@teselagen/ove 0.3.11 → 0.3.12
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/index.js +362 -209
- package/index.mjs +362 -209
- package/index.umd.js +339 -232
- package/package.json +1 -1
- package/src/AlignmentView/AlignmentVisibilityTool.js +1 -1
- package/src/AlignmentView/EditTrackNameDialog.js +1 -5
- package/src/AlignmentView/HorizontalPanelDragHandle.js +2 -2
- package/src/AlignmentView/Minimap.js +12 -12
- package/src/AlignmentView/PairwiseAlignmentView.js +1 -1
- package/src/AlignmentView/getGapMap.js +1 -1
- package/src/AlignmentView/getTrackFromEvent.js +1 -1
- package/src/AlignmentView/index.js +32 -37
- package/src/AutoAnnotate.js +48 -48
- package/src/CircularView/Cutsites.js +3 -3
- package/src/CircularView/Labels/index.js +7 -7
- package/src/CircularView/Labels/relaxLabels_DEPRECATED.js +5 -5
- package/src/CircularView/RotateCircularViewSlider.js +1 -1
- package/src/CircularView/SelectionLayer.js +2 -2
- package/src/CircularView/drawAnnotations.js +3 -3
- package/src/CircularView/getAngleForPositionMidpoint.js +1 -1
- package/src/CircularView/index.d.ts +11 -11
- package/src/CircularView/index.js +9 -9
- package/src/CreateAnnotationsPage.js +7 -5
- package/src/CreateCustomEnzyme/index.js +1 -5
- package/src/CutsiteFilter/AdditionalCutsiteInfoDialog.js +11 -11
- package/src/CutsiteFilter/index.js +12 -12
- package/src/DigestTool/AddLaddersDialog.js +1 -1
- package/src/DigestTool/DigestTool.js +3 -3
- package/src/DigestTool/Ladder.js +8 -8
- package/src/DigestTool/ladderDefaults.js +1 -2
- package/src/Editor/CommandHotkeyHandler.js +1 -1
- package/src/Editor/DropHandler.js +2 -2
- package/src/Editor/index.js +14 -14
- package/src/Editor/userDefinedHandlersAndOpts.js +2 -0
- package/src/FindBar/index.js +6 -6
- package/src/GlobalDialogUtils.js +6 -0
- package/src/LinearView/ZoomLinearView.js +1 -1
- package/src/LinearView/index.js +7 -7
- package/src/MenuBar/index.js +1 -1
- package/src/MenuBar/viewSubmenu.js +1 -1
- package/src/PCRTool/PCRTool.js +19 -19
- package/src/Reflex/Browser.js +4 -5
- package/src/Reflex/ReflexContainer.js +3 -3
- package/src/Reflex/ReflexElement.js +2 -2
- package/src/RowItem/Axis.js +1 -1
- package/src/RowItem/Caret/index.js +1 -1
- package/src/RowItem/Chromatograms/Chromatogram.js +3 -3
- package/src/RowItem/CutsiteSelectionLayers.js +1 -1
- package/src/RowItem/Cutsites.js +1 -1
- package/src/RowItem/Labels.js +2 -2
- package/src/RowItem/Orfs.js +2 -2
- package/src/RowItem/Sequence.js +4 -4
- package/src/RowItem/StackedAnnotations/PointedAnnotation.js +3 -3
- package/src/RowItem/StackedAnnotations/getStructuredBases.js +1 -1
- package/src/RowItem/Translations/AASliver.js +71 -75
- package/src/RowItem/Translations/index.js +1 -1
- package/src/RowItem/getCutsiteLabelHeights.js +1 -1
- package/src/RowItem/index.js +14 -8
- package/src/RowView/estimateRowHeight.js +5 -5
- package/src/RowView/index.d.ts +7 -7
- package/src/RowView/index.js +11 -12
- package/src/SimpleCircularOrLinearView.js +6 -6
- package/src/StatusBar/MeltingTemp.js +3 -3
- package/src/ToolBar/ToolbarItem.js +2 -2
- package/src/ToolBar/alignmentTool.js +9 -9
- package/src/ToolBar/editTool.js +1 -1
- package/src/ToolBar/findTool.js +2 -2
- package/src/ToolBar/importTool.js +1 -1
- package/src/ToolBar/index.js +2 -2
- package/src/ToolBar/oligoTool.js +1 -1
- package/src/ToolBar/orfTool.js +1 -6
- package/src/ToolBar/printTool.js +2 -2
- package/src/ToolBar/visibilityTool.js +1 -1
- package/src/VersionHistoryView/index.js +2 -2
- package/src/commands/index.js +236 -230
- package/src/createVectorEditor/index.js +4 -4
- package/src/fileUtils.js +18 -18
- package/src/helperComponents/AddOrEditAnnotationDialog/index.js +22 -15
- package/src/helperComponents/AddOrEditFeatureDialog/index.js +2 -2
- package/src/helperComponents/AddOrEditPartDialog/index.js +2 -2
- package/src/helperComponents/AddOrEditPrimerDialog/index.js +5 -5
- package/src/helperComponents/EnzymesDialog/index.js +17 -22
- package/src/helperComponents/GoToDialog.js +5 -1
- package/src/helperComponents/MergeFeaturesDialog/index.js +3 -3
- package/src/helperComponents/PinchHelper/PinchHelper.js +1 -1
- package/src/helperComponents/PrintDialog/index.js +4 -4
- package/src/helperComponents/PropertiesDialog/CutsiteProperties.js +3 -3
- package/src/helperComponents/PropertiesDialog/GenbankView.js +1 -1
- package/src/helperComponents/PropertiesDialog/GeneralProperties.js +5 -5
- package/src/helperComponents/PropertiesDialog/GenericAnnotationProperties.js +136 -138
- package/src/helperComponents/PropertiesDialog/OrfProperties.js +3 -3
- package/src/helperComponents/PropertiesDialog/PrimerProperties.js +1 -1
- package/src/helperComponents/PropertiesDialog/TranslationProperties.js +2 -2
- package/src/helperComponents/PropertiesDialog/index.js +3 -3
- package/src/helperComponents/RemoveDuplicates/index.js +3 -3
- package/src/helperComponents/SelectDialog.js +3 -3
- package/src/helperComponents/UncontrolledSliderWithPlusMinusBtns.js +5 -5
- package/src/helperComponents/createSimpleDialog.js +1 -1
- package/src/helperComponents/partTagSearch.js +2 -5
- package/src/helperComponents/withHover.js +3 -3
- package/src/redux/alignments.js +6 -6
- package/src/redux/annotationVisibility.js +4 -4
- package/src/redux/featureLengthsToHide.js +1 -1
- package/src/redux/frameTranslations.js +3 -3
- package/src/redux/middleware.js +2 -2
- package/src/redux/panelsShown.js +19 -19
- package/src/redux/partLengthsToHide.js +1 -1
- package/src/redux/primerLengthsToHide.js +1 -1
- package/src/redux/readOnly.js +1 -4
- package/src/redux/selectionLayer.js +1 -1
- package/src/redux/sequenceData/features.js +1 -1
- package/src/redux/sequenceData/upsertDeleteActionGenerator.js +1 -1
- package/src/redux/sequenceDataHistory.js +5 -5
- package/src/redux/toolBar.js +2 -4
- package/src/redux/utils/createMetaAction.js +2 -2
- package/src/redux/versionHistory.js +1 -2
- package/src/selectors/annotationSearchSelector.js +4 -4
- package/src/selectors/circularSelector.js +1 -1
- package/src/selectors/cutsiteLabelColorSelector.js +1 -1
- package/src/selectors/filteredCutsitesSelector.js +6 -6
- package/src/selectors/filteredFeaturesSelector.js +4 -4
- package/src/selectors/filteredPartsSelector.js +5 -5
- package/src/selectors/filteredPrimersSelector.js +3 -3
- package/src/selectors/isEnzymeFilterAndSelector.js +1 -1
- package/src/selectors/orfsSelector.js +1 -1
- package/src/selectors/restrictionEnzymesSelector.js +2 -2
- package/src/selectors/searchLayersSelector.js +7 -7
- package/src/selectors/sequenceLengthSelector.js +1 -1
- package/src/selectors/sequenceSelector.js +1 -1
- package/src/selectors/tagsToBoldSelector.js +1 -1
- package/src/selectors/translationsSelector.js +7 -7
- package/src/updateEditor.js +1 -1
- package/src/utils/PassThrough.js +1 -1
- package/src/utils/addWrappedAddons.js +1 -1
- package/src/utils/annotationTypes.js +2 -2
- package/src/utils/combineReducersDontIgnoreKeys.js +1 -1
- package/src/utils/editorUtils.js +2 -2
- package/src/utils/massageTickSpacing.js +1 -1
- package/src/utils/onlyUpdateForKeysDeep.js +1 -1
- package/src/utils/pureNoFunc.js +1 -1
- package/src/utils/shouldRerender.js +1 -1
- package/src/utils/showFileDialog.js +6 -7
- package/src/utils/updateLabelsForInViewFeatures.js +1 -1
- package/src/utils/useAnnotationLimits.js +1 -1
- package/src/withEditorInteractions/Keyboard.js +2 -3
- package/src/withEditorInteractions/createSequenceInputPopup.js +4 -4
- package/src/withEditorInteractions/index.js +93 -55
- package/src/withEditorProps/index.js +40 -37
package/index.umd.js
CHANGED
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@@ -23998,7 +23998,7 @@
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var ownKeys$9 = typeof Reflect !== "undefined" && Reflect.ownKeys ? Reflect.ownKeys : hasGetOwnPropertySymbols ? function (obj) {
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return Object.getOwnPropertyNames(obj).concat(Object.getOwnPropertySymbols(obj));
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} : /* istanbul ignore next */Object.getOwnPropertyNames;
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function toPrimitive$
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function toPrimitive$3(value) {
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return value === null ? null : typeof value === "object" ? "" + value : value;
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}
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function hasProp(target, prop) {
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@@ -24927,7 +24927,7 @@
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return this.name_ + "[" + this.value_ + "]";
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};
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_proto.valueOf = function valueOf() {
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return toPrimitive$
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return toPrimitive$3(this.get());
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};
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_proto[_Symbol$toPrimitive] = function () {
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return this.valueOf();
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return this.name_ + "[" + this.derivation.toString() + "]";
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};
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_proto.valueOf = function valueOf() {
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return toPrimitive$
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return toPrimitive$3(this.get());
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};
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_proto[_Symbol$toPrimitive$1] = function () {
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return this.valueOf();
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}
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};
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var
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if (hasRequired_descriptors) return _descriptors;
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hasRequired_descriptors = 1;
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// Thank's IE8 for his funny defineProperty
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_descriptors = !_fails(function () {
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return Object.defineProperty({}, 'a', { get: function () { return 7; } }).a != 7;
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});
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return _descriptors;
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}
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// Thank's IE8 for his funny defineProperty
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var _descriptors = !_fails(function () {
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return Object.defineProperty({}, 'a', { get: function () { return 7; } }).a != 7;
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});
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var _domCreate;
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var hasRequired_domCreate;
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return _domCreate;
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}
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var _ie8DomDefine
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function require_ie8DomDefine () {
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if (hasRequired_ie8DomDefine) 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 () { return 7; } }).a != 7;
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});
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return _ie8DomDefine;
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}
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var _ie8DomDefine = !_descriptors && !_fails(function () {
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return Object.defineProperty(require_domCreate()('div'), 'a', { get: function () { return 7; } }).a != 7;
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});
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// 7.1.1 ToPrimitive(input [, PreferredType])
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var isObject$6 = _isObject;
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throw TypeError("Can't convert object to primitive value");
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};
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var anObject = _anObject;
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var IE8_DOM_DEFINE = require_ie8DomDefine();
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var toPrimitive = _toPrimitive$1;
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var dP = Object.defineProperty;
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var anObject$5 = _anObject;
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var IE8_DOM_DEFINE$1 = _ie8DomDefine;
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var toPrimitive$2 = _toPrimitive$1;
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var dP$3 = Object.defineProperty;
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return _objectDp;
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}
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_objectDp.f = _descriptors ? Object.defineProperty : function defineProperty(O, P, Attributes) {
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anObject$5(O);
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P = toPrimitive$2(P, true);
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anObject$5(Attributes);
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if (IE8_DOM_DEFINE$1) try {
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return dP$3(O, P, Attributes);
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} catch (e) { /* empty */ }
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if ('get' in Attributes || 'set' in Attributes) throw TypeError('Accessors not supported!');
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if ('value' in Attributes) O[P] = Attributes.value;
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return O;
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};
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};
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};
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var createDesc$3 = _propertyDesc;
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return dP$2.f(object, key, createDesc$3(1, value));
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} : function (object, key, value) {
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object[key] = value;
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var DESCRIPTORS =
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var DESCRIPTORS = _descriptors;
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var _redefine = _hide;
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var dP$1 =
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var _wksExports = _wks.exports;
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$export$3($export$3.S + $export$3.F * !
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$export$3($export$3.S + $export$3.F * !_descriptors, 'Object', { defineProperty: _objectDp.f });
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if (name.charAt(0) != '_' && !(name in $Symbol)) defineProperty$4($Symbol, name, { value: wksExt$1.f(name) });
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58102
|
var toIObject$1 = _toIobject;
|
|
58126
58103
|
var toPrimitive$1 = _toPrimitive$1;
|
|
58127
58104
|
var has$8 = _has;
|
|
58128
|
-
var IE8_DOM_DEFINE =
|
|
58105
|
+
var IE8_DOM_DEFINE = _ie8DomDefine;
|
|
58129
58106
|
var gOPD$2 = Object.getOwnPropertyDescriptor;
|
|
58130
58107
|
|
|
58131
|
-
_objectGopd.f =
|
|
58108
|
+
_objectGopd.f = _descriptors ? gOPD$2 : function getOwnPropertyDescriptor(O, P) {
|
|
58132
58109
|
O = toIObject$1(O);
|
|
58133
58110
|
P = toPrimitive$1(P, true);
|
|
58134
58111
|
if (IE8_DOM_DEFINE) try {
|
|
@@ -58140,7 +58117,7 @@
|
|
|
58140
58117
|
// ECMAScript 6 symbols shim
|
|
58141
58118
|
var global$1 = _globalExports;
|
|
58142
58119
|
var has$7 = _has;
|
|
58143
|
-
var DESCRIPTORS =
|
|
58120
|
+
var DESCRIPTORS = _descriptors;
|
|
58144
58121
|
var $export$2 = _export;
|
|
58145
58122
|
var redefine = _redefine;
|
|
58146
58123
|
var META = _metaExports.KEY;
|
|
@@ -58163,7 +58140,7 @@
|
|
|
58163
58140
|
var gOPNExt = _objectGopnExt;
|
|
58164
58141
|
var $GOPD = _objectGopd;
|
|
58165
58142
|
var $GOPS = _objectGops;
|
|
58166
|
-
var $DP =
|
|
58143
|
+
var $DP = _objectDp;
|
|
58167
58144
|
var $keys$1 = _objectKeys;
|
|
58168
58145
|
var gOPD$1 = $GOPD.f;
|
|
58169
58146
|
var dP = $DP.f;
|
|
@@ -113755,13 +113732,7 @@
|
|
|
113755
113732
|
return {};
|
|
113756
113733
|
}
|
|
113757
113734
|
const mergedOpts = getMergedOpts(topLevelOptions, ownProps);
|
|
113758
|
-
const {
|
|
113759
|
-
formName,
|
|
113760
|
-
urlConnected,
|
|
113761
|
-
history,
|
|
113762
|
-
defaults,
|
|
113763
|
-
onlyOneFilter
|
|
113764
|
-
} = mergedOpts;
|
|
113735
|
+
const { formName, urlConnected, history, defaults, onlyOneFilter } = mergedOpts;
|
|
113765
113736
|
function updateSearch(val) {
|
|
113766
113737
|
setTimeout(function() {
|
|
113767
113738
|
dispatch(change(formName, "reduxFormSearchInput", val || ""));
|
|
@@ -113800,12 +113771,7 @@
|
|
|
113800
113771
|
action(...args, currentParams);
|
|
113801
113772
|
};
|
|
113802
113773
|
});
|
|
113803
|
-
const {
|
|
113804
|
-
variables,
|
|
113805
|
-
selectedEntities,
|
|
113806
|
-
mergedOpts,
|
|
113807
|
-
...restStateProps
|
|
113808
|
-
} = stateProps;
|
|
113774
|
+
const { variables, selectedEntities, mergedOpts, ...restStateProps } = stateProps;
|
|
113809
113775
|
const changeFormValue = (...args) => dispatchProps.dispatch(change(formName, ...args));
|
|
113810
113776
|
const tableParams = {
|
|
113811
113777
|
changeFormValue,
|
|
@@ -117701,7 +117667,9 @@
|
|
|
117701
117667
|
return doNotTriggerClick();
|
|
117702
117668
|
}
|
|
117703
117669
|
const parentEl = r.current?.closest(".bp3-dialog-container");
|
|
117704
|
-
const dialogs = document.querySelectorAll(
|
|
117670
|
+
const dialogs = document.querySelectorAll(
|
|
117671
|
+
".bp3-dialog-container"
|
|
117672
|
+
);
|
|
117705
117673
|
const numDialogs = dialogs?.length;
|
|
117706
117674
|
if (numDialogs > 1) {
|
|
117707
117675
|
const topMostDialog = dialogs[numDialogs - 1];
|
|
@@ -118040,6 +118008,7 @@
|
|
|
118040
118008
|
marginBottom: 10,
|
|
118041
118009
|
marginLeft: 20,
|
|
118042
118010
|
fontSize: 10
|
|
118011
|
+
/* color: Colors.RED1 */
|
|
118043
118012
|
}
|
|
118044
118013
|
},
|
|
118045
118014
|
userMatchedHeader && [
|
|
@@ -120028,10 +119997,7 @@
|
|
|
120028
119997
|
if (props.filesWIssues.length > 0) {
|
|
120029
119998
|
const reduxFormEntitiesArray = [];
|
|
120030
119999
|
const finishedFiles = props.filesWIssues.map((f, i) => {
|
|
120031
|
-
const {
|
|
120032
|
-
reduxFormEntities,
|
|
120033
|
-
reduxFormCellValidation
|
|
120034
|
-
} = formValueSelector(`editableCellTable-${i}`)(
|
|
120000
|
+
const { reduxFormEntities, reduxFormCellValidation } = formValueSelector(`editableCellTable-${i}`)(
|
|
120035
120001
|
state,
|
|
120036
120002
|
"reduxFormEntities",
|
|
120037
120003
|
"reduxFormCellValidation"
|
|
@@ -132275,7 +132241,14 @@
|
|
|
132275
132241
|
}
|
|
132276
132242
|
}),
|
|
132277
132243
|
branch(({ navTo }) => navTo, withRouter$1)
|
|
132278
|
-
)(function({
|
|
132244
|
+
)(function({
|
|
132245
|
+
navTo,
|
|
132246
|
+
context,
|
|
132247
|
+
staticContext,
|
|
132248
|
+
didMount,
|
|
132249
|
+
willUnmount,
|
|
132250
|
+
...props
|
|
132251
|
+
}) {
|
|
132279
132252
|
let MenuItemComp = MenuItem;
|
|
132280
132253
|
if (navTo) {
|
|
132281
132254
|
MenuItemComp = MenuItemLink;
|
|
@@ -133333,11 +133306,7 @@
|
|
|
133333
133306
|
return handlers;
|
|
133334
133307
|
}
|
|
133335
133308
|
|
|
133336
|
-
const withCommand = (mappings) => (WrappedComponent) => ({
|
|
133337
|
-
cmd,
|
|
133338
|
-
cmdOptions = {},
|
|
133339
|
-
...props
|
|
133340
|
-
}) => {
|
|
133309
|
+
const withCommand = (mappings) => (WrappedComponent) => ({ cmd, cmdOptions = {}, ...props }) => {
|
|
133341
133310
|
const mappedProps = {};
|
|
133342
133311
|
Object.keys(mappings).forEach((k) => {
|
|
133343
133312
|
mappedProps[k] = mappings[k] === "execute" ? (event) => cmd.execute({ event }) : typeof mappings[k] === "function" ? mappings[k](cmd, props) : cmd[mappings[k]];
|
|
@@ -134484,9 +134453,9 @@
|
|
|
134484
134453
|
}
|
|
134485
134454
|
},
|
|
134486
134455
|
{
|
|
134487
|
-
|
|
134488
|
-
|
|
134489
|
-
|
|
134456
|
+
1: false,
|
|
134457
|
+
2: false,
|
|
134458
|
+
3: false,
|
|
134490
134459
|
"-1": false,
|
|
134491
134460
|
"-2": false,
|
|
134492
134461
|
"-3": false
|
|
@@ -135215,9 +135184,14 @@
|
|
|
135215
135184
|
|
|
135216
135185
|
function checkIfPotentiallyCircularRangesOverlap(range, comparisonRange) {
|
|
135217
135186
|
return splitRangeIntoTwoPartsIfItIsCircular(range, Infinity).some(function(splitRange) {
|
|
135218
|
-
return splitRangeIntoTwoPartsIfItIsCircular(comparisonRange, Infinity).some(
|
|
135219
|
-
|
|
135220
|
-
|
|
135187
|
+
return splitRangeIntoTwoPartsIfItIsCircular(comparisonRange, Infinity).some(
|
|
135188
|
+
function(splitComparisonRange) {
|
|
135189
|
+
return checkIfNonCircularRangesOverlap(
|
|
135190
|
+
splitRange,
|
|
135191
|
+
splitComparisonRange
|
|
135192
|
+
);
|
|
135193
|
+
}
|
|
135194
|
+
);
|
|
135221
135195
|
});
|
|
135222
135196
|
}
|
|
135223
135197
|
|
|
@@ -135227,15 +135201,19 @@
|
|
|
135227
135201
|
return overlaps;
|
|
135228
135202
|
} else if (overlaps.length === 2) {
|
|
135229
135203
|
if (overlaps[0].start === 0 && overlaps[1].end + 1 === sequenceLength && !originalRangeLinear) {
|
|
135230
|
-
return [
|
|
135231
|
-
|
|
135232
|
-
|
|
135233
|
-
|
|
135204
|
+
return [
|
|
135205
|
+
{
|
|
135206
|
+
start: overlaps[1].start,
|
|
135207
|
+
end: overlaps[0].end
|
|
135208
|
+
}
|
|
135209
|
+
];
|
|
135234
135210
|
} else if (overlaps[1].start === 0 && overlaps[0].end + 1 === sequenceLength && !originalRangeLinear) {
|
|
135235
|
-
return [
|
|
135236
|
-
|
|
135237
|
-
|
|
135238
|
-
|
|
135211
|
+
return [
|
|
135212
|
+
{
|
|
135213
|
+
start: overlaps[0].start,
|
|
135214
|
+
end: overlaps[1].end
|
|
135215
|
+
}
|
|
135216
|
+
];
|
|
135239
135217
|
} else {
|
|
135240
135218
|
return overlaps;
|
|
135241
135219
|
}
|
|
@@ -135243,17 +135221,29 @@
|
|
|
135243
135221
|
const firstOverlap = overlaps[0];
|
|
135244
135222
|
const secondOverlap = overlaps[1];
|
|
135245
135223
|
const thirdOverlap = overlaps[2];
|
|
135246
|
-
let collapsedOverlaps = collapseOverlapsGeneratedFromRangeComparisonIfPossible(
|
|
135224
|
+
let collapsedOverlaps = collapseOverlapsGeneratedFromRangeComparisonIfPossible(
|
|
135225
|
+
[firstOverlap, secondOverlap],
|
|
135226
|
+
sequenceLength,
|
|
135227
|
+
optionalOriginalRange
|
|
135228
|
+
);
|
|
135247
135229
|
if (collapsedOverlaps.length === 1) {
|
|
135248
135230
|
collapsedOverlaps.push(thirdOverlap);
|
|
135249
135231
|
return collapsedOverlaps;
|
|
135250
135232
|
} else {
|
|
135251
|
-
collapsedOverlaps = collapseOverlapsGeneratedFromRangeComparisonIfPossible(
|
|
135233
|
+
collapsedOverlaps = collapseOverlapsGeneratedFromRangeComparisonIfPossible(
|
|
135234
|
+
[firstOverlap, thirdOverlap],
|
|
135235
|
+
sequenceLength,
|
|
135236
|
+
optionalOriginalRange
|
|
135237
|
+
);
|
|
135252
135238
|
if (collapsedOverlaps.length === 1) {
|
|
135253
135239
|
collapsedOverlaps.push(secondOverlap);
|
|
135254
135240
|
return collapsedOverlaps;
|
|
135255
135241
|
} else {
|
|
135256
|
-
collapsedOverlaps = collapseOverlapsGeneratedFromRangeComparisonIfPossible(
|
|
135242
|
+
collapsedOverlaps = collapseOverlapsGeneratedFromRangeComparisonIfPossible(
|
|
135243
|
+
[secondOverlap, thirdOverlap],
|
|
135244
|
+
sequenceLength,
|
|
135245
|
+
optionalOriginalRange
|
|
135246
|
+
);
|
|
135257
135247
|
if (collapsedOverlaps.length === 1) {
|
|
135258
135248
|
collapsedOverlaps.push(firstOverlap);
|
|
135259
135249
|
return collapsedOverlaps;
|
|
@@ -135275,11 +135265,18 @@
|
|
|
135275
135265
|
}
|
|
135276
135266
|
|
|
135277
135267
|
function convertRangeTo0Based(range) {
|
|
135278
|
-
return convertRangeIndices(range, {
|
|
135268
|
+
return convertRangeIndices(range, {
|
|
135269
|
+
inclusive1BasedStart: true,
|
|
135270
|
+
inclusive1BasedEnd: true
|
|
135271
|
+
});
|
|
135279
135272
|
}
|
|
135280
135273
|
|
|
135281
135274
|
function convertRangeTo1Based(range) {
|
|
135282
|
-
return convertRangeIndices(
|
|
135275
|
+
return convertRangeIndices(
|
|
135276
|
+
range,
|
|
135277
|
+
{},
|
|
135278
|
+
{ inclusive1BasedStart: true, inclusive1BasedEnd: true }
|
|
135279
|
+
);
|
|
135283
135280
|
}
|
|
135284
135281
|
|
|
135285
135282
|
function provideInclusiveOptions(funToWrap) {
|
|
@@ -135384,7 +135381,11 @@
|
|
|
135384
135381
|
let endMoved = true;
|
|
135385
135382
|
if (range.end >= position) {
|
|
135386
135383
|
if (position + maxLength - range.start > range.end - position) {
|
|
135387
|
-
newRange.end = normalizePositionByRangeLength(
|
|
135384
|
+
newRange.end = normalizePositionByRangeLength(
|
|
135385
|
+
position - 1,
|
|
135386
|
+
maxLength,
|
|
135387
|
+
false
|
|
135388
|
+
);
|
|
135388
135389
|
} else {
|
|
135389
135390
|
newRange.start = position;
|
|
135390
135391
|
endMoved = false;
|
|
@@ -135457,19 +135458,31 @@
|
|
|
135457
135458
|
if (range.start > range.end) {
|
|
135458
135459
|
return expandOrContractCircularRangeToPosition(range, position, maxLength);
|
|
135459
135460
|
} else {
|
|
135460
|
-
return expandOrContractNonCircularRangeToPosition(
|
|
135461
|
+
return expandOrContractNonCircularRangeToPosition(
|
|
135462
|
+
range,
|
|
135463
|
+
position);
|
|
135461
135464
|
}
|
|
135462
135465
|
}
|
|
135463
135466
|
|
|
135464
135467
|
function translateRange(rangeToBeAdjusted, translateBy, rangeLength) {
|
|
135465
135468
|
return lodashExports.assign({}, rangeToBeAdjusted, {
|
|
135466
|
-
start: normalizePositionByRangeLength(
|
|
135467
|
-
|
|
135469
|
+
start: normalizePositionByRangeLength(
|
|
135470
|
+
rangeToBeAdjusted.start + translateBy,
|
|
135471
|
+
rangeLength
|
|
135472
|
+
),
|
|
135473
|
+
end: normalizePositionByRangeLength(
|
|
135474
|
+
rangeToBeAdjusted.end + translateBy,
|
|
135475
|
+
rangeLength
|
|
135476
|
+
)
|
|
135468
135477
|
});
|
|
135469
135478
|
}
|
|
135470
135479
|
|
|
135471
135480
|
function flipRelativeRange(innerRange, outerRange, sequenceLength, options) {
|
|
135472
|
-
const isFullyContained = isRangeWithinRange(
|
|
135481
|
+
const isFullyContained = isRangeWithinRange(
|
|
135482
|
+
innerRange,
|
|
135483
|
+
outerRange,
|
|
135484
|
+
sequenceLength
|
|
135485
|
+
);
|
|
135473
135486
|
if (isFullyContained) {
|
|
135474
135487
|
return flipFullyContainedRange(innerRange, outerRange, sequenceLength);
|
|
135475
135488
|
} else {
|
|
@@ -135477,40 +135490,91 @@
|
|
|
135477
135490
|
}
|
|
135478
135491
|
}
|
|
135479
135492
|
function flipNonFullyContainedRange(innerRange, outerRange, sequenceLength, options) {
|
|
135480
|
-
const outerFullyContained = isRangeWithinRange(
|
|
135493
|
+
const outerFullyContained = isRangeWithinRange(
|
|
135494
|
+
outerRange,
|
|
135495
|
+
innerRange,
|
|
135496
|
+
sequenceLength
|
|
135497
|
+
);
|
|
135481
135498
|
let flippedInnerRange;
|
|
135482
135499
|
if (outerFullyContained) {
|
|
135483
|
-
const expandBy1 = getRangeLength(
|
|
135484
|
-
|
|
135485
|
-
|
|
135486
|
-
|
|
135487
|
-
|
|
135488
|
-
|
|
135489
|
-
|
|
135490
|
-
|
|
135491
|
-
|
|
135492
|
-
|
|
135500
|
+
const expandBy1 = getRangeLength(
|
|
135501
|
+
{
|
|
135502
|
+
start: innerRange.start,
|
|
135503
|
+
end: outerRange.start
|
|
135504
|
+
},
|
|
135505
|
+
sequenceLength
|
|
135506
|
+
) - 1;
|
|
135507
|
+
flippedInnerRange = expandOrContractRangeByLength(
|
|
135508
|
+
outerRange,
|
|
135509
|
+
expandBy1,
|
|
135510
|
+
false,
|
|
135511
|
+
sequenceLength
|
|
135512
|
+
);
|
|
135513
|
+
const expandBy2 = getRangeLength(
|
|
135514
|
+
{
|
|
135515
|
+
end: innerRange.end,
|
|
135516
|
+
start: outerRange.end
|
|
135517
|
+
},
|
|
135518
|
+
sequenceLength
|
|
135519
|
+
) - 1;
|
|
135520
|
+
flippedInnerRange = expandOrContractRangeByLength(
|
|
135521
|
+
flippedInnerRange,
|
|
135522
|
+
expandBy2,
|
|
135523
|
+
true,
|
|
135524
|
+
sequenceLength
|
|
135525
|
+
);
|
|
135493
135526
|
} else {
|
|
135494
|
-
const overlaps = getOverlapsOfPotentiallyCircularRanges(
|
|
135527
|
+
const overlaps = getOverlapsOfPotentiallyCircularRanges(
|
|
135528
|
+
innerRange,
|
|
135529
|
+
outerRange,
|
|
135530
|
+
sequenceLength
|
|
135531
|
+
);
|
|
135495
135532
|
if (overlaps.length >= 1) {
|
|
135496
135533
|
let overlapExtendsForward;
|
|
135497
135534
|
const firstOverlap = overlaps[0];
|
|
135498
135535
|
overlapExtendsForward = firstOverlap.start !== outerRange.start;
|
|
135499
|
-
const flippedTruncatedInner = flipFullyContainedRange(
|
|
135536
|
+
const flippedTruncatedInner = flipFullyContainedRange(
|
|
135537
|
+
firstOverlap,
|
|
135538
|
+
outerRange,
|
|
135539
|
+
sequenceLength
|
|
135540
|
+
);
|
|
135500
135541
|
const lengthToExtend = getRangeLength(innerRange, sequenceLength) - getRangeLength(flippedTruncatedInner, sequenceLength);
|
|
135501
|
-
flippedInnerRange = expandOrContractRangeByLength(
|
|
135542
|
+
flippedInnerRange = expandOrContractRangeByLength(
|
|
135543
|
+
flippedTruncatedInner,
|
|
135544
|
+
lengthToExtend,
|
|
135545
|
+
overlapExtendsForward,
|
|
135546
|
+
sequenceLength
|
|
135547
|
+
);
|
|
135502
135548
|
} else {
|
|
135503
|
-
throw new Error(
|
|
135549
|
+
throw new Error(
|
|
135550
|
+
"This case (relative ranges that do not overlap) is unsupported! "
|
|
135551
|
+
);
|
|
135504
135552
|
}
|
|
135505
135553
|
}
|
|
135506
135554
|
return flippedInnerRange;
|
|
135507
135555
|
}
|
|
135508
135556
|
function flipFullyContainedRange(innerRange, outerRange, sequenceLength, options) {
|
|
135509
135557
|
const translateBy = -outerRange.start;
|
|
135510
|
-
const translatedOuterRange = translateRange(
|
|
135511
|
-
|
|
135512
|
-
|
|
135513
|
-
|
|
135558
|
+
const translatedOuterRange = translateRange(
|
|
135559
|
+
outerRange,
|
|
135560
|
+
translateBy,
|
|
135561
|
+
sequenceLength
|
|
135562
|
+
);
|
|
135563
|
+
const translatedInnerRange = translateRange(
|
|
135564
|
+
innerRange,
|
|
135565
|
+
translateBy,
|
|
135566
|
+
sequenceLength
|
|
135567
|
+
);
|
|
135568
|
+
const translatedFlippedInnerRange = flipNonOriginSpanningContainedRange(
|
|
135569
|
+
translatedInnerRange,
|
|
135570
|
+
translatedOuterRange,
|
|
135571
|
+
sequenceLength
|
|
135572
|
+
);
|
|
135573
|
+
const flippedInnerRange = translateRange(
|
|
135574
|
+
translatedFlippedInnerRange,
|
|
135575
|
+
-translateBy,
|
|
135576
|
+
sequenceLength
|
|
135577
|
+
);
|
|
135514
135578
|
return flippedInnerRange;
|
|
135515
135579
|
}
|
|
135516
135580
|
function flipNonOriginSpanningContainedRange(innerRange, outerRange, sequenceLength) {
|
|
@@ -135682,9 +135746,15 @@
|
|
|
135682
135746
|
}
|
|
135683
135747
|
|
|
135684
135748
|
function zeroSubrangeByContainerRange(subRange, containerRange, sequenceLength) {
|
|
135685
|
-
const trimmedSubRange = trimRangeByAnotherRange(
|
|
135749
|
+
const trimmedSubRange = trimRangeByAnotherRange(
|
|
135750
|
+
subRange,
|
|
135751
|
+
containerRange,
|
|
135752
|
+
sequenceLength
|
|
135753
|
+
);
|
|
135686
135754
|
if (trimmedSubRange) {
|
|
135687
|
-
throw new Error(
|
|
135755
|
+
throw new Error(
|
|
135756
|
+
"subRange must be fully contained by containerRange! Otherwise this function does not make sense"
|
|
135757
|
+
);
|
|
135688
135758
|
}
|
|
135689
135759
|
const newSubrange = {};
|
|
135690
135760
|
newSubrange.start = subRange.start - containerRange.start;
|
|
@@ -135711,12 +135781,24 @@
|
|
|
135711
135781
|
}
|
|
135712
135782
|
|
|
135713
135783
|
function getZeroedRangeOverlaps(annotation, selection, sequenceLength) {
|
|
135714
|
-
const overlaps = collapseOverlapsGeneratedFromRangeComparisonIfPossible(
|
|
135784
|
+
const overlaps = collapseOverlapsGeneratedFromRangeComparisonIfPossible(
|
|
135785
|
+
getOverlapsOfPotentiallyCircularRanges(
|
|
135786
|
+
annotation,
|
|
135787
|
+
selection,
|
|
135788
|
+
sequenceLength
|
|
135789
|
+
),
|
|
135790
|
+
sequenceLength,
|
|
135791
|
+
annotation
|
|
135792
|
+
);
|
|
135715
135793
|
const zeroedOverlaps = overlaps.map((overlap) => {
|
|
135716
|
-
return zeroSubrangeByContainerRange(
|
|
135717
|
-
|
|
135718
|
-
|
|
135719
|
-
|
|
135794
|
+
return zeroSubrangeByContainerRange(
|
|
135795
|
+
overlap,
|
|
135796
|
+
{
|
|
135797
|
+
start: selection.start,
|
|
135798
|
+
end: normalizePositionByRangeLength(selection.start - 1, sequenceLength)
|
|
135799
|
+
},
|
|
135800
|
+
sequenceLength
|
|
135801
|
+
);
|
|
135720
135802
|
});
|
|
135721
135803
|
return zeroedOverlaps;
|
|
135722
135804
|
}
|
|
@@ -142422,7 +142504,7 @@
|
|
|
142422
142504
|
calculateTemperature: function(sequence, type, A, R, C, Na) {
|
|
142423
142505
|
if (typeof type === "undefined") {
|
|
142424
142506
|
type = this.TABLE_BRESLAUER;
|
|
142425
|
-
} else if (type != this.TABLE_BRESLAUER &&
|
|
142507
|
+
} else if (type != this.TABLE_BRESLAUER && type != this.TABLE_UNIFIED && type != this.TABLE_SUGIMOTO) {
|
|
142426
142508
|
throw new Error("Invalid table type!");
|
|
142427
142509
|
}
|
|
142428
142510
|
if (!A) {
|
|
@@ -150681,12 +150763,7 @@
|
|
|
150681
150763
|
return matches;
|
|
150682
150764
|
}
|
|
150683
150765
|
function findSequenceMatchesTopStrand(sequence, searchString, options = {}) {
|
|
150684
|
-
const {
|
|
150685
|
-
isCircular,
|
|
150686
|
-
isAmbiguous,
|
|
150687
|
-
isProteinSequence,
|
|
150688
|
-
isProteinSearch
|
|
150689
|
-
} = options;
|
|
150766
|
+
const { isCircular, isAmbiguous, isProteinSequence, isProteinSearch } = options;
|
|
150690
150767
|
let searchStringToUse = escapeStringRegexp(searchString);
|
|
150691
150768
|
if (isAmbiguous) {
|
|
150692
150769
|
if (isProteinSearch || isProteinSequence) {
|
|
@@ -150768,7 +150845,10 @@
|
|
|
150768
150845
|
|
|
150769
150846
|
function getComplementSequenceString(sequence, isRna) {
|
|
150770
150847
|
let complementSeqString = "";
|
|
150771
|
-
const complementMap = lodashExports.merge(
|
|
150848
|
+
const complementMap = lodashExports.merge(
|
|
150849
|
+
DNAComplementMap,
|
|
150850
|
+
isRna ? { a: "u", A: "U" } : { a: "t", A: "T" }
|
|
150851
|
+
);
|
|
150772
150852
|
for (let i = 0; i < sequence.length; i++) {
|
|
150773
150853
|
let complementChar = complementMap[sequence[i]];
|
|
150774
150854
|
if (!complementChar) {
|
|
@@ -163439,10 +163519,7 @@
|
|
|
163439
163519
|
});
|
|
163440
163520
|
}
|
|
163441
163521
|
});
|
|
163442
|
-
const toRet = lodashExports.filter(
|
|
163443
|
-
resultArray,
|
|
163444
|
-
(r) => r?.parsedSequence?.sequence?.length
|
|
163445
|
-
);
|
|
163522
|
+
const toRet = lodashExports.filter(resultArray, (r) => r?.parsedSequence?.sequence?.length);
|
|
163446
163523
|
if (toRet.length)
|
|
163447
163524
|
return toRet;
|
|
163448
163525
|
return onFileParsed(resultArray);
|
|
@@ -163544,10 +163621,7 @@
|
|
|
163544
163621
|
messages: ["Error while parsing JBEI format"]
|
|
163545
163622
|
});
|
|
163546
163623
|
}
|
|
163547
|
-
const toRet = lodashExports.filter(
|
|
163548
|
-
resultArray,
|
|
163549
|
-
(r) => r?.parsedSequence?.sequence?.length
|
|
163550
|
-
);
|
|
163624
|
+
const toRet = lodashExports.filter(resultArray, (r) => r?.parsedSequence?.sequence?.length);
|
|
163551
163625
|
if (toRet.length)
|
|
163552
163626
|
return toRet;
|
|
163553
163627
|
return onFileParsed(resultArray);
|
|
@@ -166822,10 +166896,7 @@
|
|
|
166822
166896
|
lastSavedIdUpdate
|
|
166823
166897
|
}, Symbol.toStringTag, { value: 'Module' }));
|
|
166824
166898
|
|
|
166825
|
-
const toggleReadOnlyMode = createMetaAction(
|
|
166826
|
-
"TOGGLE_READ_ONLY_MODE",
|
|
166827
|
-
lodashExports.noop
|
|
166828
|
-
);
|
|
166899
|
+
const toggleReadOnlyMode = createMetaAction("TOGGLE_READ_ONLY_MODE", lodashExports.noop);
|
|
166829
166900
|
const updateReadOnlyMode = createMetaAction("UPDATE_READ_ONLY_MODE");
|
|
166830
166901
|
const readOnly = createReducer(
|
|
166831
166902
|
{
|
|
@@ -169804,6 +169875,9 @@
|
|
|
169804
169875
|
overrideName: `AddOrEdit${nameUpper}DialogOverride`,
|
|
169805
169876
|
dialogType,
|
|
169806
169877
|
props: {
|
|
169878
|
+
...annotation.isEditLocked && {
|
|
169879
|
+
readOnly: typeof annotation.isEditLocked === "string" ? annotation.isEditLocked : "This annotation is locked"
|
|
169880
|
+
},
|
|
169807
169881
|
dialogProps: {
|
|
169808
169882
|
title: annotation && annotation.id ? `Edit ${nameUpper}` : `New ${nameUpper}`
|
|
169809
169883
|
},
|
|
@@ -170445,7 +170519,8 @@
|
|
|
170445
170519
|
editorName,
|
|
170446
170520
|
sequenceData: sequenceDataFromProps,
|
|
170447
170521
|
allowSeqDataOverride,
|
|
170448
|
-
allowMultipleFeatureDirections
|
|
170522
|
+
allowMultipleFeatureDirections,
|
|
170523
|
+
readOnly
|
|
170449
170524
|
} = ownProps;
|
|
170450
170525
|
const editorState = getEditorState(state, editorName);
|
|
170451
170526
|
const meta = { editorName };
|
|
@@ -170505,6 +170580,7 @@
|
|
|
170505
170580
|
const f = getFindTool(findTool, matchesTotal);
|
|
170506
170581
|
return {
|
|
170507
170582
|
...editorState,
|
|
170583
|
+
readOnly: readOnly || editorState.readOnly,
|
|
170508
170584
|
meta,
|
|
170509
170585
|
annotationToAdd,
|
|
170510
170586
|
...newSelection && { selectionLayer: newSelection },
|
|
@@ -188651,7 +188727,7 @@ double click --> edit`}`;
|
|
|
188651
188727
|
}
|
|
188652
188728
|
|
|
188653
188729
|
const name = "@teselagen/ove";
|
|
188654
|
-
const version = "0.3.
|
|
188730
|
+
const version = "0.3.11";
|
|
188655
188731
|
const main = "./src/index.js";
|
|
188656
188732
|
const exports$1 = {
|
|
188657
188733
|
".": {
|
|
@@ -189261,7 +189337,7 @@ double click --> edit`}`;
|
|
|
189261
189337
|
isHidden: isProtein
|
|
189262
189338
|
},
|
|
189263
189339
|
deleteSequence: {
|
|
189264
|
-
isDisabled: (props) => props.readOnly && readOnlyDisabledTooltip || !props.onDelete,
|
|
189340
|
+
isDisabled: (props) => props.disableBpEditing && bpEditingDisabledTooltip || props.readOnly && readOnlyDisabledTooltip || !props.onDelete,
|
|
189265
189341
|
isHidden: (props) => !props.onDelete,
|
|
189266
189342
|
handler: (props) => props.onDelete(props.sequenceData)
|
|
189267
189343
|
},
|
|
@@ -189460,6 +189536,7 @@ double click --> edit`}`;
|
|
|
189460
189536
|
};
|
|
189461
189537
|
});
|
|
189462
189538
|
const readOnlyDisabledTooltip = "Sorry this function is not allowed in Read-Only Mode";
|
|
189539
|
+
const bpEditingDisabledTooltip = "Sequence Editing Disabled";
|
|
189463
189540
|
const noSelection = ({ selectionLayer = {} }) => !(selectionLayer.start > -1 && selectionLayer.end > -1) && "Selection Required";
|
|
189464
189541
|
const triggerClipboardCommand = (type) => {
|
|
189465
189542
|
const wrapper = document.querySelector(".veVectorInteractionWrapper");
|
|
@@ -189491,8 +189568,8 @@ double click --> edit`}`;
|
|
|
189491
189568
|
handler: lodashExports.noop
|
|
189492
189569
|
},
|
|
189493
189570
|
cut: {
|
|
189494
|
-
isDisabled: (props) => props.readOnly && readOnlyDisabledTooltip || props.sequenceLength === 0,
|
|
189495
|
-
isHidden: (props) => props.readOnly,
|
|
189571
|
+
isDisabled: (props) => props.disableBpEditing && bpEditingDisabledTooltip || props.readOnly && readOnlyDisabledTooltip || props.sequenceLength === 0,
|
|
189572
|
+
isHidden: (props) => props.readOnly || props.disableBpEditing,
|
|
189496
189573
|
handler: () => {
|
|
189497
189574
|
triggerClipboardCommand("cut");
|
|
189498
189575
|
},
|
|
@@ -189517,7 +189594,7 @@ double click --> edit`}`;
|
|
|
189517
189594
|
},
|
|
189518
189595
|
paste: {
|
|
189519
189596
|
isDisabled: (props) => props.readOnly && readOnlyDisabledTooltip,
|
|
189520
|
-
isHidden: (props) => props.readOnly,
|
|
189597
|
+
isHidden: (props) => props.readOnly || props.disableBpEditing,
|
|
189521
189598
|
handler: () => triggerClipboardCommand("paste"),
|
|
189522
189599
|
hotkey: "mod+v"
|
|
189523
189600
|
},
|
|
@@ -189671,12 +189748,12 @@ double click --> edit`}`;
|
|
|
189671
189748
|
hotkey: "mod+i"
|
|
189672
189749
|
},
|
|
189673
189750
|
complementSelection: {
|
|
189674
|
-
isHidden: (props) => props.readOnly || isProtein(props),
|
|
189751
|
+
isHidden: (props) => props.readOnly || isProtein(props) || props.disableBpEditing,
|
|
189675
189752
|
isDisabled: (props) => props.readOnly && readOnlyDisabledTooltip || noSelection(props),
|
|
189676
189753
|
handler: (props) => props.handleComplementSelection()
|
|
189677
189754
|
},
|
|
189678
189755
|
complementEntireSequence: {
|
|
189679
|
-
isHidden: (props) => props.readOnly || isProtein(props),
|
|
189756
|
+
isHidden: (props) => props.readOnly || isProtein(props) || props.disableBpEditing,
|
|
189680
189757
|
isDisabled: (props) => props.readOnly && readOnlyDisabledTooltip || props.sequenceLength === 0,
|
|
189681
189758
|
handler: (props) => props.handleComplementSequence()
|
|
189682
189759
|
},
|
|
@@ -189828,13 +189905,13 @@ double click --> edit`}`;
|
|
|
189828
189905
|
// }
|
|
189829
189906
|
// },
|
|
189830
189907
|
reverseComplementSelection: {
|
|
189831
|
-
isDisabled: (props) => props.readOnly && readOnlyDisabledTooltip || noSelection(props),
|
|
189908
|
+
isDisabled: (props) => props.readOnly && readOnlyDisabledTooltip || noSelection(props) || props.disableBpEditing,
|
|
189832
189909
|
isHidden: (props) => props.readOnly || isProtein(props),
|
|
189833
189910
|
handler: (props) => props.handleReverseComplementSelection(),
|
|
189834
189911
|
hotkey: "mod+e"
|
|
189835
189912
|
},
|
|
189836
189913
|
reverseComplementEntireSequence: {
|
|
189837
|
-
isHidden: (props) => props.readOnly || isProtein(props),
|
|
189914
|
+
isHidden: (props) => props.readOnly || isProtein(props) || props.disableBpEditing,
|
|
189838
189915
|
isDisabled: (props) => props.readOnly && readOnlyDisabledTooltip || props.sequenceLength === 0,
|
|
189839
189916
|
handler: (props) => props.handleReverseComplementSequence()
|
|
189840
189917
|
},
|
|
@@ -189984,7 +190061,7 @@ double click --> edit`}`;
|
|
|
189984
190061
|
isDisabled: (props) => props.readOnly && readOnlyDisabledTooltip || props.sequenceLength === 0
|
|
189985
190062
|
},
|
|
189986
190063
|
rotateToCaretPosition: {
|
|
189987
|
-
isHidden: (props) => props.readOnly || isProtein(props),
|
|
190064
|
+
isHidden: (props) => props.readOnly || isProtein(props) || props.disableBpEditing,
|
|
189988
190065
|
isDisabled: (props) => props.readOnly && readOnlyDisabledTooltip || props.caretPosition === -1 && "You must first place cursor" || !props.sequenceData.circular && "Disabled for Linear Sequences" || props.sequenceLength === 0,
|
|
189989
190066
|
handler: (props) => props.handleRotateToCaretPosition(),
|
|
189990
190067
|
hotkey: "mod+b"
|
|
@@ -189993,13 +190070,13 @@ double click --> edit`}`;
|
|
|
189993
190070
|
};
|
|
189994
190071
|
const cirularityCommandDefs = {
|
|
189995
190072
|
circular: {
|
|
189996
|
-
isHidden: (props) => props.readOnly || isProtein(props),
|
|
190073
|
+
isHidden: (props) => props.readOnly || isProtein(props) || props.disableBpEditing,
|
|
189997
190074
|
isDisabled: (props) => props.readOnly && readOnlyDisabledTooltip,
|
|
189998
190075
|
handler: (props) => props.updateCircular(true),
|
|
189999
190076
|
isActive: (props) => props && props.sequenceData.circular
|
|
190000
190077
|
},
|
|
190001
190078
|
linear: {
|
|
190002
|
-
isHidden: (props) => props.readOnly,
|
|
190079
|
+
isHidden: (props) => props.readOnly || props.disableBpEditing,
|
|
190003
190080
|
isDisabled: (props) => props.readOnly && readOnlyDisabledTooltip,
|
|
190004
190081
|
handler: (props) => props.updateCircular(false),
|
|
190005
190082
|
isActive: (props) => props && !props.sequenceData.circular
|
|
@@ -190026,29 +190103,27 @@ double click --> edit`}`;
|
|
|
190026
190103
|
}
|
|
190027
190104
|
];
|
|
190028
190105
|
const labelToggleCommandDefs = {};
|
|
190029
|
-
["feature", "part", "cutsite", "primer", ...nicheAnnotations].forEach(
|
|
190030
|
-
|
|
190031
|
-
|
|
190032
|
-
|
|
190033
|
-
|
|
190034
|
-
|
|
190035
|
-
|
|
190036
|
-
|
|
190037
|
-
|
|
190038
|
-
|
|
190039
|
-
|
|
190040
|
-
|
|
190041
|
-
|
|
190042
|
-
|
|
190043
|
-
|
|
190044
|
-
|
|
190045
|
-
|
|
190046
|
-
|
|
190047
|
-
|
|
190048
|
-
|
|
190049
|
-
|
|
190050
|
-
}
|
|
190051
|
-
);
|
|
190106
|
+
["feature", "part", "cutsite", "primer", ...nicheAnnotations].forEach((_type) => {
|
|
190107
|
+
let rest = {};
|
|
190108
|
+
let type = _type;
|
|
190109
|
+
if (_type.type) {
|
|
190110
|
+
type = _type.type.slice(0, -1);
|
|
190111
|
+
rest = _type;
|
|
190112
|
+
}
|
|
190113
|
+
const cmdId = `toggle${lodashExports.upperFirst(type)}Labels`;
|
|
190114
|
+
const plural = type + "s";
|
|
190115
|
+
labelToggleCommandDefs[cmdId] = {
|
|
190116
|
+
toggle: ["show", "hide"],
|
|
190117
|
+
handler: (props) => props.annotationLabelVisibilityToggle(plural),
|
|
190118
|
+
isHidden: (props) => {
|
|
190119
|
+
return props && props.typesToOmit && props.typesToOmit[plural] === false;
|
|
190120
|
+
},
|
|
190121
|
+
...rest,
|
|
190122
|
+
isActive: (props) => {
|
|
190123
|
+
return props && props.annotationLabelVisibility[plural];
|
|
190124
|
+
}
|
|
190125
|
+
};
|
|
190126
|
+
});
|
|
190052
190127
|
const editAnnotationCommandDefs = ["feature", "part", "primer"].reduce(
|
|
190053
190128
|
(acc, key) => {
|
|
190054
190129
|
acc[`edit${lodashExports.upperFirst(key)}`] = {
|
|
@@ -191621,8 +191696,12 @@ double click --> edit`}`;
|
|
|
191621
191696
|
caretPosition = -1,
|
|
191622
191697
|
selectionLayer = { start: -1, end: -1 },
|
|
191623
191698
|
readOnly,
|
|
191624
|
-
onPaste
|
|
191699
|
+
onPaste,
|
|
191700
|
+
disableBpEditing
|
|
191625
191701
|
} = this.props;
|
|
191702
|
+
if (disableBpEditing) {
|
|
191703
|
+
return window.toastr.warning("Sorry the underlying sequence is locked");
|
|
191704
|
+
}
|
|
191626
191705
|
if (readOnly) {
|
|
191627
191706
|
return window.toastr.warning("Sorry the sequence is Read-Only");
|
|
191628
191707
|
}
|
|
@@ -191663,6 +191742,7 @@ double click --> edit`}`;
|
|
|
191663
191742
|
sequenceData,
|
|
191664
191743
|
selectionLayer,
|
|
191665
191744
|
copyOptions,
|
|
191745
|
+
disableBpEditing,
|
|
191666
191746
|
readOnly
|
|
191667
191747
|
} = this.props;
|
|
191668
191748
|
const onCut = this.props.onCut || this.props.onCopy || lodashExports.noop;
|
|
@@ -191688,7 +191768,7 @@ double click --> edit`}`;
|
|
|
191688
191768
|
);
|
|
191689
191769
|
if (!(this.sequenceDataToCopy || {}).textToCopy && !seqData.sequence.length)
|
|
191690
191770
|
return window.toastr.warning(
|
|
191691
|
-
`No Sequence Selected To ${isCut && !readOnly ? "Cut" : "Copy"}`
|
|
191771
|
+
`No Sequence Selected To ${isCut && !(readOnly || disableBpEditing) ? "Cut" : "Copy"}`
|
|
191692
191772
|
);
|
|
191693
191773
|
const clipboardData = e.clipboardData;
|
|
191694
191774
|
const textToCopy = (this.sequenceDataToCopy || {}).textToCopy !== void 0 ? this.sequenceDataToCopy.textToCopy : seqData.isProtein ? seqData.proteinSequence : seqData.sequence;
|
|
@@ -191696,7 +191776,7 @@ double click --> edit`}`;
|
|
|
191696
191776
|
clipboardData.setData("text/plain", textToCopy);
|
|
191697
191777
|
clipboardData.setData("application/json", JSON.stringify(seqData));
|
|
191698
191778
|
e.preventDefault();
|
|
191699
|
-
if (isCut && !readOnly) {
|
|
191779
|
+
if (isCut && !(readOnly || disableBpEditing) && !disableBpEditing) {
|
|
191700
191780
|
this.handleDnaDelete(false);
|
|
191701
191781
|
onCut(
|
|
191702
191782
|
e,
|
|
@@ -191709,7 +191789,7 @@ double click --> edit`}`;
|
|
|
191709
191789
|
document.body.removeEventListener("copy", this.handleCopy);
|
|
191710
191790
|
}
|
|
191711
191791
|
window.toastr.success(
|
|
191712
|
-
`Selection ${isCut && !readOnly ? "Cut" : "Copied"}`
|
|
191792
|
+
`Selection ${isCut && !(readOnly || disableBpEditing) && !disableBpEditing ? "Cut" : "Copied"}`
|
|
191713
191793
|
);
|
|
191714
191794
|
this.sequenceDataToCopy = void 0;
|
|
191715
191795
|
};
|
|
@@ -191720,14 +191800,18 @@ double click --> edit`}`;
|
|
|
191720
191800
|
caretPosition = -1,
|
|
191721
191801
|
selectionLayer = { start: -1, end: -1 },
|
|
191722
191802
|
sequenceData = { sequence: "" },
|
|
191723
|
-
readOnly
|
|
191803
|
+
readOnly,
|
|
191804
|
+
disableBpEditing
|
|
191724
191805
|
// updateSequenceData,
|
|
191725
191806
|
// wrappedInsertSequenceDataAtPositionOrRange
|
|
191726
191807
|
// handleInsert
|
|
191727
191808
|
} = this.props;
|
|
191728
191809
|
const sequenceLength = sequenceData.sequence.length;
|
|
191729
191810
|
const isReplace = selectionLayer.start > -1;
|
|
191730
|
-
if (
|
|
191811
|
+
if (disableBpEditing) {
|
|
191812
|
+
return window.toastr.warning("Sorry the underlying sequence is locked");
|
|
191813
|
+
}
|
|
191814
|
+
if (readOnly || disableBpEditing) {
|
|
191731
191815
|
window.toastr.warning("Sorry the sequence is Read-Only");
|
|
191732
191816
|
} else {
|
|
191733
191817
|
createSequenceInputPopup({
|
|
@@ -191755,13 +191839,17 @@ double click --> edit`}`;
|
|
|
191755
191839
|
selectionLayer = { start: -1, end: -1 },
|
|
191756
191840
|
sequenceData = { sequence: "" },
|
|
191757
191841
|
readOnly,
|
|
191842
|
+
disableBpEditing,
|
|
191758
191843
|
updateSequenceData,
|
|
191759
191844
|
wrappedInsertSequenceDataAtPositionOrRange,
|
|
191760
191845
|
caretPositionUpdate
|
|
191761
191846
|
// handleInsert
|
|
191762
191847
|
} = this.props;
|
|
191763
191848
|
const sequenceLength = sequenceData.sequence.length;
|
|
191764
|
-
if (
|
|
191849
|
+
if (disableBpEditing) {
|
|
191850
|
+
return window.toastr.warning("Sorry the underlying sequence is locked");
|
|
191851
|
+
}
|
|
191852
|
+
if (readOnly || disableBpEditing) {
|
|
191765
191853
|
return window.toastr.warning("Sorry the sequence is Read-Only");
|
|
191766
191854
|
}
|
|
191767
191855
|
if (sequenceLength > 0) {
|
|
@@ -191892,7 +191980,7 @@ double click --> edit`}`;
|
|
|
191892
191980
|
};
|
|
191893
191981
|
// eslint-disable-next-line no-unused-vars
|
|
191894
191982
|
getCopyOptions = (annotation) => {
|
|
191895
|
-
const { sequenceData, readOnly, selectionLayer } = this.props;
|
|
191983
|
+
const { sequenceData, readOnly, disableBpEditing, selectionLayer } = this.props;
|
|
191896
191984
|
const { isProtein } = sequenceData;
|
|
191897
191985
|
const makeTextCopyable = (transformFunc, className, action = "copy") => {
|
|
191898
191986
|
return new Clipboard$1(`.${className}`, {
|
|
@@ -191952,7 +192040,7 @@ double click --> edit`}`;
|
|
|
191952
192040
|
}
|
|
191953
192041
|
};
|
|
191954
192042
|
return [
|
|
191955
|
-
...readOnly ? [] : [
|
|
192043
|
+
...readOnly || disableBpEditing ? [] : [
|
|
191956
192044
|
{
|
|
191957
192045
|
text: "Replace",
|
|
191958
192046
|
...this.insertHelper
|
|
@@ -192026,21 +192114,14 @@ double click --> edit`}`;
|
|
|
192026
192114
|
this.openVeCopyAAReverse && this.openVeCopyAAReverse.destroy();
|
|
192027
192115
|
},
|
|
192028
192116
|
didMount: ({ className }) => {
|
|
192029
|
-
this.openVeCopyAAReverse = makeTextCopyable(
|
|
192030
|
-
(selectedSeqData)
|
|
192031
|
-
|
|
192032
|
-
|
|
192033
|
-
|
|
192034
|
-
|
|
192035
|
-
|
|
192036
|
-
|
|
192037
|
-
return {
|
|
192038
|
-
...revSeqData,
|
|
192039
|
-
textToCopy
|
|
192040
|
-
};
|
|
192041
|
-
},
|
|
192042
|
-
className
|
|
192043
|
-
);
|
|
192117
|
+
this.openVeCopyAAReverse = makeTextCopyable((selectedSeqData) => {
|
|
192118
|
+
const revSeqData = getReverseComplementSequenceAndAnnoations(selectedSeqData);
|
|
192119
|
+
const textToCopy = isProtein ? revSeqData.proteinSequence.toUpperCase() : getAminoAcidStringFromSequenceString(revSeqData.sequence);
|
|
192120
|
+
return {
|
|
192121
|
+
...revSeqData,
|
|
192122
|
+
textToCopy
|
|
192123
|
+
};
|
|
192124
|
+
}, className);
|
|
192044
192125
|
}
|
|
192045
192126
|
},
|
|
192046
192127
|
{
|
|
@@ -192147,11 +192228,12 @@ double click --> edit`}`;
|
|
|
192147
192228
|
({ nearestCaretPos, shiftHeld, event }) => {
|
|
192148
192229
|
this.updateSelectionOrCaret(shiftHeld, nearestCaretPos);
|
|
192149
192230
|
const {
|
|
192150
|
-
readOnly
|
|
192231
|
+
readOnly,
|
|
192232
|
+
disableBpEditing
|
|
192151
192233
|
// sequenceData: { circular }
|
|
192152
192234
|
} = this.props;
|
|
192153
192235
|
const menu = [
|
|
192154
|
-
...readOnly ? [] : [
|
|
192236
|
+
...readOnly || disableBpEditing ? [] : [
|
|
192155
192237
|
{
|
|
192156
192238
|
text: "Insert",
|
|
192157
192239
|
...this.insertHelper
|
|
@@ -192197,8 +192279,7 @@ double click --> edit`}`;
|
|
|
192197
192279
|
overlapsSelf: annotation.overlapsSelf
|
|
192198
192280
|
});
|
|
192199
192281
|
return [
|
|
192200
|
-
"
|
|
192201
|
-
"deletePart",
|
|
192282
|
+
...getEditDeleteHandlers("Part", annotation),
|
|
192202
192283
|
"--",
|
|
192203
192284
|
...this.getSelectionMenuOptions(annotation),
|
|
192204
192285
|
"--",
|
|
@@ -192240,8 +192321,7 @@ double click --> edit`}`;
|
|
|
192240
192321
|
event.persist();
|
|
192241
192322
|
const { readOnly, annotationsToSupport: { parts } = {} } = this.props;
|
|
192242
192323
|
return [
|
|
192243
|
-
"
|
|
192244
|
-
"deleteFeature",
|
|
192324
|
+
...getEditDeleteHandlers("Feature", annotation),
|
|
192245
192325
|
...this.getSelectionMenuOptions(annotation),
|
|
192246
192326
|
...readOnly ? [] : [
|
|
192247
192327
|
...parts && [
|
|
@@ -192308,8 +192388,7 @@ double click --> edit`}`;
|
|
|
192308
192388
|
end: annotation.end
|
|
192309
192389
|
});
|
|
192310
192390
|
return [
|
|
192311
|
-
"
|
|
192312
|
-
"deletePrimer",
|
|
192391
|
+
...getEditDeleteHandlers("Primer", annotation),
|
|
192313
192392
|
...this.getSelectionMenuOptions(annotation),
|
|
192314
192393
|
"showRemoveDuplicatesDialogPrimers",
|
|
192315
192394
|
"viewPrimerProperties"
|
|
@@ -192519,6 +192598,28 @@ double click --> edit`}`;
|
|
|
192519
192598
|
end: newSelectionLayerEnd % newSeqData.sequence.length
|
|
192520
192599
|
});
|
|
192521
192600
|
};
|
|
192601
|
+
function getEditDeleteHandlers(type, annotation) {
|
|
192602
|
+
return [
|
|
192603
|
+
...annotation.isEditLocked ? [
|
|
192604
|
+
{
|
|
192605
|
+
shouldDismissPopover: false,
|
|
192606
|
+
text: /* @__PURE__ */ React$3.createElement(
|
|
192607
|
+
"div",
|
|
192608
|
+
{
|
|
192609
|
+
style: {
|
|
192610
|
+
fontSize: 11,
|
|
192611
|
+
fontStyle: "italic",
|
|
192612
|
+
color: "rgba(0,0,0,.5)"
|
|
192613
|
+
}
|
|
192614
|
+
},
|
|
192615
|
+
typeof annotation.isEditLocked === "string" ? annotation.isEditLocked : `Note: This Annotation is Locked`
|
|
192616
|
+
)
|
|
192617
|
+
}
|
|
192618
|
+
] : [],
|
|
192619
|
+
`edit${type}`,
|
|
192620
|
+
...annotation.isEditLocked ? [] : [`delete${type}`]
|
|
192621
|
+
];
|
|
192622
|
+
}
|
|
192522
192623
|
|
|
192523
192624
|
const style$i = '';
|
|
192524
192625
|
|
|
@@ -199676,7 +199777,11 @@ double click --> edit`}`;
|
|
|
199676
199777
|
}
|
|
199677
199778
|
}
|
|
199678
199779
|
],
|
|
199679
|
-
withDialogProps: {
|
|
199780
|
+
withDialogProps: {
|
|
199781
|
+
title: "Go To",
|
|
199782
|
+
height: 190,
|
|
199783
|
+
onCloseHook: tryToRefocusEditor
|
|
199784
|
+
}
|
|
199680
199785
|
});
|
|
199681
199786
|
|
|
199682
199787
|
const validate$1 = (val, vals, props) => {
|
|
@@ -202336,6 +202441,7 @@ double click --> edit`}`;
|
|
|
202336
202441
|
overlapsSelf,
|
|
202337
202442
|
start,
|
|
202338
202443
|
end,
|
|
202444
|
+
readOnly,
|
|
202339
202445
|
getAdditionalEditAnnotationComps,
|
|
202340
202446
|
advancedOptions,
|
|
202341
202447
|
advancedDefaultOpen,
|
|
@@ -202430,10 +202536,11 @@ double click --> edit`}`;
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"tg-upsert-annotation"
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)
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},
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typeof readOnly === "string" ? /* @__PURE__ */ React$3.createElement(Callout, { intent: "primary", style: { marginBottom: 10 } }, readOnly) : null,
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/* @__PURE__ */ React$3.createElement(
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InputField,
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{
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disabled:
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disabled: readOnly,
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inlineLabel: true,
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tooltipError: true,
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autoFocus: true,
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@@ -205371,15 +205478,15 @@ ${seqDataToCopy}\r
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}
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// Edge 20+
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static isEdge() {
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return Browser.isBrowser() &&
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return Browser.isBrowser() && !Browser.isIE() && !!window.StyleMedia;
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}
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// Chrome 1+
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static isChrome() {
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return Browser.isBrowser() &&
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return Browser.isBrowser() && !!window.chrome && !!window.chrome.webstore;
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}
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// Blink engine detection
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static isBlink() {
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return Browser.isBrowser() && (
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return Browser.isBrowser() && (Browser.isChrome() || Browser.isOpera()) && !!window.CSS;
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}
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static getUserAgent() {
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return typeof navigator === "undefined" ? "" : navigator.userAgent;
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@@ -207045,6 +207152,8 @@ ${seqDataToCopy}\r
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"hideSingleImport",
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"beforeAnnotationCreate",
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"disableSetReadOnly",
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"allowAnnotationEditLocking",
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"disableBpEditing",
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"showReadOnly",
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"showCircularity",
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"onHiddenEnzymeAdd",
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@@ -208458,9 +208567,7 @@ ${seqDataToCopy}\r
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AnchorButton,
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{
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onClick: () => {
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deleteAnnotation(
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annotationPropertiesSelectedEntities
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);
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deleteAnnotation(annotationPropertiesSelectedEntities);
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},
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className: "tgDeleteAnnsBtn",
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intent: "danger",
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