimitive$2(value) {
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return value === null ? null : typeof value === "object" ? "" + value : value;
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}
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__name(toPrimitive$
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__name(toPrimitive$2, "toPrimitive$2");
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function hasProp(target, prop2) {
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return objectPrototype$2.hasOwnProperty.call(target, prop2);
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}
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@@ -27019,7 +27019,7 @@ var __async = (__this, __arguments, generator) => {
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return this.name_ + "[" + this.value_ + "]";
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}, "toString2");
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_proto.valueOf = /* @__PURE__ */ __name(function valueOf() {
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return toPrimitive$
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return toPrimitive$2(this.get());
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}, "valueOf");
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_proto[_Symbol$toPrimitive] = function() {
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return this.valueOf();
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@@ -27204,7 +27204,7 @@ var __async = (__this, __arguments, generator) => {
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return this.name_ + "[" + this.derivation.toString() + "]";
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}, "toString2");
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_proto.valueOf = /* @__PURE__ */ __name(function valueOf() {
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return toPrimitive$
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return toPrimitive$2(this.get());
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}, "valueOf");
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_proto[_Symbol$toPrimitive$1] = function() {
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return this.valueOf();
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@@ -40904,11 +40904,20 @@ ${latestSubscriptionCallbackError.current.stack}
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return true;
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}
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}, "_fails");
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var _descriptors
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var _descriptors;
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var hasRequired_descriptors;
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function require_descriptors() {
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if (hasRequired_descriptors)
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return _descriptors;
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hasRequired_descriptors = 1;
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_descriptors = !_fails(function() {
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return Object.defineProperty({}, "a", { get: function() {
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return 7;
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} }).a != 7;
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});
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return _descriptors;
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}
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__name(require_descriptors, "require_descriptors");
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var _domCreate;
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var hasRequired_domCreate;
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function require_domCreate() {
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@@ -40924,11 +40933,20 @@ ${latestSubscriptionCallbackError.current.stack}
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return _domCreate;
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}
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__name(require_domCreate, "require_domCreate");
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var _ie8DomDefine
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var _ie8DomDefine;
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var hasRequired_ie8DomDefine;
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function require_ie8DomDefine() {
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if (hasRequired_ie8DomDefine)
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return _ie8DomDefine;
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hasRequired_ie8DomDefine = 1;
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_ie8DomDefine = !require_descriptors() && !_fails(function() {
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return Object.defineProperty(require_domCreate()("div"), "a", { get: function() {
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return 7;
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} }).a != 7;
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});
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return _ie8DomDefine;
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}
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__name(require_ie8DomDefine, "require_ie8DomDefine");
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var isObject$5 = _isObject;
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var _toPrimitive$1 = /* @__PURE__ */ __name(function(it, S2) {
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if (!isObject$5(it))
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@@ -40942,25 +40960,33 @@ ${latestSubscriptionCallbackError.current.stack}
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return val2;
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throw TypeError("Can't convert object to primitive value");
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}, "_toPrimitive$1");
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var
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var hasRequired_objectDp;
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function require_objectDp() {
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if (hasRequired_objectDp)
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return _objectDp;
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hasRequired_objectDp = 1;
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var anObject2 = _anObject;
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var IE8_DOM_DEFINE2 = require_ie8DomDefine();
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var toPrimitive2 = _toPrimitive$1;
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var dP2 = Object.defineProperty;
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_objectDp.f = require_descriptors() ? Object.defineProperty : /* @__PURE__ */ __name(function defineProperty2(O2, P2, Attributes) {
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anObject2(O2);
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P2 = toPrimitive2(P2, true);
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anObject2(Attributes);
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if (IE8_DOM_DEFINE2)
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try {
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return dP2(O2, P2, Attributes);
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} catch (e2) {
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}
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if ("get" in Attributes || "set" in Attributes)
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throw TypeError("Accessors not supported!");
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if ("value" in Attributes)
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O2[P2] = Attributes.value;
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return O2;
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}, "defineProperty");
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return _objectDp;
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}
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__name(require_objectDp, "require_objectDp");
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var _propertyDesc = /* @__PURE__ */ __name(function(bitmap, value) {
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return {
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enumerable: !(bitmap & 1),
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};
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var dP$2 =
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var dP$2 = require_objectDp();
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var createDesc$3 = _propertyDesc;
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var _hide =
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var _hide = require_descriptors() ? function(object2, key2, value) {
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return dP$2.f(object2, key2, createDesc$3(1, value));
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} : function(object2, key2, value) {
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object2[key2] = value;
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var _objectGops = {};
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_objectGops.f = Object.getOwnPropertySymbols;
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var _objectPie = {};
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function require_objectPie() {
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if (hasRequired_objectPie)
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return _objectPie;
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hasRequired_objectPie = 1;
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_objectPie.f = {}.propertyIsEnumerable;
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return _objectPie;
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}
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__name(require_objectPie, "require_objectPie");
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var defined$1 = _defined;
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var _toObject = /* @__PURE__ */ __name(function(it) {
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return Object(defined$1(it));
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if (hasRequired_objectAssign)
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return _objectAssign;
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hasRequired_objectAssign = 1;
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var DESCRIPTORS2 =
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var DESCRIPTORS2 = require_descriptors();
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var getKeys2 = _objectKeys;
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var gOPS2 = _objectGops;
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var pIE2 =
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var pIE2 = require_objectPie();
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var toObject2 = _toObject;
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var IObject2 = _iobject;
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}, "_iterStep");
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var _iterators = {};
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var _redefine = _hide;
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var dP$1 =
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var dP$1 = require_objectDp();
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var anObject$4 = _anObject;
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var getKeys$1 = _objectKeys;
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var _objectDps =
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var _objectDps = require_descriptors() ? Object.defineProperties : /* @__PURE__ */ __name(function defineProperties2(O2, Properties2) {
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anObject$4(O2);
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var keys2 = getKeys$1(Properties2);
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};
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$exports.store = store$2;
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var TAG$1 = _wksExports("toStringTag");
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}, "_isArrayIter");
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var $defineProperty$1 = require_objectDp();
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var createDesc$2 = _propertyDesc;
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var _createProperty = /* @__PURE__ */ __name(function(object2, index2, value) {
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}, "_default$8");
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var $export$3 = _export;
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$export$3($export$3.S + $export$3.F * !
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$export$3($export$3.S + $export$3.F * !require_descriptors(), "Object", { defineProperty: require_objectDp().f });
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var $Object$1 = _coreExports.Object;
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var META$1 = _uid("meta");
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var setDesc = require_objectDp().f;
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}, "_wksDefine");
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var gOPS$1 = _objectGops;
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var pIE$1 =
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var pIE$1 = require_objectPie();
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var _enumKeys = /* @__PURE__ */ __name(function(it) {
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return windowNames && toString$2.call(it) == "[object Window]" ? getWindowNames(it) : gOPN$1(toIObject$2(it));
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var pIE = require_objectPie();
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var createDesc$1 = _propertyDesc;
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var toIObject$1 = _toIobject;
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var IE8_DOM_DEFINE =
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var IE8_DOM_DEFINE = require_ie8DomDefine();
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]);
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const IconToUse = isButton ? Button : Icon;
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const IconInner = /* @__PURE__ */ React$2.createElement(IconToUse, __spreadValues(__spreadValues({}, iconProps), rest));
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let toReturn;
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const toolTipOrPopoverProps = __spreadValues({
|
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disabled: disabled || !isPopover && window.Cypress && !window.Cypress.allowInfoHelperTooltips,
|
|
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popoverClassName: "tg-info-helper-popover bp3-tooltip",
|
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|
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modifiers: popoverOverflowModifiers
|
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}, popoverProps);
|
|
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if (displayToSide) {
|
|
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|
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toReturn = /* @__PURE__ */ React$2.createElement(React$2.Fragment, null, IconInner, /* @__PURE__ */ React$2.createElement("span", { style: { paddingLeft: 5, fontStyle: "italic" } }, content2 || children));
|
|
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|
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} else if (isPopover) {
|
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toReturn = /* @__PURE__ */ React$2.createElement(Popover, __spreadProps(__spreadValues({}, toolTipOrPopoverProps), { target: IconInner }));
|
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} else {
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toReturn = /* @__PURE__ */ React$2.createElement(Tooltip, __spreadProps(__spreadValues({}, toolTipOrPopoverProps), { target: IconInner }));
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}
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const El = isInline ? "span" : "div";
|
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return /* @__PURE__ */ React$2.createElement(
|
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El,
|
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{
|
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style: __spreadValues(__spreadValues(__spreadValues({}, clickable ? { cursor: "pointer" } : {}), isInline ? {} : { display: "flex" }), style2),
|
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className: classNames$1(
|
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"info-helper-wrapper",
|
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{
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},
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},
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);
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}, "InfoHelper");
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const getIdOrCodeOrIndex = /* @__PURE__ */ __name((record, rowIndex) => {
|
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if (record.id || record.id === 0) {
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|
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|
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DateRangeInput2.prototype.componentDidUpdate = function(prevProps, prevState) {
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if (((_a2 = prevProps.startInputProps) === null || _a2 === void 0 ? void 0 : _a2.inputRef) !== ((_b2 = this.props.startInputProps) === null || _b2 === void 0 ? void 0 : _b2.inputRef)) {
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this.handleStartInputRef = refHandler(this, "startInputElement", (_d2 = this.props.startInputProps) === null || _d2 === void 0 ? void 0 : _d2.inputRef);
|
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|
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return /* @__PURE__ */ React$2.createElement(TgSelect$1, __spreadValues({}, propsToUse));
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var _n = _m, { ModalComponent } = _n, rest = __objRest(_n, ["ModalComponent"]);
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|
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const [additionalProps, setAdditionalProps] = reactExports.useState(false);
|
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|
const comp = /* @__PURE__ */ React$2.createElement(
|
|
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|
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const Loading = /* @__PURE__ */ __name(({
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+
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|
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|
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|
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|
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|
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+
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|
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|
|
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|
+
const [longerThan200MS, setLongerThan200MS] = reactExports.useState(false);
|
|
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|
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reactExports.useEffect(() => {
|
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|
+
const timeoutId = setTimeout(() => {
|
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|
+
setLongerThan200MS(true);
|
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|
}, 200);
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containerStyle = {},
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} = this.props;
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const style2 = __spreadValues(__spreadValues({}, userStyle), inDialog && { minHeight: 120 });
|
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const LoaderComp = bounce || inDialog ? BounceLoader : DNALoader;
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if (loading || !children) {
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|
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if (!displayInstantly && !longerThan200MS && (!bounce && !inDialog || withTimeout)) {
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|
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return /* @__PURE__ */ React$2.createElement("div", null);
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return /* @__PURE__ */ React$2.createElement(
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{
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className: "tg-loader-container tg-flex justify-center align-center",
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style: __spreadValues(__spreadValues({
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width: "100%"
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}, containerStyle), centeredInPage && {
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|
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zIndex: 20,
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height: 10,
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position: "fixed",
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})
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},
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/* @__PURE__ */ React$2.createElement(LoaderComp, { style: style2, className })
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);
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|
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} else {
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return children || null;
|
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return () => {
|
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clearTimeout(timeoutId);
|
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|
+
};
|
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|
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}, []);
|
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|
+
const style2 = __spreadValues(__spreadValues({}, userStyle), inDialog && { minHeight: 120 });
|
|
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|
+
const LoaderComp = bounce || inDialog ? BounceLoader : DNALoader;
|
|
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|
+
if (loading || !children) {
|
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|
+
if (!displayInstantly && !longerThan200MS && (!bounce && !inDialog || withTimeout)) {
|
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|
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return /* @__PURE__ */ React$2.createElement("div", null);
|
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}
|
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|
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return /* @__PURE__ */ React$2.createElement(
|
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"div",
|
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|
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{
|
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className: "tg-loader-container tg-flex justify-center align-center",
|
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|
+
style: __spreadValues(__spreadValues({
|
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|
+
width: "100%"
|
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|
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}, containerStyle), centeredInPage && {
|
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|
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width: void 0,
|
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|
+
zIndex: 20,
|
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|
+
height: 10,
|
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|
+
position: "fixed",
|
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|
+
top: "50%",
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|
+
left: "50%",
|
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|
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transform: "translate(-50%, 0)"
|
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|
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})
|
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|
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},
|
|
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|
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/* @__PURE__ */ React$2.createElement(LoaderComp, { style: style2, className })
|
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|
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);
|
|
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|
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} else {
|
|
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|
+
return children || null;
|
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97384
|
}
|
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|
-
};
|
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|
-
__name(_Loading, "Loading");
|
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|
-
let Loading = _Loading;
|
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|
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}, "Loading");
|
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|
function AdvancedOptions({
|
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|
children,
|
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|
content: content2,
|
|
@@ -97398,14 +97415,14 @@ ${latestSubscriptionCallbackError.current.stack}
|
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97415
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), isOpen2 && /* @__PURE__ */ React$2.createElement("div", { style: { marginTop: 10 } }, content2 || children));
|
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}
|
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|
__name(AdvancedOptions, "AdvancedOptions");
|
|
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|
-
function DropdownButton(
|
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|
-
var
|
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|
+
function DropdownButton(_o) {
|
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var _p = _o, {
|
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|
disabled,
|
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97421
|
menu,
|
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|
noRightIcon,
|
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|
popoverProps,
|
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|
className
|
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|
-
} =
|
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|
+
} = _p, rest = __objRest(_p, [
|
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|
"disabled",
|
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97427
|
"menu",
|
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|
"noRightIcon",
|
|
@@ -100758,14 +100775,14 @@ ${latestSubscriptionCallbackError.current.stack}
|
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|
}
|
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|
}),
|
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|
branch(({ navTo }) => navTo, withRouter$1)
|
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|
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)(function(
|
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|
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var
|
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|
+
)(function(_q) {
|
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|
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var _r = _q, {
|
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navTo,
|
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context,
|
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|
staticContext,
|
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|
didMount,
|
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|
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|
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|
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} =
|
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|
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} = _r, props = __objRest(_r, [
|
|
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|
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|
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100787
|
"context",
|
|
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|
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|
|
@@ -100959,7 +100976,7 @@ ${latestSubscriptionCallbackError.current.stack}
|
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100976
|
);
|
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|
}
|
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|
__name(doesSearchValMatchText, "doesSearchValMatchText");
|
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|
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let MenuBar$1 = (
|
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|
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let MenuBar$1 = (_s = class extends React$2.Component {
|
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|
constructor(props) {
|
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super(props);
|
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__publicField(this, "state", {
|
|
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|
|
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101221
|
);
|
|
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101222
|
}), extraContent);
|
|
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|
}
|
|
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|
-
}, __name(
|
|
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|
+
}, __name(_s, "MenuBar"), __publicField(_s, "defaultProps", {
|
|
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101225
|
className: "",
|
|
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101226
|
style: {}
|
|
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|
-
}),
|
|
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|
+
}), _s);
|
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101228
|
const isDivider = /* @__PURE__ */ __name((item) => item.divider !== void 0, "isDivider");
|
|
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101229
|
function getAllMenuTextsAndHandlers(menu, enhancers, context, path2 = []) {
|
|
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101230
|
if (!menu)
|
|
@@ -101355,7 +101372,7 @@ ${latestSubscriptionCallbackError.current.stack}
|
|
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|
);
|
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|
}
|
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|
__name(HotkeysDialog, "HotkeysDialog");
|
|
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|
-
let FillWindow$1 = (
|
|
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|
+
let FillWindow$1 = (_t = class extends React$2.Component {
|
|
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|
constructor(props) {
|
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|
super(props);
|
|
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|
rerenderOnWindowResize(this);
|
|
@@ -101403,7 +101420,7 @@ ${latestSubscriptionCallbackError.current.stack}
|
|
|
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|
return ReactDOM$1.createPortal(inner2, window.document.body);
|
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|
return inner2;
|
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|
}
|
|
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|
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}, __name(
|
|
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|
+
}, __name(_t, "FillWindow"), _t);
|
|
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101424
|
var relativeTime$1 = { exports: {} };
|
|
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101425
|
(function(module2, exports3) {
|
|
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|
!function(r2, e2) {
|
|
@@ -101451,16 +101468,6 @@ ${latestSubscriptionCallbackError.current.stack}
|
|
|
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101468
|
var relativeTimeExports = relativeTime$1.exports;
|
|
101452
101469
|
const relativeTime = /* @__PURE__ */ getDefaultExportFromCjs(relativeTimeExports);
|
|
101453
101470
|
dayjs.extend(relativeTime);
|
|
101454
|
-
const _Timeline = class _Timeline extends reactExports.Component {
|
|
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|
-
render() {
|
|
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|
-
return /* @__PURE__ */ React$2.createElement("div", { className: "tg-timeline" }, this.props.children.length > 1 && /* @__PURE__ */ React$2.createElement("div", { className: "tg-timeline-line" }), this.props.children);
|
|
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|
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}
|
|
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|
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};
|
|
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|
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__name(_Timeline, "Timeline");
|
|
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|
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__publicField(_Timeline, "propTypes", {
|
|
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|
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children: PropTypes$1.arrayOf(PropTypes$1.element)
|
|
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|
-
});
|
|
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|
-
let Timeline = _Timeline;
|
|
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|
const ptIconWrapper = /* @__PURE__ */ __name((path2, viewboxDefault = 24, rest) => {
|
|
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|
return /* @__PURE__ */ React$2.createElement("span", { className: "bp3-icon" }, /* @__PURE__ */ React$2.createElement(
|
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101473
|
"svg",
|
|
@@ -108774,123 +108781,167 @@ ${latestSubscriptionCallbackError.current.stack}
|
|
|
108774
108781
|
return proteinAlphabet[letter.toUpperCase()];
|
|
108775
108782
|
}
|
|
108776
108783
|
__name(getAminoAcidFromSequenceTriplet, "getAminoAcidFromSequenceTriplet");
|
|
108777
|
-
function
|
|
108784
|
+
function getNextTriplet(index2, sequenceString, exonRange) {
|
|
108785
|
+
let triplet = "";
|
|
108786
|
+
let internalIndex;
|
|
108787
|
+
const codonPositions = [];
|
|
108788
|
+
const isBaseInExon = /* @__PURE__ */ __name((baseIndex) => exonRange.some(
|
|
108789
|
+
(r2) => isPositionWithinRange(baseIndex, r2, sequenceString.length, true, false)
|
|
108790
|
+
), "isBaseInExon");
|
|
108791
|
+
for (internalIndex = index2; internalIndex < sequenceString.length; internalIndex++) {
|
|
108792
|
+
if (triplet.length === 3) {
|
|
108793
|
+
break;
|
|
108794
|
+
}
|
|
108795
|
+
if (isBaseInExon(internalIndex)) {
|
|
108796
|
+
triplet += sequenceString[internalIndex];
|
|
108797
|
+
codonPositions.push(internalIndex);
|
|
108798
|
+
}
|
|
108799
|
+
}
|
|
108800
|
+
return { triplet, basesRead: internalIndex - index2, codonPositions };
|
|
108801
|
+
}
|
|
108802
|
+
__name(getNextTriplet, "getNextTriplet");
|
|
108803
|
+
function getTranslatedSequenceProperties(originalSequenceString, forward, optionalSubrangeRange, isProteinSequence) {
|
|
108778
108804
|
const originalSequenceStringLength = isProteinSequence ? originalSequenceString.length * 3 : originalSequenceString.length;
|
|
108779
108805
|
let sequenceString = originalSequenceString;
|
|
108780
|
-
|
|
108806
|
+
const translationRange = { start: 0, end: originalSequenceStringLength - 1 };
|
|
108781
108807
|
if (optionalSubrangeRange) {
|
|
108782
108808
|
sequenceString = getSequenceWithinRange(
|
|
108783
108809
|
optionalSubrangeRange,
|
|
108784
108810
|
originalSequenceString
|
|
108785
108811
|
);
|
|
108786
|
-
|
|
108812
|
+
translationRange.start = optionalSubrangeRange.start;
|
|
108813
|
+
translationRange.end = optionalSubrangeRange.end;
|
|
108787
108814
|
}
|
|
108788
108815
|
const sequenceStringLength = isProteinSequence ? sequenceString.length * 3 : sequenceString.length;
|
|
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|
-
|
|
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|
-
|
|
108791
|
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|
|
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|
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|
|
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|
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|
|
108794
|
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|
|
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|
-
|
|
108796
|
-
|
|
108797
|
-
{
|
|
108798
|
-
start: 0,
|
|
108799
|
-
end: revCompGapLength - 1
|
|
108800
|
-
},
|
|
108801
|
-
startOffset,
|
|
108816
|
+
if (!isProteinSequence && !forward) {
|
|
108817
|
+
sequenceString = getReverseComplementSequenceString(sequenceString);
|
|
108818
|
+
}
|
|
108819
|
+
const absoluteExonRange = !isProteinSequence && optionalSubrangeRange && optionalSubrangeRange.locations ? optionalSubrangeRange.locations : [translationRange];
|
|
108820
|
+
const exonRange = absoluteExonRange.map((range2) => {
|
|
108821
|
+
let outputRange = translateRange(
|
|
108822
|
+
range2,
|
|
108823
|
+
-translationRange.start,
|
|
108802
108824
|
originalSequenceStringLength
|
|
108803
108825
|
);
|
|
108804
|
-
if (
|
|
108805
|
-
|
|
108806
|
-
|
|
108807
|
-
|
|
108808
|
-
|
|
108809
|
-
|
|
108810
|
-
aminoAcidIndex,
|
|
108811
|
-
sequenceIndex: codonRange.start + i2,
|
|
108812
|
-
codonRange,
|
|
108813
|
-
fullCodon: false
|
|
108814
|
-
});
|
|
108815
|
-
}
|
|
108816
|
-
aminoAcidIndex--;
|
|
108826
|
+
if (!forward) {
|
|
108827
|
+
outputRange = flipRelativeRange(
|
|
108828
|
+
outputRange,
|
|
108829
|
+
{ start: 0, end: sequenceStringLength - 1 },
|
|
108830
|
+
sequenceStringLength
|
|
108831
|
+
);
|
|
108817
108832
|
}
|
|
108833
|
+
return outputRange;
|
|
108834
|
+
});
|
|
108835
|
+
return {
|
|
108836
|
+
sequenceString,
|
|
108837
|
+
translationRange,
|
|
108838
|
+
sequenceStringLength,
|
|
108839
|
+
originalSequenceStringLength,
|
|
108840
|
+
exonRange
|
|
108841
|
+
};
|
|
108842
|
+
}
|
|
108843
|
+
__name(getTranslatedSequenceProperties, "getTranslatedSequenceProperties");
|
|
108844
|
+
function positionInCdsToPositionInMainSequence(index2, forward, translationRange, mainSequenceLength) {
|
|
108845
|
+
let outputRange = translateRange(
|
|
108846
|
+
{ start: index2, end: index2 },
|
|
108847
|
+
translationRange.start,
|
|
108848
|
+
mainSequenceLength
|
|
108849
|
+
);
|
|
108850
|
+
if (!forward) {
|
|
108851
|
+
outputRange = flipRelativeRange(
|
|
108852
|
+
outputRange,
|
|
108853
|
+
translationRange,
|
|
108854
|
+
mainSequenceLength
|
|
108855
|
+
);
|
|
108818
108856
|
}
|
|
108819
|
-
|
|
108857
|
+
return outputRange.start;
|
|
108858
|
+
}
|
|
108859
|
+
__name(positionInCdsToPositionInMainSequence, "positionInCdsToPositionInMainSequence");
|
|
108860
|
+
function getAminoAcidDataForEachBaseOfDna(originalSequenceString, forward, optionalSubrangeRange, isProteinSequence) {
|
|
108861
|
+
const {
|
|
108862
|
+
sequenceString,
|
|
108863
|
+
translationRange,
|
|
108864
|
+
sequenceStringLength,
|
|
108865
|
+
originalSequenceStringLength,
|
|
108866
|
+
exonRange
|
|
108867
|
+
} = getTranslatedSequenceProperties(
|
|
108868
|
+
originalSequenceString,
|
|
108869
|
+
forward,
|
|
108870
|
+
optionalSubrangeRange,
|
|
108871
|
+
isProteinSequence
|
|
108872
|
+
);
|
|
108873
|
+
const aminoAcidDataForEachBaseOfDNA = [];
|
|
108874
|
+
for (let index2 = 0; index2 < sequenceStringLength; index2 += 3) {
|
|
108820
108875
|
let aminoAcid;
|
|
108876
|
+
const aminoAcidIndex = index2 / 3;
|
|
108877
|
+
let codonPositionsInCDS;
|
|
108878
|
+
let basesRead;
|
|
108821
108879
|
if (isProteinSequence) {
|
|
108822
|
-
|
|
108880
|
+
codonPositionsInCDS = [0, 1, 2].map((i2) => index2 + i2);
|
|
108881
|
+
basesRead = 3;
|
|
108882
|
+
aminoAcid = proteinAlphabet[sequenceString[index2 / 3].toUpperCase()];
|
|
108823
108883
|
} else {
|
|
108824
|
-
|
|
108825
|
-
|
|
108826
|
-
|
|
108827
|
-
|
|
108828
|
-
|
|
108829
|
-
|
|
108830
|
-
|
|
108831
|
-
|
|
108832
|
-
|
|
108833
|
-
|
|
108834
|
-
|
|
108835
|
-
|
|
108836
|
-
|
|
108884
|
+
const {
|
|
108885
|
+
triplet,
|
|
108886
|
+
basesRead: _basesRead,
|
|
108887
|
+
codonPositions
|
|
108888
|
+
} = getNextTriplet(index2, sequenceString, exonRange);
|
|
108889
|
+
basesRead = _basesRead;
|
|
108890
|
+
codonPositionsInCDS = codonPositions;
|
|
108891
|
+
aminoAcid = triplet.length === 3 ? getAminoAcidFromSequenceTriplet(triplet) : getAminoAcidFromSequenceTriplet("xxx");
|
|
108892
|
+
}
|
|
108893
|
+
const absoluteCodonPositions = codonPositionsInCDS.map(
|
|
108894
|
+
(i2) => positionInCdsToPositionInMainSequence(
|
|
108895
|
+
i2,
|
|
108896
|
+
forward,
|
|
108897
|
+
translationRange,
|
|
108898
|
+
originalSequenceStringLength
|
|
108899
|
+
)
|
|
108837
108900
|
);
|
|
108838
|
-
|
|
108839
|
-
|
|
108840
|
-
|
|
108841
|
-
|
|
108842
|
-
|
|
108843
|
-
|
|
108844
|
-
|
|
108845
|
-
|
|
108846
|
-
|
|
108847
|
-
|
|
108848
|
-
|
|
108849
|
-
|
|
108850
|
-
|
|
108851
|
-
|
|
108852
|
-
|
|
108853
|
-
|
|
108854
|
-
|
|
108855
|
-
|
|
108856
|
-
|
|
108857
|
-
|
|
108858
|
-
|
|
108859
|
-
|
|
108860
|
-
|
|
108861
|
-
|
|
108862
|
-
|
|
108863
|
-
|
|
108864
|
-
|
|
108865
|
-
|
|
108866
|
-
|
|
108867
|
-
|
|
108868
|
-
|
|
108901
|
+
const codonRange = forward ? {
|
|
108902
|
+
start: absoluteCodonPositions[0],
|
|
108903
|
+
end: absoluteCodonPositions[codonPositionsInCDS.length - 1]
|
|
108904
|
+
} : {
|
|
108905
|
+
start: absoluteCodonPositions[codonPositionsInCDS.length - 1],
|
|
108906
|
+
end: absoluteCodonPositions[0]
|
|
108907
|
+
};
|
|
108908
|
+
let positionInCodon = 0;
|
|
108909
|
+
for (let i2 = 0; i2 < basesRead; i2++) {
|
|
108910
|
+
const posInCds = i2 + index2;
|
|
108911
|
+
if (codonPositionsInCDS.includes(posInCds)) {
|
|
108912
|
+
aminoAcidDataForEachBaseOfDNA.push({
|
|
108913
|
+
aminoAcid,
|
|
108914
|
+
positionInCodon,
|
|
108915
|
+
aminoAcidIndex,
|
|
108916
|
+
sequenceIndex: absoluteCodonPositions[i2],
|
|
108917
|
+
codonRange,
|
|
108918
|
+
fullCodon: codonPositionsInCDS.length === 3
|
|
108919
|
+
});
|
|
108920
|
+
positionInCodon++;
|
|
108921
|
+
} else {
|
|
108922
|
+
aminoAcidDataForEachBaseOfDNA.push({
|
|
108923
|
+
aminoAcid: null,
|
|
108924
|
+
positionInCodon: null,
|
|
108925
|
+
aminoAcidIndex: null,
|
|
108926
|
+
sequenceIndex: positionInCdsToPositionInMainSequence(
|
|
108927
|
+
posInCds,
|
|
108928
|
+
forward,
|
|
108929
|
+
translationRange,
|
|
108930
|
+
originalSequenceStringLength
|
|
108931
|
+
),
|
|
108932
|
+
codonRange: null,
|
|
108933
|
+
fullCodon: null
|
|
108934
|
+
});
|
|
108935
|
+
}
|
|
108869
108936
|
}
|
|
108870
|
-
|
|
108871
|
-
const lengthOfEndBpsNotCoveredByAminoAcids = sequenceStringLength - aminoAcidDataForEachBaseOfDNA.length;
|
|
108872
|
-
codonRange = translateRange(
|
|
108873
|
-
{
|
|
108874
|
-
start: sequenceStringLength - lengthOfEndBpsNotCoveredByAminoAcids,
|
|
108875
|
-
end: sequenceStringLength - 1
|
|
108876
|
-
},
|
|
108877
|
-
startOffset,
|
|
108878
|
-
originalSequenceStringLength
|
|
108879
|
-
);
|
|
108880
|
-
for (let j2 = 0; j2 < lengthOfEndBpsNotCoveredByAminoAcids; j2++) {
|
|
108881
|
-
aminoAcidDataForEachBaseOfDNA.push({
|
|
108882
|
-
aminoAcid: getAminoAcidFromSequenceTriplet("xxx"),
|
|
108883
|
-
//fake xxx triplet returns the gap amino acid
|
|
108884
|
-
positionInCodon: j2,
|
|
108885
|
-
aminoAcidIndex,
|
|
108886
|
-
sequenceIndex: codonRange.start + j2,
|
|
108887
|
-
fullCodon: false,
|
|
108888
|
-
codonRange
|
|
108889
|
-
});
|
|
108937
|
+
index2 += basesRead - codonPositionsInCDS.length;
|
|
108890
108938
|
}
|
|
108891
108939
|
if (sequenceStringLength !== aminoAcidDataForEachBaseOfDNA.length) {
|
|
108892
108940
|
throw new Error("something went wrong!");
|
|
108893
108941
|
}
|
|
108942
|
+
if (!forward) {
|
|
108943
|
+
aminoAcidDataForEachBaseOfDNA.reverse();
|
|
108944
|
+
}
|
|
108894
108945
|
return aminoAcidDataForEachBaseOfDNA;
|
|
108895
108946
|
}
|
|
108896
108947
|
__name(getAminoAcidDataForEachBaseOfDna, "getAminoAcidDataForEachBaseOfDna");
|
|
@@ -120290,7 +120341,7 @@ ${latestSubscriptionCallbackError.current.stack}
|
|
|
120290
120341
|
const xmlNode = xmlNode$1;
|
|
120291
120342
|
const readDocType = DocTypeReader;
|
|
120292
120343
|
const toNumber = strnum;
|
|
120293
|
-
let OrderedObjParser$1 = (
|
|
120344
|
+
let OrderedObjParser$1 = (_u = class {
|
|
120294
120345
|
constructor(options) {
|
|
120295
120346
|
this.options = options;
|
|
120296
120347
|
this.currentNode = null;
|
|
@@ -120329,7 +120380,7 @@ ${latestSubscriptionCallbackError.current.stack}
|
|
|
120329
120380
|
this.saveTextToParentTag = saveTextToParentTag;
|
|
120330
120381
|
this.addChild = addChild;
|
|
120331
120382
|
}
|
|
120332
|
-
}, __name(
|
|
120383
|
+
}, __name(_u, "OrderedObjParser"), _u);
|
|
120333
120384
|
function addExternalEntities(externalEntities) {
|
|
120334
120385
|
const entKeys = Object.keys(externalEntities);
|
|
120335
120386
|
for (let i2 = 0; i2 < entKeys.length; i2++) {
|
|
@@ -120885,7 +120936,7 @@ ${latestSubscriptionCallbackError.current.stack}
|
|
|
120885
120936
|
const OrderedObjParser = OrderedObjParser_1;
|
|
120886
120937
|
const { prettify } = node2json;
|
|
120887
120938
|
const validator$1 = validator$2;
|
|
120888
|
-
let XMLParser$1 = (
|
|
120939
|
+
let XMLParser$1 = (_v = class {
|
|
120889
120940
|
constructor(options) {
|
|
120890
120941
|
this.externalEntities = {};
|
|
120891
120942
|
this.options = buildOptions(options);
|
|
@@ -120935,7 +120986,7 @@ ${latestSubscriptionCallbackError.current.stack}
|
|
|
120935
120986
|
this.externalEntities[key2] = value;
|
|
120936
120987
|
}
|
|
120937
120988
|
}
|
|
120938
|
-
}, __name(
|
|
120989
|
+
}, __name(_v, "XMLParser"), _v);
|
|
120939
120990
|
var XMLParser_1 = XMLParser$1;
|
|
120940
120991
|
const EOL = "\n";
|
|
120941
120992
|
function toXml(jArray, options) {
|
|
@@ -128756,7 +128807,7 @@ ${seq.sequence}
|
|
|
128756
128807
|
};
|
|
128757
128808
|
__name(_FASTAParser, "FASTAParser");
|
|
128758
128809
|
let FASTAParser = _FASTAParser;
|
|
128759
|
-
let Parser$1 = (
|
|
128810
|
+
let Parser$1 = (_w = class {
|
|
128760
128811
|
constructor(args) {
|
|
128761
128812
|
this.fastaParser = void 0;
|
|
128762
128813
|
this.eof = false;
|
|
@@ -128980,7 +129031,7 @@ ${seq.sequence}
|
|
|
128980
129031
|
}
|
|
128981
129032
|
});
|
|
128982
129033
|
}
|
|
128983
|
-
}, __name(
|
|
129034
|
+
}, __name(_w, "Parser"), _w);
|
|
128984
129035
|
function _callback(callback2) {
|
|
128985
129036
|
if (process && process.nextTick)
|
|
128986
129037
|
process.nextTick(callback2);
|
|
@@ -147915,7 +147966,7 @@ double click --> edit`}`;
|
|
|
147915
147966
|
fill: color2 || "gray"
|
|
147916
147967
|
}
|
|
147917
147968
|
)),
|
|
147918
|
-
!isFiller && /* @__PURE__ */ React$2.createElement(
|
|
147969
|
+
(!isFiller || isTruncatedEnd && isTruncatedStart) && /* @__PURE__ */ React$2.createElement(
|
|
147919
147970
|
"text",
|
|
147920
147971
|
{
|
|
147921
147972
|
fontSize: 25,
|
|
@@ -147992,18 +148043,39 @@ double click --> edit`}`;
|
|
|
147992
148043
|
subrangeStartRelativeToAnnotationStart,
|
|
147993
148044
|
aminoAcids
|
|
147994
148045
|
);
|
|
148046
|
+
let prevAaSliver;
|
|
148047
|
+
let nextAaSliver = aminoAcidsForSubrange[1];
|
|
148048
|
+
const lastIndex = aminoAcidsForSubrange.length - 1;
|
|
147995
148049
|
const translationSVG = aminoAcidsForSubrange.map(
|
|
147996
148050
|
function(aminoAcidSliver, index2) {
|
|
147997
|
-
|
|
147998
|
-
|
|
147999
|
-
|
|
148051
|
+
if (aminoAcidSliver.positionInCodon === null) {
|
|
148052
|
+
prevAaSliver = aminoAcidSliver;
|
|
148053
|
+
nextAaSliver = aminoAcidsForSubrange[index2 + 2];
|
|
148054
|
+
return /* @__PURE__ */ React$2.createElement(
|
|
148055
|
+
"rect",
|
|
148056
|
+
{
|
|
148057
|
+
x: index2 * charWidth2,
|
|
148058
|
+
y: height2 / 2 - height2 / 16,
|
|
148059
|
+
width: charWidth2,
|
|
148060
|
+
height: height2 / 8,
|
|
148061
|
+
fill: "grey",
|
|
148062
|
+
stroke: "black",
|
|
148063
|
+
strokeWidth: 1
|
|
148064
|
+
}
|
|
148065
|
+
);
|
|
148066
|
+
}
|
|
148067
|
+
const isEndFiller = (index2 === 0 || (prevAaSliver == null ? void 0 : prevAaSliver.positionInCodon) === null) && aminoAcidSliver.positionInCodon === (annotation.forward ? 2 : 0);
|
|
148068
|
+
const isStartFiller = (index2 === lastIndex || (nextAaSliver == null ? void 0 : nextAaSliver.positionInCodon) === null) && aminoAcidSliver.positionInCodon === (annotation.forward ? 0 : 2);
|
|
148069
|
+
let isTruncatedEnd = (index2 === 0 || (prevAaSliver == null ? void 0 : prevAaSliver.positionInCodon) === null) && aminoAcidSliver.positionInCodon === 1;
|
|
148070
|
+
let isTruncatedStart = (index2 === lastIndex || (nextAaSliver == null ? void 0 : nextAaSliver.positionInCodon) === null) && aminoAcidSliver.positionInCodon === 1;
|
|
148000
148071
|
if (!annotation.forward) {
|
|
148001
148072
|
const holder = isTruncatedEnd;
|
|
148002
148073
|
isTruncatedEnd = isTruncatedStart;
|
|
148003
148074
|
isTruncatedStart = holder;
|
|
148004
148075
|
}
|
|
148005
|
-
const isStartFiller = index2 === aminoAcidsForSubrange.length - 1 && aminoAcidSliver.positionInCodon === (annotation.forward ? 0 : 2);
|
|
148006
148076
|
if (aminoAcidSliver.positionInCodon !== 1 && !isStartFiller && !isEndFiller) {
|
|
148077
|
+
prevAaSliver = aminoAcidSliver;
|
|
148078
|
+
nextAaSliver = aminoAcidsForSubrange[index2 + 2];
|
|
148007
148079
|
return null;
|
|
148008
148080
|
}
|
|
148009
148081
|
const { gapsInside, gapsBefore } = getGaps(aminoAcidSliver.codonRange);
|
|
@@ -148020,10 +148092,12 @@ double click --> edit`}`;
|
|
|
148020
148092
|
} else {
|
|
148021
148093
|
color2 = aminoAcid.color;
|
|
148022
148094
|
}
|
|
148095
|
+
prevAaSliver = aminoAcidSliver;
|
|
148096
|
+
nextAaSliver = aminoAcidsForSubrange[index2 + 2];
|
|
148023
148097
|
return /* @__PURE__ */ React$2.createElement(
|
|
148024
148098
|
AASliver$1,
|
|
148025
148099
|
{
|
|
148026
|
-
isFiller: isEndFiller || isStartFiller,
|
|
148100
|
+
isFiller: isEndFiller || isStartFiller || isTruncatedEnd && isTruncatedStart,
|
|
148027
148101
|
isTruncatedEnd,
|
|
148028
148102
|
isTruncatedStart,
|
|
148029
148103
|
onClick: function(event) {
|
|
@@ -148254,7 +148328,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
|
|
|
148254
148328
|
"editorName"
|
|
148255
148329
|
])(Labels$1);
|
|
148256
148330
|
const DrawLabel = withHover(
|
|
148257
|
-
(
|
|
148331
|
+
(_x = class extends React$2.Component {
|
|
148258
148332
|
render() {
|
|
148259
148333
|
const {
|
|
148260
148334
|
hovered,
|
|
@@ -148358,7 +148432,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
|
|
|
148358
148432
|
}
|
|
148359
148433
|
));
|
|
148360
148434
|
}
|
|
148361
|
-
}, __name(
|
|
148435
|
+
}, __name(_x, "DrawLabelInner"), _x)
|
|
148362
148436
|
);
|
|
148363
148437
|
const labelClassNames = {
|
|
148364
148438
|
cutsites: "veCutsiteLabel",
|
|
@@ -150235,7 +150309,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
|
|
|
150235
150309
|
}
|
|
150236
150310
|
__name(showFileDialog, "showFileDialog");
|
|
150237
150311
|
const name = "@teselagen/ove";
|
|
150238
|
-
const version = "0.5.
|
|
150312
|
+
const version = "0.5.13";
|
|
150239
150313
|
const main = "./src/index.js";
|
|
150240
150314
|
const type = "module";
|
|
150241
150315
|
const exports$1 = {
|
|
@@ -150315,8 +150389,8 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
|
|
|
150315
150389
|
cutsites: 100
|
|
150316
150390
|
}
|
|
150317
150391
|
}), "useAnnotationLimits");
|
|
150318
|
-
function LimitAnnotations(
|
|
150319
|
-
var
|
|
150392
|
+
function LimitAnnotations(_y) {
|
|
150393
|
+
var _z = _y, { type: type2 } = _z, rest = __objRest(_z, ["type"]);
|
|
150320
150394
|
const [limits = {}, setLimits] = useAnnotationLimits();
|
|
150321
150395
|
return /* @__PURE__ */ React$2.createElement(MenuItem, __spreadValues({ icon: "blank", shouldDismissPopover: false }, rest), [50, 100, 200, 400].map((n2) => /* @__PURE__ */ React$2.createElement(
|
|
150322
150396
|
MenuItem,
|
|
@@ -156618,7 +156692,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
|
|
|
156618
156692
|
__name(_Minimap, "Minimap");
|
|
156619
156693
|
let Minimap = _Minimap;
|
|
156620
156694
|
const YellowScrollHandle = view(
|
|
156621
|
-
(
|
|
156695
|
+
(_A = class extends React$2.Component {
|
|
156622
156696
|
render() {
|
|
156623
156697
|
const {
|
|
156624
156698
|
scrollHandleWidth,
|
|
@@ -156773,7 +156847,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
|
|
|
156773
156847
|
)
|
|
156774
156848
|
);
|
|
156775
156849
|
}
|
|
156776
|
-
}, __name(
|
|
156850
|
+
}, __name(_A, "YellowScrollHandleInner"), _A)
|
|
156777
156851
|
);
|
|
156778
156852
|
function getTrimmedRangesToDisplay({ trimmedRange, seqLen }) {
|
|
156779
156853
|
if (!trimmedRange)
|
|
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}, rest);
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}
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__name(getRangeAnglesSpecial, "getRangeAnglesSpecial");
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function PositionAnnotationOnCircle(
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var
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function PositionAnnotationOnCircle(_B) {
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var _C = _B, {
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children,
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height: height2 = 0,
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sAngle = 0,
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eAngle = 0,
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forward = true
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} =
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} = _C, rest = __objRest(_C, [
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"children",
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"height",
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"sAngle",
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}),
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tgFormValues("from", "to")
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)(
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(
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(_D = class extends React$2.Component {
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constructor() {
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super(...arguments);
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__publicField(this, "updateTempHighlight", /* @__PURE__ */ __name(({ isStart, isEnd } = {}) => (val2) => {
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))
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);
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}
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}, __name(
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+
}, __name(_D, "SelectDialog"), _D)
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);
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const normalizeToInt = /* @__PURE__ */ __name((val2) => {
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const int2 = Math.round(val2);
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return track2;
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}
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__name(getTrackFromEvent, "getTrackFromEvent");
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const PerformantSelectionLayer = view((
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var
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const PerformantSelectionLayer = view((_E) => {
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var _F = _E, { easyStore: easyStore2 } = _F, rest = __objRest(_F, ["easyStore"]);
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const seqLen = rest.sequenceLength - 1;
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return /* @__PURE__ */ React$2.createElement(
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SelectionLayer$3,
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})
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)
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)(AlignmentView);
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const PerformantCaret = view((
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var
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const PerformantCaret = view((_G) => {
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var _H = _G, { easyStore: easyStore2 } = _H, rest = __objRest(_H, ["easyStore"]);
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return /* @__PURE__ */ React$2.createElement(Caret$2, __spreadValues({ caretPosition: easyStore2.caretPosition }, rest));
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});
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function cleanTracks(alignmentTracks) {
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}, toolbarItemProps))
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);
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function CutsiteToolDropDown(
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var
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function CutsiteToolDropDown(_I) {
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var _J = _I, {
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editorName,
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toggleDropdown,
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annotationVisibilityShow: annotationVisibilityShow2,
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withDigestTool,
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createNewDigest: createNewDigest2
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} =
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} = _J, rest = __objRest(_J, [
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});
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const OrfToolDropdown = withEditorProps(
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(
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+
(_K = class extends React$2.Component {
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constructor(props) {
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this.commands = getCommands(this);
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}, __name(
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}, __name(_K, "OrfDropdown"), _K)
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);
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const opts = [
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{ label: "DNA", value: "DNA" },
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return /* @__PURE__ */ React$2.createElement(Provider, { store }, /* @__PURE__ */ React$2.createElement(VersionHistoryView$1, __spreadValues({}, __spreadValues({}, props))));
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}
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__name(StandaloneVersionHistoryView, "StandaloneVersionHistoryView");
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function createVectorEditor(_node,
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var
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function createVectorEditor(_node, _L = {}) {
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var _M = _L, { editorName = "StandaloneEditor" } = _M, rest = __objRest(_M, ["editorName"]);
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if (!store) {
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}
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return editor;
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function createVersionHistoryView(node2,
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var
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function createVersionHistoryView(node2, _N = {}) {
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var _O = _N, { editorName = "StandaloneVersionHistoryView" } = _O, rest = __objRest(_O, ["editorName"]);
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}
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var renderElement = /* @__PURE__ */ __name(function(element2, opts2) {
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var ownerDocument, defaultView, resourceOptions, contextOptions, windowOptions, windowBounds, context, foreignObjectRendering, cloneOptions, documentCloner, clonedElement, container, _a2, width, height2, left2, top2, backgroundColor2, renderOptions, canvas, renderer, root2, renderer;
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var _b2, _c2, _d2, _e, _f, _g, _h, _j, _k, _l, _m, _o, _p,
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var _b2, _c2, _d2, _e, _f, _g, _h, _j, _k, _l, _m, _o, _p, _q, _r, _s2, _t2;
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return __generator(this, function(_u2) {
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switch (_u2.label) {
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case 0:
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scale: (_o = (_m = opts2.scale) !== null && _m !== void 0 ? _m : defaultView.devicePixelRatio) !== null && _o !== void 0 ? _o : 1,
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x: ((_p = opts2.x) !== null && _p !== void 0 ? _p : 0) + left2,
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y: ((
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width: (
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y: ((_q = opts2.y) !== null && _q !== void 0 ? _q : 0) + top2,
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width: (_r = opts2.width) !== null && _r !== void 0 ? _r : Math.ceil(width),
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height: (_s2 = opts2.height) !== null && _s2 !== void 0 ? _s2 : Math.ceil(height2)
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};
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if (!foreignObjectRendering)
|